WO2015042564A1 - Methods for treating or preventing transthyretin (ttr) associated diseases - Google Patents

Methods for treating or preventing transthyretin (ttr) associated diseases Download PDF

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WO2015042564A1
WO2015042564A1 PCT/US2014/056923 US2014056923W WO2015042564A1 WO 2015042564 A1 WO2015042564 A1 WO 2015042564A1 US 2014056923 W US2014056923 W US 2014056923W WO 2015042564 A1 WO2015042564 A1 WO 2015042564A1
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rnai agent
ttr
nucleotides
administered
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WO2015042564A8 (en
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Kallanthottahil G. Rajeev
Tracy Zimmermann
Muthiah Manoharan
Martin Maier
Satyanarayana Kuchimanchi
Klaus CHARISSE
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Alnylam Pharmaceuticals, Inc.
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    • C—CHEMISTRY; METALLURGY
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/321—2'-O-R Modification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/322—2'-R Modification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3515—Lipophilic moiety, e.g. cholesterol

Definitions

  • Transthyretin (also known as prealbumin) is found in serum and cerebrospinal fluid (CSF). TTR transports retinol-binding protein (RBP) and thyroxine (T4) and also acts as a carrier of retinol (vitamin A) through its association with RBP in the blood and the CSF. Transthyretin is named for its transport of thyroxine and retinol. TTR also functions as a protease and can cleave proteins including apoA-I (the major HDL apolipoprotein), amyloid ⁇ -peptide, and neuropeptide Y. See Liz, M.A. et al. (2010) IUBMB Life, 62(6):429-435.
  • apoA-I the major HDL apolipoprotein
  • amyloid ⁇ -peptide amyloid ⁇ -peptide
  • neuropeptide Y neuropeptide Y. See Liz, M.A. et al. (2010) IUBMB Life,
  • TTR is a tetramer of four identical 127-amino acid subunits (monomers) that are rich in beta sheet structure. Each monomer has two 4-stranded beta sheets and the shape of a prolate ellipsoid. Antiparallel beta-sheet interactions link monomers into dimers. A short loop from each monomer forms the main dimer-dimer interaction. These two pairs of loops separate the opposed, convex beta-sheets of the dimers to form an internal channel.
  • the liver is the major site of TTR expression. Other significant sites of expression include the choroid plexus, retina (particularly the retinal pigment epithelium) and pancreas.
  • Amyloidosis is a general term for the group of amyloid diseases that are characterized by amyloid deposits. Amyloid diseases are classified based on their precursor protein; for example, the name starts with "A” for amyloid and is followed by an abbreviation of the precursor protein, e.g., ATTR for amloidogenic transthyretin. Ibid.
  • TTR-associated diseases There are numerous TTR-associated diseases, most of which are amyloid diseases.
  • Normal-sequence TTR is associated with cardiac amyloidosis in people who are elderly and is termed senile systemic amyloidosis (SSA) (also called senile cardiac amyloidosis (SCA) or cardiac amyloidosis).
  • SSA senile systemic amyloidosis
  • SCA senile cardiac amyloidosis
  • SSA senile cardiac amyloidosis
  • SSA senile cardiac amyloidosis
  • SSA senile cardiac amyloidosis
  • SSA senile cardiac amyloidosis
  • SSA senile cardiac amyloidosis
  • SSA senile cardiac amyloidosis
  • SSA senile cardiac amyloidosis
  • SSA senile cardiac amyloidosis
  • SSA senile cardiac
  • Abnormal amyloidogenic proteins may be either inherited or acquired through somatic mutations. Guan, J. et al. (Nov. 4, 2011) Current perspectives on cardiac amyloidosis, Am J Physiol Heart Circ Physiol, doi: 10.1152/ajpheart.00815.2011. Transthyretin associated ATTR is the most frequent form of hereditary systemic amyloidosis. Lobato, L. (2003) J. Nephrol., 16:438-442. TTR mutations accelerate the process of TTR amyloid formation and are the most important risk factor for the development of ATTR. More than 85 amyloidogenic TTR variants are known to cause systemic familial amyloidosis. TTR mutations usually give rise to systemic amyloid deposition, with particular involvement of the peripheral nervous system, although some mutations are associated with cardiomyopathy or vitreous opacities. Ibid.
  • the V30M mutation is the most prevalent TTR mutation. See, e.g., Lobato, L. (2003) J Nephrol, 16:438-442.
  • the V122I mutation is carried by 3.9% of the African American population and is the most common cause of FAC. Jacobson, D.R. et al.
  • the present invention provides methods of treating or preventing a TTR- associated disease in a subject using the RNAi agents, e.g. double stranded RNAi agents, of the invention, targeting the Transthyretin (TTR) gene.
  • RNAi agents e.g. double stranded RNAi agents
  • TTR Transthyretin
  • the present invention is based, at least in part, on the discovery that RNAi agents that comprise particular chemical modifications show a superior ability to inhibit expression of TTR.
  • Agents including a certain pattern of chemical modifications (e.g., an alternating pattern) and a ligand are shown herein to be effective in silencing the activity of the TTR gene.
  • consecutive nucleotides show surprisingly enhanced TTR gene silencing activity.
  • a single such chemical motif is present in the agent, it is preferred to be at or near the cleavage region for enhancing of the gene silencing activity.
  • Cleavage region is the region surrounding the cleavage site, i.e., the site on the target mRNA at which cleavage occurs.
  • the present invention provides methods of treating or preventing a TTR-associated disease in a subject.
  • the methods include administering to the subject an RNAi agent at a dose of about 7.5 mg/kg, daily for five days, followed by a dose of about 7.5 mg/kg weekly for about five weeks, thereby treating or preventing the TTR-associated disease in the subject.
  • RNAi agents suitable for use in the methods of the invention include double stranded RNAi agents RNAi agents, e.g., double stranded RNAi agents, that inhibit expression of a transthyretin (TTR) gene.
  • TTR transthyretin
  • the double stranded RNAi agent includes a sense strand complementary to an antisense strand.
  • the antisense strand includes a region complementary to a part of an mRNA encoding transthyretin. Each strand has 14 to 30 nucleotides, and the double stranded RNAi agent is represented by formula (III):
  • the sense strand is conjugated to at least one ligand, e.g. , at least one ligand, e.g., at least one ligand attached to the 3' end of the sense strand.
  • the ligand may be conjugated to the antisense strand.
  • the present invention provides methods of treating or preventing a TTR-associated disease in a subject.
  • the methods include administering to the subject an RNAi agent at a dose of about 500 mg, daily for five days, followed by a weekly dose of about 500 mg, thereby treating or preventing the TTR-associated disease in the subject.
  • RNAi agents suitable for use in the methods of the invention include double stranded RNAi agents RNAi agents, e.g. , double stranded RNAi agents, that inhibit expression of a transthyretin (TTR) gene.
  • TTR transthyretin
  • the double stranded RNAi agent includes a sense strand complementary to an antisense strand.
  • the antisense strand includes a region complementary to a part of an mRNA encoding transthyretin. Each strand has 14 to 30 nucleotides, and the double stranded RNAi agent is represented by formula (III):
  • TTR expression in a sample derived from the subject is inhibited by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60% or at least about 70% at least about 80%, or at least about 90%.
  • the subject is a human.
  • the subject is a subject suffering from a TTR-associated disease. In other embodiments, the subject is a subject at risk for developing a TTR- associated disease.
  • the subject is a subject who carries a TTR gene mutation that is associated with the development of a TTR-associated disease.
  • the subject has a TTR-associated amyloidosis and the method reduces an amyloid TTR deposit in the subject.
  • the RNAi agent is administered to the subject by an administration means selected from the group consisting of subcutaneous, intravenous, intramuscular, intrabronchial, intrapleural, intraperitoneal, intraarterial, lymphatic, cerebrospinal, and any combinations thereof.
  • the RNAi agent is administered to the subject via subcutaneous or intravenous administration.
  • the RNAi agent is administered to the subject via subcutaneous administration.
  • the subcutaneous administration is subcutaneous injection of the RNAi agent.
  • the subcutaneous injection may be at an anatomical location selected from the group consisting of the abdomen of the subject, the thigh of the subject, and the upper arm of the subject.
  • the RNAi agent is administered to the subject as a split 500 mg dose at two different anatomical locations.
  • the subcutaneous administration includes administration via a subcutaneous pump or subcutaneous depot. In one embodiment, the subcutaneous administration comprises administration via a subcutaneous infusion pump. In one embodiment, the RNAi agent is administered to the subject as a single 500 mg dose. In one embodiment, the RNAi agent is administered to the subject over of period of 5-20, 5- 10, 5- 15, 10- 15, 10-20, or 15-20 minutes. In another embodiment, the RNAi agent is administered to the subject over of period of 15 minutes or less, 10 minutes or less, or 5 minutes or less.
  • the RNAi agent is administered to the subject as a single dose 500 mg dose. In another embodiment, the RNAi agent is administered to the subject as a split 500 mg dose.
  • administering the RNAi agent does not result in an inflammatory response in the subject as assessed based on the level of a cytokine or chemokine selected from the group consisting of G-CSF, IFN- ⁇ , IL- 10, IL- 12 (p70), ILip, IL- lra, IL-6, IL-8, IP-10, MCP- 1, ⁇ - ⁇ , ⁇ - ⁇ , TNFa, and any combinations thereof, in a sample from the subject.
  • a cytokine or chemokine selected from the group consisting of G-CSF, IFN- ⁇ , IL- 10, IL- 12 (p70), ILip, IL- lra, IL-6, IL-8, IP-10, MCP- 1, ⁇ - ⁇ , ⁇ - ⁇ , TNFa, and any combinations thereof, in a sample from the subject.
  • each N b and N b ' independently represents an oligonucleotide sequence including 1-5 modified nucleotides.
  • formula (III) is represented as formula (IIIc):
  • the duplex region is 15-30 nucleotide pairs in length. In some embodiments, the duplex region is 17-23 nucleotide pairs in length, 17-25 nucleotide pairs in length, 23-27 nucleotide pairs in length, 19-21 nucleotide pairs in length, or 21-23 nucleotide pairs in length.
  • the modifications on the nucleotides are selected from the group consisting of LNA, UNA, CRN, cEt, HNA, CeNA, 2'-methoxyethyl, 2'-0-alkyl, 2'-0-allyl, 2'-C- allyl, 2'-fluoro, 2'-deoxy, 2'-hydroxyl, and combinations thereof.
  • the modifications on the nucleotides are 2'-0-methyl or 2'-fluoro.
  • the ligand is one or more N-acetylgalactosamine
  • the ligand is attached to the 3' end of the sense strand.
  • the RNAi agent is conjugated to the ligand as shown in the following schematic
  • the RNAi agent is conjugated to the ligand as shown in the following schematic
  • the sense strand has a total of 21 nucleotides and the antisense strand has a total of 23 nucleotides.
  • linkages between n p ' include phosphorothioate linkages. In some such embodiments, the linkages between n p ' are phosphorothioate linkages.
  • the RNAi agent is selected from the group of agents listed in Table 1.
  • the present invention provides methods of treating or preventing a TTR-associated disease in a subject.
  • the methods include administering to the subject an RNAi agent at a dose of about 500 mg, daily for five days, followed by a weekly dose of about 500 mg, wherein the RNAi agent is AD-51547, having the following structure: sense: 5 ' - UfgGfg AfuUfuCf AfUfgUfaacCfaAfgAfL96-3 ' (SEQ ID NO:2211 ) antisense: 5'- uCfuUfgGfUfUfaCfaugAfaAfuCfcCfasUfsc-3' (SEQ ID NO:2217) wherein lowercase nucleotides (a, u, g, c) indicate 2'-0-methyl nucleotides; Nf (e.g. , Af) indicates a 2' -fluoro nucleotide; s indicates a
  • the subject is a subject suffering from a TTR-associated disease. In other embodiments, the subject is a subject at risk for developing a TTR- associated disease.
  • the subject is a subject who carries a TTR gene mutation that is associated with the development of a TTR-associated disease.
  • the TTR-associated disease is selected from the group consisting of senile systemic amyloidosis (SSA), systemic familial amyloidosis, familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy (FAC), leptomeningeal/Central Nervous System (CNS) amyloidosis, and hyperthyroxinemia.
  • SSA senile systemic amyloidosis
  • FAP familial amyloidotic polyneuropathy
  • FAC familial amyloidotic cardiomyopathy
  • CNS central Nervous System
  • the subject has a TTR-associated amyloidosis and the method reduces an amyloid TTR deposit in the subject.
  • the subcutaneous administration includes administration via a subcutaneous pump or subcutaneous depot. In one embodiment, the subcutaneous administration comprises administration via a subcutaneous infusion pump. In one embodiment, the RNAi agent is administered to the subject as a single 500 mg dose. In one embodiment, the RNAi agent is administered to the subject over of period of 5-20, 5- 10, 5- 15, 10- 15, 10-20, or 15-20 minutes. In another embodiment, the RNAi agent is administered to the subject over of period of 15 minutes or less, 10 minutes or less, or 5 minutes or less.
  • the RNAi agent is administered to the subject as a single dose 500 mg dose. In another embodiment, the RNAi agent is administered to the subject as a split 500 mg dose.
  • kits for performing the methods of the invention include an RNAi agent of the invention, such as AD-51547, having the following structure:
  • kits may optionally contain means for administering the RNAi agent to the subject, such as an injection device or an infusion pump.
  • Figure 1 is a graph depicting that administering to mice a single subcutaneous dose of a GalN Ac-conjugated RNAi agent targeting TTR resulted in dose-dependent suppression of TTR mRNA.
  • Figure 2 is a graph depicting that administering to mice a single subcutaneous dose of 7.5 mg/kg or 30 mg/kg of a GalN Ac conjugated RNAi agent targeting TTR resulted in long lasting suppression of TTR mRNA.
  • Figure 4 is a graph depicting improved silencing activity of RNAi agents modified relative to the parent AD-45163.
  • Figure 5 is a graph depicting improved silencing activity of RNAi agents modified relative to the parent AD-45165.
  • Figure 6 is a graph depicting improved free uptake silencing following 4 hour incubation with RNAi agents modified relative to the parent AD-45163.
  • Figure 10 is a graph depicting silencing of TTR mRNA in transgenic mice that express hTTR V30M following administration of a single subcutaneous dose of RNAi agents AD-51544, AD-51545, AD-45163, AD-51546, AD-51547, or AD-45165.
  • Figure 12 is a graph depicting TTR protein suppression in transgenic mice that express hTTR V30M following administration of a single subcutaneous dose of 5 mg/kg or lmg/kg of RNAi agents AD-51546, AD-51547, or AD-45165.
  • Figure 13 depicts the protocol for post-dose blood draws in monkeys that received 5x5mg/kg RNAi agent (top line) or lx25mg/kg RNAi agent (bottom line).
  • Figures 14A and 14B are graphs depicting suppression of TTR protein in non- human primates following subcutaneous administration of five 5 mg/kg doses ( Figure 14A) or a single 25mg/kg dose ( Figure 14B) of AD-45163, AD-51544, AD-51545, AD- 51546, or AD-51547.
  • Figure 15 is a graph depicting suppression of TTR protein in non-human primates following subcutaneous administration of AD-51547 at 2.5 mg/kg (white squares), 5 mg/kg (black squares) or 10 mg/kg (patterned squares) per dose, or administration of PBS as a negative control (gray squares).
  • Figures 16A- 16D are graphs depicting serum levels of IL-6 (A), TNF alpha (B), G-CSF (C), and CRP (D) in human subjects administered the indicated doses of AD- 51547.
  • Figure 18 is a graph depicting the mean TTR knockdown relative to baseline in human subjects administered a single dose of AD-51547 as indicated.
  • Figure 19 is a graph depicting the mean TTR knockdown relative to baseline in human subjects administered a multiple dose of 2.5 mg/kg, 5 mg/kg, or 10 mg/kg of
  • strand comprising a sequence refers to an
  • RNAi agent refers to a complex of ribonucleic acid molecules, having a duplex structure comprising two anti-parallel and substantially complementary, as defined below, nucleic acid strands.
  • nucleic acid strands In general, the majority of nucleotides of each strand are ribonucleotides, but as described in detail herein, each or both strands can also include one or more non-ribonucleotides, e.g., a deoxyribonucleotide and/or a modified nucleotide.
  • an "RNAi agent” may include ribonucleotides with chemical modifications; an RNAi agent may include substantial modifications at multiple nucleotides. Such modifications may include all types of modifications disclosed herein or known in the art. Any such modifications, as used in a siRNA type molecule, are encompassed by "RNAi agent" for the purposes of this specification and claims.
  • the two strands forming the duplex structure may be different portions of one larger RNA molecule, or they may be separate RNA molecules. Where the two strands are part of one larger molecule, and therefore are connected by an uninterrupted chain of nucleotides between the 3 '-end of one strand and the 5 '-end of the respective other strand forming the duplex structure, the connecting RNA chain is referred to as a "hairpin loop.” Where the two strands are connected covalently by means other than an uninterrupted chain of nucleotides between the 3 '-end of one strand and the 5 '-end of the respective other strand forming the duplex structure, the connecting structure is referred to as a "linker.”
  • the RNA strands may have the same or a different number of nucleotides.
  • RNAi agent may comprise one or more nucleotide overhangs.
  • siRNA is also used herein to refer to an RNAi agent as described above.
  • nucleotide overhang refers to the unpaired nucleotide or nucleotides that protrude from the duplex structure of an RNAi agent when a 3 '-end of one strand of the RNAi agent extends beyond the 5 '-end of the other strand, or vice versa.
  • Bount or “blunt end” means that there are no unpaired nucleotides at that end of the double stranded RNAi agent, i.e., no nucleotide overhang.
  • RNAi agent is a dsRNA that is double- stranded over its entire length, i.e., no nucleotide overhang at either end of the molecule.
  • the RNAi agents of the invention include RNAi agents with nucleotide overhangs at one end (i.e., agents with one overhang and one blunt end) or with nucleotide overhangs at both ends.
  • the term "complementary,” when used to describe a first nucleotide sequence in relation to a second nucleotide sequence, refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as will be understood by the skilled person.
  • Such conditions can, for example, be stringent conditions, where stringent conditions may include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50°C or 70°C for 12- 16 hours followed by washing.
  • “Complementary” sequences may also include, or be formed entirely from, non-Watson-Crick base pairs and/or base pairs formed from non-natural and modified nucleotides, in as far as the above requirements with respect to their ability to hybridize are fulfilled.
  • non- Watson-Crick base pairs includes, but not limited to, G:U Wobble or Hoogstein base pairing.
  • inhibitor as used herein, is used interchangeably with “reducing,” “silencing,” “downregulating,” “suppressing” and other similar terms, and includes any level of inhibition.
  • “Inhibiting expression of a TTR gene” includes any level of inhibition of a TTR gene, e.g., at least partial suppression of the expression of a TTR gene, such as an inhibition of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%. at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%.
  • TTR gene may be assessed based on the level of any variable associated with TTR gene expression, e.g., TTR mRNA level, TTR protein level, retinol binding protein level, vitamin A level, or the number or extent of amyloid deposits. Inhibition may be assessed by a decrease in an absolute or relative level of one or more of these variables compared with a control level.
  • the control level may be any type of control level that is utilized in the art, e.g., a pre-dose baseline level, or a level determined from a similar subject, cell, or sample that is untreated or treated with a control (such as, e.g., buffer only control or inactive agent control).
  • contacting a cell with an RNAi agent includes contacting a cell by any possible means.
  • Contacting a cell with an RNAi agent includes contacting a cell in vitro with the RNAi agent or contacting a cell in vivo with the RNAi agent.
  • the contacting may be done directly or indirectly.
  • the RNAi agent may be put into physical contact with the cell by the individual performing the method, or alternatively, the RNAi agent may be put into a situation that will permit or cause it to subsequently come into contact with the cell.
  • a cell might also be contacted in vitro with an RNAi agent and subsequently transplanted into a subject.
  • a "patient” or “subject,” as used herein, is intended to include either a human or non-human animal, preferably a mammal, e.g., a monkey. Most preferably, the subject or patient is a human.
  • TTR-associated disease is intended to include any disease associated with the TTR gene or protein. Such a disease may be caused, for example, by excess production of the TTR protein, by TTR gene mutations, by abnormal cleavage of the TTR protein, by abnormal interactions between TTR and other proteins or other endogenous or exogenous substances.
  • a "TTR-associated disease” includes any type of TTR amyloidosis (ATTR) wherein TTR plays a role in the formation of abnormal extracellular aggregates or amyloid deposits.
  • TTR-associated diseases include senile systemic amyloidosis (SSA), systemic familial amyloidosis, familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy (FAC),
  • TTR amyloidosis e.g. , central Nervous System (CNS) amyloidosis, amyloidotic vitreous opacities, carpal tunnel syndrome, and hyperthyroxinemia.
  • Symptoms of TTR amyloidosis include sensory neuropathy (e.g. , paresthesia, hypesthesia in distal limbs), autonomic neuropathy (e.g.
  • RNAi agent that, when administered to a subject who does not yet experience or display symptoms of a TTR-associated disease, but who may be predisposed to the disease, is sufficient to prevent or ameliorate the disease or one or more symptoms of the disease.
  • Symptoms that may be ameliorated include sensory neuropathy (e.g.
  • autonomic neuropathy e.g., gastrointestinal dysfunction, such as gastric ulcer, or orthostatic hypotension
  • motor neuropathy seizures, dementia, myelopathy, polyneuropathy, carpal tunnel syndrome, autonomic insufficiency, cardiomyopathy, vitreous opacities, renal insufficiency, nephropathy, substantially reduced mBMI (modified Body Mass Index), cranial nerve dysfunction, and corneal lattice dystrophy.
  • Ameliorating the disease includes slowing the course of the disease or reducing the severity of later-developing disease.
  • the "prophylactically effective amount” may vary depending on the RNAi agent, how the agent is administered, the degree of risk of disease, and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.
  • a “therapeutically-effective amount” or “prophylacticaly effective amount” also includes an amount of an RNAi agent that produces some desired local or systemic effect at a reasonable benefit/risk ratio applicable to any treatment.
  • RNAi gents employed in the methods of the present invention may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment.
  • sample includes a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject.
  • biological fluids include blood, serum and serosal fluids, plasma, cerebrospinal fluid, ocular fluids, lymph, urine, saliva, and the like.
  • Tissue samples may include samples from tissues, organs or localized regions.
  • samples may be derived from particular organs, parts of organs, or fluids or cells within those organs.
  • samples may be derived from the liver (e.g. , whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g.
  • hepatocytes the retina or parts of the retina (e.g., retinal pigment epithelium), the central nervous system or parts of the central nervous system (e.g., ventricles or choroid plexus), or the pancreas or certain cells or parts of the pancreas.
  • a "sample derived from a subject” refers tocerebro spinal fluid obtained from the subject.
  • a “sample derived from a subject” refers to blood or plasma drawn from the subject.
  • a “sample derived from a subject” refers to liver tissue (or subcomponents thereof) or retinal tissue (or subcomponents thereof) derived from the subject.
  • the present invention provides RNAi agents with superior gene silencing activity. It is shown herein and in PCT Publication No. WO 2013/075035 (the entire contents of which are incorporated by reference) that a superior result may be obtained by introducing one or more motifs of three identical modifications on three consecutive nucleotides into a sense strand and/or antisense strand of a RNAi agent, particularly at or near the cleavage site. The sense strand and antisense strand of the RNAi agent may otherwise be completely modified. The introduction of these motifs interrupts the modification pattern, if present, of the sense and/or antisense strand.
  • the RNAi agent also optionally conjugates with a GalNAc derivative ligand, for instance on the sense strand. The resulting RNAi agents present superior gene silencing activity.
  • RNAi agents e.g., double stranded RNAi agents, capable of inhibiting the expression of a target gene (i.e., a TTR gene) in vivo.
  • the RNAi agent comprises a sense strand and an antisense strand.
  • Each strand of the RNAi agent can range from 12-30 nucleotides in length.
  • each strand can be between 14-30 nucleotides in length, 17-30 nucleotides in length, 25-30 nucleotides in length, 27-30 nucleotides in length, 17-23 nucleotides in length, 17-21 nucleotides in length, 17-19 nucleotides in length, 19-25 nucleotides in length, 19-23 nucleotides in length, 19-21 nucleotides in length, 21-25 nucleotides in length, or 21-23 nucleotides in length.
  • RNAi agent a duplex double stranded RNA
  • the duplex region of an RNAi agent may be 12-30 nucleotide pairs in length.
  • the duplex region can be between 14-30 nucleotide pairs in length, 17-30 nucleotide pairs in length, 27-30 nucleotide pairs in length, 17 - 23 nucleotide pairs in length, 17-21 nucleotide pairs in length, 17-19 nucleotide pairs in length, 19-25 nucleotide pairs in length, 19-23 nucleotide pairs in length, 19- 21 nucleotide pairs in length, 21-25 nucleotide pairs in length, or 21-23 nucleotide pairs in length.
  • the duplex region is selected from 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27.
  • the RNAi agent may contain one or more overhang regions and/or capping groups of RNAi agent at 3 '-end, or 5 '-end or both ends of a strand.
  • the overhang can be 1-6 nucleotides in length, for instance 2-6 nucleotides in length, 1-5 nucleotides in length, 2-5 nucleotides in length, 1-4 nucleotides in length, 2-4 nucleotides in length, 1-3 nucleotides in length, 2-3 nucleotides in length, or 1-2 nucleotides in length.
  • the overhangs can be the result of one strand being longer than the other, or the result of two strands of the same length being staggered.
  • the overhang can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be other sequence.
  • the first and second strands can also be joined, e.g., by additional bases to form a hairpin, or by other non-base linkers.
  • RNAi agents provided by the present invention include agents with chemical modifications as disclosed, for example, in U.S. Provisional Application No.
  • the nucleotides in the overhang region of the RNAi agent can each independently be a modified or unmodified nucleotide including, but no limited to 2'-sugar modified, such as, 2-F, 2'-0-methyl, thymidine (T), 2 -0-methoxyethyl-5- methyluridine (Teo), 2 -0-methoxyethyladenosine (Aeo), 2 -0-methoxyethyl-5- methylcytidine (m5Ceo), and any combinations thereof.
  • TT can be an overhang sequence for either end on either strand.
  • the overhang can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be other sequence.
  • the RNAi agent may contain only a single overhang, which can strengthen the interference activity of the RNAi, without affecting its overall stability.
  • the single- stranded overhang is located at the 3 '-terminal end of the sense strand or, alternatively, at the 3 '-terminal end of the antisense strand.
  • the RNAi may also have a blunt end, located at the 5 '-end of the antisense strand (or the 3 '-end of the sense strand) or vice versa.
  • the antisense strand of the RNAi has a nucleotide overhang at the 3 '-end, and the 5 '-end is blunt. While the Applicants are not bound by theory, the theoretical mechanism is that the asymmetric blunt end at the 5 '-end of the antisense strand and 3 '-end overhang of the antisense strand favor the guide strand loading into RISC process.
  • the RNAi agent is a double ended bluntmer of 19 nt in length, wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides at positions 7,8,9 from the 5'end.
  • the antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5'end.
  • the RNAi agent is a double ended bluntmer of 20 nt in length, wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides at positions 8,9,10 from the 5'end.
  • the antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5'end.
  • the RNAi agent is a double ended bluntmer of 21 nt in length, wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides at positions 9, 10, 11 from the 5'end.
  • the antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5'end.
  • the RNAi agent comprises a 21 nucleotides (nt) sense strand and a 23 nucleotides (nt) antisense strand, wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides at positions 9,10,11 from the 5'end; the antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5'end, wherein one end of the RNAi agent is blunt, while the other end comprises a 2 nt overhang.
  • the 2 nt overhang is at the 3 '-end of the antisense.
  • the RNAi agent further comprises a ligand (preferably GalNAc 3 ).
  • antisense strand is sufficiently complementary to a target RNA along at least 19 ribonucleotides of antisense strand length to reduce target gene expression when the double stranded nucleic acid is introduced into a mammalian cell; and wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides, where at least one of the motifs occurs at or near the cleavage site.
  • the antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at or near the cleavage site.
  • the RNAi agent further comprises a ligand.
  • the sense strand of the RNAi agent contains at least one motif of three identical modifications on three consecutive nucleotides, where one of the motifs occurs at the cleavage site in the sense strand.
  • the antisense strand of the RNAi agent can also contain at least one motif of three identical modifications on three consecutive nucleotides, where one of the motifs occurs at or near the cleavage site in the antisense strand
  • the sense strand of the RNAi agent may contain at least one motif of three identical modifications on three consecutive nucleotides at the cleavage site of the strand; and the antisense strand may have at least one motif of three identical modifications on three consecutive nucleotides at or near the cleavage site of the strand.
  • the sense strand and the antisense strand can be so aligned that one motif of the three nucleotides on the sense strand and one motif of the three nucleotides on the antisense strand have at least one nucleotide overlap, i.e., at least one of the three nucleotides of the motif in the sense strand forms a base pair with at least one of the three nucleotides of the motif in the antisense strand.
  • at least two nucleotides may overlap, or all three nucleotides may overlap.
  • the sense strand of the RNAi agent may contain more than one motif of three identical modifications on three consecutive nucleotides.
  • the first motif should occur at or near the cleavage site of the strand and the other motifs may be wing modifications.
  • the term "wing modification" herein refers to a motif occurring at another portion of the strand that is separated from the motif at or near the cleavage site of the same strand.
  • the wing modification is either adajacent to the first motif or is separated by at least one or more nucleotides.
  • the motifs are immediately adjacent to each other than the chemistry of the motifs are distinct from each other and when the motifs are separated by one or more nucleotide than the chemistries can be the same or different.
  • Two or more wing modifications may be present. For instance, when two wing modifications are present, each wing modification may occur at one end relative to the first motif which is at or near cleavage site or on either side of the lead motif.
  • the wing modification on the sense strand or antisense strand of the RNAi agent typically does not include the first one or two terminal nucleotides at the 3 '-end, 5 '-end or both ends of the strand.
  • the RNAi agent comprises the pattern of the alternating motif of 2'-0-methyl modification and 2'-F modification on the sense strand initially has a shift relative to the pattern of the alternating motif of 2'-0-methyl modification and 2'-F modification on the antisense strand initially, i.e., the 2'-0-methyl modified nucleotide on the sense strand base pairs with a 2'-F modified nucleotide on the antisense strand and vice versa.
  • the 1 position of the sense strand may start with the 2'- F modification
  • the 1 position of the antisense strand may start with the 2'- O- methyl modification.
  • the RNAi agent may further comprise at least one phosphorothioate or methylphosphonate internucleotide linkage.
  • methylphosphonate internucleotide linkage modification may occur on any nucleotide of the sense strand or antisense strand or both in any position of the strand.
  • the internucleotide linkage modification may occur on every nucleotide on the sense strand or antisense strand; each internucleotide linkage modification may occur in an alternating pattern on the sense strand or antisense strand; or the sense strand or antisense strand may contain both internucleotide linkage modifications in an alternating pattern.
  • the alternating pattern of the internucleotide linkage modification on the sense strand may be the same or different from the antisense strand, and the alternating pattern of the internucleotide linkage modification on the sense strand may have a shift relative to the alternating pattern of the internucleotide linkage modification on the antisense strand.
  • the RNAi comprises the phosphorothioate or
  • the overhang region may contain two nucleotides having a phosphorothioate or methylphosphonate internucleotide linkage between the two nucleotides.
  • Internucleotide linkage modifications also may be made to link the overhang nucleotides with the terminal paired nucleotides within duplex region. For example, at least 2, 3, 4, or all the overhang nucleotides may be linked through phosphorothioate or
  • methylphosphonate internucleotide linkage and optionally, there may be additional phosphorothioate or methylphosphonate internucleotide linkages linking the overhang nucleotide with a paired nucleotide that is next to the overhang nucleotide.
  • additional phosphorothioate or methylphosphonate internucleotide linkages linking the overhang nucleotide with a paired nucleotide that is next to the overhang nucleotide.
  • these terminal three nucleotides may be at the 3 '-end of the antisense strand.
  • the RNAi agent comprises mismatch(es) with the target, within the duplex, or combinations thereof.
  • the mistmatch can occur in the overhang region or the duplex region.
  • the base pair can be ranked on the basis of their propensity to promote dissociation or melting (e.g. , on the free energy of association or dissociation of a particular pairing, the simplest approach is to examine the pairs on an individual pair basis, though next neighbor or similar analysis can also be used).
  • A:U is preferred over G:C
  • G:U is preferred over G:C
  • Mismatches e.g. , non-canonical or other than canonical pairings (as described elsewhere herein) are preferred over canonical (A:T, A:U, G:C) pairings; and pairings which include a universal base are preferred over canonical pairings.
  • the RNAi agent comprises at least one of the first 1, 2, 3, 4, or 5 base pairs within the duplex regions from the 5'- end of the antisense strand can be chosen independently from the group of: A:U, G:U, I:C, and mismatched pairs, e.g. , non-canonical or other than canonical pairings or pairings which include a universal base, to promote the dissociation of the antisense strand at the 5'-end of the duplex.
  • the nucleotide at the 1 position within the duplex region from the 5 '-end in the antisense strand is selected from the group consisting of A, dA, dU, U, and dT.
  • At least one of the first 1, 2 or 3 base pair within the duplex region from the 5'- end of the antisense strand is an AU base pair.
  • the first base pair within the duplex region from the 5'- end of the antisense strand is an AU base pair.
  • the sense strand sequence may be represented by formula
  • i and j are each independently 0 or 1 ;
  • each N a independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;
  • i is 1 and j is 0, or i is 0 and j is 1, or both i and j are 1.
  • the sense strand can therefore be represented by the following formulas:
  • k and 1 are each independently 0 or 1 ;
  • p' and q' are each independently 0-6;
  • each N a ' independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;
  • N b ' and Y' do not have the same modification
  • ⁇ ' ⁇ ' ⁇ ', ⁇ ' and Z'Z'Z' each independently represent one motif of three identical modifications on three consecutive nucleotides.
  • the N a ' and/or N b ' comprise modifications of alternating pattern.
  • ⁇ ' motif is all 2'-OMe modified nucleotides.
  • k is 1 and 1 is 0, or k is 0 and 1 is 1, or both k and 1 are 1.
  • the antisense strand can therefore be represented by the following formulas:
  • N b represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides.
  • Each N a ' independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
  • N b ' represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides.
  • Each N a ' independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
  • Each N a ' independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
  • N b is 0, 1, 2, 3, 4, 5 or 6.
  • Each of X', Y' and Z' may be the same or different from each other.
  • Each nucleotide of the sense strand and antisense strand may be independently modified with LNA, UNA, CRN, cEt, HNA, CeNA, 2'-methoxyethyl, 2'-0-methyl, 2'- O-allyl, 2'-C- allyl, 2'-hydroxyl, 2'-deoxy or 2'-fluoro.
  • each nucleotide of the sense strand and antisense strand is independently modified with 2'-0-methyl or 2'- fluoro.
  • Each X, Y, Z, X', Y' and Z' in particular, may represent a 2'-0-methyl modification or a 2' -fluoro modification.
  • the sense strand of the RNAi agent may contain YYY motif occurring at 9, 10 and 11 positions of the strand when the duplex region is 21 nt, the count starting from the 1 st nucleotide from the 5 '-end, or optionally, the count starting at the 1 st paired nucleotide within the duplex region, from the 5'- end; and Y represents 2'- F modification.
  • the sense strand may additionally contain XXX motif or ZZZ motifs as wing modifications at the opposite end of the duplex region; and XXX and ZZZ each independently represents a 2'-OMe modification or 2'-F modification.
  • the sense strand represented by any one of the above formulas (la), (lb) and (Ic) forms a duplex with a antisense strand being represented by any one of formulas (Ila), (lib) and (lie), respectively.
  • i, j, k, and 1 are each independently 0 or 1;
  • each N b and N b independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides
  • each n p ', n p , n q ', and n q independently represents an overhang nucleotide; and XXX, YYY, ZZZ, X'X'X', Y'Y'Y', and Z'Z'Z' each independently represent one motif of three identical modifications on three consecutive nucleotides.
  • i is 1 and j is 0; or i is 0 and j is 1; or both i and j are 1.
  • k is 1 and 1 is 0; k is 0 and 1 is 1; or both k and 1 are 1.
  • each N a independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or Omodified nucleotides.
  • Each N a independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or Omodified nucleotides.
  • Each N a independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or Omodified nucleotides.
  • Each N a independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or Omodified nucleotides.
  • Each N a independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7,
  • N a , N a independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or Omodified nucleotides.
  • Each N a , N a independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
  • Each of N a , N a ', N b and N b independently comprises modifications of alternating pattern.
  • the acyclic group is selected from serinol backbone or diethanolamine backbone.
  • D1200 D1201, D1202, D1203, D1204, D1205, D1206, D1207, D1208, D1209, D1210,
  • RNAi agents of the invention may optionally be conjugated to one or more ligands.
  • the ligand can be attached to the sense strand, antisense strand or both strands, at the 3 '-end, 5 '-end or both ends.
  • the ligand may be conjugated to the sense strand.
  • the ligand is conjgated to the 3 '-end of the sense strand.
  • the ligand is a GalNAc ligand.
  • the ligand is GalNAc 3 :
  • RNAi agents of the present invention A wide variety of entities can be coupled to the RNAi agents of the present invention.
  • Preferred moieties are ligands, which are coupled, preferably covalently, either directly or indirectly via an intervening tether.
  • Ligands in general can include therapeutic modifiers, e.g., for enhancing uptake; diagnostic compounds or reporter groups e.g., for monitoring distribution; cross-linking agents; and nuclease-resistance conferring moieties.
  • therapeutic modifiers e.g., for enhancing uptake
  • diagnostic compounds or reporter groups e.g., for monitoring distribution
  • cross-linking agents e.g., for monitoring distribution
  • nuclease-resistance conferring moieties lipids, steroids, vitamins, sugars, proteins, peptides, polyamines, and peptide mimics.
  • Ligands can include a naturally occurring substance, such as a protein ⁇ e.g., human serum albumin (HSA), low-density lipoprotein (LDL), high-density lipoprotein (HDL), or globulin); a carbohydrate ⁇ e.g., a dextran, pullulan, chitin, chitosan, inulin, cyclodextrin or hyaluronic acid); or a lipid.
  • the ligand may also be a recombinant or synthetic molecule, such as a synthetic polymer, e.g., a synthetic polyamino acid, an oligonucleotide ⁇ e.g., an aptamer).
  • polyamino acids examples include polyamino acid is a polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydride copolymer, poly(L-lactide-co-glycolied) copolymer, divinyl ether-maleic anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyurethane, poly(2-ethylacryllic acid), N-isopropylacrylamide polymers, or polyphosphazine.
  • PLL polylysine
  • poly L-aspartic acid poly L-glutamic acid
  • styrene-maleic acid anhydride copolymer poly(L-lactide-co-glycolied) copolymer
  • divinyl ether-maleic anhydride copolymer divinyl ether-
  • ligands include dyes, intercalating agents (e.g., acridines), cross-linkers (e.g., psoralene, mitomycin C), porphyrins (TPPC4, texaphyrin,
  • intercalating agents e.g., acridines
  • cross-linkers e.g., psoralene, mitomycin C
  • porphyrins TPPC4, texaphyrin
  • Ligands can be proteins, e.g., glycoproteins, or peptides, e.g., molecules having a specific affinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified cell type such as a cancer cell, endothelial cell, or bone cell.
  • Ligands may also include hormones and hormone receptors. They can also include non-peptidic species, such as lipids, lectins, carbohydrates, vitamins, cofactors, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose, multivalent fucose, or aptamers.
  • the ligand can be, for example, a lipopolysaccharide, an activator of p38 MAP kinase, or an activator of NF-KB.
  • RGD peptides cyclic peptides containing RGD, RGD peptides that include D-amino acids, as well as synthetic RGD mimics.
  • RGD one can use other moieties that target the integrin ligand.
  • ligands can be used to control proliferating cells and angiogeneis.
  • Preferred conjugates of this type of ligand target PECAM-1, VEGF, or other cancer gene, e.g., a cancer gene described herein.
  • the ligands can all have same properties, all have different properties or some ligands have the same properties while others have different properties.
  • a ligand can have targeting properties, have endosomolytic activity or have PK modulating properties.
  • all the ligands have different properties.
  • ligands can be attached to one or both strands.
  • a double- stranded iRNA agent contains a ligand conjugated to the sense strand.
  • a double- stranded iRNA agent contains a ligand conjugated to the antisense strand.
  • the position can also be attached to a conjugate moiety, such as in an abasic residue.
  • Internucleosidic linkages can also bear conjugate moieties.
  • phosphorus-containing linkages e.g. , phosphodiester, phosphorothioate,
  • q 2A ,q 2B ,q 3A ,q 3B ,q4 ,, ⁇ ,q 4B ,q 5A ,q 5B and i q 5C represent .
  • p2A p2B p3A p3B p4A p4B p5A p5B p5C r 2A r 2B r 3A r 3B r 4A r 4B r 4A r 5B r 5C each independently for each occurrence absent, CO, NH, O, S, OC(O), NHC(O), CH 2 , CH 2 NHorCH 2 0;
  • R a is H or amino acid side chain.
  • the buffer solution further comprises an agent for controlling the osmolarity of the solution, such that the osmolarity is kept at a desired value, e.g. , at the physiologic values of the human plasma.
  • Solutes which can be added to the buffer solution to control the osmolarity include, but are not limited to, proteins, peptides, amino acids, non-metabolized polymers, vitamins, ions, sugars, metabolites, organic acids, lipids, or salts.
  • the agent for controlling the osmolarity of the solution is a salt.
  • the agent for controlling the osmolarity of the solution is sodium chloride or potassium chloride.
  • the RNAi agent preparation includes at least a second therapeutic agent (e.g., an agent other than an RNA or a DNA).
  • a second therapeutic agent e.g., an agent other than an RNA or a DNA
  • an RNAi agent composition for the treatment of a TTR-associated disease e.g., a transthyretin- related hereditary amyloidosis (familial amyloid polyneuropathy, FAP)
  • FAP transthyretin- related hereditary amyloidosis
  • a known drug for the amelioration of FAP e.g., Tafamidis (INN, or Fx-1006A or Vyndaqel).
  • a formulated RNAi agent composition can assume a variety of states.
  • the composition is at least partially crystalline, uniformly crystalline, and/or anhydrous (e.g., it contains less than 80, 50, 30, 20, or 10% of water).
  • the RNAi agent is in an aqueous phase, e.g., in a solution that includes water.
  • aqueous phase or the crystalline compositions can be incorporated into a delivery vehicle, e.g., a liposome (particularly for the aqueous phase) or a particle (e.g., a microparticle as can be appropriate for a crystalline composition).
  • a delivery vehicle e.g., a liposome (particularly for the aqueous phase) or a particle (e.g., a microparticle as can be appropriate for a crystalline composition).
  • the RNAi agent composition is formulated in a manner that is compatible with the intended method of administration, as described herein.
  • the composition is prepared by at least one of the following methods: spray drying, lyophilization, vacuum drying, evaporation, fluid bed drying, or a combination of these techniques; or sonication with a lipid, freeze-drying, condensation and other self- assembly.
  • RNAi agent preparation can be formulated in combination with another agent, e.g., another therapeutic agent or an agent that stabilizes RNAi agent, e.g., a protein that complexes with the RNAi agent to form an iRNP.
  • another agent e.g., another therapeutic agent or an agent that stabilizes RNAi agent, e.g., a protein that complexes with the RNAi agent to form an iRNP.
  • Still other agents include chelators, e.g., EDTA (e.g., to remove divalent cations such as Mg 2+ ), salts, RNAse inhibitors (e.g., a broad specificity RNAse inhibitor such as RNAsin) and so forth.
  • compositions comprise a therapeutically- or
  • prophylactically effective amount of one or more of the the dsRNA agents in any of the preceding embodiments taken alone or formulated together with one or more pharmaceutically acceptable carriers (additives), excipient and/or diluents.
  • compositions of the invention include the step of bringing into association an RNAi agent of the present invention with the carrier and, optionally, one or more accessory ingredients.
  • the compositions are prepared by uniformly and intimately bringing into association an RNAi agent of the present invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.
  • the pharmaceutical compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral
  • drenches aqueous or non-aqueous solutions or
  • phrases "pharmaceutically acceptable” is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
  • pharmaceutically-acceptable carrier means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body.
  • a pharmaceutically-acceptable material such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body.
  • manufacturing aid e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid
  • solvent encapsulating material involved in carrying or transport
  • compositions may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy.
  • amount of RNAi agent which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, and the particular mode of
  • RNAi agent which can be combined with a carrier material to produce a single dosage form will generally be that amount of the RNAi agent which produces a desired effect, e.g., therapeutic or prophylactic effect. Generally, out of one hundred per cent, this amount will range from about 0.1 per cent to about ninety-nine percent of RNAi agent, preferably from about 5 per cent to about 70 per cent, most preferably from about 10 per cent to about 30 per cent.
  • RNAi agent in order to prolong the effect of an RNAi agent, it is desirable to slow the absorption of the agent from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material having poor water solubility. The rate of absorption of the RNAi agent then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally-administered RNAi agent may be accomplished by dissolving or suspending the agent in an oil vehicle.
  • RNAi agent of the invention can be formulated for delivery in a membranous molecular assembly, e.g., a liposome or a micelle.
  • liposome refers to a vesicle composed of amphiphilic lipids arranged in at least one bilayer, e.g., one bilayer or a plurality of bilayers. Liposomes include unilamellar and multilamellar vesicles that have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the RNAi agent composition.
  • the lipophilic material isolates the aqueous interior from an aqueous exterior, which typically does not include the RNAi agent composition, although in some examples, it may.
  • Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomal bilayer fuses with bilayer of the cellular membranes. As the merging of the liposome and cell progresses, the internal aqueous contents that include the RNAi agent are delivered into the cell where the RNAi agent can specifically bind to a target RNA and can mediate RNAi. In some cases the liposomes are also specifically targeted, e.g., to direct the RNAi agent to particular cell types.
  • a liposome containing an RNAi agent can be prepared by a variety of methods.
  • the lipid component of a liposome is dissolved in a detergent so that micelles are formed with the lipid component.
  • the lipid component can be an amphipathic cationic lipid or lipid conjugate.
  • the detergent can have a high critical micelle concentration and may be nonionic. Exemplary detergents include cholate, CHAPS, octylglucoside, deoxycholate, and lauroyl sarcosine.
  • the RNAi agent preparation is then added to the micelles that include the lipid component.
  • the cationic groups on the lipid interact with the RNAi agent and condense around the RNAi agent to form a liposome.
  • the detergent is removed, e.g., by dialysis, to yield a liposomal preparation of RNAi agent.
  • a carrier compound that assists in condensation can be added during the condensation reaction, e.g., by controlled addition.
  • the carrier compound can be a polymer other than a nucleic acid (e.g., spermine or spermidine). pH can also be adjusted to favor condensation.
  • Liposome formation can also include one or more aspects of exemplary methods described in Feigner, P. L. et al., Proc. Natl. Acad. Set, USA 8:7413-7417, 1987; U.S. Pat. No. 4,897,355; U.S. Pat. No. 5,171,678;
  • Liposomes that are pH-sensitive or negatively-charged entrap nucleic acid molecules rather than complex with them. Since both the nucleic acid molecules and the lipid are similarly charged, repulsion rather than complex formation occurs.
  • nucleic acid molecules are entrapped within the aqueous interior of these liposomes.
  • pH-sensitive liposomes have been used to deliver DNA encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 19, (1992) 269-274).
  • liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine.
  • Neutral liposome compositions for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl
  • phosphatidylcholine DPPC
  • Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE).
  • DOPE dioleoyl phosphatidylethanolamine
  • Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC.
  • PC phosphatidylcholine
  • Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.
  • liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect encapsulated RNAi agents in their internal compartments from metabolism and degradation (Rosoff, in
  • Liposome formulations Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.
  • a positively charged synthetic cationic lipid, N-[l-(2,3-dioleyloxy)propyl]- ⁇ , ⁇ , ⁇ -trimethylammonium chloride can be used to form small liposomes that interact spontaneously with nucleic acid to form lipid-nucleic acid complexes which are capable of fusing with the negatively charged lipids of the cell membranes of tissue culture cells, resulting in delivery of RNAi agent (see, e.g., Feigner, P. L. et al., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987 and U.S. Pat. No. 4,897,355 for a description of DOTMA and its use with DNA).
  • RNAi agent see, e.g., Feigner, P. L. et al., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987 and U.S. Pat. No. 4,897,355 for a
  • a DOTMA analogue, l,2-bis(oleoyloxy)-3-(trimethylammonia)propane (DOTAP) can be used in combination with a phospholipid to form DNA-complexing vesicles.
  • LipofectinTM Bethesda Research Laboratories, Gaithersburg, Md. is an effective agent for the delivery of highly anionic nucleic acids into living tissue culture cells that comprise positively charged DOTMA liposomes which interact spontaneously with negatively charged polynucleotides to form complexes. When enough positively charged liposomes are used, the net charge on the resulting complexes is also positive.
  • DOTAP cationic lipid, l,2-bis(oleoyloxy)-3,3-(trimethylammonia)propane
  • cationic lipid compounds include those that have been conjugated to a variety of moieties including, for example, carboxyspermine which has been conjugated to one of two types of lipids and includes compounds such as 5- carboxyspermylglycine dioctaoleoylamide (“DOGS”) (TransfectamTM, Promega, Madison, Wisconsin) and dipalmitoylphosphatidylethanolamine 5-carboxyspermyl- amide (“DPPES”) (see, e.g., U.S. Pat. No. 5,171,678).
  • DOGS 5- carboxyspermylglycine dioctaoleoylamide
  • DPES dipalmitoylphosphatidylethanolamine 5-carboxyspermyl- amide
  • Another cationic lipid conjugate includes derivatization of the lipid with cholesterol ("DC-Chol") which has been formulated into liposomes in combination with DOPE (See, Gao, X. and Huang, L., Biochim. Biophys. Res. Commun. 179:280, 1991). Lipopolylysine, made by conjugating polylysine to DOPE, has been reported to be effective for transfection in the presence of serum (Zhou, X. et al., Biochim. Biophys. Acta 1065:8, 1991). For certain cell lines, these liposomes containing conjugated cationic lipids, are said to exhibit lower toxicity and provide more efficient transfection than the DOTMA-containing compositions.
  • Other commercially available cationic lipid products include DMRIE and DMRIE-HP (Vical, La Jolla, California) and
  • DOSPA Lipofectamine
  • Liposomal formulations are particularly suited for topical administration, liposomes present several advantages over other formulations. Such advantages include reduced side effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at the desired target, and the ability to administer RNAi agent into the skin.
  • liposomes are used for delivering RNAi agent to epidermal cells and also to enhance the penetration of RNAi agent into dermal tissues, e.g., into skin.
  • the liposomes can be applied topically. Topical delivery of drugs formulated as liposomes to the skin has been documented (see, e.g., Weiner et al., Journal of Drug Targeting, 1992, vol.
  • Papahadjopoulos D. Meth. Enz. 101:512-527, 1983; Wang, C. Y. and Huang, L., Proc. Natl. Acad. Sci. USA 84:7851-7855, 1987).
  • Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol.
  • Non-ionic liposomal formulations comprising Novasome I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome II (glyceryl distearate/ cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver a drug into the dermis of mouse skin.
  • Such formulations with RNAi agent are useful for treating a dermatological disorder.
  • Liposomes that include RNAi agent can be made highly deformable. Such deformability can enable the liposomes to penetrate through pore that are smaller than the average radius of the liposome.
  • transfersomes are a type of deformable liposomes. Transferosomes can be made by adding surface edge activators, usually surfactants, to a standard liposomal composition. Transfersomes that include RNAi agent can be delivered, for example, subcutaneously by infection in order to deliver RNAi agent to keratinocytes in the skin. In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient.
  • these transferosomes can be self-optimizing (adaptive to the shape of pores, e.g., in the skin), self-repairing, and can frequently reach their targets without fragmenting, and often self-loading.
  • Other formulations amenable to the present invention are described in United States provisional application serial Nos. 61/018,616, filed January 2, 2008; 61/018,611, filed January 2, 2008; 61/039,748, filed March 26, 2008; 61/047,087, filed April 22, 2008 and 61/051,528, filed May 8, 2008.
  • PCT application no PCT/US2007/080331, filed October 3, 2007 also describes formulations that are amenable to the present invention.
  • RNAi agent or a precursor, e.g., a larger dsiRNA which can be processed into a siRNA, or a DNA which encodes a siRNA or precursor
  • compositions can include a surfactant.
  • the siRNA is formulated as an emulsion that includes a surfactant.
  • HLB hydrophile/lipophile balance
  • hydrophilic group provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in “Pharmaceutical Dosage Forms,” Marcel Dekker, Inc., New York, NY, 1988, p. 285).
  • Nonionic surfactants find wide application in pharmaceutical products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure.
  • Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters.
  • Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and
  • ethoxylated/propoxylated block polymers are also included in this class.
  • the polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.
  • Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates.
  • the most important members of the anionic surfactant class are the alkyl sulfates and the soaps.
  • Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.
  • amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.
  • RNAi agents of the invention can also be provided as micellar formulations.
  • Micelles are defined herein as a particular type of molecular assembly in which amphipathic molecules are arranged in a spherical structure such that all the
  • hydrophobic portions of the molecules are directed inward, leaving the hydrophilic portions in contact with the surrounding aqueous phase.
  • the converse arrangement exists if the environment is hydrophobic.
  • a mixed micellar formulation suitable for delivery through transdermal membranes may be prepared by mixing an aqueous solution of the siRNA composition, an alkali metal Cg to C 22 alkyl sulphate, and a micelle forming compound.
  • exemplary micelle forming compounds include lecithin, hyaluronic acid, pharmaceutically acceptable salts of hyaluronic acid, glycolic acid, lactic acid, chamomile extract, cucumber extract, oleic acid, linoleic acid, linolenic acid, monoolein, monooleates, monolaurates, borage oil, evening of primrose oil, menthol, trihydroxy oxo cholanyl glycine and pharmaceutically acceptable salts thereof, glycerin, polyglycerin, lysine, polylysine, triolein, polyoxyethylene ethers and analogues thereof, polidocanol alkyl ethers and analogues thereof, chenodeoxycholate, deoxy
  • a first micellar composition which contains the siRNA composition and at least the alkali metal alkyl sulphate.
  • the first micellar composition is then mixed with at least three micelle forming compounds to form a mixed micellar composition.
  • the micellar composition is prepared by mixing the siRNA composition, the alkali metal alkyl sulphate and at least one of the micelle forming compounds, followed by addition of the remaining micelle forming compounds, with vigorous mixing.
  • Phenol and/or m-cresol may be added to the mixed micellar composition to stabilize the formulation and protect against bacterial growth.
  • phenol and/or m-cresol may be added with the micelle forming ingredients.
  • An isotonic agent such as glycerin may also be added after formation of the mixed micellar composition.
  • the formulation can be put into an aerosol dispenser and the dispenser is charged with a propellant.
  • the propellant which is under pressure, is in liquid form in the dispenser.
  • the ratios of the ingredients are adjusted so that the aqueous and propellant phases become one, i.e., there is one phase. If there are two phases, it is necessary to shake the dispenser prior to dispensing a portion of the contents, e.g., through a metered valve.
  • the dispensed dose of pharmaceutical agent is propelled from the metered valve in a fine spray.
  • Propellants may include hydrogen-containing chlorofluorocarbons, hydrogen- containing fluorocarbons, dimethyl ether and diethyl ether.
  • HFA 134a (1,1,1,2 tetrafluoroethane) may be used.
  • the specific concentrations of the essential ingredients can be determined by relatively straightforward experimentation.
  • an RNAi agent of the invention may be incorporated into a particle, e.g., a microparticle.
  • Microparticles can be produced by spray-drying, but may also be produced by other methods including lyophilization, evaporation, fluid bed drying, vacuum drying, or a combination of these techniques. IV. Methods For Inhibiting TTR Expression
  • the present invention also provides methods of inhibiting expression of a transthyretin (TTR) in a cell.
  • the methods include contacting a cell with an RNAi agent, e.g., double stranded RNAi agent, in an amount effective to inhibit expression of TTR in the cell, thereby inhibiting expression of TTR in the cell.
  • an RNAi agent e.g., double stranded RNAi agent
  • RNAi agent e.g., a double stranded RNAi agent
  • Contacting a cell in vivo with the RNAi agent includes contacting a cell or group of cells within a subject, e.g., a human subject, with the RNAi agent. Combinations of in vitro and in vivo methods of contacting a cell are also possible. Contacting a cell may be direct or indirect, as discussed above. Furthermore, contacting a cell may be accomplished via a targeting ligand, including any ligand described herein or known in the art. In preferred embodiments, the targeting ligand is a carbohydrate moiety, e.g. , a GalNAc 3 ligand, or any other ligand that directs the RNAi agent to a site of interest, e.g. , the liver of a subject.
  • the targeting ligand is a carbohydrate moiety, e.g. , a GalNAc 3 ligand, or any other ligand that directs the
  • inhibitor as used herein, is used interchangeably with “reducing,” “silencing,” “downregulating”, “suppressing”, and other similar terms, and includes any level of inhibition.
  • TTR tumor necrosis factor receptor
  • any TTR gene such as, e.g. , a mouse TTR gene, a rat TTR gene, a monkey TTR gene, or a human TTR gene
  • the TTR gene may be a wild-type TTR gene, a mutant TTR gene (such as a mutant TTR gene giving rise to amyloid deposition), or a transgenic TTR gene in the context of a genetically manipulated cell, group of cells, or organism.
  • “Inhibiting expression of a TTR gene” includes any level of inhibition of a TTR gene, e.g. , at least partial suppression of the expression of a TTR gene.
  • the expression of the TTR gene may be assessed based on the level, or the change in the level, of any variable associated with TTR gene expression, e.g. , TTR mRNA level, TTR protein level, or the number or extent of amyloid deposits. This level may be assessed in an individual cell or in a group of cells, including, for example, a sample derived from a subject.
  • Inhibition may be assessed by a decrease in an absolute or relative level of one or more variables that are associated with TTR expression compared with a control level.
  • the control level may be any type of control level that is utilized in the art, e.g., a pre- dose baseline level, or a level determined from a similar subject, cell, or sample that is untreated or treated with a control (such as, e.g., buffer only control or inactive agent control).
  • expression of a TTR gene is inhibited by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%,at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%. at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%.
  • Inhibition of the expression of a TTR gene may be manifested by a reduction of the amount of mRNA expressed by a first cell or group of cells (such cells may be present, for example, in a sample derived from a subject) in which a TTR gene is transcribed and which has or have been treated (e.g., by contacting the cell or cells with an RNAi agent of the invention, or by administering an RNAi agent of the invention to a subject in which the cells are or were present) such that the expression of a TTR gene is inhibited, as compared to a second cell or group of cells substantially identical to the first cell or group of cells but which has not or have not been so treated (control cell(s)).
  • the inhibition is assessed by expressing the level of mRNA in treated cells as a percentage of the level of mRNA in control cells, using the following formula:
  • TTR gene silencing may be determined in any cell expressing TTR, either constitutively or by genomic engineering, and by any assay known in the art.
  • the liver is the major site of TTR expression. Other significant sites of expression include the choroid plexus, retina and pancreas.
  • Inhibition of the expression of a TTR protein may be manifested by a reduction in the level of the TTR protein that is expressed by a cell or group of cells (e.g., the level of protein expressed in a sample derived from a subject).
  • the inhibiton of protein expression levels in a treated cell or group of cells may similarly be expressed as a percentage of the level of protein in a control cell or group of cells.
  • a control cell or group of cells that may be used to assess the inhibition of the expression of a TTR gene includes a cell or group of cells that has not yet been contacted with an RNAi agent of the invention.
  • the control cell or group of cells may be derived from an individual subject (e.g., a human or animal subject) prior to treatment of the subject with an RNAi agent.
  • the level of TTR mRNA that is expressed by a cell or group of cells, or the level of circulating TTR mRNA may be determined using any method known in the art for assessing mRNA expression.
  • the level of expression of TTR in a sample is determined by detecting a transcribed polynucleotide, or portion thereof, e.g., mRNA of the TTR gene.
  • RNA may be extracted from cells using RNA extraction techniques including, for example, using acid phenol/guanidine isothiocyanate extraction (RNAzol B; Biogenesis), RNeasy RNA preparation kits (Qiagen) or PAXgene (PreAnalytix, Switzerland).
  • RNAzol B acid phenol/guanidine isothiocyanate extraction
  • RNeasy RNA preparation kits Qiagen
  • PAXgene PreAnalytix, Switzerland.
  • the level of expression of TTR is determined using a nucleic acid probe.
  • probe refers to any molecule that is capable of selectively binding to a specific TTR. Probes can be synthesized by one of skill in the art, or derived from appropriate biological preparations. Probes may be specifically designed to be labeled. Examples of molecules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic molecules.
  • Isolated mRNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, polymerase chain reaction (PCR) analyses and probe arrays.
  • One method for the determination of mRNA levels involves contacting the isolated mRNA with a nucleic acid molecule (probe) that can hybridize to TTR mRNA.
  • the mRNA is immobilized on a solid surface and contacted with a probe, for example by running the isolated mRNA on an agarose gel and transferring the mRNA from the gel to a membrane, such as nitrocellulose.
  • the probe(s) are immobilized on a solid surface and the mRNA is contacted with the probe(s), for example, in an Affymetrix gene chip array.
  • a skilled artisan can readily adapt known mRNA detection methods for use in determining the level of TTR mRNA.
  • An alternative method for determining the level of expression of TTR in a sample involves the process of nucleic acid amplification and/or reverse transcriptase (to prepare cDNA) of for example mRNA in the sample, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88: 189-193), self sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87: 1874-1878),
  • the level of expression of TTR is determined by quantitative fluorogenic RT-PCR (i.e., the TaqManTM System).
  • TTR mRNA The expression levels of TTR mRNA may be monitored using a membrane blot
  • TTR expression level may also comprise using nucleic acid probes in solution.
  • the level of mRNA expression is assessed using branched DNA (bDNA) assays or real time PCR (qPCR).
  • bDNA branched DNA
  • qPCR real time PCR
  • the level of TTR protein expression may be determined using any method known in the art for the measurement of protein levels. Such methods include, for example, electrophoresis, capillary electrophoresis, high performance liquid
  • HPLC high resolution liquid chromatography
  • TLC thin layer chromatography
  • the efficacy of the methods of the invention can be monitored by detecting or monitoring a reduction in an amyloid TTR deposit.
  • Reducing an amyloid TTR deposit includes any decrease in the size, number, or severity of TTR deposits, or to a prevention or reduction in the formation of TTR deposits, within an organ or area of a subject, as may be assessed in vitro or in vivo using any method known in the art. For example, some methods of assessing amyloid deposits are described in Gertz, M.A. & Rajukumar, S.V. (Editors) (2010), Amyloidosis: Diagnosis and Treatment, New York: Humana Press.
  • Methods of assessing amyloid deposits may include biochemical analyses, as well as visual or computerized assessment of amyloid deposits, as made visible, e.g., using immunohistochemical staining, fluorescent labeling, light microscopy, electron microscopy, fluorescence microscopy, or other types of microscopy.
  • Invasive or noninvasive imaging modalities including, e.g., CT, PET, or NMR/MRI imaging may be employed to assess amyloid deposits.
  • the methods of the invention may reduce TTR deposits in any number of tissues or regions of the body including but not limited to the heart, liver, spleen, esophagus, stomach, intestine (ileum, duodenum and colon), brain, sciatic nerve, dorsal root ganglion, kidney and retina.
  • sample refers to a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject.
  • biological fluids include blood, serum and serosal fluids, plasma, lymph, urine, cerebrospinal fluid, saliva, ocular fluids, and the like.
  • Tissue samples may include samples from tissues, organs or localized regions.
  • samples may be derived from particular organs, parts of organs, or fluids or cells within those organis.
  • samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g.
  • hepatocytes the retina or parts of the retina (e.g., retinal pigment epithelium), the central nervous system or parts of the central nervous system (e.g., ventricles or choroid plexus), or the pancreas or certain cells or parts of the pancreas.
  • a "sample derived from a subject” refers to blood or plasma drawn from the subject.
  • a "sample derived from a subject” refers to liver tissue or retinal tissue derived from the subject.
  • the RNAi agent is administered to a subject such that the RNAi agent is delivered to a specific site within the subject.
  • the inhibition of expression of TTR may be assessed using measurements of the level or change in the level of TTR mRNA or TTR protein in a sample derived from fluid or tissue from the specific site within the subject.
  • the site is selected from the group consisting of liver, choroid plexus, retina, and pancreas.
  • the site may also be a subsection or subgroup of cells from any one of the aforementioned sites (e.g., hepatocytes or retinal pigment epithelium).
  • the site may also include cells that express a particular type of receptor (e.g. , hepatocytes that express the asialogycloprotein receptor).
  • the present invention also provides methods for treating or preventing a TTR- associated disease in a subject.
  • the methods include administering to the subject a therapeutically effective amount or prophylactically effective amount of an RNAi agent of the invention.
  • a "subject” includes either a human or a non-human animal, preferably a vertebrate, and more preferably a mammal.
  • a subject may include a transgenic organism.
  • the subject is a human, such as a human suffering from or predisposed to developing a TTR-associated disease.
  • the subject is suffering from a TTR-associated disease.
  • the subject is a subject at risk for developing a TTR-associated disease, e.g. , a subject with a TTR gene mutation that is associated with the development of a TTR associated disease, a subject with a family history of TTR-associated disease, or a subject who has signs or symptoms suggesting the development of TTR
  • amyloidosis is amyloidosis.
  • TTR-associated disease includes any disease caused by or associated with the formation of amyloid deposits in which the fibril precurosors consist of variant or wild-type TTR protein. Mutant and wild-type TTR give rise to various forms of amyloid deposition (amyloidosis). Amyloidosis involves the formation and aggregation of misfolded proteins, resulting in extracellular deposits that impair organ function. Climical syndromes associated with TTR aggregation include, for example, senile systemic amyloidosis (SSA); systemic familial amyloidosis; familial amyloidotic polyneuropathy (FAP); familial amyloidotic cardiomyopathy (FAC); and
  • leptomeningeal amyloidosis also known as leptomeningeal or meningocerebrovascular amyloidosis, central nervous system (CNS) amyloidosis, or amyloidosis VII form.
  • CNS central nervous system
  • RNAi agents of the invention are administered to subjects suffering from familial amyloidotic
  • SSA senile systemic amyloidosis
  • SCA senile cardiac amyloidosis
  • TTR amyloidosis amyloidosis
  • ATTR amyloidosis-transthyretin type
  • RNAi agents of the invention are administered to subjects suffering from transthyretin (TTR)-related familial amyloidotic polyneuropathy (FAP). Such subjects may suffer from ocular manifestations, such as vitreous opacity and glaucoma. It is known to one of skill in the art that amyloidogenic transthyretin (ATTR) synthesized by retinal pigment epithelium (RPE) plays important roles in the progression of ocular amyloidosis.
  • TTR transthyretin
  • FAP familial amyloidotic polyneuropathy
  • RNAi agent can be delivered in a manner suitable for targeting a particular tissue, such as the eye.
  • Modes of ocular delivery include retrobulbar, subcutaneous eyelid, subconjunctival, subtenon, anterior chamber or intravitreous injection (or internal injection or infusion).
  • Specific formulations for ocular delivery include eye drops or ointments.
  • TTR-associated disease is hyperthyroxinemia, also known as hyperthyroxinemia
  • distransthyretinemic hyperthyroxinemia or "dysprealbuminemic hyperthyroxinemia”. This type of hyperthyroxinemia may be secondary to an increased association of thyroxine with TTR due to a mutant TTR molecule with increased affinity for thyroxine.
  • RNAi agents of the invention may be administered to a subject using any mode of administration known in the art, including, but not limited to subcutaneous, intravenous, intramuscular, intraocular, intrabronchial, intrapleural, intraperitoneal, intraarterial, lymphatic, cerebrospinal, and any combinations thereof.
  • the administration is via a depot injection.
  • a depot injection may release the RNAi agent in a consistent way over a prolonged time period.
  • RNAi agent that, when administered to a subject who does not yet experience or display symptoms of a TTR-associated disease, but who may be predisposed to the disease, is sufficient to prevent or ameliorate the disease or one or more symptoms of the disease.
  • Symptoms that may be ameliorated include sensory neuropathy (e.g.
  • the "prophylactically effective amount” may vary depending on the RNAi agent, how the agent is administered, the degree of risk of disease, and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.
  • Any of these schedules may optionally be repeated for one or more iterations.
  • the number of iterations may depend on the achievement of a desired effect, e.g., the suppression of a TTR gene, retinol binding protein level, vitamin A level, and/or the achievement of a therapeutic or prophylactic effect, e.g. , reducing an amyloid deposit or reducing a symptom of a TTR-associated disease.
  • AD-43527 The mouse/rat cross-reactive GalNAc-conjugate, AD-43527, was chosen for in vivo evaluation in WT C57BL/6 mice for silencing of TTR mRNA in liver.
  • the sequence of each strand of AD-43527 is shown below.
  • AD-43527 was administered to female C57BL/6 mice (6-10 weeks, 5 per group) via subcutaneous injection at a dose volume of ⁇ /g at a dose of 30, 15, 7.5, 3.5, 1.75 or 0.5 mg/kg of AD-43527. Control animals received PBS by subcutaneous injection at the same dose volume.
  • Liver lysis mixture (a mixture of 1 volume of lysis mixture, 2 volume of nuclease-free water and ⁇ of Proteinase-K/ml for a final concentration of 20mg/ml) was incubated at 65 °C for 35 minutes. 5 ⁇ 1 of liver lysate and 95 ⁇ of working probe set (TTR probe for gene target and GAPDH for endogenous control) were added into the Capture Plate. Capture Plates were incubated at 53 °C +1 °C (aprx. 16-20hrs).
  • the hydroxyprolinol-ligand moiety was then coupled to a solid support via a succinate linker or was converted to phosphoramidite via standard phosphitylation conditions to obtain the desired carbohydrate conjugate building blocks.
  • Fluorophore labeled siRNAs were synthesized from the corresponding phosphoramidite or solid support, purchased from Biosearch Technologies.
  • the oleyl lithocholic (GalNAc) 3 polymer support made in house at a loading of 38.6 ⁇ /gram.
  • the Mannose (Man) polymer support was also made in house at a loading of 42.0 ⁇ /gram.
  • TSA.3HF trihydrofluoride
  • pyridine-HF and DMSO (3:4:6) and heated at 60°C for 90 minutes to remove the ie/t-butyldimethylsilyl (TBDMS) groups at the 2' position.
  • TDMS ie/t-butyldimethylsilyl
  • oligonucleotides were analyzed by high-performance liquid chromatography (HPLC) prior to purification and selection of buffer and column depends on nature of the sequence and or conjugated ligand.
  • oligonucleotides were diluted in water to 150 ⁇ and then pipetted in special vials for CGE and LC/MS analysis. Compounds were finally analyzed by LC-ESMS and CGE.
  • Lowercase nucleotides are 2'-0-methyl nucleotides; Nf (e.g., Af) is a 2'-fluoro nucleotide; s is a phosphothiorate linkage; L96 indicates a GalNAc 3 ligand.
  • Human Hep3B cells or rat H.II.4.E cells were grown to near confluence at 37 °C in an atmosphere of 5% C02 in RPMI (ATCC) supplemented with 10% FBS, streptomycin, and glutamine (ATCC) before being released from the plate by trypsinization.
  • Transfection was carried out by adding 14.8 ⁇ of Opti-MEM plus 0.2 ⁇ of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad CA. cat # 13778- 150) to 5 ⁇ of siRNA duplexes per well into a 96- well plate and incubated at room temperature for 15 minutes.
  • Cells were harvested and lysed in 150 ⁇ of Lysis/Binding Buffer then mixed for 5 minutes at 850rpm using an Eppendorf Thermomixer (the mixing speed was the same throughout the process).
  • Ten microliters of magnetic beads and 80 ⁇ Lysis/Binding Buffer mixture were added to a round bottom plate and mixed for 1 minute. Magnetic beads were captured using magnetic stand and the supernatant was removed without disturbing the beads. After removing the supernatant, the lysed cells were added to the remaining beads and mixed for 5 minutes. After removing the supernatant, magnetic beads were washed 2 times with 150 ⁇ Wash Buffer A and mixed for 1 minute. Beads were capture again and supernatant removed.
  • Beads were then washed with 150 ⁇ Wash Buffer B, captured and supernatant was removed. Beads were next washed with 150 ⁇ Elution Buffer, captured and supernatant removed. Beads were allowed to dry for 2 minutes. After drying, 50 ⁇ of Elution Buffer was added and mixed for 5 minutes at 70°C. Beads were captured on magnet for 5 minutes. 40 ⁇ of supernatant was removed and added to another 96 well plate.
  • RNA samples were added into 5 ⁇ total RNA.
  • cDNA was generated using a Bio-Rad C-1000 or S-1000 thermal cycler (Hercules, CA) through the following steps: 25 °C 10 min, 37 °C 120 min, 85 °C 5 sec, 4 °C hold.
  • IC 50 S were calculated using a 4 parameter fit model using XLFit and normalized to cells transfected with AD-1955 (sense sequence:
  • UCGAAGuCUcAGCGuAAGdTsdT (SEQ ID NO: 2203)) or naive cells over the same dose range, or to its own lowest dose.
  • IC 50 S were calculated for each individual transfection as well as in combination, where a single IC 50 was fit to the data from both transfections.
  • Example 5 In vitro Silencing Activity of Chemically Modified RNAi Agents that Target TTR
  • RNAi agents AD-45165, AD-51546 and AD-51547 are provided in Table 2 below.
  • the regions of complementarity to the TTR mRNA are as follows: the region of complementarity of RNAi agents AD-45165, AD-51546 and AD-51547 is
  • RNAi agents AD-45163, AD-51544, and AD-51545 is a region or complemetarity of RNAi agents AD-45163, AD-51544, and AD-51545.
  • TTCATGTAACCAAGAGTATTCCAT SEQ ID NO: 2205.
  • the IC 50 for each modified siRNA was determined in Hep3B cells (a human hepatoma cell line) by standard reverse transfection using Lipofectamine RNAiMAX.
  • reverse transfection was carried out by adding 5 ⁇ ⁇ of Opti-MEM to 5 ⁇ ⁇ of siRNA duplex per well into a 96-well plate along with 10 ⁇ ⁇ of Opti-MEM plus 0.5 ⁇ ⁇ of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad CA. cat # 13778-150) and incubating at room temperature for 15-20 minutes. Following incubation, 100 ⁇ ⁇ of complete growth media without antibiotic containing 12,000-15,000 Hep3B cells was then added to each well.
  • Free uptake silencing in primary cynomolgus hepatocytes was assessed following incubation with TTR siRNA for either 4 hours or 24 hours. Silencing was measured at 24 hours from the initial exposure.
  • 96-well culture plates were coated with 0.05 -0.1 collagen (Sigma C3867-1VL) at room temperature, 24 hours prior to the start of the experiment.
  • siRNAs were diluted in pre- warmed Plating Media consisting of DMEM supplemented with GIBCO' s Maintenance Media Kit (Serum-Free, Life Technologies CM4000), and added to the collagen-coated 96-well culture plates. Cryopreserved primary cynomolgus hepatocytes were rapidly thawed in a 37 °C water bath, and immediately diluted in Plating Media to a
  • TTR and GAPDH mRNA concentration of 360,000 cells/mL.
  • a volume of cell suspension was gently pipetted on top of the pre-plated siRNAs such that the final cell count was 18,000 cells/well.
  • the plate was lightly swirled to mix and spread cells evenly across the wells and placed in a 37 °C, 5% C0 2 incubator for 24 hours prior to lysis and analysis of TTR and GAPDH mRNA by bDNA (Quantigene, Affymetrix).
  • the media was decanted after 4 hours of exposure to the cells, and replaced with fresh Plating Media for the remaining 20 hours of incubation.
  • Downstream analysis for TTR and GAPDH mRNA was the same as described above.
  • siRNAs were titrated from ⁇ to 0.24nM by 4 fold serial dilution.
  • Table 2 In vitro Activity Summary for Alternating TTR-GalNAc and Variants with Triplet Motifs
  • Lowercase nucleotides (a, u, g, c) indicate 2'-0-methyl nucleotides; Nf (e.g., Af) indicates a 2'-fluoro nucleotide; s indicates a phosphothiorate linkage;
  • L96 indicates a GalNAc 3 ligand; bold nucleotides indicate changes relative to the corresponding parent agent. Each bold nucleotide is at the center of a triplet motif.
  • RNAi agents with alternating chemical modifications and a GalNAc 3 ligand provided an IC 50 in Hep3B cells of about 0.01 nM.
  • agents modified relative to the parent agents, for example, by the addition of one or more repeating triplets of 2'-fluoro and 2'-0-methyl modifications showed unexpectedly enhanced silencing activity, achieving IC 50 values in Hep3B cells that were 5-8 fold better than the corresponding parent agent.
  • RNAi agents modified relative to the parent AD-45163 also showed enhanced free uptake silencing.
  • the modified agents showed more than double the silencing activity of the parent after a 24 hour incubation period and nearly 10 times the silencing activity of the parent after a 4 hour incubation period.
  • RNAi agents modified relative to the parent AD-45165 also showed enhanced free uptake silencing.
  • the modified agents showed 2-3 times the silencing activity of the parent after a 24 hour incubation period and 5-8 times the silencing activity of the parent after a 4 hour incubation period.
  • RNAi agents presented herein e.g., AD-51544, AD-51545, AD-51546, and AD-51547, all showed unexpectedly good inhibition of TTR mRNA in in vitro silencing experiments.
  • RNAi agents in PBS buffer
  • PBS control mice were administered to mice (2 male and 2 female) of 18-24 months of age in a single subcutaneous dose of 5 mg/kg or 1 mg/kg. After approximately 48 hours, mice were anesthetized with 200 ⁇ of ketamine, and then exsanguinated by severing the right caudal artery. Whole blood was isolated and plasma was isolated and stored at -80°C until assaying. Liver tissue was collected, flash-frozen and stored at -80°C until processing.
  • Efficacy of treatment was evaluated by (i) measurement of TTR mRNA in liver at 48 hours post-dose, and (ii) measurement of TTR protein in plasma at pre-bleed and at 48 hours post-dose.
  • TTR liver mRNA levels were assayed utilizing the Branched DNA assays- QuantiGene 2.0 (Panomics cat #: QS0011). Briefly, mouse liver samples were ground and tissue lysates were prepared. Liver lysis mixture (a mixture of 1 volume of lysis mixture, 2 volume of nuclease-free water and lOul of Proteinase- K/ml for a final concentration of 20mg/ml) was incubated at 65 °C for 35 minutes.
  • Component 2 then dried by centrifuging for 1 minute at 240g.
  • ⁇ of pre- Amplifier Working Reagent was added into the Capture Plate, which was sealed with aluminum foil and incubated for 1 hour at 55°C ⁇ 1°C. Following 1 hour incubation, the wash step was repeated, then ⁇ of Amplifier Working Reagent was added. After 1 hour, the wash and dry steps were repeated, and ⁇ of Label Probe was added. Capture plates were incubated 50 °C +1 °C for 1 hour. The plate was then washed with IX Wash Buffer, dried and ⁇ Substrate was added into the Capture Plate.
  • Capture Plates were read using the SpectraMax Luminometer following a 5 to 15 minute incubation.bDNA data were analyzed by subtracting the average background from each triplicate sample, averaging the resultant triplicate GAPDH (control probe) and TTR (experimental probe) values, and then computing the ratio: (experimental probe-background)/(control probe- background).
  • Plasma TTR levels were assayed utilizing the commercially available kit "AssayMax Human Prealbumin ELISA Kit” (AssayPro, St. Charles, MO, Catalog # EP3010-1) according to manufacturer's guidelines. Briefly, mouse plasma was diluted 1: 10,000 in IX mix diluents and added to pre-coated plates along with kit standards, and incubated for 2 hours at room temperature followed by 5X washes with kit wash buffer. Fifty microliters of biotinylated prealbumin antibody was added to each well and incubated for 1 hr at room temperature, followed by 5X washes with wash buffer.
  • Figure 10 shows that the RNAi agents modified relative to the parent agents AD-45163 and AD-45165 showed RNA silencing activity that was similar or more potent compared with that of the parent agents.
  • Figure 11 shows that the agents AD-51544 and AD-51545 showed dose dependent silencing activity and that the silencing activity of these agents at a dose of 5mg/kg was similar to that of the corresponding parent AD-45163.
  • Figure 12 shows that the agents AD-51546 and AD-51547 also showed dose-dependent silencing activity. Furthermore, the silencing activity of AD-51546 and AD-51547 at a dose of 5mg/kg was superior to that of the corresponding parent AD-45165.
  • RNAi agents AD-45163, AD-51544, AD- 51545, AD-51546, and AD-51547 achieved similar or higher concentrations in the liver when administered subcutaneously than when administered by IV bolus.
  • the liver pharmacokinetic parameters are presented in Tables 5 and 6 below.
  • the peak concentration (C max ) and area under the curve (AUCo-kst) in the liver were two to three times higher after subcutaneous administration as compared with IV administration of the same agent at the same dose. Liver exposures were highest for AD-51547 and lowest for AD-51545.
  • the mean resident time (MRT) and elimination half-life were longer for AD-51546 and AD-51547 compared with AD-51544 and AD-51545.
  • AD-51546 and AD-51547 were 40 hours for AD- 51546 and 25 hours for AD-51547, whereas the MRTs for AD-51544 and AD-51545 were lower (about 6-9 hours).
  • the elimination half life of AD-51546 and AD-51547 was also higher (41-53 hours) than was the elimination half life of AD-51544 and AD- 51545 (6-10 hours).
  • RNAi agents AD-51544, AD-51545, AD-51546, and AD- 51547 were also assessed in monkeys. The results demonstrated that the antisense and sense strands of AD-51544, AD-51545, and AD-51547 showed serum stability over a period of about 24 hours (data not shown).
  • RNA silencing activity of RNAi agents AD-45163, AD-51544, AD-51545, AD-51546, and AD-51547 was assessed by measuring suppression of TTR protein in serum of cynomologous monkeys following subcutaneous administration of five 5 mg/kg doses (one dose each day for 5 days) or a single 25mg/kg dose.
  • Pre-dose TTR protein levels in serum were assessed by averaging the levels at 11 days prior to the first dose, 7 days prior to the first dose, and 1 day prior to the first dose.
  • Post-dose serum levels of TTR protein were assessed by determining the level in serum beginning at 1 day after the final dose (i.e.
  • study day 5 in the 5x5 mg/kg group and study day 1 in the 1x25 mg/kg group until 49 days after the last dose (i.e., study day 53 in the 5x5 mg/kg group and study day 49 in the 1x25 mg/kg group). See Figure 13.
  • TTR protein levels were assessed as described in Example 6. The results are shown in Figures 14A and 14B and in Tables 7 and 8.
  • a maximal suppression of TTR protein of up to about 50% was achieved in the groups that received 25 mg/kg of AD-45163, AD-51544, AD-51546, and AD-51547 (see Table 8).
  • a greater maximal suppression of TTR protein of about 70% was achieved in the groups that received 5x5 mg/kg of AD-45163, AD-51544, AD-51546, and AD-51547 (see Table 7).
  • the agent AD-51545 produced a lesser degree of suppression in both administration protocols.
  • better suppression was achieved in the 5x5 mg/kg protocol than in the 1x25 mg/kg protocol.
  • Table 7 Fraction Serum Transthyretin Relative to Pre-dose in Cynomolgus Monkeys ( 5 mg/kg daily for 5 days)
  • RNAi agents that target TTR including AD-45163, AD-51544, AD-51545, AD-51546, and AD-51547
  • each agent was tested in a whole blood assay using blood from three human donors.
  • the agents were either 300 nM DOTAP transfected or 1 ⁇ without transfection reagent (free siRNA).
  • RNAi agents were injected subcutaneously in CD1 mice at a dose of 125 mg/kg. No cytokine induction was observed at 2, 4, 6, 24, or 48 hours after subcutaneous injection of AD-45163. No significant cytokine induction was observed at 6 or 24 hours after subcucutaneous injection of AD-51544, AD-51545, AD- 51546, or AD-51547.
  • RNAi agents including AD- 45163, AD-51544, AD-51545, AD-51546, and AD-51547
  • AD- 45163, AD-51544, AD-51545, AD-51546, and AD-51547 were tested by subcutaneous injection of 5 and 25 mg in non-human primates (cynomologous monkeys) with dose volumes between 1-2 ml per site. No erythema or edema was observed at injection sites.
  • rats were injected with a single subcutaneous dose of 100, 250, 500, or 750 mg/kg of AD-45163 (see Table 9).
  • the following assessments were made: clinical signs of toxicity, body weight, hematology, clinical chemistry and coagulation, organ weights (liver & spleen); gross and microscopic evaluation (kidney, liver, lung, lymph node, spleen, testes, thymus, aorta, heart, intestine (small and large).
  • MONO metal-oxide-semiconductor
  • RNA silencing activity of RNAi agent AD-51547 was assessed by measuring suppression of TTR protein in the serum of cynomologous monkeys following subcutaneous administration of a "loading phase" of the RNAi agent: five daily doses of either 2.5 mg/kg, 5 mg/kg or 10 mg/kg (one dose each day for 5 days) followed by a "maintenance phase" of the RNAi agent: weekly dosing of either 2.5 mg/kg, 5 mg/kg or 10 mg/kg for 4 weeks.
  • Pre-dose TTR protein levels in serum were assessed by averaging the levels at 11 days prior to the first dose, 7 days prior to the first dose, and 1 day prior to the first dose.
  • Post-dose serum levels of TTR protein were assessed by determining the level in serum relative to pre-dose beginning at 1 day after the loading phase was completed until 40 days after the last dose of the maintenance phase (i.e., study day 70).
  • TTR protein levels were assessed as described in Example 6. The results are shown in Figure 15.
  • a maximal suppression of TTR protein of up to about 80% was achieved in all of the groups that received either 2.5 mg/kg, 5 mg/kg or 10 mg/kg of AD-51547.
  • Nadir knockdown was achieved in all of the groups by about day 14, the suppression sustained at nadir knockdown levels with a weekly maintenance dose of either 2.5 mg/kg, 5 mg/kg or 10 mg/kg of AD-51547.
  • the levels of TTR had not returned to baseline more than 40 days after the day of administration of the last maintenance dose for the 5 and 2.5 mg/kg dose levels.
  • Cohorts 1-4 each including 4 male subjects, were administered subcutaneously a single dose of AD-51547 at 1.25 mg/kg, 2.5 mg/kg, 5.0 mg/kg, or 10 mg/kg.
  • Cohorts 5-7 each including 4 male subjects, were administered subcutaneously multiple doses of AD-51547.
  • the schedule for multi-dose administration was a daily dose of AD-51547 at 2.5 mg/kg, 5.0 mg/kg, or 10 mg/kg for five days, followed by a single dose of AD-51547 at 2.5 mg/kg, 5 mg/kg, or 10 mg/kg once per week for five weeks.
  • the median age of the subjects enrolled in the trial was 35 years of age (ranging in age from 25 to 47) and the mean serum TTR level at the time of study entry was 270 ⁇ (+/- 47 ⁇ g/ml).
  • Figure 20 shows the serum TTR knockdown by dose group.
  • AD-51547 multiple doses were generally safe and well tolerated. There was no evidence of inflammation (cytokine, CRP), no evidence of abnormalities in liver function tests, renal function, or hematologic parameters, and transient erythema most common reaction at the injection site. As shown in Figures 18 and 19, the knockdown of serum TTR was greater than 80% and this level of knockdown was maintained at a dose of > 5 mg/kg of AD-51547 dosed weekly. There was statistically significant dose-dependent knockdown of serum TTR at doses of > 2.5 mg/kg. In addition, TTR knockdown was sustained for at least 14 days after the last dose of 2.5 and 5.0 mg/kg. Equivalents:

Abstract

The present invention provides methods for treating or preventing transthyretin-(TTR-) associated diseases using RNAi agents, e.g., double stranded RNAi agents, that target the transthyretin (TTR) gene.

Description

METHODS FOR TREATING OR PREVENTING TRANSTHYRETIN (TTR)
ASSOCIATED DISEASES
Related Applications
This application claims the benefit of priority to U.S. Provisional Patent
Application No. 61/881,257, filed September 23, 2013, the entire contents of which are incorporated herein by reference.
This application is related to U.S. Provisional Application No. 61/561,710, filed on November 18, 2011, International Application No. PCT/US2012/065601, filed on November 16, 2012, U.S. Provisional Application No. 61/615,618, filed on March 26, 2012, U.S. Provisional Application No. 61/680,098, filed on August 6, 2012, U.S.
Application No. 14/358,972, filed on May 16, 2014, and International Application No. PCT/US2012/65691, filed November 16, 2012, the entire contents of each of which are hereby incorporated herein by reference.
Sequence Listing
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on September 22, 2014, is named 121301-00820_SL.txt and is 593,216 bytes in size.
Background of the Invention
Transthyretin (TTR) (also known as prealbumin) is found in serum and cerebrospinal fluid (CSF). TTR transports retinol-binding protein (RBP) and thyroxine (T4) and also acts as a carrier of retinol (vitamin A) through its association with RBP in the blood and the CSF. Transthyretin is named for its transport of thyroxine and retinol. TTR also functions as a protease and can cleave proteins including apoA-I (the major HDL apolipoprotein), amyloid β-peptide, and neuropeptide Y. See Liz, M.A. et al. (2010) IUBMB Life, 62(6):429-435.
TTR is a tetramer of four identical 127-amino acid subunits (monomers) that are rich in beta sheet structure. Each monomer has two 4-stranded beta sheets and the shape of a prolate ellipsoid. Antiparallel beta-sheet interactions link monomers into dimers. A short loop from each monomer forms the main dimer-dimer interaction. These two pairs of loops separate the opposed, convex beta-sheets of the dimers to form an internal channel. The liver is the major site of TTR expression. Other significant sites of expression include the choroid plexus, retina (particularly the retinal pigment epithelium) and pancreas.
Transthyretin is one of at least 27 distinct types of proteins that is a precursor protein in the formation of amyloid fibrils. See Guan, J. et al. (Nov. 4, 2011) Current perspectives on cardiac amyloidosis, Am J Physiol Heart Circ Physiol,
doi: 10.1152/ajpheart.00815.2011. Extracellular deposition of amyloid fibrils in organs and tissues is the hallmark of amyloidosis. Amyloid fibrils are composed of misfolded protein aggregates, which may result from either excess production of or specific mutations in precursor proteins. The amyloidogenic potential of TTR may be related to its extensive beta sheet structure; X-ray crystallographic studies indicate that certain amyloidogenic mutations destabilize the tetrameric structure of the protein. See, e.g., Saraiva M.J.M. (2002) Expert Reviews in Molecular Medicine, 4(12): 1-11.
Amyloidosis is a general term for the group of amyloid diseases that are characterized by amyloid deposits. Amyloid diseases are classified based on their precursor protein; for example, the name starts with "A" for amyloid and is followed by an abbreviation of the precursor protein, e.g., ATTR for amloidogenic transthyretin. Ibid.
There are numerous TTR-associated diseases, most of which are amyloid diseases. Normal-sequence TTR is associated with cardiac amyloidosis in people who are elderly and is termed senile systemic amyloidosis (SSA) (also called senile cardiac amyloidosis (SCA) or cardiac amyloidosis). SSA often is accompanied by microscopic deposits in many other organs. TTR amyloidosis manifests in various forms. When the peripheral nervous system is affected more prominently, the disease is termed familial amyloidotic polyneuropathy (FAP). When the heart is primarily involved but the nervous system is not, the disease is called familial amyloidotic cardiomyopathy (FAC). A third major type of TTR amyloidosis is leptomeningeal amyloidosis, also known as leptomeningeal or meningocerebrovascular amyloidosis, central nervous system (CNS) amyloidosis, or amyloidosis VII form. Mutations in TTR may also cause amyloidotic vitreous opacities, carpal tunnel syndrome, and euthyroid hyperthyroxinemia, which is a non-amyloidotic disease thought to be secondary to an increased association of thyroxine with TTR due to a mutant TTR molecule with increased affinity for thyroxine. See, e.g., Moses et al. (1982) /. Clin. Invest., 86, 2025-2033.
Abnormal amyloidogenic proteins may be either inherited or acquired through somatic mutations. Guan, J. et al. (Nov. 4, 2011) Current perspectives on cardiac amyloidosis, Am J Physiol Heart Circ Physiol, doi: 10.1152/ajpheart.00815.2011. Transthyretin associated ATTR is the most frequent form of hereditary systemic amyloidosis. Lobato, L. (2003) J. Nephrol., 16:438-442. TTR mutations accelerate the process of TTR amyloid formation and are the most important risk factor for the development of ATTR. More than 85 amyloidogenic TTR variants are known to cause systemic familial amyloidosis. TTR mutations usually give rise to systemic amyloid deposition, with particular involvement of the peripheral nervous system, although some mutations are associated with cardiomyopathy or vitreous opacities. Ibid.
The V30M mutation is the most prevalent TTR mutation. See, e.g., Lobato, L. (2003) J Nephrol, 16:438-442. The V122I mutation is carried by 3.9% of the African American population and is the most common cause of FAC. Jacobson, D.R. et al.
(1997) N. Engl. J. Med. 336 (7): 466-73. It is estimated that SSA affects more than 25% of the population over age 80. Westermark, P. et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 87 (7): 2843-5.
Accordingly, there is a need in the art for effective treatments for TTR-associated diseases.
Summary of the Invention
The present invention provides methods of treating or preventing a TTR- associated disease in a subject using the RNAi agents, e.g. double stranded RNAi agents, of the invention, targeting the Transthyretin (TTR) gene. The present invention is based, at least in part, on the discovery that RNAi agents that comprise particular chemical modifications show a superior ability to inhibit expression of TTR. Agents including a certain pattern of chemical modifications (e.g., an alternating pattern) and a ligand are shown herein to be effective in silencing the activity of the TTR gene. Furthermore, agents including one or more motifs of three identical modifications on three
consecutive nucleotides, including one such motif at or near the cleavage site of the agents, show surprisingly enhanced TTR gene silencing activity. When a single such chemical motif is present in the agent, it is preferred to be at or near the cleavage region for enhancing of the gene silencing activity. Cleavage region is the region surrounding the cleavage site, i.e., the site on the target mRNA at which cleavage occurs.
Accordingly, in one aspect, the present invention provides methods of treating or preventing a TTR-associated disease in a subject. The methods include administering to the subject an RNAi agent at a dose of about 7.5 mg/kg, daily for five days, followed by a dose of about 7.5 mg/kg weekly for about five weeks, thereby treating or preventing the TTR-associated disease in the subject. RNAi agents suitable for use in the methods of the invention include double stranded RNAi agents RNAi agents, e.g., double stranded RNAi agents, that inhibit expression of a transthyretin (TTR) gene. The double stranded RNAi agent includes a sense strand complementary to an antisense strand. The antisense strand includes a region complementary to a part of an mRNA encoding transthyretin. Each strand has 14 to 30 nucleotides, and the double stranded RNAi agent is represented by formula (III):
sense: 5' np -Na -(X X X) rNb - Y Y Y -Nb -(Z Z Z¾ -Na - nq 3'
antisense: 3' np'-NaHX'X'X k-Nb'-YTT'-Nb'-(ZZZ')i-Na'- nq' 5'
(HI).
In Formula III, i, j, k, and 1 are each independently 0 or 1 ; p, p', q, and q' are each independently 0-6; each Na and Na' independently represents an oligonucleotide sequence including 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence including at least two differently modified nucleotides; each Nb and Nb' independently represents an oligonucleotide sequence including 0-10 nucleotides which are either modified or unmodified or combinations thereof; each np, np', nq, and nq' independently represents an overhang nucleotide; XXX, YYY, ZZZ, Χ'Χ'Χ', ΥΎΎ', and ZZZ' each independently represents one motif of three identical modifications on three consecutive nucleotides; modifications on Nb differ from the modification on Y and modifications on Nb' differ from the modification on Y'. In some embodiments, the sense strand is conjugated to at least one ligand, e.g. , at least one ligand, e.g., at least one ligand attached to the 3' end of the sense strand. In other embodiments, the ligand may be conjugated to the antisense strand.
In another aspect, the present invention provides methods of treating or preventing a TTR-associated disease in a subject. The methods include administering to the subject an RNAi agent at a dose of about 500 mg, daily for five days, followed by a weekly dose of about 500 mg, thereby treating or preventing the TTR-associated disease in the subject. RNAi agents suitable for use in the methods of the invention include double stranded RNAi agents RNAi agents, e.g. , double stranded RNAi agents, that inhibit expression of a transthyretin (TTR) gene. The double stranded RNAi agent includes a sense strand complementary to an antisense strand. The antisense strand includes a region complementary to a part of an mRNA encoding transthyretin. Each strand has 14 to 30 nucleotides, and the double stranded RNAi agent is represented by formula (III):
sense: 5' np -Na -(X X X) rNb - Y Y Y -Nb -(Z Z Z¾ -Na - nq 3'
antisense: 3' np'-Na'-(X'X'X')k-Nb'-Y'Y'Y'-Nb'-(Z'Z'Z')i-Na'- nq' 5'
(III).
In Formula III, i, j, k, and 1 are each independently 0 or 1 ; p, p', q, and q' are each independently 0-6; each Na and Na' independently represents an oligonucleotide sequence including 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence including at least two differently modified nucleotides; each Nb and Nb' independently represents an oligonucleotide sequence including 0-10 nucleotides which are either modified or unmodified or combinations thereof; each np, np', nq, and nq' independently represents an overhang nucleotide; XXX, YYY, ZZZ, Χ'Χ'Χ', Y'Y'Y', and Z'Z'Z' each independently represents one motif of three identical modifications on three consecutive nucleotides; modifications on Nb differ from the modification on Y and modifications on Nb' differ from the modification on Y'. In some embodiments, the sense strand is conjugated to at least one ligand, e.g. , at least one ligand, e.g., at least one ligand attached to the 3' end of the sense strand. In other embodiments, the ligand may be conjugated to the antisense strand.
In some embodiments, TTR expression in a sample derived from the subject is inhibited by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60% or at least about 70% at least about 80%, or at least about 90%.
In some embodiments, the subject is a human.
In some embodiments, the subject is a subject suffering from a TTR-associated disease. In other embodiments, the subject is a subject at risk for developing a TTR- associated disease.
In some embodiments, the subject is a subject who carries a TTR gene mutation that is associated with the development of a TTR-associated disease.
In certain embodiments, the TTR-associated disease is selected from the group consisting of senile systemic amyloidosis (SSA), systemic familial amyloidosis, familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy (FAC), leptomeningeal/Central Nervous System (CNS) amyloidosis, and hyperthyroxinemia.
In some embodiments, the subject has a TTR-associated amyloidosis and the method reduces an amyloid TTR deposit in the subject.
In some embodiments, the RNAi agent is administered to the subject by an administration means selected from the group consisting of subcutaneous, intravenous, intramuscular, intrabronchial, intrapleural, intraperitoneal, intraarterial, lymphatic, cerebrospinal, and any combinations thereof. In certain embodiments, the RNAi agent is administered to the subject via subcutaneous or intravenous administration. In preferred embodiments, the RNAi agent is administered to the subject via subcutaneous administration. In one embodiment, the subcutaneous administration is subcutaneous injection of the RNAi agent. The subcutaneous injection may be at an anatomical location selected from the group consisting of the abdomen of the subject, the thigh of the subject, and the upper arm of the subject. In one embodiment, the RNAi agent is administered to the subject as a split 500 mg dose at two different anatomical locations.
In some such embodiments, the subcutaneous administration includes administration via a subcutaneous pump or subcutaneous depot. In one embodiment, the subcutaneous administration comprises administration via a subcutaneous infusion pump. In one embodiment, the RNAi agent is administered to the subject as a single 500 mg dose. In one embodiment, the RNAi agent is administered to the subject over of period of 5-20, 5- 10, 5- 15, 10- 15, 10-20, or 15-20 minutes. In another embodiment, the RNAi agent is administered to the subject over of period of 15 minutes or less, 10 minutes or less, or 5 minutes or less.
In one embodiment, the RNAi agent is administered to the subject as a single dose 500 mg dose. In another embodiment, the RNAi agent is administered to the subject as a split 500 mg dose.
In one embodiment, the weekly dose is administered to the subject chronically.
In certain embodiments, the RNAi agent is administered to the subject such that the RNAi agent is delivered to a specific site within the subject. In some such embodiments, the site is selected from the group consisting of liver, choroid plexus, retina, and pancreas. In preferred embodiments, the site is the liver. In some embodiments, the delivery of the RNAi agent is mediated by asialoglycoprotein receptor (ASGP-R) present in hepatocytes.
In other embodiments, the method further includes assessing the level of TTR mRNA expression or TTR protein expression in a sample derived from the subject.
In preferred embodiments, administering the RNAi agent does not result in an inflammatory response in the subject as assessed based on the level of a cytokine or chemokine selected from the group consisting of G-CSF, IFN-γ, IL- 10, IL- 12 (p70), ILip, IL- lra, IL-6, IL-8, IP-10, MCP- 1, ΜΙΡ-Ια, ΜΙΡ- Ιβ, TNFa, and any combinations thereof, in a sample from the subject.
In some embodiments, the RNAi agent is administered using a pharmaceutical composition, e.g., a liposome.
In some embodiments, the RNAi agent is administered in a solution. In some such embodiments, the RNAi agent is administered in an unbuffered solution. In one embodiment, the RNAi agent is administered in saline or water. In other embodiments, the RNAi agent is administred with a buffer solution, such as an acetate buffer, a citrate buffer, a prolamine buffer, a carbonate buffer, or a phosphate buffer or any combination thereof. In some embodiments, the buffer solution is phosphate buffered saline (PBS).
In one embodiment, the unbuffered solution is sterile water. The RNAi agent may be administered as a solution in sterile water having a concentration of RNAi agent of about 150 mg/ml to about 300 mg/ml, about 150 mg/ml to about 200 mg/ml, about 100 mg/ml to about 350 mg/ml, e.g., about 100 mg/ml, 150 mg/ml, 200 mg/ml, 250 mg/ml, or about 350 mg/ml.
In some embodiments, i is 1 ; j is 1 ; or both i and j are 1.
In some embodiments, k is 1 ; 1 is 1 ; or both k and 1 are 1.
In some embodiments, i is 0; j is 1.
In some embodiments, i is 1, j is 0.
In some embodiments, k is 0; 1 is 1.
In some embodiments, k is 1 ; 1 is 0.
In some embodiments, XXX is complementary to X'X'X', YYY is
complementary to ΥΎΎ', and ZZZ is complementary to Z'Z'Z'.
In some embodiments, the YYY motif occurs at or near the cleavage site of the sense strand.
In some embodiments, the ΥΎΎ' motif occurs at the 11, 12 and 13 positions of the antisense strand from the 5 '-end.
In some embodiments, the Y' is 2'-0-methyl.
In some embodiments, the Y' is 2'-fluoro.
In some embodiments, formula (III) is represented as formula (Ilia):
sense: 5' np -Na - Y Y Y -Nb -Z Z Z -Na-nq 3'
antisense: 3' np'-Na'-YYY'-Nb'-Z'Z'Z'-Na'nq' 5'
(Ilia).
In formula Ilia, each Nb and Nb' independently represents an oligonucleotide sequence including 1-5 modified nucleotides.
In some embodiments, formula (III) is represented as formula (Illb):
sense: 5' np-Na-X X X -Nb-Y Y Y -Na-nq 3'
antisense: 3' np'-Na'-X'X'X'-Nb'-YYY'-Na'-nq' 5'
(nib).
In formula Illb each Nb and Nb' independently represents an oligonucleotide sequence including 1-5 modified nucleotides. In some embodiments, formula (III) is represented as formula (IIIc):
sense: 5' np-Na-X X X -Nb-Y Y Y -Nb-Z Z Z -Na-nq 3' antisense: 3' np'-Na'-X'X'X'-Nb'-Y'Y'Y'-Nb'-Z'Z'Z'-Na'-nq' 5'
(IIIc).
In formula IIIc, each Nb and -Nb' independently represents an oligonucleotide sequence including 1-5 modified nucleotides and each Na and Na' independently represents an oligonucleotide sequence including 2-10 modified nucleotides.
In many embodiments, the duplex region is 15-30 nucleotide pairs in length. In some embodiments, the duplex region is 17-23 nucleotide pairs in length, 17-25 nucleotide pairs in length, 23-27 nucleotide pairs in length, 19-21 nucleotide pairs in length, or 21-23 nucleotide pairs in length.
In certain embodiments, each strand has 15-30 nucleotides.
In some embodiments, the modifications on the nucleotides are selected from the group consisting of LNA, UNA, CRN, cEt, HNA, CeNA, 2'-methoxyethyl, 2'-0-alkyl, 2'-0-allyl, 2'-C- allyl, 2'-fluoro, 2'-deoxy, 2'-hydroxyl, and combinations thereof. In some preferred embodiments, the modifications on the nucleotides are 2'-0-methyl or 2'-fluoro.
In some embodiments, the ligand is one or more N-acetylgalactosamine
(GalNAc) derivatives attached through a bivalent or trivalent branched linker. In particular embodiments, the ligand is
Figure imgf000010_0001
In some embodiments, the ligand is attached to the 3' end of the sense strand.
In some embodiments, the RNAi agent is conjugated to the ligand as shown in the following schematic
Figure imgf000011_0001
wherein X is O or S.
In some embodiments, the RNAi agent is conjugated to the ligand as shown in the following schematic
Figure imgf000011_0002
In some embodiments, the RNAi agent further includes at least one
phosphorothioate or methylphosphonate intemucleotide linkage. In some embodiments, the phosphorothioate or methylphosphonate intemucleotide linkage is at the 3 '-terminal of one strand. In some embodiments, the strand is the antisense strand. In other embodiments, the strand is the sense strand.
In certain embodiments, the base pair at the 1 position of the 5'-end of the duplex is an AU base pair.
In some embodiments, the Y nucleotides contain a 2'-fluoro modification.
In some embodiments, the Y' nucleotides contain a 2'-0-methyl modification. In some embodiments, p'>0. In some such embodiments, each n is
complementary to the target mRNA. In other such embodiments, each n is non- complementary to the target mRNA. In some embodiments, p, p', q and q' are 1-6. In some preferred embodiments, p' = 1 or 2. In some preferred embodiments, p -2. In some such embodiments, q'=0, p=0, q=0, and p' overhang nucleotides are
complementary to the target mRNA. In other such embodiments, q'=0, p=0, q=0, and p' overhang nucleotides are non-complementary to the target mRNA. In some embodiments, the sense strand has a total of 21 nucleotides and the antisense strand has a total of 23 nucleotides.
In certain embodiments, linkages between np' include phosphorothioate linkages. In some such embodiments, the linkages between np' are phosphorothioate linkages.
In some embodiments, the RNAi agent is selected from the group of agents listed in Table 1.
In preferred embodiments, the RNAi agent is selected from the group consisting of AD-51544, AD-51545, AD-51546, and AD-51547.
In an even more preferred embodiment, the RNAi agent is AD-51547 having the following structure:
sense: 5 ' - UfgGfg AfuUfuCf AfUfgUfaacCfaAfgAfL96-3 ' (SEQ ID NO: 2211 ) antisense: 5'- uCfuUfgGfUfUfaCfaugAfaAfuCfcCfasUfsc-3' (SEQ ID NO: 2217) wherein lowercase nucleotides (a, u, g, c) indicate 2'-0-methyl nucleotides; Nf (e.g. , Af) indicates a 2' -fluoro nucleotide; s indicates a phosphothiorate linkage; L96 indicates a GalNAc3 ligand.
In one aspect, the present invention provides methods of treating or preventing a TTR-associated disease in a subject. The methods include administering to the subject an RNAi agent at a dose of about 500 mg, daily for five days, followed by a weekly dose of about 500 mg, wherein the RNAi agent is AD-51547, having the following structure: sense: 5 ' - UfgGfg AfuUfuCf AfUfgUfaacCfaAfgAfL96-3 ' (SEQ ID NO:2211 ) antisense: 5'- uCfuUfgGfUfUfaCfaugAfaAfuCfcCfasUfsc-3' (SEQ ID NO:2217) wherein lowercase nucleotides (a, u, g, c) indicate 2'-0-methyl nucleotides; Nf (e.g. , Af) indicates a 2' -fluoro nucleotide; s indicates a phosphothiorate linkage; L96 indicates a GalNAc ligand, thereby treating or preventing the TTR-associated disease in the subject.
In some embodiments, the subject is a human.
In some embodiments, the subject is a subject suffering from a TTR-associated disease. In other embodiments, the subject is a subject at risk for developing a TTR- associated disease.
In some embodiments, the subject is a subject who carries a TTR gene mutation that is associated with the development of a TTR-associated disease.
In certain embodiments, the TTR-associated disease is selected from the group consisting of senile systemic amyloidosis (SSA), systemic familial amyloidosis, familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy (FAC), leptomeningeal/Central Nervous System (CNS) amyloidosis, and hyperthyroxinemia. In some embodiments, the subject has a TTR-associated amyloidosis and the method reduces an amyloid TTR deposit in the subject.
In some embodiments, the RNAi agent is administered to the subject via subcutaneous administration. In one embodiment, the subcutaneous administration is subcutaneous injection of the RNAi agent. The subcutaneous injection may be at an anatomical location selected from the group consisting of the abdomen of the subject, the thigh of the subject, and the upper arm of the subject. In one embodiment, the RNAi agent is administered to the subject as a split 500 mg dose at two different anatomical locations.
In some such embodiments, the subcutaneous administration includes administration via a subcutaneous pump or subcutaneous depot. In one embodiment, the subcutaneous administration comprises administration via a subcutaneous infusion pump. In one embodiment, the RNAi agent is administered to the subject as a single 500 mg dose. In one embodiment, the RNAi agent is administered to the subject over of period of 5-20, 5- 10, 5- 15, 10- 15, 10-20, or 15-20 minutes. In another embodiment, the RNAi agent is administered to the subject over of period of 15 minutes or less, 10 minutes or less, or 5 minutes or less.
In one embodiment, the RNAi agent is administered to the subject as a single dose 500 mg dose. In another embodiment, the RNAi agent is administered to the subject as a split 500 mg dose.
In one embodiment, the weekly dose is administered to the subject chronically. In one aspect, the present invention provides kits for performing the methods of the invention. The kits include an RNAi agent of the invention, such as AD-51547, having the following structure:
sense: 5 ' - UfgGfg AfuUfuCf AfUfgUfaacCfaAfgAfL96-3 ' (SEQ ID NO:2211 ) antisense: 5'- uCfuUfgGfUfUfaCfaugAfaAfuCfcCfasUfsc-3' (SEQ ID NO:2217) wherein lowercase nucleotides (a, u, g, c) indicate 2'-0-methyl nucleotides; Nf (e.g. , Af) indicates a 2'-fluoro nucleotide; s indicates a phosphothiorate linkage; L96 indicates a GalNAc3 ligand and instructions for use.
The kits may optionally contain means for administering the RNAi agent to the subject, such as an injection device or an infusion pump.
The RNAi agent may be provided in the kits at a concentration suitable for administration to a subject. For example, in some embodiments, an RNAi agent is formulated in sterile water for injection at a concentration of about 50-500 mg/ml, about 150 mg/ml to about 300 mg/ml, about 150 mg/ml to about 200 mg/ml, about 100 mg/ml to about 350 mg/ml, e.g., about 50 mg/ml, about 100 mg/ml, about 150 mg/ml, about 200 mg/ml, about 250 mg/ml, about 300 mg/ml, about 350 mg/ml, about 400 mg/ml, about 450 mg/ml, or about 500 mg/ml.
The present invention is further illustrated by the following detailed description and drawins.
Brief Description of the Drawings
Figure 1 is a graph depicting that administering to mice a single subcutaneous dose of a GalN Ac-conjugated RNAi agent targeting TTR resulted in dose-dependent suppression of TTR mRNA.
Figure 2 is a graph depicting that administering to mice a single subcutaneous dose of 7.5 mg/kg or 30 mg/kg of a GalN Ac conjugated RNAi agent targeting TTR resulted in long lasting suppression of TTR mRNA.
Figure 3 depicts the human TTR mRNA sequence.
Figure 4 is a graph depicting improved silencing activity of RNAi agents modified relative to the parent AD-45163.
Figure 5 is a graph depicting improved silencing activity of RNAi agents modified relative to the parent AD-45165.
Figure 6 is a graph depicting improved free uptake silencing following 4 hour incubation with RNAi agents modified relative to the parent AD-45163.
Figure 7 is a graph depicting improved free uptake silencing following 24 hour incubation with RNAi agents modified relative to the parent AD-45163.
Figure 8 is a graph depicting improved free uptake silencing following 4 hour incubation with RNAi agents modified relative to the parent AD-45165.
Figure 9 is a graph depicting improved free uptake silencing following 24 hour incubation with RNAi agents modified relative to the parent AD-45165.
Figure 10 is a graph depicting silencing of TTR mRNA in transgenic mice that express hTTR V30M following administration of a single subcutaneous dose of RNAi agents AD-51544, AD-51545, AD-45163, AD-51546, AD-51547, or AD-45165.
Figure 11 is a graph depicting TTR protein suppression in transgenic mice that express hTTR V30M following administration of a single subcutaneous dose of 5 mg/kg or lmg/kg of RNAi agents AD-51544, AD-51545, or AD-45163.
Figure 12 is a graph depicting TTR protein suppression in transgenic mice that express hTTR V30M following administration of a single subcutaneous dose of 5 mg/kg or lmg/kg of RNAi agents AD-51546, AD-51547, or AD-45165. Figure 13 depicts the protocol for post-dose blood draws in monkeys that received 5x5mg/kg RNAi agent (top line) or lx25mg/kg RNAi agent (bottom line).
Figures 14A and 14B are graphs depicting suppression of TTR protein in non- human primates following subcutaneous administration of five 5 mg/kg doses ( Figure 14A) or a single 25mg/kg dose ( Figure 14B) of AD-45163, AD-51544, AD-51545, AD- 51546, or AD-51547.
Figure 15 is a graph depicting suppression of TTR protein in non-human primates following subcutaneous administration of AD-51547 at 2.5 mg/kg (white squares), 5 mg/kg (black squares) or 10 mg/kg (patterned squares) per dose, or administration of PBS as a negative control (gray squares).
Figures 16A- 16D are graphs depicting serum levels of IL-6 (A), TNF alpha (B), G-CSF (C), and CRP (D) in human subjects administered the indicated doses of AD- 51547.
Figures 17A- 17D are graphs depicting serum levels of aspartate transferase (A), alanine transferase (B), total bilirubin (C), and creatinine (D) in human subjects administered the indicated doses of AD-51547.
Figure 18 is a graph depicting the mean TTR knockdown relative to baseline in human subjects administered a single dose of AD-51547 as indicated.
Figure 19 is a graph depicting the mean TTR knockdown relative to baseline in human subjects administered a multiple dose of 2.5 mg/kg, 5 mg/kg, or 10 mg/kg of
AD-51547 for 5 days (qdx5) followed by weekly doses of the same amounts for 5 weeks (qwx5).
Figure 20 is a Table showing the knockdown of serum TTR by dose group. Detailed Description of the Invention
The present invention provides RNAi agents, e.g. , double stranded RNAi agents, and compositions targeting the Transthyretin (TTR) gene. The present invention also provides methods of inhibiting expression of TTR and methods of treating or preventing a TTR-associated disease in a subject using the RNAi agents, e.g., double stranded RNAi agents, of the invention. The present invention is based, at least in part, on the discovery that RNAi agents that comprise particular chemical modifications show a superior ability to inhibit expression of TTR. Agents including a certain pattern of chemical modifications (e.g. , an alternating pattern) and a ligand are shown herein to be effective in silencing the activity of the TTR gene. Furthermore, agents including one or more motifs of three identical modifications on three consecutive nucleotides, including one such motif at or near the cleavage site of the agents, show surprisingly enhanced TTR gene silencing activity. When a single such chemical motif is present in the agent, it is preferred to be at or near the cleavage region for enhancing of the gene silencing activity. Cleavage region is the region surrounding the cleavage site, i.e., the site on the target mRNA at which cleavage occurs.
I. Definitions
In order that the present invention may be more readily understood, certain terms are first defined. In addition, it should be noted that whenever a value or range of values of a parameter are recited, it is intended that values and ranges intermediate to the recited values are also intended to be part of this invention.
The articles "a" and "an" are used herein to refer to one or to more than one {i.e., to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element, e.g., a plurality of elements.
The term "including" is used herein to mean, and is used interchangeably with, the phrase "including but not limited to".
The term "or" is used herein to mean, and is used interchangeably with, the term "and/or," unless context clearly indicates otherwise.
As used herein, a "transthyretin" ("TTR") refers to the well known gene and protein. TTR is also known as prealbumin, HsT2651, PALB, and TB PA. TTR functions as a transporter of retinol-binding protein (RBP), thyroxine (T4) and retinol, and it also acts as a protease. The liver secretes TTR into the blood, and the choroid plexus secretes TTR into the cerebrospinal fluid. TTR is also expressed in the pancreas and the retinal pigment epithelium. The greatest clinical relevance of TTR is that both normal and mutant TTR protein can form amyloid fibrils that aggregate into
extracellular deposits, causing amyloidosis. See, e.g., Saraiva M.J.M. (2002) Expert Reviews in Molecular Medicine, 4(12): 1-11 for a review. The molecular cloning and nucleotide sequence of rat transthyretin, as well as the distribution of mRNA expression, was described by Dickson, P.W. et al. (1985) J. Biol. Chem. 260(13)8214-8219. The X- ray crystal structure of human TTR was described in Blake, C.C. et al. (1974) J Mol Biol 88, 1-12. The sequence of a human TTR mRNA transcript can be found at National Center for Biotechnology Information (NCBI) RefSeq accession number NM_000371. The sequence of mouse TTR mRNA can be found at RefSeq accession number
NM_013697.2, and the sequence of rat TTR mRNA can be found at RefSeq accession number NM 012681.1 As used herein, "target sequence" refers to a contiguous portion of the nucleotide sequence of an mRNA molecule formed during the transcription of a TTR gene, including mRNA that is a product of RNA processing of a primary transcription product.
As used herein, the term "strand comprising a sequence" refers to an
oligonucleotide comprising a chain of nucleotides that is described by the sequence referred to using the standard nucleotide nomenclature.
"G," "C," "A" and "U" each generally stand for a nucleotide that contains guanine, cytosine, adenine, and uracil as a base, respectively. "T" and "dT" are used interchangeably herein and refer to a deoxyribonucleotide wherein the nucleobase is thymine, e.g., deoxyribothymine, 2'-deoxythymidine or thymidine. However, it will be understood that the term "ribonucleotide" or "nucleotide" or "deoxyribonucleotide" can also refer to a modified nucleotide, as further detailed below, or a surrogate replacement moiety. The skilled person is well aware that guanine, cytosine, adenine, and uracil may be replaced by other moieties without substantially altering the base pairing properties of an oligonucleotide comprising a nucleotide bearing such replacement moiety. For example, without limitation, a nucleotide comprising inosine as its base may base pair with nucleotides containing adenine, cytosine, or uracil. Hence, nucleotides containing uracil, guanine, or adenine may be replaced in the nucleotide sequences of the invention by a nucleotide containing, for example, inosine. Sequences comprising such
replacement moieties are embodiments of the invention.
A "double stranded RNAi agent," double- stranded RNA (dsRNA) molecule, also referred to as "dsRNA agent," "dsRNA", "siRNA", "iRNA agent," as used
interchangeably herein, refers to a complex of ribonucleic acid molecules, having a duplex structure comprising two anti-parallel and substantially complementary, as defined below, nucleic acid strands. In general, the majority of nucleotides of each strand are ribonucleotides, but as described in detail herein, each or both strands can also include one or more non-ribonucleotides, e.g., a deoxyribonucleotide and/or a modified nucleotide. In addition, as used in this specification, an "RNAi agent" may include ribonucleotides with chemical modifications; an RNAi agent may include substantial modifications at multiple nucleotides. Such modifications may include all types of modifications disclosed herein or known in the art. Any such modifications, as used in a siRNA type molecule, are encompassed by "RNAi agent" for the purposes of this specification and claims.
In another embodiment, the RNAi agent may be a single- stranded siRNA that is introduced into a cell or organism to inhibit a target mRNA. Single- stranded RNAi agents bind to the RISC endonuclease Argonaute 2, which then cleaves the target mRNA. The single- stranded siRNAs are generally 15-30 nucleotides and are chemically modified. The design and testing of single- stranded siRNAs are described in U.S. Patent No. 8,101,348 and in Lima et al, (2012) Cell 150: 883-894, the entire contents of each of which are hereby incorporated herein by reference. Any of the antisense nucleotide sequences described herein may be used as a single- stranded siRNA as described herein or as chemically modified by the methods described in Lima et al., (2012) Cell
150;:883-894.
The two strands forming the duplex structure may be different portions of one larger RNA molecule, or they may be separate RNA molecules. Where the two strands are part of one larger molecule, and therefore are connected by an uninterrupted chain of nucleotides between the 3 '-end of one strand and the 5 '-end of the respective other strand forming the duplex structure, the connecting RNA chain is referred to as a "hairpin loop." Where the two strands are connected covalently by means other than an uninterrupted chain of nucleotides between the 3 '-end of one strand and the 5 '-end of the respective other strand forming the duplex structure, the connecting structure is referred to as a "linker." The RNA strands may have the same or a different number of nucleotides. The maximum number of base pairs is the number of nucleotides in the shortest strand of the dsRNA minus any overhangs that are present in the duplex. In addition to the duplex structure, an RNAi agent may comprise one or more nucleotide overhangs. The term "siRNA" is also used herein to refer to an RNAi agent as described above.
In another aspect, the agent is a single- stranded antisense RNA molecule. An antisense RNA molecule is complementary to a sequence within the target mRNA. Antisense RNA can inhibit translation in a stoichiometric manner by base pairing to the mRNA and physically obstructing the translation machinery, see Dias, N. et al., (2002) Mol Cancer Ther 1:347-355. The antisense RNA molecule may have about 15-30 nucleotides that are complementary to the target mRNA. For example, the antisense RNA molecule may have a sequence of at least 15, 16, 17, 18, 19, 20 or more contiguous nucleotides from one of the antisense sequences of Table 1.
As used herein, a "nucleotide overhang" refers to the unpaired nucleotide or nucleotides that protrude from the duplex structure of an RNAi agent when a 3 '-end of one strand of the RNAi agent extends beyond the 5 '-end of the other strand, or vice versa. "Blunt" or "blunt end" means that there are no unpaired nucleotides at that end of the double stranded RNAi agent, i.e., no nucleotide overhang. A "blunt ended" RNAi agent is a dsRNA that is double- stranded over its entire length, i.e., no nucleotide overhang at either end of the molecule. The RNAi agents of the invention include RNAi agents with nucleotide overhangs at one end (i.e., agents with one overhang and one blunt end) or with nucleotide overhangs at both ends.
The term "antisense strand" refers to the strand of a double stranded RNAi agent which includes a region that is substantially complementary to a target sequence (e.g. , a human TTR mRNA). As used herein, the term "region complementary to part of an mRNA encoding transthyretin" refers to a region on the antisense strand that is substantially complementary to part of a TTR mRNA sequence. Where the region of complementarity is not fully complementary to the target sequence, the mismatches are most tolerated in the terminal regions and, if present, are generally in a terminal region or regions, e.g., within 6, 5, 4, 3, or 2 nucleotides of the 5' and/or 3' terminus.
The term "sense strand," as used herein, refers to the strand of a dsRNA that includes a region that is substantially complementary to a region of the antisense strand.
As used herein, the term "cleavage region" refers to a region that is located immediately adjacent to the cleavage site. The cleavage site is the site on the target at which cleavage occurs. In some embodiments, the cleavage region comprises three bases on either end of, and immediately adjacent to, the cleavage site. In some embodiments, the cleavage region comprises two bases on either end of, and
immediately adjacent to, the cleavage site. In some embodiments, the cleavage site specifically occurs at the site bound by nucleotides 10 and 11 of the antisense strand, and the cleavage region comprises nucleotides 11, 12 and 13.
As used herein, and unless otherwise indicated, the term "complementary," when used to describe a first nucleotide sequence in relation to a second nucleotide sequence, refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as will be understood by the skilled person. Such conditions can, for example, be stringent conditions, where stringent conditions may include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50°C or 70°C for 12- 16 hours followed by washing. Other conditions, such as physiologically relevant conditions as may be encountered inside an organism, can apply. The skilled person will be able to determine the set of conditions most appropriate for a test of complementarity of two sequences in accordance with the ultimate application of the hybridized nucleotides.
Sequences can be "fully complementary" with respect to each when there is base-pairing of the nucleotides of the first nucleotide sequence with the nucleotides of the second nucleotide sequence over the entire length of the first and second nucleotide sequences. However, where a first sequence is referred to as "substantially complementary" with respect to a second sequence herein, the two sequences can be fully complementary, or they may form one or more, but generally not more than 4, 3 or 2 mismatched base pairs upon hybridization, while retaining the ability to hybridize under the conditions most relevant to their ultimate application. However, where two oligonucleotides are designed to form, upon hybridization, one or more single stranded overhangs, such overhangs shall not be regarded as mismatches with regard to the determination of complementarity. For example, a dsRNA comprising one
oligonucleotide 21 nucleotides in length and another oligonucleotide 23 nucleotides in length, wherein the longer oligonucleotide comprises a sequence of 21 nucleotides that is fully complementary to the shorter oligonucleotide, may yet be referred to as "fully complementary" for the purposes described herein.
"Complementary" sequences, as used herein, may also include, or be formed entirely from, non-Watson-Crick base pairs and/or base pairs formed from non-natural and modified nucleotides, in as far as the above requirements with respect to their ability to hybridize are fulfilled. Such non- Watson-Crick base pairs includes, but not limited to, G:U Wobble or Hoogstein base pairing.
The terms "complementary," "fully complementary" and "substantially complementary" herein may be used with respect to the base matching between the sense strand and the antisense strand of a dsRNA, or between the antisense strand of a dsRNA and a target sequence, as will be understood from the context of their use.
As used herein, a polynucleotide that is "substantially complementary to at least part of a messenger RNA (mRNA) refers to a polynucleotide that is substantially complementary to a contiguous portion of the mRNA of interest (e.g., an mRNA encoding TTR) including a 5' UTR, an open reading frame (ORF), or a 3' UTR. For example, a polynucleotide is complementary to at least a part of a TTR mRNA if the sequence is substantially complementary to a non-interrupted portion of an mRNA encoding TTR.
The term "inhibiting," as used herein, is used interchangeably with "reducing," "silencing," "downregulating," "suppressing" and other similar terms, and includes any level of inhibition.
The phrase "inhibiting expression of a TTR," as used herein, includes inhibition of expression of any TTR gene (such as, e.g., a mouse TTR gene, a rat TTR gene, a monkey TTR gene, or a human TTR gene) as well as variants or mutants of a TTR gene. Thus, the TTR gene may be a wild-type TTR gene, a mutant TTR gene (such as a mutant TTR gene giving rise to systemic amyloid deposition), or a transgenic TTR gene in the context of a genetically manipulated cell, group of cells, or organism. "Inhibiting expression of a TTR gene" includes any level of inhibition of a TTR gene, e.g., at least partial suppression of the expression of a TTR gene, such as an inhibition of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%. at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%.
The expression of a TTR gene may be assessed based on the level of any variable associated with TTR gene expression, e.g., TTR mRNA level, TTR protein level, retinol binding protein level, vitamin A level, or the number or extent of amyloid deposits. Inhibition may be assessed by a decrease in an absolute or relative level of one or more of these variables compared with a control level. The control level may be any type of control level that is utilized in the art, e.g., a pre-dose baseline level, or a level determined from a similar subject, cell, or sample that is untreated or treated with a control (such as, e.g., buffer only control or inactive agent control).
The phrase "contacting a cell with an RNAi agent," as used herein, includes contacting a cell by any possible means. Contacting a cell with an RNAi agent, e.g., a double stranded RNAi agent, includes contacting a cell in vitro with the RNAi agent or contacting a cell in vivo with the RNAi agent. The contacting may be done directly or indirectly. Thus, for example, the RNAi agent may be put into physical contact with the cell by the individual performing the method, or alternatively, the RNAi agent may be put into a situation that will permit or cause it to subsequently come into contact with the cell.
Contacting a cell in vitro may be done, for example, by incubating the cell with the RNAi agent. Contacting a cell in vivo may be done, for example, by injecting the RNAi agent into or near the tissue where the cell is located, or by injecting the RNAi agent into another area, e.g., the bloodstream or the subcutaneous space, such that the agent will subsequently reach the tissue where the cell to be contacted is located. For example, the RNAi agent may contain and/or be coupled to a ligand, e.g., a GalNAc3 ligand, that directs the RNAi agent to a site of interest, e.g., the liver. Combinations of in vitro and in vivo methods of contacting are also possible. In connection with the methods of the invention, a cell might also be contacted in vitro with an RNAi agent and subsequently transplanted into a subject. A "patient" or "subject," as used herein, is intended to include either a human or non-human animal, preferably a mammal, e.g., a monkey. Most preferably, the subject or patient is a human.
A "TTR-associated disease," as used herein, is intended to include any disease associated with the TTR gene or protein. Such a disease may be caused, for example, by excess production of the TTR protein, by TTR gene mutations, by abnormal cleavage of the TTR protein, by abnormal interactions between TTR and other proteins or other endogenous or exogenous substances. A "TTR-associated disease" includes any type of TTR amyloidosis (ATTR) wherein TTR plays a role in the formation of abnormal extracellular aggregates or amyloid deposits. TTR-associated diseases include senile systemic amyloidosis (SSA), systemic familial amyloidosis, familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy (FAC),
leptomeningeal/Central Nervous System (CNS) amyloidosis, amyloidotic vitreous opacities, carpal tunnel syndrome, and hyperthyroxinemia.Symptoms of TTR amyloidosis include sensory neuropathy (e.g. , paresthesia, hypesthesia in distal limbs), autonomic neuropathy (e.g. , gastrointestinal dysfunction, such as gastric ulcer, or orthostatic hypotension), motor neuropathy, seizures, dementia, myelopathy, polyneuropathy, carpal tunnel syndrome, autonomic insufficiency, cardiomyopathy, vitreous opacities, renal insufficiency, nephropathy, substantially reduced mBMI (modified Body Mass Index), cranial nerve dysfunction, and corneal lattice dystrophy.
"Therapeutically effective amount," as used herein, is intended to include the amount of an RNAi agent that, when administered to a patient for treating a TTR associated disease, is sufficient to effect treatment of the disease (e.g., by diminishing, ameliorating or maintaining the existing disease or one or more symptoms of disease). The "therapeutically effective amount" may vary depending on the RNAi agent, how the agent is administered, the disease and its severity and the history, age, weight, family history, genetic makeup, stage of pathological processes mediated by TTR expression, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.
"Prophylactically effective amount," as used herein, is intended to include the amount of an RNAi agent that, when administered to a subject who does not yet experience or display symptoms of a TTR-associated disease, but who may be predisposed to the disease, is sufficient to prevent or ameliorate the disease or one or more symptoms of the disease. Symptoms that may be ameliorated include sensory neuropathy (e.g. , paresthesia, hypesthesia in distal limbs), autonomic neuropathy (e.g., gastrointestinal dysfunction, such as gastric ulcer, or orthostatic hypotension), motor neuropathy, seizures, dementia, myelopathy, polyneuropathy, carpal tunnel syndrome, autonomic insufficiency, cardiomyopathy, vitreous opacities, renal insufficiency, nephropathy, substantially reduced mBMI (modified Body Mass Index), cranial nerve dysfunction, and corneal lattice dystrophy. Ameliorating the disease includes slowing the course of the disease or reducing the severity of later-developing disease. The "prophylactically effective amount" may vary depending on the RNAi agent, how the agent is administered, the degree of risk of disease, and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.
A "therapeutically-effective amount" or "prophylacticaly effective amount" also includes an amount of an RNAi agent that produces some desired local or systemic effect at a reasonable benefit/risk ratio applicable to any treatment. RNAi gents employed in the methods of the present invention may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment.
The term "sample," as used herein, includes a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject. Examples of biological fluids include blood, serum and serosal fluids, plasma, cerebrospinal fluid, ocular fluids, lymph, urine, saliva, and the like. Tissue samples may include samples from tissues, organs or localized regions. For example, samples may be derived from particular organs, parts of organs, or fluids or cells within those organs. In certain embodiments, samples may be derived from the liver (e.g. , whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g. , hepatocytes), the retina or parts of the retina (e.g., retinal pigment epithelium), the central nervous system or parts of the central nervous system (e.g., ventricles or choroid plexus), or the pancreas or certain cells or parts of the pancreas. In some embodiments, a "sample derived from a subject" refers tocerebro spinal fluid obtained from the subject. In preferred embodiments, a "sample derived from a subject" refers to blood or plasma drawn from the subject. In further embodiments, a "sample derived from a subject" refers to liver tissue (or subcomponents thereof) or retinal tissue (or subcomponents thereof) derived from the subject.
II. RNAi Agents
The present invention provides RNAi agents with superior gene silencing activity. It is shown herein and in PCT Publication No. WO 2013/075035 (the entire contents of which are incorporated by reference) that a superior result may be obtained by introducing one or more motifs of three identical modifications on three consecutive nucleotides into a sense strand and/or antisense strand of a RNAi agent, particularly at or near the cleavage site. The sense strand and antisense strand of the RNAi agent may otherwise be completely modified. The introduction of these motifs interrupts the modification pattern, if present, of the sense and/or antisense strand. The RNAi agent also optionally conjugates with a GalNAc derivative ligand, for instance on the sense strand. The resulting RNAi agents present superior gene silencing activity.
The inventors surprisingly discovered that when the sense strand and antisense strand of the RNAi agent are completely modified, having one or more motifs of three identical modifications on three consecutive nucleotides at or near the cleavage site of at least one strand of a RNAi agent superiorly enhanced the gene silencing acitivity of the RNAi agent.
Accordingly, the invention provides RNAi agents, e.g., double stranded RNAi agents, capable of inhibiting the expression of a target gene (i.e., a TTR gene) in vivo. The RNAi agent comprises a sense strand and an antisense strand. Each strand of the RNAi agent can range from 12-30 nucleotides in length. For example, each strand can be between 14-30 nucleotides in length, 17-30 nucleotides in length, 25-30 nucleotides in length, 27-30 nucleotides in length, 17-23 nucleotides in length, 17-21 nucleotides in length, 17-19 nucleotides in length, 19-25 nucleotides in length, 19-23 nucleotides in length, 19-21 nucleotides in length, 21-25 nucleotides in length, or 21-23 nucleotides in length.
The sense strand and antisense strand typically form a duplex double stranded RNA ("dsRNA"), also referred to herein as an "RNAi agent." The duplex region of an RNAi agent may be 12-30 nucleotide pairs in length. For example, the duplex region can be between 14-30 nucleotide pairs in length, 17-30 nucleotide pairs in length, 27-30 nucleotide pairs in length, 17 - 23 nucleotide pairs in length, 17-21 nucleotide pairs in length, 17-19 nucleotide pairs in length, 19-25 nucleotide pairs in length, 19-23 nucleotide pairs in length, 19- 21 nucleotide pairs in length, 21-25 nucleotide pairs in length, or 21-23 nucleotide pairs in length. In another example, the duplex region is selected from 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27.
In one embodiment, the RNAi agent may contain one or more overhang regions and/or capping groups of RNAi agent at 3 '-end, or 5 '-end or both ends of a strand. The overhang can be 1-6 nucleotides in length, for instance 2-6 nucleotides in length, 1-5 nucleotides in length, 2-5 nucleotides in length, 1-4 nucleotides in length, 2-4 nucleotides in length, 1-3 nucleotides in length, 2-3 nucleotides in length, or 1-2 nucleotides in length. The overhangs can be the result of one strand being longer than the other, or the result of two strands of the same length being staggered. The overhang can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be other sequence. The first and second strands can also be joined, e.g., by additional bases to form a hairpin, or by other non-base linkers.
The RNAi agents provided by the present invention include agents with chemical modifications as disclosed, for example, in U.S. Provisional Application No.
61/561,710, filed on November 18, 2011, International Application No.
PCT/US2011/051597, filed on September 15, 2010, and PCT Publication WO
2009/073809, the entire contents of each of which are incorporated herein by reference.
In one embodiment, the nucleotides in the overhang region of the RNAi agent can each independently be a modified or unmodified nucleotide including, but no limited to 2'-sugar modified, such as, 2-F, 2'-0-methyl, thymidine (T), 2 -0-methoxyethyl-5- methyluridine (Teo), 2 -0-methoxyethyladenosine (Aeo), 2 -0-methoxyethyl-5- methylcytidine (m5Ceo), and any combinations thereof. For example, TT can be an overhang sequence for either end on either strand.The overhang can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be other sequence.
The 5'- or 3'- overhangs at the sense strand, antisense strand or both strands of the RNAi agent may be phosphorylated. In some embodiments, the overhang region contains two nucleotides having a phosphorothioate between the two nucleotides, where the two nucleotides can be the same or different. In one embodiment, the overhang is present at the 3 '-end of the sense strand, antisense strand or both strands. In one embodiment, this 3 '-overhang is present in the antisense strand.In one embodiment, this 3 '-overhang is present in the sense strand.
The RNAi agent may contain only a single overhang, which can strengthen the interference activity of the RNAi, without affecting its overall stability. For example, the single- stranded overhang is located at the 3 '-terminal end of the sense strand or, alternatively, at the 3 '-terminal end of the antisense strand. The RNAi may also have a blunt end, located at the 5 '-end of the antisense strand (or the 3 '-end of the sense strand) or vice versa. Generally, the antisense strand of the RNAi has a nucleotide overhang at the 3 '-end, and the 5 '-end is blunt. While the Applicants are not bound by theory, the theoretical mechanism is that the asymmetric blunt end at the 5 '-end of the antisense strand and 3 '-end overhang of the antisense strand favor the guide strand loading into RISC process.
In one embodiment, the RNAi agent is a double ended bluntmer of 19 nt in length, wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides at positions 7,8,9 from the 5'end. The antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5'end.
In one embodiment, the RNAi agent is a double ended bluntmer of 20 nt in length, wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides at positions 8,9,10 from the 5'end. The antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5'end.
In one embodiment, the RNAi agent is a double ended bluntmer of 21 nt in length, wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides at positions 9, 10, 11 from the 5'end. The antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5'end.
In one embodiment, the RNAi agent comprises a 21 nucleotides (nt) sense strand and a 23 nucleotides (nt) antisense strand, wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides at positions 9,10,11 from the 5'end; the antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5'end, wherein one end of the RNAi agent is blunt, while the other end comprises a 2 nt overhang. Preferably, the 2 nt overhang is at the 3 '-end of the antisense. Optionally, the RNAi agent further comprises a ligand (preferably GalNAc3).
In one embodiment, the RNAi agent comprises a sense and an antisense strand, wherein the sense strand is 25-30 nucleotide residues in length, wherein starting from the 5' terminal nucleotide (position 1) positions 1 to 23 of the first strand comprise at least 8 ribonucleotides; antisense strand is 36-66 nucleotide residues in length and, starting from the 3' terminal nucleotide, comprises at least 8 ribonucleotides in the positions paired with positions 1- 23 of sense strand to form a duplex; wherein at least the 3 ' terminal nucleotide of antisense strand is unpaired with sense strand, and up to 6 consecutive 3' terminal nucleotides are unpaired with sense strand, thereby forming a 3' single stranded overhang of 1-6 nucleotides; wherein the 5' terminus of antisense strand comprises from 10-30 consecutive nucleotides which are unpaired with sense strand, thereby forming a 10-30 nucleotide single stranded 5' overhang; wherein at least the sense strand 5' terminal and 3' terminal nucleotides are base paired with nucleotides of antisense strand when sense and antisense strands are aligned for maximum
complementarity, thereby forming a substantially duplexed region between sense and antisense strands; and antisense strand is sufficiently complementary to a target RNA along at least 19 ribonucleotides of antisense strand length to reduce target gene expression when the double stranded nucleic acid is introduced into a mammalian cell; and wherein the sense strand contains at least one motif of three 2'-F modifications on three consecutive nucleotides, where at least one of the motifs occurs at or near the cleavage site. The antisense strand contains at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at or near the cleavage site.
In one embodiment, the RNAi agent comprises sense and antisense strands, wherein the RNAi agent comprises a first strand having a length which is at least 25 and at most 29 nucleotides and a second strand having a length which is at most 30 nucleotides with at least one motif of three 2'-0-methyl modifications on three consecutive nucleotides at position 11,12,13 from the 5' end; wherein the 3' end of the first strand and the 5' end of the second strand form a blunt end and the second strand is 1-4 nucleotides longer at its 3' end than the first strand, wherein the duplex region which is at least 25 nucleotides in length, and the second strand is sufficiently complemenatary to a target mRNA along at least 19 nt of the second strand length to reduce target gene expression when the RNAi agent is introduced into a mammalian cell, and wherein dicer cleavage of the RNAi agent preferentially results in an siRNA comprising the 3' end of the second strand, thereby reducing expression of the target gene in the mammal.
Optionally, the RNAi agent further comprises a ligand.
In one embodiment, the sense strand of the RNAi agent contains at least one motif of three identical modifications on three consecutive nucleotides, where one of the motifs occurs at the cleavage site in the sense strand.
In one embodiment, the antisense strand of the RNAi agent can also contain at least one motif of three identical modifications on three consecutive nucleotides, where one of the motifs occurs at or near the cleavage site in the antisense strand
For RNAi agent having a duplex region of 17-23 nucleotides in length, the cleavage site of the antisense strand is typically around the 10, 11 and 12 positions from the 5 '-end. Thus, the motifs of three identical modifications may occur at the 9, 10, 11 positions; 10, 11, 12 positions; 11, 12, 13 positions; 12, 13, 14 positions; or 13, 14, 15 positions of the antisense strand, the count starting from the 1st nucleotide from the 5 '-end of the antisense strand, or, the count starting from the 1st paired nucleotide within the duplex region from the 5'- end of the antisense strand. The cleavage site in the antisense strand may also change according to the length of the duplex region of the RNAi from the 5 '-end.
The sense strand of the RNAi agent may contain at least one motif of three identical modifications on three consecutive nucleotides at the cleavage site of the strand; and the antisense strand may have at least one motif of three identical modifications on three consecutive nucleotides at or near the cleavage site of the strand. When the sense strand and the antisense strand form a dsRNA duplex, the sense strand and the antisense strand can be so aligned that one motif of the three nucleotides on the sense strand and one motif of the three nucleotides on the antisense strand have at least one nucleotide overlap, i.e., at least one of the three nucleotides of the motif in the sense strand forms a base pair with at least one of the three nucleotides of the motif in the antisense strand. Alternatively, at least two nucleotides may overlap, or all three nucleotides may overlap.
In one embodiment, the sense strand of the RNAi agent may contain more than one motif of three identical modifications on three consecutive nucleotides. The first motif should occur at or near the cleavage site of the strand and the other motifs may be wing modifications. The term "wing modification" herein refers to a motif occurring at another portion of the strand that is separated from the motif at or near the cleavage site of the same strand. The wing modification is either adajacent to the first motif or is separated by at least one or more nucleotides. When the motifs are immediately adjacent to each other than the chemistry of the motifs are distinct from each other and when the motifs are separated by one or more nucleotide than the chemistries can be the same or different. Two or more wing modifications may be present. For instance, when two wing modifications are present, each wing modification may occur at one end relative to the first motif which is at or near cleavage site or on either side of the lead motif.
Like the sense strand, the antisense strand of the RNAi agent may contain at least two motifs of three identical modifications on three consecutive nucleotides, with at least one of the motifs occurring at or near the cleavage site of the strand. This antisense strand may also contain one or more wing modifications in an alignment similar to the wing modifications that is present on the sense strand.
In one embodiment, the wing modification on the sense strand or antisense strand of the RNAi agent typically does not include the first one or two terminal nucleotides at the 3 '-end, 5 '-end or both ends of the strand.
In another embodiment, the wing modification on the sense strand or antisense strand of the RNAi agent typically does not include the first one or two paired nucleotides within the duplex region at the 3 '-end, 5 '-end or both ends of the strand.
When the sense strand and the antisense strand of the RNAi agent each contain at least one wing modification, the wing modifications may fall on the same end of the duplex region, and have an overlap of one, two or three nucleotides.
When the sense strand and the antisense strand of the RNAi agent each contain at least two wing modifications, the sense strand and the antisense strand can be so aligned that two modifications each from one strand fall on one end of the duplex region, having an overlap of one, two or three nucleotides; two modifications each from one strand fall on the other end of the duplex region, having an overlap of one, two or three
nucleotides; two modifications one strand fall on each side of the lead motif, having an overlap of one, two or three nucleotides in the duplex region.
In one embodiment, every nucleotide in the sense strand and antisense strand of the RNAi agent, including the nucleotides that are part of the motifs, may be modified. Each nucleotide may be modified with the same or different modification which can include one or more alteration of one or both of the non-linking phosphate oxygens and/or of one or more of the linking phosphate oxygens; alteration of a constituent of the ribose sugar, e.g., of the 2' hydroxyl on the ribose sugar; wholesale replacement of the phosphate moiety with "dephospho" linkers; modification or replacement of a naturally occurring base; and replacement or modification of the ribose-phosphate backbone.
As nucleic acids are polymers of subunits, many of the modifications occur at a position which is repeated within a nucleic acid, e.g., a modification of a base, or a phosphate moiety, or a non-linking O of a phosphate moiety. In some cases the modification will occur at all of the subject positions in the nucleic acid but in many cases it will not. By way of example, a modification may only occur at a 3' or 5' terminal position, may only occur in a terminal region, e.g., at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand. A modification may occur in a double strand region, a single strand region, or in both. A modification may occur only in the double strand region of a RNA or may only occur in a single strand region of a RNA. For example, a phosphorothioate modification at a non-linking O position may only occur at one or both termini, may only occur in a terminal region, e.g., at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand, or may occur in double strand and single strand regions, particularly at termini. The 5' end or ends can be phosphorylated.
It may be possible, e.g., to enhance stability, to include particular bases in overhangs, or to include modified nucleotides or nucleotide surrogates, in single strand overhangs, e.g., in a 5' or 3' overhang, or in both. For example, it can be desirable to include purine nucleotides in overhangs. In some embodiments all or some of the bases in a 3' or 5' overhang may be modified, e.g., with a modification described herein.
Modifications can include, e.g., the use of modifications at the 2' position of the ribose sugar with modifications that are known in the art, e.g., the use of deoxyribonucleotides, 2'-deoxy-2'-fluoro (2'-F) or 2'-0-methyl modified instead of the ribosugar of the nucleobase, and modifications in the phosphate group, e.g., phosphorothioate modifications. Overhangs need not be homologous with the target sequence.
In one embodiment, each residue of the sense strand and antisense strand is independently modified with locked nucleic acid (LNA), unlocked nucleic acid (UNA), conformational^ restricted nucleotide (CRN), constrained ethyl nucleotide (cEt), HNA, CeNA, 2'-methoxyethyl, 2'- O-methyl, 2'-0-allyl, 2'-C- allyl, 2'-deoxy, 2'-hydroxyl, or 2'-fluoro. The strands can contain more than one modification. In one embodiment, each residue of the sense strand and antisense strand is independently modified with 2'- O-methyl or 2'-fluoro.
At least two different modifications are typically present on the sense strand and antisense strand. Those two modifications may be the 2'- O-methyl or 2'-fluoro modifications, or others.
In one embodiment, the Na and/or Nb comprise modifications of an alternating pattern. The term "alternating motif as used herein refers to a motif having one or more modifications, each modification occurring on alternating nucleotides of one strand. The alternating nucleotide may refer to one per every other nucleotide or one per every three nucleotides, or a similar pattern. For example, if A, B and C each represent one type of modification to the nucleotide, the alternating motif can be "ABABABABABAB...," "AABBAABBAABB ... ," "AABAABAABAAB ... ," "AAABAAABAAAB
"AAABBB AAABBB ... ," or "ABCABCABCABC ...," etc.
The type of modifications contained in the alternating motif may be the same or different. For example, if A, B, C, D each represent one type of modification on the nucleotide, the alternating pattern, i.e., modifications on every other nucleotide, may be the same, but each of the sense strand or antisense strand can be selected from several possibilities of modifications within the alternating motif such as "ABABAB...", "ACACAC..." "BDBDBD..." or "CDCDCD...," etc.
In one embodiment, the RNAi agent of the invention comprises the modification pattern for the alternating motif on the sense strand relative to the modification pattern for the alternating motif on the antisense strand is shifted. The shift may be such that the modified group of nucleotides of the sense strand corresponds to a differently modified group of nucleotides of the antisense strand and vice versa. For example, the sense strand when paired with the antisense strand in the dsRNA duplex, the alternating motif in the sense strand may start with "ABABAB" from 5 '-3' of the strand and the alternating motif in the antisense strand may start with "BAB ABA" from 5 '-3 Of the strand within the duplex region. As another example, the alternating motif in the sense strand may start with "AABBAABB" from 5 '-3' of the strand and the alternating motif in the antisenese strand may start with "BBAABBAA" from 5 '-3' of the strand within the duplex region, so that there is a complete or partial shift of the modification patterns between the sense strand and the antisense strand.
In one embodiment, the RNAi agent comprises the pattern of the alternating motif of 2'-0-methyl modification and 2'-F modification on the sense strand initially has a shift relative to the pattern of the alternating motif of 2'-0-methyl modification and 2'-F modification on the antisense strand initially, i.e., the 2'-0-methyl modified nucleotide on the sense strand base pairs with a 2'-F modified nucleotide on the antisense strand and vice versa. The 1 position of the sense strand may start with the 2'- F modification, and the 1 position of the antisense strand may start with the 2'- O- methyl modification.
The introduction of one or more motifs of three identical modifications on three consecutive nucleotides to the sense strand and/or antisense strand interrupts the initial modification pattern present in the sense strand and/or antisense strand. This interruption of the modification pattern of the sense and/or antisense strand by introducing one or more motifs of three identical modifications on three consecutive nucleotides to the sense and/or antisense strand surprisingly enhances the gene silencing acitivty to the target gene.
In one embodiment, when the motif of three identical modifications on three consecutive nucleotides is introduced to any of the strands, the modification of the nucleotide next to the motif is a different modification than the modification of the motif. For example, the portion of the sequence containing the motif is
"...NaYYYNb...," where "Y" represents the modification of the motif of three identical modifications on three consecutive nucleotide, and "Na" and "Nb" represent a modification to the nucleotide next to the motif "γγγ" that is different than the modification of Y, and where Na and Nb can be the same or different modifications. Altnematively, Na and/or Nb may be present or absent when there is a wing modification present.
The RNAi agent may further comprise at least one phosphorothioate or methylphosphonate internucleotide linkage. The phosphorothioate or
methylphosphonate internucleotide linkage modification may occur on any nucleotide of the sense strand or antisense strand or both in any position of the strand. For instance, the internucleotide linkage modification may occur on every nucleotide on the sense strand or antisense strand; each internucleotide linkage modification may occur in an alternating pattern on the sense strand or antisense strand; or the sense strand or antisense strand may contain both internucleotide linkage modifications in an alternating pattern. The alternating pattern of the internucleotide linkage modification on the sense strand may be the same or different from the antisense strand, and the alternating pattern of the internucleotide linkage modification on the sense strand may have a shift relative to the alternating pattern of the internucleotide linkage modification on the antisense strand.
In one embodiment, the RNAi comprises the phosphorothioate or
methylphosphonate internucleotide linkage modification in the overhang region. For example, the overhang region may contain two nucleotides having a phosphorothioate or methylphosphonate internucleotide linkage between the two nucleotides.
Internucleotide linkage modifications also may be made to link the overhang nucleotides with the terminal paired nucleotides within duplex region. For example, at least 2, 3, 4, or all the overhang nucleotides may be linked through phosphorothioate or
methylphosphonate internucleotide linkage, and optionally, there may be additional phosphorothioate or methylphosphonate internucleotide linkages linking the overhang nucleotide with a paired nucleotide that is next to the overhang nucleotide. For instance, there may be at least two phosphorothioate internucleotide linkages between the terminal three nucleotides, in which two of the three nucleotides are overhang nucleotides, and the third is a paried nucleotide next to the overhang nucleotide. Preferably, these terminal three nucleotides may be at the 3 '-end of the antisense strand.
In one embodiment, the RNAi agent comprises mismatch(es) with the target, within the duplex, or combinations thereof. The mistmatch can occur in the overhang region or the duplex region. The base pair can be ranked on the basis of their propensity to promote dissociation or melting (e.g. , on the free energy of association or dissociation of a particular pairing, the simplest approach is to examine the pairs on an individual pair basis, though next neighbor or similar analysis can also be used). In terms of promoting dissociation: A:U is preferred over G:C; G:U is preferred over G:C; and I:C is preferred over G:C (I=inosine). Mismatches, e.g. , non-canonical or other than canonical pairings (as described elsewhere herein) are preferred over canonical (A:T, A:U, G:C) pairings; and pairings which include a universal base are preferred over canonical pairings.
In one embodiment, the RNAi agent comprises at least one of the first 1, 2, 3, 4, or 5 base pairs within the duplex regions from the 5'- end of the antisense strand can be chosen independently from the group of: A:U, G:U, I:C, and mismatched pairs, e.g. , non-canonical or other than canonical pairings or pairings which include a universal base, to promote the dissociation of the antisense strand at the 5'-end of the duplex. In one embodiment, the nucleotide at the 1 position within the duplex region from the 5 '-end in the antisense strand is selected from the group consisting of A, dA, dU, U, and dT. Alternatively, at least one of the first 1, 2 or 3 base pair within the duplex region from the 5'- end of the antisense strand is an AU base pair. For example, the first base pair within the duplex region from the 5'- end of the antisense strand is an AU base pair.
In one embodiment, the sense strand sequence may be represented by formula
(I):
5' np-Na-(X X X )i-Nb-Y Y Y -Nb-(Z Z Z )rNa-nq 3' (I)
wherein:
i and j are each independently 0 or 1 ;
p and q are each independently 0-6;
each Na independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;
each Nb independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides;
each np and nq independently represent an overhang nucleotide;
wherein Nb and Y do not have the same modification; and
XXX, YYY and ZZZ each independently represent one motif of three identical modifications on three consecutive nucleotides. Preferably YYY is all 2'-F modified nucleotides.
In one embodiment, the Na and/or Nb comprise modifications of alternating pattern.
In one embodiment, the YYY motif occurs at or near the cleavage site of the sense strand. For example, when the RNAi agent has a duplex region of 17-23 nucleotides in length, the YYY motif can occur at or the vicinity of the cleavage site {e.g. : can occur at positions 6, 7, 8, 7, 8, 9, 8, 9, 10, 9, 10, 11, 10, 11,12 or 11, 12, 13) of - the sense strand, the count starting from the 1st nucleotide, from the 5 '-end; or optionally, the count starting at the 1st paired nucleotide within the duplex region, from the 5'- end.
In one embodiment, i is 1 and j is 0, or i is 0 and j is 1, or both i and j are 1. The sense strand can therefore be represented by the following formulas:
5' np-Na-YYY-Nb-ZZZ-Na-nq 3' (la);
5' np-Na-XXX-Nb-YYY-Na-nq 3' (lb); or
5' np-Na-XXX-Nb-YYY-Nb-ZZZ-Na-nq 3' (Ic). When the sense strand is represented by formula (la), Nb represents an oligonucleotide sequence comprising 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na independently can represent an oligonucleotide sequence comprising 2-20, 2- 15, or 2-10 modified nucleotides.
When the sense strand is represented as formula (lb), Nb represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na can independently represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
When the sense strand is represented as formula (Ic), each Nb independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Preferably, Nb is 0, 1, 2, 3, 4, 5 or 6 Each Na can independently represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
Each of X, Y and Z may be the same or different from each other.
In one embodiment, the antisense strand sequence of the RNAi may be represented by formula (II):
5' nq-Na'-(Z'Z'Z')k-Nb'-YTT'-Nb'-(X'X'X')i-N'a-np' 3' (II)
wherein:
k and 1 are each independently 0 or 1 ;
p' and q' are each independently 0-6;
each Na' independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;
each Nb' independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides;
each np' and nq' independently represent an overhang nucleotide;
wherein Nb' and Y' do not have the same modification;
and
Χ'Χ'Χ', ΥΎΎ' and Z'Z'Z' each independently represent one motif of three identical modifications on three consecutive nucleotides.
In one embodiment, the Na' and/or Nb' comprise modifications of alternating pattern.
The ΥΎΎ' motif occurs at or near the cleavage site of the antisense strand. For example, when the RNAi agent has a duplex region of 17-23 nt in length, the ΥΎΎ' motif can occur at positions 9, 10, 11;10, 11, 12; 11, 12, 13; 12, 13, 14 ; or 13, 14, 15 of the antisense strand, with the count starting from the 1st nucleotide, from the 5 '-end; or optionally, the count starting at the Is paired nucleotide within the duplex region, from the 5'- end. Preferably, the ΥΎΎ' motif occurs at positions 11, 12, 13.
In one embodiment, ΥΎΎ' motif is all 2'-OMe modified nucleotides.
In one embodiment, k is 1 and 1 is 0, or k is 0 and 1 is 1, or both k and 1 are 1. The antisense strand can therefore be represented by the following formulas:
5' nq<-Na'-Z'Z'Z'-Nb'-Y'Y'Y'-Na'-np< 3' (Ila);
5' nq<-Na'-Y'Y'Y'-Nb'-X'X'X'-np< 3' (lib); or
5' nq-Na'- Z'Z'Z'-Nb'-Y'Y'Y'-Nb'- X'X'X'-Na'-np< 3' (lie).
When the antisense strand is represented by formula (Ila), Nb represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na' independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
When the antisense strand is represented as formula (lib), Nb' represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na' independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
When the antisense strand is represented as formula (lie), each Nb'
independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na' independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
Preferably, Nb is 0, 1, 2, 3, 4, 5 or 6.
Each of X', Y' and Z' may be the same or different from each other.
Each nucleotide of the sense strand and antisense strand may be independently modified with LNA, UNA, CRN, cEt, HNA, CeNA, 2'-methoxyethyl, 2'-0-methyl, 2'- O-allyl, 2'-C- allyl, 2'-hydroxyl, 2'-deoxy or 2'-fluoro. For example, each nucleotide of the sense strand and antisense strand is independently modified with 2'-0-methyl or 2'- fluoro. Each X, Y, Z, X', Y' and Z', in particular, may represent a 2'-0-methyl modification or a 2' -fluoro modification.
In one embodiment, the sense strand of the RNAi agent may contain YYY motif occurring at 9, 10 and 11 positions of the strand when the duplex region is 21 nt, the count starting from the 1st nucleotide from the 5 '-end, or optionally, the count starting at the 1st paired nucleotide within the duplex region, from the 5'- end; and Y represents 2'- F modification. The sense strand may additionally contain XXX motif or ZZZ motifs as wing modifications at the opposite end of the duplex region; and XXX and ZZZ each independently represents a 2'-OMe modification or 2'-F modification. In one embodiment the antisense strand may contain ΥΎΎ' motif occurring at positions 11, 12, 13 of the strand, the count starting from the 1st nucleotide from the 5 '-end, or optionally, the count starting at the 1st paired nucleotide within the duplex region, from the 5'- end; and Y' represents 2'-0-methyl modification. The antisense strand may additionally contain X'X'X' motif or Z'Z'Z' motifs as wing modifications at the opposite end of the duplex region; and X'X'X' and Z'Z'Z' each independently represents a 2'-OMe modification or 2'-F modification.
The sense strand represented by any one of the above formulas (la), (lb) and (Ic) forms a duplex with a antisense strand being represented by any one of formulas (Ila), (lib) and (lie), respectively.
Accordingly, the RNAi agents of the invention may comprise a sense strand and an antisense strand, each strand having 14 to 30 nucleotides, the RNAi duplex represented by formula (III):
sense: 5' np -Na-(X X X); -Nb- Y Y Y -Nb -(Z Z Z)rNa-nq 3'
antisense: 3' np '-Na '-(X'X'X')k-Nb '-Y'Y'Y'-Nb '-(Z'Z'Z')i-Na '-nq 5'
(III)
wherein:
i, j, k, and 1 are each independently 0 or 1;
p, p', q, and q' are each independently 0-6;
each Na and Na independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;
each Nb and Nb independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides;
wherein
each np', np, nq', and nq independently represents an overhang nucleotide; and XXX, YYY, ZZZ, X'X'X', Y'Y'Y', and Z'Z'Z' each independently represent one motif of three identical modifications on three consecutive nucleotides.
In one embodiment, i is 1 and j is 0; or i is 0 and j is 1; or both i and j are 1. In another embodiment, k is 1 and 1 is 0; k is 0 and 1 is 1; or both k and 1 are 1.
Exemplary combinations of the sense strand and antisense strand forming a RNAi duplex include the formulas below:
5' np -Na -Y Y Y -Nb -Z Z Z -Na-nq 3'
3' np -Na -Y'Y'Y'-Nb -Z'Z'Z'-Na nq 5'
(Ilia)
5' np-Na- X X X -Nb -Y Y Y - Na-nq 3' 3' np '-Na' -X'X'X'-Nb -Y'Y'Y'-Na -nq 5'
(nib)
5' np -Na -X X X -Nb-Y Y Y -Nb- Z Z Z -Na-nq 3'
3' np '-Na -X'X'X'-Nb -Y'YY'-Nb -Z'Z'Z'-Na-nq 5'
(IIIc)
When the RNAi agent is represented by formula (Ilia), each Nb independently represents an oligonucleotide sequence comprising 1-10, 1-7, 1-5 or 1-4 modified nucleotides. Each Na independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
When the RNAi agent is represented as formula (Illb), each Nb, Nb'
independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or Omodified nucleotides. Each Na independently represents an
oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
When the RNAi agent is represented as formula (IIIc), each Nb, Nb'
independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or Omodified nucleotides. Each Na, Na independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides. Each of Na, Na', Nb and Nb independently comprises modifications of alternating pattern.
Each of X, Y and Z in formulas (III), (Ilia), (Illb) and (IIIc) may be the same or different from each other.
When the RNAi agent is represented by formula (III), (Ilia), (Illb) or (IIIc), at least one of the Y nucleotides may form a base pair with one of the Y' nucleotides. Alternatively, at least two of the Y nucleotides form base pairs with the corresponding Y' nucleotides; or all three of the Y nucleotides all form base pairs with the
corresponding Y' nucleotides.
When the RNAi agent is represented by formula (Ilia) or (IIIc), at least one of the Z nucleotides may form a base pair with one of the Z' nucleotides. Alternatively, at least two of the Z nucleotides form base pairs with the corresponding Z' nucleotides; or all three of the Z nucleotides all form base pairs with the corresponding Z' nucleotides.
When the RNAi agent is represented as formula (Illb) or (IIIc), at least one of the
X nucleotides may form a base pair with one of the X' nucleotides. Alternatively, at least two of the X nucleotides form base pairs with the corresponding X' nucleotides; or all three of the X nucleotides all form base pairs with the corresponding X' nucleotides.
In one embodiment, the modification on the Y nucleotide is different than the modification on the Y' nucleotide, the modification on the Z nucleotide is different than the modification on the Z' nucleotide, and/or the modification on the X nucleotide is different than the modification on the X' nucleotide.
In one embodiment, the RNAi agent is a multimer containing at least two duplexes represented by formula (III), (Ilia), (Illb) or (IIIc), wherein the duplexes are connected by a linker. The linker can be cleavable or non-cleavable. Optionally, the multimer further comprise a ligand. Each of the duplexes can target the same gene or two different genes; or each of the duplexes can target same gene at two different target sites.
In one embodiment, the RNAi agent is a multimer containing three, four, five, six or more duplexes represented by formula (III), (Ilia), (Illb) or (IIIc), wherein the duplexes are connected by a linker. The linker can be cleavable or non-cleavable.
Optionally, the multimer further comprises a ligand. Each of the duplexes can target the same gene or two different genes; or each of the duplexes can target same gene at two different target sites.
In one embodiment, two RNAi agents represented by formula (III), (Ilia), (Illb) or (IIIc) are linked to each other at the 5' end, and one or both of the 3' ends of the are optionally conjugated to to a ligand. Each of the agents can target the same gene or two different genes; or each of the agents can target same gene at two different target sites.
Various publications describe multimeric RNAi agents . Such publications include WO2007/091269, US Patent No. 7858769, WO2010/141511, WO2007/117686, WO2009/014887 and WO2011/031520 the entire contents of which are hereby incorporated herein by reference.
The RNAi agent that contains conjugations of one or more carbohydrate moieties to a RNAi agent can optimize one or more properties of the RNAi agent. In many cases, the carbohydrate moiety will be attached to a modified subunit of the RNAi agent. For example, the ribose sugar of one or more ribonucleotide subunits of a dsRNA agent can be replaced with another moiety, e.g., a non-carbohydrate (preferably cyclic) carrier to which is attached a carbohydrate ligand. A ribonucleotide subunit in which the ribose sugar of the subunit has been so replaced is referred to herein as a ribose replacement modification subunit (RRMS). A cyclic carrier may be a carbocyclic ring system, i.e., all ring atoms are carbon atoms, or a heterocyclic ring system, i.e., one or more ring atoms may be a heteroatom, e.g., nitrogen, oxygen, sulfur. The cyclic carrier may be a monocyclic ring system, or may contain two or more rings, e.g. fused rings. The cyclic carrier may be a fully saturated ring system, or it may contain one or more double bonds.
The ligand may be attached to the polynucleotide via a carrier. The carriers include (i) at least one "backbone attachment point," preferably two "backbone attachment points" and (ii) at least one "tethering attachment point." A "backbone attachment point" as used herein refers to a functional group, e.g. a hydroxyl group, or generally, a bond available for, and that is suitable for incorporation of the carrier into the backbone, e.g. , the phosphate, or modified phosphate, e.g., sulfur containing, backbone, of a ribonucleic acid. A "tethering attachment point" (TAP) in some embodiments refers to a constituent ring atom of the cyclic carrier, e.g., a carbon atom or a heteroatom (distinct from an atom which provides a backbone attachment point), that connects a selected moiety. The moiety can be, e.g. , a carbohydrate, e.g.
monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide and polysaccharide. Optionally, the selected moiety is connected by an intervening tether to the cyclic carrier. Thus, the cyclic carrier will often include a functional group, e.g., an amino group, or generally, provide a bond, that is suitable for incorporation or tethering of another chemical entity, e.g. , a ligand to the constituent ring.
The RNAi agents may be conjugated to a ligand via a carrier, wherein the carrier can be cyclic group or acyclic group; preferably, the cyclic group is selected from pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [l,3]dioxolane, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl and and decalin;
preferably, the acyclic group is selected from serinol backbone or diethanolamine backbone.
In certain specific embodiments, the RNAi agent of the invention is an agent selected from the group of agents listed in Table 1 and consisting of D 1000, D1001, D1002, D1003, D1004, D1005, D1006, D1007, D1008, D1009, D1010, D1011, D1012, D1013, D1014, D1015, D1016, D1017, D1018, D1019, D1020, D1021, D1022, D1023, D1024, D1025, D1026, D1027, D1028, D1029, D1030, D1031, D1032, D1033, D1034, D1035, D1036, D1037, D1038, D1039, D1040, D1041, D1042, D1043, D1044, D1045, D1046, D1047, D1048, D1049, D1050, D1051, D1052, D1053, D1054, D1055, D1056, D1057, D1058, D1059, D1060, D1061, D1062, D1063, D1064, D1065, D1066, D1067, D1068, D1069, D1070, D1071, D1072, D1073, D1074, D1075, D1076, D1077, D1078, D1079, D1080, D1081, D1082, D1083, D1084, D1085, D1086, D1087, D1088, D1089, D1090, D1091, D1092, D1093, D1094, D1095, D1096, D1097, D1098, D1099, D1100, D1101, D1102, D1103, D1104, D1105, D1106, D1107, D1108, D1109, D1110, Dl l l l, D1112, D1113, D1114, D1115, D1116, D1117, D1118, D1119, D1120, D1121, D1122, D1123, D1124, D1125, D1126, D1127, D1128, D1129, D1130, D1131, D1132, D1133, D1134, D1135, D1136, D1137, D1138, D1139, D1140, D1141, D1142, D1143, D1144, D1145, D1146, D1147, D1148, D1149, D1150, D1151, D1152, D1153, D1154, D1155, D1156, D1157, D1158, D1159, D1160, D1161, D1162, D1163, D1164, D1165, D1166,
D1167, D1168, D1169, D1170, D1171, D1172, D1173, D1174, D1175, D1176, D1177,
D1178, D1179, D1180, D1181, D1182, D1183, D1184, D1185, D1186, D1187, D1188,
D1189, D1190, D1191, D1192, D1193, D1194, D1195, D1196, D1197, D1198, D1199,
D1200, D1201, D1202, D1203, D1204, D1205, D1206, D1207, D1208, D1209, D1210,
D1211, D1212, D1213, D1214, D1215, D1216, D1217, D1218, D1219, D1220, D1221,
D1222, D1223, D1224, D1225, D1226, D1227, D1228, D1229, D1230, D1231, D1232,
D1233, D1234, D1235, D1236, D1237, D1238, D1239, D1240, D1241, D1242, D1243,
D1244, D1245, D1246, D1247, D1248, D1249, D1250, D1251, D1252, D1253, D1254,
D1255, D1256, D1257, D1258, D1259, D1260, D1261, D1262, D1263, D1264, D1265,
D1266, D1267, D1268, D1269, D1270, D1271, D1272, D1273, D1274, D1275, D1276,
D1277, D1278, D1279, D1280, D1281, D1282, D1283, D1284, D1285, D1286, D1287,
D1288, D1289, D1290, D1291, D1292, D1293, D1294, D1295, D1296, D1297, D1298,
D1299, D1300, D1301, D1302, D1303, D1304, D1305, D1306, D1307, D1308, D1309,
D1310, D1311, D1312, D1313, D1314, D1315, D1316, D1317, D1318, D1319, D1320,
D1321, D1322, D1323, D1324, D1325, D1326, D1327, D1328, D1329, D1330, D1331,
D1332, D1333, D1334, D1335, D1336, D1337, D1338, D1339, D1340, D1341, D1342,
D1343, D1344, D1345, D1346, D1347, D1348, D1349, D1350, D1351, D1352, D1353,
D1354, D1355, D1356, D1357, D1358, D1359, D1360, D1361, D1362, D1363, D1364,
D1365, D1366, D1367, D1368, D1369, D1370, D1371, D1372, D1373, D1374, D1375,
D1376, D1377, D1378, D1379, D1380, D1381, D1382, D1383, D1384, D1385, D1386,
D1387, D1388, D1389, D1390, D1391, D1392, D1393, D1394, D1395, D1396, D1397,
D1398, D1399, D1400, D1401, D1402, D1403, D1404, D1405, D1406, D1407, D1408,
D1409, D1410, D1411, D1412, D1413, D1414, D1415, D1416, D1417, D1418, D1419,
D1420, D1421, D1422, D1423, D1424, D1425, D1426, D1427, D1428, D1429, D1430,
D1431, D1432, D1433, D1434, D1435, D1436, D1437, D1438, D1439, D1440, D1441,
D1442, D1443, D1444, D1445, D1446, D1447, D1448, D1449, D1450, D1451, D1452,
D1453, D1454, D1455, D1456, D1457, D1458, D1459, D1460, D1461, D1462, D1463,
D1464, D1465, D1466, D1467, D1468, D1469, D1470, D1471, D1472, D1473, D1474,
D1475, D1476, D1477, D1478, D1479, D1480, D1481, D1482, D1483, D1484, D1485,
D1486, D1487, D1488, D1489, D1490, D1491, D1492, D1493, D1494, D1495, D1496,
D1497, D1498, D1499, . D1500, D1501, D1502, D1503, D1504, D1505, D1506,
D1507, D1508, D1509, D1510, D1511, D1512, D1513, D1514, D1515, D1516, D1517,
D1518, D1519, D1520, D1521, D1522, D1523, D1524, D1525, D1526, D1527, D1528,
D1529, D1530, D1531, D1532, D1533, D1534, D1535, D1536, D1537, D1538, D1539,
D1540, D1541, D1542, D1543, D1544, D1545, D1546, D1547, D1548, D1549, D1550, D1551, D1552, D1553, D1554, D1555, D1556, D1557, D1558, D1559, D1560, D1561,
D1562, D1563, D1564, D1565, D1566, D1567, D1568, D1569, D1570, D1571, D1572,
D1573, D1574, D1575, D1576, D1577, D1578, D1579, D1580, D1581, D1582, D1583,
D1584, D1585, D1586, D1587, D1588, D1589, D1590, D1591, D1592, D1593, D1594,
D1595, D1596, D1597, D1598, D1599, D1600, D1601, D1602, D1603, D1604, D1605,
D1606, D1607, D1608, D1609, D1610, D1611, D1612, D1613, D1614, D1615, D1616,
D1617, D1618, D1619, D1620, D1621, D1622, D1623, D1624, D1625, D1626, D1627,
D1628, D1629, D1630, D1631, D1632, D1633, D1634, D1635, D1636, D1637, D1638,
D1639, D1640, D1641, D1642, D1643, D1644, D1645, D1646, D1647, D1648, D1649,
D1650, D1651, D1652, D1653, D1654, D1655, D1656, D1657, D1658, D1659, D1660,
D1661, D1662, D1663, D1664, D1665, D1666, D1667, D1668, D1669, D1670, D1671,
D1672, D1673, D1674, D1675, D1676, D1677, D1678, D1679, D1680, D1681, D1682,
D1683, D1684, D1685, D1686, D1687, D1688, D1689, D1690, D1691, D1692, D1693,
D1694, D1695, D1696, D1697, D1698, D1699, D1700, D1701, D1702, D1703, D1704,
D1705, D1706, D1707, D1708, D1709, D1710, D1711, D1712, D1713, D1714, D1715,
D1716, D1717, D1718, D1719, D1720, D1721, D1722, D1723, D1724, D1725, D1726,
D1727, D1728, D1729, D1730, D1731, D1732, D1733, D1734, D1735, D1736, D1737,
D1738, D1739, D1740, D1741, D1742, D1743, D1744, D1745, D1746, D1747, D1748,
D1749, D1750, D1751, D1752, D1753, D1754, D1755, D1756, D1757, D1758, D1759,
D1760, D1761, D1762, D1763, D1764, D1765, D1766, D1767, D1768, D1769, D1770,
D1771, D1772, D1773, D1774, D1775, D1776, D1777, D1778, D1779, D1780, D1781,
D1782, D1783, D1784, D1785, D1786, D1787, D1788, D1789, D1790, D1791, D1792,
D1793, D1794, D1795, D1796, D1797, D1798, D1799, D1800, D1801, D1802, D1803,
D1804, D1805, D1806, D1807, D1808, D1809, D1810, D1811, D1812, D1813, D1814,
D1815, D1816, D1817, D1818, D1819, D1820, D1821, D1822, D1823, D1824, D1825,
D1826, D1827, D1828, D1829, D1830, D1831, D1832, D1833, D1834, D1835, D1836,
D1837, D1838, D1839, D1840, D1841, D1842, D1843, D1844, D1845, D1846, D1847,
D1848, D1849, D1850, D1851, D1852, D1853, D1854, D1855, D1856, D1857, D1858,
D1859, D1860, D1861, D1862, D1863, D1864, D1865, D1866, D1867, D1868, D1869,
D1870, D1871, D1872, D1873, D1874, D1875, D1876, D1877, D1878, D1879, D1880,
D1881, D1882, D1883, D1884, D1885, D1886, D1887, D1888, D1889, D1890, D1891,
D1892, D1893, D1894, D1895, D1896, D1897, D1898, D1899, D1900, D1901, D1902,
D1903, D1904, D1905, D1906, D1907, D1908, D1909, D1910, D1911, D1912, D1913,
D1914, D1915, D1916, D1917, D1918, D1919, D1920, D1921, D1922, D1923, D1924,
D1925, D1926, D1927, D1928, D1929, D1930, D1931, D1932, D1933, D1934, D1935,
D1936, D1937, D1938, D1939, D1940, D1941, D1942, D1943, D1944, D1945, D1946, D1947, D1948, D1949, D1950, D1951, D1952, D1953, D1954, D1955, D1956, D1957, D1958, D1959, D1960, D1961, D1962, D1963, D1964, D1965, D1966, D1967, D1968, D1969, D1970, D1971, D1972, D1973, D1974, D1975, D1976, D1977, D1978, D1979, D1980, D1981, D1982, D1983, D1984, D1985, D1986, D1987, D1988, D1989, D1990, D1991, D1992, D1993, D1994, D1995, D1996, D1997, D1998, D1999, D2000, D2001, D2002, D2003, D2004, D2005, D2006, D2007, D2008, D2009, D2010, D2011, D2012, D2013, D2014, D2015, D2016, D2017, D2018, D2019, D2020, D2021, D2022, D2023, D2024, D2025, D2026, D2027, D2028, D2029, D2030, D2031, D2032, D2033, D2034, D2035, D2036, D2037, D2038, D2039, D2040, D2041, D2042, D2043, D2044, D2045, D2046, D2047, D2048, D2049, D2050, D2051, D2052, D2053, D2054, D2055, D2056, D2057, D2058, D2059, D2060, D2061, D2062, D2063, D2064, D2065, D2066, D2067, D2068, D2069, D2070, D2071, D2072, D2073, D2074, D2075, D2076, D2077, D2078, D2079, D2080, D2081, D2082, D2083, D2084, D2085, D2086, D2087, D2088, D2089, D2090 and D2091.
These agents may further comprise a ligand, such as a GalNAc ligand.
Ligands
The RNAi agents of the invention, e.g., double stranded RNAi agents, may optionally be conjugated to one or more ligands. The ligand can be attached to the sense strand, antisense strand or both strands, at the 3 '-end, 5 '-end or both ends. For instance, the ligand may be conjugated to the sense strand. In preferred embodiments, the ligand is conjgated to the 3 '-end of the sense strand. In one preferred embodiment, the ligand is a GalNAc ligand. In particularly preferred embodiments, the ligand is GalNAc3:
Figure imgf000042_0001
A wide variety of entities can be coupled to the RNAi agents of the present invention. Preferred moieties are ligands, which are coupled, preferably covalently, either directly or indirectly via an intervening tether.
In preferred embodiments, a ligand alters the distribution, targeting or lifetime of the molecule into which it is incorporated. In preferred embodiments a ligand provides an enhanced affinity for a selected target, e.g., molecule, cell or cell type, compartment, receptor e.g., a cellular or organ compartment, tissue, organ or region of the body, as, e.g., compared to a species absent such a ligand. Ligands providing enhanced affinity for a selected target are also termed targeting ligands.
Some ligands can have endosomolytic properties. The endosomolytic ligands promote the lysis of the endosome and/or transport of the composition of the invention, or its components, from the endosome to the cytoplasm of the cell. The endosomolytic ligand may be a polyanionic peptide or peptidomimetic which shows pH-dependent membrane activity and fusogenicity. In one embodiment, the endosomolytic ligand assumes its active conformation at endosomal pH. The "active" conformation is that conformation in which the endosomolytic ligand promotes lysis of the endosome and/or transport of the composition of the invention, or its components, from the endosome to the cytoplasm of the cell. Exemplary endosomolytic ligands include the GALA peptide (Subbarao et al., Biochemistry, 1987, 26: 2964-2972), the EALA peptide (Vogel et al., J. Am. Chem. Soc, 1996, 118: 1581-1586), and their derivatives (Turk et al., Biochem. Biophys. Acta, 2002, 1559: 56-68). In one embodiment, the endosomolytic component may contain a chemical group {e.g., an amino acid) which will undergo a change in charge or protonation in response to a change in pH. The endosomolytic component may be linear or branched.
Ligands can improve transport, hybridization, and specificity properties and may also improve nuclease resistance of the resultant natural or modified oligoribonucleotide, or a polymeric molecule comprising any combination of monomers described herein and/or natural or modified ribonucleotides.
Ligands in general can include therapeutic modifiers, e.g., for enhancing uptake; diagnostic compounds or reporter groups e.g., for monitoring distribution; cross-linking agents; and nuclease-resistance conferring moieties. General examples include lipids, steroids, vitamins, sugars, proteins, peptides, polyamines, and peptide mimics.
Ligands can include a naturally occurring substance, such as a protein {e.g., human serum albumin (HSA), low-density lipoprotein (LDL), high-density lipoprotein (HDL), or globulin); a carbohydrate {e.g., a dextran, pullulan, chitin, chitosan, inulin, cyclodextrin or hyaluronic acid); or a lipid. The ligand may also be a recombinant or synthetic molecule, such as a synthetic polymer, e.g., a synthetic polyamino acid, an oligonucleotide {e.g., an aptamer). Examples of polyamino acids include polyamino acid is a polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydride copolymer, poly(L-lactide-co-glycolied) copolymer, divinyl ether-maleic anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyurethane, poly(2-ethylacryllic acid), N-isopropylacrylamide polymers, or polyphosphazine. Example of polyamines include: polyethylenimine, polylysine (PLL), spermine, spermidine, polyamine, pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine, arginine, amidine, protamine, cationic lipid, cationic porphyrin, quaternary salt of a polyamine, or an alpha helical peptide.
Ligands can also include targeting groups, e.g. , a cell or tissue targeting agent, e.g. , a lectin, glycoprotein, lipid or protein, e.g., an antibody, that binds to a specified cell type such as a kidney cell. A targeting group can be a thyrotropin, melanotropin, lectin, glycoprotein, surfactant protein A, Mucin carbohydrate, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose, multivalent fucose, glycosylated polyaminoacids, multivalent galactose, transferrin, bisphosphonate, polyglutamate, polyaspartate, a lipid, cholesterol, a steroid, bile acid, folate, vitamin B 12, biotin, an RGD peptide, an RGD peptide mimetic or an aptamer.
Other examples of ligands include dyes, intercalating agents (e.g., acridines), cross-linkers (e.g., psoralene, mitomycin C), porphyrins (TPPC4, texaphyrin,
Sapphyrin), polycyclic aromatic hydrocarbons (e.g., phenazine, dihydrophenazine), artificial endonucleases or a chelator (e.g., EDTA), lipophilic molecules, e.g. , cholesterol, cholic acid, adamantane acetic acid, 1-pyrene butyric acid,
dihydrotestosterone, l,3-Bis-0(hexadecyl)glycerol, geranyloxyhexyl group,
hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid, myristic acid,03-(oleoyl)lithocholic acid, 03-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine)and peptide conjugates (e.g., antennapedia peptide, Tat peptide), alkylating agents, phosphate, amino, mercapto, PEG (e.g., PEG-40K), MPEG, [MPEG]2, polyamino, alkyl, substituted alkyl, radiolabeled markers, enzymes, haptens (e.g., biotin), transport/absorption facilitators (e.g., aspirin, vitamin E, folic acid), synthetic ribonucleases (e.g., imidazole, bisimidazole, histamine, imidazole clusters, acridine- imidazole conjugates, Eu3+ complexes of tetraazamacrocycles), dinitrophenyl, HRP, or AP.
Ligands can be proteins, e.g., glycoproteins, or peptides, e.g., molecules having a specific affinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified cell type such as a cancer cell, endothelial cell, or bone cell. Ligands may also include hormones and hormone receptors. They can also include non-peptidic species, such as lipids, lectins, carbohydrates, vitamins, cofactors, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose, multivalent fucose, or aptamers. The ligand can be, for example, a lipopolysaccharide, an activator of p38 MAP kinase, or an activator of NF-KB.
The ligand can be a substance, e.g., a drug, which can increase the uptake of the iRNA agent into the cell, for example, by disrupting the cell' s cytoskeleton, e.g. , by disrupting the cell's microtubules, microfilaments, and/or intermediate filaments. The drug can be, for example, taxon, vincristine, vinblastine, cytochalasin, nocodazole, japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or myoservin.
The ligand can increase the uptake of the oligonucleotide into the cell by, for example, activating an inflammatory response. Exemplary ligands that would have such an effect include tumor necrosis factor alpha (TNFalpha), interleukin-1 beta, or gamma interferon.
In one aspect, the ligand is a lipid or lipid-based molecule. Such a lipid or lipid- based molecule preferably binds a serum protein, e.g. , human serum albumin (HSA). An HSA binding ligand allows for distribution of the conjugate to a target tissue, e.g. , a non-kidney target tissue of the body. For example, the target tissue can be the liver, including parenchymal cells of the liver. Other molecules that can bind HSA can also be used as ligands. For example, naproxen or aspirin can be used. A lipid or lipid-based ligand can (a) increase resistance to degradation of the conjugate, (b) increase targeting or transport into a target cell or cell membrane, and/or (c) can be used to adjust binding to a serum protein, e.g. , HSA.
A lipid based ligand can be used to modulate, e.g., control the binding of the conjugate to a target tissue. For example, a lipid or lipid-based ligand that binds to HSA more strongly will be less likely to be targeted to the kidney and therefore less likely to be cleared from the body.A lipid or lipid-based ligand that binds to HSA less strongly can be used to target the conjugate to the kidney.
In a preferred embodiment, the lipid based ligand binds HSA. Preferably, it binds HSA with a sufficient affinity such that the conjugate will be preferably distributed to a non-kidney tissue. However, it is preferred that the affinity not be so strong that the HSA-ligand binding cannot be reversed.
In another preferred embodiment, the lipid based ligand binds HSA weakly or not at all, such that the conjugate will be preferably distributed to the kidney. Other moieties that target to kidney cells can also be used in place of or in addition to the lipid based ligand.
In another aspect, the ligand is a moiety, e.g. , a vitamin, which is taken up by a target cell, e.g. , a proliferating cell. These are particularly useful for treating disorders characterized by unwanted cell proliferation, e.g., of the malignant or non-malignant type, e.g., cancer cells. Exemplary vitamins include vitamin A, E, and K. Other exemplary vitamins include B vitamins, e.g., folic acid, B 12, riboflavin, biotin, pyridoxal or other vitamins or nutrients taken up by cancer cells. Also included are HAS, low density lipoprotein (LDL) and high-density lipoprotein (HDL).
In another aspect, the ligand is a cell-permeation agent, preferably a helical cell- permeation agent. Preferably, the agent is amphipathic. An exemplary agent is a peptide such as tat or antennopedia. If the agent is a peptide, it can be modified, including a peptidylmimetic, invertomers, non-peptide or pseudo-peptide linkages, and use of D-amino acids. The helical agent is preferably an alpha-helical agent, which preferably has a lipophilic and a lipophobic phase.
The ligand can be a peptide or peptidomimetic. A peptidomimetic (also referred to herein as an oligopeptidomimetic) is a molecule capable of folding into a defined three-dimensional structure similar to a natural peptide. The peptide or peptidomimetic moiety can be about 5-50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long. A peptide or peptidomimetic can be, for example, a cell permeation peptide, cationic peptide, amphipathic peptide, or hydrophobic peptide (e.g. , consisting primarily of Tyr, Trp or Phe). The peptide moiety can be a dendrimer peptide, constrained peptide or crosslinked peptide. In another alternative, the peptide moiety can include a hydrophobic membrane translocation sequence (MTS). An exemplary hydrophobic MTS -containing peptide is RFGF having the amino acid sequence AAVALLPAVLLALLAP (SEQ ID NO:4). An RFGF analogue (e.g. , amino acid sequence AALLPVLLAAP) (SEQ ID NO:5) containing a hydrophobic MTS can also be a targeting moiety. The peptide moiety can be a "delivery" peptide, which can carry large polar molecules including peptides, oligonucleotides, and protein across cell membranes. For example, sequences from the HIV Tat protein (GRKKRRQRRRPPQ) (SEQ ID NO:6) and the Drosophila Antennapedia protein (RQIKTWFQNRRMKWKK) (SEQ ID NO:7) have been found to be capable of functioning as delivery peptides. A peptide or peptidomimetic can be encoded by a random sequence of DNA, such as a peptide identified from a phage-display library, or one-bead-one-compound (OBOC) combinatorial library (Lam et ah , Nature, 354:82-84, 1991). Preferably the peptide or peptidomimetic tethered to an iRNA agent via an incorporated monomer unit is a cell targeting peptide such as an arginine-glycine-aspartic acid (RGD)-peptide, or RGD mimic. A peptide moiety can range in length from about 5 amino acids to about 40 amino acids. The peptide moieties can have a structural modification, such as to increase stability or direct conformational properties. Any of the structural
modifications described below can be utilized.An RGD peptide moiety can be used to target a tumor cell, such as an endothelial tumor cell or a breast cancer tumor cell (Zitzmann et al., Cancer Res., 62:5139-43, 2002). An RGD peptide can facilitate targeting of an iRNA agent to tumors of a variety of other tissues, including the lung, kidney, spleen, or liver (Aoki et al., Cancer Gene Therapy 8:783-787, 2001).
Preferably, the RGD peptide will facilitate targeting of an iRNA agent to the kidney. The RGD peptide can be linear or cyclic, and can be modified, e.g., glycosylated or methylated to facilitate targeting to specific tissues. For example, a glycosylated RGD peptide can deliver an iRNA agent to a tumor cell expressing αγβ3 (Haubner et al. , Jour. Nucl. Med., 42:326-336, 2001). Peptides that target markers enriched in proliferating cells can be used. For example, RGD containing peptides and peptidomimetics can target cancer cells, in particular cells that exhibit an integrin. Thus, one could use RGD peptides, cyclic peptides containing RGD, RGD peptides that include D-amino acids, as well as synthetic RGD mimics. In addition to RGD, one can use other moieties that target the integrin ligand. Generally, such ligands can be used to control proliferating cells and angiogeneis. Preferred conjugates of this type of ligand target PECAM-1, VEGF, or other cancer gene, e.g., a cancer gene described herein.
A "cell permeation peptide" is capable of permeating a cell, e.g., a microbial cell, such as a bacterial or fungal cell, or a mammalian cell, such as a human cell. A microbial cell-permeating peptide can be, for example, an a-helical linear peptide (e.g., LL-37 or Ceropin PI), a disulfide bond-containing peptide (e.g., a -defensin, β-defensin or bactenecin), or a peptide containing only one or two dominating amino acids (e.g., PR-39 or indolicidin). A cell permeation peptide can also include a nuclear localization signal (NLS). For example, a cell permeation peptide can be a bipartite amphipathic peptide, such as MPG, which is derived from the fusion peptide domain of HIV-1 gp41 and the NLS of SV40 large T antigen (Simeoni et al., Nucl. Acids Res. 31 :2717-2724, 2003).
In one embodiment, a targeting peptide can be an amphipathic a-helical peptide. Exemplary amphipathic α-helical peptides include, but are not limited to, cecropins, lycotoxins, paradaxins, buforin, CPF, bombinin-like peptide (BLP), cathelicidins, ceratotoxins, S. clava peptides, hagfish intestinal antimicrobial peptides (HFIAPs), magainines, brevinins-2, dermaseptins, melittins, pleurocidin, H2A peptides, Xenopus peptides, esculentinis-1, and caerins. A number of factors will preferably be considered to maintain the integrity of helix stability. For example, a maximum number of helix stabilization residues will be utilized (e.g., leu, ala, or lys), and a minimum number helix destabilization residues will be utilized (e.g., proline, or cyclic monomeric units. The capping residue will be considered (for example Gly is an exemplary N-capping residue and/or C-terminal amidation can be used to provide an extra H-bond to stabilize the helix. Formation of salt bridges between residues with opposite charges, separated by i + 3, or i + 4 positions can provide stability. For example, cationic residues such as lysine, arginine, homo-arginine, ornithine or histidine can form salt bridges with the anionic residues glutamate or aspartate.
Peptide and peptidomimetic ligands include those having naturally occurring or modified peptides, e.g., D or L peptides; α, β, or γ peptides; N-methyl peptides;
azapeptides; peptides having one or more amide, i.e., peptide, linkages replaced with one or more urea, thiourea, carbamate, or sulfonyl urea linkages; or cyclic peptides.
The targeting ligand can be any ligand that is capable of targeting a specific receptor. Examples are: folate, GalNAc, galactose, mannose, mannose-6P, clusters of sugars such as GalNAc cluster, mannose cluster, galactose cluster, or an apatamer. A cluster is a combination of two or more sugar units. The targeting ligands also include integrin receptor ligands, Chemokine receptor ligands, transferrin, biotin, serotonin receptor ligands, PSMA, endothelin, GCPII, somatostatin, LDL and HDL ligands. The ligands can also be based on nucleic acid, e.g., an aptamer. The aptamer can be unmodified or have any combination of modifications disclosed herein.
Endosomal release agents include imidazoles, poly or oligoimidazoles, PEIs, peptides, fusogenic peptides, polycaboxylates, polyacations, masked oligo or poly cations or anions, acetals, polyacetals, ketals/polyketyals, orthoesters, polymers with masked or unmasked cationic or anionic charges, dendrimers with masked or unmasked cationic or anionic charges.
PK modulator stands for pharmacokinetic modulator. PK modulators include lipophiles, bile acids, steroids, phospholipid analogues, peptides, protein binding agents, PEG, vitamins etc. Examplary PK modulators include, but are not limited to, cholesterol, fatty acids, cholic acid, lithocholic acid, dialkylglycerides, diacylglyceride,
phospholipids, sphingolipids, naproxen, ibuprofen, vitamin E, biotin etc.
Oligonucleotides that comprise a number of phosphorothioate linkages are also known to bind to serum protein, thus short oligonucleotides, e.g. , oligonucleotides of about 5 bases, 10 bases, 15 bases or 20 bases, comprising multiple phosphorothioate linkages in the backbaone are also amenable to the present invention as ligands (e.g. , as PK modulating ligands).
In addition, aptamers that bind serum components (e.g. , serum proteins) are also amenable to the present invention as PK modulating ligands.
Other ligand conjugates amenable to the invention are described in U.S. Patent
Applications USSN: 10/916,185, filed August 10, 2004; USSN: 10/946,873, filed September 21, 2004; USSN: 10/833,934, filed August 3, 2007; USSN: 11/115,989 filed April 27, 2005 and USSN: 11/944,227 filed November 21, 2007, which are incorporated by reference in their entireties for all purposes.
When two or more ligands are present, the ligands can all have same properties, all have different properties or some ligands have the same properties while others have different properties. For example, a ligand can have targeting properties, have endosomolytic activity or have PK modulating properties. In a preferred embodiment, all the ligands have different properties.
Ligands can be coupled to the oligonucleotides at various places, for example, 3 '-end, 5 '-end, and/or at an internal position. In preferred embodiments, the ligand is attached to the oligonucleotides via an intervening tether, e.g., a carrier described herein. The ligand or tethered ligand may be present on a monomer when the monomer is incorporated into the growing strand. In some embodiments, the ligand may be incorporated via coupling to a "precursor" monomer after the "precursor" monomer has been incorporated into the growing strand. For example, a monomer having, e.g., an amino-terminated tether (i.e., having no associated ligand), e.g., TAP-(CH2)nNH2 may be incorporated into a growing oligonucelotide strand. In a subsequent operation, i.e., after incorporation of the precursor monomer into the strand, a ligand having an electrophilic group, e.g., a pentafluorophenyl ester or aldehyde group, can subsequently be attached to the precursor monomer by coupling the electrophilic group of the ligand with the terminal nucleophilic group of the precursor monomer' s tether.
In another example, a monomer having a chemical group suitable for taking part in Click Chemistry reaction may be incorporated, e.g., an azide or alkyne terminated tether/linker.In a subsequent operation, i.e., after incorporation of the precursor monomer into the strand, a ligand having complementary chemical group, e.g. an alkyne or azide can be attached to the precursor monomer by coupling the alkyne and the azide together.
For double- stranded oligonucleotides, ligands can be attached to one or both strands. In some embodiments, a double- stranded iRNA agent contains a ligand conjugated to the sense strand. In other embodiments, a double- stranded iRNA agent contains a ligand conjugated to the antisense strand.
In some embodiments, ligand can be conjugated to nucleobases, sugar moieties, or internucleosidic linkages of nucleic acid molecules. Conjugation to purine
nucleobases or derivatives thereof can occur at any position including, endocyclic and exocyclic atoms. In some embodiments, the 2-, 6-, 7-, or 8-positions of a purine nucleobase are attached to a conjugate moiety. Conjugation to pyrimidine nucleobases or derivatives thereof can also occur at any position. In some embodiments, the 2-, 5-, and 6-positions of a pyrimidine nucleobase can be substituted with a conjugate moiety. Conjugation to sugar moieties of nucleosides can occur at any carbon atom. Example carbon atoms of a sugar moiety that can be attached to a conjugate moiety include the 2', 3', and 5' carbon atoms. The position can also be attached to a conjugate moiety, such as in an abasic residue. Internucleosidic linkages can also bear conjugate moieties. For phosphorus-containing linkages (e.g. , phosphodiester, phosphorothioate,
phosphorodithiotate, phosphoroamidate, and the like), the conjugate moiety can be attached directly to the phosphorus atom or to an O, N, or S atom bound to the phosphorus atom. For amine- or amide-containing internucleosidic linkages (e.g., PNA), the conjugate moiety can be attached to the nitrogen atom of the amine or amide or to an adjacent carbon atom.
Any suitable ligand in the field of RNA interference may be used, although the ligand is typically a carbohydrate e.g. monosaccharide (such as GalNAc), disaccharide, trisaccharide, tetrasaccharide, polysaccharide.
Linkers that conjugate the ligand to the nucleic acid include those discussed above. For example, the ligand can be one or more GalNAc (N-acetylglucosamine) derivatives attached through a bivalent or trivalent branched linker.
In one embodiment, the dsRNA of the invention is conjugated to a bivalent and trivalent branched linkers include the structures shown in any of formula (IV) - (VII):
Figure imgf000051_0001
Formula IV) Formula (V)
Figure imgf000051_0002
Formula (VII) wherein:
q 2A ,q 2B ,q 3A ,q 3B ,q4 ,,Α,q 4B ,q 5A ,q 5B and i q 5C represent . i ·nd iepend iently f r-or eac ih_ occurrence 0-20 and wherein the repeating unit can be the same or different;
p2A p2B p3A p3B p4A p4B p5A p5B p5C r 2A r 2B r 3A r 3B r 4A r 4B r 4A r 5B r 5C each independently for each occurrence absent, CO, NH, O, S, OC(O), NHC(O), CH2, CH2NHorCH20;
Q2A, Q2B, Q3A, Q3B, Q4A, Q4B, Q5A, Q5B, Q5C are independently for each occurrence absent, alkylene, substituted alkylene wherin one or more methylenes can be interrupted or terminated by one or more of O, S, S(O), S02, N(RN), C(R')=C(R"), C≡C or C(O);
R2A, R2B, R3A, R3B, R4A, R4B, R5A, R5B, R5C are each independently for each
-C(0)-CH(Ra)-
Figure imgf000051_0003
,«ivf ^ T or heterocyclyl; L2A, L2B, L3A, L3B, L4A, L4B, L5A, L5B and L5C represent the ligand; i.e. each independently for each occurrence a monosaccharide (such as GalNAc), disaccharide, trisaccharide, tetrasaccharide, oligosaccharide, or polysaccharide; and
Ra is H or amino acid side chain.
Trivalent conjugating GalNAc derivatives are particularly useful for use with RNAi agents for inhibiting the expression of a target gene, such as those of formula (VII):
Figure imgf000052_0001
Formula (VII) wherein L , L and L represent a monosaccharide, such as GalNAc derivative.
Examples of suitable bivalent and trivalent branched linker groups conjugating derivatives include, but are not limited to, the following compounds:
Figure imgf000052_0002
Figure imgf000053_0001
51
Figure imgf000054_0001
In other embodiments, the RNAi agent of the invention is an agent selected from the group consisting of AD-45163, AD-45165, AD-51544, AD-51545, AD-51546, and AD-51547.
III. Pharmaceutical Compositions
The RNAi agents of the invention may be formulated for administration in any convenient way for use in human or veterinary medicine, by analogy with other pharmaceuticals. The pharmaceutical compositions comprising RNAi agents of the invention may be, for example, solutions with or without a buffer, or compositions containing pharmaceutically acceptable carriers. Such compositions include, for example, aqueous or crystalline compositions, liposomal formulations, micellar formulations, emulsions, and gene therapy vectors. In the methods of the invention, the RNAi agent may be administered in a solution. A free RNAi agent may be administered in an unbuffered solution, e.g. , in saline or in water.
In one embodiment, the RNAi agent is formulated in sterile water for injection at a concentration suitable for administration to a subject. For example, is some embodiments, an RNAi agent of the invention is formulated in sterile water for injection at a concentration of about 50-500 mg/ml, e.g., about 50 mg/ml, about 100 mg/ml, about 150 mg/ml, about 200 mg/ml, about 250 mg/ml, about 300 mg/ml, about 350 mg/ml, about 400 mg/ml, about 450 mg/ml, or about 500 mg/ml.
The free siRNA may also be administred in a suitable buffer solution. The buffer solution may comprise acetate, citrate, prolamine, carbonate, or phosphate, or any combination thereof. In a preferred embodiment, the buffer solution is phosphate buffered saline (PBS). The pH and osmolarity of the buffer solution containing the RNAi agent can be adjusted such that it is suitable for administering to a subject.
In some embodiments, the buffer solution further comprises an agent for controlling the osmolarity of the solution, such that the osmolarity is kept at a desired value, e.g. , at the physiologic values of the human plasma. Solutes which can be added to the buffer solution to control the osmolarity include, but are not limited to, proteins, peptides, amino acids, non-metabolized polymers, vitamins, ions, sugars, metabolites, organic acids, lipids, or salts. In some embodiments, the agent for controlling the osmolarity of the solution is a salt. In certain embodiments, the agent for controlling the osmolarity of the solution is sodium chloride or potassium chloride.
In other embodiments, the RNAi agent is formulated as a composition that includes one or more RNAi agents and a pharmaceutically acceptable carrier. As used herein the language "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
In one embodiment, the RNAi agent preparation includes at least a second therapeutic agent (e.g., an agent other than an RNA or a DNA). For example, an RNAi agent composition for the treatment of a TTR-associated disease, e.g., a transthyretin- related hereditary amyloidosis (familial amyloid polyneuropathy, FAP), may include a known drug for the amelioration of FAP, e.g., Tafamidis (INN, or Fx-1006A or Vyndaqel).
A formulated RNAi agent composition can assume a variety of states. In some examples, the composition is at least partially crystalline, uniformly crystalline, and/or anhydrous (e.g., it contains less than 80, 50, 30, 20, or 10% of water). In another example, the RNAi agent is in an aqueous phase, e.g., in a solution that includes water.
The aqueous phase or the crystalline compositions can be incorporated into a delivery vehicle, e.g., a liposome (particularly for the aqueous phase) or a particle (e.g., a microparticle as can be appropriate for a crystalline composition). Generally, the RNAi agent composition is formulated in a manner that is compatible with the intended method of administration, as described herein. For example, in particular embodiments the composition is prepared by at least one of the following methods: spray drying, lyophilization, vacuum drying, evaporation, fluid bed drying, or a combination of these techniques; or sonication with a lipid, freeze-drying, condensation and other self- assembly.
An RNAi agent preparation can be formulated in combination with another agent, e.g., another therapeutic agent or an agent that stabilizes RNAi agent, e.g., a protein that complexes with the RNAi agent to form an iRNP. Still other agents include chelators, e.g., EDTA (e.g., to remove divalent cations such as Mg2+), salts, RNAse inhibitors (e.g., a broad specificity RNAse inhibitor such as RNAsin) and so forth.
In one embodiment, the RNAi agent preparation includes another siRNA compound, e.g., a second RNAi agent that can mediate RNAi with respect to a second gene, or with respect to the same gene. Still other preparation can include at least 3, 5, ten, twenty, fifty, or a hundred or more different RNAi agent species. Such RNAi agents can mediate RNAi with respect to a similar number of different genes.
The iRNA agents of the invention may be formulated for pharmaceutical use. Pharmaceutically acceptable compositions comprise a therapeutically- or
prophylactically effective amount of one or more of the the dsRNA agents in any of the preceding embodiments, taken alone or formulated together with one or more pharmaceutically acceptable carriers (additives), excipient and/or diluents.
Methods of preparing pharmaceutical compositions of the invention include the step of bringing into association an RNAi agent of the present invention with the carrier and, optionally, one or more accessory ingredients. In general, the compositionsare prepared by uniformly and intimately bringing into association an RNAi agent of the present invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product. The pharmaceutical compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral
administration, for example, drenches (aqueous or non-aqueous solutions or
suspensions), tablets, e.g. , those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; (3) topical application, for example, as a cream, ointment, or a controlled- release patch or spray applied to the skin; (4) intravaginally or intrarectally, for example, as a pessary, cream or foam; (5) sublingually; (6) ocularly; (7) transdermally; or (8) nasally. Delivery using subcutaneous or intravenous methods can be particularly advantageous.
The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
The phrase "pharmaceutically- acceptable carrier" as used herein means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be "acceptable" in the sense of being compatible with the other ingredients of the compositionand not injurious to the patient. Some examples of materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium state, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer' s solution; (19) ethyl alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents, such as polypeptides and amino acids (23) serum component, such as serum albumin, HDL and LDL; and (22) other non-toxic compatible substances employed in pharmaceuticalcompositions.
The compositions may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. The amount of RNAi agent which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, and the particular mode of
administration. The RNAi agent which can be combined with a carrier material to produce a single dosage form will generally be that amount of the RNAi agent which produces a desired effect, e.g., therapeutic or prophylactic effect. Generally, out of one hundred per cent, this amount will range from about 0.1 per cent to about ninety-nine percent of RNAi agent, preferably from about 5 per cent to about 70 per cent, most preferably from about 10 per cent to about 30 per cent.
In certain embodiments, a composition of the present invention comprises an excipient selected from the group consisting of cyclodextrins, celluloses, liposomes, micelle forming agents, e.g., bile acids, and polymeric carriers, e.g., polyesters and polyanhydrides; and an RNAi agent of the present invention. In certain embodiments, an aforementioned composition renders orally bioavailable an RNAi agent of the present invention.
In some cases, in order to prolong the effect of an RNAi agent, it is desirable to slow the absorption of the agent from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material having poor water solubility. The rate of absorption of the RNAi agent then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally-administered RNAi agent may be accomplished by dissolving or suspending the agent in an oil vehicle.
Liposomes
An RNAi agent of the invention can be formulated for delivery in a membranous molecular assembly, e.g., a liposome or a micelle. As used herein, the term "liposome" refers to a vesicle composed of amphiphilic lipids arranged in at least one bilayer, e.g., one bilayer or a plurality of bilayers. Liposomes include unilamellar and multilamellar vesicles that have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the RNAi agent composition. The lipophilic material isolates the aqueous interior from an aqueous exterior, which typically does not include the RNAi agent composition, although in some examples, it may. Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomal bilayer fuses with bilayer of the cellular membranes. As the merging of the liposome and cell progresses, the internal aqueous contents that include the RNAi agent are delivered into the cell where the RNAi agent can specifically bind to a target RNA and can mediate RNAi. In some cases the liposomes are also specifically targeted, e.g., to direct the RNAi agent to particular cell types.
A liposome containing an RNAi agent can be prepared by a variety of methods. In one example, the lipid component of a liposome is dissolved in a detergent so that micelles are formed with the lipid component. For example, the lipid component can be an amphipathic cationic lipid or lipid conjugate. The detergent can have a high critical micelle concentration and may be nonionic. Exemplary detergents include cholate, CHAPS, octylglucoside, deoxycholate, and lauroyl sarcosine. The RNAi agent preparation is then added to the micelles that include the lipid component. The cationic groups on the lipid interact with the RNAi agent and condense around the RNAi agent to form a liposome. After condensation, the detergent is removed, e.g., by dialysis, to yield a liposomal preparation of RNAi agent.
If necessary a carrier compound that assists in condensation can be added during the condensation reaction, e.g., by controlled addition. For example, the carrier compound can be a polymer other than a nucleic acid (e.g., spermine or spermidine). pH can also be adjusted to favor condensation.
Methods for producing stable polynucleotide delivery vehicles, which incorporate a polynucleotide/cationic lipid complex as structural components of the delivery vehicle, are further described in, e.g., WO 96/37194, the entire contents of which are incorporated herein by reference. Liposome formation can also include one or more aspects of exemplary methods described in Feigner, P. L. et al., Proc. Natl. Acad. Set, USA 8:7413-7417, 1987; U.S. Pat. No. 4,897,355; U.S. Pat. No. 5,171,678;
Bangham, et al. M. Mol. Biol. 23:238, 1965; Olson, et al. Biochim. Biophys. Acta 557:9, 1979; Szoka, et al. Proc. Natl. Acad. Sci. 75: 4194, 1978; Mayhew, et al. Biochim.
Biophys. Acta 775: 169, 1984; Kim, et al. Biochim. Biophys. Acta 728:339, 1983; and Fukunaga, et al. Endocrinol. 115:757, 1984. Commonly used techniques for preparing lipid aggregates of appropriate size for use as delivery vehicles include sonication and freeze-thaw plus extrusion (see, e.g., Mayer, et al. Biochim. Biophys. Acta 858: 161, 1986). Microfluidization can be used when consistently small (50 to 200 nm) and relatively uniform aggregates are desired (Mayhew, et al. Biochim. Biophys. Acta 775: 169, 1984). These methods are readily adapted to packaging RNAi agent preparations into liposomes.
Liposomes that are pH-sensitive or negatively-charged entrap nucleic acid molecules rather than complex with them. Since both the nucleic acid molecules and the lipid are similarly charged, repulsion rather than complex formation occurs.
Nevertheless, some nucleic acid molecules are entrapped within the aqueous interior of these liposomes. pH-sensitive liposomes have been used to deliver DNA encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 19, (1992) 269-274).
One major type of liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine. Neutral liposome compositions, for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl
phosphatidylcholine (DPPC). Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC. Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.
Examples of other methods to introduce liposomes into cells in vitro and in vivo include U.S. Pat. No. 5,283,185; U.S. Pat. No. 5,171,678; WO 94/00569; WO 93/24640; WO 91/16024; Feigner, J. Biol. Chem. 269:2550, 1994; Nabel, Proc. Natl. Acad. Sci. 90: 11307, 1993; Nabel, Human Gene Ther. 3:649, 1992; Gershon, Biochem. 32:7143, 1993; and Strauss EMBO J. 11:417, 1992.
In one embodiment, cationic liposomes are used. Cationic liposomes possess the advantage of being able to fuse to the cell membrane. Non-cationic liposomes, although not able to fuse as efficiently with the plasma membrane, are taken up by macrophages in vivo and can be used to deliver RNAi agents to macrophages.
Further advantages of liposomes include: liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect encapsulated RNAi agents in their internal compartments from metabolism and degradation (Rosoff, in
"Pharmaceutical Dosage Forms," Lieberman, Rieger and Banker (Eds.), 1988, volume 1, p. 245). Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes. A positively charged synthetic cationic lipid, N-[l-(2,3-dioleyloxy)propyl]- Ν,Ν,Ν-trimethylammonium chloride (DOTMA) can be used to form small liposomes that interact spontaneously with nucleic acid to form lipid-nucleic acid complexes which are capable of fusing with the negatively charged lipids of the cell membranes of tissue culture cells, resulting in delivery of RNAi agent (see, e.g., Feigner, P. L. et al., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987 and U.S. Pat. No. 4,897,355 for a description of DOTMA and its use with DNA).
A DOTMA analogue, l,2-bis(oleoyloxy)-3-(trimethylammonia)propane (DOTAP) can be used in combination with a phospholipid to form DNA-complexing vesicles. Lipofectin™ Bethesda Research Laboratories, Gaithersburg, Md.) is an effective agent for the delivery of highly anionic nucleic acids into living tissue culture cells that comprise positively charged DOTMA liposomes which interact spontaneously with negatively charged polynucleotides to form complexes. When enough positively charged liposomes are used, the net charge on the resulting complexes is also positive. Positively charged complexes prepared in this way spontaneously attach to negatively charged cell surfaces, fuse with the plasma membrane, and efficiently deliver functional nucleic acids into, for example, tissue culture cells. Another commercially available cationic lipid, l,2-bis(oleoyloxy)-3,3-(trimethylammonia)propane ("DOTAP")
(Boehringer Mannheim, Indianapolis, Indiana) differs from DOTMA in that the oleoyl moieties are linked by ester, rather than ether linkages.
Other reported cationic lipid compounds include those that have been conjugated to a variety of moieties including, for example, carboxyspermine which has been conjugated to one of two types of lipids and includes compounds such as 5- carboxyspermylglycine dioctaoleoylamide ("DOGS") (Transfectam™, Promega, Madison, Wisconsin) and dipalmitoylphosphatidylethanolamine 5-carboxyspermyl- amide ("DPPES") (see, e.g., U.S. Pat. No. 5,171,678).
Another cationic lipid conjugate includes derivatization of the lipid with cholesterol ("DC-Chol") which has been formulated into liposomes in combination with DOPE (See, Gao, X. and Huang, L., Biochim. Biophys. Res. Commun. 179:280, 1991). Lipopolylysine, made by conjugating polylysine to DOPE, has been reported to be effective for transfection in the presence of serum (Zhou, X. et al., Biochim. Biophys. Acta 1065:8, 1991). For certain cell lines, these liposomes containing conjugated cationic lipids, are said to exhibit lower toxicity and provide more efficient transfection than the DOTMA-containing compositions. Other commercially available cationic lipid products include DMRIE and DMRIE-HP (Vical, La Jolla, California) and
Lipofectamine (DOSPA) (Life Technology, Inc., Gaithersburg, Maryland). Other cationic lipids suitable for the delivery of oligonucleotides are described in WO
98/39359 and WO 96/37194.
Liposomal formulations are particularly suited for topical administration, liposomes present several advantages over other formulations. Such advantages include reduced side effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at the desired target, and the ability to administer RNAi agent into the skin. In some implementations, liposomes are used for delivering RNAi agent to epidermal cells and also to enhance the penetration of RNAi agent into dermal tissues, e.g., into skin. For example, the liposomes can be applied topically. Topical delivery of drugs formulated as liposomes to the skin has been documented (see, e.g., Weiner et al., Journal of Drug Targeting, 1992, vol. 2,405-410 and du Plessis et al., Antiviral Research, 18, 1992, 259-265; Mannino, R. J. and Fould- Fogerite, S., Biotechniques 6:682-690, 1988; Itani, T. et al. Gene 56:267-276. 1987; Nicolau, C. et al. Meth. Enz. 149: 157-176, 1987; Straubinger, R. M. and
Papahadjopoulos, D. Meth. Enz. 101:512-527, 1983; Wang, C. Y. and Huang, L., Proc. Natl. Acad. Sci. USA 84:7851-7855, 1987).
Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol. Non-ionic liposomal formulations comprising Novasome I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome II (glyceryl distearate/ cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver a drug into the dermis of mouse skin. Such formulations with RNAi agent are useful for treating a dermatological disorder.
Liposomes that include RNAi agent can be made highly deformable. Such deformability can enable the liposomes to penetrate through pore that are smaller than the average radius of the liposome. For example, transfersomes are a type of deformable liposomes. Transferosomes can be made by adding surface edge activators, usually surfactants, to a standard liposomal composition. Transfersomes that include RNAi agent can be delivered, for example, subcutaneously by infection in order to deliver RNAi agent to keratinocytes in the skin. In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient. In addition, due to the lipid properties, these transferosomes can be self-optimizing (adaptive to the shape of pores, e.g., in the skin), self-repairing, and can frequently reach their targets without fragmenting, and often self-loading. Other formulations amenable to the present invention are described in United States provisional application serial Nos. 61/018,616, filed January 2, 2008; 61/018,611, filed January 2, 2008; 61/039,748, filed March 26, 2008; 61/047,087, filed April 22, 2008 and 61/051,528, filed May 8, 2008. PCT application no PCT/US2007/080331, filed October 3, 2007 also describes formulations that are amenable to the present invention.
Surfactants
Surfactants find wide application in formulations such as emulsions (including microemulsions) and liposomes (see above). RNAi agent (or a precursor, e.g., a larger dsiRNA which can be processed into a siRNA, or a DNA which encodes a siRNA or precursor) compositions can include a surfactant. In one embodiment, the siRNA is formulated as an emulsion that includes a surfactant. The most common way of classifying and ranking the properties of the many different types of surfactants, both natural and synthetic, is by the use of the hydrophile/lipophile balance (HLB). The nature of the hydrophilic group provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in "Pharmaceutical Dosage Forms," Marcel Dekker, Inc., New York, NY, 1988, p. 285).
If the surfactant molecule is not ionized, it is classified as a nonionic surfactant. Nonionic surfactants find wide application in pharmaceutical products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure. Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and
ethoxylated/propoxylated block polymers are also included in this class. The polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.
If the surfactant molecule carries a negative charge when it is dissolved or dispersed in water, the surfactant is classified as anionic. Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates. The most important members of the anionic surfactant class are the alkyl sulfates and the soaps.
If the surfactant molecule carries a positive charge when it is dissolved or dispersed in water, the surfactant is classified as cationic. Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.
If the surfactant molecule has the ability to carry either a positive or negative charge, the surfactant is classified as amphoteric. Amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.
The use of surfactants in drug products, formulations and in emulsions has been reviewed (Rieger, in "Pharmaceutical Dosage Forms," Marcel Dekker, Inc., New York, NY, 1988, p. 285).
Micelles and other Membranous Formulations
The RNAi agents of the invention can also be provided as micellar formulations.
"Micelles" are defined herein as a particular type of molecular assembly in which amphipathic molecules are arranged in a spherical structure such that all the
hydrophobic portions of the molecules are directed inward, leaving the hydrophilic portions in contact with the surrounding aqueous phase. The converse arrangement exists if the environment is hydrophobic.
A mixed micellar formulation suitable for delivery through transdermal membranes may be prepared by mixing an aqueous solution of the siRNA composition, an alkali metal Cg to C22 alkyl sulphate, and a micelle forming compound. Exemplary micelle forming compounds include lecithin, hyaluronic acid, pharmaceutically acceptable salts of hyaluronic acid, glycolic acid, lactic acid, chamomile extract, cucumber extract, oleic acid, linoleic acid, linolenic acid, monoolein, monooleates, monolaurates, borage oil, evening of primrose oil, menthol, trihydroxy oxo cholanyl glycine and pharmaceutically acceptable salts thereof, glycerin, polyglycerin, lysine, polylysine, triolein, polyoxyethylene ethers and analogues thereof, polidocanol alkyl ethers and analogues thereof, chenodeoxycholate, deoxycholate, and mixtures thereof. The micelle forming compounds may be added at the same time or after addition of the alkali metal alkyl sulphate. Mixed micelles will form with substantially any kind of mixing of the ingredients but vigorous mixing in order to provide smaller size micelles.
In one method a first micellar composition is prepared which contains the siRNA composition and at least the alkali metal alkyl sulphate. The first micellar composition is then mixed with at least three micelle forming compounds to form a mixed micellar composition. In another method, the micellar composition is prepared by mixing the siRNA composition, the alkali metal alkyl sulphate and at least one of the micelle forming compounds, followed by addition of the remaining micelle forming compounds, with vigorous mixing. Phenol and/or m-cresol may be added to the mixed micellar composition to stabilize the formulation and protect against bacterial growth. Alternatively, phenol and/or m-cresol may be added with the micelle forming ingredients. An isotonic agent such as glycerin may also be added after formation of the mixed micellar composition.
For delivery of the micellar formulation as a spray, the formulation can be put into an aerosol dispenser and the dispenser is charged with a propellant. The propellant, which is under pressure, is in liquid form in the dispenser. The ratios of the ingredients are adjusted so that the aqueous and propellant phases become one, i.e., there is one phase. If there are two phases, it is necessary to shake the dispenser prior to dispensing a portion of the contents, e.g., through a metered valve. The dispensed dose of pharmaceutical agent is propelled from the metered valve in a fine spray.
Propellants may include hydrogen-containing chlorofluorocarbons, hydrogen- containing fluorocarbons, dimethyl ether and diethyl ether. In certain embodiments, HFA 134a (1,1,1,2 tetrafluoroethane) may be used.
The specific concentrations of the essential ingredients can be determined by relatively straightforward experimentation. For absorption through the oral cavities, it is often desirable to increase, e.g., at least double or triple, the dosage for through injection or administration through the gastrointestinal tract.
Particles
In another embodiment, an RNAi agent of the invention may be incorporated into a particle, e.g., a microparticle. Microparticles can be produced by spray-drying, but may also be produced by other methods including lyophilization, evaporation, fluid bed drying, vacuum drying, or a combination of these techniques. IV. Methods For Inhibiting TTR Expression
The present invention also provides methods of inhibiting expression of a transthyretin (TTR) in a cell. The methods include contacting a cell with an RNAi agent, e.g., double stranded RNAi agent, in an amount effective to inhibit expression of TTR in the cell, thereby inhibiting expression of TTR in the cell.
Contacting of a cell with an RNAi agent, e.g., a double stranded RNAi agent, may be done in vitro or in vivo. Contacting a cell in vivo with the RNAi agent includes contacting a cell or group of cells within a subject, e.g., a human subject, with the RNAi agent. Combinations of in vitro and in vivo methods of contacting a cell are also possible. Contacting a cell may be direct or indirect, as discussed above. Furthermore, contacting a cell may be accomplished via a targeting ligand, including any ligand described herein or known in the art. In preferred embodiments, the targeting ligand is a carbohydrate moiety, e.g. , a GalNAc3 ligand, or any other ligand that directs the RNAi agent to a site of interest, e.g. , the liver of a subject.
The term "inhibiting," as used herein, is used interchangeably with "reducing," "silencing," "downregulating", "suppressing", and other similar terms, and includes any level of inhibition.
The phrase "inhibiting expression of a TTR" is intended to refer to inhibition of expression of any TTR gene (such as, e.g. , a mouse TTR gene, a rat TTR gene, a monkey TTR gene, or a human TTR gene) as well as variants or mutants of a TTR gene. Thus, the TTR gene may be a wild-type TTR gene, a mutant TTR gene (such as a mutant TTR gene giving rise to amyloid deposition), or a transgenic TTR gene in the context of a genetically manipulated cell, group of cells, or organism.
"Inhibiting expression of a TTR gene" includes any level of inhibition of a TTR gene, e.g. , at least partial suppression of the expression of a TTR gene. The expression of the TTR gene may be assessed based on the level, or the change in the level, of any variable associated with TTR gene expression, e.g. , TTR mRNA level, TTR protein level, or the number or extent of amyloid deposits. This level may be assessed in an individual cell or in a group of cells, including, for example, a sample derived from a subject.
Inhibition may be assessed by a decrease in an absolute or relative level of one or more variables that are associated with TTR expression compared with a control level. The control level may be any type of control level that is utilized in the art, e.g., a pre- dose baseline level, or a level determined from a similar subject, cell, or sample that is untreated or treated with a control (such as, e.g., buffer only control or inactive agent control).
In some embodiments of the methods of the invention, expression of a TTR gene is inhibited by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%,at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%. at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%.
Inhibition of the expression of a TTR gene may be manifested by a reduction of the amount of mRNA expressed by a first cell or group of cells (such cells may be present, for example, in a sample derived from a subject) in which a TTR gene is transcribed and which has or have been treated (e.g., by contacting the cell or cells with an RNAi agent of the invention, or by administering an RNAi agent of the invention to a subject in which the cells are or were present) such that the expression of a TTR gene is inhibited, as compared to a second cell or group of cells substantially identical to the first cell or group of cells but which has not or have not been so treated (control cell(s)). In preferred embodiments, the inhibition is assessed by expressing the level of mRNA in treated cells as a percentage of the level of mRNA in control cells, using the following formula:
(mRNA in control cells) - (mRNA in treated cells) . ^„
— · 100%
(mRNA in control cells)
Alternatively, inhibition of the expression of a TTR gene may be assessed in terms of a reduction of a parameter that is functionally linked to TTR gene expression, e.g., TTR protein expression, retinol binding protein level, vitamin A level, or presence of amyloid deposits comprising TTR. TTR gene silencing may be determined in any cell expressing TTR, either constitutively or by genomic engineering, and by any assay known in the art. The liver is the major site of TTR expression. Other significant sites of expression include the choroid plexus, retina and pancreas.
Inhibition of the expression of a TTR protein may be manifested by a reduction in the level of the TTR protein that is expressed by a cell or group of cells (e.g., the level of protein expressed in a sample derived from a subject). As explained above for the assessment of mRNA suppression, the inhibiton of protein expression levels in a treated cell or group of cells may similarly be expressed as a percentage of the level of protein in a control cell or group of cells.
A control cell or group of cells that may be used to assess the inhibition of the expression of a TTR gene includes a cell or group of cells that has not yet been contacted with an RNAi agent of the invention. For example, the control cell or group of cells may be derived from an individual subject (e.g., a human or animal subject) prior to treatment of the subject with an RNAi agent.
The level of TTR mRNA that is expressed by a cell or group of cells, or the level of circulating TTR mRNA, may be determined using any method known in the art for assessing mRNA expression. In one embodiment, the level of expression of TTR in a sample is determined by detecting a transcribed polynucleotide, or portion thereof, e.g., mRNA of the TTR gene. RNA may be extracted from cells using RNA extraction techniques including, for example, using acid phenol/guanidine isothiocyanate extraction (RNAzol B; Biogenesis), RNeasy RNA preparation kits (Qiagen) or PAXgene (PreAnalytix, Switzerland). Typical assay formats utilizing ribonucleic acid
hybridization include nuclear run-on assays, RT-PCR, RNase protection assays (Melton et ah, Nuc. Acids Res. 12:7035), Northern blotting, in situ hybridization, and microarray analysis. Circulating TTR mRNA may be detected using methods the described in PCT/US2012/043584, the entire contents of which are hereby incorporated herein by reference.
In one embodiment, the level of expression of TTR is determined using a nucleic acid probe. The term "probe", as used herein, refers to any molecule that is capable of selectively binding to a specific TTR. Probes can be synthesized by one of skill in the art, or derived from appropriate biological preparations. Probes may be specifically designed to be labeled. Examples of molecules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic molecules.
Isolated mRNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, polymerase chain reaction (PCR) analyses and probe arrays. One method for the determination of mRNA levels involves contacting the isolated mRNA with a nucleic acid molecule (probe) that can hybridize to TTR mRNA. In one embodiment, the mRNA is immobilized on a solid surface and contacted with a probe, for example by running the isolated mRNA on an agarose gel and transferring the mRNA from the gel to a membrane, such as nitrocellulose. In an alternative embodiment, the probe(s) are immobilized on a solid surface and the mRNA is contacted with the probe(s), for example, in an Affymetrix gene chip array. A skilled artisan can readily adapt known mRNA detection methods for use in determining the level of TTR mRNA.
An alternative method for determining the level of expression of TTR in a sample involves the process of nucleic acid amplification and/or reverse transcriptase (to prepare cDNA) of for example mRNA in the sample, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88: 189-193), self sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87: 1874-1878),
transcriptional amplification system (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86: 1173-1177), Q-Beta Replicase (Lizardi et al. (1988) Bio/Technology 6: 1197), rolling circle replication (Lizardi et al., U.S. Pat. No. 5,854,033) or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers. In particular aspects of the invention, the level of expression of TTR is determined by quantitative fluorogenic RT-PCR (i.e., the TaqMan™ System).
The expression levels of TTR mRNA may be monitored using a membrane blot
(such as used in hybridization analysis such as Northern, Southern, dot, and the like), or microwells, sample tubes, gels, beads or fibers (or any solid support comprising bound nucleic acids). See U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which are incorporated herein by reference. The determination of TTR expression level may also comprise using nucleic acid probes in solution.
In preferred embodiments, the level of mRNA expression is assessed using branched DNA (bDNA) assays or real time PCR (qPCR). The use of these methods is described and exemplified in the Examples presented herein.
The level of TTR protein expression may be determined using any method known in the art for the measurement of protein levels. Such methods include, for example, electrophoresis, capillary electrophoresis, high performance liquid
chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion
chromatography, fluid or gel precipitin reactions, absorption spectroscopy, a
colorimetric assays, spectrophotometric assays, flow cytometry, immunodiffusion (single or double), Immunoelectrophoresis, Western blotting, radioimmunoassay (RIA), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, electrochemiluminescence assays, and the like.
In some embodiments, the efficacy of the methods of the invention can be monitored by detecting or monitoring a reduction in an amyloid TTR deposit. Reducing an amyloid TTR deposit, as used herein, includes any decrease in the size, number, or severity of TTR deposits, or to a prevention or reduction in the formation of TTR deposits, within an organ or area of a subject, as may be assessed in vitro or in vivo using any method known in the art. For example, some methods of assessing amyloid deposits are described in Gertz, M.A. & Rajukumar, S.V. (Editors) (2010), Amyloidosis: Diagnosis and Treatment, New York: Humana Press. Methods of assessing amyloid deposits may include biochemical analyses, as well as visual or computerized assessment of amyloid deposits, as made visible, e.g., using immunohistochemical staining, fluorescent labeling, light microscopy, electron microscopy, fluorescence microscopy, or other types of microscopy. Invasive or noninvasive imaging modalities, including, e.g., CT, PET, or NMR/MRI imaging may be employed to assess amyloid deposits.
The methods of the invention may reduce TTR deposits in any number of tissues or regions of the body including but not limited to the heart, liver, spleen, esophagus, stomach, intestine (ileum, duodenum and colon), brain, sciatic nerve, dorsal root ganglion, kidney and retina.
The term "sample" as used herein refers to a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject. Examples of biological fluids include blood, serum and serosal fluids, plasma, lymph, urine, cerebrospinal fluid, saliva, ocular fluids, and the like. Tissue samples may include samples from tissues, organs or localized regions. For example, samples may be derived from particular organs, parts of organs, or fluids or cells within those organis. In certain embodiments, samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g. , hepatocytes), the retina or parts of the retina (e.g., retinal pigment epithelium), the central nervous system or parts of the central nervous system (e.g., ventricles or choroid plexus), or the pancreas or certain cells or parts of the pancreas. In preferred embodiments, a "sample derived from a subject" refers to blood or plasma drawn from the subject. In further
embodiments, a "sample derived from a subject" refers to liver tissue or retinal tissue derived from the subject.
In some embodiments of the methods of the invention, the RNAi agent is administered to a subject such that the RNAi agent is delivered to a specific site within the subject. The inhibition of expression of TTR may be assessed using measurements of the level or change in the level of TTR mRNA or TTR protein in a sample derived from fluid or tissue from the specific site within the subject. In preferred embodiments, the site is selected from the group consisting of liver, choroid plexus, retina, and pancreas. The site may also be a subsection or subgroup of cells from any one of the aforementioned sites (e.g., hepatocytes or retinal pigment epithelium). The site may also include cells that express a particular type of receptor (e.g. , hepatocytes that express the asialogycloprotein receptor).
V. Methods for Treating or Preventing a TTR- Associated Disease
The present invention also provides methods for treating or preventing a TTR- associated disease in a subject. The methods include administering to the subject a therapeutically effective amount or prophylactically effective amount of an RNAi agent of the invention.
As used herein, a "subject" includes either a human or a non-human animal, preferably a vertebrate, and more preferably a mammal. A subject may include a transgenic organism. Most preferably, the subject is a human, such as a human suffering from or predisposed to developing a TTR-associated disease.
In some embodiments, the subject is suffering from a TTR-associated disease. In other embodiments, the subject is a subject at risk for developing a TTR-associated disease, e.g. , a subject with a TTR gene mutation that is associated with the development of a TTR associated disease, a subject with a family history of TTR-associated disease, or a subject who has signs or symptoms suggesting the development of TTR
amyloidosis.
A "TTR-associated disease," as used herein, includes any disease caused by or associated with the formation of amyloid deposits in which the fibril precurosors consist of variant or wild-type TTR protein. Mutant and wild-type TTR give rise to various forms of amyloid deposition (amyloidosis). Amyloidosis involves the formation and aggregation of misfolded proteins, resulting in extracellular deposits that impair organ function. Climical syndromes associated with TTR aggregation include, for example, senile systemic amyloidosis (SSA); systemic familial amyloidosis; familial amyloidotic polyneuropathy (FAP); familial amyloidotic cardiomyopathy (FAC); and
leptomeningeal amyloidosis, also known as leptomeningeal or meningocerebrovascular amyloidosis, central nervous system (CNS) amyloidosis, or amyloidosis VII form.
In some embodiments of the methods of the invention, RNAi agents of the invention are administered to subjects suffering from familial amyloidotic
cardiomyopathy (FAC) and senile systemic amyloidosis (SSA). Normal- sequence TTR causes cardiac amyloidosis in people who are elderly and is termed senile systemic amyloidosis (SSA) (also called senile cardiac amyloidosis (SCA) or cardiac
amyloidosis). SSA often is accompanied by microscopic deposits in many other organs. TTR mutations accelerate the process of TTR amyloid formation and are the most important risk factor for the development of clinically significant TTR amyloidosis (also called ATTR (amyloidosis-transthyretin type)). More than 85 amyloidogenic TTR variants are known to cause systemic familial amyloidosis.
In some embodiments of the methods of the invention, RNAi agents of the invention are administered to subjects suffering from transthyretin (TTR)-related familial amyloidotic polyneuropathy (FAP). Such subjects may suffer from ocular manifestations, such as vitreous opacity and glaucoma. It is known to one of skill in the art that amyloidogenic transthyretin (ATTR) synthesized by retinal pigment epithelium (RPE) plays important roles in the progression of ocular amyloidosis. Previous studies have shown that panretinal laser photocoagulation, which reduced the RPE cells, prevented the progression of amyloid deposition in the vitreous, indicating that the effective suppression of ATTR expression in RPE may become a novel therapy for ocular amyloidosis (see, e.g. , Kawaji, T., et al., Ophthalmology. (2010) 117: 552-555). The methods of the invention are useful for treatment of ocular manifestations of TTR related FAP, e.g. , ocular amyloidosis. The RNAi agent can be delivered in a manner suitable for targeting a particular tissue, such as the eye. Modes of ocular delivery include retrobulbar, subcutaneous eyelid, subconjunctival, subtenon, anterior chamber or intravitreous injection (or internal injection or infusion). Specific formulations for ocular delivery include eye drops or ointments.
Another TTR-associated disease is hyperthyroxinemia, also known as
"dystransthyretinemic hyperthyroxinemia" or "dysprealbuminemic hyperthyroxinemia". This type of hyperthyroxinemia may be secondary to an increased association of thyroxine with TTR due to a mutant TTR molecule with increased affinity for thyroxine.
See, e.g., Moses et al. (1982) J. Clin. Invest., 86, 2025-2033.
The RNAi agents of the invention may be administered to a subject using any mode of administration known in the art, including, but not limited to subcutaneous, intravenous, intramuscular, intraocular, intrabronchial, intrapleural, intraperitoneal, intraarterial, lymphatic, cerebrospinal, and any combinations thereof.
In preferred embodiments, the agents are administered to the subject
subcutaneously. In some embodiments, a subject is administered a single dose of an
RNAi agent via subcutaneous injection, e.g., abdominal, thigh, or upper arm injection. In other embodiments, a subject is administered a split dose of an RNAi agent via subcutaneous injection. In one embodiment, the split dose of the RNAi agent is administered to the subject via subcutaneous injection at two different anatomical locations on the subject. For example, the subject may be subcutaneously injected with a split dose of about 250 mg {e.g., about half of a 500 mg dose) in the right arm and about 250 mg in the left arm.
In some embodiments, the administration is via a depot injection. A depot injection may release the RNAi agent in a consistent way over a prolonged time period.
Thus, a depot injection may reduce the frequency of dosing needed to obtain a desired effect, e.g., a desired inhibition of TTR, or a therapeutic or prophylactic effect. A depot injection may also provide more consistent serum concentrations. Depot injections may include subcutaneous injections or intramuscular injections. In preferred embodiments, the depot injection is a subcutaneous injection.
In some embodiments, the administration is via a pump. The pump may be an external pump or a surgically implanted pump. In certain embodiments, the pump is a subcutaneously implanted osmotic pump. In other embodiments, the pump is an infusion pump. An infusion pump may be used for intravenous, subcutaneous, arterial, or epidural infusions. In preferred embodiments, the infusion pump is a subcutaneous infusion pump. In other embodiments, the pump is a surgically implanted pump that delivers the RNAi agent to the liver.
In embodiments in which the RNAi agent is administered via a subcutaneous infusion pump, a single dose of the RNAi agent may be administered to the subject over a period of time of about 45 minutes to about 5 minutes, e.g., about 45 minutes, about 40 minutes, about 35 minutes, about 30 minutes, about 25 minutes, about 20 minutes, about 15 minutes, about 10 minutes, or about 5 minutes.
Other modes of administration include epidural, intracerebral,
intracerebroventricular, nasal administration, intraarterial, intracardiac, intraosseous infusion, intrathecal, and intravitreal, and pulmonary.The mode of administration may be chosen based upon whether local or systemic treatment is desired and based upon the area to be treated. The route and site of administration may be chosen to enhance targeting.
In some embodiments, the RNAi agent is administered to a subject in an amount effective to inhibit TTR expression in a cell within the subject. The amount effective to inhibit TTR expression in a cell within a subject may be assessed using methods discussed above, including methods that involve assessment of the inhibition of TTR mRNA, TTR protein, or related variables, such as amyloid deposits.
In some embodiments, the RNAi agent is administered to a subject in a therapeutically or prophylactically effective amount.
"Therapeutically effective amount," as used herein, is intended to include the amount of an RNAi agent that, when administered to a patient for treating a TTR associated disease, is sufficient to effect treatment of the disease (e.g., by diminishing, ameliorating or maintaining the existing disease or one or more symptoms of disease). The "therapeutically effective amount" may vary depending on the RNAi agent, how the agent is administered, the disease and its severity and the history, age, weight, family history, genetic makeup, stage of pathological processes mediated by TTR expression, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.
"Prophylactically effective amount," as used herein, is intended to include the amount of an RNAi agent that, when administered to a subject who does not yet experience or display symptoms of a TTR-associated disease, but who may be predisposed to the disease, is sufficient to prevent or ameliorate the disease or one or more symptoms of the disease. Symptoms that may be ameliorated include sensory neuropathy (e.g. , paresthesia, hypesthesia in distal limbs), autonomic neuropathy (e.g., gastrointestinal dysfunction, such as gastric ulcer, or orthostatic hypotension), motor neuropathy, seizures, dementia, myelopathy, polyneuropathy, carpal tunnel syndrome, autonomic insufficiency, cardiomyopathy, vitreous opacities, renal insufficiency, nephropathy, substantially reduced mBMI (modified Body Mass Index), cranial nerve dysfunction, and corneal lattice dystrophy. Ameliorating the disease includes slowing the course of the disease or reducing the severity of later-developing disease. The "prophylactically effective amount" may vary depending on the RNAi agent, how the agent is administered, the degree of risk of disease, and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.
A "therapeutically-effective amount" or "prophylacticaly effective amount" also includes an amount of an RNAi agent that produces some desired local or systemic effect at a reasonable benefit/risk ratio applicable to any treatment. RNAi agents employed in the methods of the present invention may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment.
As used herein, the phrases "therapeutically effective amount" and
"prophylactically effective amount" also include an amount that provides a benefit in the treatment, prevention, or management of pathological processes or symptom(s) of pathological processes mediated by TTR expression. Symptoms of TTR amyloidosis include sensory neuropathy (e.g. paresthesia, hypesthesia in distal limbs), autonomic neuropathy (e.g. , gastrointestinal dysfunction, such as gastric ulcer, or orthostatic hypotension), motor neuropathy, seizures, dementia, myelopathy, polyneuropathy, carpal tunnel syndrome, autonomic insufficiency, cardiomyopathy, vitreous opacities, renal insufficiency, nephropathy, substantially reduced mBMI (modified Body Mass Index), cranial nerve dysfunction, and corneal lattice dystrophy.
The dose of an RNAi agent that is administered to a subject may be tailored to balance the risks and benefits of a particular dose, for example, to achieve a desired level of TTR gene suppression (as assessed, e.g., based on TTR mRNA suppression, TTR protein expression, or a reduction in an amyloid deposit, as defined above) or a desired therapeutic or prophylactic effect, while at the same time avoiding undesirable side effects.
In one embodiment, an iRNA agent of the invention is administered to a subject as a weight-based dose. A "weight-based dose" (e.g., a dose in mg/kg) is a dose of the iRNA agent that will change depending on the subject's weight. In another
embodiement, an iRNA agent is administered to a subject as a fixed dose. A "fixed dose" (e.g., a dose in mg) means that one dose of an iRNA agent is used for all subjects regardless of any specific subject-related factors, such as weight. In one particular embodiment, a fixed dose of an iRNA agent of the invention is based on a
predetermined weight or age.
In one embodiment, the RNAi agent is administered as a weight-based of between about 0.25 mg/kg to about 50 mg/kg, e.g., between about 0.25 mg/kg to about 0.5 mg/kg, between about 0.25 mg/kg to about 1 mg/kg, between about 0.25 mg/kg to about 5 mg/kg, between about 0.25 mg/kg to about 10 mg/kg, between about 1 mg/kg to about 10 mg/kg, between about 5 mg/kg to about 15 mg/kg, between about 10 mg/kg to about 20 mg/kg, between about 15 mg/kg to about 25 mg/kg, between about 20 mg/kg to about 30 mg/kg, between about 25 mg/kg to about 35 mg/kg, or between about 40 mg/kg to about 50 mg/kg.
In some embodiments, the RNAi agent is administered as a weight-based dose of about 0.25 mg/kg, about 0.5 mg/kg, about 1 mg/kg, about 2 mg/kg, about 3 mg/kg, about 4 mg/kg, about 5 mg/kg, about 6 mg/kg, about 7 mg/kg, about 8 mg/kg, about 9 mg/kg, about 10 mg/kg, about 11 mg/kg, about 12 mg/kg, about 13 mg/kg, about 14 mg/kg, about 15 mg/kg, about 16 mg/kg, about 17 mg/kg, about 18 mg/kg, about 19 mg/kg, about 20 mg/kg, about 21 mg/kg, about 22 mg/kg, about 23 mg/kg, about 24 mg/kg, about 25 mg/kg, about 26 mg/kg, about 27 mg/kg, about 28 mg/kg, about 29 mg/kg, 30 mg/kg, about 31 mg/kg, about 32 mg/kg, about 33 mg/kg, about 34 mg/kg, about 35 mg/kg, about 36 mg/kg, about 37 mg/kg, about 38 mg/kg, about 39 mg/kg, about 40 mg/kg, about 41 mg/kg, about 42 mg/kg, about 43 mg/kg, about 44 mg/kg, about 45 mg/kg, about 46 mg/kg, about 47 mg/kg, about 48 mg/kg, about 49 mg/kg or about 50 mg/kg.
In some embodiments, the RNAi agent is administered as a fixed dose of between about 100 mg to about 900 mg, e.g., between about 100 mg to about 850 mg, between about 100 mg to about 800 mg, between about 100 mg to about 750 mg, between about 100 mg to about 700 mg, between about 100 mg to about 650 mg, between about 100 mg to about 600 mg, between about 100 mg to about 550 mg, between about 100 mg to about 500 mg, between about 200 mg to about 850 mg, between about 200 mg to about 800 mg, between about 200 mg to about 750 mg, between about 200 mg to about 700 mg, between about 200 mg to about 650 mg, between about 200 mg to about 600 mg, between about 200 mg to about 550 mg, between about 200 mg to about 500 mg, between about 300 mg to about 850 mg, between about 300 mg to about 800 mg, between about 300 mg to about 750 mg, between about 300 mg to about 700 mg, between about 300 mg to about 650 mg, between about 300 mg to about 600 mg, between about 300 mg to about 550 mg, between about 300 mg to about 500 mg, between about 400 mg to about 850 mg, between about 400 mg to about 800 mg, between about 400 mg to about 750 mg, between about 400 mg to about 700 mg, between about 400 mg to about 650 mg, between about 400 mg to about 600 mg, between about 400 mg to about 550 mg, or between about 400 mg to about 500 mg. In some embodiments, the RNAi agent is administered as a fixed dose of about 100 mg, about 125 mg, about 150 mg, about 175 mg, 200 mg, about 225 mg, about 250 mg, about 275 mg, about 300 mg, about 325 mg, about 350 mg, about 375 mg, about 400 mg, about 425 mg, about 450 mg, about 475 mg, about 500 mg, about 525 mg, about 550 mg, about 575 mg, about 600 mg, about 625 mg, about 650 mg, about 675 mg, about 700 mg, about 725 mg, about 750 mg, about 775 mg, about 800 mg, about 825 mg, about 850 mg, about 875 mg, or about 900 mg.
In some embodiments, the RNAi agent is administered in two or more doses. If desired to facilitate repeated or frequent infusions, implantation of a delivery device, e.g. , a pump, semi-permanent stent (e.g. , intravenous, intraperitoneal, intracisternal or intracapsular), or reservoir may be advisable. In some embodiments, the number or amount of subsequent doses is dependent on the achievement of a desired effect, e.g., the suppression of a TTR gene, or the achievement of a therapeutic or prophylactic effect, e.g., reducing an amyloid deposit or reducing a symptom of a TTR- associated disease.
In some embodiments, the RNAi agent is administered according to a schedule. For example, the RNAi agent may be administered twice per week, three times per week, four times per week, or five times per week. In some embodiments, the schedule involves regularly spaced administrations, e.g. , hourly, every four hours, every six hours, every eight hours, every twelve hours, daily, every 2 days, every 3 days, every 4 days, every 5 days, weekly, biweekly, or monthly. In other embodiments, the schedule involves closely spaced administrations followed by a longer period of time during which the agent is not administered. For example, the schedule may involve an initial set of doses that are administered in a relatively short period of time (e.g., about every 6 hours, about every 12 hours, about every 24 hours, about every 48 hours, or about every 72 hours) followed by a longer time period (e.g., about 1 week, about 2 weeks, about 3 weeks, about 4 weeks, about 5 weeks, about 6 weeks, about 7 weeks, or about 8 weeks) during which the RNAi agent is not administered. In one embodiment, the RNAi agent is initially administered hourly and is later administered at a longer interval (e.g., daily, weekly, biweekly, or monthly). In another embodiment, the RNAi agent is initially administered daily and is later administered at a longer interval (e.g., weekly, biweekly, or monthly). In certain embodiments, the longer interval increases over time or is determined based on the achievement of a desired effect.
In a specific embodiment, the RNAi agent is administered once daily during a first week, followed by weekly dosing starting on the eighth day of administration. In another specific embodiment, the RNAi agent is administered every other day during a first week followed by weekly dosing starting on the eighth day of administration. In another embodiment, the RNAi agent is administered once daily for five days during a first week, followed by weekly dosing administration.
Any of these schedules may optionally be repeated for one or more iterations. The number of iterations may depend on the achievement of a desired effect, e.g., the suppression of a TTR gene, retinol binding protein level, vitamin A level, and/or the achievement of a therapeutic or prophylactic effect, e.g. , reducing an amyloid deposit or reducing a symptom of a TTR-associated disease.
In some embodiments, the RNAi agent is administered with other therapeutic agents or other therapeutic regimens. For example, other agents or other therapeutic regimens suitable for treating a TTR-associated disease may include a liver transplant, which can reduce mutant TTR levels in the body; Tafamidis (Vyndaqel), which kinetically stabilizes the TTR tetramer preventing tetramer dissociation required for TTR amyloidogenesis; and diuretics, which may be employed, for example, to reduce edema in TTR amyloidosis with cardiac involvement.
In one embodiment, a subject is administered an initial dose and one or more maintenance doses of an RNAi agent. The maintenance dose or doses can be the same or lower than the initial dose, e.g., one-half of the initial dose. A maintenance regimen can include treating the subject with a dose or doses ranging from 0.01 μg to 15 mg/kg of body weight per day, e.g., 10 mg/kg, 1 mg/kg, 0.1 mg/kg, 0.01 mg/kg, 0.001 mg/kg, or 0.00001 mg/kg of bodyweight per day, or a dose or doses of about 100 mg to about 900 mg, e.g., about 125 mg, about 150 mg, about 175 mg, 200 mg, about 225 mg, about 250 mg, about 275 mg, about 300 mg, about 325 mg, about 350 mg, about 375 mg, about 400 mg, about 425 mg, about 450 mg, about 475 mg, about 500 mg, about 525 mg, about 550 mg, about 575 mg, about 600 mg, about 625 mg, about 650 mg, about 675 mg, about 700 mg, about 725 mg, about 750 mg, about 775 mg, about 800 mg, about 825 mg, about 850 mg, about 875 mg, or about 900 mg per week. The
maintenance doses are, for example, administered no more than once every 2 days, once every 5 days, once every 7 days, once every 10 days, once every 14 days, once every 21 days, or once every 30 days. Further, the treatment regimen may last for a period of time which will vary depending upon the nature of the particular disease, its severity and the overall condition of the patient. In certain embodiments the dosage may be delivered no more than once per day, e.g., no more than once per 24, 36, 48, or more hours, e.g. , no more than once every 5 or 8 days. Following treatment, the patient can be monitored for changes in his/her condition. The dosage of the RNAi agent may either be increased in the event the patient does not respond significantly to current dosage levels, or the dose may be decreased if an alleviation of the symptoms of the disease state is observed, if the disease state has been ablated, or if undesired side-effects are observed.
VI. Kits
The present invention also provides kits for performing any of the methods of the invention. Such kits include one or more RNAi agent(s) and instructions for use, e.g., instructions for inhibiting expression of a TTR in a cell by contacting the cell with the RNAi agent(s) in an amount effective to inhibit expression of the TTR. The kits may optionally further comprise means for contacting the cell with the RNAi agent (e.g. , an injection device or an infusion pump), or means for measuring the inhibition of TTR (e.g., means for measuring the inhibition of TTR mRNA or TTR protein). Such means for measuring the inhibition of TTR may comprise a means for obtaining a sample from a subject, such as, e.g. , a plasma sample. The kits of the invention may optionally further comprise means for administering the RNAi agent(s) to a subject or means for determining the therapeutically effective or prophylactically effective amount.
Suitable RNAi agents for inclusion in the kits of the invention include any one of the RNAi agents listed in Table 1 or Table 2. In one embodiment, the RNAi agent is selected from the group consisting of AD-51544, AD-51545, AD-51546, and AD- 51547. In another embodiemtn, the RNAi agent is AD-51547.
The RNAi agent may be provided in any convenient form, such as a solution in sterile water for injection. In one embodiment, the the RNAi agent is provided as a 200 mg/ml solution in sterile water for injection.
This invention is further illustrated by the following examples which should not be construed as limiting. The contents of all references and published patents and patent applications cited throughout the application are hereby incorporated herein by reference. EXAMPLES
Example 1: Inhibition of TTR with TTR-GalNAc conjugates
A single dose of the TTR RNAi agent AD-43527 was administered to mice subcutaneously and TTR mRNA levels were determined 72 hours post administration.
The mouse/rat cross-reactive GalNAc-conjugate, AD-43527, was chosen for in vivo evaluation in WT C57BL/6 mice for silencing of TTR mRNA in liver. The sequence of each strand of AD-43527 is shown below.
Strand: s= sense; as= antisense
Figure imgf000079_0003
The ligand used was GalNAc3:
Figure imgf000079_0001
This GalNAc3 ligand was conjugated to the 3 '-end of the sense strand using the linker and tether as shown below:
Figure imgf000079_0002
The structure of the resulting GalNAc3 conjugated sense strand is shown in the following schematic:
Figure imgf000080_0001
Additional RNAi agents that target TTR and have the following sequences and modifications were synthesized and assayed.
Mouse/rat cross reactive TTR RNAi agents
Figure imgf000080_0002
Human/cyno cross reactive TTR RNAi agents; parent duplex is AD-18328 [having a sense strand 5'-3' sequence of GuAAccAAGAGuAuuccAudTdT (SEQ ID NO: 12) and antisense strand 5' to 3' sequence of AUGGAAuACUCUUGGUuACdTdT (SEQ ID NO: 13) with the following modifications: alternating 2'F/2'OMe w/2 PS on AS.
Figure imgf000080_0003
L96 = GalNAc3; lowercase nts (a,u,g,c) are 2'-0-methyl nucleotides, Nf (i. e. , Af) is a 2'- fluoro nucleotide; Ql l is cholesterol; s is phosphorothioate.
AD-43527 was administered to female C57BL/6 mice (6-10 weeks, 5 per group) via subcutaneous injection at a dose volume of ΙΟμΙ/g at a dose of 30, 15, 7.5, 3.5, 1.75 or 0.5 mg/kg of AD-43527. Control animals received PBS by subcutaneous injection at the same dose volume.
After approximately seventy two hours, mice were anesthetized with 200 μΐ of ketamine, and then exsanguinated by severing the right caudal artery. Liver tissue was collected, flash-frozen and stored at -80°C until processing. Efficacy of treatment was evaluated by measurement of TTR mRNA in the liver at 72 hours post-dose. TTR liver mRNA levels were assayed utilizing the Branched DNA assays- QuantiGene 1.0 (Panomics). Briefly, mouse liver samples were ground and tissue lysates were prepared. Liver lysis mixture (a mixture of 1 volume of lysis mixture, 2 volume of nuclease-free water and ΙΟμΙ of Proteinase-K/ml for a final concentration of 20mg/ml) was incubated at 65 °C for 35 minutes. 5μ1 of liver lysate and 95 μΐ of working probe set (TTR probe for gene target and GAPDH for endogenous control) were added into the Capture Plate. Capture Plates were incubated at 53 °C +1 °C (aprx. 16-20hrs). The next day, the Capture Plates were washed 3 times with IX Wash Buffer (nuclease-free water, Buffer Component 1 and Wash Buffer Component 2), then dried by centrifuging for 1 minute at 240g. ΙΟΟμΙ of Amplifier Probe mix per well was added into the Capture Plate, which was sealed with aluminum foil and incubated for 1 hour at 46°C ±1°C. Following a 1 hour incubation, the wash step was repeated, then ΙΟΟμΙ of Label Probe mix per well was added. Capture plates were incubated at 46 °C +1 °C for 1 hour. The plates were then washed with IX Wash Buffer, dried and ΙΟΟμΙ substrate per well was added into the Capture Plates. Capture Plates were incubated for 30 minutes at 46°C followed by incubation for 30 minutes at room temperature. Plates were read using the SpectraMax Luminometer following
incubation.bDNA data were analyzed by subtracting the average background from each duplicate sample, averaging the resultant duplicate GAPDH (control probe) and TTR (experimental probe) values, and then computing the ratio: (experimental probe- background)/(control probe-background). The average TTR mRNA level was calculated for each group and normalized to the PBS group average to give relative TTR mRNA as a % of the PBS control group.
The results are shown in Figure 1. The GalNAc conjugated RNAi agent targeting TTR had an ED50 of approximately 5 mg/kg for TTR mRNA knockdown. These results demonstrate that GalNAc conjugated RNAi agents that target TTR are effective at inhibiting expression of TTR mRNA. Example 2: Inhibition of TTR with TTR-GalNAc conjugates is durable
Mice were administered a subcutaneous dose (either 7.5 or 30.0 mg/kg) of AD- 43527, a GalNAc conjugated RNAi agent that targets TTR. The TTR mRNA levels in the liver were evaluated at 1, 3, 5, 7, 10, 13, 15, 19, 26, 33, and 41 days post treatment using the method described in Example 1. The results are shown in Figure 2. At day 19, administration of 30.0 mg/kg GalNAc conjugated RNAi agents still showed about 50% silencing. Full recovery of expression occurred at day 41.
These results demonstrated that the inhibition provided by GalNAc conjugated siRNA targeting TTR is durable, lasting up to 3, 5, 7, 10, 13, 15, 19, 26 or 33 days post treatment.
Example 3. RNA Synthesis and Duplex Annealing
1. Oligonucleotide Synthesis
Oligonucleotides were synthesized on an AKTAoligopilot synthesizer or an ABI
394 synthsizer. Commercially available controlled pore glass solid support (dT-CPG, 500A, Prime Synthesis) and RNA phosphoramidites with standard protecting groups, 5'- O-dimethoxytrityl N6-benzoyl-2'-i-butyldimethylsilyl-adenosine-3'-O-N,N'- diisopropyl-2-cyanoethylphosphoramidite, 5'-0-dimethoxytrityl-N4-acetyl-2'-i- butyldimethylsilyl-cytidine-3'-O-N,N'-diisopropyl-2-cyanoethylphosphoramidite, 5'-O- dimethoxytrityl-N2--isobutryl-2'-i-butyldimethylsilyl-guanosine-3'-O-N,N'-diisopropyl- 2-cyanoethylphosphoramidite, and 5' -0-dimethoxytrityl-2'-i-butyldimethylsilyl -undines' -O-N,N'-diisopropyl-2-cyanoethylphosphoramidite (Pierce Nucleic Acids
Technologies) were used for the oligonucleotide synthesis unless otherwise specified. The 2'-F phosphoramidites, 5'-0-dimethoxytrityl-N4-acetyl-2'-fluro-cytidine-3'-O- Ν,Ν' -diisopropyl-2-cyanoethyl-phosphoramidite and 5 ' -O-dimethoxytrityl-2' -fluro- uridine-3'-O-N,N'-diisopropyl-2-cyanoethyl-phosphoramidite were purchased from (Promega). All phosphoramidites were used at a concentration of 0.2M in acetonitrile (CH3CN) except for guanosine which was used at 0.2M concentration in 10% THF/ANC (v/v). Coupling/recycling time of 16 minutes was used. The activator was 5-ethyl thiotetrazole (0.75M, American International Chemicals), for the PO-oxidation
Iodine/Water/Pyridine was used and the PS-oxidation PADS (2 %) in 2,6-lutidine/ACN (1: 1 v/v) was used.
Ligand conjugated strands were synthesized using a solid support containing the corresponding ligand. For example, the introduction of a carbohydrate moiety/ligand (for e.g., GalNAc) at the 3 '-end of a sequence was achieved by starting the synthesis with the corresponding carbohydrate solid support. Similarly a cholesterol moiety at the 3 '-end was introduced by starting the synthesis on the cholesterol support. In general, the ligand moiety was tethered to iraw5,-4-hydroxyprolinol via a tether of choice as described in the previous examples to obtain a hydroxyprolinol-ligand moiety. The hydroxyprolinol-ligand moiety was then coupled to a solid support via a succinate linker or was converted to phosphoramidite via standard phosphitylation conditions to obtain the desired carbohydrate conjugate building blocks. Fluorophore labeled siRNAs were synthesized from the corresponding phosphoramidite or solid support, purchased from Biosearch Technologies. The oleyl lithocholic (GalNAc)3 polymer support made in house at a loading of 38.6 μιηοΐ/gram. The Mannose (Man) polymer support was also made in house at a loading of 42.0 μιηοΐ/gram.
Conjugation of the ligand of choice at the desired position, for example at the 5'- end of the sequence, was achieved by coupling of the corresponding phosphoramidite to the growing chain under standard phosphoramidite coupling conditions unless otherwise specified. An extended 15 minute coupling of 0.1M solution of phosphoramidite in anhydrous CH CN in the presence of 5-(ethylthio)-lH-tetrazole activator to a solid bound oligonucleotide. Oxidation of the internucleotide phosphite to the phosphate was carried out using standard iodine- water as reported in Beaucage, S.L. (2008) Solid- phase synthesis of siRNA oligonucleotides. Curr. Opin. Drug Discov. Devel., 11, 203- 216; Mueller, S., Wolf, J. and Ivanov, S.A. (2004) Current Strategies for the Synthesis of RNA. Curr. Org. Synth., 1, 293-307; Xia, J., Noronha, A., Toudjarska, I., Li, F., Akinc, A., Braich, R., Frank- Kamenetsky, M., Rajeev, K.G., Egli, M. and Manoharan, M. (2006) Gene Silencing Activity of siRNAs with a Ribo-difluorotoluyl Nucleotide. ACS Chem. Biol., 1, 176-183 or by treatment with ie/t-butyl
hydroperoxide/acetonitrile/water (10: 87: 3) with a 10 minute oxidation wait time conjugated oligonucleotide. Phosphorothioate was introduced by the oxidation of phosphite to phosphorothioate by using a sulfur transfer reagent such as DDTT
(purchased from AM Chemicals), PADS and or Beaucage reagent The cholesterol phosphoramidite was synthesized in house, and used at a concentration of 0.1 M in dichloromethane. Coupling time for the cholesterol phosphoramidite was 16 minutes. 2. Deprotection- 1 (Nucleobase Deprotection)
After completion of synthesis, the support was transferred to a 100 ml glass bottle (VWR). The oligonucleotide was cleaved from the support with simultaneous deprotection of base and phosphate groups with 80 mL of a mixture of ethanolic ammonia [ammonia: ethanol (3: 1)] for 6.5h at 55°C. The bottle was cooled briefly on ice and then the ethanolic ammonia mixture was filtered into a new 250 ml bottle. The CPG was washed with 2 x 40 mL portions of ethanol/water (1: 1 v/v). The volume of the mixture was then reduced to ~ 30 ml by roto-vap. The mixture was then frozen on dry ice and dried under vacuum on a speed vac. 3. Deprotection-II (Removal of 2' TBDMS group)
The dried residue was resuspended in 26 ml of triethylamine, triethylamine
trihydrofluoride (TEA.3HF) or pyridine-HF and DMSO (3:4:6) and heated at 60°C for 90 minutes to remove the ie/t-butyldimethylsilyl (TBDMS) groups at the 2' position. The reaction was then quenched with 50 ml of 20mM sodium acetate and pH adjusted to 6.5, and stored in freezer until purification.
4. Analysis
The oligonucleotides were analyzed by high-performance liquid chromatography (HPLC) prior to purification and selection of buffer and column depends on nature of the sequence and or conjugated ligand.
5. HPLC Purification
The ligand conjugated oligonucleotides were purified by reverse phase preparative HPLC. The unconjugated oligonucleotides were purified by anion-exchange HPLC on a TSK gel column packed in house. The buffers were 20 mM sodium phosphate (pH 8.5) in 10% CH3CN (buffer A) and 20 mM sodium phosphate (pH 8.5) in 10% CH3CN, 1M NaBr (buffer B). Fractions containing full-length oligonucleotides were pooled, desalted, and lyophilized. Approximately 0.15 OD of desalted oligonucleotidess were diluted in water to 150 μΐ and then pipetted in special vials for CGE and LC/MS analysis. Compounds were finally analyzed by LC-ESMS and CGE.
6. RNAi Agent preparation
For the preparation of an RNAi agent, equimolar amounts of sense and antisense strand were heated in lxPBS at 95°C for 5 minutes and slowly cooled to room temperature. The integrity of the duplex was confirmed by HPLC analysis. Table 1 below reflects the RNAi agents which target human or rodent TTR mRNA.
Table 1: RNAi Agents and Results of In Vitro Screening
Figure imgf000085_0001
Figure imgf000086_0001
Figure imgf000087_0001
Figure imgf000088_0001
Figure imgf000089_0001
Figure imgf000090_0001
Figure imgf000091_0001
Figure imgf000092_0001
Figure imgf000093_0001
Figure imgf000094_0001
Figure imgf000095_0001
Figure imgf000096_0001
Figure imgf000097_0001
Figure imgf000098_0001
Figure imgf000099_0001
Figure imgf000100_0001
Figure imgf000101_0001
Figure imgf000102_0001
Figure imgf000103_0001
Figure imgf000104_0001
Figure imgf000105_0001
Figure imgf000106_0001
Figure imgf000107_0001
Figure imgf000108_0001
Figure imgf000109_0001
Figure imgf000110_0001
Figure imgf000111_0001
Figure imgf000112_0001
Figure imgf000113_0001
Figure imgf000114_0001
Figure imgf000115_0001
Figure imgf000116_0001
Figure imgf000117_0001
Figure imgf000118_0001
Figure imgf000119_0001
Figure imgf000120_0001
Figure imgf000121_0001
Figure imgf000122_0001
Figure imgf000123_0001
Figure imgf000124_0001
Figure imgf000125_0001
Lowercase nucleotides (a, u, g, c) are 2'-0-methyl nucleotides; Nf (e.g., Af) is a 2'-fluoro nucleotide; s is a phosphothiorate linkage; L96 indicates a GalNAc3 ligand.
Example 4: In vitro screening of RNAi Agents
Cell culture and transfections
Human Hep3B cells or rat H.II.4.E cells (ATCC, Manassas, VA) were grown to near confluence at 37 °C in an atmosphere of 5% C02 in RPMI (ATCC) supplemented with 10% FBS, streptomycin, and glutamine (ATCC) before being released from the plate by trypsinization. Transfection was carried out by adding 14.8 μΐ of Opti-MEM plus 0.2 μΐ of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad CA. cat # 13778- 150) to 5 μΐ of siRNA duplexes per well into a 96- well plate and incubated at room temperature for 15 minutes. 80 μΐ of complete growth media without antibiotic containing ~2 xl04 Hep3B cells were then added to the siRNA mixture. Cells were incubated for either 24 or 120 hours prior to RNA purification. Single dose experiments were performed at ΙΟηΜ and O. lnM final duplex concentration and dose response experiments were done using 8, 4 fold serial dilutions with a maximum dose of ΙΟηΜ final duplex concentration.
Total RNA isolation using DYNABEADS mRNA Isolation Kit (Invitrogen, part #: 610- 12)
Cells were harvested and lysed in 150 μΐ of Lysis/Binding Buffer then mixed for 5 minutes at 850rpm using an Eppendorf Thermomixer (the mixing speed was the same throughout the process). Ten microliters of magnetic beads and 80 μΐ Lysis/Binding Buffer mixture were added to a round bottom plate and mixed for 1 minute. Magnetic beads were captured using magnetic stand and the supernatant was removed without disturbing the beads. After removing the supernatant, the lysed cells were added to the remaining beads and mixed for 5 minutes. After removing the supernatant, magnetic beads were washed 2 times with 150 μΐ Wash Buffer A and mixed for 1 minute. Beads were capture again and supernatant removed. Beads were then washed with 150 μΐ Wash Buffer B, captured and supernatant was removed. Beads were next washed with 150 μΐ Elution Buffer, captured and supernatant removed. Beads were allowed to dry for 2 minutes. After drying, 50 μΐ of Elution Buffer was added and mixed for 5 minutes at 70°C. Beads were captured on magnet for 5 minutes. 40 μΐ of supernatant was removed and added to another 96 well plate.
cDNA synthesis using ABI High capacity cDNA reverse transcription kit (Applied Biosystems, Foster City, CA, Cat #4368813)
A master mix of 1 μΐ 10X Buffer, 0.4μ1 25X dNTPs, Ιμΐ Random primers, 0.5 μΐ Reverse Transcriptase, 0.5 μΐ RNase inhibitor and 1.6μ1 of H20 per reaction were added into 5 μΐ total RNA. cDNA was generated using a Bio-Rad C-1000 or S-1000 thermal cycler (Hercules, CA) through the following steps: 25 °C 10 min, 37 °C 120 min, 85 °C 5 sec, 4 °C hold.
Real time PCR
2μ1 of cDNA were added to a master mix containing 0.5μ1 GAPDH TaqMan
Probe (Applied Biosystems Cat #4326317E (human) Cat # 4308313 (rodent)), 0.5μ1 TTR TaqMan probe (Applied Biosystems cat # HS00174914 _ml (human) cat # Rn00562124_ml (rat)) and 5μ1 Lightcycler 480 probe master mix (Roche Cat
#04887301001) per well in a 384 well plate (Roche cat # 04887301001). Real time PCR was done in a Roche LC 480 Real Time PCR machine (Roche). Each duplex was tested in at least two independent transfections and each transfection was assayed in duplicate, unless otherwise noted.
To calculate relative fold change, real time data were analyzed using the AACt method and normalized to assays performed with cells transfected with lOnM AD-1955, or mock transfected cells. IC50S were calculated using a 4 parameter fit model using XLFit and normalized to cells transfected with AD-1955 (sense sequence:
cuuAcGcuGAGuAcuucGAdTsdT (SEQ ID NO: 2202); antisense sequence:
UCGAAGuCUcAGCGuAAGdTsdT (SEQ ID NO: 2203)) or naive cells over the same dose range, or to its own lowest dose. IC50S were calculated for each individual transfection as well as in combination, where a single IC50 was fit to the data from both transfections.
The results of gene silencing of the exemplary siRNA duplex with various motif modifications of the invention are shown in Table 1 above. Example 5: In vitro Silencing Activity of Chemically Modified RNAi Agents that Target TTR
The following experiments demonstrated the beneficial effects of chemical modifications, including the introduction of triplet repeat motifs, together with a GalNAc3 ligand, on the silencing activity of RNAi agents that target TTR. The sequences of the agents investigated are provided in Table 2 below. The regions of complementarity to the TTR mRNA are as follows: the region of complementarity of RNAi agents AD-45165, AD-51546 and AD-51547 is
GGATGGGATTTCATGTAACCAAGA (SEQ ID NO: 2204) and the region or complemetarity of RNAi agents AD-45163, AD-51544, and AD-51545 is
TTCATGTAACCAAGAGTATTCCAT (SEQ ID NO: 2205).
Protocol for assessment of ICsn in Hep3B cells
The IC50 for each modified siRNA was determined in Hep3B cells (a human hepatoma cell line) by standard reverse transfection using Lipofectamine RNAiMAX. In brief, reverse transfection was carried out by adding 5 μΐ^ of Opti-MEM to 5 μΐ^ of siRNA duplex per well into a 96-well plate along with 10 μΐ^ of Opti-MEM plus 0.5 μΐ^ of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad CA. cat # 13778-150) and incubating at room temperature for 15-20 minutes. Following incubation, 100 μΐ^ of complete growth media without antibiotic containing 12,000-15,000 Hep3B cells was then added to each well. Cells were incubated for 24 hours at 37°C in an atmosphere of 5% C02 prior to lysis and analysis of TTR and GAPDH mRNA by bDNA (Quantigene). Seven different siRNA concentrations ranging from ΙΟηΜ to 0.6pM were assessed for IC50 determination and TTR/GAPDH for siRNA transfected cells was normalized to cells transfected with ΙΟηΜ Luc siRNA. The results are shown in Table 2.
Protocol for assessment of free-uptake ICsn
Free uptake silencing in primary cynomolgus hepatocytes was assessed following incubation with TTR siRNA for either 4 hours or 24 hours. Silencing was measured at 24 hours from the initial exposure. In brief, 96-well culture plates were coated with 0.05 -0.1 collagen (Sigma C3867-1VL) at room temperature, 24 hours prior to the start of the experiment. On the day of assay, siRNAs were diluted in pre- warmed Plating Media consisting of DMEM supplemented with GIBCO' s Maintenance Media Kit (Serum-Free, Life Technologies CM4000), and added to the collagen-coated 96-well culture plates. Cryopreserved primary cynomolgus hepatocytes were rapidly thawed in a 37 °C water bath, and immediately diluted in Plating Media to a
concentration of 360,000 cells/mL. A volume of cell suspension was gently pipetted on top of the pre-plated siRNAs such that the final cell count was 18,000 cells/well. The plate was lightly swirled to mix and spread cells evenly across the wells and placed in a 37 °C, 5% C02 incubator for 24 hours prior to lysis and analysis of TTR and GAPDH mRNA by bDNA (Quantigene, Affymetrix). In the case of the 4h incubation with siRNA, the media was decanted after 4 hours of exposure to the cells, and replaced with fresh Plating Media for the remaining 20 hours of incubation. Downstream analysis for TTR and GAPDH mRNA was the same as described above. For a typical dose reponse curve, siRNAs were titrated from ΙμΜ to 0.24nM by 4 fold serial dilution. Table 2: In vitro Activity Summary for Alternating TTR-GalNAc and Variants with Triplet Motifs
Figure imgf000129_0001
Lowercase nucleotides (a, u, g, c) indicate 2'-0-methyl nucleotides; Nf (e.g., Af) indicates a 2'-fluoro nucleotide; s indicates a phosphothiorate linkage;
L96 indicates a GalNAc3 ligand; bold nucleotides indicate changes relative to the corresponding parent agent. Each bold nucleotide is at the center of a triplet motif.
The results are provided in Table 2 and demonstrate that modified RNAi agents that target TTR provide enhanced silencing activity.
Results: Improved Activity of Modified RNAi Agents
Parent RNAi agents with alternating chemical modifications and a GalNAc3 ligand provided an IC50 in Hep3B cells of about 0.01 nM. As shown in Figures 4-5 and in Table 2, agents modified relative to the parent agents, for example, by the addition of one or more repeating triplets of 2'-fluoro and 2'-0-methyl modifications, showed unexpectedly enhanced silencing activity, achieving IC50 values in Hep3B cells that were 5-8 fold better than the corresponding parent agent.
Results: Free Uptake ICsnS in Hep3B cells
As shown in Table 2 and Figures 6-7, RNAi agents modified relative to the parent AD-45163 also showed enhanced free uptake silencing. The modified agents showed more than double the silencing activity of the parent after a 24 hour incubation period and nearly 10 times the silencing activity of the parent after a 4 hour incubation period.
As shown in Table 2 and Figures 8-9, RNAi agents modified relative to the parent AD-45165 also showed enhanced free uptake silencing. The modified agents showed 2-3 times the silencing activity of the parent after a 24 hour incubation period and 5-8 times the silencing activity of the parent after a 4 hour incubation period.
Taken collectively, these results demonstrate that the modified RNAi agents presented herein, e.g., AD-51544, AD-51545, AD-51546, and AD-51547, all showed unexpectedly good inhibition of TTR mRNA in in vitro silencing experiments.
Example 6: TTR mRNA silencing and TTR Protein Suppression in Transgenic Mice
To assess the efficacy of the RNAi agents AD-45163, AD-51544, AD-51545, AD45165, AD-51546, and AD-51547, these agents were administered to transgenic mice that express human transthyretin with the V30M mutation (see Santos, SD., Fernaandes, R., and Saraiva, MJ. (2010) Neurobiology of Aging, 31, 280-289). The V30M mutation is known to cause familial amyloid polyneuropathy type I in humans. See, e.g., Lobato, L. (2003) J Nephrol, 16(3):438-42.
The RNAi agents (in PBS buffer) or PBS control were administered to mice (2 male and 2 female) of 18-24 months of age in a single subcutaneous dose of 5 mg/kg or 1 mg/kg. After approximately 48 hours, mice were anesthetized with 200 μΐ of ketamine, and then exsanguinated by severing the right caudal artery. Whole blood was isolated and plasma was isolated and stored at -80°C until assaying. Liver tissue was collected, flash-frozen and stored at -80°C until processing.
Efficacy of treatment was evaluated by (i) measurement of TTR mRNA in liver at 48 hours post-dose, and (ii) measurement of TTR protein in plasma at pre-bleed and at 48 hours post-dose. TTR liver mRNA levels were assayed utilizing the Branched DNA assays- QuantiGene 2.0 (Panomics cat #: QS0011). Briefly, mouse liver samples were ground and tissue lysates were prepared. Liver lysis mixture (a mixture of 1 volume of lysis mixture, 2 volume of nuclease-free water and lOul of Proteinase- K/ml for a final concentration of 20mg/ml) was incubated at 65 °C for 35 minutes. 20μ1 of Working Probe Set (TTR probe for gene target and GAPDH for endogenous control) and 80ul of tissue-lysate were then added into the Capture Plate. Capture Plates were incubated at 55 °C +1 °C (aprx. 16-20hrs). The next day, the Capture Plates were washed 3 times with IX Wash Buffer (nuclease-free water, Buffer Component 1 and Wash Buffer
Component 2), then dried by centrifuging for 1 minute at 240g. ΙΟΟμΙ of pre- Amplifier Working Reagent was added into the Capture Plate, which was sealed with aluminum foil and incubated for 1 hour at 55°C ±1°C. Following 1 hour incubation, the wash step was repeated, then ΙΟΟμΙ of Amplifier Working Reagent was added. After 1 hour, the wash and dry steps were repeated, and ΙΟΟμΙ of Label Probe was added. Capture plates were incubated 50 °C +1 °C for 1 hour. The plate was then washed with IX Wash Buffer, dried and ΙΟΟμΙ Substrate was added into the Capture Plate. Capture Plates were read using the SpectraMax Luminometer following a 5 to 15 minute incubation.bDNA data were analyzed by subtracting the average background from each triplicate sample, averaging the resultant triplicate GAPDH (control probe) and TTR (experimental probe) values, and then computing the ratio: (experimental probe-background)/(control probe- background).
Plasma TTR levels were assayed utilizing the commercially available kit "AssayMax Human Prealbumin ELISA Kit" (AssayPro, St. Charles, MO, Catalog # EP3010-1) according to manufacturer's guidelines. Briefly, mouse plasma was diluted 1: 10,000 in IX mix diluents and added to pre-coated plates along with kit standards, and incubated for 2 hours at room temperature followed by 5X washes with kit wash buffer. Fifty microliters of biotinylated prealbumin antibody was added to each well and incubated for 1 hr at room temperature, followed by 5X washes with wash buffer. Fifty microliters of streptavidin-peroxidase conjugate was added to each well and plates were incubated for 30 minutes at room temperature followed by washing as previously described. The reaction was developed by the addition of 50 μΐ/well of chromogen substrate and incubation for 10 minutes at room temperature with stopping of reaction by the addition of 50 μΐ/well of stop solution. Absorbance at 450 nm was read on a Versamax microplate reader (Molecular Devices, Sunnyvale, CA) and data were analyzed utilizing the Softmax 4.6 software package (Molecular Devices).
The results are shown in Figures 10-12. Figure 10 shows that the RNAi agents modified relative to the parent agents AD-45163 and AD-45165 showed RNA silencing activity that was similar or more potent compared with that of the parent agents. Figure 11 shows that the agents AD-51544 and AD-51545 showed dose dependent silencing activity and that the silencing activity of these agents at a dose of 5mg/kg was similar to that of the corresponding parent AD-45163. Figure 12 shows that the agents AD-51546 and AD-51547 also showed dose-dependent silencing activity. Furthermore, the silencing activity of AD-51546 and AD-51547 at a dose of 5mg/kg was superior to that of the corresponding parent AD-45165.
Example 7: Serum and Liver Pharmacokinetic Profiles of RNAi Agents that Target TTR in Mice
To assess the pharmacokinetic profiles of the RNAi agents AD-45163, AD-
51544, AD-51545, AD-51546, and AD-51547, these agents, in PBS buffer, were administered to C57BL/6 mice using a single IV bolus or subcutaneous (SC) administration. The plasma concentrations and liver concentrations of the agents were assessed at various timepoints after the administration. The plasma pharmacokinetic parameters are presented in Tables 3 and 4 below. The mean resident time (MRT) in plasma was about 0.2 hours after IV dosing and about 1 hour after SC dosing. At a dose of 25 mg/kg, the agents AD-51544, AD-51545, AD- 51546, and AD-51547 showed similar plasma pharmacokinetic properties. Each of these agents had more than 75% bioavailability from the subcutaneous space. Their bioavailability was superior to that of the parent agent AD-45163 that was administered at a higher dose of 30 mg/kg. The subcutaneous bioavailability of AD-51544 and AD- 51547 was about 100%, whereas that of AD-51545 was 90% and that of and AD-51546 was 76%.
Table 3: Summary of Plasma PK Parameter Estimates After SC Administration of TTR-GalNAc siRNAs in Mice
Figure imgf000133_0001
Table 4: Plasma siRNA PK Parameters in Mice after an IV Bolus or SC Dose of AD-51544, 51545, 51546 or 51547 at 25 mg kg
Figure imgf000134_0001
The results also indicated that the RNAi agents AD-45163, AD-51544, AD- 51545, AD-51546, and AD-51547 achieved similar or higher concentrations in the liver when administered subcutaneously than when administered by IV bolus. The liver pharmacokinetic parameters are presented in Tables 5 and 6 below. The peak concentration (Cmax) and area under the curve (AUCo-kst) in the liver were two to three times higher after subcutaneous administration as compared with IV administration of the same agent at the same dose. Liver exposures were highest for AD-51547 and lowest for AD-51545. The mean resident time (MRT) and elimination half-life were longer for AD-51546 and AD-51547 compared with AD-51544 and AD-51545.
Following subcutaneous administration, the approximate MRTs were 40 hours for AD- 51546 and 25 hours for AD-51547, whereas the MRTs for AD-51544 and AD-51545 were lower (about 6-9 hours). The elimination half life of AD-51546 and AD-51547 was also higher (41-53 hours) than was the elimination half life of AD-51544 and AD- 51545 (6-10 hours).
Table 5: Summary of Liver PK Parameter Estimates After SC Administration of TTR-GalNAc siRNAs in Mice
Figure imgf000136_0001
Table 6: Liver siRNA PK Parameters in Mice after an IV Bolus or SC Dose of AD-51544 51545, 51546 or 51547 at 25 mg/kg
Figure imgf000137_0001
Example 8: In vitro Stability of RNAi Agents in Monkey Serum
The serum stability of RNAi agents AD-51544, AD-51545, AD-51546, and AD- 51547 was also assessed in monkeys. The results demonstrated that the antisense and sense strands of AD-51544, AD-51545, and AD-51547 showed serum stability over a period of about 24 hours (data not shown).
Example 9: RNAi Agents Produce Lasting Suppression of TTR Protein in Non- Human Primates
The RNA silencing activity of RNAi agents AD-45163, AD-51544, AD-51545, AD-51546, and AD-51547 was assessed by measuring suppression of TTR protein in serum of cynomologous monkeys following subcutaneous administration of five 5 mg/kg doses (one dose each day for 5 days) or a single 25mg/kg dose. Pre-dose TTR protein levels in serum were assessed by averaging the levels at 11 days prior to the first dose, 7 days prior to the first dose, and 1 day prior to the first dose. Post-dose serum levels of TTR protein were assessed by determining the level in serum beginning at 1 day after the final dose (i.e. , study day 5 in the 5x5 mg/kg group and study day 1 in the 1x25 mg/kg group) until 49 days after the last dose (i.e., study day 53 in the 5x5 mg/kg group and study day 49 in the 1x25 mg/kg group). See Figure 13.
TTR protein levels were assessed as described in Example 6. The results are shown in Figures 14A and 14B and in Tables 7 and 8.
A maximal suppression of TTR protein of up to about 50% was achieved in the groups that received 25 mg/kg of AD-45163, AD-51544, AD-51546, and AD-51547 (see Table 8). A greater maximal suppression of TTR protein of about 70% was achieved in the groups that received 5x5 mg/kg of AD-45163, AD-51544, AD-51546, and AD-51547 (see Table 7). The agent AD-51545 produced a lesser degree of suppression in both administration protocols. Significant suppression of about 20% or more persisted for up to 49 days after the last dose of AD-51546 and AD-51547 in both the 1x25 mg/kg and 5x5 mg/kg protocols. Generally, better suppression was achieved in the 5x5 mg/kg protocol than in the 1x25 mg/kg protocol. Table 7 Fraction Serum Transthyretin Relative to Pre-dose in Cynomolgus Monkeys ( 5 mg/kg daily for 5 days)
Figure imgf000139_0001
Example 10: Tolerability of RNAi Agents that Target TTR
In Cytokine Evaluation in Whole Blood Assay
To assess the tolerability of RNAi agents that target TTR (including AD-45163, AD-51544, AD-51545, AD-51546, and AD-51547), each agent was tested in a whole blood assay using blood from three human donors. The agents were either 300 nM DOTAP transfected or 1 μΜ without transfection reagent (free siRNA). There was less than a two fold change for the following cytokines/chemokines: G-CSF, IFN-γ, IL-10, IL-12 (p70), ILip, IL-lra, IL-6, IL-8, IP-10, MCP-1, ΜΙΡ-Ια, ΜΙΡ-Ιβ, TNFa. (Results not shown).
In Vivo Evaluation
To assess in vivo tolerability, RNAi agents were injected subcutaneously in CD1 mice at a dose of 125 mg/kg. No cytokine induction was observed at 2, 4, 6, 24, or 48 hours after subcutaneous injection of AD-45163. No significant cytokine induction was observed at 6 or 24 hours after subcucutaneous injection of AD-51544, AD-51545, AD- 51546, or AD-51547.
To further assess in vivo tolerability, multiple RNAi agents (including AD- 45163, AD-51544, AD-51545, AD-51546, and AD-51547) were tested by subcutaneous injection of 5 and 25 mg in non-human primates (cynomologous monkeys) with dose volumes between 1-2 ml per site. No erythema or edema was observed at injection sites. Single SC Dose Rat Tolerability Study
To assess toxicity, rats were injected with a single subcutaneous dose of 100, 250, 500, or 750 mg/kg of AD-45163 (see Table 9). The following assessments were made: clinical signs of toxicity, body weight, hematology, clinical chemistry and coagulation, organ weights (liver & spleen); gross and microscopic evaluation (kidney, liver, lung, lymph node, spleen, testes, thymus, aorta, heart, intestine (small and large).
Table 9: Single SC Dose Rat Tolerability Study: 100, 250, 500 & 750 mg/kg of AD- 45163 in Sprague Dawley Rats
Figure imgf000141_0002
The results showed no test article-related clinical signs of toxicity, effects on body weight, organ weights, or clinical chemistry. No histopathology was observed in heart, kidneys, testes, spleen, liver, and thymus. There was a non-adverse, slight test article-related increase in WBC (†68 , primarily attributed to increase in NEUT and
MONO) at 750 mg/kg. These results indicate that a single-dose of up to 750 mg/kg is well tolerated in rats.
Tolerability of Repeated Subcutaneous Administrations in Rats
To assess the tolerability of repeated subcutaneous administrations of AD-45163, daily subcutaneous injections of 300 mg/kg were given for 5 days, and a necropsy was performed on day 6. The study design is shown in Table 10.
Table 10: Five Day Repeat Dose Tolerability Study in Rat
Figure imgf000141_0001
The following outcome variables were assessed: clinical signs, body weights, hematology, clinical chemistry and coagulation, organ weights, gross and microscopic evaluation (liver, spleen, kidney, heart, GI tract and first and last injection site). The results showed no test article-related clinical signs, body weight or organ weight effects, and also no test article -related findings in clinical hematology or chemistry. There was a possible slight prolongation of activated partial thromboplastin time (APTT) on day 6 (20.4 vs. 17.4 sec). Histopathology revealed no test article-related findings in the liver, spleen, heart, and GI tract. In the kidney, minimal to slight hypertrophy of the tubular epithelium (not adverse) was observed. At the last injection site, there was minimal multifocal mononuclear infiltration, not adverse. These results indicate that five daily 300 mg/kg doses of the parent RNAi agent AD-45163 are well tolerated in rats.
Example 11: RNAi Agents Produce Lasting Suppression of TTR Protein in Non- Human Primates
The RNA silencing activity of RNAi agent AD-51547 was assessed by measuring suppression of TTR protein in the serum of cynomologous monkeys following subcutaneous administration of a "loading phase" of the RNAi agent: five daily doses of either 2.5 mg/kg, 5 mg/kg or 10 mg/kg (one dose each day for 5 days) followed by a "maintenance phase" of the RNAi agent: weekly dosing of either 2.5 mg/kg, 5 mg/kg or 10 mg/kg for 4 weeks. Pre-dose TTR protein levels in serum were assessed by averaging the levels at 11 days prior to the first dose, 7 days prior to the first dose, and 1 day prior to the first dose. Post-dose serum levels of TTR protein were assessed by determining the level in serum relative to pre-dose beginning at 1 day after the loading phase was completed until 40 days after the last dose of the maintenance phase (i.e., study day 70).
TTR protein levels were assessed as described in Example 6. The results are shown in Figure 15.
A maximal suppression of TTR protein of up to about 80% was achieved in all of the groups that received either 2.5 mg/kg, 5 mg/kg or 10 mg/kg of AD-51547. Nadir knockdown was achieved in all of the groups by about day 14, the suppression sustained at nadir knockdown levels with a weekly maintenance dose of either 2.5 mg/kg, 5 mg/kg or 10 mg/kg of AD-51547. The levels of TTR had not returned to baseline more than 40 days after the day of administration of the last maintenance dose for the 5 and 2.5 mg/kg dose levels.
Example 12: Phase I Clinical Trial of AD-51547
A Phase I, randomized, double-blind, placebo-controlled, single and multi-dose, dose escalation study was conducted in normal healthy volunteers to evaluate the safety, tolerability, pharmacokinetics and pharmacodynamics of subcutaneously administered AD-51547 as described below.
Seven cohorts, as described below, were included in this study.
Cohorts 1-4, each including 4 male subjects, were administered subcutaneously a single dose of AD-51547 at 1.25 mg/kg, 2.5 mg/kg, 5.0 mg/kg, or 10 mg/kg.
Cohorts 5-7, each including 4 male subjects, were administered subcutaneously multiple doses of AD-51547. The schedule for multi-dose administration was a daily dose of AD-51547 at 2.5 mg/kg, 5.0 mg/kg, or 10 mg/kg for five days, followed by a single dose of AD-51547 at 2.5 mg/kg, 5 mg/kg, or 10 mg/kg once per week for five weeks.
The pharmacodynamic effect of ALN-TTRsc was followed through serial measurements of serum TTR
The median age of the subjects enrolled in the trial was 35 years of age (ranging in age from 25 to 47) and the mean serum TTR level at the time of study entry was 270 μ^πύ (+/- 47 μg/ml).
All treatment emergent adverse effects were mild or moderate in severity.
Injection site reactions were clinically mild. There were no study discontinuations, flulike symptoms, or changes in cytokines or CRP (Figures 16A-D), liver function tests or renal function (Figures 17A-D), or hematologic parameters.
The knockdown of TTR levels in the single dose cohorts and in the multi-dose cohorts, shown as a percent mean TTR knockdown relative to baseline, are shown in Figures 18 and 19, respectively.
Figure 20 shows the serum TTR knockdown by dose group.
In summary, multiple doses of AD-51547 were generally safe and well tolerated. There was no evidence of inflammation (cytokine, CRP), no evidence of abnormalities in liver function tests, renal function, or hematologic parameters, and transient erythema most common reaction at the injection site. As shown in Figures 18 and 19, the knockdown of serum TTR was greater than 80% and this level of knockdown was maintained at a dose of > 5 mg/kg of AD-51547 dosed weekly. There was statistically significant dose-dependent knockdown of serum TTR at doses of > 2.5 mg/kg. In addition, TTR knockdown was sustained for at least 14 days after the last dose of 2.5 and 5.0 mg/kg. Equivalents:
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments and methods described herein. Such equivalents are intended to be encompassed by the scope of the following claims.

Claims

We claim:
1. A method of treating or preventing a TTR- associated disease in a subject, comprising administering to said subject an RNAi agent at a dose of about 7.5 mg/kg, daily for five days, followed by a dose of about 7.5 mg/kg weekly for about five weeks, wherein the RNAi agent is a double stranded RNAi agent comprising a sense strand complementary to an antisense strand, wherein said antisense strand comprises a region complementary to part of an mRNA encoding transthyretin (TTR), wherein each strand has about 14 to about 30 nucleotides, wherein said double stranded RNAi agent is represented by formula (III):
sense: 5' np -Na -(X X X)rNb -Y Y Y -Nb -(Z Z Z¾ -Na - nq 3'
antisense: 3' np'-Na'-(X'X'X')k-Nb'-Y'Y'Y'-Nb'-(Z'Z'Z')i-Na'- nq' 5'
(III)
wherein:
i, j, k, and 1 are each independently 0 or 1;
p, p', q, and q' are each independently 0-6;
each Na and Na' independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;
each Nb and Nb' independently represents an oligonucleotide sequence comprising 0-10 nucleotides which are either modified or unmodified or combinations thereof;
each np, np', nq, and nq' independently represents an overhang nucleotide;
XXX, YYY, ZZZ, Χ'Χ'Χ', ΥΎΎ', and Z'Z'Z' each independently represent one motif of three identical modifications on three consecutive nucleotides;
modifications on Nb differ from the modification on Y and modifications on Nb' differ from the modification on Y'; and
wherein the sense strand is conjugated to at least one ligand, thereby treating or preventing said TTR-associated disease in said subject.
2. A method of treating or preventing a TTR-associated disease in a subject, comprising administering to said subject an RNAi agent at a dose of about 500 mg, daily for five days, followed by a weekly dose of about 500 mg, wherein the RNAi agent is a double stranded RNAi agent comprising a sense strand complementary to an antisense strand, wherein said antisense strand comprises a region complementary to part of an mRNA encoding transthyretin (TTR), wherein each strand has about 14 to about 30 nucleotides, wherein said double stranded RNAi agent is represented by formula (III):
sense: 5' np -Na -(X X X)rNb -Y Y Y -Nb -(Z Z Z¾ -Na - nq 3'
antisense: 3' np'-NaHX'X'X k-Nb'-YTT'-Nb'-(ZZ'Z')i-Na'- nq' 5'
(III)
wherein:
i, j, k, and 1 are each independently 0 or 1;
p, p', q, and q' are each independently 0-6;
each Na and Na' independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;
each Nb and Nb' independently represents an oligonucleotide sequence comprising 0-10 nucleotides which are either modified or unmodified or combinations thereof;
each np, np', nq, and nq' independently represents an overhang nucleotide;
XXX, YYY, ZZZ, Χ'Χ'Χ', ΥΎΎ', and Z'Z'Z' each independently represent one motif of three identical modifications on three consecutive nucleotides;
modifications on Nb differ from the modification on Y and modifications on Nb' differ from the modification on Y'; and
wherein the sense strand is conjugated to at least one ligand, thereby treating or preventing said TTR-associated disease in said subject.
3. The method of claim 1 or 2, wherein TTR expression in a sample derived from said subject is inhibited by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90%.
4. The method of claim 1 or 2, wherein said subject is a human.
5. The method of claim 1 or 2, wherein said subject is a subject suffering from a TTR-associated disease.
6. The method of claim 1 or 2, wherein said subject is a subject at risk for developing a TTR-associated disease.
7. The method of claim 1 or 2, wherein said subject carries a TTR gene mutation that is associated with the development of a TTR-associated disease.
8. The method of claim 1 or 2, wherein said TTR-associated disease is selected from the group consisting of senile systemic amyloidosis (SSA), systemic familial amyloidosis, familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy (FAC), leptomeningeal/Central Nervous System (CNS) amyloidosis, and hyperthyroxinemia.
9. The method of claim 1 or 2, wherein said subject has a TTR-associated amyloidosis and said method reduces an amyloid TTR deposit in said subject.
10. The method of claim 1 or 2, wherein said RNAi agent is administered to said subject by an administration means selected from the group consisting of subcutaneous, intravenous, intramuscular, intrabronchial, intrapleural, intraperitoneal, intraarterial, lymphatic, cerebrospinal, and any combinations thereof.
11. The method of claim 1 or 2, wherein said RNAi agent is administered to said subject via subcutaneous, intramuscular or intravenous administration.
12. The method of claim 1 or 2, wherein said RNAi agent is administered to said subject via subcutaneous administration.
13. The method of claim 12, wherein said subcutaneous administration is subcutaneous injection of the RNAi agent.
14. The method of claim 13, wherein the subcutaneous injection is at an anatomical location selected from the group consisting of the abdomen of the subject, the thigh of the subject, and the upper arm of the subject.
15. The method of claim 13 or 14, wherein the RNAi agent is administered to the subject as a split 500 mg dose at two different anatomical locations.
16. The method of claim 12, wherein said subcutaneous administration of the RNAi agent comprises administration via a subcutaneous pump or subcutaneous depot.
17. The method of claim 16, wherein said subcutaneous administration comprises administration via a subcutaneous infusion pump.
18. The method of claim 17, wherein the RNAi agent is administered to the subject as a single 500 mg dose.
19. The method of claim 18, wherein the RNAi agent is administered to the subject over a period of 5-20 minutes.
20. The method of claim 18, wherein the RNAi agent is administered to the subject over a period of 15 minutes or less.
21. The method of claim 2, wherein the RNAi agent is administered to the subject as a single 500 mg dose.
22. The method of claim 2, wherein the RNAi agent is administered to the subject as a split 500 mg dose.
23. The method of claim 2, wherein the weekly dose is administered to the subject chronically.
24. The method of claim 1 or 2, wherein said RNAi agent is administered to said subject, such that said RNAi agent is delivered to a specific site within said subject.
25. The method of claim 24, wherein said site is selected from the group consisting of liver, choroid plexus, retina, and pancreas.
26. The method of claim 24 wherein said site is the liver.
27. The method of claim 24, wherein delivery of said RNAi agent is mediated by an asialoglycoprotein receptor (ASGP-R) present in hepatocytes.
28. The method of claim 1 or 2, further comprising assessing the level of
TTR mRNA expression or TTR protein expression in a sample derived from the subject.
29. The method of claim 1 or 2, wherein administering said RNAi agent does not result in an inflammatory response in said subject as assessed based on the level of a cytokine or chemokine selected from the group consisting of G-CSF, IFN-γ, IL-10, IL- 12 (p70), ILip, IL-lra, IL-6, IL-8, IP-10, MCP-1, ΜΙΡ-Ια, ΜΙΡ-Ιβ, TNFa, and any combinations thereof, in a sample from said subject.
30. The method of claim 1 or 2, wherein said RNAi agent is administered using a pharmaceutical composition.
31. The method of claim 30, wherein said siRNA is administered in an unbuffered solution.
32. The method of claim 31, wherein said unbuffered solution is saline or water.
33. The method of claim 32, wherein said unbuffered solution is sterile water.
34. The method of claim 33, wherein said RNAi agent is administered as a solution of 200 mg/ml of RNAi agent.
35. The method of claim 30, wherein said siRNA is administered with a buffer solution.
36. The method of claim 35, wherein said buffer solution comprises acetate, citrate, prolamine, carbonate, or phosphate or any combination thereof.
37. The method of claim 36, wherein said buffer solution is phosphate buffered saline (PBS).
38. The method of claim 30, wherein said pharmaceutical composition is a liposome.
39. The method of claim 1 or 2, wherein i is 1; j is 1; or both i and j are 1.
40. The method of claim 1 or 2, wherein k is 1; 1 is 1; or both k and 1 are 1.
41. The method of claim 1 or 2, wherein XXX is complementary to X'X'X', YYY is complementary to ΥΎΎ', and ZZZ is complementary to Z'Z'Z'.
42. The method of claim 1 or 2, wherein the YYY motif occurs at or near the cleavage site of the sense strand.
43. The method of claim 1 or 2, wherein the ΥΎΎ' motif occurs at the 11, 12 and 13 positions of the antisense strand from the 5 '-end.
44. The method of claim 43, wherein the Y' is 2'-0-methyl.
45. The method of claim 1 or 2, wherein formula (III) is represented as formula (Ilia):
sense: 5' np -Na - Y Y Y -Nb -Z Z Z -Na-nq 3'
antisense: 3' np'-Na'-Y'Y'Y'-Nb'-Z'Z'Z'-Na'nq' 5'
(Ilia)
wherein each Nb and Nb' independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides.
46. The method of claim 1 or 2, wherein formula (III) is represented as formula (Illb):
sense: 5' np-Na-X X X -Nb-Y Y Y -Na-nq 3'
antisense: 3' np'-Na'-X'X'X'-Nb'-YYY'-Na'-nq' 5'
(nib) wherein each Nb and Nb' independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides.
47. The method claim 1 or 2, wherein formula (III) is represented as formula (IIIc):
sense: 5' np-Na-X X X -Nb-Y Y Y -Nb-Z Z Z -Na-nq 3'
antisense: 3' np'-Na'-X'X'X'-Nb'-Y'Y'Y'-Nb'-Z'Z'Z'-Na'-nq' 5'
(IIIc)
wherein each Nb and Nb' independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides and each Na and Na' independently represents an oligonucleotide sequence comprising 2-10 modified nucleotides.
48. The method of claim 1 or 2, wherein the duplex region is 15-30 nucleotide pairs in length.
49. The method of claim 48, wherein the duplex region is 17-23 nucleotide pairs in length.
50. The method of claim 48, wherein the duplex region is 17-25 nucleotide pairs in length.
51. The method of claim 48, wherein the duplex region is 23-27 nucleotide pairs in length.
52. The R method of claim 48, wherein the duplex region is 19-21 nucleotide pairs in length.
53. The method of claim 51, wherein the duplex region is 21-23 nucleotide pairs in length.
54. The method of claim 1 or 2, wherein each strand has 15-30 nucleotides.
55. The method of claim 1 or 2, wherein the modifications on the nucleotides are selected from the group consisting of LNA, UNA, CRN, cEt, HNA, CeNA, r-methoxyethyl, 2'-0-alkyl, 2'-0-allyl, 2'-C- allyl, 2'-fluoro, 2'-deoxy, 2'- hydroxyl, and combinations thereof.
56. The method of claim 55, wherein the modifications on the nucleotides are 2 -0-methyl,2'-fluoro or both.
57. The method of claim 1 or 2, wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker. e ligand is
Figure imgf000152_0001
59. The method of claim 1 or 2, wherein the ligand is attached to the 3' end of the sense strand.
60. The method of claim 59, wherein the RNAi agent is conjugated to the ligand as shown in the following schematic
Figure imgf000152_0002
wherein X is O or S.
61. The method of claim 60, wherein the RNAi agent is conjugated to the ligand as shown in the following schematic
Figure imgf000153_0001
62. The method of claim 1 or 2, further comprising at least one
phosphorothioate or methylphosphonate internucleotide linkage.
63. The method of claim 62, wherein the phosphorothioate or
methylphosphonate internucleotide linkage is at the 3 '-terminal of one strand.
64. The method of claim 63, wherein said strand is the antisense strand.
65. The method of claim 63, wherein said strand is the sense strand.
66. The method of claim 1 or 2, wherein the base pair at the 1 position of the 5 '-end of the antisense strand of the duplex is an AU base pair.
67. The method of claim 1 or 2, wherein the Y nucleotides contain a 2'- fluoro modification.
68. The method of claim 1 or 2, wherein the Y' nucleotides contain a 2'-0- methyl modification.
69. The method of claim 1 or 2, wherein p'>0.
70. The method of claim 1 or 2, wherein p -2.
71. The method of claim 70, wherein q'=0, p=0, q=0, and p' overhang nucleotides are complementary to the target mRNA.
72. The method of claim 70, wherein q'=0, p=0, q=0, and p' overhang nucleotides are non-complementary to the target mRNA.
73. The method of claim 70, wherein the sense strand has a total of 21 nucleotides and the antisense strand has a total of 23 nucleotides.
74. The method of any one of claims 69-73, wherein at least one np' is linked to a neighboring nucleotide via a phosphorothioate linkage.
75. The method of claim 74, wherein all np' are linked to neighboring nucleotides via phosphorothioate linkages.
76. The method of claim 1 or 2, wherein the RNAi agent is selected from the group of RNAi agents listed in Table 1.
77. The method of claim 1 or 2, wherein the RNAi agent is selected from the group consisting of AD-51544, AD-51545, AD-51546, and AD-51547.
78.The method of claim 77, wherein the RNAi agent is AD-51547.
79. A method of treating or preventing a TTR-associated disease in a subject, comprising administering to said subject an RNAi agent at a dose of about 500 mg, daily for five days, followed by a weekly dose of about 500 mg, wherein the RNAi agent is AD-51547, thereby treating or preventing said TTR-associated disease in said subject.
80. The method of claim 79, wherein said subject is a human.
81. The method of claim 79, wherein said subject is a subject suffering from a TTR-associated disease.
82. The method of claim 79, wherein said subject is a subject at risk for developing a TTR-associated disease.
83. The method of claim 79, wherein said subject carries a TTR gene mutation that is associated with the development of a TTR-associated disease.
84. The method of claim 79, wherein said TTR-associated disease is selected from the group consisting of senile systemic amyloidosis (SSA), systemic familial amyloidosis, familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy (FAC), leptomeningeal/Central Nervous System (CNS) amyloidosis, and hyperthyroxinemia.
85. The method of claim 79, wherein said subject has a TTR-associated amyloidosis and said method reduces an amyloid TTR deposit in said subject.
86. The method of claim 79, wherein said RNAi agent is administered to said subject via subcutaneous administration.
87. The method of claim 86, wherein said subcutaneous administration of the RNAi agent is subcutaneous injection of the RNAi agent.
88. The method of claim 87, wherein the subcutaneous injection is at an anatomical location selected from the group consisting of the abdomen of the subject, the thigh of the subject, and the upper arm of the subject.
89. The method of claim 87 or 88, wherein the RNAi agent is administered to the subject as a split 500 mg dose at two different anatomical locations.
90. The method of claim 86, wherein said subcutaneous administration comprises administration via a subcutaneous pump or subcutaneous depot.
91. The method of claim 90, wherein said subcutaneous administration comprises administration via a subcutaneous infusion pump.
92. The method of claim 91, wherein the RNAi agent is administered to the subject over of period of 5-20 minutes.
93. The method of claim 92, wherein the RNAi agent is administered to the subject over of period of 15 minutes or less.
94. The method of claim 2, wherein the RNAi agent is administered to the subject as a single 500 mg dose.
95. The method of claim 79, wherein said RNAi agent is administered to the subject as a split 500 mg dose.
96. The method of claim 79, wherein the weekly dose is administered to the subject chronically.
97. A kit for performing the method of claim 1, comprising
a) said RNAi agent, and
b) instructions for use, and
c) optionally, means for administering said RNAi agent to said subject.
98. A kit for performing the method of claim 2, comprising
a) said RNAi agent, and
b) instructions for use, and
c) optionally, means for administering said RNAi agent to said subject.
99. A kit for performing the method of claim 79, comprising
a) said RNAi agent, and
b) instructions for use, and
c) optionally, means for administering said RNAi agent to said subject.
100. The kit of claim 98 or 99, wherein said RNAi agent is present in said kit as a 200 mg/ml solution of the RNAi agent in sterile water.
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