CA2147593C

CA2147593C - Dual purpose tissue fixative

Info

Publication number: CA2147593C
Application number: CA002147593A
Authority: CA
Inventors: Hyman C. Birnboim
Original assignee: Cancer Care Ontario
Current assignee: Cancer Care Ontario
Priority date: 1994-04-22
Filing date: 1995-04-21
Publication date: 2008-07-29
Anticipated expiration: 2015-04-21
Also published as: US5976829A; CA2147593A1

Abstract

A dual purpose tissue fixative is described. The fixative comprises a cross-linking aldehyde, alcohol, a chelating agent and a non-amine buffer. More particularly, the tissue fixative comprises 0.1-2 % w/v formaldehyde, 45-90% w/w alcohol, 1-10 mM of a chelating agent and 1-50 mM of a non-nitrogen buffer. The tissue fixative permits the recovery of high molecular weight DNA and RNA from the tissue sample for molecular genetic analysis. The tissue fixative also preserves the morphology and immunogenicity of the tissue allowing for pathology analysis. The tissue fixative is compared to 95% alcohol and a standard fixative such as 10% BNF.

Description

DUKL PURPOSE ~_'i SSUL F':, :~?'!'--, VE
FTjLD OF THL TNVFbI?'TON

The present inventiorl relates to a dual purpose tissue f i:=at 1.*vG, TTie t issue f i3:at i ve permit s the recovery of h'i gh rriolGcular weight nucleic acids (DNA and RNA) frorn the tissue sample for molecular geriet ic analys 1s. The f'i1.at ive also preserves the morphology ai',a immunogenicity of the t'lssue allowing for pathology analysis.

Lr3VL'PITTOhT .
BACKGROUND OF T'I49 The analysis of tissue samples removed at surgery or aut opsy can reveal important clues in our understanding of various pathological states. For example, the .analys.is of the DNA obtained from tumor biopsy can provide valuable insight into the genetic defects that underlie malignant transformation. Freshly obtained sample.s must immediately be stored in a t is sue f ipat ive in order to prevent decompos it i on .
The. ideal f ixat ive should ( i)_permit recovery of high .molecular weight nucleic acids (DNA and RNA) from the sample for molecular analysis and -(ii) preserve the morphology and immunogenicity of specimens allowing routine anat onrical patholog,y investigation.

A commonly used fixative i.s 10% buffered neutral formalin (B1-qF) Samples stored in 'BNF are adeguate for p?thology analysis. However BNF degrades nucleic acids and thereforp samples are not useful for the extraction of high molecular weight.DNA or RNA. Solutions of 95% ethanol have been shown to b.e..effect ive in preserving DNA in a iimited.. number of _ , _ cases. However, samples stored in 95% ethanol are not sat isfactory for the pathologist. Consequently, when one wants to obtain samples for both DNA extraction and pathology it is necessary to talre the fresh biopsy sample and store part of it in BNF and another part in, for example, liquid nitrogen. This conventional method requires that a technician is on call during surgery in order to properly store the s arrip l e .

Ttierefore, in view of the foregoing it is desirable to develop a tissue fixative that permits the recovery, weeks or even months after fixation, of high molecular weight nucleic acids for molecular genetic analysis, while at the same time preserving the morphology of the sample for analysis by the pathologist.

SU)-IMARY OF TFir INVENTION

The present invention solves the problem of the prior art fixatives as it allows the recovery of substantially intact nucleic acids (both DNA and RNA) from a tissue sample and also adequately preserves the sample for pathological analysis.

In particular, the present invention provides a tissue fixative comprising:

- a cross-linking aldehyde;
- alcohol;

- a chelating agent; and - a non-nitrogen containing buffer.

More particularly, the tissue fixative comprises about:

79683-i - 0.1-2% w/v formaldehyde;
- 45-90% w/w alcohol;

- 1-10 mM of a chelating agent; and - 1-50 mM of a non-nitrogen-containing buffer.

The aldehyde is selected from those capable of cross-linking proteins. The aldehyde itiay be selected from, for exaniple, formaldehyde, gluteraldehyde, and the like.

The alcohol is preferably a.low molecular weight alcohol such as methanol or ethanol. The alcohol may also be composed of a mixture of two or more alcohols. In a preferred embodiment, the alcohol is methanol.

The chelating agent is preferably one that is soluble in alcohol and has a high affinity for divalent cations in 'tissue. A preferred chelating agent is trans-l-2-diamiriocyclohexane-N,N,N',N'-tetraacetic acid (CDTA).

The non-nitrogen containing buffer is preferably a phosphate buffer such as potassium or sodium phosphate or mixtures thereof. The buffer should act to control the pH of the tissue sample during fixation. In a preferred embodiment, the buffer maintains the pH of the sample from about 6.0 to about 8.5, since acidic agents can cause depurination and breakdown of the nucleic acids. More preferably, the buffer should maintain the sample at a pH of about 7.3.

In a more preferred embodiment, the tissue fixative comprises about:

- 0.75% w/v formaldehyde;
- 55% w/w methanol;

- 5 mM trans-1-2-diaminocyclohexane-N,N,N1,Nl-tetraacetic acid (GD't'A) ; and -15 mM potassium phosphate and 15.8 mM sodium phosphate as buffer.

BRIEF DESCRIPTICN OF THE DRATn1INGS

Figure 1 represents agarose gels showing the comparison of the high molecular weight DNAs and their EcoRl sensitivity when extracted from a colonic adenocarcinoma and variously fixed for different time periods.

Figure 2 represents agarose gels illustrating a Ki-ras gene fragment obtained by PCR amplification of DNA extracted from rectal mucosa specimens that were fixed for four months in various fixatives.

Figure 3 represents agarose gels showing the total nucleic acid extracted from rat livers fixed for four weeks in the fixative of the present invention after various extraction procedures.

Figure 4A represents agarose gels showing DNA extracted from samples fixed in 10% BNF, at various time points.

Figure 4B represents agarose gels showing DNA extracted from samples fixed in the fixative of the invention, at various time 2 0 points.

Figure 5 represents a resected segment of a human colon fixed in the fixative of the present invention.

Figure 6 represents stained sections of an invasive carcinoma of the colon. Figure 6A represents a sample fixed in 10%
BNF and Figure 6B represents a sample fixed in the fixative of the present invention.

DETAILED DESCRIPTION OF THE INVENTION
E~cample 1 Preparat 9.on of Pref erred Fixative The preparation of a preferred tissue f ixat ive according to the present invention is described below. Each of the components of the fixative may be obtained for example as described below:

1) 10% neutral buffered formalin, Anacxiemia Cat. No.
R2400.

(Compositionl1000 ml : 100 ml of 37% formaldehyde, 4 g sodium phosphate monobasic, 6.5 g sodium phosphate dibasic) 2) Methanol, Fisher Cat. No. A412B.

3) CDTA, Sigma Cat. No. D1383, Trans-1-2-diaminocyclohexane- N,N,N',N'-tetraacetic acid, F.W.
34.6.3.

4) Potassium phosphate, dibasic, anhydrous. K2HPO4,F.W.
174.18, Fisher, Cat. No. P-288.

The CDTA chelator and potassium phosphate buffer are first prepared together as follows:

1) Add 3 L of ddH2O to a 4 L Winchester, with glass funnel.

2) Weigh out 53.56 g of K2HPO4 and 35.5 g CDTA in plastic weighing boats. Transfer to Winchester with powder funnel. Rinse funnel and weighing boats with 1.1 L
ddH2O

into Winchester.

3) Cap and shake by hand until all solute dissolves.
4) Measure pH of a 5 mL saniple of solution.

This combined solution is designated "CKP".

The tissue fixative is prepared in a 40 L carboy as follows:

1) Add 24 L Methanol, to the 24 L mark.

2) Add 8 L of 10% neutral buffered formalin, using a 2 L
cylirider.

3) Add 8 L CKP solution using a 2 L cylinder.
4) Mix with a stirring paddle for 3 min.

5) Remove 25 mL and dilute with 25 mL water. Save for xneasurement of pH using pH meter within 1 hour.
Final Concentrations:

Methanol 55% (w/w) Formaldehyde 0.75% (w/v) Y2HPO4 15.0 mM

Na phosphate 15.8 mM
CDTA 5 mM

Final pH of 1; 1 dilution in water = 7.3 Preparation of Other Fixatives Several other fixatives according to the present invention were also prepared. The stock reagents used were as follows:

1. 6.7 M Formaldehyde. Commercial "37V formaldehyde is 13.3 M in 10-14$ methanol. Immediately before use, dilute 12.5 triL of 13.3 N formaldehyde in 12.5 mL of water to make 6.7 M
formaldehyde. Boil geritly in a 60 mL Erlenmeyer flaslc in the fume hood for 5 min to degrade paraformaldehyde. Cool to room temperature.

2. Met hano l .
3. Ethanol.

4. DMF. Dimethylformamide.

5. CDTA (0.5 M, pH 7.0). Chelating agent. Cyclohexane diamine-tetraacetate.

6. Phosphate buffer. pfl 6.8. Prepared by mixing equal volumes of 1 M NaH2PO4 and 1 M Na2HPO4.

7. Postassium phosphate dibasic buffer. K2HPO4.

The various fixatives shown in Table 1 were prepared by mixing the stock solutions according to the procedure in Example 1. The resulting concentrations of each of the components are shown in Table 1. These fixatives were tested and shown to be useful.

Example 3 Comparison of Dual Purpose Fixative With Other Fixatives The integrity of the DNA extracted from Duke's B3 colonic adenocarcinoma was compared from samples fixed in the tissue fixative prepared in Example 1 versus samples fixed in 95%
alcohol or 10% BNF. Samples of surgically removed carcinoma were placed in each of the three fixatives. DNA was extracted from the samples at 3 days and at 8 months. The DNA was extracted using a method developed by the present inventor and described iri Methods in Enzymology (1992) 216:154-159.
Briefly, the DHA is extracted using proteinase K digestion and phenol-chloroform extraction in the presence of an amine.
Portions of the DNA. were digested with the restriction enzyme EcoRl. One microgram of the DNA was applied to a 0.8% agarose gel in 40 mM Tris buffer containing 20 mM sodium acetate, 1 mM
CDTA. The results are shown in Figure 1 in which:

Larze 1 contains molecular weight markers.

Lane 2 contains DNA extracted from an unfixed sample.
Lane 3 contains DNA digested with EcoRl.

Lane 4 contains DNA extracted from a sample fixed in ettianol for three days.

Lane 5 contains DNA extracted from a sample fixed with ethanol for three days and digested with EcoRl.

Lane 6 contains DNA extracted from a sample fixed with the Example 1 f ixat ive for three days.

Lane 7 contains DNA extracted from a sample fixed with the Example 1 fixative for three days and digested with EcoRl.

Lane 8 contains DNA extracted from a sample fixed with formaliri for three clays.

Larie 9 contains DNA extracted from a sample fixed with formalin for three days arid digested with EcoRl.

Lane 1 0 contains DNA ext ract ed from a sample fixed in ethanol for eight months.

Lane 11 contains DNA extracted from a sample fixed with ethanol for eight months and digested with EcoR1.

Lane 12 contains DNA extracted from a sample fixed with the Example 1 f ixat ive for eight months.

Lane 13 contains DNA extracted from a sample fixed with the Example 1 fixative for eight months and digested with EcoRl.

Lane 14 contains DNA ext ract ed from a sample fixed with formalin for eight months.

Lane 15 contains DNA extracted from a sample fixed with formalin for eight months and digested with EcoRl.

The results indicate that DNA extracted from a sample fixed in the Example 1 fixative shows a similar profile as DNA
extracted from samples fixed in ethanol. Both yield high molecular weight, EcoRl digestible DNA. Samples fixed in BNF
clearly demonstrate extensive DNA degradation.

Example 4 PCR Amplification of the Ki-ras Oncogene from DNA Extracted from Fixed Samples Portions of a surgically obtained rectal mucosa were fixed in each of the Example 1 fixative, 10% BNF and ethanol for four months. DNA was extracted from each sample as described in Exaniple 3. The extracted DNA was subJected to 30 cycles of PCR amplification with primers for the Ki-ras cellular oncogene.

The results, shown in Figure 2, demonstrate that DNA
extracted from samples fixed in the Example 1 fixative are ameriabl.e to PCR amplification as evidenced by the presence of the 174 bp I:i- ras oncogene in the sample. Samples fixed in BNF did not yield any PCR amplification product.

Example 5 Total Nucleic Acid Analysis of Fixed Rat Livers An intact rat liver was fixed for four weeks in the Example 1 fixative. Two hundred mg wet weight portions were removed and the DNA was extracted by 3 variations of the nucleic acid extraction procedure. The extraction procedures differed with respect to the pH of the extracting solution.
Solution 1 had a pH of 7.2, solution 2 had a pH of 8.0 and solution 3 had a pH of 6.8. The extracted nucleic acid was applied to a 1.2% agarose gel in 10 mM phosphate buffer in triplicate. The results are shown in Figure 3. Lanes 1-6 represents samples extracted in solution 1, Lanes 7-9 represent samples extracted in solution 2 and Lanes 10-12 represents samples extracted in solution 3. The top band in each sample represents DNA, while the lower two bands represent RNA. The results indicate that nucleic acids, includincx RNA, can be extracted for up to four weeks after t issue f ixat ion iri tt-ie Example 1 f ixat ive . Ext ract iria the nucleic acids at a pH between about 6.5 and 7.0 is optimal for the ext ract ion of RNA f r. om the samples.

79n8s-1 Exampl e 6 Comparison of the Present Fixative and 10% BNF on D1IA
Dearadation Samples of a modified Duke's C2 colonic adenocarcinoma were placed in the Example 1 fixative or in 10% BNF. At various time points, DNA was extracted from the samples as described previously. The samples were electrophoresecl on an agarose gel as shown in Figure 4. Figure 4A represents DNA
from samples fixed in 10% BNF and Figure 4B represent DNA from samples fixed in the Example 1 fixative. The lanes are as follows:

Lane 1: phage DNA Hind III digest Lane 2: DNA ext ract ed from a sample fixed f o r 3 days Lane 3: DNA extracted from a sample fixed for 1 week Lane 4: DNA extracted from a sample fixed for 2 weeks Lane 5; DNA extracted from a sample fixed for 1 month Lane 6: DNA ext ract ed from a sample fixed for 2 months Lane 7: DNA extracted from a sample fixed for 4 months Lane 8: DNA ext ract ed from a sample fixed f o r 8 months (F1g.4B only) The results indicate that DNA obtained from samples fixed in 10% BNF was extensively degraded after one week in the fixative. On the other hand, the DNA extracted from samples fixed in the present fixative remained intact for several mont hs .
Example 7 Pathological Analysis of Samples fixed in the Present Fixative A resected segment of a human colon was fixed for 1 week in the E ample 1 fixative and photographed as shown in Figure 5. The photograph demonst rat es that a sample fixed in the fixative according to the invention appears as if it was freshly resected. In contrast, it is known that samples fixed in formaldehyde turn grey in color. Samples fixed in alcohol have the disadvantage that they become brittle and difficult to handle. The results of Figure 5 show that samples fixed In the fixative according to the invention better maintain the gross morphological properties of the tissue.

Example 8 Comr)arison of Tissue Sections Fixed with the Present Fixative versus 10% BNF

Haematoxylin and eosin stained sections of an invasive carcinoma of the colon had been fixed in either 10% BNF or the Example 1 fixative. The results are shown in Figure 6 wherein Figure 6A represents tissue fixed in 10% BNF and Figure 6B
represents tissue fixed in the Example 1 fixative. The results illustrate that samples fixed in the Example 1 fixative are indistinguishable histologically from sections preserved in BNF.

Example 9 Immunoreactivity Profile of Tissue Fixed in Various Fixatives A human colorectal cancer sample was portioned and separate samples were fixed in each of 10% BrdF, ethanol and the Example 1 fixative. The samples were fixed from periods ranging from three days to two months. The samples were tested for tY--e presences of various antigens using commercially available antibodies. The results, shown in Table 2, iridicate that samples fixed in the Example 1 fixative show similar immunoreactivity profiles. Furthermore, the immurioreactivity compared favourably with that obtained in samples fixed in alcohol. based fixatives, such as Carnoys.

Example 10 Quant itat ion of DNA Obtained from Samples Samples of a human colorectal cancer and an ulcerative colitis were stored in either the Example 1 fixative or 10%
BNF. DNA was extracted from the samples as described previously. The amount of DNA was determined spectrophotometrically. The results, shown in Table 3, demonstrate that the total recovery of DNA is greater from samples fixed in the Example 1 fixative versus samples fixed in 10% BNF.

SummarY

The above experiments demonstrate that the fixative according to the present invention is capable of preserving the DNA and RNA in tissue samples for up to several months or longer. The results also indicate that samples fixed in the present fixative are morphologically similar to freshly ,'9n8~'-1 obtained samples and are useful for analysis by the pathologlst.

While the above described examples 3-10 use the fixative as prepared in Example 1, it is to be appreciated that various modifications can be made to the tissue fixative and still be within the scope of the present invention. For example, the percentages of the various components can be varied as described irl Example 2 and still produce a useful fixative. Furthermore, additional ingredients such as dimethylformamide, formamide, dimethylsulfoxide or ethylene glycol may also be added to the fixative. Other additives may include low concentrations of detergents or other organic solvents.

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a z s_ ~=Q o E' O v o d xa Xd x xUaxin g w w -.a - N K7 1f) p a N JSCaCQ.>=uM~c,W) QUANTlTAT1ON OF PURE, HIGH MOLECULAR WEIGHT DNA
FROM HUMAN LARGE BO1i10E1. (SURGICAL SAMPLES) EDA9PAR/SON OF E'XAMPLE / FOXATIVE AlVD /0 % BNF F/XAT/VE

DNA Recovered ( g/mg wet weight)a Clinical Diagnosis (specimen) lExomple I Fixative 10% BNFb 1. Colorectal cancer Normal tissue 1.99 0.26 (n=10)' 1..16 0.30 (n=4)2 Malignant tumour 3.60 0.29 (n=18)4 1.88 0.18 (n=12)',3 2. Ulcerative colitis Normal tissue 2.35 0.20 (n=12)' 1.45 0.09 (n=4)2 Involved tissue 3.14 0.21 (n=1 1)42.26 0.30 (n.=4)1=3 Averages All samplesc 2.89 0.16 (n=51)5 1.75 0.13 (n=24)6 Statistical comparisons. Unlike superscripts denote statistically significant differences within each diagnostic group.

b 10%BNF = 10% Buffered Neutral Formalin fixative.

Recovery of DNA from Example I fixed tissue greater than from 10% BNF
fixed tissue (p 0.005).

Claims

1. A tissue fixative comprising:

a protein cross-linking aldehyde;
alcohol;

CDTA as a chelating agent; and a phosphate buffer.

2. A tissue fixative according to claim 1 comprising:
about 0.1-2% w/v of the aldehyde;

alcohol;
about 1-10 mM of the CDTA chelating agent; and about 1-50 mM of the phosphate buffer.

3. A tissue fixative according to claim 1 comprising:
0.75% w/v formaldehyde;

55% w/v methanol;

mM of the CDTA chelating agent; and mM potassium phosphate and 15.8 mM sodium phosphate as the buffer.

4. A tissue fixative according to claim 1 or 2, wherein the pH is approximately 6.0-8.5.

5. A tissue fixative according to any one of claims 1 to 3, wherein the pH is approximately 7.3.