Analysis of DNA in fresh and fixed tissue by the polymerase chain reaction.

The polymerase chain reaction (PCR) was used to amplify viral or oncogene sequences from frozen or formalin-fixed, paraffin-embedded tissue sections. Methods for preparing fixed, embedded colonic tissue for PCR amplification of c-K-ras sequences from genomic DNA and for amplification of viral DNA from other tissues, including brain, lung, and liver, were evaluated. The effect of formalin fixation on the efficiency of amplification was also determined. While there seemed to be only a modest variation in the efficiency of the PCR for amplification of single-copy human genes, regardless of the methods used for tissue preparation, amplification of viral DNA sequences against a human genomic DNA background was more efficient when the DNA was purified to some degree before amplification of the tissue. We used the PCR to examine frozen and fixed embedded tissue sections for the presence of Epstein-Barr virus (EBV) and cytomegalovirus (CMV) DNA. One patient with a heart-lung transplant succumbed to a lymphoproliferative disorder, and EBV genome was present in tissues with abnormal lymphoid infiltrates. CMV was also present in bronchial lavages from the same patient, where cytologic diagnosis was not apparent. Another patient with a liver transplant showed CMV genome in multiple liver biopsies, with negative histologic results for CMV. In vitro DNA amplification with the PCR demonstrated sensitivity superior to that of histology in detecting CMV and EBV in the cases examined.     

PCR detection of HIV proviral DNA (gag) in the brains of patients with AIDS: comparison between results using fresh frozen and paraffin wax embedded specimens.

AIMS--To adapt the polymerase chain reaction (PCR) technique of HIV detection to paraffin wax embedded brain tissue and to compare the results with those obtained using frozen tissue. METHODS--HIV antigen and HIV proviral DNA were detected in specimens of frontal lobe using immunohistochemistry and PCR, respectively. DNA was extracted from fresh tissue using standard methods whereas the technique for extracting DNA from paraffin wax embedded tissue was partly modified. RESULTS--Twenty cases were examined. HIV DNA was detected in 16 cases in frozen specimens. Of these, 15 were also positive when paraffin wax embedded material was analysed. CONCLUSIONS--This study shows that HIV proviral DNA can be detected in formalin fixed, paraffin wax embedded brain tissue by PCR. The results obtained from paraffin wax embedded specimens showed a similar degree of reliability to those from fresh frozen brain. Factors such as fixative, fixation time, and delay in performing post mortem examinations did not seem to influence PCR amplification as positive results were obtained with specimens left in fixative for up to eight months, as well as in cases where post mortem examinations had been delayed for up to four days.     

Two techniques for electron opaque staining of elastic fibres using tannic acid in fresh and formalin fixed tissue.

Two electron microscopic staining techniques, one using tannic acid-glutaraldehyde as a fixative, and the other using tannic acid-uranyl acetate solution as a stain on ultra-thin sections of glutaraldehyde fixed material, were directly compared for elastic fibre staining on several human and animal tissues. Various concentrations of tannic acid were compared using both techniques. The two techniques were also compared on formalin fixed tissues. The use of tannic acid-uranyl acetate solution as a stain on processed tissue is by far the more consistent technique and achieves equally good results on glutaraldehyde or formalin fixed tissue. It is suggested that the use of the term tannic acid technique/method should be reserved for this particular method to achieve a meaningful interpretation of results in scientific papers.     

Immunohistochemical retrieval of the principal HIV antigens p24, gp41, and gp120 in formalin fixed tissue: an investigation using HIV infected lymphoblasts and postmortem brain tissue from AIDS cases.

This paper describes the use of an autoclaving procedure followed by immunocytochemistry to enhance the detection of the human immunodeficiency virus (HIV) antigens p24, gp41, and gp120. This procedure greatly improved the detection rate of the p24 and gp41 HIV surface antigens in formalin fixed, paraffin wax embedded, HIV positive central nervous system (CNS) tissue while restricting staining to areas of the CNS showing evidence of neuropathology. However, the technique did not improve retrieval of the gp120 antigen in either HIV positive, formalin fixed CNS tissue or HIV infected T lymphoblasts. The inclusion of the high temperature autoclave step was validated using both HIV infected lymphoblasts and pre-adsorption of the specific antibodies with the appropriate recombinant HIV proteins. Using the methodology described here, formalin fixed CNS tissue from potential or known HIV positive cases can be processed reliably and safely. To ensure the reliability of this technique, it is recommended that an assessment of both the p24 and gp41 antigens is undertaken.     

Direct multiplex amplification of DNA from a formalin fixed, paraffin wax embedded tissue section.

The extraction of DNA from formalin fixed, paraffin wax embedded tissue can be problematical, with long protocols producing low yields. This report describes a very simple and useful method for amplifying DNA from formalin fixed, paraffin wax embedded tissue without the need for prior DNA extraction. This method allows direct polymerase chain reaction (PCR) based molecular analysis of fixed tissue. It is an invaluable method if clinical biopsy specimens are to be investigated, because extraction of uncontaminated DNA from such small samples can be very difficult or even impossible. It will also facilitate the study of intratumour heterogeneity, with the analysis of multiple small areas from within a single tumour section. In addition, this method can be used for other samples where only a few tests are to be carried out and a stock of DNA is not required, thus shortening the analysis time.     

An alternative protocol for DNA extraction from formalin fixed and paraffin wax embedded tissue

BACKGROUND: DNA extraction from paraffin wax embedded tissue requires special protocols, and most described methods report an amplification success rate of 60-80%. AIMS: To propose a simple and inexpensive protocol consisting of xylene/ethanol dewaxing, followed by a kit based extraction. METHOD: Xylene/ethanol dewaxing was followed by a long rehydration step and a kit based DNA extraction step. RESULTS: This method produced a 100% amplification success rate for fragments of 121 to 227 bp for tamponated formalin fixed paraffin wax embedded tissue. CONCLUSION: This cost effective and non-laborious protocol can successfully extract DNA from tamponated formalin fixed paraffin wax embedded tissue and should facilitate the molecular analysis of a large number of archival specimens in retrospective studies.     

Quantification of human cytomegalovirus DNA by real-time PCR

A quantitative real-time PCR assay was developed to measure human cytomegalovirus (HCMV) DNA load in peripheral blood leukocytes (PBLs). The HCMV DNA load in PBLs was normalized by means of the quantification of a cellular gene (albumin). The results of the real-time PCR assay correlated with those of the HCMV pp65-antigenemia assay (P < 0.0001).     

Variability in beta-globin and HPV DNA amplification by PCR from fixed tissues.

Paraffin-embedded tissues from a variety of sources and treated with different fixatives were tested for beta-globin and HPV amplification by polymerase chain reaction (PCR). In tests of tissues collected in the previous 2 to 3 yr, excellent rates (87% to 93%) for beta-globin amplification were obtained for specimens fixed in buffered formalin, Bouin's, and Hartmann's solutions. In contrast, the rate of beta-globin amplification was low for tissues fixed in Hollande's solution (7%) and in Hartmann's solution with eosin (33%). The results of beta-globin amplification from archival tissues stored for variable time periods showed no decrease in the amplification rate with longer periods of storage. Human papillomaviruses (HPVs) were identified in 17% of globin negative and in 43% of globin positive tissues. HPV-16 amplification was more efficient when the targeted DNA sequence was small. Variability in amplification depends not only on the type of fixative used, but also on other ill-defined factors. Therefore, conditions for optimal amplification should be determined before undertaking studies of archival material.     

Definitive identification of human T cells in formalin fixed paraffin wax embedded tissue.

The use of a new monoclonal antibody, BF1, which reacts in routinely fixed tissues, directed against the beta chain of the T cell antigen receptor was assessed to determine its reactivity in a variety of normal tissues as well as in a number of B and T cell tumours and other lymphoid disorders. It reacted with all five of the unequivocal T cell tumours tested. BF1 will have widespread use in the assessment of lymphoid tissues in patients with the acquired immune deficiency syndrome (AIDS) and the differential diagnosis of tumours.     

Extraction of genomic DNA from paraffin-embedded tissue sections of human fetuses fixed and stored in formalin for long periods

The advent of polymerase chain reaction (PCR) technology has increased the interest in fetal specimens housed in anatomy museums, as they may represent a unique source of genetic material for the study of uncommon or rare pathological conditions such as congenital malformations, neoplastic processes and parasitic as well as other infectious diseases. The aim of this study is to evaluate the quality of genomic DNA extracted from paraffin-embedded tissue sections of human fetuses that have been maintained in formalin for several years. Fetal tissues were embedded in paraffin, and tissue sections were submitted to ethanol/xylene dewaxing, followed by DNA extraction with ammonium acetate. DNA fragments were amplified from DNA extracted from formalin-fixed tissue sections, but not from Bouin-fixed tissues (average yield of 13.7mug/ml from 10 umbilical cord sections of 10mum; A(260):A(280)=1.55,). The addition of bovine serum albumim increased the yield of PCR amplification. Genomic DNA can be reliably amplified from paraffin-embedded human fetal tissues that had been fixed in formalin during 19 years and used for microdissection studies. This simple, cost-effective, and non-laborious method should facilitate the molecular analysis of a large number of specimens fixed for long periods of time.     

Covalent binding of formalin fixed paraffin embedded brain tissue sections to glass slides suitable for in situ hybridization

A novel method for covalently binding formalin fixed paraffin embedded (FFPE) tissue sections to glass microscope slides is validated suitable for in situ hybridization (ISH). Using the organosilane methodology of Maples (1985), 100% tissue adhesion is reported with no nonspecific probe binding, staining, or autoradiographic artefacts. JC viral nucleic acid sequences are successfully detected in FFPE progressive multifocal leukoencephalopathy brain tissue and the Tm of the hybridized product is estimated. From the Tm the most stringent washing condition resulting in an optimal signal to noise ratio is determined. A comparison is made between currently used methods of tissue adhesion and the proposed organosilane methodology. This methodology greatly facilitates studies of conditions for ISH and elucidation of mechanisms of viral infections requiring consecutive FFPE sections. It is also applicable to studies using cryosections and cultured cells.     

Biomechanical comparison of Thiel embalmed and fresh frozen nerve tissue

The aim of this study was to determine the effect of Thiel embalming on the biomechanical properties of nerve tissue, to validate the use of Thiel embalmed     

Quantification of human polyomavirus JC in brain tissue and cerebrospinal fluid of patients with progressive multifocal leukoencephalopathy by competitive PCR

Activation of human polyomavirus JC (JCV) infection is the cause of the central nervous system (CNS) disease progressive multifocal leukoencephalopathy (PML). Previous studies with uncontrolled quantification systems suggested that the virus load in the CNS correlates with the state of disease and might reflect therapeutic effects. Therefore the aim of this study was the development of a competitive system with standard PCR techniques that allowed rapid detection of JCV subtypes, simultaneous differentiation of the two human polyomaviruses JCV and BKV and absolute quantification of the virus burden in initial diagnosis and progressive disease states. Subtype- and species-specificity of the PCR was achieved with the development of a degenerative PCR primer pair that detected JCV DNA in a range regularly found in PML samples, but did not amplify BKV DNA. The accuracy of the system was evaluated by quantification of known amounts of cloned JCV DNA with a competitive JCV-specific template that exhibited a comparable amplification rate to that of the native product. The calibration study demonstrated a linear correlation over a wide range of DNA concentrations on the background of buffer or JCV-negative diagnostic samples. The reliability of the system for PML diagnosis was analysed by calibration and determination of the virus burden in tissue and cerebrospinal fluid (CSF) of 11 PML patients confirming the accuracy in both types of samples under diagnostic conditions. Comparison of the JCV DNA concentration in tissue and CSF by a tightly controlled quantification technique revealed for the first time differences in a range of about four orders of magnitude and a variable virus load in CSF samples taken at comparable states of disease. This pointed to an individual course of virus shedding and demonstrates that a controlled competitive PCR system of high accuracy is essential for reliable quantification of virus DNA either in initial diagnosis, in progressive disease or for the evaluation of therapeutic effects.     

Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens

Molecular tools for tissue profiling, such as expression microarrays and real-time PCR, generally require collection of fresh frozen tissues as sources of high-quality RNA. The fragile nature of RNA prompted us to examine the effects of storage time and transport conditions with regard to RNA integrity and gene expression in nonfixed surgical human specimens. At surgery, fresh normal tonsil and colon tissue was cut into pieces and snap frozen. Additional fresh tissue pieces were (i) left at room temperature, (ii) kept on ice, (iii) in normal saline or (iv) in a commercial RNA-stabilizing buffer (RNAlater) and snap frozen after 0.5, 1, 3, 6 and 16 h. Structural RNA integrity was analysed by microchip electrophoresis. Surprisingly, RNA remained stable in both tissue types under all conditions tested for up to 6-16 h. Gene expression by real-time PCR of cfos, HIF1alpha, Bcl2, PCNA, TGFbeta1 and SMAD7 was analysed at different storage time points in tonsil tissue. Expression levels were essentially stable when samples were kept on ice, while marked regulation of single genes was observed during storage at room temperature, in normal saline and in RNAlater. Furthermore, we analysed selected tissue types from the local biobank representing 47 normal and malignant tissues transported on ice for up to 2-3 h before biobanking. RNA prepared from 45 of the 47 samples exhibited distinct ribosomal peaks indicating intact RNA. This study shows that RNA degradation is a minor problem during handling of fresh human tissue before biobanking. Our data indicate that nonfixed tissue specimens may be transported on ice for hours without any major influence on RNA quality and expression of the selected genes. However, further studies are warranted to clarify the impact of transport logistics on global gene expression.     

Immunoarchitecture of normal human bone marrow: a study of frozen and fixed tissue sections.

To provide baseline information on the immunoarchitecture of normal bone marrow, we studied cryostat-cut, frozen, and paraffin-embedded, fixed tissue sections prepared from 21 core biopsies of normal bone marrow obtained during bone marrow harvests for transplantation. A large panel of antibodies was applied that included, for frozen tissue, Leu-6 (CD1), T11 (CD2), Leu-3a (CD4), Leu-1 (CD5), Leu-2a (CD8), J5 (CD10), My7 (CD13), Leu-11 (CD16), B4 (CD19), B1 (CD20), B2 (CD21), Tac (CD25), My9 (CD33), T200 (CD45), NKH-1 (CD56), kappa and lambda chains, beta F1, Ki-67, HLA-DR, TQ1, and keratin, and for fixed tissue, leukocyte common antigen (CD45), L26 (CD20), LN1 (CDw75), LN2 (CD74), LN3, LN4, LN5, MB1 (CD45R), MB2, MT1 (CD43), MT2 (CD45R), UCHL1 (CD45R0), BM1, Ki-1 (CD30), Leu-M1 (CD15), lysozyme, KP1 (CD68), actin, S100, neuron-specific enolase, vimentin, and keratin. On fresh-frozen sections CD19 and CD2 were the most reliable and sensitive markers for B and T cells, staining 5% and 9% of marrow cells, respectively. Immunoglobulins generally showed heavy background staining, which frequently precluded an accurate assessment. The CD4 to CD8 ratio in the bone marrow was reversed from that of peripheral blood. On fixed tissues, leukocyte common antigen was found in 14% of the marrow cells, corresponding roughly to the lymphocyte population. L26, a pan-B-cell marker, stained 3% of the marrow cells. Among the other B-cell markers, LN1 and MB2 stained a large number of cells (40% to 70%), indicating reactivity with cells of the myeloid or erythroid series in addition to lymphocytes. Among the T-cell markers, UCHL1 and MT1 stained 66% and 50% of the cells, respectively, which could be explained by their cross-reactivity with myeloid cells. Nonspecific myelomonocytic markers (Leu-M1, KP1, and lysozyme) also showed reactivity in a high percentage of cells. No particular architectural distribution patterns of B or T lymphocytes were noted in either frozen or fixed bone marrow specimens. The results of this study provide normal baseline data for the immunohistologic application of hematopoietic and lymphoid markers on frozen or fixed bone marrow biopsy specimens.