Validation of a standardized extraction method for formalin-fixed paraffin-embedded tissue samples

BackgroundFormalin-fixed paraffin-embedded (FFPE) samples can be DNA-extracted and used for human papillomavirus (HPV) genotyping. The xylene-based gold standard for extracting FFPE samples is laborious, suboptimal and involves health hazards for the personnel involved.ObjectivesTo compare extraction with the standard xylene method to a xylene-free method used in an HPV LabNet Global Reference Laboratory at the Centers for Disease Control (CDC); based on a commercial method with an extra heating step.Study designFifty FFPE samples were randomly selected from a national audit of all cervical cancer cases diagnosed in Sweden during 10 years. For each case-block, a blank-block was sectioned, as a control for contamination. For xylene extraction, the standard WHO Laboratory Manual protocol was used. For the CDC method, the manufacturers’ protocol was followed except for an extra heating step, 120 °C for 20 min. Samples were extracted and tested in parallel with β-globin real-time PCR, HPV16 real-time PCR and HPV typing using modified general primers (MGP)-PCR and Luminex assays.ResultsFor a valid result the blank-block had to be betaglobin-negative in all tests and the case-block positive for beta-globin. Overall, detection was improved with the heating method and the amount of HPV-positive samples increased from 70% to 86% (p = 0.039). For all samples where HPV type concordance could be evaluated, there was 100% type concordance.ConclusionsA xylene-free and robust extraction method for HPV-DNA typing in FFPE material is currently in great demand. Our proposed standardized protocol appears to be generally useful.     

Applicability of next-generation sequencing to decalcified formalin-fixed and paraffin-embedded chronic myelomonocytic leukaemia samples

Decalcified formalin-fixed and paraffin-embedded (dFFPE) bone marrow trephines remain the primary source of gDNA in hematopathological diagnostics. Here, we investigated the applicability of next-generation sequencing (NGS) to dFFPE samples. Chronic myelomonocytic leukaemia (CMML) is a haematopoietic stem cell malignancy delineated by genetic heterogeneity. Recently characteristic mutations have been identified for this entity in a distinct group of genes (TET2, CBL, KRAS). We comparatively investigated DNA extracted from fresh mononuclear cells as well as dFFPE samples from four CMML patients employing a commercially available primer set covering the above mentioned and well characterized mutational hotspots in CMML followed by an amplicon based next-generation deep-sequencing (NGS) approach. As we observed high quality run data as well as complete concordance between both sample types in all cases, we further validated the potential of NGS in hematopathology on a larger cohort of CMML patients (n=39), detecting sequence variations in 84.6% of patients. Sequence analysis revealed 92 variants, including five known polymorphisms, ten silent mutations, 36 missense mutations, 14 nonsense mutations, 24 frame shift mutations and three potential splice site mutations. Our findings ultimately demonstrate the applicability of NGS to dFFPE biopsy specimen in CMML and thus allowing the pathologist to evaluate prognostically relevant mutations at a high resolution and further contribute to risk stratification for the individual patient.     

A simple method for isolation of DNA from formalin-fixed paraffin-embedded samples for PCR.

A simple method of processing formalin-fixed, paraffin-embedded tissue sections for DNA amplification by polymerase chain reaction (PCR) is described. In this procedure, deparaffinized sections are readily subjected to DNA isolation simply by boiling and the released DNA can be directly employed for PCR. The method allows analysis of single-copy genes or viral sequences at least up to 300 base pairs long in one working day. This method is particularly useful in analysing retrospective materials when the simplicity and low cost of the assay are preferable. Furthermore, the simplicity of the procedure reduces the risk of contamination.     

Development of an immunohistochemical assay for the detection of babesiosis in formalin-fixed, paraffin-embedded tissue samples

The hemoparasite Babesia can cause life-threatening infections to neonates, elderly and immunocompromised people, and people who have undergone splenectomy. By using pooled hamster serum samples collected 21 days after infection with Babesia microti, we developed an immunohistochemical assay for formalin-fixed, paraffin-embedded tissue (FFPET) samples and blood smears. By use of the immunohistochemical assay, parasites were detected inside erythrocytes present in the heart, spleen, and liver of experimentally and naturally infected animals. FFPET samples from 2 fatal and 1 nonfatal human cases demonstrated immunohistochemical assay-positive parasites in circulating erythrocytes in various organs, including lymph nodes and spleen. In addition, air-dried blood smears from 4 patients showed positive immunohistochemical staining inside the erythrocytes. The immunohistochemical assay showed cross-reactivity against the Babesia WA-1 strain but did not react against Babesia bigemina or Plasmodium falciparum. The immunohistochemical assay for Babesia microti successfully detected parasites in human and animal FFPET samples and blood smears. This technique will be useful for the diagnosis of clinically suspected cases and for differentiating Babesia microti infection from malaria. Application of this technique to animal models will better define pathogenic mechanisms, including the possible recognition of exoerythrocytic tissue stages.     

Expression profiling of Epstein-Barr virus-encoded microRNAs from paraffin-embedded formalin-fixed primary Epstein-Barr virus-positive B-cell lymphoma samples

Epstein-Barr virus (EBV) is implicated in a range of B-cell malignancies and expresses unique microRNAs (EBV-miRNAs). Due to the requirements for high-quality RNA, studies profiling EBV-miRNA in EBV-positive lymphomas have been restricted to cell-lines or frozen samples. However, the most commonly available archived patient material is paraffin-embedded formalin-fixed (FFPE) tissue. This has impeded the widespread profiling of EBV-miRNA expression in clinical samples. The requirements for accurate EBV-miRNA real-time RT-PCR quantitation in FFPE tissues representing a broad-spectrum of EBV-positive lymphomas were determined systematically, including where the neoplastic cells are sparse relative to the non-malignant infiltrate. The level of cellular EBV-load correlated strongly with the sum of EBV-miRNA expression and the number of EBV-miRNAs detectable. As calibrators for cellular EBV-load, the sum EBV-miRNA was optimal to EBV-genome copy number and EBER2 expression level, with the added advantage of not requiring additional assays. EBV-miRNA was profiled reliably within archival FFPE tissue in 14/23 patients, but not in tissues with low abundance EBV. This method enabled specific and simultaneous detection of numerous EBV-miRNAs in FFPE lymphoma samples that contain EBV at high to medium levels, making it as a useful tool for studies of EBV-miRNA in the majority of diagnostic biopsies.     

RNA expression analysis of formalin-fixed paraffin-embedded tumors

RNA expression analysis is an important tool in cancer research, but a limitation has been the requirement for high-quality RNA, generally derived from frozen samples. Such tumor sets are often small and lack clinical annotation, whereas formalin-fixed paraffin-embedded (FFPE) materials are abundant. Although RT-PCR-based methods from FFPE samples are finding clinical application, genome-wide microarray analysis has proven difficult. Here, we report expression profiling on RNA from 157 FFPE tumors. RNA was extracted from 2- to 8-year-old FFPE or frozen tumors of known and unknown histologies. Total RNA was analyzed, reverse-transcribed and used for the synthesis of labeled aRNA after two rounds of amplification. Labeled aRNA was hybridized to a 3'-based 22K spot oligonucleotide arrays, and compared to a labeled reference by two-color microarray analysis. After normalization, gene expression profiles were compared by unsupervised hierarchical clustering. Using this approach, at least 24% of unselected FFPE samples produced RNA of sufficient quality for microarray analysis. From our initial studies, we determined criteria based on spectrophotometric analyses and a novel TaqMan-based assay to predict which samples were of sufficient quality for microarray analysis before hybridization. These criteria were validated on an independent set of tumors with a 100% success rate (20 of 20). Unsupervised analysis of informative gene expression profiles distinguished tumor type and subtype, and identified tumor tissue of origin in three unclassified carcinomas. Although only a minority of FFPE blocks could be analyzed, we show that informative RNA expression analysis can be derived from selected FFPE samples.     

Demonstration of AA-protein in formalin-fixed, paraffin-embedded tissues.

AA-protein was identified by SDS-acrylamide electrophoresis in amyloid fibrils fixed in formalin after isolation from fresh-frozen tissues obtained from patients with familial Mediterranean fever (FMF) amyloidosis and idiopathic AA-amyloidosis and, following deparaffination, rehydration and homogenization of embedded formalin-fixed tissues of old autopsy cases of the hereditary amyloidosis of FMF and amyloidosis acquired in association with tuberculosis, bronchiectasis, and rheumatoid arthritis. That AA-protein is unaltered by formalin was firmly established by agar gel diffusion using specific rabbit anti-AA serum. By contrast, AL proteins could not be demonstrated either in formalin-fixed amyloid fibrils derived from fresh-frozen tissues of a patient with presumably AL-amyloidosis dominated by cardiomegaly and one with AL-kappa amyloidosis or in blocks of cases of familial neuropathic amyloidosis, multiple myeloma, and idiopathic amyloidosis with cardiopathy. AA-protein is not denatured by formalin and retains its typical electrophoretic, chromatographic, and immunologic characteristics even 30 years after fixation and paraffin-embedding.     

Antigen unmasking on formalin-fixed,paraffin-embedded tissue sections

Enzymatic and non-enzymatic treatments for antigen unmasking on formalin-fixed, paraffin-embedded, dewaxed sections were optimized and compared by the use of a panel of antibodies of diagnostic relevance (anti-cytokeratins, vimentin. S-100. T- and B-cell receptors, Ki-67/MIB 1, muscle actin). Non-enzymatic unmasking was obtained by boiling the slides in a microwave oven in 0.01 M salt solution (pH 6) or in 6 M urea. Trypsin or pronase digestion was used for comparison and found to be necessary for some of the reagents. The investigation was then extended to 256 antibodies; the epitopic amino acid sequence was known for 48 of them. We found that enzymatic and non-enzymatic antigen unmasking are not dependent on the epitope sequence, but some antigens benefit selectively from one treatment but not from the other. Denaturation of proteins is the likely mechanism which leads to immunodetection on microwave oven-boiled slides; this suggestion is supported by the use of denaturating solutions and by the observation that endogenous enzymes were inactivated and a few antigens were no longer immunodetectable after boiling. Non-enzymatic methods for antigen unmasking are a powerful new tool for broadening the use of antibodies for immunostaining formalin-fixed, paraffin-embedded sections and should be used in parallel with the traditional enzymatic methods.     

Immunofluorescence studies on formalin-fixed and paraffin-embedded material.

In an attempt to apply immunomorphologic techniques to formalin-fixed material, various tissues were studied by indirect immunofluorescence. To minimize nonspecific background staining, formalin-fixed paraffin sections were treated with pronase prior to incubation with the antisera. This technique was published by Huang in 1975 to study hepatitis B core and surface antigen in formalin-fixed liver-tissue. Our examination demonstrate that this technique might enable the morphologist to identify immunoglobulins in formalin-fixed tissues and so to get new criteria for their diagnosis.     

Detection of early myocardial infarction in formalin-fixed, paraffin-embedded tissue

Whether the early infarct area in formalin-fixed, paraffin-embedded tissue could be delineated by the immunohistochemical method using myoglobin-antibody was studied in 23 pig hearts without collateral circulation. Five hearts were examined at 20 minutes, 2 hours, 4 hours, and 6 hours after occlusion of the distal one third of the left anterior descending coronary artery, respectively. Three pigs were killed 24 hours after occlusion. Heart rate and aortic pressure before and after occlusion did not change in any groups. The subepicardial and subendocardial regional blood flows were reduced to almost zero in all hearts after occlusion (0.88 +/- 0.10 to 0.02 +/- 0.02 mL/g/min). Slight myoglobin defects in the ischemic tissue were noted in the five pigs examined 2 hours after occlusion and definite myoglobin defects were detected in all pigs examined at 4, 6, and 24 hours after occlusion. Nitrotetrazorium blue stain of myocardial tissue before formalin fixation showed slight demarcation of the ischemic area at 4 hours after occlusion and definite demarcation at 6 and 24 hours after occlusion. Slight demarcation was noted at 2 hours after occlusion in Masson trichrome stain and 4 hours after occlusion in the hematoxylin-eosin stain. However, definite demarcation of the ischemic area was seen in Masson trichrome stain only at 24 hours after occlusion and was not noted in hematoxylin-eosin stain even at 24 hours after occlusion. Our previous electron microscopic study revealed that, in the pig heart, irreversible cellular damage was transmurally seen at two hours after occlusion of the coronary artery. Therefore, a definite myoglobin defect reflects irreversible cellular damage such as infarction.(ABSTRACT TRUNCATED AT 250 WORDS)     

Immunohistochemical detection of Yersinia pestis in formalin-fixed, paraffin-embedded tissue

Yersinia pestis infection usually is limited to lymph nodes (bubo); rarely, if bacteria are aerosolized, pneumonic plague occurs. We developed an immunohistochemical assay using a monoclonal anti-fraction 1 Y pestis antibody for formalin-fixed tissues. We studied 6 cases using this technique. Respiratory symptoms were prominent in 2 cases; histologically, one showed intra-alveolar inflammation, and the other had alveolar hemorrhage and edema. By using the immunohistochemical assay, we found intact Yersinia and granular bacterial antigen staining in alveoli, bronchi, and blood vessels. Of the remaining cases, 2 had septicemia and 2 had a bubo. Pathologic changes included lymphocyte depletion, necrosis, edema, and foamy macrophages in lymph nodes; multiple abscesses in the spleen; fibrin thrombi in glomeruli; and unremarkable lungs. By using the immunohistochemical assay, we identified intact bacteria inside monocytes and granular antigen staining in blood vessels. The immunohistochemical assay provided a fast, nonhazardous method for diagnosing plague. The immunohistochemical assay localizes bacteria, retaining tissue morphologic features, and can help define transmission mechanisms.     

Enhanced phylogenetic resolution of Newcastle disease outbreaks using complete viral genome sequences from formalin-fixed paraffin-embedded tissue samples

Virus Genes - Highly virulent Newcastle disease virus (NDV) causes Newcastle disease (ND), which is a threat to poultry production worldwide. Effective disease management requires approaches to...     

Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays

Oligonucleotide microarrays are widely used to investigate gene expression in a large-scale approach. A major limitation is the dependency on frozen material to obtain high-quality ribonucleic acid because most clinical specimens are formalin-fixed and paraffin-embedded (FFPE). The ability to analyze these samples using microarrays would enlarge the investigable sample stocks manifold. We conducted a comparison of snap-frozen and FFPE tissues investigating two malignomas. Gene expression profiles were obtained from both materials of the tumors. Independently processed triplicates of snap-frozen and FFPE specimen, respectively, were two-round-amplified and hybridized on Affymetrix GeneChips (Palo Alto, CA, USA). Differentially expressed genes were identified in both FFPE and frozen material. All replicates had a correlation coefficient (R) of greater than 0.95 after normalization. Only direct comparison of FFPE to frozen replicates resulted in a mean R of 0.86, rendering a "mixed" investigation unfeasible. More than 50% (419 genes) of the more than fivefold differentially expressed genes (800 in FFPE, 685 in frozen material) were detected concomitantly regardless of the material used, which is similar to other comparisons of different gene expression analysis platforms. Thus, global gene expression analyses using solely FFPE material seem to be feasible with nearly comparable results to frozen tissue studies.     

Direct immunofluorescence of skin using formalin-fixed paraffin-embedded sections.

The technique of direct immunofluorescence has been applied to skin biopsy specimens fixed in formalin and embedded in paraffin wax. The results have been compared with those obtained by using snap-frozen biopsy specimens from the same patients. Trypsinisation of the dewaxed material allowed subsequent detection of immunoglobulins, complement, and fibrinogen. When compared to the fluorescence in the snap-frozen specimens, the staining in the paraffin sections was less bright and there was a higher rate of negatives. Even so, it was possible to establish the diagnosis in most cases of pemphigus, pemphigoid, and lupus erythematosus.