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PubMed1999

Molecular genetic testing from paraffin-embedded tissue distinguishes nonmolar hydropic abortion from hydatidiform mole.

BACKGROUND: Diagnosis of hydatidiform mole by histology and ploidy analysis is limited by overlap of criteria for nonmolar hydropic abortion, complete mole, and partial mole. With early presentation, diagnosis is difficult due to limited tissue and lack of clinical features. Accurate diagnosis of these entities is important for both prognosis and patient management. We assessed a polymerase chain reaction (PCR) assay for polymorphic short tandem repeats (STR) for discrimination between nonmolar hydropic abortion, complete mole, and partial mole based on the genetic composition of molar pregnancies. METHODS: Seventeen cases of products of conception (POC) diagnosed by histology and flow cytometry ploidy analysis were studied retrospectively. PCR was performed using maternal and chorionic villus DNA extracted from microdissected, formalin-fixed, paraffin-embedded tissue sections. Allelic patterns for up to eight well-characterized polymorphic STR loci were determined using the GenePrint Fluorescent STR System (Promega Corporation, Madison, WI). The presence of three villus alleles at a single locus was interpreted as partial mole. Detection of only one allele in the villi, different from all maternal allele(s) at the same locus, was interpreted as a complete mole. RESULTS: This technique identified eight complete moles previously diagnosed as complete mole (3), hydatidiform mole, otherwise unspecified (1), hydropic villi (2), hydropic villi versus partial mole (1), and partial mole (1). The diagnoses of five partial moles by the molecular assay were consistent with the diagnoses by histology and flow cytometry. One nonmolar gestation was identified, which had been diagnosed previously as hydropic villi. In three cases, maternal DNA amplification was insufficient for definitive diagnosis. CONCLUSION: Molecular genetic testing of POC from paraffin-embedded tissue accurately distinguishes complete mole, partial mole, and nonmolar hydropic abortion. Identification of triploidy by flow cytometry can confirm a histological impression of partial mole. Histological and ploidy analysis of POC results in underdiagnosis of complete moles.

Abortion, Spontaneous↗
PubMed1996

Monoclonal antibodies detecting components of the bovine immune system in formaldehyde-fixed paraffin-embedded tissue specimens.

Although the use of monoclonal antibodies in the diagnosis of fixed human material is a daily routine, the lack of suitable reagents recognizing epitopes resistant to formaldehyde fixation is an obvious limit to extending this approach to veterinary research and practice. To find reagents that retain their binding capacity to the recognized epitopes in formaldehyde-fixed samples, bovine lymphoid tissue sections were immunostained using various antigen retrieval procedures with monoclonal antibodies raised against ruminant leukocyte cell surface molecules. As a results, a set of antibodies could be established that allowed the identification of different immune cell types including all or a distinct subpopulation of B and T lymphocytes, monocytes, macrophages, granulocytes, red blood cells, and vascular endothelial cells.

Animals↗
PubMed2006

Optimization of recovery of RNA from formalin-fixed, paraffin-embedded tissue.

Formalin-fixed, paraffin-embedded (FFPE) tissue is the most common specimen available for application of diagnostic assays on tissue after microscopic examination. Not only is there a substantial archive of tissue available, but FFPE tissue remains the best method of preparation for microscopic examination in a routine clinical environment. Molecular assays, especially reverse transcription and polymerase chain reaction and expression array-based assays, offer significant potential as diagnostic, prognostic, and predictive tools, but require high quality RNA. Herein, we have optimized a reliable RNA extraction method for FFPE tissue. It is based on deparaffinization at high temperature coupled with a 3-day lysis at 65 degrees C. The average total RNA yield is 4.5 to 5.5 pg per 1 microm of archival FFPE tissue, and 260/280 ratios are between 1.80 and 1.95. The extracted RNA has a modal fragment length between 100 and 200 nt by the Bioanalyzer analysis. Although modal lengths of RNA fragments were shorter, reverse transcription and polymerase chain reaction was able to amplify amplicons in range of 300 bp. Pretreatment with RNA, later followed by formalin fixation, did not result in improving the RNA quality, but did improve RNA yield. Our method improves the utility of FFPE tissue for molecular profiling studies.

Animals↗
PubMed1993

The identification of equid herpesvirus 1 in paraffin-embedded tissues from aborted fetuses by polymerase chain reaction and immunohistochemistry.

Paraffin-embedded organ samples from 28 aborted fetuses and three foals, partly archival and partly sampled in 1991, were examined by polymerase chain reaction (PCR) and immunohistochemistry for the presence of DNA and antigens, respectively, specific for equine herpesvirus 1 (EHV-1). Virologic examination had been performed on 23 of the aborted fetuses. DNA fragments specific for EHV-1 were identified by PCR, and EHV-1 antigens were identified in situ by immunohistochemistry, with an agreement between the methods of 94% (kappa = 0.85). Compared with virus isolation, PCR agreement was 87% (kappa 0.69), and IH agreement was 82% (kappa = 0.47). These results showed that there was moderate to almost perfect agreement among the different methods and that PCR and immunohistochemistry are powerful tools for the identification of EHV-1 in paraffin-embedded tissues. The techniques give more rapid results than virus isolation and also detect inactivated virus, which are not identified by standard virus isolation. These techniques also make retrospective studies possible.

Abortion, Veterinary↗
PubMed1998

DNA-Flow cytometric analysis of bladder TCC using paraffin-embedded tissues.

A retrospective study of DNA flow cytometry (FCM) in paraffin-embedded tissues of urinary bladder transitional cell carcinoma (TCC) was performed on 239 biopsy samples taken from 81 patients in the period from 1984 to 1994. 210 (87%) were analysable. Of these samples 21 patients had multiple biopsies taken from large tumours and/or bladder mucosa showing an endoscopically normal appearance. DNA-FCM results have been evaluated comparing ploidy and histopathological grade, clinical stage and different clinical status, i.e., first diagnosis, recurrence and patients who died from bladder cancer. Our results indicate that 'diploid' FCM correlated with a better prognosis, whilst DNA aneuploid correlated with malignancy and a poorer prognosis. There was a trend to an increasing incidence of DNA aneuploidy as the grade of the tumour rose and the proportion of biopsies with aneuploidy was significantly higher in malignant tissue samples, recurrences and in biopsies from patients who died from TCC than in other groups. In 12 patients from whom several biopsies were obtained, samples from recurrences had significantly higher DNA aneuploidy than those from the first diagnosis.

Adult↗
PubMed1994

Molecular biological analysis of paraffin-embedded tissues.

Molecular biology techniques have been adapted to the analysis of paraffin-embedded tissues (PETs), expanding their clinical utility. In vitro amplification with the polymerase chain reaction (PCR) promises to be the most useful means of retrospective analysis because it can be performed successfully on nucleic acids that have been partially degraded during fixation, paraffin embedding, and the extraction process. Five clinical situations in which DNA analysis of PETs can be helpful are: (1) confirmatory molecular diagnosis of lymphoma in which fresh tissue has not been obtained at the time of surgery, (2) identification of infectious agents, (3) genetic characterization of a putative inherited disease in which the affected individual has died, (4) confirmation of donor cell malignancy in transplant recipients, and (5) specimen identification. The role of the pathologist in molecular diagnosis will grow because of the feasibility of using PETs, a venue unique to our profession.

DNA↗
PubMed1983

Immunohistochemical staining on hydroxyethyl-methacrylate-embedded tissues.

Hydroxyethyl-methacrylate (GMA) embedding has recently been proposed for light microscopy studies. In the present investigation extracellular protein antigens were localized on GMA-embedded renal biopsy tissue. Conventionally frozen sections were compared with GMA sections from 55 renal specimens for the detection of extracellular protein antigens. Sections were directly stained with fluorescein- or peroxidase-conjugated antisera against immunoglobulin (Ig) G, IgA, IgM, C3, C1q, and fibrinogen. Results obtained using these two methods showed a 74-89% agreement, depending on the antigen under study. Some discrepancy between GMA and frozen sections was observed in three cases of renal amyloidosis and those cases presenting focal or trace reactions; the differences did not, however, influence the diagnosis. Prerequisites for antigen recovery on GMA sections were a) choice of fixative; b) abrupt dehydration of specimens; and c) treatment of sections with nonspecific protease. The improved localization and the lower background staining obtained led to easy and immediate detection of antigens on GMA sections despite the reduced antigenicity due to the embedding process.

Acrylates↗
PubMed1994

[Microwave oven in immunohistochemistry. An important tool for determination of antigens in formalin-fixed and paraffin-embedded tissue].

Immunocytochemical methods are important tools for identifying antigens in tissue sections and cell smears. Some antigens were retrieved in formalin-fixed and paraffin-embedded tissues by means of a microwave technique. This method also increased the sensitivity of the immunohistochemical detection of several other antigens. Altogether, microwave boiling of the tissue sections in citrate buffer clearly improved the immunoreactivity for cytokeratin 18, oestrogen receptor, Ki-67 protein, PCNA, p53 protein, retinoblastoma gene protein and c-erbB-2 protein. This new technique, which can be applied in every pathology laboratory, will facilitate the application of immunohistochemical methods for research and diagnostic work.

Epitopes↗
PubMed2002

Methacarn fixation for genomic DNA analysis in microdissected, paraffin-embedded tissue specimens.

We recently found methacarn to be a versatile fixative for analysis of RNA and protein applicable for microdissected specimens from paraffin-embedded tissue (PET). In this study we investigated the performance of methacarn for genomic DNA analysis using microdissected rat tissues. We found that extensive portions of DNA up to 2.8 kb could be amplified by nested PCR using DNA templates extracted by a simple and rapid extraction procedure from a 1 x 1-mm area of cerebral cortex of a 10-microm-thick section. By nested PCR, a 522-bp fragment from a single cell could be amplified in 20% of cresyl violet-stained Purkinje cells, and the minimal number of cells required, as estimated using hippocampal neurons, was on the order of 10-20. Although tissue staining with hematoxylin and eosin affected the PCR, amplification of a 522-bp fragment was successful, with 150-270 cells by 35 cycles of single-step PCR. Immunostaining resulted in a substantial decrease of yield and degradation of extracted DNA. However, even after immunostaining, a 184-bp DNA fragment could be amplified with 150-270 cells by 35 cycles of PCR. The results thus demonstrate the superior performance of methacarn to that reported with formalin in genomic DNA analysis using microdissected PET specimens.

Acetic Acid↗
PubMed1983

Plasma cell lesions of the head and neck: immunofluorescent determination of clonality from formalin-fixed, paraffin-embedded tissue.

An immunofluorescent technique was used on formalin-fixed, paraffin-embedded tissue to characterize and diagnose plasma cell lesions of the head and neck. Infiltrates were classified as either monoclonal or polyclonal with rhodamine and fluorescein staining of light chains and heavy chains. In the cases in which histopathologic diagnoses were relatively certain, immunofluorescence provided good correlation. In those cases in which histopathologic diagnoses were equivocal, immunofluorescence distinguished between reactive and neoplastic infiltrates through the determination of clonality of the infiltrates.

Clone Cells↗
PubMed1988

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)

Animals↗
PubMed2002

Detection of SYT-SSX fusion transcripts in paraffin-embedded tissues of synovial sarcoma by reverse transcription-polymerase chain reaction.

OBJECTIVE: To assess the feasibility of detecting SYT-SSX fusion transcripts in paraffin-embedded tissues of synovial sarcoma by reverse transcription-polymerase chain reaction (RT-PCR). METHODS: RT-PCR was used to amplify the SYT-SSX fusion transcripts using archival formalin-fixed paraffin-embedded tumor specimens from a series of 37 synovial sarcoma cases. To investigate the specificity of the SYT-SSX fusion transcripts, a variety of non-synovial sarcoma tumors were included in the study as negative controls. The detected messages derived from fusion genes were confirmed by subsequent sequence analysis. RESULTS: SYT-SSX fusion transcripts were detected in 33 of 37 (89.2%) synovial sarcomas. None of the 34 cases of non-synovial sarcoma tumors showed amplified products of SYT-SSX fusion transcripts, although PBGD mRNA was detected in all specimens. Among 33 SYT-SSX-positive synovial sarcomas, 22 tumors had an SYT-SSX 1 fusion transcript, whereas 6 tumors had an SYT-SSX2 fusion transcript. Fusion types can not be distinguished in the remaining 5 cases. There was a significant relationship between SYT-SSX fusion type and histologic subtype. All 10 biphasic synovial sarcomas had the SYT-SSX1 fusion, whereas all tumors with SYT-SSX2 were of monophasic morphology (P < 0.05). CONCLUSIONS: RT-PCR can be applied to archival formalin-fixed paraffin-embedded tumor tissues as a sensitive and reliable technique for the diagnosis and differential diagnosis of synovial sarcoma. There is an association between SYT-SSX fusion type and histological subtype. SYT-SSX2 fusion transcripts can only be found in monophasic synovial sarcoma.

Adolescent↗
PubMed2005

Comparison of archival plasma and formalin-fixed paraffin-embedded tissue for genotyping in hepatocellular carcinoma.

Biobanks containing formalin-fixed paraffin-embedded tissue, as well as frozen serum or plasma, are important resources for molecular epidemiologic studies. However, few studies have compared the reliability of formalin-fixed tissue samples and archival plasma samples for genotyping. We determined the genotype of four proposed genetic risk factors for hepatocellular carcinoma [hereditary hemochromatosis (HFE 63 and 282), alpha(1)-antitrypsin deficiency (AAT 342) and cystic fibrosis (CFTR 508)] on formalin-fixed tissue samples, stored for up to 25 years, from 318 patients diagnosed with hepatocellular carcinoma and on plasma or serum samples from 31 of these patients. The genotypes were analyzed by RFLP or allele-specific amplification as well as by TaqMan assays. In addition, genotyping was attempted after whole genome amplification by multiple displacement amplification (MDA). Genotyping was successful in 94% of the tissue samples and successful and identical to the tissue samples from the same subjects in 98% of the plasma/serum samples. DNA from plasma samples could be amplified >5,000-fold by MDA and genotyping after MDA gave identical results to the genotyping of the same subjects before whole genome amplification. MDA amplification of the tissue samples was not successful. In summary, archival plasma was found to be an adequate source of efficiently amplifiable DNA. MDA on plasma samples allows analysis of multiple genotypes in epidemiologic studies.

Carcinoma, Hepatocellular↗
PubMed1991

A new method for transfer of polyethylene glycol-embedded tissue sections to silanated slides for immunocytochemistry.

Polyethylene glycol (PEG) is an excellent embedding medium for immunohistochemical studies. It provides structural preservation superior to frozen sections and increased sensitivity of antigen detection compared with paraffin sections. One limitation of PEG embedment is that PEG sections are difficult to handle and adhere poorly to glass slides. Here we present a simple and effective method for embedding tissues in PEG and transferring the resultant sections onto silanated glass slides. In addition, a method for silver enhanced colloidal gold immunostaining was combined with common dye staining to demonstrate the excellent structure preservation and sensitive antigen detection. Bovine chorionic membrane was fixed with Bouin's fixative, embedded in polyethylene glycol (PEG) 1500, cut into 5-microns sections, flattened over agarose blocks (10 x 10 x 2 mm3), and blotted onto Digene silanated slides. Slides were then washed in PBS, which removed the PEG and agarose blocks. Tissue sections were immunocytochemically stained with dilute antiserum raised in a rabbit against purified bovine placental retinol binding protein (bpRBP). Sections were washed and incubated with 1-nm colloidal gold-labeled goat anti-rabbit IgG. The immunogold particles were enhanced by silver staining (IGSS). Specimens were observed and photographed with an Olympus epipolarization microscope. The new method offered excellent morphological preservation of cell structure and the epipolarization microscopy provided high sensitivity for detection of specific immunogold-silver particles.

Animals↗
PubMed1993

Cellular localisation of messenger RNAs in rat testis: application of digoxigenin-labelled ribonucleotide probes to embedded tissue.

In an attempt to identify key changes involved in normal spermatogenesis we have developed methods to enable the study of gene expression by the various subpopulations of testicular cells by use of in-situ hybridisation histochemistry. The use of digoxigenin-labelled ribonucleotide and oligonucleotide probes on testicular tissue perfusion-fixed with Bouin's fixative and embedded in paraffin, polystyrene or methacrylate, has been used to accurately localise three transcripts to three different cell types (Sertoli cells, pachytene spermatocytes, and step 7-12 spermatids) within the seminiferous tubule. The ability to produce semi-thin sections of polystyrene- or methacrylate-embedded tissue and successfully to apply digoxigenin-labelled ribonucleotide or oligonucleotide probes resulted in far greater resolution and unequivocal localisation of mRNA in testicular cells than was previously possible by use of thicker paraffin or frozen sections hybridised with 35S-labelled riboprobes. A comparison of the different embedding media versus digoxigenin-labelled oligonucleotide or ribonucleotide probes is made and we demonstrate the relative sensitivities and merits of each combination.

Animals↗
PubMed2003

Differentiation between porcine epidemic diarrhea virus and transmissible gastroenteritis virus in formalin-fixed paraffin-embedded tissues by multiplex RT-nested PCR and comparison with in situ hybridization.

Porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) were detected and differentiated in formalin-fixed, paraffin-embedded tissues from experimentally and naturally infected pigs by multiplex reverse transcription-nested polymerase chain reaction (RT-nPCR). The results of this new method were compared with in situ hybridization. A method based on xylene deparaffinization followed by proteinase K digestion yielded RNA of a suitable quality for reliable and consistent multiplex RT-nPCR analyses. PEDV and TGEV cDNAs were detected in jejunal tissues from experimentally and naturally infected pigs by multiplex RT-nPCR. Distinct positive signals for PEDV and TGEV were also detected in the same jejunal tissues by in situ hybridization. The rate of conformity between multiplex RT-nPCR and in situ hybridization was 100% for the detection of PEDV and TGEV in formalin-fixed paraffin-embedded jejunal tissues.

Animals↗