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Results for “Paraffin Embedding”

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At least 523 records · Page 29Linked to original sources

PubMed1997

Paraffin-embedded tissue as a source of RNA for gene expression analysis in oral malignancy.

OBJECTIVE: To assess the feasibility of using archival oral mucosal tissue to examine gene expression at the ribonucleic acid (RNA) level. MATERIALS AND METHODS: We describe the isolation of RNA from 8 microns sections of formalin-fixed paraffin-embedded oral mucosal tissue. RNA was reverse transcribed and three candidate genes amplified by polymerase chain reaction (PCR). The ribosomal protein S14 gene is a housekeeping gene which has been used as an internal standard in several quantitative PCR protocols. The thymidine kinase (TK) gene is expressed at low levels in most tissues and, with a well-documented genomic organisation, is a useful tool for discrimination between genomic DNA and cDNA. The RI alpha gene is reported to be overexpressed in many cancer cell lines, in malignant tissue and in vitro transformed cells. RESULTS: The S14 gene, the TK gene and the RI alpha gene of the cAMP-dependent protein kinase (PKA) were amplified successfully from formalin-fixed paraffin-embedded tissue sections. The TK primer pair is a useful additional tool in the unambiguous identification of RNA-derived species. CONCLUSION: RNA suitable for reverse transcribed (RT)-PCR was extracted from archival oral mucosal tissue. This should permit rapid sequence analysis of transcribed tumor suppressor genes and oncogenes in this material. Furthermore, the RT-PCR approach described may allow quantification of gene expression in oral mucosal archival material processed in a standard fashion.

Carcinoma, Squamous Cell↗

PubMed2004

Detection of the M30 neoepitope as a new tool to quantify liver apoptosis: timing and patterns of positivity on frozen and paraffin-embedded sections.

One of the first stages of apoptosis is cytokeratin cleavage mediated by caspases, which is associated with the expression of a neoepitope, the cleavage site of cytokeratin 18, identifiable by the M30 monoclonal antibody. The aim of this study was to evaluate the timing of neoantigen expression and its modifications in the various morphologic stages of apoptosis on frozen and paraffin-embedded sections from liver biopsies of patients with chronic hepatitis or transplanted liver. The appearance of this neoepitope coincides with the gradual disappearance of cytokeratins, with the appearance of nuclear DNA fragmentation, and with the presence of Councilman bodies. The staining patterns on paraffin-embedded sections of liver specimens were similar to those found in frozen sections, with a reduced sensitivity. The M30 antibody is correlated with apoptosis, and its specificity for epithelial cells makes this method the first choice for routine evaluation of apoptosis in liver epithelial cells.

Antibodies, Monoclonal↗

PubMed1990

Production of a monoclonal antibody as immunohistochemical marker on paraffin embedded tissues using a new immunization method.

This report describes a method for the production of murine monoclonal antibodies (MAbs) against cellular antigens preserved during formol fixation and paraffin embedding of human tissues in an attempt to select markers that would be useful in immunopathology. Hybridomas were prepared using spleen cells from mice immunized with cell suspensions obtained from formalin-fixed paraffin block sections of a human breast carcinoma. A monoclonal antibody 83 D4 was selected, which was reactive with paraffin embedded breast carcinoma tissues, but not with normal breast. The reactive antigen has a high molecular weight (400-1000 kD) and was detected on the cell surface of live human breast cancer cell lines and on frozen tissues sections. These results demonstrate that the MAb 83 D4 identifies a native breast tumor associated epitope conserved during tissue fixation and embedding and could be used as an immunohistochemical marker.

Antibodies, Monoclonal↗

PubMed1996

Sonification as a means of enhancing the detection of gene expression levels from formalin-fixed, paraffin-embedded biopsies.

We describe a novel approach for the isolation and quantification of mRNA from archival specimens by using oligo(dT)25 paramagnetic beads and the reverse transcription polymerase chain reaction (RT-PCR). A preliminary study is conducted to evaluate experimental conditions and the effects of varied periods of sonification on the yield of mRNA isolated from formalin-fixed, paraffin-embedded human biopsy samples. Validation of this approach will involve the comparison of observed beta-actin gene expression levels among different samples from the same patient after various periods of sonification. The novelty of this method is that it offers a means of analyzing archival samples using semiquantitative RT-PCR following sonification-enhanced mRNA extraction. The utility of this protocol allows for gene expression studies to be done effectively using the formalin-fixed, paraffin-embedded archival samples that are commonly available in all hospital pathology departments.

Actins↗

PubMed2006

RCL2, a new fixative, preserves morphology and nucleic acid integrity in paraffin-embedded breast carcinoma and microdissected breast tumor cells.

Methacarn and RCL2, a new noncrosslinking fixative, were compared to formalin-fixed or frozen tissue samples of the same invasive breast carcinoma and were evaluated for their effects on tissue morphology and immunohistochemistry as well as DNA and RNA integrity. The histomorphology of methacarn- or RCL2-fixed paraffin-embedded tumors was similar to that observed with the matched formalin-fixed tissues. Immunohistochemistry using various antibodies showed comparable results with either fixative, leading to accurate breast tumor diagnosis and determination of estrogen and progesterone receptors, and HER2 status. Methacarn and RCL2 fixation preserved DNA integrity as demonstrated by successful amplification and sequencing of large DNA amplicons. Similarly, high-quality RNA could be extracted from methacarn- or RCL2-fixed paraffin-embedded MCF-7 cells, whole breast tumor tissues, or microdissected breast tumor cells, as assessed by electropherogram profiles and real-time reverse transcriptase-polymerase chain reaction quantification of various genes. Moreover, tissue morphology and RNA integrity were preserved after 8 months of storage. Altogether, these results indicate that methacarn, as previously shown, and RCL2, a promising new fixative, have great potential for performing both morphological and molecular analyses on the same fixed tissue sample, even after laser-capture microdissection, and can open new doors for investigating small target lesions such as premalignant breast lesions.

Breast Neoplasms↗

PubMed1998

Detection of tyrosinase mRNA in formalin-fixed, paraffin-embedded archival sections of melanoma, using the reverse transcriptase in situ polymerase chain reaction.

Most studies of the reverse transcriptase in situ polymerase chain reaction technique have reported results from assessments of cultured cells, frozen sections, and cytospin preparations. For application to routine diagnosis, it will be necessary to adapt the technique for use with formalin-fixed, paraffin-embedded tissues, the materials that are generally available. We have evaluated the feasibility of such an approach, using surgical pathology archival material from 25 UCLA patients: 15 tissues from primary and metastatic melanoma, 7 from nonmelanocytic tumors, including cancer of the lung, colon, kidney and skin and a thyroid adenoma, and 3 nontumorous tissues. Seven of 15 melanoma tissues gave a strong positive signal, 5 gave a weak signal, and 3 were negative. None of the 10 nonmelanoma tissues gave a positive signal. The specific reaction product was mainly located in the cytoplasm. None of the nonmelanocytic tumors or normal tissues demonstrated this pattern of cytoplasmic staining. Some nonspecific nuclear staining was observed in melanocytic and nonmelanocytic tumors and must not be overread as a true positive result. It is possible to detect tyrosinase mRNA in formalin-fixed, paraffin-embedded tissue sections of melanoma, but the technique remains too demanding for routine application.

Formaldehyde↗

PubMed2004

A new immunofluorostaining method using red fluorescence of PerCP on formalin-fixed paraffin-embedded tissues.

Immunofluorostaining, a versatile tissue staining method, is used in biomedical research because of its clear contrast and precise quantification of positive signals. However, its application in clinical diagnosis has been limited. A major obstacle is high fluorescent background of formalin-fixed, paraffin-embedded tissue sections (paraffin sections). On paraffin sections, strong and broad fluorescence of the section overlapping that of conventional fluorescent dyes such as fluorescein isothiocyanate (FITC) prevents detection of target immunofluorescence. To circumvent the background, we selected an albuminous dye, peridinin chlorophyll a protein (PerCP), for immunostaining of human tumor sections with tumor-reactive monoclonal antibodies. Red fluorescence of PerCP clearly distinguished the tumor region within the yellow-green autofluorescence of the section. Furthermore, it was possible to observe tissue morphology simultaneously without any counterstaining; autofluorescence served as counterstaining in this method. Digital quantification of PerCP-stained image intensity correlated (r2>0.99) well with extracted PerCP amount, indicating the usefulness of image quantification. We conclude that this new and simple immunofluorostaining method can be applied to pathological diagnosis of a wide range of conditions, including cancer.

Animals↗

PubMed2006

Cytogenetic and clinicopathological characterization by fluorescence in situ hybridization on paraffin-embedded tissue sections of twenty-six cases with malignant lymphoma of small intestine.

OBJECTIVE: In small intestinal malignant lymphoma (SIML), the correlation between specific chromosomal abnormalities and clinicopathological features remains unclear. The aim of this study was to determine the frequency of chromosomal translocations involving the BCL1, BCL2, c-MYC, BCL6 and MALT1 genes by using fluorescence in situ hybridization directly on paraffin-embedded tissue sections (tissue-FISH). MATERIAL AND METHODS: Twenty-six cases diagnosed as having SIML between 1996 and 2003 were the subjects of the clinicopathological investigation conducted in this study. Tissue-FISH was performed with specific probes on paraffin-embedded tissue sections as described previously. RESULTS: The primary site was frequently located at the duodenum (9 cases, 35%). In accordance with the World Health Organization classification, 14 (53%) cases were diagnosed as having diffuse large B-cell lymphoma (DLBCL) and 6 (23%) as marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MALT). Macroscopically, DLBCL and MALT lymphoma displayed various macroscopic features. Cytogenetically, IGH-BCL2 translocation was detected in 3 (21%) out of 14 DLBCL cases, but in none of the MALT lymphomas. BCL6 translocation was detected in 5 (35%) of 14 DLBCL cases and in 1 (17%) of 6 MALT lymphoma cases (17%). API2-MALT1 translocation was detected in 1 (7%) of 14 DLBCL cases and in 1 (17%) of 6 MALT lymphoma cases. CONCLUSIONS: The duodenum was preferentially involved in SIML. DLBCL and MALT lymphoma showed various macroscopic features. Tissue-FISH analysis disclosed that DLBCL is cytogenetically heterogeneous. Furthermore, our study validated tissue-FISH as an additional promising diagnostic tool for detecting specific chromosomal translocations in NHL.

Adolescent↗

PubMed2006

Detection of specific human papillomavirus types in paraffin-embedded sections of cervical carcinomas.

Human papillomaviruses (HPV) are the causative agents of most cervical carcinomas. A complete understanding of the HPV types that cause cervical carcinoma is needed as vaccines are designed. Fresh tissues are not always available for such studies. We therefore sought to determine the feasibility of HPV studies using formalin-fixed, paraffin-embedded sections of 56 cervical carcinomas, correlating typing information with the pathology and physical state of the HPV sequences within cells. Sections from each specimen were used to extract and purify DNA. Specific HPV types were identified using a PCR/reverse blot strip assay. Tyramide signal-amplified, fluorescent DNA in situ hybridization (FISH) was used to localize HPV within cells. Human beta-globin sequences were amplified in DNA from all specimens. HPV sequences from oncogenic types were identified in 52 of 56 (92.9%) by PCR/reverse blot strip assay, and in one additional case using an HPV 16 multiplex PCR assay. HPV 16 was the most commonly detected type, present in most cases as a solitary isolate. Thirty- five of 42 HPV 16 or HPV 18 PCR-positive specimens were also positive in the FISH assay, in most cases in a pattern consistent with viral integration. We conclude that HPV typing from formalin-fixed, paraffin-embedded sections of cervical carcinomas is possible, with a sensitivity that is similar to that found in studies using fresh tissue.

Animals↗

PubMed1988

Detection of human papillomavirus DNA in cell scrapes and formalin-fixed, paraffin-embedded tissue of the uterine cervix by filter in situ hybridisation.

Filter in situ hybridisation (FISH) was used to detect the presence of DNA of human papillomavirus (HPV) types 6/11 or 16/18 in cell scrapes (CYTOFISH) and formalin-fixed, paraffin-embedded biopsies (HISTOFISH) taken from the uterine cervices of 19 women. Paraffin tissue sections collected for HISTOFISH were either digested with pepsin or lysed with alkali/Triton X-100. The digest or lysate of the tissue sections and cell scrapes were applied to nylon or nitrocellulose membranes for nucleic acid hybridisation using 32P-labeled HPV-DNA probes. CYTOFISH and HISTOFISH were compared directly by taking samples for each method from the cervices of the same women. Of 19 women examined by colposcopy, cytology, and histology, eight were assessed as normal and 11 had evidence of a cervical disorder and/or the presence of HPV infection. Whereas no HPV-DNA was detected in the normal cases, the presence of HPV-DNAs was detected by both CYTOFISH and HISTOFISH in 11 cases with histological evidence of HPV infection and/or dysplasia. In these HPV positive cases, eight contained HPV 16/18, two HPV 6/11, and one a mixed infection of HPV 6/11/16/18. The high correlation between the results of CYTOFISH and HISTOFISH shows that formalin-fixed, paraffin-embedded cervical biopsies are suitable specimens for the detection and typing of HPV-DNA by FISH. Both CYTOFISH and HISTOFISH should facilitate studies on the prevalence and distribution of HPVs and their association with neoplasia.

Autoradiography↗

PubMed1990

Immunophenotyping of acute leukemias using paraffin-embedded tissue sections.

In a study of 55 patients with either acute lymphoid leukemia (ALL; 25 cases) or acute myeloid leukemia (AML; 30 cases), paraffin-embedded bone marrow particle sections were examined with a panel of monoclonal and polyclonal antibodies reactive toward lymphoid and myeloid-associated antigens, using the alkaline phosphatase-anti-alkaline phosphatase (APAAP) technique. All cases were previously classified according to the French-American-British (FAB) Co-operative Group, and cases of ALL were immunophenotyped by flow cytometry. Results indicated that myeloid-associated antibodies (Mac 387, KP 1 [CD68], antielastase, antilactoferrin, and antilysozyme) did not react with any case of ALL, M1-AML, or M6-AML, whereas at least one of these antibodies reacted with 20 of 21 (95%) cases of M2, M3, M4, and M5-AML. Anti-glycophorin C marked cases of M6-AML, whereas anti-CD3 labeled T-cell ALL. None of the antibodies tested specifically identified cases of B-cell ALL. The authors conclude that use of a selected panel of antibodies on paraffin-embedded bone marrow particle sections may be of value in the diagnosis and immunophenotypic classification of many cases of acute leukemias.

Acute Disease↗

PubMed1994

Detection of T-cell clonality in paraffin-embedded tissues.

In lymph node diagnosis, difficulties are frequently encountered with the differential diagnosis of reactive and neoplastic T-cell proliferations. Immunohistochemistry is of limited use, and fresh frozen material for DNA studies is not available in many cases. We have established a polymerase chain reaction (PCR) technique to amplify rearranged T-cell receptor (TCR)-gamma sequences from paraffin-embedded material. Our method differs from other techniques previously described in that it uses four sets of family-specific variable (V)gamma primers. Clonality of the investigated T cells is reflected not only by the varying lengths of amplified products but also by differences in the relative amount of rearranged V gamma families. Preliminary studies indicate that this approach can provide information about the presence of predominant T-cell clones within the sample and thus help to classify the lymph node lesion. With this technique we were able to confirm clonality in seven of 12 T-cell lymphomas in paraffin-embedded tissues.

Adult↗

PubMed1993

HER-2 and INT-2 amplification estimated by quantitative PCR in paraffin-embedded ovarian cancer tissue samples.

Competitive polymerase chain reaction (PCR) systems were developed for rapid and quantitative estimation of HER-2 (c-erbB-2) and INT-2 oncogene amplification in paraffin-embedded ovarian cancer tissue samples. The beta-globin gene was used as reference and DNA from paraffin-embedded placenta tissue as single copy control. Reliability of the PCR method could be demonstrated by comparing dot blot data with PCR data of identical tumour samples. The PCR method was used to determine HER-2 and INT-2 copy numbers in 196 ovarian cancer samples. HER-2 and INT-2 were found to be amplified in 40 and 19%, respectively. In 8% HER-2 copy numbers were greater than five, but no high INT-2 copies were noted. Kaplan-Meier estimates did not reveal significant association with overall survival. Indirect correlation between HER-2 and INT-2 amplification was observed. The present PCR system is a valuable method for prospective and retrospective studies.

Base Sequence↗

PubMed1995

Detection of bcl-1 gene rearrangement and B-cell clonality in mantle cell lymphoma using formalin-fixed, paraffin-embedded tissues.

Mantle cell lymphoma (MCL) has recently emerged as a distinct clinicopathologic entity with characteristic molecular genetic features. Specifically, MCL are clonal B-cell neoplasms and often harbor bcl-1 gene rearrangements. Although this genetic profile is well documented, scant or no data are available on the molecular assessment of MCL using formalin-fixed, paraffin-embedded tissue as a sample source. The polymerase chain reaction (PCR) was employed to study bcl-1 and immunoglobulin heavy chain (IgH) gene rearrangements (B-cell clonality) using formalin-fixed tissue from 12 cases of MCL. In addition, 12 cases of low grade B-cell lymphoma and 5 cases of reactive lymphocytic hyperplasia were studied as comparison controls. A hemi-nested PCR assay was developed to identify major translocation cluster (MTC) bcl-1 gene rearrangements, whereas IgH gene rearrangements were evaluated by both a single-step and hemi-nested approach. Bcl-1 gene rearrangements were amplified in 4 of 12 (33%) MCL, but in none of the controls. With the hemi-nested approach, B-cell monoclonality was demonstrated in 11 of 12 (92%) MCL; 6 of 6 (100%) small lymphocytic lymphomas; 1 of 2 marginal zone lymphomas; 1 of 4 follicular lymphomas; and 0 of 5 reactive lymphocytic hyperplasias. When one-step PCR was used for B-cell clonality assessment, the overall detection rate was lower, specifically: 8 of 12 (67%) MCL; 4 of 6 (67%) small lymphocytic lymphomas; 1 of 2 marginal zone lymphomas; 0 of 4 follicular lymphomas; and 0 of 5 reactive lymphocytic hyperplasias were identified as monoclonal. We have demonstrated that MTC bcl-1 gene rearrangements can be amplified from formalin-fixed tissue. In addition, monoclonal B-cell populations from MCL are better amplified with a hemi-nested approach rather than a single-step PCR assay. With specialized nucleic acid isolation techniques and appropriate PCR protocol design, formalin-fixed, paraffin-embedded tissue is an adequate source of DNA for assessing MTC bcl-1 and IgH gene rearrangements.

B-Lymphocytes↗

PubMed1993

Immunohistochemical assessment of cellular proliferation in the developing human CNS using formalin-fixed paraffin-embedded material.

Assessment of cell proliferation in the developing human brain has been limited to counting mitotic cells, since the other procedures currently used for determination of the mitotic activity either depend on experimental manipulation of the tissue, e.g., labeling with radioactive thymidine precursors or with bromodeoxyuridine, or on frozen sections of the tissue, e.g., Ki-67 immunoreactivity. As most of the developing human brain material available is formalin fixed and paraffin embedded, these procedures are not practical. An immunohistochemical technique based on a monoclonal antibody directed against a proliferating cell nuclear antigen (PCNA) was used for detecting cellular proliferation in the developing human brain. Known progenitor cells in proliferating zones showed distinct PCNA-reactivity, but the method also revealed new areas of cell proliferation in fixed paraffin-embedded tissue blocks from the developing human brain.

Antibodies, Monoclonal↗

PubMed2000

Monoclonal antibodies recognizing CD5, CD10 and CD23 in formalin-fixed, paraffin-embedded tissue: production and assessment of their value in the diagnosis of small B-cell lymphoma.

AIMS: Assessment of the expression of antigens CD5, CD10 and CD23 can be of value in the differential diagnosis of small B-cell lymphoma. Correct subclassification is important since optimal treatment regimes differ between the subtypes. The aim of this study was to generate monoclonal antibodies recognizing these antigens in paraffin-embedded tissue and to assess their efficacy using a panel of cases of small B-cell lymphoma of various subtypes. METHODS AND RESULTS: For each antibody synthetic recombinant protein and conventional murine hybridoma technology was employed. Monoclonal antibodies effective in formalin-fixed, paraffin-embedded tissue were successfully generated, designated NCL-CD5-4C7, NCL-CD10-270 and NCL-CD23-1B12, respectively. A series of 58 cases of small B-cell lymphoma including examples of each subtype (lymphocytic, follicle centre cell, mantle cell, marginal zone and lymphoplasmacytoid) was assembled and immunostaining for the respective antigens carried out using the monoclonal antibodies produced. Our results indicate that the antibodies are specific for their respective antigens and give the predicted phenotypic profile in the small B-cell lymphoma subtypes. CONCLUSIONS: These novel monoclonal antibodies may be of value in routine diagnostic practice.

Animals↗

PubMed1998

Incidental early detection of a splenic marginal zone lymphoma by polymerase chain reaction analysis of paraffin-embedded tissue.

Splenic marginal zone lymphoma (SMZL) most commonly presents with splenomegaly and stage IV disease. To our knowledge, there have been only two reported cases of SMZL without associated splenomegaly; one was detected incidentally after a bicycle accident. This previously reported case represented an early-stage SMZL with monoclonality confirmed by immunohistochemistry. We report a case of early-stage SMZL detected incidentally following a motor vehicle accident; monoclonality was confirmed by polymerase chain reaction analysis of paraffin-embedded tissue owing to the inability of confirmation by immunohistochemical techniques. We describe our findings and emphasize the importance of recognizing early stages of SMZL in incidental splenectomies by polymerase chain reaction analysis of paraffin-embedded tissue. Frozen tissue is not generally available in such cases.

Accidents, Traffic↗

PubMed1995

Detection and sequence confirmation of Sin Nombre virus RNA in paraffin-embedded human tissues using one-step RT-PCR.

Sin Nombre virus (SNV) is the causative agent of hantavirus pulmonary syndrome (HPS). SNV RNA can be detected in fresh or frozen autopsy tissue samples by reverse transcriptase polymerase chain reaction (RT-PCR), and virus antigens can be identified by immunohistochemistry. A method was developed for demonstration of SNV RNA in formalin-fixed, paraffin-embedded tissues by RT-PCR. Virus genomes were detected in 8 of 12 (66.7%) fixed human tissue samples that were positive by immunohistochemistry, and RT-PCR prior to tissue fixation. By comparison with nucleotide sequences determined previously in fresh or frozen tissues of the same patients, identical genomic sequences were obtained, proving the authenticity of the PCR products. The study demonstrates that detection of SNV RNA in formalin-fixed, paraffin-embedded archival tissue by RT-PCR is feasible. This method allows retrospective studies on the phylogenetic epidemiology of SNV in North America.

Base Sequence↗