SEARCH · PubMed Health

Results for “Paraffin Embedding”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources

PubMed1997

Detection of CD44 splice variants in formalin-fixed, paraffin-embedded specimens of human skin cancer.

The standard form of CD44 (CD44s) and CD44 isoforms, containing sequences encoded by one or several of 10 different variant CD44 exons (v1-v10), are thought to play a crucial role in the growth and metastasis of certain human tumors. Recently, monoclonal antibodies (mAbs) directed against all CD44 isoforms (panCD44), or against epitopes encoded by specific variant exons (CD44v) have been developed, which unfortunately only stain cryopreserved tissues. We wished to develop a technique to unmask chemically CD44s and CD44v epitopes in paraffin-embedded specimens of human skin cancers, so that they would be accessible for these mAbs. To address this issue, CD44s and CD44v expression was compared in cryopreserved and in formalin-fixed, paraffin-embedded biopsies obtained from the same basal cell carcinomas (BCC), squamous cell carcinomas (SCC), primary malignant melanomas (PMM) and metastatic malignant melanomas (MMM). Formalin-fixed tumors were deparaffinized and treated briefly with an antigen retrieval fluid (TUFTM) at 95 degrees C or left untreated. In untreated paraffin-embedded tissues, no CD44s or CD44v staining was detected. In contrast, in antigen retrieval fluid-treated biopsies CD44s and CD44v expression was identical to that in cryopreserved specimens of the same tumor with the exception of mAbs detecting v7/8 and v10. We conclude that antigen retrieval unmasks certain epitopes in formalin-fixed, paraffin-embedded tissues, thus facilitating future research on the relevance of CD44s and CD44v expression for human skin carcinogenesis.

Alternative Splicing↗

PubMed2004

RT-PCR analysis of RNA extracted from Bouin-fixed and paraffin-embedded lymphoid tissues.

In the present study, we have investigated whether RNA can be efficiently isolated from Bouin-fixed or formalin-fixed, paraffin-embedded lymphoid tissue specimens. To this aim, we applied a new and simple method that includes the combination of proteinase K digestion and column purification. By this method, we demonstrated that the amplification of long fragments could be accomplished after a pre-heating step before cDNA synthesis associated with the use of enzymes that work at high temperature. By means of PCR using different primers for two examined genes (glyceraldehyde-3-phosphate dehydrogenase [GAPDH]- and CD40), we amplified segments of cDNA obtained by reverse transcription of the isolated RNA extracted from Bouin-fixed or formalin-fixed paraffin-embedded tissues. Amplified fragments of the expected sizes were obtained for both genes tested indicating that this method is suitable for the isolation of high-quality RNA. To explore the possibility for giving accurate real time quantitative RT-PCR results, cDNA obtained from matched frozen, Bouin-fixed and formalin-fixed neoplastic samples (two diffuse large cell lymphomas, one plasmacytoma) was tested for the following target genes: CD40, Aquaporin-3, BLIMP1, IRF4, Syndecan-1. Delta threshold cycle (DeltaC(T)) values for Bouin-fixed and formalin-fixed paraffin-embedded tissues and their correlation with those for frozen samples showed an extremely high correlation (r > 0.90) for all of the tested genes. These results show that the method of RNA extraction we propose is suitable for giving accurate real time quantitative RT-PCR results.

Acetic Acid↗

PubMedDate not supplied

[Evaluation of 3 methods of DNA extraction from paraffin-embedded material for the amplification of genomic DNA using PCR].

There are several protocols reported in the literature for the extraction of genomic DNA from formalin-fixed paraffin-embedded samples. Genomic DNA is utilized in molecular analyses, including PCR. This study compares three different methods for the extraction of genomic DNA from formalin-fixed paraffin-embedded (inflammatory fibrous hyperplasia) and non-formalin-fixed (normal oral mucosa) samples: phenol with enzymatic digestion, and silica with and without enzymatic digestion. The amplification of DNA by means of the PCR technique was carried out with primers for the exon 7 of human keratin type 14. Amplicons were analyzed by means of electrophoresis in an 8% polyacrylamide gel with 5% glycerol, followed by silver-staining visualization. The phenol/enzymatic digestion and the silica/enzymatic digestion methods provided amplicons from both tissue samples. The method described is a potential aid in the establishment of the histopathologic diagnosis and in retrospective studies with archival paraffin-embedded samples.

DNA↗

PubMed1998

PMP-22 gene duplications and deletions identified in archival, paraffin-embedded sural nerve biopsy specimens: correlation to structural changes.

We retrospectively analyzed paraffin-embedded sural nerve biopsy specimens from cases suspected of having dominantly inherited motor and sensory neuropathy (HMSN) or hereditary neuropathy with liability to pressure palsy (HNPP), with respect to their proportional DNA content at chromosome 17p11.2-12, encompassing the PMP-22 gene, using polymerase chain reaction (PCR). Of 19 cases in whom HMSN Ia had been suspected on clinical, neurophysiological, and histopathological grounds, 14 showed a duplication on chromosome 17p11.2-12. A deletion in the identical chromosomal region could be identified in all of the suspected cases with HNPP. In 5 cases showing neither duplication, deletion, nor a point mutation in the exons of the PMP-22 gene on heteroduplex DNA analysis, the histopathological findings strongly suggested a diagnosis of chronic inflammatory demyelinating polyneuropathy in 2 cases, and HMSN Ib, or HMSN non-a non-b, and HMSN III in 3 cases. It is shown for the first time that archival, formalin-fixed, paraffin-embedded sural nerve biopsy samples can be used for establishing the diagnosis of PMP-22 diseases, i.e., HMSN Ia and HNPP, by PCR amplification of the region coding for the PMP-22 gene.

Adult↗

PubMed2001

Detection of occult melanoma cells in paraffin-embedded histologically negative sentinel lymph nodes using a reverse transcriptase polymerase chain reaction assay.

PURPOSE: Detection of occult metastasis before the development of clinical disease could allow more accurate staging, appropriate follow-up procedures, and adjuvant therapies in patients with malignant melanoma (MM). The sentinel lymph node (SLN) has been proposed as a reliable predictor of metastatic disease in the lymphatic basin draining the primary melanoma. In this study, we screened both paraffin-embedded SLNs and peripheral-blood (PB) samples from MM patients at various stage of disease using a multimarker reverse transcriptase polymerase chain reaction (RT-PCR) assay. The prognostic significance of the presence of PCR-positive markers was also evaluated. PATIENTS AND METHODS: Total RNA was obtained from paraffin-embedded SLN sections and PB samples of 75 MM patients. RT-PCR was performed using tyrosinase and MelanA/MART1 as melanoma-associated markers. Radiolabeled PCR products were analyzed on denaturing polyacrylamide gels. RESULTS: Good sensitivity of the RT-PCR assay on archival tissues was demonstrated after comparison of RT-PCR results on frozen and paraffin-embedded SLNs from 16 MM patients. Significant correlation between the disease stage and marker expression in both PB and SLN samples was observed; the highest value was for patients who were positive for both markers in SLN (P =.006). Progression of disease was significantly associated with the total number of PCR-positive markers in both PB (P =.034) and SLN (P =.001) samples. CONCLUSION: Although sensitivity is lowered by the use of paraffin-embedded specimens, our data indicate that RT-PCR analysis of serial sections from archival SLNs may be helpful in improving detection of occult micrometastases, thus improving staging of patients with melanoma.

Biomarkers, Tumor↗

PubMed1999

Monoclonal antibody-based immunohistochemical detection of porcine epidemic diarrhea virus antigen in formalin-fixed, paraffin-embedded intestinal tissues.

An immunohistochemistry technique was developed for the diagnosis of porcine epidemic diarrhea virus (PEDV). The technique was tested on formalin-fixed, paraffin-embedded intestinal tissues from piglets naturally infected with PEDV. Five different monoclonal antibodies (MAbs) were tested in this study. PEDV antigen was consistently detected in the PLP (4% paraformaldehyde, 100 mM L-lysine dihydrochloride, 10 mM sodium m-periodate in phosphate-buffered saline)-fixed PEDV-infected Vero cells or formalin-fixed, paraffin-embedded intestinal tissues from piglets naturally infected with PEDV. The C9-2-2 MAb gave the strongest reactivity and least background staining, detecting 10 of 10 infected pigs. The positive reaction was cytoplasmic. Positive enterocytes were distributed over the tip and along the sides of atrophied or fused villi in the jejunum and ileum. Positive-staining cells were not detected in the crypts. No staining was observed in cecum and colon. No positive cells were observed when the C9-2-2 MAb was reacted with the tissue sections from noninfected piglets or from transmissible gastroenteritus virus (TGEV)- and rotavirus-infected piglets. The selected anti-PEDV MAbs tested on formalin-fixed, paraffin-embedded tissue sections are useful for diagnosis when virus isolation is not available. This method would be of particular value in countries where both PEDV and TGEV are epizootic and would aid in differentiating between PEDV and TGEV infection.

Animals↗

PubMed1987

Immunophenotyping of non-Hodgkin's lymphomas using a panel of antibodies on paraffin-embedded tissues.

The use of monoclonal and polyclonal antibodies for the immunophenotyping of non-Hodgkin's lymphomas in paraffin-embedded tissue has been limited by the fact that most antigens on lymphoid cells are denatured by histologic fixation, dehydration, and embedment. In this article the authors have analyzed a small panel of antibodies which represent exceptions to this rule, in that they identify denaturation-resistant determinants on leukocyte antigens in paraffin-embedded tissue. Monoclonal antibodies L26 [corrected] and 4KB5 label preferentially B cells, monoclonal antibody UCHL1 stains predominantly T cells, and monoclonal antibody MAC 387 reacts with granulocytes and some macrophages. A polyclonal antiserum raised against purified CD3 (T3) antigen, a T-cell-specific molecule, was also employed. This antibody panel was used to immunophenotype routinely processed tissue biopsy specimens from 61 non-Hodgkin's lymphomas (all of which had been previously phenotyped in cryostat sections). The lineage of the neoplastic cells was correctly identified in 32 of 34 (94%) cases of B-cell lymphoma, in 19 of 19 (100%) cases of T-cell neoplasm, and in 2 of 4 (50%) cases of histiocytic malignancy. It is concluded that this combination of antibodies is helpful in immunophenotyping non-Hodgkin's lymphomas when only paraffin-embedded tissue sections are available, although additional reagents of higher specificity are required to improve the identification of lymphomas.

Antibodies, Monoclonal↗

PubMed1997

Comparison of formalin, ethanol, and Histochoice fixation on the PCR amplification from paraffin-embedded breast cancer tissue.

The polymerase chain reaction (PCR) has been successfully employed for the laboratory analyses of genetic and infectious disorders using DNA extracted from paraffin-embedded tissues. However, fixative type and fixation time influenced PCR reactions and in some circumstances amplification fragments could not be efficiently generated. In this study, we determined the effects of three commonly used fixatives including ethanol, formalin and Histochoice, on the PCR amplification of DNA from paraffin-embedded breast cancer tissue. The effect of fixatives and fixation times was measured by the ability of the extracted DNA to serve as a template for the amplification of 280 and 530 base pair DNA fragments. On amplifying DNA, positive reactions were uniformly seen in the ethanol specimens. The next best fixative was Histochoice with positive results almost constantly observed in the PCR reactions performed. Formalin fixation sometimes compromised DNA amplification. Our results are consistent with previous reports investigating the effect of ethanol and formalin fixation on DNA amplification by PCR. Moreover, this is the first study showing that paraffin-embedded tissues fixed with Histochoice can be efficiently used for PCR gene amplification.

Breast Neoplasms↗

PubMed2003

[Amplification of beta-catenin gene in the paraffin-embedded epidermal tissue].

OBJECTIVE: To establish a method of extracting DNA from the paraffin-embedded epidermal tissue and examine the amplification of beta-catenin gene by polymerase chain reaction (PCR) analysis. METHODS: Exon 3 of the beta-catenin gene was amplified by PCR in 14 paraffin-embedded Bowen's disease (BD) of various weight and years. RESULTS: The amplification of exon 3 of beta-catenin gene was successful in all the 10 mg and 20 mg samples, but not in the 5 mg samples. The amplification of exon 3 of beta-catenin gene was successful in 9 samples embedded within 10 years, and in only 2 of the 5 samples embedded more than 10 years. CONCLUSION: Epidermal tissue whose weight is 10 mg or more within 10 years of embedding can be used in the amplification of purpose gene by PCR.

Cytoskeletal Proteins↗

PubMed1980

ESR investigation of paraffin-embedded ocular melanomas.

Ocular melanomas embedded in paraffin wax for histological examination have been studied by electron spin resonance (ESR) spectroscopy. A free-radical signal was detected at the g = 2.003 section of the spectrum. The amplitude of this signal was correlated with the number of melanin granules in microscopical slides made from the tumour. This positive correlation can make ESR spectroscopy suitable for estimating the melanin content in the embedded melanoma blocks. Additional paramagnetic signals can also be detected. The clarification of their significance needs, however, further ESR measurements.

Electron Spin Resonance Spectroscopy↗

PubMed2005

Impact of formalin-fixation and paraffin-embedding on the ratio between mRNA copy numbers of differently expressed genes.

Several studies have shown that specific mRNA sequences can be successfully detected in formalin-fixed, paraffin-embedded tissues using reverse transcriptase-polymerase chain reaction (RT-PCR). Here, we test the hypothesis that gene expression levels can be accurately quantified in formalin-fixed, paraffin-embedded tissues by determining the ratio between the copy number of the mRNA molecule of interest and the mRNA copy number of a so-called housekeeping gene. The mRNA copy numbers of the variably expressed multiple drug resistance gene (MDR)-1 and four housekeeping genes (hypoxanthine phosphoribosyl-transferase-1, glyceraldehyde-3-phosphate dehydrogenase, beta-actin, and elongation factor-1a) were quantified by real-time-quantitative RT-PCR before and after formalin-fixation and paraffin-embedding of 576 tissue samples (heart, kidney, spleen, liver) from three beagle dogs. The results indicate that fixation and embedding drastically altered the ratios between the different mRNA copy numbers and that the relative expression levels of MDR-1 per any of the housekeeping genes were artificially increased or decreased up to more than tenfold. It would thus appear questionable to normalize quantitative expression data from fixed and embedded tissues by using housekeeping genes as reference. In contrast, tissue autolysis of up to 24 h and long-term storage of embedded tissues of up to 20 years had no additional effects.

Animals↗

PubMed1994

Application of dual parameter analysis in flow cytometric DNA measurements of paraffin-embedded samples.

In a comparison of flow cytometric DNA measurements on fresh and paraffin-embedded material from primary squamous cell carcinomas of the head and neck region, we discovered that previously undetected aneuploid clones could be detected by dual parameter analysis of cytokeratin and DNA applied to disintegrated cells from paraffin sections. Using this new approach the correlation coefficient between DNA-indices from fresh and paraffin-embedded material increased from 0.423 to 0.904.

Aneuploidy↗

PubMed1999

Immunolocalisation of PIVKA-II in paraffin-embedded specimens of hepatocellular carcinoma.

AIMS/BACKGROUND: Although serum PIVKA-II has been widely used as a tumor marker for hepatocellular carcinoma (HCC), little information is available concerning tissue PIVKA-II, and detection of tissue PIVKA-II in paraffin-embedded tissue specimens of HCC is also considered difficult. METHODS: Paraffin-embedded HCC tissues obtained at autopsy from 22 patients were subjected to immunohistochemical staining using the antibody MU-3 (Eisai Co., Ltd.) after microwave antigen retrieval. RESULTS: PIVKA-II was mainly detected in the cytoplasm of HCC cells. The intensity of tissue PIVKA-II staining was not correlated with serum PIVKA-II levels or with the histotogical differentiation of HCC. However PIVKA-II staining tended to be more intense in tissue from patients with portal tumor thrombus, distant metastases, or a longer duration of HCC. CONCLUSION: This method of immunohistochemical staining is easy and simple to use and may be helpful for detecting tissue PIVKA-II in paraffin-embedded HCC specimens.

Adult↗

PubMed1993

Immunomycology: rapid and specific immunocytochemical identification of fungi in formalin-fixed, paraffin-embedded material.

We report the rapid (less than 1 hr), immunocytochemical identification of various fungi in formalin-fixed, paraffin-embedded tissues using antisera originally developed for use in immunodiffusion assays. Primary antisera directed towards fungal genera including Aspergillus, Blastomyces, Candida, Coccidioides, Cryptococcus, Histoplasma, and Sporothrix were examined. The specificity of each antiserum was evaluated by the presence or absence of crossreactivity with other morphologically similar fungi in both paraffin-embedded pure fungal cultures and tissues with culture-confirmed fungal infections. Each antiserum reacted strongly with the fungus to which it had been raised, whether examined in pure culture or infected tissues. The antisera raised against Candida, Cryptococcus, and Sporothrix did not exhibit cross-reactivity with any other fungus tested. However, the antisera raised to Aspergillus, Blastomyces, Coccidioides, and Histoplasma demonstrated significant crossreactivity with other genera of fungi, thus precluding their routine use in diagnostic immunocytochemistry. The results indicate that immunocytochemistry may provide an important adjunct to other methods, such as immunodiffusion or complement fixation assays and histochemical stains such as the Grocott methenamine silver or periodic acid-Schiff, when attempts are made to specifically identify certain fungi in formalin-fixed, paraffin-embedded tissues before mycology culture results are available.

Antigens, Fungal↗

PubMed2000

New comprehensive denaturing-gradient-gel- electrophoresis assay for KRAS mutation detection applied to paraffin-embedded tumours.

A comprehensive mutation detection assay is presented for the entire coding region and all splice site junctions of the KRAS oncogene. The assay is based on denaturing gradient gel electrophoresis and applicable to archival paraffin-embedded tumour material. All KRAS amplicons are analysed within two lanes of a DGGE gel under a single set of experimental conditions. Six known codon 12 mutations in genomic DNA from different paraffin-embedded tumours could readily be detected. When testing 35 paraffin-embedded Dukes' C colorectal carcinomas for unknown mutations, 12 tumours were found with mutations in codons 12 or 13. None of the tumours appeared to have a codon 61 mutation. In nine tumours, however, 11 additional sequence variations were found outside the hot-spot codons. None of these occurred in germline DNA from 57 individuals. Of these variations, three are considered as significant mutations, as they result in a non-conservative substitution of amino acid residues essential for the functioning of the KRAS protein. Thus, in total, 15 of the 35 Dukes' C tumours (43%) had a KRAS mutation of functional significance. Moreover, a novel exon 4B polymorphism was found to occur in 10 of the 35 tumours. The results of this study suggest that in restricting analysis of KRAS to hot-spot mutation sites only, significant information may be missed.

Colorectal Neoplasms↗

PubMed1999

Assessment of DNA content in formalin-fixed, paraffin-embedded tissue of lung cancer by laser scanning cytometer.

A new cytometric device, a laser scanning cytometer was developed to overcome the limitations of flow cytometry (FCM) and image analyses. The purpose of this study was to develop a method that allows laser scanning cytometry (LSC) to be used for measuring the cellular DNA content of paraffin-embedded tissues. Paraffin-embedded lung cancer tissue from 30 patients was analyzed by both FCM (p-FCM) and LSC (p-LSC). In addition, touch preparations from fresh frozen tissues were prepared to provide material for LSC (f-LSC). The limits of agreement for the DNA indices (DI) measured by p-LSC and p-FCM were -0.07 to 0.07, indicating that for a given case, these methods would be expected to differ by no more than 0.07. The limits of agreement for comparisons between the other materials and methods were wider and depended upon the size of the measurements. Agreement between f-LSC and p-FCM was good for small DI values, but poor for large values. Agreement between f-LSC and p-LSC was poor for small and large DI values, but good for moderately sized values. Discordancies in DNA ploidy status between different materials and methods may have been caused by either the heterogeneity within tumors, sampling errors or differences in the interpretation of histograms. This method allows a comparison of the results of DNA analysis with histologic findings from hematoxylineosin-stained sections and the prognosis of the patients.

Aneuploidy↗

PubMed1998

Expression of KAI1 in paraffin-embedded normal, hyperplastic and neoplastic prostate and prostate carcinoma cell lines.

Expression of KAI1, a tumor metastasis suppressor gene, was studied with different fixatives in frozen and paraffin-embedded sections of human and rat prostate carcinoma cell lines and human prostate lesions by immunohistochemistry. Immunoreactivity of the membrane antigen in cell lines was associated with known expression levels in these lines and the fixative used. Formalin and paraformaldehyde helped maintain the immunoreactivity of cells. In human prostate, frozen sections revealed diffuse reactivity of the antigen in normal and neoplastic tissues while paraffin-embedded tissues usually showed focal reactivity, although more than 50% of cases with normal epithelium and adenocarcinomas were reactive. In some cases, pretreatment with trypsin enhanced immunoreactivity. Benign prostatic hyperplasia (BPH) showed the most intense diffuse immunoreactivity, which suggested enhanced expression. Prostatic intraepithelial neoplasia (PIN) also often expressed high levels of KAI1. Three of five metastases were reactive but two primaries and their metastases were not. Lymphocytes in primary carcinomas and lymphocytes and germinal center cells in lymph nodes were immunoreactive, while adjacent primary or metastatic prostate adenocarcinoma epithelium was not immunoreactive. Although paraffin-embedded human tissues were not optimal for determining levels of expression of KAI1, they did show immunoreactivity that could have prognostic value and showed the specific cytoplasmic localization of the protein in cells.

Adenocarcinoma↗

PubMed2000

Anti-CD10 immunoperoxidase staining of paraffin-embedded acute leukemias: comparison with flow cytometric immunophenotyping.

CD10 is common in B-precursor acute lymphoblastic leukemia (ALL) but is rare in acute myeloid leukemia (AML). However, until recently, analysis for CD10 has generally required fresh or frozen tissue. 56C6 is a monoclonal antibody that is now commercially available for the detection of CD10 in routinely processed paraffin-embedded tissue. Immunoperoxidase stains for CD10 on paraffin-embedded bone marrow core biopsy specimens (B5-fixed, decalcified) and marrow aspirate clots (formalin-fixed) were compared with flow cytometric immunophenotyping for CD10 on fresh cell suspensions in 20 cases of AML and in 30 cases of ALL. CD10 detection by immunohistochemistry agreed with CD10 by flow cytometry in 98% (49 of 50) of acute leukemias. The results matched in 100% (20 of 20) of AML. Five percent (1 of 20) of AMLs expressed CD10. Two of the AMLs with monocytoid differentiation were interpreted as negative for CD10 by flow cytometry, although these had nonspecific dim immunofluorescence for multiple markers, including CD10, and these cases were negative by immunohistochemistry. CD10 detection by immunohistochemistry agreed with CD10 by flow cytometry in 97% (29 of 30) of ALL. Eighty-four percent (21 of 25) of B-precursor ALL and 40% (2/5) of T-lineage ALL expressed CD10 by immunohistochemistry. In 1 case of B-precursor ALL, CD10 was dimly positive in 24% of the blasts by flow cytometry but negative by immunohistochemistry. We conclude that immunohistochemical staining of paraffin-embedded tissue, either B5- or formalin-fixed, is an effective method for the detection of CD10 in acute leukemia. This technique is useful in distinguishing AML from ALL.

Acute Disease↗