Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Tissue Embedding”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 73 records · Page 4Linked to original sources
PubMed2000

CD10 expression in follicular lymphoma versus reactive follicular hyperplasia: evaluation in paraffin-embedded tissue.

The differentiation of reactive follicular hyperplasia (RFH) from follicular lymphoma (FL) may be a diagnostic challenge and require the use of adjuvant studies. Antibodies to CD10 have been used with flow cytometry and frozen tissue sections and recently have become available for use with paraffin-embedded tissue. We sought to investigate the utility of CD10 in the differentiation of RFH from FL in paraffin-embedded tissue. Twenty-three cases of FL and 19 cases of RFH were evaluated after immunostaining with antibodies to CD3, CD20, BCL2, and CD10 antigens. Intensity of CD10 expression was graded. CD10 expression was present in 87% of cases of FL. Follicles demonstrated strong positivity in 70%. One CD10-positive case of FL showed equivocal staining for BCL2 and one an absence of staining for BCL2. Weaker but definite staining was present in 17%, and 13% were negative for CD10. In contrast, none of the cases of RFH was strongly positive for CD10 expression, with 26% demonstrating weak immunostaining, one case showing equivocal staining, and 68% being entirely negative. CD3, CD20, and BCL2 stained appropriately in all cases. These findings indicate that immunohistochemical staining of paraffin-embedded tissue sections for CD10 may help differentiate reactive from neoplastic follicular lesions.

Antigens, CD20↗
PubMed2004

Effect of formalin, acetone, and RNAlater fixatives on tissue preservation and different size amplicons by real-time PCR from paraffin-embedded tissue.

RNA recovered from paraffin-embedded tissue has been reported to be a suitable substrate for polymerase chain reaction. During tissue fixation and paraffin embedding, RNA undergoes degradation, but with certain restrictions, it can be used for gene expression studies. At the same time, formalin-fixed, paraffin embedded histopathology archives contain an unestimable collection, which could be analyzed to investigate changes in mRNA expression in pathologic processes. To decide for future tissue conservation of pathology samples, it would be reasonable to satisfy both histologic and molecular biologic needs. The effect of three different fixation methods, RNAlater (SIGMA R 0901, St Louis, MO), acetone, and formalin, were compared by histology, immunohistochemistry, and real-time PCR. To assess tissue structure preservation and antigenicity, hematoxylin-eosin staining and immunohistochemistry were performed; to assess RNA quality, RNA was extracted and the transcription of different amplicon sizes (121, 225, 406 bp for GAPDH; 166, 310, 536 bp for beta globin) were examined on human endometrium samples. The most adequate tissue preservation was found in case of formalin fixation, while there were no significant differences in the three fixatives' yields for various size real-time PCR amplicons. Longer amplicons (above approximately 225 bp) have limited use for gene expression studies, while shorter amplicons could give more reliable results.

Adult↗
PubMed1985

Flow cytometric determination of DNA ploidy level in nuclei isolated from paraffin-embedded tissue.

Nuclei, isolated from paraffin-embedded tissue, were stained with propidium iodide (PI) and found suitable for DNA analysis by flow cytometry (FCM). DNA-derived fluorescence intensity, however, was always decreased and had a much higher intersample variability as compared to results obtained with fresh material. Using chicken red blood cells (CRBC) as a model system, we found the lower fluorescence intensity to be due to the formalin fixation step in tissue processing. The intersample variability was found to be at least partly caused by variations in the duration of fixation. Overnight trypsinization improved the fluorescence intensity but did not reduce the intersample variability. Under all conditions tested PI binding to CRBC appeared to be saturable. Since fresh diploid or red blood cells could not be used to standardize DNA histograms, an alternative approach was developed in which nuclei from paraffin-embedded normal and tumor tissue of the same specimen were mixed. With this method DNA indices (DI) of 24 colorectal cancers were found to be closely correlated (r = 0.9877, P less than 0.001) with DI obtained with fresh tumor tissue from the same patients. The correlation of the percentages of S-phase nuclei between paraffin-extracted and fresh samples (r = 0.5875, P less than 0.05) was as high as could be expected, taking sampling differences into account. This method is an important tool for the retrospective analysis of FCM-derived DNA parameters in relation to diagnosis and prognosis of neoplasms.

Animals↗
PubMed1978

Immunofluorescence studies of canine distemper encephalitis on paraffin-embedded tissue.

A paraffin-embedding technique for fluorescent antibody studies of canine distemper encephalitis was developed. Specific fluorescence was demonstrated in all brain tissue from dogs with canine distemper, and when compared with tissue on cryostat sections, the paraffin-embedded tissue showed superior preservation of tissue architecture. The preservation of viral antigen was good, and the appearance of fluorescence in gray- and white-matter lesions was described. In gray matter, extensive fluorescence was found mainly in neurons; fluorescence in white matter was less extensive and was mainly associated with astrocytes.

Animals↗
PubMed2005

A method to generate antigen-specific mAb capable of staining formalin-fixed, paraffin-embedded tissue sections.

Abnormalities in HLA class I antigen expression are frequently found in malignant tumors. Their potential role in the clinical course of the disease and in the outcome of T cell-based immunotherapy has stimulated interest in the characterization of the molecular mechanisms underlying HLA class I antigen abnormalities in malignant cells. Multiple mechanisms have been identified. Among them are abnormalities in antigen processing machinery (APM) component expression. In spite of this information, APM component expression in malignant lesions has been investigated only to a limited extent because of the lack of availability, for most APM components, of monoclonal antibodies (mAb) which stain formalin-fixed, paraffin-embedded tissues. The latter are the substrate of choice in immunohistochemical (IHC) reactions. To overcome this limitation, we have developed a simple and reproducible method to generate APM component-specific mAb which stain formalin-fixed, paraffin-embedded tissue sections. This method involves five steps: (i) immunogenic amino acid sequences, which display low homology with their mouse counterparts when possible, are identified in APM components and utilized to synthesize peptides; (ii) BALB/c mice are immunized with keyhole limpet hemocyanin (KLH)-conjugated synthetic peptides and with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)-purified recombinant APM component proteins; (iii) immunized mice, which develop high titer APM component-specific antibodies, are utilized to generate hybridomas which are screened for APM component-specific antibody production by Western blotting assays, with lymphoid cell lysates; (iv) identified APM component-specific mAb are characterized in their specificity and in their reactivity with permeabilized cells in ELISA and/or flow cytometry; and (v) mAb, with the appropriate reactivity pattern, are tested in IHC reactions with formalin-fixed, paraffin-embedded tissue sections. The use of the methodology we have developed resulted in the generation of a panel of APM component-specific mAb capable of staining formalin-fixed, paraffin-embedded tissue sections in IHC reactions. These reagents will facilitate the analysis of APM component expression in tissues under physiological and pathological conditions. In addition, the methodology we have described is likely to be applicable to other antigenic systems to develop mAb capable of detecting protein components of interest in formalin-fixed, paraffin-embedded tissue sections.

Amino Acid Sequence↗
PubMed2004

Fluorescence in situ hybridization on formalin-fixed and paraffin-embedded tissue: optimizing the method.

Fluorescence in situ hybridization (FISH) is widely used to study numerical and structural genetic abnormalities in both metaphase and interphase cells. The technique is based on the hybridization of labeled probes to complementary sequences in the DNA or RNA of the cells. Interphase FISH is most often applied on cytologic material such as hematologic smears or imprints, but the method is also used to study genetic changes in tissue sections when morphology is important or when cytologic material is not available. In cases in which the presence of intact nuclei is of importance, such as quantitation of signals as in triploidy, it is possible to isolate nuclei from paraffin-embedded tissue. However, using formalin-fixed paraffin-embedded tissue, either in thin sections or as isolated nuclei, one encounters a range of technical problems, paralleling those met in immunohistochemistry. Variations in time lapse between removal of tissue and fixation, duration of fixation, enzymatic pretreatment, hybridization conditions, and posthybridization washing conditions are important factors in the hybridization. In this study, we have listed the results of a systematic approach to improve FISH on isolated nuclei and tissue sections from formalin-fixed, paraffin-embedded tissue.

Chromosome Aberrations↗
PubMed1995

Isolation of nucleic acid from paraffin embedded tissue for PCR amplification and sequencing of TcR V beta genes.

PCR analysis of DNA and RNA from fresh and frozen tissue is now a routine practice in most laboratories. Furthermore DNA extracted from paraffin embedded tissue is routinely used for clonality studies and for HLA typing. However the use of RNA from paraffin embedded tissue is more problematical due to degradation and only short sequences are suitable for amplification. In this report we examine the suitability of extracted nucleic acid from paraffin embedded tissue for the PCR amplification of TcR V beta genes and sequencing of resultant PCR products.

Amino Acid Sequence↗
PubMed1986

Immunocytochemical localization of protein antigens in large sections of tissues embedded in water-soluble embedding media.

JB4 and Immunobed are water-soluble embedding media used for embedding large blocks of tissue. Immunobed was specifically designed for immunocytochemistry because ethanol extraction of an additive in the monomer of the resin is reported to render tissue sections permeable to immunoglobulins. We have modified the manufacturer's protocol to accomplish localization of two protein antigens in tissues embedded in either JB4 or Immunobed. Luteinizing hormone-beta (LH beta) was localized in sections of rat and bovine pituitary tissues and bovine placental lactogen (bPL) was localized in sections of placentomes from bovine placentas. Sections received one of the following pre-treatments: absolute EtOH; NaHCO3 buffer, pH 6-10; EtOH followed by NaHCO3 buffer; one of several enzymes; EtOH followed by enzyme; NaHCO3 buffer followed by enzyme. Anti-LH beta stained only pituitary gonadotrophs and anti-bPL stained only placental binucleate cells, as assessed by absorption controls. Pre-treatment with enzyme was required for staining of sections, but an alkaline pH change (NaHCO3) had little or no effect. Ethanol pretreatment had little or no effect alone or in conjunction with NaHCO3 or enzyme. Sections were sufficiently thin (1.5 micron) to afford resolution of structure, but suitably large (approximately 2 cm2) to minimize problems of sampling.

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↗
PubMed2002

Inexpensive holder for hand-trimming resin-embedded tissues.

A simple and inexpensive mount for securely holding resin-embedded tissues for trimming prior to sectioning for light or electron microscopy is described. The unit is composed of a base plate from which a 12.7-mm drill chuck protrudes. A tissue block is clamped into a microtome chuck and that is mounted in the drill chuck. A standard dissecting microscope is placed over the unit and used to magnify the block for trimming. Total cost of materials is estimated to be $20-40 USD.

Microscopy, Electron↗
PubMed1976

Science and art in preparing tissues embedded in plastic for light microscopy, with special reference to glycol methacrylate, glass knives and simple stains.

Plastic embedding preserves tissue structure much more faithfully than does paraffin. Acrylic polymerization is innocuous to dye-binding groups in sections. The water solubility of glycol methacrylate monomer and the hydrophilic properties of the polymer allow for convenience in dehydration and for versatility in staining sections. Five years of experience with glycol methacrylate (GMA) embedding for light microscopy is summarized. Methods for purifying GMA monomer are cited. Procedures for fixing, dehydrating, embedding, polymerizing, sectioning and staining, using GMA, are explained. A method is provided for making glass knives long enough to cut large blocks. Simple, reliable, quick staining methods are outlined. When compared with paraffin, GMA offers opportunities for simpler, quicker procedures and yields sections of superior quality, greater information content, and less distortion.

Acrylates↗
PubMed2002

Extraction and amplification of DNA from formalin-fixed, paraffin-embedded tissues.

Formalin-fixed, paraffin-embedded tissue (PET) is an invaluable resource for retrospective molecular genetic studies, but the extraction of high-quality genomic DNA from the PET may be problematic. We report a simple method that significantly improves the ability to amplify DNA recovered from formalin-fixed PET. Based on the standard procedure of a commercially available DNA preparation kit, the QIAamp DNA mini kit or the HighPure DNA preparation kit, we developed this method by eliminating the xylene/ethanol extraction step and adding a heat-treatment step. With this method, we have observed a five- to 10-fold increase in amplification efficiency of a fragment in a range of 90 to 386 base pairs. We also have obtained much higher amplification efficiencies for a multiplex polymerase chain reaction.

Base Sequence↗
PubMed1992

Detection of Cryptosporidium parvum DNA in fixed, paraffin-embedded tissue by the polymerase chain reaction.

The objective of this project was to demonstrate detection of Cryptosporidium parvum DNA in fixed, paraffin-embedded tissue using the polymerase chain reaction (PCR). DNA was purified from six samples of fixed, paraffin-embedded tissue that were histologically positive for C. parvum and used in the PCR. Previously developed oligonucleotide primers specific for C. parvum were used to amplify a 452-base target sequence, and a 20-base synthetic probe labeled with digoxigenin-11-dUTP was used to detect the amplification product by chemiluminescence. All six samples were positive by PCR; negative controls showed no amplification or hybridization. This approach could provide a sensitive and specific method for detection of parasite material in fixed, paraffin-embedded tissue samples, and prove to be of significant value in retrospective studies of archival material.

Animals↗
PubMed1996

Detection of Mycobacterium tuberculosis in formaldehyde solution-fixed, paraffin-embedded tissue by polymerase chain reaction in Pott's disease.

STUDY DESIGN: Twenty-five formaldehyde solution-fixed, paraffin-embedded tissue blocks from vertebral biopsy specimen materials with presumptive diagnosis of tuberculous spondylitis and nonspecific vertebral osteomyelitis were studied. OBJECTIVES: To evaluate the sensitivity and specificity of polymerase chain reaction in detecting Mycobacterium tuberculosis in formaldehyde solution-fixed, paraffin-embedded tissue samples from histologically proved tuberculous spondylitis. SUMMARY OF BACKGROUND DATA: Diagnosis of a mycobacterial infection is a long and tedious process; because of the slow growth rate of mycobacteria on solid media, identification and antibiotic sensitivity testing can take up to 10 weeks, but the sensitivity of culture can be as low as 50%. Direct microscopy is insensitive because clinical samples may contain only few organisms. Recently, polymerase chain reaction has been applied in the rapid amplification and identification of many organisms, including mycobacteria. METHODS: The DNAs were extracted from 25 paraffin-embedded tissue blocks. An insertion element IS 6110 (Integrated DNA Tec. Inc., Corrallville, IA), a DNA sequence unique to Mycobacterium complex (M. tuberculosis and the subspecies Mycobacterium bovis), was amplified by polymerase chain reaction. Polymerase chain reaction results were compared with those of Mycobacterium culture, acid-fast bacilli staining, and histologic findings. RESULTS: Polymerase chain reaction was positive in 18 cases of 19 tuberculous spondylitis. Three of the polymerase chain reaction test results were positive with concomitant negative culture and positive acid-fast bacilli staining. There were six chronic nonspecific infections, and polymerase chain reaction results were negative in five cases; in the single positive case, DNA amplification results remained positive even after three repeated tests. CONCLUSION: Polymerase chain reaction has a sensitivity of 94.7%, specificity of 83.3%, positive predictive value of 94.7%, and a negative predictive value of 83.3%. Accuracy was calculated as 92%.

Fixatives↗
PubMed2000

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

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

Biopsy↗
PubMed1994

Effects of fixative and fixation time on the extraction and polymerase chain reaction amplification of RNA from paraffin-embedded tissue. Comparison of two housekeeping gene mRNA controls.

A number of reports have indicated that RNA recovered from paraffin-embedded tissue can be used as a substrate in the polymerase chain reaction (PCR). Although it is established that RNA in paraffin-embedded tissue undergoes significant degradation, the specific contributions of different fixatives and fixation times to this degradation are not known. Mouse splenic tissue was harvested and fixed immediately for 2, 8, or 24 h in either formalin, Omnifix II, or Carnoy's fixative and then processed and embedded in paraffin. RNA was extracted from deparaffinized cubes of tissue using an adaptation of the technique described by Chomczynski and Sacchi. RNA was reverse transcribed using a random hexamer primed reaction. PCR amplification for cDNAs of the housekeeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and hypoxanthine phosphoribosyltransferase (HPRT) mRNAs was then performed. Although GAPDH amplification is used routinely on fresh and frozen tissues, we show that the presence of DNA contamination in the RNA preparations limits its usefulness in paraffin-embedded tissue. Amplifiable HPRT mRNA sequences were detected in nine of 12 samples fixed in Omnifix II, in four of 12 samples fixed in Carnoy's fixative, and in none of 12 formalin-fixed samples. Because of primer selection to preclude amplification of genomic HPRT, DNA contamination is not an issue when HPRT is amplified. Thus, HPRT represents the control system of choice for the evaluation of RNA in PET. The techniques described provide a rapid, uniform, and reproducible method of obtaining RNA from PET for molecular analysis, but they indicate limited utility for retrospective analysis of archival tissues.

Animals↗
PubMed2004

Detection of hepatitis C virus RNA in paraffin-embedded tissues from patients with non-Hodgkin's lymphoma.

The aim of this study is to detect the possible role of hepatitis C Virus (HCV) in lymphomagenesis. HCV-RNA and anti-HCV antibodies were studied in tissue and serum samples taken from patients with non-Hodgkin's Lymphoma (NHL). The prevalence of HCV, the clinical presentation of these cases, and association with histologic subtypes were determined. RT-PCR was used to detect the HCV-RNA in serum and tissue samples. The anti-HCV antibodies were tested with microparticle enzyme immunoassay. Immunohistochemistry with the ABC method was used to detect the HCV core protein in HCV-RNA(+) cases. RNA could be detected in 30 of 35 cases, and other tests were performed in these 30 samples. HCV-RNA was detected in 11 tissue samples (11/30, 37%). HCV core protein was studied in 10 of 11 HCV-RNA(+) cases, and 1-3% nuclear staining was found in only 2 samples. Serologically, HCV-RNA was detected in 7 of 30 samples (23.3%) and anti-HCV antibody was detected in 3 of 30 samples (10%). Detection of HCV-RNA in 37% of the lymphoma tissue samples suggests that HCV may have a role or is a contributing factor in the pathogenesis of lymphoma. The very low HCV core protein in lymphoma tissues may be due to the low viral load in lymphoid tissues and/or higher sensitivity of the PCR method. Detection of anti-HCV antibody in only three cases may be associated with undetectable levels of antibodies due to the immune deficiency in cases with NHL.

Adolescent↗