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PubMed1989

The effect of fixatives and paraffin embedding on the histochemical reactivity of a monoclonal antibody against human type IV collagen (JK-199).

A new monoclonal antibody (JK-199) was found to react with basement membranes on paraffin-embedded tissue sections without prior enzyme digestion. JK-199 was shown to react with isolated type IV collagen treated by any of four different fixatives--PLP, 4% formalin, modified Zamboni's (0.2% picric acid, 4% paraformaldehyde in 0.1 M phosphate buffer, pH 7.4) or Bouin's--applied for 6 h at room temperature and incubated at 60 degrees C for 30 min to simulate routine tissue processing. None of the fixatives was able to alter the reactivity of JK-199 with isolated type IV collagen. In the human placenta, specific and intense staining of basement membranes was demonstrated on paraffin sections fixed with any of the four fixatives. In human skin, basement membranes were fully demonstrated on paraffin sections fixed by PLP fixative or by 4% formalin, but only partially on sections fixed by picric acid-containing fixatives. Optimal results, i.e., with the least non-specific or incomplete staining, were obtained on PLP-fixed paraffin-embedded tissues. In PLP-fixed paraffin sections of the kidney, skeletal muscle, and small intestine, all basement membranes were stained intensely by this antibody (JK-199) at the expected locations. The results indicate that JK-199 may be widely applicable for the analysis of basement membrane kinetics, including developmental processes or pathological conditions.

Antibodies, Monoclonal↗

PubMed2003

Comparison of polymerase chain reaction with histopathologic features for diagnosis of tuberculosis in formalin-fixed, paraffin-embedded histologic specimens.

Objective.-To investigate the relationship between various histopathologic features and the results of the tuberculosis (TB)-polymerase chain reaction (PCR) method in routinely submitted histologic specimens for the histopathologic diagnosis of TB. Design.-We used 95 formalin-fixed, paraffin-embedded tissue blocks from 81 patients who were clinically suspected of having TB. We assessed the presence of histopathologic features including well-formed granuloma, poorly formed granuloma, caseous necrosis, and Langhans-type giant cells. We performed nested PCR for IS6110 and Ziehl-Neelsen staining for acid-fast bacilli (AFB). Results.-Of the 81 patients studied, 53 patients had chronic granulomatous inflammation, whereas 28 patients had only chronic inflammation without definite granulomatous inflammation. Of the 53 cases with chronic granulomatous inflammation, 17 (32%) were AFB positive and 36 (68%) were TB-PCR positive. Among cases with chronic granulomatous inflammation, the percentage that were positive and negative by TB-PCR differed significantly with the presence of various histopathologic features. All of the 13 cases with well-formed granuloma, caseous necrosis, and Langhans-type giant cells were TB-PCR positive; however, 10 (36%) of the 28 cases with chronic inflammation without granulomatous lesions were also TB-PCR positive. Conclusions.-TB-PCR is a rapid, sensitive method for the diagnosis of TB in routinely processed formalin-fixed, paraffin-embedded histologic specimens and is readily available in histopathology laboratories. We recommend use of TB-PCR when TB is suspected clinically, especially in cases of chronic inflammation without definite evidence of granulomatous inflammation.

Chronic Disease↗

PubMed1989

Human papillomavirus detection in paraffin-embedded cervical carcinomas and metastases of the carcinomas by the polymerase chain reaction.

The polymerase chain reaction (PCR) is used for human papillomavirus (HPV) detection in paraffin-embedded tissue. The specificity of the reaction is unaffected by the method of fixation used before embedding into paraffin. Five HPV 16, 18, 31, and 33 DNA in situ hybridization (DISH)-negative cervical carcinomas were subjected to the PCR. In two patients, HPV 16 DNA could be detected in the cervical squamous cell carcinomas and also in their lymph node metastases. One patient with an adeno-carcinoma of the cervix was found positive for HPV-18. A lymph node of this patient was HPV 18 positive as well. In the tumors of the remaining two patients, no HPV 16, 18, or 33 DNA was detected by the PCR. Both negative patients had cervical squamous cell carcinomas. One had a bladder metastasis, whereas the other had a lymph node metastasis and an additional distant metastasis in the lung. HPV DNA positivity in cervical carcinomas correlated with HPV prevalence in the metastases. This relationship can be of use for diagnostic purposes in the pathologic analysis of metastases.

Blotting, Southern↗

PubMed2001

Degenerate oligonucleotide primed-polymerase chain reaction-based array comparative genomic hybridization for extensive amplicon profiling of breast cancers : a new approach for the molecular analysis of paraffin-embedded cancer tissue.

We have developed a protocol for degenerate oligonucleotide-primed-polymerase chain reaction-based array comparative genomic hybridization (array CGH) that, when combined with a laser microdissection technique, allows the analysis of cancer cell populations isolated from routine, formalin-fixed, paraffin-embedded tissue samples. Comparison of copy number changes detected by degenerate oligonucleotide-primed-polymerase chain reaction-based array CGH to those detected by conventional array CGH or fluorescence in situ hybridization, demonstrated that amplifications can be reliably detected. Using a genomic microarray containing 57 oncogenes, we screened a total of 28 breast cancer samples and obtained a detailed amplicon profile that is the most comprehensive to date in human breast cancer. The array CGH method described here will allow the genetic analysis of paraffin-embedded human cancer materials for example in the context of clinical trials.

Breast Neoplasms↗

PubMed2003

Immunohistochemical detection of SWC3, CD2, CD3, CD4 and CD8 antigens in paraformaldehyde fixed and paraffin embedded porcine lymphoid tissue.

Identification of the different cell types of the immune system is important for in situ studies on the pathogenesis of infectious diseases in various animals, including the pig. Unfortunately, many monoclonal anti-leukocyte antibodies are only useful for staining frozen tissue sections with inherent poor tissue morphology, and are not readily adapted to formaldehyde fixed and paraffin embedded tissue with well preserved morphology. Seven well characterised monoclonal antibodies against porcine leukocyte antigens were tested on neutral buffered paraformaldehyde fixed and paraffin embedded porcine tissue sections using the highly sensitive tyramide signal amplification system. Combining this method with different antigen retrieval techniques enabled us to detect CD2, CD3, CD4, CD8 and SWC3 antigen expressing cells in porcine lymphoid tissue. Thus, we describe herein methods for the detection of several major cell types of the porcine immune system in fixed tissue with optimal preservation of histological details.

Animals↗

PubMed2001

Hemochromatosis (HFE) gene sequence analysis of formalin-fixed, paraffin-embedded liver biopsy specimens.

BACKGROUND: Hereditary hemochromatosis (HH) is a common disease predominantly characterized by mutations of the HFE gene. METHODS AND RESULTS: We investigated the utility of HFE gene sequence analysis in the diagnosis of HH in 61 prospectively accrued formalin-fixed, paraffin-embedded liver biopsy specimens with clinical or histologic features suggestive of HH. Mutations in codons 63 or 282 of the HFE gene were identified by direct sequencing; in 21 of these samples, quantitative hepatic iron testing was also performed. Changes characteristic of HH were present in 16 (26%) of the cases, and 54% of the cases showed HFE gene mutations. The most common alteration was homozygous mutation of codon 282 (11 cases, 18%), followed by the combined 63 + 282 heterozygous mutation (3 cases, 5%). Two cases (3%) showed biallelic mutation of codon 63. The other 28 cases (46%) showed no sequence abnormalities. Weak iron staining did not exclude HH; intense staining did not reliably predict HH. CONCLUSION: When HH is clinically and/or histologically suspected, HFE gene sequencing of formalin-fixed, paraffin-embedded liver biopsy specimens is a rapid and cost-effective approach to genotypic diagnosis of HH.

Age Factors↗

PubMed1998

Rapid microsatellite analysis of paraffin embedded tumour specimens from patients with hereditary non-polyposis colorectal cancer.

In screening for hereditary non-polyposis colorectal cancer (HNPCC)--an autosomal dominant disorder characterised by mutations in mismatch repair genes--detection of microsatellite instability is an important diagnostic criterion. The mono- or dinucleotide repeat DNA sequences are usually amplified from formalin fixed, paraffin embedded tissue by polymerase chain reaction after numerous time consuming steps including deparaffinisation, DNA extraction, and purification. A rapid single step method for direct DNA analysis is described, based on preincubation of paraffin embedded tissue with Triton X-100 followed by DNA amplification with fluorescence labelled primers and electrophoresis in an automated sequencer. This procedure allows precise allele sizing and analysis of genetic instability, is more efficient and time saving, reduces the risk of contamination, and is therefore of particular interest in screening for HNPCC.

Colorectal Neoplasms, Hereditary Nonpolyposis↗

PubMed1994

Angioimmunoblastic lymphadenopathy type of T-cell lymphoma and angioimmunoblastic lymphadenopathy: a clinicopathological and molecular biological study of 13 Chinese patients using polymerase chain reaction and paraffin-embedded tissues.

The morphological classification of angioimmunoblastic lymphadenopathy (AILD) or T-cell lymphoma of AILD-type (AILD-TCL) is still a subject of considerable difficulty and controversy. The aim of the current study was to examine the value of clinical, morphological, immunohistochemical variables in paraffin-embedded tissues in predicting the clonality of the respective lesion. Fifteen lymph node biopsies derived from 13 patients from Chengdu, China, were diagnosed as AILD or AILD-TCL and included in this study. The specimens were examined using a panel of monoclonal antibodies and a scoring system of morphological features. Clonality of the paraffin-embedded material was investigated using a novel polymerase chain reaction-technique to amplify rearranged T-cell receptor (TCR)-gamma sequences. Additional experiments were carried out to investigate the presence of clonal rearrangements of the immunoglobulin heavy chain (IgH) locus. We found clonal rearrangements of the TCR-gamma locus in 9 out of 15 lymph node biopsies. In 3 patients, the predominant cell clones carried clonal IgH and TCR-gamma rearrangements whereas 1 patient with polyclonal TCR-gamma pattern displayed IgH-monoclonality. The statistical evaluation of morphological and immunohistochemical data indicated that no single variable was able significantly to predict the clonality of the lesion. Furthermore, demonstrable clonality for the TCR-gamma or the IgH loci of a lesion did not correlate with a bad clinical course. Our data correlate with findings of other studies investigating AILD-TCL in Caucasian populations.

Adult↗

PubMed1998

Improved mRNA in situ hybridization on formaldehyde-fixed and paraffin-embedded tissue using signal amplification with different haptenized tyramides.

We report an optimized in situ hybridization (ISH) protocol with a rapid signal amplification procedure based on catalyzed reporter deposition (CARD) to increase the sensitivity of non-isotopic mRNA ISH on formaldehyde-fixed and paraffin-embedded tissue. The CARD method is based on the deposition of haptenized tyramide molecules in the vicinity of hybridized probes catalyzed by horseradish peroxidase. Commercially available and newly synthesized haptenized tyramides, including digoxigenin-, biotin-, di- and trinitrophenyl- as well as fluorescein-tyramide, were compared. The haptenized tyramides were visualized using peroxidase conjugated anti-hapten antibodies followed by the diaminobenzidine reaction. As a test system, we applied digoxigenin-labeled oligonucleotides to detect insulin and vasoactive intestinal polypeptide mRNA in pancreatic endocrine tumors and liver metastases. Our results indicate that specificity, sensitivity, and applicability of oligonucleotide mRNA ISH can be significantly improved by using chemically digoxigenin-labeled oligonucleotide probes and signal amplification by CARD. Furthermore, all tested tyramides provided approximately equal amplification efficiency. In conclusion, CARD signal amplification should further promote mRNA ISH studies on paraffin-embedded tissues and allow for multiple-target nucleic acid detection in situ.

Dinitrophenols↗

PubMed1991

Improved prognostic impact of S-phase values from paraffin-embedded breast and prostate carcinomas after correcting for nuclear slicing.

Nuclear debris may significantly interfere with the analysis of S-phase fraction (SPF) from paraffin-embedded tumors. We used a background subtraction algorithm to compensate for the effects of slicing of tumor cell nuclei during preparation of paraffin-embedded specimens. DNA histograms were analyzed from 88 node-negative breast and from 78 prostatic carcinomas. Median SPFs corrected for nuclear slicing were lower than uncorrected ones in both breast cancer (7.6% vs. 5.7%) and prostate cancer (6.7% vs. 4.2%). The median SPF value in each group was used as a cut-off point in survival studies. As compared with the uncorrected SPFs, corrected SPF levels resulted in a more significant survival difference between breast cancer patients with above and below median SPF (p = 0.0014 vs. p = 0.014) and in a higher relative risk (RR) of death (4.5 vs. 3.1). The same was true for prostate cancer survival (p less than 0.0001 vs. p = 0.002) and RR (5.3 vs. 3.1). Compared with the exponential background subtraction method, the sliced nuclei correction was more reproducible and could be applied in all evaluable histograms without the risk of overcompensation. In conclusion, our results support the use of background correction with the sliced nuclei model in DNA flow cytometric studies of archival tissues.

Breast Neoplasms↗

PubMed2002

Molecular detection of the synovial sarcoma translocation t(X;18) by real-time polymerase chain reaction in paraffin-embedded material.

The t(X;18) translocation is known to be a useful marker for the diagnosis of synovial sarcoma. In this study, the authors describe a new real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method to detect SYT/SSX fusion transcripts using paraffin-embedded and frozen tumor specimens. A series of 38 soft tissue sarcomas were analyzed. Diagnosis was based on clinical, histologic, and immunohistochemical examination. The fusion transcripts were detected in 16 of 17 synovial sarcoma samples (the 17th sample was not suitable for molecular analysis). No t(X;18)-fusion transcript was PCR-amplified in the 21 nonsynovial sarcoma mesenchymal tumors. Therefore, real-time PCR amplification appears to be a powerful, rapid, specific, and sensitive technique that can be used routinely to diagnose the synovial sarcoma t(X;18) translocation. In addition, the t(X;18) can be detected not only on frozen but also on paraffin-embedded tumor samples.

Biomarkers, Tumor↗

PubMed1993

[Analysis of the Duchenne muscular dystrophy gene with PCR analysis in paraffin-embedded tissue. A new diagnostic possibility].

Analysis of DNA from archival, paraffin-embedded muscle tissue allowed tracing of the mutated dystrophin gene in two families with Duchenne muscular dystrophy. There were no living patients in these families. In one family this diagnosis contributed to the birth of a normal male, in the other family to the demonstration of carrier status. These analyses, based on the polymerase chain reaction, are relatively rapid and simple, and lend increased value to old tissue samples stored in pathology departments.

DNA↗

PubMed1989

Demonstration of human immunodeficiency virus by colorimetric in situ hybridization: a rapid technique for formalin-fixed paraffin-embedded material.

A colorimetric method of in situ hybridization has been developed for the rapid detection of human immunodeficiency virus (HIV) in formalin-fixed paraffin-embedded material. Following optimization of digestion conditions, biotin-labeled DNA probes are detected with an alkaline phosphatase conjugate. The method is verified using fixed paraffin-embedded cell blocks of HIV-infected and uninfected lymphocyte cell cultures. Hybridization specifically detects both viral RNA and proviral DNA. Formalin fixation for intervals up to 21 d did not significantly hamper the signal under the appropriate digestion conditions; however, Trump's fixation for even 12 h greatly reduced the intensity of the hybridization. This technique for in situ hybridization is amenable to automation, provides results within 6 h, and results in good morphologic preservation. A key feature of the technique is the use of human placental DNA as an endogenous positive control to optimize the empirically determined conditions for protein digestion.

Cells, Cultured↗

PubMed1996

Excision of selected skin tumours using Mohs' micrographic surgery with horizontal paraffin-embedded sections.

Histological interpretation of frozen sections made during Mohs' micrographic surgery may be difficult, depending on the morphological and staining characteristics of the tumour and on the nature of the associated inflammatory infiltrate. We have employed an adaptation of micrographic surgery in which horizontal, formalin-fixed, paraffin-embedded sections were used to improve histological assessment in the excision of 18 non-melanoma skin tumours in which frozen sections had been or were likely to be unsatisfactory. We describe our experience of this method in the management of squamous cell carcinomas (11), extramammary Paget's disease (two), microcystic adnexal cell carcinomas (two), dermatofibrosarcoma protuberans (two), and primary cutaneous neuroendocrine carcinoma (Merkel cell carcinoma) (one). The use of horizontal paraffin-embedded sections lengthens the duration of the procedure but facilitates accurate assessment of histological sections in selected tumours.

Adult↗

PubMed2005

Species identification of mycobacteria in paraffin-embedded tissues: frequent detection of nontuberculous mycobacteria.

Diagnosis of infections caused by mycobacteria, especially nontuberculous mycobacteria still represents a difficult task both in microbiology and pathology. The aim of this study was to determine the frequency of mycobacterial DNA detectable by PCR in formalin-fixed paraffin-embedded tissues showing suspicious granulomatous lesions. A total of 190 archival specimens were analyzed, using a nested PCR protocol, which amplifies a fragment of the mycobacterial 65-kDa heat-shock protein gene. Restriction fragment-length polymorphisms and sequencing were utilized to further analyze the obtained PCR products. Corresponding microbiological culture results were available for 41 cases. We detected mycobacterial DNA in 119 cases (63%), of which 71 (60%) were positive for Mycobacterium tuberculosis complex DNA and 41 (34%) for DNA of nontuberculous mycobacteria. Seven cases (6%) could not be subtyped for technical reasons. The largest group of nontuberculous mycobacteria comprised 29 cases (25% of the 119 positive cases), which were assigned to Mycobacterium fortuitum complex. Mycobacterium avium-intracellulare complex was detected in eight (7%) cases, Mycobacterium gordonae in three (2.5%) and Mycobacterium rhodesiae in a single case (0.8%). All cases of Mycobacterium tuberculosis were unequivocally identified by restriction fragment-length polymorphism analysis. In contrast, sequencing provided a gain of information over restriction fragment-length polymorphism analysis in 37% of the nontuberculous mycobacteria cases (15 of 41). Alignment studies on DNA of nontuberculous mycobacteria showed frequent sequence variations, supporting the existence of sequevars. Comparison of molecular data to available results of microbiological culture assays showed a good concordance of 83%. In conclusion, amplification and sequencing of the mycobacterial 65-kDa heat-shock protein gene is an excellent tool for species identification of mycobacteria, especially nontuberculous mycobacteria, in formalin-fixed paraffin-embedded tissues.

Base Sequence↗

PubMed2005

FISH is superior to PCR in detecting t(14;18)(q32;q21)-IgH/bcl-2 in follicular lymphoma using paraffin-embedded tissue samples.

Detection of t(14;18)(q32;q21)-IgH/bcl-2, which is present in 70% to 95% of follicular lymphomas (FLs), might aid in diagnosing FL. The efficacy of routine polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH) techniques in detecting t(14;18) in paraffin-embedded tissue samples was compared on 5 normal tonsils and 28 FLs demonstrated to be t(14;18)+ by previous karyotyping. There was technical failure in 14 (50%) of the FLs by PCR, likely due to B-5 fixation, and 4 (14%) of FLs by FISH, likely due to advanced specimen age. In the remaining successful cases, 5 (36%) of 14 were positive by PCR and 24 (100%) of 24 were positive by FISH. All 5 normal tonsils were negative by both methods. FISH is superior to PCR for detecting t(14;18) from paraffin-embedded tissue samples because it is more sensitive and equally specific.

Chromosomes, Human, Pair 14↗

PubMedDate not supplied

Immunohistochemical detection of P-glycoprotein on frozen and paraffin-embedded tissue sections of normal and malignant tissues.

In this study the reactivity of the monoclonal antibodies (mabs) C 219, C 494 and 4E3 was compared on frozen and paraffin-embedded normal tissues and tumors. On frozen tissues we used an indirect immunoperoxidase method, while on paraffin sections a streptavidin-biotin method without antigen retrieval methods was used. In normal tissues all mabs were reactive with colon epithelium in frozen and paraffin-embedded sections. The bile canaliculi in the liver showed the most extensive reaction with C 219 in frozen sections, and to a lesser extent with C 494 and 4E3. C 219 reacted with the pancreatic acinar and ductal epithelium, whereas C 494 and 4E3 reacted predominantly in the stroma. The kidney showed positivity for all mabs in the collecting ducts and isolated solitary cells were reactive in the spleen. In the skin the eccrine part of the sweat glands was reactive for all mabs in paraffin sections. The lung, prostate and breast were negative for all mabs. Only in paraffin sections of various tissues did the C 494 appear to be reactive with nerve fibers and ganglion cells. Colon cancers were positive for P-170 with all mabs tested. In breast carcinoma C 494 showed positive reactions in 8/26 frozen and 4/22 paraffin sections, while 4E3 was reactive with 20/25 frozen but only with 1/21 paraffin sections. C 219 gave similar results in frozen (22/26) and paraffin (17/26) sections of breast cancer. Ovarian carcinomas were positive with C 494 in 11/20 of the frozen and in 11/15 of the paraffin sections, while 4E3 again reacted more weakly in paraffin (5/15) than in frozen (15/20) sections. C 219 gave positive reactions in all ovarian carcinomas in frozen (20/20) and paraffin sections (14/14). In the tumors, the most intense reaction for all mabs was obtained in the colon, followed by the ovary and breast. Enhanced staining was seen in paraffin sections for mab C 494 in ovarian carcinoma. By demonstrating the presence of both an external and internal epitope on frozen sections, the combined use of 4E3 and C 219 gave complementary information about the expression of P-170.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2002

Patterns of immunoglobulin staining in paraffin-embedded malignant lymphomas.

The demonstration of immunoglobulin light chain restriction in paraffin-embedded B cell lymphomas is a capricious and difficult procedure that has been abandoned by many diagnostic laboratories. Using a combination of microwave antigen retrieval performed in a pressure cooker and proteolytic digestion with trypsin, we were able to demonstrate immunoglobulin light chain restriction in 66 B cell lymphomas comprising 25 follicular lymphomas, 29 diffuse large cell lymphomas, 6 small lymphocytic lymphomas, 2 mantle cell lymphomas, 1 nodal marginal zone lymphoma, 1 Burkitt lymphoma, 1 hairy cell leukemia, and 1 plasmacytoma. There was concordance of results in 13 cases in which flow cytometry immunoglobulin analyzes were performed. Perinuclear staining was demonstrated in all cases with dot-like staining of the Golgi present in 23 cases. Perinuclear staining occurred in combination with cytoplasmic staining in 12 cases and membrane staining in 8 cases with 12 lymphomas showing more than two patterns of staining.

Flow Cytometry↗