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A new monoclonal antibody for detection of EGF-receptors in western blots and paraffin-embedded tissue sections.

The prognostic significance of the epidermal growth factor receptor status (EGF-R-status) for certain human tumors requires the development of antibodies useful for clinical application. We used purified receptor preparations to generate monoclonal antibodies immunoreactive with the EGF-R purified from placenta membranes and A431 tumors. Four of the hybridomas contained antibodies (R2, R3, R5, and R9) which recognized both antigens. Antibody R3 was shown to display the following properties: it binds with a KD value of about 10(-9)-10(-10) M to the receptor, a half maximal inhibition of EGF-binding is achieved at 5 x 10(-8) M, and in Western blots of cell membranes R3 specifically detects the EGF-R at 0.1 micrograms/ml. R3 inhibits EGF-dependent clonogenic growth of NRK cells and completely blocks EGF stimulated autophosphorylation of the receptor. Moreover, R3 also detects EGF-R in paraffin-embedded tissue sections taken from human salivary gland, term placenta, and adult skin and mammary carcinomas. Thus, R3 can be used in retrospective diagnostic clinical studies and might help to develop new immunotherapeutic intervention.

Animals↗

Improved technique for analysis of formalin-fixed, paraffin-embedded tumors by fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) and specific DNA probes for peri-centromeric repeat regions and unique sequence loci have made it possible to study chromosomal aberrations from interphase tumor nuclei. Large-scale retrospective studies on the prognostic value of interphase cytogenetics would become feasible if these techniques were readily applicable to nuclei from archival formalin-fixed tumor tissues. We describe here an improved technique for interphase FISH analysis of tumors that have been extensively fixed in formalin. The protocol aims at improving probe penetration and hybridization efficiency by inducing chromatin decondensation and swelling of the nuclei with a heat treatment in a 90 degrees C glycerol solution prior to hybridization. Using this cell pretreatment, FISH results on the detection of chromosome copy number aberrations and amplification of the c-erbB-2 oncogene from formalin-fixed, paraffin-embedded tissues were highly concordant with those from fresh tissues. In contrast to previously described methods, separate adjustments of denaturation or proteinase K digestion are not required for each sample. This method facilitates retrospective analyses of large series of tumors and is also useful for applying FISH to routine diagnostic purposes using formalin-fixed material.

Breast Neoplasms↗

NCL-CD10-270: a new monoclonal antibody recognizing CD10 in paraffin-embedded tissue.

CD10 (CALLA) antigen is expressed in a wide variety of epithelial and nonepithelial tissues, but its most significant application is in the diagnosis and classification of certain types of malignant lymphoma and leukemia. CD10 is expressed in a high percentage of cases of acute lymphoblastic leukemia (ALL), follicular lymphoma, Burkitt's lymphoma, and some hematopoietic tumors. Although the antigen is not lineage specific, CD10 expression is widely used to define subgroups within B-ALL and is a useful tool for detecting the presence of leukemic blasts in the bloodstream. Currently available monoclonal antibodies to CD10 have been found to be effective only in fresh-frozen tissue and for techniques such as flow cytometry. We have used a recombinant protein corresponding to the whole of CD10 to generate a monoclonal antibody that is effective in paraffin-embedded tissue sections. We have used this antibody to assay for the presence of CD10 on a range of normal and pathological tissues. Strong staining was seen in lymphoid germinal centers, renal tubules, glomeruli, syncytiotrophoblast, hepatic parenchymal canaliculi, B-lineage ALL, follicle center cell lymphoma, and a proportion of cases of large-B-cell lymphoma. We believe that this antibody will be of value in the characterization of malignant lymphoma, in particular the differential diagnosis of small-B-cell lymphoma and subtyping of lymphoblastic leukemia, as well as the investigation of the significance of expression of CD10 in other normal and pathological tissues.

Animals↗

Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA.

Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polymerase Phi29 can be used for the random-primed amplification of whole genomes, although the amplification may introduce bias in gene dosage. We have performed a detailed investigation of this technique in archival fresh-frozen and formalin-fixed/paraffin-embedded tumor DNA by using cDNA microarray-based comparative genomic hybridization. Phi29 amplified DNA from matched pairs of fresh-frozen and formalin-fixed/paraffin-embedded tumor samples with similar efficiency. The distortion in gene dosage representation in the amplified DNA was nonrandom and reproducibly involved distinct genomic loci. Regional amplification efficiency was significantly linked to regional GC content of the template genome. The biased gene representation in amplified tumor DNA could be effectively normalized by using amplified reference DNA. Our data suggest that genome-wide gene dosage alterations in clinical tumor samples can be reliably assessed from a few hundred tumor cells. Therefore, this amplification method should lend itself to high-throughput genetic analyses of limited sources of tumor, such as fine-needle biopsies, laser-microdissected tissue, and small paraffin-embedded specimens.

Chromosome Aberrations↗

Molecular diagnosis of synovial sarcoma: RT-PCR detection of SYT-SSX1/2 fusion transcripts in paraffin-embedded tissue.

BACKGROUND: Synovial sarcomas comprise up to 10 percent of malignant soft tissue tumors, and most are characterized by the chromosomal translocation t(X;18) (pl 1.2;q11.2), which results in the expression of SYT-SSX fusion transcripts. These tumors include two major histological subtypes, biphasic and monophasic. Diagnosing biphasic synovial sarcomas does not usually pose a problem, whereas the monophasic spindle-cell form can be difficult to distinguish from other spindle-cell neoplasms using histological and immunohistochemical profiles only. MATERIAL/METHODS: We investigated the presence of SYT-SSX1/2 chimeric RNA in tumors from 7 patients. We applied amplification of the specific fusion transcripts by reverse transcriptase-polymerase chain reaction (RT-PCR) in fresh, frozen tumors. We also developed a method useful for RT-PCR SYT-SSX fusion transcript detection in formalin-fixed, paraffin-embedded tissue. RESULTS: We found that both histological subtypes of synovial sarcoma were SYT-SSX positive. Moreover, we observed a correlation between histological subtype and type of SYT-SSX fusion transcript. Biphasic synovial sarcoma expressed the SYT-SSX1 fusion transcript, whereas the monophasic subtype expressed the SYT-SSX2 fusion transcript. CONCLUSIONS: The detection of SYT-SSX1/2 fusion transcripts by RT-PCR is a valuable diagnostic marker of synovial sarcoma which can be used for the reclassification of cases whose diagnosis is difficult by routine methods.

Adult↗

Analysis of BCR/ABL abnormalities in mRNA from 20-year-old paraffin-embedded tissue for BCR/ABL rearrangement by polymerase chain reaction.

We studied whether it is possible to obtain sufficient mRNA from old paraffin-embedded samples of spleen and bone marrow for reverse transcription and polymerase chain reaction analysis. Spleen tissue from 6 subjects with chronic myelogenous leukemia was studied for rearrangement of BCR and ABL genes. Analysis was successful in 4 cases. These data indicate the feasibility of retrospective analysis of tissue samples of special interest by molecular techniques.

Adult↗

Hepatitis C virus RNA detection by in situ RT-PCR in formalin-fixed paraffin-embedded liver tissue. Comparison with serum and tissue results.

The purpose of this study was to localize HCV RNA in formalin-fixed paraffin-embedded liver biopsies of 15 patients with chronic hepatitis C using in situ RT-PCR method. The results were compared to serum and tissue extract analysis of HCV RNA. HCV RNA was detected in 80% of the sera tested, in 40% of the corresponding hepatic tissue extract and in 60% of the tissue sections tested by in situ RT-PCR. Compared to the serum positive cases, 67% of the cases were positive with in situ RT-PCR and 41% were positive with tissue extract detection. 50% of the cases in situ RT-PCR positive were also positive with tissue extract detection. These results underlined the complementarity of the different methods of viral detection for the precise diagnosis of hepatitis C.

Formaldehyde↗

Detection of fusion gene transcripts in fresh-frozen and formalin-fixed paraffin-embedded tissue sections of soft-tissue sarcomas after laser capture microdissection and rt-PCR.

The diagnosis of small round cell sarcomas is often very difficult, especially when only small biopsy specimens are available for examination. Recent studies have shown that some sarcomas have specific recurrent chromosomal translocations producing chimeric gene fusions, which can be detected by reverse transcription-polymerase chain reaction (RT-PCR), fluorescent in situ hybridization (FISH), or cytogenetic analysis. In this study, 12 cases of well-defined sarcomas including Ewings sarcoma/primitive neuroectodermal tumors (ES/PNET), synovial sarcoma (SS), alveolar rhabdomyosarcoma (ARMS), and desmoplastic small round cell tumors (DSRCT) were used to collect specific numbers of cells by laser capture microdissection (LCM), subsequently used for RT-PCR to detect specific chimeric gene transcripts. Tumor cells from fresh-frozen (FS) tissue sections and paraffin-embedded (PS) tissue sections from the same cases were compared directly to evaluate the sensitivity of FS and PS sections as the starting material for analysis. Samples were used for RNA extraction, RT-PCR analysis, and Southern hybridization with fluorescein-labeled internal probes followed by enhance chemiluminescence (ECL) detection. The fusion gene transcripts could be detected using 50 cells from FS materials in all cases and from 1 cell in 9 of 12 cases. For PS, a positive signal could be detected using 200 to 1000 cells in all cases, while weaker signals were detected using 50 cells in most cases. These results indicate that the fusion gene products from small round cell sarcomas can be detected by RT-PCR with 10 to 200 cells from FS and PS tissues. The sensitivity of RT-PCR with FS was 10- to 50-fold greater than with PS. These results also suggest that RT-PCR analysis for sarcoma fusion gene products can be successfully performed when only a few cells are available for analysis, although this is not recommended for routine clinical use.

Blotting, Southern↗

Sensitive detection of clonal immunoglobulin rearrangements in frozen and paraffin embedded tissues by polymerase chain reaction heteroduplex analysis.

Molecular detection of a clonal population of B or T cells through analysis of rearranged antigen receptor genes is an essential adjunct to the morphologic, flow cytometric, and immunohistochemical evaluation of tissue specimens for the presence of leukemia or lymphoma. Combining polymerase chain reaction (PCR) with heteroduplex annealing and polyacrylamide gel electrophoresis (PAGE) has been used to detect clonal T-cell receptor rearrangements, particularly in skin biopsy specimens. The authors have developed a similar PCR heteroduplex assay for detection of clonal VDJ immunoglobulin gene rearrangements using two sets of primers based on relatively conserved consensus regions in the J(H) and framework I and 2 regions of the immunoglobulin heavy chain V region gene. This method is able to detect a clonal rearrangement when the clone comprises as little as 1% of the population in a polyclonal B-cell background. It may be used on fresh, frozen, or paraffin-embedded tissue and detects a clonal population in a majority of lymphoma subtypes. Compared with conventional PCR analysis, this method requires only a short additional cycle of denaturation and slow renaturation before PAGE. Interpretation is simplified as the clonal PCR product migrates away from the polyclonal background products.

Antibodies, Monoclonal↗

Application of in situ hybridization with a novel phenytoin-labeled probe to conventional formalin-fixed, paraffin-embedded tissue sections.

Non-isotopic in situ hybridization with a novel phenytoin (PHE)-labeled probe was developed. The mixture of cloned cytomegalovirus (CMV) DNA fragments was labeled by random primer technique using PHE-11(spacer)-dUTP, instead of dTTP. The tissue sections were treated with 0.2 N HCl and with proteinase K (1 microgram/ml), and then heated at 70 degrees C in the presence of 50 or 75% formamide. The sections were hybridized with PHE-labeled probe at 37 degrees C overnight. The hybridization signal was visualized by alkaline phosphatase-5-bromo-4-chloro-3-indolyl phosphate (BCIP)/4-nitroblue tetazolium (NBT) system. Strong hybridization signals were detected in sections of the small intestine and the placenta, even when denatured in the presence of 50% formamide. In the case of small intestine, CMV DNA was also detected in the endothelial cells of the mucosa where apparent infected cell was not observed histologically. In the sections of the submaxillary gland, the lung, the adrenal gland and the ovary, hybridization signal was not detected when denatured in the presence of 50% formamide, but detected after denaturation with 75% formamide. Thus, in situ hybridization with the novel PHE-labeled probe is applicable to conventional formalin-fixed, paraffin-embedded tissue sections.

Adrenal Glands↗

[Value of PCR amplification from formalin-fixed paraffin-embedded tissues in the diagnosis of Mycobacterium tuberculosis infection].

Mycobacterium tuberculosis infection remains a major health problem throughout the world. In France, tuberculosis is endemic, particularly in the Paris area (Ile-de-France) and in the south (Provence Alpes côte d'Azur) where immigration is greater than in other countries in northern Europe. Culture is the gold standard for diagnosis of tuberculosis and is the only method enabling a study of strain sensitivity to treatment. Histology contributes to diagnosis in most cases by revealing typical necrotizing granulomatous lesions. The diagnosis is then confirmed by the detection of acid-fast bacilli with Ziehl-Neelsen staining. However, the Ziehl-Neelsen stain is not sensitive and does not allow identification of different species. The polymerase chain reaction (PCR) DNA amplification method has been used to detect M. tuberculosis in formalin-fixed paraffin-embedded tissues. The aim of the present study was to investigate the value of this method for the diagnosis of M. tuberculosis infection. The results obtained with PCR assay were compared to those obtained with histological and microbiological methods (direct examination and culture). Sixty-three specimens (mainly lymph node and lung specimens) exhibiting a positive culture for M. tuberculosis were analyzed. Tuberculosis granulomas were noted in 32/63 cases, tuberculoid granulomas in 18/63, pyoepitheloid granuloms in 10/63, and non-specific inflammation in 3/63. Ziehl-Neelsen staining was positive in 11/63 cases. PCR assay on tissue sections was positive for M. tuberculosis in 58/63 cases. Controls of the PCR method (granulomas due to other mycobacterial species, foreign body granulomas, sarcoidosis granulomas) were all negative. This study shows that PCR from deparaffinized sections, 1) greatly increases the sensitivity of diagnosis of tuberculosis, 2) enables the diagnosis of M. tuberculosis infection. However, although this method reduces the time to diagnosis, culture remains the gold standard for identification of the mycobacterium and for determining the sensitivity of the isolated strain to treatment.

Adult↗

Clonality analysis of B-cell lymphoma in fresh-frozen and paraffin-embedded tissues: the effects of variable polymerase chain reaction parameters.

To investigate the sensitivity of polymerase chain reaction (PCR)-based detection of B-cell monoclonality and the effects of several variables, we analyzed 119 cases of B-cell lymphomas with proven IgH gene rearrangements, testing fresh-frozen and formalin-fixed materials in parallel. Using fresh-frozen tissue, 83 cases (70%) were positive with one-step PCR and high-stringency annealing. Two groups of false-negative cases were identified, Group I (16 cases) showing no PCR products, and Group II (20 cases) showing polyclonal smear patterns. Seminested PCR and/or lowered annealing stringency revealed nine additional positive cases in Group I but none in Group II. Amplification with bcl-2/JH primers resulted in five more positive cases. The overall positive rate in the fresh-frozen category was 81% (97 of 119). Parallel analysis was performed on formalin-fixed, paraffin-embedded material from 61 cases, and a high concordance rate (89%) was observed. The results indicated that fresh and formalin-fixed specimens are comparable in this PCR-based assay, and that the two groups of false-negative results can be accounted for by different reasons. In addition, we reviewed the current literature, discussed the diagnostic applications of this technique, and listed the core elements of a proposed PCR protocol that should be suitable for most laboratories.

Base Sequence↗

Prognostication of astrocytoma patient survival by Ki-67 (MIB-1), PCNA, and S-phase fraction using archival paraffin-embedded samples.

The prognostic power of three proliferation estimation methods, Ki-67 (MIB-1) and PCNA immunohistochemistry, and flow cytometry (S-phase and S + G2/M fractions, respectively), were evaluated in 50 cases of astrocytoma. Each proliferation index showed a strong association with the grade of malignancy (grades I-IV). The MIB-1 labelling index (LI) provided additional information, as it could be used for the discrimination of grade II and grade III astrocytomas (P = 0.0357). All three proliferation estimation methods also had strong prognostic potential (MIB-1 LI: P < 0.0001; PCNA Li: P < 0.0001; S-phase: P = 0.0004; S + G2/M: P = 0.0124). According to the receiver operating characteristics (ROC) curve, the MIB-1 LI showed generally the best sensitivity and specificity in placing the patients correctly into groups of survivors and non-survivors, which was further confirmed in the multivariate analysis. Only 4 per cent of the patients having high MIB-1 scores (> 15.3 per cent) were alive after 2-years' follow-up. In contrast, 72 per cent of patients with tumours of low proliferation activity survived. It appears that Ki-67 (MIB-1) immunolabelling using archival paraffin-embedded samples is of value in predicting prognosis in astrocytic tumours.

Astrocytoma↗

Constant detection of CD2, CD3, CD4, and CD5 in fixed and paraffin-embedded tissue using the peroxidase-mediated deposition of biotin-tyramide.

Immunohistochemical methods are widely used for diagnostic purposes in histopathology. However, the use of most monoclonal anti-leukocyte antibodies is limited to frozen tissues. Initially, it was believed that formalin fixation in particular, which is the gold standard for morphological tissue preservation, destroys most of the antigen binding sites. In recent years, protease digestion and the introduction of microwave techniques have significantly enhanced the sensitivity of immunohistochemical techniques, and a variety of hidden antigen sites in formalin-fixed tissue have been retrieved for initially unreactive antibodies. It therefore became clear that many of the leukocyte antigens are not irreversibly destroyed but are most probably masked during the fixation process. We developed a technique combining optimized pretreatment of formalin-fixed tissue with a dramatic enhancement of the immunohistochemical sensitivity and named it the ImmunoMax method. The ImmunoMax method proves that by optimizing the technique at the following three levels it is possible to detect formalin-sensitive leukocyte antigens: (a) standard fixation of the tissue; (b) sufficient antigen unmasking; and (c) increasing the substrate turnover by multiplication of binding sites with subsequent enhancement of the immunohistochemical reaction. Using this optimized ImmunoMax method, we were able to detect CD2, CD3, CD4, and CD5 with conventional monoclonal antibodies in formalin-fixed, paraffin-embedded tissue specimens of various lymphoid tissues.

Antigens, CD↗

Single-cell immunohistochemical mutation load assay (SCIMLA) using human paraffin-embedded tissues.

It would be advantageous to measure mutation load in situ in order to determine the relationship between a high mutation load and increased risk for cancer or other diseases and to evaluate sources of possible mutagen exposure. Previously, in situ mutation detection assays have been plagued with multiple rounds of amplification and high rates of false-positives and false-negatives. The single cell immunohistochemical mutation load assay (SCIMLA) was developed to measure somatic mutation frequency, pattern, and spectrum in normal tissues with a single round of amplification. The P53 gene was utilized as a mutation reporter because of the unusual property that missense mutations often cause P53 protein to accumulate in the cell, allowing the mutant proteins to be detected by immunohistochemical staining. Alternative reporter genes with stabilized mutant proteins may be envisioned. Single cells that stain positively for P53 protein overabundance (red cells) were microdissected from ethanol-fixed and paraffin-embedded tissues. A novel stimulated-PCR (S-PCR) protocol permitted successful amplification of a 1.8-kb segment of the P53 gene (i.e., exons 5-9) in 87% of single mammary cells. Subsequent sequence analysis demonstrated that 35% of the amplified red-stained epithelial cells from normal breast tissue have missense mutations at evolutionarily conserved amino acids. Jackpot mutations, presumably due to clonal expansion, were common. False-positive missense mutations at conserved residues were observed in 3% of the clear cells (i.e., without red stain), presumably due to DNA polymerase error in early PCR cycles. The allele dropout rate was measured at 40% of the amplified cells. SCIMLA is applicable to a variety of tissues, utilizes a single amplification of an endogenous gene, displays mutant cells in situ, and may be adapted to other species.

Base Sequence↗

Evaluation of the predictive value of Her-2/neu gene expression on osteosarcoma therapy in laser-microdissected paraffin-embedded tissue.

Histologic response to chemotherapy is currently the strongest prognostic factor in high-grade osteosarcoma, but it can only be assessed after several weeks of therapy. Thus, detection of chemosensitivity at the time of diagnosis would be of great clinical importance. The expression of the proto-oncogene Her-2/neu has been shown to be of predictive value in breast cancer and has also been considered as prognostic marker for osteosarcomas, but reports of mainly immunohistochemical studies are controversial. Therefore, the aim of this study was to investigate Her-2/neu gene expression in laser-microdissected osteosarcoma cells. Laser microdissection enables the precise isolation of morphological defined cells from archival tissue specimens and is in combination with the highly sensitive real-time RT-PCR technique a valuable tool for cell-specific analysis of gene expression. Through optimization of current protocols, we could show that this technique can be successfully applied on formalin-fixed, paraffin-embedded and decalcified osteosarcoma tissue with high sensitivity and reproducibility. In all 17 osteosarcoma biopsies analyzed, we could detect Her-2/neu gene expression. Expression correlated significantly with the response to preoperative chemotherapy, which was assessed histologically according to the six-grade scale of Salzer-Kuntschik. Risk assessment on the basis of increased Her-2/neu gene expression matched the histologic findings in 16 out of 17 cases (94%). These data demonstrate the reliability of laser microdissection in the analysis of gene expression and suggest a possible role of Her-2/neu as prognostic marker for therapy outcome in osteosarcomas.

Antineoplastic Agents↗

Interphase cytogenetics in paraffin-embedded sections from renal cortical neoplasms. Correlation with cytogenetic and flow cytometric DNA ploidy analyses.

Nonisotopic in situ hybridization (ISH) was performed on archival tissue sections from six renal cortical neoplasms and corresponding normal kidney tissue using pericentrometric (alpha-satellite) probes to chromosomes 1, 3, 7, 8, 10, 11, 12, 16, and 17. The results were correlated with classic cytogenetic analyses and flow cytometric DNA ploidy findings of these neoplasms. Our study shows that intratissue and intertissue ISH spot counts were generally homogeneous in normal kidney tissue and markedly heterogenous in tumor specimens. In all cases the correlation between the DNA Index and the ISH spot numbers was statistically significant. A correlation between modal and numerical chromosomal findings by cytogenetic analysis and ISH spot counts was found in three cases and was discordant in three cases. Our results also show that chromosomes 1, 3, 7, and 17 appear to manifest more propensity for aneuploidy than chromosomes 8, 10, 11, 12, and 16. We conclude that 1) numerical chromosomal aberrations by interphase in-situ hybridization correlate with DNA ploidy analysis in these tumors; 2) certain chromosomes may be more prone to aneuploidy than others; 3) determination of monosomy by ISH is less reliable on paraffin-embedded sections; and 4) the ISH technique complements conventional cytogenetic analysis in providing more information for the determination of cytogenetic aberrations and clonal heterogeneity in solid neoplasms.

Adenocarcinoma, Clear Cell↗

Duplex PCR for differential identification of Mycobacterium bovis, M. avium, and M. avium subsp. paratuberculosis in formalin- fixed paraffin-embedded tissues from cattle.

We previously isolated and sequenced two genomic segments of Mycobacterium avium subsp. paratuberculosis, namely, f57, a species-specific sequence, and the p34 gene, coding for a 34-kDa antigenic protein. Comparison of sequences upstream of the p34 open reading frame (us-p34) from M. avium subsp. paratuberculosis and M. tuberculosis showed a 79-base deletion in M. tuberculosis. Sequence analysis of the p34 genes in another two species, M. bovis (strain BCG) and M. avium (strain D4), confirmed the differences observed between tuberculous and nontuberculous species. A duplex diagnostic PCR strategy based on coamplification of nonhomologous us-p34 and species-specific f57 sequences was therefore developed. Duplex PCR yielded three different patterns, specific either for tuberculous bacilli (M. tuberculosis, M. bovis, and M. africanum), for both nontuberculous mycobacteria M. avium and M. intracellulare, or for M. avium subsp. paratuberculosis. The specificity of this single-step DNA-based assay was assessed on DNA from cultured mycobacterial strains, as well as on a panel of formalin-fixed and paraffin-embedded tissues from cattle. Molecular assay results from tissular DNA were compared to conventional bacteriological and histological test results, including those obtained by Ziehl-Neelsen staining on tissue biopsy specimens. Molecular discrimination was successful and confirmed the value of duplex us-p34 and f57 sequence amplification for differential diagnosis of tuberculosis, paratuberculosis, or infections caused by other members of the M. avium complex.

Animals↗