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PubMed1997

Fetal and adult hair follicle. An immunohistochemical study of anticytokeratin antibodies in formalin-fixed and paraffin-embedded tissue.

The expression of cytokeratins (CK), involucrin, vimentin, CD34, and alpha-smooth-muscle actin was studied in fetal and adult hair follicles. The first stage of the developing hair follicle is characterized by palisaded, elongated epithelial cells budding from the epidermal basal layer. These cells express CK5/6, CK14, CK17, CK19, and vimentin. During the following weeks of gestation, different structures in the developing hair follicle can be identified and characterized. The matrical cells display only CK19. The keratinocytes of the outer root sheath express CK5/6, CK14, CK17, CK19, and involucrin; those of the inner root sheath, CK4, CK18, and involucrin; those of the isthmus, the same profile as the ORS. In the infundibulum, the basal-layer keratinocytes express CK5/6, CK14, CK17, and CK19, whereas in the suprabasal layers CK1, CK4, CK10, CK14, and CK17 are seen. The adult hair follicle in anagen fails to express CK19 in the matrical cells and isthmus and both CK17 and CK19 in the infundibulum. These profiles of intermediate filaments and other markers appear to be potentially useful in categorizing neoplasms with apparent follicular differentiation.

Actins↗
PubMed1998

Microsatellite instability is rare in the clinical course of myelodysplastic syndrome studied with DNA from fresh and paraffin-embedded tissues.

Microsatellite instability (MSI) has been reported to occur in various types of malignant neoplasms. We performed a polymerase-chain-reaction-based assay for MSI between the initial and the most recently available ("latest") samples from 23 patients with myelodysplastic syndrome (MDS). Of these patients, 15 were informative at more than three microsatellite loci. Seven patients showed an increase in leukemic cells while 8 patients did not during the interval between the two analyses. Only 1 of the patients, who had refractory anemia with excess blasts, which changed to acute myelogenous leukemia, showed microsatellite alteration at the analysis times. Among all 23 patients, two alterations were detected in the 42 informative paired samples that showed an increase in leukemic cells (4.8%), while none was detected in the 59 paired samples without such an increase. In total, therefore only two alterations were detected among 101 informative paired samples (2%). This indicates that MSI is rare in the clinical course of MDS irrespective of disease status, and is consequently not a critical genetic event for disease progression in most MDS patients.

Adult↗
PubMed1995

Biologic characteristics of T1 papillary bladder cancer. Flow cytometric study of paraffin-embedded material.

DNA ploidy, proliferative activity (evaluated in terms of the proliferative index [PI]) and epidermal growth factor receptors (EGF-R) expression in primary bladder cancer in 52 patients were studied by means of flow cytometry and immunohistochemistry. Forty of the 52 tumors yielded evaluable DNA histograms: 22 were diploid (55%) and 18 aneuploid (45%) (median DNA index = 1.5). Ninety-five percent of the tumors were positive for EGF-R expression. The median PI value of the entire case series, estimated with a mathematical model, was 5.4%, or 6.7% in diploid tumors and 12.1% in aneuploid ones. EGF-R expression was higher in aneuploid than diploid tumors. Most of the well-differentiated tumors were diploid, while aneuploid populations and positivity for EGF-R expression were more frequent in poorly and moderately differentiated tumors. No differences in proliferative activity were observed in relation to grade. Overexpression of EGF-R in aneuploid tumors and a relationship between it, proliferative activity and grading were observed. The disease-free survival rates were 72% and 91% for patients with aneuploid and diploid tumors, respectively.

Aneuploidy↗
PubMed1994

DNA of Mycobacterium tuberculosis in formalin-fixed, paraffin-embedded tissue in tuberculosis and sarcoidosis detected by polymerase chain reaction.

Infection with Mycobacterium tuberculosis is a major cause of death worldwide. Identification of mycobacteria in tissue sections is usually easily achieved by acid-fast stains, but this method sometimes gives unsatisfactory results. The authors therefore compared conventional staining techniques and polymerase chain reaction (PCR) for mycobacterial DNA sequences in 24 selected tissue samples from patients with tuberculosis. In all samples, either positive or negative with acid-fast stain, mycobacterial DNA fragments were detected. In addition, tissue samples from patients with clinically proven sarcoidosis were included as controls. Surprisingly, strong signals for mycobacterial DNA were found in 2 of 15 cases. Polymerase chain reaction is a useful technique in the demonstration of mycobacterial DNA fragments in patients with clinically suspected tuberculosis who have acid fast stain-negative histology. An epithelioid granulomatous reaction in the lung, negative by acid-fast stain and positive for mycobacterial DNA by PCR, however, does not permit a diagnosis of tuberculosis, because a positive result can also be obtained in cases of sarcoidosis. In some cases of sarcoidosis, the causal agent might be either cell wall defective mycobacteria or persistent intracellular DNA from mycobacteria.

Base Sequence↗
PubMed2006

Detection of the t(11;18) API2/MALT1 translocation associated with gastric MALT lymphoma in routine formalin-fixed, paraffin-embedded small endoscopic biopsy specimens by robust real-time RT-PCR.

The t(11;18)(q21;q21) API2/MALT1 translocation is a specific chromosomal abnormality in extranodal marginal B-cell lymphomas of the mucosa-associated lymphoid tissue (MALT) type, particularly in those occurring in the stomach and lungs. Identification of t(11;18) may aid in the diagnosis of MALT lymphoma and strongly predicts resistance of gastric MALT lymphoma to Helicobacter pylori eradication therapy. We developed a robust real-time reverse transcription-polymerase chain reaction (RT-PCR) procedure to efficiently detect t(11;18) in virtually all types of specimens used in routine diagnostic workups. We blindly tested 40 samples from 38 patients with gastric MALT lymphoma; 10 (25%) of 40 samples, or 8 (21%) of 38 patients were positive for t(11;18). In contrast, t(11;18) was not detected in 8 cases of gastric large B-cell lymphoma, 11 cases of chronic active gastritis, and 16 samples unrelated to lymphoma. Our findings suggest that real-time RT-PCR for t(11;18) may be a valuable tool with much relevance in the current clinical management scheme.

Biopsy↗
PubMed2001

Quantitation of human herpes virus 8 DNA in paraffin-embedded biopsies of HIV-associated and classical Kaposi's sarcoma by PCR.

BACKGROUND: Kaposi's sarcoma occurs in patients seropositive and seronegative for the human immunodeficiency virus (HIV) and has been associated with human herpes virus 8 (HHV8). The purpose of this study was to determine and to compare the amount of HHV8 DNA in formalin-fixed tissue sections of Kaposi's sarcoma. METHODS: From 27 biopsies of Kaposi's sarcoma patients, tissue sections were taken and deparaffinized. Four patients were HIV seronegative and 13 were HIV seropositive. After extraction of DNA copy numbers of HHV8 and beta-globin were determined in every sample by quantitative PCR ELISA using an internal quantitation standard. Results were expressed as HHV8 per beta-globin. RESULTS: No significant differences were found between biopsies from HIV-positive and HIV-negative patients (14.8+/-19.6 HHV8 per 1000 beta-globin in HIV-positive versus 18.0+/-23.5 in HIV-negative patients). CONCLUSIONS: These data suggest that HHV8 viral load in Kaposi's sarcoma is relatively low and does not differ in HIV-positive and HIV-negative samples. The importance of viral load determination for prognosis or treatment monitoring remains to be elucidated.

AIDS-Related Opportunistic Infections↗
PubMed1992

Hairy cell leukemia. Diagnosis of bone marrow involvement in paraffin-embedded sections with monoclonal antibody DBA.44.

The new monoclonal antibody DBA.44 recognizes an unknown fixation-resistant B-cell differentiation antigen expressed by mantle zone lymphocytes, reactive immunoblasts, monocytoid B cells, and a small proportion of high- and low-grade lymphomas. Among node-based lymphomas, the strongest membrane staining was observed in centroblastic, immunoblastic, and monocytoid B-cell lymphomas. In studying bone marrow biopsy specimens from 166 patients with hairy cell leukemia, strong positive staining of surface membrane 'hairy' features of leukemic cells was observed in routinely fixed and decalcified bone marrow biopsy specimens of nearly all cases. The antibody distinguished hairy cell leukemia from the more common B-cell chronic lymphocytic leukemia and bone marrow infiltrates of typical lymph node-based lymphomas by immunomorphologic criteria. DBA.44 was valuable to (1) confirm the diagnosis of hairy cell leukemia, (2) estimate the bone marrow density of hairy cell leukemia before and after treatment, and (3) make the diagnosis of hairy cell leukemia in ambiguous cases, which are all properties that indicate its usefulness in the practice of diagnostic hematopathology.

Adult↗
PubMed1995

Non-radioactive localization of nucleic acids by direct in situ PCR and in situ RT-PCR in paraffin-embedded sections.

Technological developments have made possible extension of polymerase chain reaction (PCR) analysis to individual cells to localize DNA/RNA with non-radioactive labels at the light microscopic level. This approach, in situ PCR, is particularly useful in resolving low-frequency message expression in mixed populations of cells and tissues. We have established a working protocol for direct in situ PCR and have utilized several controls to validate our results. In this report we outline the procedures for detecting either DNA or RNA in a rapid and reproducible manner. We evaluate the sequential steps required for this analysis, such as protease hydrolysis, DNAse digestion, "hot start" capabilities, and detection methods. We have applied these methods in several applications, including detection of the p53 gene in human tumor samples, localization of insulin-like growth factor-IA mRNA in cell lines with low levels of expression, and distribution of transferrin mRNA in lung cancer cell lines and tumors. We demonstrate from this study that the in situ PCR technique is an investigative approach capable of detecting specific DNA/RNA sequences at the cellular level and of identifying cells with low levels of mRNA expression.

Base Sequence↗
PubMed1993

Diagnostic tools for differentiating pleural mesothelioma from lung adenocarcinoma in paraffin embedded tissue. II. Design of an expert system and its application to the diagnosis of mesothelioma.

A panel of 14 antibodies (panepithelial antibody Lu-5, anti-keratin-18, anti-keratin-7, Ber-EP4, anti-Leu-M1, HEA-125, anti-carcinoembryonic antigen, anti-blood group-related antigens A, B, H, B72.3, anti-placental alkaline phosphatase, anti-vimentin and BMA-120), which have been evaluated for use in differentiating mesothelioma from lung adenocarcinoma, was applied to a group of 24 suspected mesotheliomas. Using the established qualitative, descriptive criteria derived from monovariate statistical analysis of the tumour control groups (definite mesotheliomas, adenocarcinomas), a definitive allocation was possible in only 25% of suspected cases. We therefore constructed two "expert systems", based on multivariate discriminant analysis with either the ALLOC 80 program for ordinal data or a newly developed analysis program for binomial data. With these two systems diagnostic allocation of suspected mesotheliomas was improved to 75% and 79%. The use of binomial data ("positive" versus "negative") in conjunction with the probability-based test system is of particular interest because the primary data are easy to record and the test results have a higher statistical probability.

Adenocarcinoma↗
PubMed1999

Detection of EWS-FLI-1 fusion in Ewing's sarcoma/peripheral primitive neuroectodermal tumor by fluorescence in situ hybridization using formalin-fixed paraffin-embedded tissue.

The balanced translocation t(11;22)(q24;q12) is specific for the Ewing's sarcoma/peripheral primitive neuroectodermal tumors (ES/PNETs) and results in the EWS/FLI-1 fusion transcript, which can be detected by reverse transcription polymerase chain reaction (RT-PCR). Recent studies also have used fluorescence in situ hybridization (FISH) to show the translocation; however, most of these have been performed on cell lines or touch preparations and short-term cultures of tumors. Moreover, the existing probes generally have shown only the break in the specific chromosomes rather than the translocation itself. We describe our findings with a new set of probes that localize to 22q12 (EWS) and 11q24 (FLI-1) and directly show the translocation as juxtaposed red-green signals on der(22) in nuclei extracted from formalin-fixed, paraffm-embedded tissues. After establishing the specificity of the probes (on metaphase spreads and interphase nuclei in two translocation-positive cell lines and normal peripheral blood lymphocytes), we evaluated 11 ES/PNETs and 10 other tumors (four alveolar rhabdomyosarcomas, three neuroblastomas, two lymphomas, one extramedullary myeloid tumor) using a two-color FISH assay. All 11 ES/PNETs showed fusion signals in 20% to 80% of evaluable nuclei. In two lymphoma cases, random overlapping signals were present in 2% and 4% of nuclei, whereas the remaining eight tumors were negative. The presence of t(11;22) was confirmed by RT-PCR in 10 of 11 ES/PNETs. We conclude that FISH analysis with this newly designed probe pair is a specific and sensitive method of detecting t(11;22) on routinely processed tissue and can be useful in the differential diagnosis of ES/PNETs from other small round blue cell tumors when only fixed tissue is available.

Adolescent↗
PubMed1994

Comparison of image (CAS 200) and flow cytometry determined DNA content of paraffin-embedded Hodgkin's disease tissue.

To assess the reliability of DNA estimation using image cytometry, deparaffinized lymph nodes from 70 patients with Hodgkin's disease were examined and the results obtained were compared with those from flow cytometry. Image analysis without discriminating between the various cell types, as found in Hodgkin's disease, revealed no separate aneuploid peak. Selecting on morphologically defined nuclear types DNA aneuploidy was detected in 20% of the cases (14/70). The aneuploid populations were limited to the population of nuclei defined as Reed-Sternberg (RS)-like or medium-sized lymphocytes. Benign lymph nodes DNA aneuploidy was not found in any of the controls. Comparison of DNA histograms obtained by image and flow cytometry showed aneuploid peaks using image cytometry in 4 of 30 diploid and 10 of 40 aneuploid flow histograms. In conclusion, image analysis using the CAS 200 system as compared to flow cytometry is more time-consuming and less sensitive to assess ploidy status, although it may provide extra information in some selected cases. Evidence is obtained that DNA aneuploidy in Hodgkin's disease is preferentially expressed by cells with the RS/H-like and medium-sized lymphocyte morphology.

Aneuploidy↗
PubMed2003

Multiplex RT-PCR for the detection of common BCR-ABL fusion transcripts in paraffin-embedded tissues from patients with chronic myeloid leukemia and acute lymphoblastic leukemia.

Diagnosis of chronic myeloid leukemia and acute lymphoblastic leukemia requires the investigation of the Philadelphia chromosome translocation t(9;22) or the molecular detection of BCR-ABL fusion transcripts. Determination of the type of fusion transcript is crucial for quantitative molecular monitoring the course of the disease during treatment. Histopathologists, who usually use formalin-fixed tissues, may be confronted with the need to investigate the BCR-ABL rearrangement when evaluating tumor forming infiltrates and bone marrow trephines from patients presenting with chronic myeloproliferative disorders. Therefore, we have established a one-tube multiplex RT-PCR for the detection of common BCR-ABL fusion transcripts (b2a2, b3a2, e1a2) in routinely processed tissues and bone marrow trephines with respect to the inevitable fragmentation of ribonucleic acids in these specimens. RT-PCR products allow distinct and unequivocal differentiation of the underlying fusion in either the Major- or minor-breakpoint cluster region. Detection of BCR-ABL fusion transcripts by multiplex RT-PCR in routinely processed and fixed tissues is a time- and cost-sparing tool for definite diagnosis of typical chronic myeloid leukemia and Philadelphia chromosome positive acute lymphoblastic leukemia.

Bone Marrow Cells↗
PubMed1997

Obtaining clone-specific primer and probe for the immunoglobulin heavy-chain gene from paraffin-embedded tissue of B-cell lymphoma: technical considerations.

The complementarity determining region (CDR) III of the immunoglobulin heavy-chain (IgH) gene is a tumor-specific marker for B-cell malignancies that has been widely exploited for the monitoring of minimal residual disease in B-precursor acute lymphocytic leukemia. There are a number of technical problems in applying the same technology for B-cell non-Hodgkin's lymphoma (B-NHL). Several procedures have been useful in overcoming these unique problems encountered in obtaining the tumor-specific sequence of the IgH-CDRIII in B-NHL, including the use of denaturing gradient gel electrophoresis or micromanipulation of tissue sections in separating the tumor-specific CDRIII products from those of contaminating normal B-lymphocytes. Minor modifications of a commercial kit greatly improve the purity of the polymerase chain reaction (PCR) products for sequencing. Modifications of the 5'-ends of the VH and IH primers, coupled with the cycle sequencing technique, make it possible to obtain unambiguous sequences on direct sequencing of short PCR products. Computer informatics and programs that facilitate the design of tumor-specific primers and probes from CDRIII sequences are described.

DNA Primers↗
PubMed2000

Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction.

Analysis of gene expression and correlation with clinical parameters has the potential to become an important factor in therapeutic decision making. The ability to analyze gene expression in archived tissues, for which clinical followup is already available, will greatly facilitate research in this area. A major obstacle to this approach, however, has been the uncertainty about whether gene expression analyses from routinely archived tissues accurately reflect expression before fixation. In the present study we have optimized the RNA isolation and reverse transcription steps for quantitative reverse transcription-polymerase chain reaction (RT-PCR) on archival material. Using tissue taken directly from the operating room, mRNAs with half-lives from 10 minutes to >8 hours were isolated and reverse transcribed. Subsequent real-time quantitative PCR methodology (TaqMan) on these cDNAs gives a measurement of gene expression in the fixed tissues comparable to that in the fresh tissue. In addition, we simulated routine pathology handling and demonstrate that this method of mRNA quantitation is insensitive to pre-fixation times (time from excision to fixation) of up to 12 hours. Therefore, it should be feasible to analyze gene expression in archived tissues where tissue collection procedures are largely unknown.

Base Sequence↗
PubMed2003

Common ALK gene rearrangement in Asian CD30+ anaplastic large cell lymphoma: an immunohistochemical and fluorescence in situ hybridisation (FISH) study on paraffin-embedded tissue.

AIMS: The most common recurrent genetic aberration in anaplastic large cell lymphoma (ALCL) is translocation involving the ALK gene that results in ectopic expression of ALK protein in lymphoid tissue. This study aims to investigate the frequency of ALK gene rearrangement in a series of Asian ALCL. METHODS: ALK gene rearrangement was detected by immunostaining of ALK protein and fluorescence in situ hybridisation (FISH) targeting at the 2p23 region. RESULTS: The expression of ALK protein was detected in 24/34 (71%) of the cases, and it was significantly higher in childhood cases (100%) when compared to adult cases (47%). The analyses by FISH were consistent with the results from immunostaining of ALK protein, but the analyses were only successful in 15/34 (44%) cases. FISH analyses detected extra copies of ALK gene in three cases, including one case that expressed ALK protein and showed 2p23 rearrangement. CONCLUSIONS: The current series revealed a high frequency of ALK gene rearrangement, especially in the children. Immunostaining of ALK protein is a reliable indication of ALK gene rearrangement, and is superior to FISH. However, FISH analysis is useful in detecting other genetic aberrations that are not related to ALK gene rearrangement.

Adolescent↗
PubMed1995

Complete hydatidiform mole in twin pregnancy: differentiation from partial mole with interphase cytogenetic and DNA cytometric analyses on paraffin embedded tissues.

Six cases of hydatidiform mole associated with normal chorionic villi and a normal embryo/fetus (in five cases) were investigated with interphase cytogenetic and DNA cytometric analyses for diagnostic purposes. DNA probes specific for the pericentromeric regions of chromosomes 1 and X and for the long arm of chromosome Y were used. In four cases a dizygotic twin pregnancy could be proven. In these cases, the histologically normal chorionic villi showed an XY DNA-diploid pattern, consistent with a normal male conceptus, and the molar chorionic villi a XX pattern. In the other two cases an identical sex chromosomal pattern was found in the normal and in the molar villi (XX/XX and XY/XY respectively). In all six cases the molar placental tissues showed prominent trophoblastic hyperplasia with DNA-polyploidy, consistent with a complete hydatidiform mole. In two cases persistent gestational trophoblastic disease developed. It is emphasized that twin pregnancies composed of a normal conceptus and a complete mole have a relatively high risk for the development of persistent trophoblastic disease and therefore, should be carefully differentiated from triploid partial moles with a relatively low risk of persistent gestational trophoblastic disease. These case reports indicate that additional interphase cytogenetic and DNA cytometric analyses are useful in this differential diagnosis.

Adult↗
PubMed1995

Non-hazardous organic solvents in the paraffin-embedding technique: a rational approach. Aliphatic monoesters for clearing and dewaxing: butyldecanoate.

The aim of this study was to substitute hazardous compounds, used in tissue processing and dewaxing, with compounds having lowest possible toxicity and inflammability without impairing the morphology, staining characteristics, or diagnostic value of the tissue sections. All aromatic compounds and aliphatic hydrocarbons (e.g. alkanes, isoparaffins, petroleum distillates, etc.) were rejected, primarily due to their high vapour pressure. Based on a theoretical study of compounds used for clearing, a number of non-hazardous potential substitutes were chosen. The following experimental study narrowed the group to three unbranched, saturated, aliphatic monoesters containing 12-14 carbon atoms. On large-scale testing of these compounds, we found butyldecanoate to be the closest to an ideal substitute for aromatic and aliphatic hydrocarbons in the histology department: the section quality is at least equal to that obtained with xylene. For dewaxing, it is used at 30-35 degrees C. Butyldecanoate is not suitable as a pre-mounting agent. In practice, this is no problem as modern mounting agents permit mounting of coverslips directly from ethanol without impairing the appearance of the section in the microscope. Butyldecanoate has only a slight odour, insignificant vapour pressure (< 0.01 kPa at 20 degrees C), and does not present a fire hazard (flash point 134 degrees C). The introduction of this compound in the laboratory poses no health hazard, and the substance is biodegradable.

Animals↗
PubMed2005

Three-dimensional reconstruction of tumor microvasculature: simultaneous visualization of multiple components in paraffin-embedded tissue.

Three-dimensional (3D) visualization of microscopic structures may provide useful information about the exact 3D configuration, and offers a useful tool to examine the spatial relationship between different components in tissues. A promising field for 3D investigation is the microvascular architecture in normal and pathological tissue, especially because pathological angiogenesis plays a key role in tumor growth and metastasis formation. This paper describes an improved method for 3D reconstruction of microvessels and other microscopic structures in transmitted light microscopy. Serial tissue sections were stained for the endothelial marker CD34 to highlight microvessels and corresponding images were selected and aligned. Alignment of stored images was further improved by automated non-rigid image registration, and automated segmentation of microvessels was performed. Using this technique, 3D reconstructions were produced of the vasculature of the normal brain. Also, to illustrate the complexity of tumor vasculature, 3D reconstructions of two brain tumors were performed: a hemangioblastoma and a glioblastoma multiforme. The possibility of multiple component visualization was shown in a 3D reconstruction of endothelium and pericytes of normal cerebellar cortex and a hemangioblastoma using alternate staining for CD34 and alpha-smooth muscle actin in serial sections, and of a GBM using immunohistochemical double staining. In conclusion, the described 3D reconstruction procedure provides a promising tool for simultaneous visualization of microscopic structures.

Brain Neoplasms↗