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PubMed2001

Factors that influence the measurement of prostate cancer DNA ploidy and proliferation in paraffin embedded tissue evaluated by flow cytometry.

DNA ploidy and proliferation have been shown in several studies to be prognostic markers for prostate cancer. Flow cytometry (FCM) is often used in the determination of ploidy and proliferation. However, FCM cannot readily distinguish among benign epithelium, stromal and inflammatory cells, high grade prostatic intraepithelial neoplasia (HGPIN), and cancer cells. In this study, we evaluated H&E histologic features of 322 radical prostatectomy formalin-fixed, paraffin-embedded tissue blocks used for determining DNA ploidy, percent S-phase (%S), and %S + %G2M by FCM. The microscopic findings included Gleason score, extent of cancer and HGPIN in the tissue block, and presence of a needle track. The amount of cancer in the block was expressed as a percentage of the total tissue surface area in quartiles: < or =25%, 26-50%, 51-75%, and > or =76%. The extent of HGPIN was recorded in rough 5% intervals. Needle track effect was defined as a combination of fibrohistiocytic reaction, fibrin clot, granuloma formation, and chronic inflammation. The associations between these histologic features and DNA ploidy and proliferation (%S and %S + %G2M) were assessed. In multivariate analyses, Gleason score, the amount of tumor in the tissue block, and the extent of HGPIN were significantly associated with ploidy. Gleason score was the only parameter significantly associated with the proliferation measure of %S. If we included %G2M as part of the proliferative fraction of the histogram, however, both Gleason score and the amount of tumor in the block were significantly associated with this measure of proliferation. The presence of a needle track was not significantly associated with DNA ploidy, %S, or %S + %G2M. In summary, prostate cancer DNA ploidy and proliferation results assessed by FCM in paraffin-embedded tissue blocks were associated with the Gleason score, amount of cancer in the tissue block, and extent of HGPIN. However, the presence of a needle track was not associated with the FCM results.

Adult↗

PubMed1993

DNA content parameters of paraffin-embedded soft tissue sarcomas: optimization of retrieval technique and comparison to fresh tissue.

DNA content analysis of formalin fixed paraffin embedded (FFPE) tissue permits determination of the influence of DNA content on the prognosis in cohorts of patients for whom the clinical outcome is known. Of key importance in such an analysis is the accuracy of DNA content determination. Variations in the quality of DNA histograms from FFPE tissues of different types prompted a comparative evaluation of the preparative methodology of FFPE soft tissue sarcomas for DNA flow cytometry. Following deparaffination and rehydration of fixed tissue, and prior to fluorochrome staining, tissue blocks of 15 DNA aneuploid soft tissue sarcomas were subjected to repeated experimental (time x concentration) enzyme exposures. The goal of these studies was to define the optimal tissue specific retrieval technique with the coefficient of variation, maintenance of DNA aneuploidy, and DNA index as endpoints. After optimizing the technique, the DNA content of 50 soft tissue neoplasms derived from FFPE specimens was compared to the corresponding fresh surgical tissue. The observed 14 percent error rate in the determination of DNA ploidy status suggest limited utility for FFPE tissue in prospective therapeutic trials of soft tissue sarcoma.

Cell Count↗

PubMed2003

Detection by the fluorescence in situ hybridization technique of MYC translocations in paraffin-embedded lymphoma biopsy samples.

The detection of chromosomal translocations by fluorescence in situ hybridization (FISH) is widely performed, but very few studies have attempted to apply this technique to paraffin-embedded routine biopsy samples. We report the analysis of paraffin sections from 36 B-cell lymphoma biopsies for MYC translocation breakpoints by FISH. The probes consisted of multi-YAC constructs that flanked the breakpoint region and that, therefore, separate upon a chromosomal translocation and generate split (or "segregated") signals (rather than a more ambiguous "co-localization" pattern, obtained when the two partners in a hybrid gene are detected). The results were assessed by a simple approach that avoids the counting of signal numbers per nucleus and so is appropriate for use in routine practice. A total of 19 of the 36 lymphomas were scored as positive for MYC translocation and this included 16 of the 20 patients in whom classic cytogenetics had shown the presence of the (8;14) translocation (or one of its two variants). We conclude that this two-colour "split-signal" technique based on breakpoint flanking probes can readily detect chromosomal translocations in paraffin sections. Furthermore, our results suggest that cases categorized as "atypical Burkitt's/Burkitt-like" lymphoma (at least for adult patients) are heterogeneous with respect to translocations involving the MYC oncogene, as well as immunophenotype and clinical features.

Adolescent↗

PubMed1987

Distinction between undifferentiated (small noncleaved) and lymphoblastic lymphoma. An immunohistologic study on paraffin-embedded, fixed tissue sections.

The morphologic differentiation between malignant lymphoma of the small noncleaved cell (SNC) type and lymphoblastic lymphoma (LBL) is at times difficult, particularly when fresh tissue is not available for immunologic studies. We have examined the reactivities of a panel of monoclonal and polyclonal antibodies, including LN-1, LN-2, and antibodies to immunoglobulin light chains, leukocyte common antigen (LCA), Leu-M1, vimentin, S-100 protein, lysozyme, and alpha-1-antitrypsin, in paraffin-embedded, B5- and formalin-fixed tissue involved by SNC or LBL. The immunophenotypes in all of the cases included in this study had been characterized previously in fresh-frozen sections or cell suspensions. Among 21 samples of B5-fixed SNC, LN-1 was reactive in 17 and LN-2 in 18 cases. Among 13 B5-fixed LBL, LN-1 was reactive in two cases and LN-2 was reactive in two cases. Each of 20 B5-fixed samples of SNC was reactive with at least one of the antibodies, whereas 10 of the 13 B5-fixed samples of LBL were negative for both antibodies. Lesser reactivity was evident in formalin-fixed tissues, with only nine of 27 SNC specimens positive for LN-1 and 16 of 27 positive for LN-2. Most or all of the SNC and LBL samples were negative for immunoglobulin light chains, Leu-M1, vimentin, S-100 protein, lysozyme, and alpha-1-antitrypsin. The majority of both SNC and LBL were positive for LCA. We conclude that LN-1, preferably in combination with LN-2, can be used for distinguishing between SNC and LBL in paraffin-embedded, B5-fixed tissue when fresh tissue is not available.

Adolescent↗

PubMed1990

DNA ploidy and cell-cycle analysis in pancreatic and ampullary carcinoma: flow cytometric study of formalin-fixed paraffin-embedded tissue.

The cellular DNA content of formalin-fixed, paraffin-embedded specimens from 47 ductal adenocarcinomas of the pancreas and 5 adenocarcinomas of the ampulla of Vater was analysed using flow cytometry. Ploidy and the fraction of cells in the S and G2M phases were determined and correlated with tumour stage and grade as well as patients' survival. Cell populations with aneuploid DNA content were observed in 15% of the tumours. The S + G2M fractions ranged between 1% and 10%. Compared to non-neoplastic tissue of the pancreas the S + G2M fraction was significantly higher in the carcinomas. Cox regression analysis revealed the S + G2M fraction as an independent prognostic factor (p less than 0.05). Ploidy was of no prognostic value for survival, but correlated weakly with tumour stage and tumour grade. All patients without lymph node metastases at time of surgery had diploid tumours. Aneuploidy was restricted to tumours in advanced stages and tended to be more frequent in high-grade tumours.

Adult↗

PubMed1992

Semiquantitative analysis of the effects of fixation and paraffin embedding on immunoreactivity of renal basement membranes to a monoclonal antibody against type IV collagen.

The effects of formalin fixation and paraffin embedding on the immunoreactivity of human kidney to a monoclonal anti-type IV collagen antibody (JK-199) were examined semiquantitatively by a modified enzyme-linked immunosorbent assay (ELISA). The intensity of immunoreactivity in paraffin sections of the tissue fixed overnight with 10% formalin was approximately 70% of that in frozen sections. Immunoreactivity reduced to this extent did not impair the specific staining of basement membranes. Paraffin sections of tissues fixed 2 days showed 50-60% of the reactivity in the frozen sections of the tissue fixed overnight; the basement membranes in Bowman's capsules were stained positively, but those in other sites were not. The paraffin sections of tissues fixed 7 or 14 days showed no specific immunostaining. The immunoreactivity for type IV collagen in the basement membranes was restored after treatment with pronase E. The immunoreactivity after the enzymatic treatment was about 150% of that in the frozen sections of the overnight fixed specimens.

Antibodies, Monoclonal↗

PubMed1991

An efficient method for the extraction of DNA from formalin-fixed, paraffin-embedded tissue by sonication.

A method was developed for fast and efficient isolation of DNA from formalin-fixed, paraffin-embedded tissue sections for subsequent use in PCRs and DNA hybridization assays. The method relies on the use of a sonicating water bath to disrupt tissue samples to which a small amount of micro-sized glass beads have been added. The sonicating glass beads provide fast and efficient physical shearing of fixed tissue sections, allowing for quick release and solubilization of the DNA. The extraction process from paraffin section to amplifiable target DNA takes 30 minutes. The method eliminates the need for repetitive solvent extractions and exhaustive proteinase K digestion. PCR amplification of human genomic and viral target sequences was successfully carried out on DNA isolated from a number of different types of normal and infected tissues.

Base Sequence↗

PubMed1997

Hepatic regeneration in humans with various liver disease as assessed by Ki-67 staining of formalin-fixed paraffin-embedded liver tissue.

The ability to document nuclear proliferation in the liver is essential to our understanding of hepatic regeneration and hepatocellular carcinoma. While numerous tests are available to provide such information in experimental animals, few can be applied to patients with liver disease. Ki-67 is a proliferating nuclear antigen present in replicating cells. Recent data indicates that staining for Ki-67 reflects nuclear proliferation in these tissues. To date, the technique has had only limited application to human liver tissues in formalin-fixed paraffin embedded tissue. In the present study, we documented Ki-67 staining in archival liver tissue from patients with mild chronic hepatitis, severe chronic hepatitis, inactive cirrhosis, hepatocellular carcinoma, and in normal livers. We found that Ki-67 staining was increased in patients with mild chronic hepatitis (labelling index 29 +/- 25), severe chronic hepatitis (labelling index 41 +/- 40), and hepatocellular carcinoma (labelling index 71 +/- 61), when compared to patients with inactive cirrhosis, (labelling index 1.4 +/- 3.1), and normal livers (labelling index 2.5 +/- 3.2). In conclusion, Ki-67 maybe useful tool to assess hepatocyte proliferation in formalin-fixed paraffin-embedded human liver tissue.

Carcinoma, Hepatocellular↗

PubMed2001

A technical note on microsatellite DNA instability studied in archival paraffin-embedded tissues.

The authors present brief overview of problems associated with analysis of microsatellite sequences in DNA from archival paraffin-embedded tissue. This methodology can serve several diagnostic and research purposes provided appropriate precautions are taken to extract DNA of acceptable quality with small admixture of contaminants. Also PCR amplification step requires some modifications compared to routine reactions involving DNA from fresh or freshly-frozen tissues.

DNA↗

PubMed1995

Detection of Borna disease virus RNA in formalin-fixed, paraffin-embedded brain tissues by nested PCR.

A method for detecting Borna disease virus (BDV) RNA in formalin-fixed, paraffin-embedded brain tissue sections was established. By digestion with proteinase K and subsequent extraction with guanidinium thiocyanate, phenol, and chloroform, we were able to efficiently release RNA from the fixed tissues. By reverse transcription of the RNA and nested PCR a 212-bp product was generated, as expected.

Animals↗

PubMed2003

Expression profiling of mouse endometrial cancers microdissected from ethanol-fixed, paraffin-embedded tissues.

Expression-profiling studies have helped define genetic changes associated with carcinogenesis. Determining which alterations in gene expression are causally associated with cancer and which result from the general dysregulation in gene expression that is characteristic of malignancies remains a problem. Transcriptional profiling of early lesions (small cancers or precancers) holds promise for identifying biologically important changes in gene expression. There are, however, technical barriers to the study of small tumors. The total number of cells available for analysis is limiting. It is also often difficult to distinguish cancer cells from normal proliferating cells in frozen sections that are typically used as a source of RNA. Here we describe an ethanol fixation and paraffin-embedding protocol that preserves tissue architecture and cellular morphology of the mouse endometrium, and allows for the recovery of high-quality RNA from microdissected cells. We performed GeneChip expression profiling using RNA from 800 to 4400 cells microdissected from ethanol-fixed, paraffin-embedded uteri. Endometrial adenocarcinomas exhibited changes in the levels of a number of messages known to be abnormally expressed in cancer, and differential expression of additional transcripts not previously implicated in carcinogenesis. We confirmed increased Amd1 expression in RNAs from mouse endometrial carcinomas that were hybridized to GeneChips and validated overexpression of this transcript in additional tumors.

Animals↗

PubMed1997

DNA ploidy by image cytometry in urothelial carcinomas. Comparison of touch imprints and paraffin-embedded biopsies from 31 patients.

OBJECTIVE: To compare DNA content measured by image cytometry from touch imprints and formalinfixed, paraffin-embedded samples in bladder carcinomas. STUDY DESIGN: Thirty-one biopsies of urothelial carcinomas were selected for a prospective study. Imprints of fresh specimens were performed. Cell suspensions were obtained from dewaxed samples by the procedure of Hedley. Sections 7 microns thick were used for carcinoma in situ and small biopsies. The DNA ploidy index was measured on Feulgen-stained slides using an image cytometer. RESULTS: From imprint analysis, seven grade 1 carcinomas (n = 9) were found to be diploid (78%). Nine grade 2 carcinomas (n = 12) exhibited aneuploidy (75%), as did all grade 3 and in situ carcinomas (n = 10). Multiploidy was demonstrated from imprints in four cases instead of the two detected from dewaxed tissue. In 27 cases (87%), G0/G1 peaks obtained from paraffin blocks showed a shift to the left. In five cases (16%), variations in the DNA index were responsible for discrepancies in the DNA ploidy evaluation between fresh imprints and dewaxed samples of the same tumors. CONCLUSION: Image cytometry on Feulgen-stained imprints of bladder biopsies is a simple and reliable procedure for assessing DNA ploidy in urothelial carcinomas, providing great sensitivity for detecting small aneuploid peaks and multiploid tumors. DNA image analysis of touch preparations is especially useful for carcinoma in situ and small biopsies unsuitable for Hedley's technique.

Aged↗

PubMed1994

Determination of hepatic iron concentration in fresh and paraffin-embedded tissue: diagnostic implications.

BACKGROUND/AIMS: Determination of hepatic iron concentration (HIC) is essential for the evaluation of hereditary hemochromatosis. Occasionally, only paraffin-embedded liver biopsy specimens are available, or fresh biopsy specimens have been placed in saline for transport. This study aimed to describe a method for extraction of liver tissue from paraffin blocks, determine the accuracy of measurement of HIC in recovered tissue compared with fresh tissue, and determine the effect of immersion in saline on HIC. METHODS: HIC was measured in both fresh and deparaffinized liver specimens (n = 41). Accurate measurements were defined as either a normal result in both specimens or a result in the deparaffinized specimen that was within 30% of the fresh measurement. RESULTS: Measurements of HIC in fresh and deparaffinized tissue showed an excellent linear relationship (r = 0.95). In deparaffinized samples > or = 0.4 mg, accurate measurements were seen in 24 out of 29 specimens, compared with 6 out of 12 specimens weighing < 0.4 mg (P < 0.01). The hepatic iron index calculated from results in deparaffinized samples > or = 0.4 mg correctly classified all patients. Immersion of fresh biopsy specimens in saline for 1 hour resulted in up to 50% iron loss (P < 0.05). CONCLUSIONS: Accurate measurement of HIC in deparaffinized liver biopsy specimens is possible. Calculation of the hepatic iron index from deparaffinized liver tissue can facilitate diagnosis of hemochromatosis when fresh tissue is not available. Samples should not be transported in saline.

Animals↗

PubMed1991

Analysis of N-ras gene mutations in medulloblastomas by polymerase chain reaction and oligonucleotide probes in formalin-fixed, paraffin-embedded tissues.

Precise data on the incidence of transforming ras oncogenes in pediatric tumors and the correlations with the histopathological properties of the tumors are very limited. Additionally the presence of ras activation in medulloblastomas has not been investigated so far. Using a combination of techniques including in vitro gene amplification by polymerase chain reaction (PCR) and detection of single base mutations by sequence-specific oligonucleotides we studied N-ras activation (mutations at codon 12, 13, and 61) in 32 medulloblastomas. DNA was isolated from 20 microns sections of formalin-fixed paraffin-embedded tissue. Mutations were found in 3 out of 32 examined medulloblastomas. In all cases only mutations of codon 61 were found: two of three mutations were C to A mutations at position 1 of the codon 61 (leading to a substitution of a glutamine residue for a lysine) and one was A to T mutation at position 3 in the same codon (glutamine-histidine). Our results indicate 10% incidence N-ras mutation in medulloblastoma, higher than in other CNS tumors studied so far. The main advantages of the procedure described are its greatly improved sensitivity, the increased speed with which tumor samples can be analyzed, and the possibility of using paraffin-embedded sections to analyze various rare tumors in retrospect.

Adolescent↗

PubMed1992

Significance of variation in DNA flow cytometric analyses from paraffin-embedded breast cancers. Evaluation of the grading efficiency of ploidy determination, DNA index, and S-phase fraction.

116 paraffin-embedded breast cancer samples were analyzed by flow cytometry. From each sample 3 consecutive 50 microns sections were cut for the study. The presence of neoplastic tissue was verified from light microscope sections cut before and after the adjacent sections. One laboratory started with one section from each block and was allowed extra sections when needed for analysis. At the end the laboratory obtained results from all 116 cases. The rest of the samples were studied by 2 other laboratories. Samples with results from 2 or 3 laboratories then allowed variability analysis and the estimation of the grading efficiency in a 2-grade system. Inconsistency in diploidy/aneuploidy distinction was present in 36 of 111 (32.4%) cases studied by two or three laboratories. This inconsistency was less obvious in samples graded as multiploid by at least one of the laboratories. The grading efficiency as analyzed from the results of 3 laboratories was 0.89, and of 2 laboratories, 0.84. The DNA index showed a slightly higher grading efficiency. At the cutoff point of 1.3, 91% of cases could be expected to be correctly classified into low ploidy and high ploidy groups (grading efficiency 0.91). The S-phase fraction had a mean grading efficiency of 0.89, a performance comparable to that of diploidy/aneuploidy distinction. In the light of the available data the flow cytometric analysis can add to the consistency of grading, especially when compared with subjective histological grading. However, the data do not suggest that flow cytometric analysis of paraffin sections as a grading method would be more consistent than quantitative histopathology from sections.

Aneuploidy↗

PubMed1991

Comparative long-term prognostic value of quantitative HER-2/neu protein expression, DNA ploidy, and morphometric and clinical features in paraffin-embedded invasive breast cancer.

Data regarding the prognostic value of HER-2/neu protein expression in breast cancer are conflicting, perhaps because of short follow-up and technical difficulties in the determination (the admixture of benign elements with the biochemical method and the subjectivity of the immunohistochemical assessment). Therefore, using digital image processing, we compared the correlation between and the prognostic value of (a) quantitative immunohistochemical HER-2/neu protein expression and (b) clinical, morphometric, and flow-cytometric DNA ploidy features; histologic grade; and biochemically assessed estrogen receptor content. Paraffin-embedded invasive breast Pancers of 82 patients with long-term follow-up were used. None of the patients had received adjuvant systemic therapy. HER-2/neu protein expression was significantly correlated with DNA index, lymph node status, and tumor size and, in the diploid tumors, was weakly correlated with the percentage of S-phase cells. Strong HER-2/neu protein expression was associated with a worse prognosis (although not significantly, p = 0.07). No differences were detected between cancers with or without axillary lymph node metastases. In survival analysis, the Multivariate Prognostic Index and the morphometric features were much stronger prognosticators than HER-2/neu protein overexpression, which, however, had additional prognostic value to that of many of the features analyzed, especially when more than 35% HER-2/neu protein levels (relative to the high expression SKBR3 cell line) were present. Combined diploidy and HER-2/neu protein content greater than 35% occurred in a small group of patients (n = 3), all of whom died. Likewise, in tetraploid cancers a combination of S-phase cells greater than or equal to 7% and HER-2/neu protein content greater than 35% was an ominous sign. In multivariate analysis, strong HER-2/neu protein overexpression was prognostically over-shadowed by the morphometric features. Nevertheless, it is important to further analyze the intriguing possibility of identifying a subgroup of breast cancer patients with a very poor outcome merely using cytometric analysis of paraffin-embedded material of the primary tumor.

Biomarkers, Tumor↗

PubMed2005

Molecular diagnosis of Ewing's sarcoma/primitive neuroectodermal tumor in formalin-fixed paraffin-embedded tissues by RT-PCR and fluorescence in situ hybridization.

Recent studies have suggested that formalin-fixed paraffin-embedded (FFPE) tissues can be used for molecular analyses by fluorescence in situ hybridization (FISH) and RT-PCR. We analyzed 18 cases of ES/PNET for the t(11;22)(q24;q12) and t(21;22)(q22;q12) fusion transcripts by RT-PCR and analyzed for EWS translocation by interphase FISH with a dual color fusion probe to compare these two approaches directly. RT-PCR detected 13 (72%) EWS-FLI-1 fusions (type I=10, type II=3) and 2 (11%) EWS-ERG fusions. Three cases could not be evaluated because the housekeeping gene phosphoglycerate kinase (internal mRNA control) was not amplified. FISH was diagnostic in 15 of 18 cases (83%). There were three discordant cases between RT-PCR and FISH (concordance of 83%). Using a combination of RT-PCR and FISH, the results were complementary. One advantage of RT-PCR analysis was that subtypes of EWS translocation could be determined specifically (type I, type II and ERG). These findings indicate that because of the difficulties and limitations associated with the molecular analysis of FFPE tissues, a combination of RT-PCR and FISH may be a better approach to enhance the sensitivity and accuracy of detecting ES/PNET translocations in FFPE tissues with suboptimally preserved nucleic acids.

Base Sequence↗

PubMed1994

Polymerase chain reaction analysis of hepatitis B virus DNA in formalin-fixed, paraffin-embedded liver biopsies from alcoholics using a simplified and standardized amplification protocol.

Sixty-seven formalin-fixed and paraffin-embedded liver biopsies from HBsAg-negative alcoholics without previous blood transfusions or intravenous drug abuse were analyzed for the presence of low-level hepatitis B virus DNA by the polymerase chain reaction. To simplify and standardize the amplification procedure, aliquots of a complete polymerase chain reaction mix were prepared and frozen for storage; random samples were tested prior to analysis of clinical material. Freezing and storage of the aliquots did not affect the activity of Taq polymerase. One large batch of ready-to-use aliquots could thus be used as a standardized polymerase chain reaction kit for all experiments. The suitability of the extracted material for polymerase chain reaction analysis was tested in two ways. First, the absence of nonspecific polymerase chain reaction inhibitors was demonstrated in all samples by amplifying cloned hepatitis B virus DNA in the presence of extracted material. Second, the integrity of the extracted DNA was tested by amplifying a segment of the beta-globin gene. Twenty-three samples were beta-globin DNA positive and thus contained sufficient amounts of nondegraded DNA. These results emphasize the importance of testing both the absence of nonspecific inhibitors and DNA integrity in DNA samples extracted from fixed tissue. Among the 23 beta-globin positive samples, 12 had cirrhosis (52.1%). Two of these samples were hepatitis B virus DNA positive (8.7%); one of these cases had cirrhosis. Thus, even in the absence of common risk factors, the incidence of hepatitis B virus in this alcoholic population was increased compared to the general population.

Alcoholism↗