Analysis Of Paraffin-embedded Tissue Research Articles

Immunodetection of NETs in Paraffin-Embedded Tissue.

The pathogenic potential of neutrophil extracellular traps (NETs) was recently described, and their detection in tissue could serve as a prognostic marker. NETs are delicate and filigree structures; hence good tissue preservation is essential for their detection. Indeed, analysis of paraffin-embedded tissue has proven superior to the study of cryo sections. Though, under favorable conditions, the presence of NETs can be detected in tissue sections stained with histological dyes, definitive identification of NETs needs the colocalization of immunofluorescent signals for both nuclear and granular (or cytoplasmic) NET components. We tested diverse antigen retrieval methods and various combinations of commercially available antibodies and present here staining protocols to detect NETs in human and murine tissue sections.

Examination of the early infection stages of koi herpesvirus (KHV) in experimentally infected carp, Cyprinus carpio L. using in situ hybridization.

Koi herpesvirus (KHV) causes a highly infectious disease afflicting common carp and koi, Cyprinus carpio L. Various molecular and antibody-based detection methods have been used to elucidate the rapid attachment and dissemination of the virus throughout carp tissues, facilitating ongoing development of effective diagnostic approaches. In situ hybridization (ISH) was used here to determine the target tissues of KHV during very early infection, after infecting carp with a highly virulent KHV isolate. Analysis of paraffin-embedded tissues (i.e. gills, skin, spleen, kidney, gut, liver and brain) during the first 8h and following 10days post-infection (hpi; dpi) revealed positive signals in skin mucus, gills and gut sections after only 1hpi. Respiratory epithelial cells were positive as early as 2hpi. Viral DNA was also detected within blood vessels of various tissues early in the infection. Notable increases in signal abundance were observed in the gills and kidney between 5 and 10 dpi, and viral DNA was detected in all tissues except brain. This study suggests that the gills and gut play an important role in the early pathogenesis of this Alloherpesvirus, in addition to skin, and demonstrates ISH as a useful diagnostic tool for confirmation of acutely infected carp.

Diagnosis of testicular carcinoma in situ‘(intratubular and microinvasive)’ seminoma and embryonal carcinoma using direct enzymatic alkaline phosphatase reactivity on frozen histological sections

Testis-sparing surgery might benefit quality of life, but can only be applied with histological examination for the presence of invasive germ cell tumour components, and the precursor carcinoma in situ (CIS). Currently, diagnosis is based on paraffin-embedded tissue, therefore a delay in further surgery is mainly unavoidable. The aim was to develop an intraoperative assessment technique using alkaline phosphatase as a marker. A total of 4093 snap-frozen samples and matched paraffin-embedded tissue of 1500 patients were included. Besides standard haematoxylin and eosin (H&E) staining, the direct enzymatic alkaline phosphatase reactivity (dAP) test (duration 15 min) was applied on frozen sections, while H&E and immunohistochemistry for detection of OCT3/4, α-fetoprotein, human chorionic gonadotrophin (hCG) and cytokeratin was performed on the paraffin-embedded slides. Endothelial cells served as control for the dAP test. Positive staining was found in all CIS (n=965), seminoma (n=1035) and embryonal carcinoma (n=584), either intratubular, microinvasive or invasive. Differentiated non-seminomas (n=1238) showed variable staining. No staining was identified in spermatocytic seminomas (n=5), testicular lymphomas (n=42), testicular rhabdomyosarcomas (n=7), Leydig cell tumours (n=31), Sertoli-cell-only nodules (n=4), (epi) dermoid cyst (n=16), normal testicular parenchyma (n=116), testicular torsion (n=32) and inflammation of the epididymis (n=19). The dAP test results matched H&E-stained parallel sections, as well paraffin-embedded tissue analysis, including immunohistochemistry. The dAP test is an informative, reproducible and easy tool to diagnose CIS, (intratubular and microinvasive) seminoma and embryonal carcinoma on frozen tissue sections, being of great value in the context of sparing surgery.

HER2 Status in Ovarian Carcinomas: A Multicenter GINECO Study of 320 Patients

BackgroundDespite a typically good response to first-line combination chemotherapy, the prognosis for patients with advanced ovarian cancer remains poor because of acquired chemoresistance. The use of targeted therapies such as trastuzumab may potentially improve outcomes for patients with ovarian cancer. HER2 overexpression/amplification has been reported in ovarian cancer, but the exact percentage of HER2-positive tumors varies widely in the literature. In this study, HER2 gene status was evaluated in a large, multicentric series of 320 patients with advanced ovarian cancer, including 243 patients enrolled in a multicenter prospective clinical trial of paclitaxel/carboplatin-based chemotherapy.Methodology/Principal FindingsThe HER2 status of primary tumors and metastases was evaluated by both immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) analysis of paraffin-embedded tissue on conventional slides. The prognostic impact of HER2 expression was analyzed. HER2 gene was overexpressed and amplified in 6.6% of analyzed tumors. Despite frequent intratumoral heterogeneity, no statistically significant difference was detected between primary tumors and corresponding metastases.Conclusions/SignificanceOur results show that the decision algorithm usually used in breast cancer (IHC as a screening test, with equivocal results confirmed by FISH) is appropriate in ovarian cancer. In contrast to previous series, HER2-positive status did not influence outcome in the present study, possibly due to the fact that patients in our study received paclitaxel/carboplatin-based chemotherapy. This raises the question of whether HER2 status and paclitaxel sensitively are linked.

Value of frozen section analysis with suspected testicular malignancy

Objectives To determine whether frozen section analysis (FSA) assists safe conservative surgery for men presenting with suspected testicular tumors. Methods We performed a retrospective review of intraoperative testicular FSA used at a single university institution during an 11-year period. The exclusion criteria included lesions of paratesticular origin, size greater than 5 cm, and the known presence of elevated tumor markers or metastatic disease. Results Eighty men underwent FSA, facilitating the diagnosis of germ cell malignancy in 51 (54.3%) of the 94 new cases encountered during this period. Malignancy was reported by FSA in 52 patients (65.0%), but was later revised in 3 to benign Leydig cell tumor after orchiectomy. Also, 2 of 27 specimens reported as benign by FSA were revised to malignant after analysis of paraffin-embedded tissue from the biopsies. Both were seminoma and required delayed orchiectomy. FSA was reported as “suspicious” (intratubular germ cell neoplasia with necrosis) in 1 patient, in whom orchiectomy was performed and malignancy confirmed. In total, orchiectomy was avoided in 25 cases (31.3%). The positive and negative predictive value for FSA in the diagnosis of testicular malignancy was 94.2% and 92.6%, respectively. Of 13 lesions 1 cm or less, 10 (76.9%) were benign. All 26 lesions greater than 3 cm were malignant. A clear correlation between lesion size and the diagnosis of malignancy was demonstrated. Conclusions FSA is a valuable tool assisting testicular preservation. Lesion size correlated with incidence of malignancy; therefore, FSA may be best used for small testicular lesions suitable for excision biopsy.

Rhabdomyosarcoma: Value of myogenin expression analysis and molecular testing in diagnosing the alveolar subtype

AbstractBACKGROUNDIdentification of the alveolar subtype of rhabdomyosarcoma (ARMS) is important, because the poor prognosis associated with this subtype necessitates a modified therapeutic regimen. At present, ARMS diagnoses are made on the basis of histologic findings and the extent of myogenin immunopositivity. Nonetheless, the absence of an alveolar pattern in the solid variant, the low degree of differentiation in certain embryonal rhabdomyosarcomas (ERMS), and the increasing use of microbiopsy samples make the diagnosis of ARMS somewhat difficult. Two specific translocations have been found in ARMS, and fusion transcripts can be detected by reverse transcriptase–polymerase chain reaction (RT‐PCR) analysis of paraffin‐embedded tissue (PET).METHODSTo assess the value of myogenin staining and molecular testing in the diagnosis of rhabdomyosarcoma, the authors examined 109 rhabdomyosarcoma samples (45 ARMS samples and 64 ERMS samples). Real‐time RT‐PCR analysis of PET was performed in all 109 rhabdomyosarcomas, and RT‐PCR analysis of frozen material was performed in 24 cases.RESULTSPAX fusion transcripts were present in 44 cases (39 ARMS and 5 ERMS) and absent in 52 cases (2 ARMS and 50 ERMS). In 13 cases (4 ARMS and 9 ERMS), the results were not interpretable. Results were concordant between paired frozen and fixed tumor samples. All 35 interpretable ERMS samples that contained < 50% myogenin‐positive cells failed to yield detectable PAX fusion transcripts. Of the 61 interpretable tumor samples (41 ARMS and 20 ERMS) that contained > 50% myogenin‐positive cells, 44 (39 ARMS and 5 ERMS) yielded detectable PAX fusion transcripts.CONCLUSIONSThe current study demonstrates that molecular detection of PAX fusion transcripts via real‐time RT‐PCR analysis of PET is a sensitive and specific method for the diagnosis of ARMS and that immunohistochemical analysis of myogenin expression can be used to select cases for such molecular testing. Although RT‐PCR analysis appears not to possess diagnostic value in tumors with < 50% tumor cell immunopositivity, it is strongly recommended for the diagnosis of tumors containing > 50% myogenin‐positive cells. Cancer 2004. © 2004 American Cancer Society.

Molecular genetic analysis of archival gliomas using diagnostic smears.

Investigation of the clinical significance of genetic alterations in gliomas requires molecular genetic analysis using samples from retrospective or prospective clinical studies. However, diagnostic tissue is often severely limited and because of fixation, paraffin-embedded tissues (PET) contain degraded DNA. Intra-operative cytological preparations (smears) archived after diagnosis may represent an additional source of clinical material for genetic analysis. In this study, tissue samples were obtained by precision microdissection of archived diagnostic smears from 20 cases (1961-1999). All samples produced polymerase chain reaction (PCR) products for the beta globin gene, but the most recent samples amplified best and gave longer amplimers. For six cases, direct comparison was made between samples microdissected from smears and the corresponding PET. Samples from smears showed improved PCR performance and similar alleles on microsatellite marker analysis. One case, with smears of uninvolved cortex and tumour tissue available for microdissection, showed allelic imbalance at 10q23 on the basis of the smear results alone. PCR products from smears were shown to be suitable for direct sequence analysis (p53 gene). A PTEN mutation, found previously in an anaplastic astrocytoma by analysis of PET, was detected in the corresponding diagnostic smear. The results of this study indicate that tissue samples microdissected from diagnostic intra-operative cytological preparations may be suitable for molecular genetic analysis of gliomas.

Identification of MEN1 Mutations in Sporadic Enteropancreatic Neuroendocrine Tumors by Analysis of Paraffin-embedded Tissue

Gastrinomas and other gastrointestinal neuroendocrine tumors may occur sporadically or as part of the inherited syndrome multiple endocrine neoplasia type 1 (MEN1). Mutations in the recently identified MEN1 gene have been described in sporadic gastrinomas and insulinomas. This study describes techniques used to identify mutations in the MEN1 gene in DNA extracted from paraffin-preserved tissue. Two novel mutations are identified in the MEN1 gene from nine archived paraffin-embedded neuroendocrine tumors, demonstrating that retrospective genetic analysis can be used to identify mutations in the MEN1 gene from preserved tissue. Conditions are provided by which paraffin-embedded tissue can be used as a source of genetic material for sequence information of sufficient quality for mutational studies of the MEN1 gene. It should also be possible to apply this retrospective genetic analysis of paraffin-embedded tissue to other disease models.

Molecular biological analysis of paraffin-embedded tissues

Molecular biology techniques have been adapted to the analysis of paraffin-embedded tissues (PETs), expanding their clinical utility. In vitro amplification with the polymerase chain reaction (PCR) promises to be the most useful means of retrospective analysis because it can be performed successfully on nucleic acids that have been partially degraded during fixation, paraffin embedding, and the extraction process. Five clinical situations in which DNA analysis of PETs can be helpful are: (1) confirmatory molecular diagnosis of lymphoma in which fresh tissue has not been obtained at the time of surgery, (2) identification of infectious agents, (3) genetic characterization of a putative inherited disease in which the affected individual has died, (4) confirmation of donor cell malignancy in transplant recipients, and (5) specimen identification. The role of the pathologist in molecular diagnosis will grow because of the feasibility of using PETs, a venue unique to our profession.

Variation in reference cells for DNA analysis of paraffin-embedded tissue.

Selection of the diploid reference cells used in flow cytometric DNA analysis of paraffin-embedded tissue is inconsistent in the literature. To determine which types of cells were most suitable for use as reference cells, benign paraffin-embedded tissue was evaluated from nine randomly selected autopsies. Benign kidney, lymph node, gastrointestinal mucosa, laryngeal mucosa, bronchial mucosa, bladder mucosa, pancreas, and, when available, prostate tissue were studied. Ten paraffin-embedded surgical specimens also were studied. In the autopsy specimens, great variability in the mean peak channels was noted on intrapatient evaluation and even more variability was present when comparing similar organs (especially lymph nodes) from different patients. Similar results were obtained using lymph nodes from surgical specimens. It is concluded that the most suitable diploid reference cells for DNA analysis of paraffin-embedded tissue are the benign cells present in the paraffin tumor block that have been processed in the same way as the tumor cells.

DNA Measurement by Image Analysis of Paraffin-Embedded Breast Carcinoma Tissue: A Comparative Investigation

Measurement of cellular DNA content may provide useful prognostic information in several human neoplasms. The DNA content by image analysis of fresh tissue has been compared with flow cytometry with good correlation, but the use of paraffin-embedded tissue for image analysis has not been studied widely. This study reports the DNA content of 54 breast carcinomas and compares the results of image analysis of paraffin-embedded tissue and results of image analysis and flow cytometry of corresponding fresh tumors. Image analysis of paraffin blocks and fresh tumors showed comparable results in 51 tumors (94%), whereas 47 tumors (87%) were similar by all three methods. The DNA indices from image analysis of fresh and paraffin-embedded tumors showed significant correlation by linear regression analysis (r = 0.96; P less than 0.001). Discordances between image analysis of fresh and paraffin-embedded tumors are the result of technical problems, such as staining and tissue preservation. Discordances between image analysis and flow cytometry reflect the advantages and pitfalls of the two techniques. These data suggest that image analysis of paraffin-embedded tissue is a viable technique that will permit the performance of retrospective studies with long-term follow-up data for the evaluation of the prognostic significance of DNA content.

Detection of Epstein-Barr Virus in Epidermal Skin Lesions of an Immunocompromised Patient

Using in-situ hybridizaiton, we showed the presence of the Epstein-Barr (EB) virus genome in epidermal cells from a patient with chronic lymphocytic leukemia and unusual cutaneous lesions characterized clinically by a maculopapular eruption and histologically by epidermal cell degeneration and lymphoid cell infiltration. Such histologic changes are similar to those seen in graft-versus-host disease. The EB virus genome was mainly detected in the basal, germinative cells of the abnormal epithelium. Specimens of our patient's healthy skin were negative. The presence of EB virus DNA in skin lesions was confirmed by polymerase chain reaction adapted for analysis of paraffin-embedded tissue. These findings indicate that EB virus can infect the human epidermis and that the viral infection may produce a distinctive cutaneous disease.

Modified Methodology to Improve Flow Cytometric Dna Histograms from Paraffin-Embedded Material

Flow Cytometric (FCM) DNA content analysis of paraffin-embedded tissues has become a widely accepted procedure in assessing the biologic course in some tumors from archival material. Difficulty in interpreting histograms is frequently due to high levels of debris, and wide coefficients of variation (CV). These may lead to underestimating near-diploid abnormality. Although the clinical significance of low-degree aneuploidy has yet to be established, the procedure reported here improved our endeavor to detect DNA Indices (DI) of at least 1.1%. Experience has shown that careful technique can result in overall improvement of DNA histograms by lowering levels of debris and % CV, dramatically so in some cases. Archival histograms can be generated that rival in quality fresh tissue results. Archival material is currently employed for diagnostic and research purposes.