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Kumarasen Cooper

Publications and source records attributed to Kumarasen Cooper.

At least 19 recordsLinked to original sources
PubMed2006

Use of multiple displacement amplification in the investigation of human papillomavirus physical status.

BACKGROUND AND AIMS: The investigation of human papillomavirus (HPV) physical status in pre-invasive cervical lesions has been restricted by the small amounts of tissue available for study. Multiple displacement amplification (MDA), a phi29 DNA polymerase based whole genome amplification technique, has the potential to help resolve this problem by yielding large amounts of high molecular weight DNA from tiny starting quantities. METHODS: Firstly, a comparison was made of restriction endonuclease fragment patterns of DNA from seven different HPV types and corresponding MDA products. Secondly, E6/E7 and LCR sequencing data from HPV16 recombinant plasmid and MDA copy DNA were correlated. Thirdly, DNA and MDA products from cervical cell lines (CaSki, HeLa, and SiHa that contain integrated HPV) and an invasive cervical carcinoma were analysed by Southern blot hybridisation. Fourthly, MDA product from CaSki cell DNA mixed with HPV18-plasmid DNA was tested for the demonstration of both episomal and integrated HPV. Finally, MDA products from HPV16 positive abnormal cervical cytological samples were assayed for integration by Southern blot hybridisation. RESULTS: DNA templates and MDA products yielded analogous data. Episomal and integrated HPV DNA were successfully detected by Southern blot assay of the cell line/HPV-plasmid model, and in MDA products of clinical samples. CONCLUSIONS: These data show that MDA has considerable potential to assist in the investigation of HPV physical status; abundant (>40 microg) DNA can be generated with high fidelity from minuscule (50 ng) starting quantities, and both episomal and integrated HPV DNA are distinguishable in MDA products from solid tumours and cytological materials.

Base Sequence↗
PubMed2006

Recommendations for quality assurance and improvement in surgical and autopsy pathology.

Current regulations require that departments of pathology have a structured and active program of quality assurance (QA) and quality improvement (QI), with the goals of enhancing patient safety, minimizing error, ensuring timely delivery of reports, and monitoring physician competence. Types of potential error may evolve over time and, as regulations become progressively more stringent, QA/QI programs need to be constantly updated. The Association of Directors of Anatomic and Surgical Pathology herein provides guidelines for QA and QI in surgical and autopsy pathology.

Humans↗
PubMed2006

Clinical and molecular differences between clear cell and papillary serous ovarian carcinoma.

PURPOSE: The aim of the current study is to compare clear cell ovarian carcinoma (CCOC) and papillary serous ovarian carcinoma (PSOC) with respect to their clinical features and expression of different regulators of cell cycle, apoptosis, and chemoresistance. EXPERIMENTAL DESIGN: Women with stage III CCOC (n = 9) and those with stage III, poorly differentiated PSOC (n = 21) seen between 1996 and 2000 and treated with cytoreductive surgery followed by paclitaxel and platinum chemotherapy were compared in their demographic features, tumor marker profile, surgical substage, results of cytoreductive surgery, thromboembolic complications, response to chemotherapy, and tumor recurrence. Tumor samples were compared in their expression of p53, Bcl(2), Bcl(x), Bax, p21, p-glycoprotein (PGP), multi-drug resistance-associated protein (MRP), lung resistance protein (LRP), and glutathione S-transferase (GST) using immunohistochemistry. RESULTS: Women with CCOC had significantly lower mean preoperative CA-125 values, lower surgical substage, less expression of p53, and more expression of p21 than women with PSOC (P = 0.037, 0.012, 0.008, and 0.009, respectively). Women with CCOC had less ascites, smaller amount of residual tumor, higher incidence of thromboembolism, chemoresistance, more expression of Bcl(2), and less expression of PGP than women with PSOC (P = 0.067, 0.078, 0.108, 0.114, 0.091, and 0.118, respectively). CONCLUSIONS: Women with CCOC exhibit certain clinical and molecular differences compared to stage- and grade-matched women with PSOC. Women with CCOC have a smaller tumor volume and manifest different expressions of p53, p21, and Bcl(2) than women with PSOC. Although further studies with larger number of patients are needed, our findings indicate that chemoresistance in CCOC is probably not p53-dependent.

Adenocarcinoma, Clear Cell↗
PubMed2006

Distribution of human papillomavirus types in ThinPrep Papanicolaou tests classified according to the Bethesda 2001 terminology and correlations with patient age and biopsy outcomes.

BACKGROUND: A survey of the distribution of human papillomavirus (HPV) types across the spectrum of cervical cytologic categories defined by the Bethesda 2001 guidelines was conducted with the objective of examining how HPV detection by polymerase chain reaction (PCR) analysis may benefit the management of patients who have abnormal Papanicolaou (Pap) test results. METHODS: DNA samples from women with no intraepithelial lesion or malignancy (NLM) (n = 300 samples); atypical squamous cells of undetermined significance (ASC-US) (n = 200 samples); low-grade squamous intraepithelial lesion (LSIL) (n = 200 samples); atypical squamous cells, cannot rule out high-grade squamous intraepithelial lesion (ASC-H) (n = 200 samples); and high-grade squamous intraepithelial lesion (HSIL) (n = 200 samples) were tested for HPV using a modified general primer (GP)5+/GP6+ PCR assay and dot-blot hybridization with type-specific oligonucleotide probes (PCR assay analytical sensitivity: 1-100 copies of HPV, depending on the HPV type, in a background of 100 ng human DNA). RESULTS: HPV was detected in 27% of NLM samples, in 89.5% of ASC-US samples, in 97.5% of LSIL samples, in 93% of ASC-H samples, and in 96.5% of HSIL samples. Thirty-seven different HPV types were identified in total. One or more of 13 high-risk (HR) HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68) were detected in 53% of samples that were diagnosed as ASC-US (59.0% of patients younger than age 30 yrs; 45.5% of patients age 30 yrs and older), in 55.5% of samples that were diagnosed as LSIL (60.0% of patients younger than age 30 yrs; 44.0% of patients age 30 yrs and older), in 80% of samples that were diagnosed as ASC-H, and in 87.5% of samples that were diagnosed as HSIL (P < 0.001). HPV-16 was detected in 17.5% of ASC-US samples, in 15.5% of LSIL samples, in 48.5% of ASC-H samples, and in 49.0% of HSIL samples (P < 0.001). Among abnormal smears, HR HPV was significantly more common in women younger than age 30 years compared with women age 30 years and older (P < 0.002). Follow-up biopsy data were obtained for 359 patients. A "benign" biopsy result was recorded for 47 of 64 women (73.5%) with ASC-US, 30 of 66 women (45.5%) with LSIL, 39 of 87 women (45.0%) with ASC-H, and 26 of 142 women (18.0%) with HSIL and was most common in women age 30 years and older (P < 0.0001). Cervical intraepithelial neoplasia (CIN) Grade I (CIN-I) was found in 14.0% of women with ASC-US, in 39.5% of women with LSIL, in 8.0% of women with ASC-H, and in 7.0% of women with HSIL. CIN-II was diagnosed in 9.5% of women with ASC-US, in 13.5% of women with LSIL, in 19.5% of women with ASC-H, and in 24.0% of women with HSIL. CIN-III was identified in 2 women (3.0%) with ASC-US, in 1 woman (1.5%) with LSIL, in 24 women (27.5%) with ASC-H, and in 71 women (50.0%) with HSIL. CONCLUSIONS: HR HPV testing by PCR of samples diagnosed according to the Bethesda 2001 guidelines may benefit the management of patients with ASC-US or patients with LSIL, especially among women age 30 years and older, by allowing exclusion from referral for biopsy of women who are negative for HR HPV types. However, the small numbers of women who had CIN-III detected after a diagnosis of ASC-US or LSIL limited the assessment of test sensitivity.

Adult↗
PubMed2006

p16INK4a immunoexpression: surrogate marker of high-risk HPV and high-grade cervical intraepithelial neoplasia.

p16INK4a has emerged as a valuable surrogate marker for high-risk human papillomavirus infection and shows increased immunoexpression with worsening grades of cervical intraepithelial neoplasia (CIN). Numerous studies have emerged in recent years supporting its role in the detection of high-grade dysplasia and have lead to the use of p16INK4a immunohistochemistry in many laboratories. However, only a few studies have examined the possible predictive or prognostic value of p16INK4a in CIN or cervical cancer. This review addresses some of the practical issues in the application of p16INK4a in everyday practice, with an emphasis on integrating the extensive data that have emerged in the literature on p16INK4a immunoreactivity in CIN. The potential role of p16INK4a immunohistochemistry in the prediction of CIN progression is also discussed.

Biomarkers, Tumor↗
PubMed2006

Recommendations for quality assurance and improvement in surgical and autopsy pathology.

Current regulations require that departments of pathology have a structured and active program of quality assurance (QA) and quality improvement (QI), with the goals of enhancing patient safety, minimizing error, ensuring timely delivery of reports, and monitoring physician competence. Types of potential error may evolve over time, and, as regulations become progressively more stringent, QA and QI programs need to be updated constantly. The Association of Directors of Anatomic and Surgical Pathology herein provides guidelines for QA and QI in surgical and autopsy pathology.

Autopsy↗
PubMed2006

The binding of thyroid transcription factor-1 and hepatocyte paraffin 1 to mitochondrial proteins in hepatocytes: a molecular and immunoelectron microscopic study.

We studied the antibodies hepatocyte paraffin 1 (Hep Par 1) and thyroid transcription factor-1 (TTF-1; clone 8G7G3/1) in normal human liver tissue with immunoelectron microscopy using renal tubules as control samples. TTF-1 (8G7G3/1) and Hep Par 1 bound exclusively to the mitochondria of hepatocytes but not to those of the renal tubular epithelium. Both antibodies labeled mitochondria in a similar pattern and density. These findings confirm that the binding site of Hep Par 1 in hepatocytes is mitochondrial. The specific binding of TTF-1 (8G7G3/1) in hepatocyte mitochondria suggests its potential usefulness for identifying hepatocellular carcinoma. Western blot analysis with cellular proteins extracted from normal human liver and thyroid tissue demonstrated that Hep Par 1 and TTF-1 (8G7G3/1) bound to a protein band of approximately 150 kd in liver cells, with TTF-1 (8G7G3/1) showing less affinity. It is likely that different epitopes to Hep Par 1 and TTF-1 (8G7G3/1) share the same protein molecule in hepatocyte mitochondria.

Antibodies, Monoclonal↗
PubMed2006

Errors and error rates in surgical pathology: an Association of Directors of Anatomic and Surgical Pathology survey.

This survey on errors in surgical pathology was commissioned by the Association of Directors of Anatomic and Surgical Pathology Council to explore broad perceptions and definitions of error in surgical pathology among its membership and to get some estimate of the perceived frequency of such errors. Overall, 41 laboratories were surveyed, with 34 responding to a confidential questionnaire. Six small, 13 medium, and 10 large laboratories (based on specimen volume), predominantly located in the United States, were surveyed (the remaining 5 laboratories did not provide this particular information). The survey questions, responses, and associated comments are presented. It is clear from this survey that we lack uniformity and consistency with respect to terminology, definitions, and the identification/documentation of errors in surgical pathology. An appeal is made for the urgent need to reach some consensus in order to address these discrepancies as we prepare to combat the issue of errors in surgical pathology.

Data Collection↗
PubMed2006

MIB-1 and MCM-2 immunohistochemical analysis does not aid in identification of serrated colorectal polyps with abnormal proliferation.

We investigated the staining characteristics of serrated polyps with abnormal proliferation (SPAP) using MIB-1 and MCM-2 to determine if they could provide assistance in delineating SPAPs from traditional hyperplastic polyps (HPs). Using published morphologic criteria we reviewed H&E slides of 107 polyps from 80 patients. Thirty-nine (36.4%) polyps met the criteria for SPAP Within a given region, polyps in the transverse colon had the largest percentage of SPAPs (50.0%) followed by the right colon (40.9%). The majority of SPAPs (82.1%) and HPs (72.1%) showed MIB-1 staining confined to the basal third of the crypts. The majority of SPAPs (59.0%) and HPs (52.9%) showed MCM-2 staining extending into the apical third of the crypts. We do not recommend MIB-1 or MCM-2 staining to differentiate SPAPs from conventional HPs, since staining characteristics are not significantly different between the 2 groups, and frequent variable crypt staining within a given polyp is difficult to interpret.

Biomarkers, Tumor↗
PubMed2005

Touchdown General Primer (GP5+/GP6+) PCR and optimized sample DNA concentration support the sensitive detection of human papillomavirus.

BACKGROUND: The GP5+/GP6+ PCR assay is a well-established HPV detection technique. This study has examined the effects of incorporating 'hot start' and 'touchdown' steps into the protocol. In addition, dTTP was substituted with dUTP to permit contamination control measures against carry-over PCR product. METHODS: Firstly, HPV-16 was amplified from SiHa cell DNA (0.1 ng-100 ng) diluted in a background of C-33A DNA (100 ng-2 microg). Secondly, the detection of small quantities (15ag-1.5pg) of HPV recombinant plasmids (types 16, 31, 33, 45, 51, 52, and 56) diluted in C-33A DNA was investigated. Thirdly, clinical sample DNA extracts (cervical smears, formalin-fixed vaginal lesions and breast tumors) were tested for HPV. Six different PCR protocols were assessed. HPV was detected by gel electrophoresis, and by Southern and dot blot hybridization. RESULTS: HPV detection sensitivity was dependent on the total amount of DNA in a PCR. Touchdown protocols supported HPV-16 detection from 1 ng or 0.5 ng SiHa cell DNA in a background of 2 microg or 1 microg C-33A DNA respectively, and from 0.1 ng of SiHa cell DNA (approximately 28 copies HPV-16) in 500 ng or 100 ng background DNA. Under standard GP5+/GP6+ annealing conditions, HPV-16 went undetected when the DNA content of a PCR was 2 microg or 1 microg, and with 500 ng C-33A DNA the sensitivity limit was 1 ng SiHa cell DNA. HPV recombinant plasmids were each detected with high (albeit varying) sensitivity by a touchdown protocol. HPV-31 was better amplified under standard annealing conditions (1.5fg in 100 ng background DNA) than by a touchdown approach (15fg detection limit). HPV-52 was not amplified by the standard protocol at the dilutions tested. Seventeen different HPV types were demonstrated in 47/65 (72%) abnormal cytology samples recorded as HPV negative by standard GP5+/GP6+ conditions. Twenty-one different HPV types were recorded in 111/114 (97%) vaginal lesions. Multiple infections were also detectable using a touchdown approach. Of 26 breast tumors, 5 (19%) tested HPV positive by the standard assay and 15/26 (58%) using a touchdown protocol. CONCLUSION: Touchdown modification of the GP5+/GP6+ PCR assay enables the detection of HPV undetected under regular assay conditions. The use of standardized DNA quantities in a PCR rather than standard sample volumes containing arbitrary amounts of DNA is supported. A touchdown approach may be beneficial as an analytical test for the re-evaluation of (apparently) HPV negative abnormal cervical cytological or histological samples, and for investigating the association of HPV with disease conditions at diverse organ sites. The clinical utility of a touchdown approach for HPV detection requires further investigation as increased assay analytical sensitivity may not necessarily equate with improved clinical sensitivity or specificity.

Journal Article↗
PubMed2005

Benign fibroblastic polyp of the colorectum.

GOALS: We present the clinicopathologic features, endoscopic appearance, and ultrastructure of a newly described mesenchymal polyp of the colorectum, termed benign fibroblastic polyp. STUDY: A total of 4 cases from our institution are analyzed using routine histopathology, immunohistochemistry, and electron microscopy, and compared with the original series of 14 cases previously described in the pathology literature. RESULTS: Benign fibroblastic polyps appear endoscopically throughout the colorectum as submucosal lesions with a hyperplastic surface component. These lesions are histologically and ultrastructurally distinct, but overlap with other mesenchymal polyps warrants additional immunohistochemical studies for definitive classification. CONCLUSIONS: Benign fibroblastic polyps of the colorectum comprise a recently described distinct entity of mesenchymal polyps that appear to follow an indolent clinical course. Their etiology is uncertain but may be linked to an exuberant tissue response following mucosal injury. Gastroenterologists should be aware of this new entity that will be increasingly diagnosed by pathologists.

Actins↗
PubMed2005

Visceral pleural invasion in lung cancer: recognizing histologic parameters that impact staging and prognosis.

Visceral pleural involvement (VPI) is a critical component in the staging of non-small cell lung carcinoma (NSCLC). Tumors < or =3 cm that involve the visceral pleura are classified as T2 lesions, underscoring the prognostic significance of this histologic parameter. Accurate staging of small NSCLCs depends on appropriately assessing the presence or absence of VPI. Elastic stains can be instrumental in detecting disruptions of the visceral pleural elastic layer by tumor, a finding that has prognostic and staging implications similar to tumor that is present on the visceral pleural surface.

Adult↗
PubMed2005

p16INK4A immunoexpression and HPV in situ hybridization signal patterns: potential markers of high-grade cervical intraepithelial neoplasia.

Integration of human papillomavirus (HPV) into the cell genome is considered to be an important event in the progression of cervical neoplasia. p16, also a useful biomarker of cervical intraepithelial neoplasia (CIN), shows increased immunoexpression with worsening grades of CIN. This study examines the correlation between p16 immunoexpression, grade of CIN, HPV type, and HPV in situ hybridization diffuse and punctate signal patterns (linked to episomal and integrated viral particles, respectively) in 44 cervical biopsies/LEEP excisions classified as CIN 1 and CIN 2/3. In 22 of 25 (88%) CIN 1 lesions, p16 immunoexpression was confined to the lower half of the epithelium, with sporadic to focal staining in 11 of 25 cases (44%). In CIN 2/3 lesions, 15 of 17 (88.2%) showed diffuse, two-thirds to full-thickness staining of the epithelium. High-risk HPV types were found in 20 (80%) CIN 1 lesions and 17 (100%) CIN 2/3 lesions. Punctate signals were detected in only 3 (13.6%) of high-risk HPV-positive CIN 1 lesions and in 17 of 17 (100%) CIN 2/3 lesions (P<0.001). p16 immunoexpression and the presence of punctate signal on HPV in situ hybridization correlated with the degree of cervical neoplasia (P<0.001). However, 3 cases of CIN 1 demonstrating punctate signals did not demonstrate a comparable CIN 2/3 p16 staining pattern. Similarly, two CIN 1 lesions with comparable CIN 2/3 p16 staining showed no evidence of viral integration. Both increased p16 immunoexpression and punctate signal correlate with CIN 2/3 grade, supporting the use of either, or both, tests to confirm CIN 2/3. Strong p16 immunostaining in CIN 1 appears independent of HPV punctate signal type.

Biomarkers, Tumor↗
PubMed2004

Human papillomavirus integration: detection by in situ hybridization and potential clinical application.

Human papillomaviruses (HPVs) are accepted as a necessary cause of cervical neoplasia. However, the benefits of testing simply for high-risk HPV types are limited because of their high prevalence in intraepithelial lesions of all grades, the majority of which regress if left untreated. One factor considered to be of key importance for the progression of intraepithelial lesions to invasive disease is integration of HPV into the host cell genome. Although questions remain about the prevalence of integration amongst pre-invasive lesions, sensitive in situ hybridization techniques utilizing tyramide reagents may aid determination of the significance of HPV infection by enabling routine detection of both high-risk HPV and its physical status. This will provide important data relevant not only to our understanding of the biology of HPV-associated neoplasia, but also potentially to clinical testing for HPV.

Disease Progression↗
PubMed2004

Factors associated with cytoreducibility among women with ovarian carcinoma.

OBJECTIVES: The aim of the current study is to investigate the clinical and molecular factors associated with cytoreduction among women with advanced stage epithelial ovarian carcinoma EOC. METHODS: Seventy-two women with FIGO stage III and IV EOC or primary peritoneal carcinoma (PPC) underwent similar attempt at surgical cytoreduction, mostly by the same surgeon. The histologic material of these patients was reviewed and the histologic subtype and grade were assigned. Immunohistochemical tests were performed for expression of molecular regulators of apoptosis (p53, p21, Bcl(2), Bcl(x), Bax) and chemoresistance (PGP, MRP, LRP, GST). The following factors were assessed for their association with complete (no residual tumor) and optimal (residual tumor < 1 cm) cytoreduction: type of carcinoma (EOC versus PPC), stage, CA-125 values, ascites, histology, tumor grade, and p53, p21, Bcl(2), Bcl(x), Bax, PGP, MRP, LRP, GST expression using the odds ratio and associated 95% confidence intervals. Significant univariate odds ratios were assessed jointly in a multivariate logistic regression model. Receiver operating characteristic curve analysis was performed to determine the CA-125 level with the maximal cytoreduction prognostic power. RESULTS: Twenty-three (31.9%) women had no residual tumor, 35 (48.6%) had 1 cm. Factors with significant univariate associations with complete cytoreduction included stage, CA-125 level, ascites, histology, and p53. p53 expression was the only factor which remained significant in the multivariate analysis (odds ratio 7.2, 95% CI 1.5, 34.9). A preoperative CA-125 value of <or=500 IU/ml best determined complete cytoreducibility. CONCLUSIONS: Innate tumor characteristics determine cytoreducibility of women with ovarian carcinoma. Pre-operative evaluation of p53 expression may be of value in predicting the outcome of cytoreductive surgery in women with advanced stage EOC.

Adult↗
PubMed2004

Granulomatous chest disease following intravesical bacillus Calmette-Guerin immunotherapy.

Bacillus Calmette-Guerin (BCG) is well accepted as an intravesicular method of treatment of bladder cancer. Although well tolerated in the majority of patients, adverse local and systemic adverse effects of this therapy have been described. In particular, lung disease complicating intravesicular use of BCG has been reported, producing 5 recognized forms of chest disease: 1) allergic interstitial lung disease, 2) miliary infection, 3) empyema, 4) diffuse alveolar damage, and 5) localized consolidative or cavitary lung disease. We report an asymptomatic form of pulmonary disease complicating intravesical BCG therapy, that of pulmonary granulomas with mediastinal and hilar lymph node enlargement.

Aged↗