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https://www.readbyqxmd.com/read/29018224/integrative-analysis-of-genomic-and-epigenomic-regulation-of-the-transcriptome-in-liver-cancer
#1
Hyun Goo Woo, Ji-Hye Choi, Sarah Yoon, Byul A Jee, Eun Ju Cho, Jeong-Hoon Lee, Su Jong Yu, Jung-Hwan Yoon, Nam-Joon Yi, Kwang-Woong Lee, Kyung-Suk Suh, Yoon Jun Kim
Hepatocellular carcinoma harbors numerous genomic and epigenomic aberrations of DNA copy numbers and DNA methylation. Transcriptomic deregulation by these aberrations plays key driver roles in heterogeneous progression of cancers. Here, we profile DNA copy numbers, DNA methylation, and messenger RNA expression levels from 64 cases of hepatocellular carcinoma specimens. We find that the frequencies of the aberrancies of the DNA copy-number-correlated (CNVcor) expression genes and the methylation-correlated expression (METcor) genes are co-regulated significantly...
October 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28994508/loss-of-brca1-associated-protein-1-bap1-expression-is-useful-in-diagnostic-cytopathology-of-malignant-mesothelioma-in-effusions
#2
Ilaria Cozzi, Florina Anca Oprescu, Emma Rullo, Valeria Ascoli
BACKGROUND: The important diagnostic challenge facing the cytopathologist is whether a mesothelial proliferation on effusions represents a malignant mesothelioma (MM) or a benign mesothelial hyperplasia (MH). Here, we evaluated the diagnostic utility of BAP1 immunohistochemistry (IHC) in distinguishing between reactive and neoplastic mesothelial cells. METHODS: In pleural and peritoneal effusions from 147 patients with diagnosed MM or with a differential diagnosis of MM and MH, the expression of BAP1 was examined by IHC on paraffin-embedded cell blocks (n = 121) and biopsies (n = 44)...
October 10, 2017: Diagnostic Cytopathology
https://www.readbyqxmd.com/read/28978163/diagnostic-accuracy-of-brca1-associated-protein-1-in-malignant-mesothelioma-a-meta-analysis
#3
Li-Ming Wang, Zhen-Wang Shi, Ji-Ling Wang, Zhi Lv, Fang-Bin Du, Qing-Bin Yang, Yong Wang
BACKGROUND: Conventional measurements are not always helpful in the diagnosis of malignant mesothelioma (MM). Increasing studies indicate that loss of BRCA1-associated protein 1 (BAP1) detected by immunohistochemistry (IHC) is a useful diagnostic marker for MM. In this meta-analysis, we investigated the diagnostic accuracy of BAP1 in MM. RESULTS: In total, 12 eligible studies with a total of 1824 patients were selected. Results indicated that loss of BAP1 sustained a pooled sensitivity of 0...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28977912/functional-role-of-setd2-bap1-parp-3-and-pbrm1-candidate-genes-on-the-regulation-of-htert-gene-expression
#4
Hannah Linne, Hemad Yasaei, Alison Marriott, Amanda Harvey, Kefah Mokbel, Robert Newbold, Terry Roberts
Narrowing the search for the critical hTERT repressor sequence(s) has identified three regions on chromosome 3p (3p12-p21.1, 3p21.2 and 3p21.3-p22). However, the precise location and identity of the sequence(s) responsible for hTERT transcriptional repression remains elusive. In order to identify critical hTERT repressor sequences located within human chromosome 3p12-p22, we investigated hTERT transcriptional activity within 21NT microcell hybrid clones containing chromosome 3 fragments. Mapping of chromosome 3 structure in a single hTERT-repressed 21NT-#3fragment hybrid clone, revealed a 490kb region of deletion localised to 3p21...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28935764/ubiquitin-recognition-of-bap1-understanding-its-enzymatic-function
#5
Pranita Hanpude, Sushmita Bhattacharya, Abhishek Kumar Singh, Tushar Kanti Maiti
BRCA1 associated protein 1 (BAP1) is a nuclear localizing UCH, having tumor suppressor activity and is widely involved in many crucial cellular processes. BAP1 has garnered attention for its links with cancer, however, the molecular mechanism in the regulation of cancer by BAP1 has not been established. Among the four UCHs, only BAP1 and UCHL5 are able to hydrolyze small and large ubiquitin adducts but UCHL5 hydrolyzes only when it is present in the PA700 complex of the proteasome. The ability of BAP1 to cleave large ubiquitin derivatives is because of its relatively longer active-site crossover loop than other UCHs...
September 21, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28910456/identification-of-alk-rearrangements-in-malignant-peritoneal-mesothelioma
#6
Yin P Hung, Fei Dong, Jaclyn C Watkins, Valentina Nardi, Raphael Bueno, Paola Dal Cin, John J Godleski, Christopher P Crum, Lucian R Chirieac
Importance: Malignant peritoneal mesothelioma is a rare, aggressive tumor arising from the peritoneal lining, induced by asbestos, therapeutic radiation, or germline mutations. Nevertheless, the molecular features remain largely unknown. Objective: To investigate anaplastic lymphoma kinase (ALK) rearrangements in a large series of peritoneal mesothelioma and characterize the mutational landscape of these tumors. Design, Setting, and Participants: We studied 88 consecutive patients (39 men, 49 women; median age 61, range 17-84 years) with peritoneal mesotheliomas diagnosed at a single institution between 2005 and 2015...
September 14, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28903138/improvement-of-genetic-testing-for-cutaneous-melanoma-in-countries-with-low-to-moderate-incidence-the-rule-of-2-vs-the-rule-of-3
#7
Juliette Delaunay, Ludovic Martin, Brigitte Bressac-de Paillerets, Gerard Duru, Olivier Ingster, Luc Thomas
Importance: Genetic testing for melanoma-prone mutation in France, a country with low to moderate incidence of melanoma, is proposed in cases with 2 invasive cutaneous melanomas and/or related cancers in the same patient, or in first- or second-degree relatives (rule of 2). In preclinical studies, these rules led to disclosure of mutation(s) in more than 10% of these families, the threshold widely accepted to justify genetic testing for cancers. Objective: To reconsider these criteria in a general population testing of patients...
September 13, 2017: JAMA Dermatology
https://www.readbyqxmd.com/read/28900502/a-bap1-mutation-specific-microrna-signature-predicts-clinical-outcomes-in-clear-cell-renal-cell-carcinoma-patients-with-wild-type-bap1
#8
Yu-Zheng Ge, Lu-Wei Xu, Chang-Cheng Zhou, Tian-Ze Lu, Wen-Tao Yao, Ran Wu, You-Cai Zhao, Xiao Xu, Zhi-Kai Hu, Min Wang, Xiao-Bing Yang, Liu-Hua Zhou, Bing Zhong, Zheng Xu, Wen-Cheng Li, Jia-Geng Zhu, Rui-Peng Jia
Background: Clear cell renal cell carcinoma (ccRCC) is the most prevalent histologic subtype of kidney cancers in adults, which could be divided into two distinct subgroups according to the BRCA1 associated protein-1 (BAP1) mutation status. In the current study, we comprehensively analyzed the genome-wide microRNA (miRNA) expression profiles in ccRCC, with the aim to identify the differentially expressed miRNAs between BAP1 mutant and wild-type tumors, and generate a BAP1 mutation-specific miRNA signature for ccRCC patients with wild-type BAP1...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28889523/the-epithelioid-bap1-negative-and-p16-positive-phenotype-predicts-prolonged-survival-in-pleural-mesothelioma
#9
Angela Chou, Christopher W Toon, Adele Clarkson, Amy Sheen, Loretta Sioson, Anthony J Gill
AIMS: Mesothelioma is a relatively uncommon but highly malignant neoplasm. Most patients die of disease within one year of diagnosis, but some have prolonged survival. Prospective identification of these longer-term survivors may help guide treatment. We therefore sought to investigate the role of p16 immunohistochemistry (IHC) both alone and in combination with other markers as a potential predictor of prolonged survival in mesothelioma. METHODS AND RESULTS: P16 IHC was performed on unselected pleural mesotheliomas biopsied from 1991 to 2014...
September 10, 2017: Histopathology
https://www.readbyqxmd.com/read/28884745/clinicopathologic-and-genetic-characteristics-of-young-patients-with-pleural-diffuse-malignant-mesothelioma
#10
Marina Vivero, Raphael Bueno, Lucian R Chirieac
Pleural diffuse malignant mesothelioma typically presents during the seventh decade of life and has poor prognosis. Recent epidemiologic studies have shown differences between young and older mesothelioma patients, but the biology of pleural mesothelioma in young patients is poorly understood. We studied the clinicopathologic and genetic characteristics in pleural mesothelioma patients aged 35 years and younger. Thirty-six consecutive pleural mesothelioma patients aged 35 years and younger were compared with 48 older patients...
September 8, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28877056/pax8-expression-in-a-subset-of-malignant-peritoneal-mesotheliomas-and-benign-mesothelium-has-diagnostic-implications-in-the-differential-diagnosis-of-ovarian-serous-carcinoma
#11
David B Chapel, Aliya N Husain, Thomas Krausz, Stephanie M McGregor
Distinguishing malignant peritoneal mesothelioma (MPM) from serous carcinoma involving the peritoneum remains a diagnostic challenge, particularly in small biopsy and cytology specimens. In this distinction, PAX8 expression has been regarded as a specific marker of serous carcinoma. In addition, BAP1 loss is reportedly specific to MPM, in the distinction from both benign mesothelial lesions and ovarian serous tumors (OSTs). Using immunohistochemistry, we examined PAX8 and BAP1 expression in 27 MPMs, 25 cases of benign mesothelium, and 45 OSTs...
September 4, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28829357/peritoneal-mesothelioma-with-residential-asbestos-exposure-report-of-a-case-with-long-survival-seventeen-years-analyzed-by-cgh-array
#12
Gabriella Serio, Federica Pezzuto, Andrea Marzullo, Anna Scattone, Domenica Cavone, Alessandra Punzi, Francesco Fortarezza, Mattia Gentile, Antonia Lucia Buonadonna, Mattia Barbareschi, Luigi Vimercati
Malignant mesothelioma is a rare and aggressive tumor with limited therapeutic options. We report a case of a malignant peritoneal mesothelioma (MPM) epithelioid type, with environmental asbestos exposure, in a 36-year-old man, with a long survival (17 years). The patient received standard treatment which included cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC). METHODS AND RESULTS: Molecular analysis with comparative genomic hybridization (CGH)-array was performed on paraffin-embedded tumoral samples...
August 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812986/epigenome-aberrations-emerging-driving-factors-of-the-clear-cell-renal-cell-carcinoma
#13
REVIEW
Ali Mehdi, Yasser Riazalhosseini
Clear cell renal cell carcinoma (ccRCC), the most common form of Kidney cancer, is characterized by frequent mutations of the von Hippel-Lindau (VHL) tumor suppressor gene in ~85% of sporadic cases. Loss of pVHL function affects multiple cellular processes, among which the activation of hypoxia inducible factor (HIF) pathway is the best-known function. Constitutive activation of HIF signaling in turn activates hundreds of genes involved in numerous oncogenic pathways, which contribute to the development or progression of ccRCC...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28810145/integrative-analysis-identifies-four-molecular-and-clinical-subsets-in-uveal-melanoma
#14
A Gordon Robertson, Juliann Shih, Christina Yau, Ewan A Gibb, Junna Oba, Karen L Mungall, Julian M Hess, Vladislav Uzunangelov, Vonn Walter, Ludmila Danilova, Tara M Lichtenberg, Melanie Kucherlapati, Patrick K Kimes, Ming Tang, Alexander Penson, Ozgun Babur, Rehan Akbani, Christopher A Bristow, Katherine A Hoadley, Lisa Iype, Matthew T Chang, Andrew D Cherniack, Christopher Benz, Gordon B Mills, Roel G W Verhaak, Klaus G Griewank, Ina Felau, Jean C Zenklusen, Jeffrey E Gershenwald, Lynn Schoenfield, Alexander J Lazar, Mohamed H Abdel-Rahman, Sergio Roman-Roman, Marc-Henri Stern, Colleen M Cebulla, Michelle D Williams, Martine J Jager, Sarah E Coupland, Bita Esmaeli, Cyriac Kandoth, Scott E Woodman
Comprehensive multiplatform analysis of 80 uveal melanomas (UM) identifies four molecularly distinct, clinically relevant subtypes: two associated with poor-prognosis monosomy 3 (M3) and two with better-prognosis disomy 3 (D3). We show that BAP1 loss follows M3 occurrence and correlates with a global DNA methylation state that is distinct from D3-UM. Poor-prognosis M3-UM divide into subsets with divergent genomic aberrations, transcriptional features, and clinical outcomes. We report change-of-function SRSF2 mutations...
August 14, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28802580/suppressive-role-of-ogt-mediated-o-glcnacylation-of-bap1-in-retinoic-acid-signaling
#15
Seungtae Moon, Yong-Kyu Lee, Sang-Wang Lee, Soo-Jong Um
BRCA1-associated protein 1 (BAP1) has been implicated in diverse biological functions, including tumor suppression. However, its regulation via glycosylation and its role in embryonic stem (ES) cells are poorly defined. BAP1 was recently reported to interact with O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT). Here, we confirmed the physical interaction and investigated its functional significance. The O-GlcNAcylation of BAP1, which requires OGT, was examined in vivo and in vitro, and was proven using alloxan, an OGT inhibitor...
October 7, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28802494/toward-a-molecular-genetic-classification-of-spitzoid-neoplasms
#16
REVIEW
Michael T Tetzlaff, Alexandre Reuben, Steven D Billings, Victor G Prieto, Jonathan L Curry
The histopathologic spectrum of Spitzoid neoplasms includes Spitz nevi, atypical Spitz tumors, and Spitzoid melanomas. Advances in molecular genetics have evolved to the point that Spitzoid lesions can now be reasonably classified according to their distinctive molecular-genetic alterations: Spitzoid lesions with (1) 11p amplification and/or HRAS mutations; (2) isolated loss of 6q23 by fluorescence in situ hybridization (FISH); (3) homozygous deletion of 9p21 by FISH; (4) BAP1 loss and BRAFV600 E mutation; (5) translocations involving any of a number of different oncogenic kinase drivers, including ROS1, ALK, NTRK1, NTRK3, MET, BRAF, and RET; and (6) TERT promoter mutations...
September 2017: Clinics in Laboratory Medicine
https://www.readbyqxmd.com/read/28793149/genotypic-and-phenotypic-features-of-bap1-cancer-syndrome-a-report-of-8-new-families-and-review-of-cases-in-the-literature
#17
Alexandra M Haugh, Ching-Ni Njauw, Jeffrey A Bubley, Anna Elisa Verzì, Bin Zhang, Emily Kudalkar, Timothy VandenBoom, Kara Walton, Brian L Swick, Raj Kumar, Huma Q Rana, Sarah Cochrane, Shelley R McCormick, Christopher R Shea, Hensin Tsao, Pedram Gerami
Importance: Patients with germline mutations in BAP1 may develop several flesh-colored melanocytic BAP1-mutated atypical intradermal tumors (MBAITs). These tumors generally develop earlier than other BAP1-associated tumors, highlighting an important role for dermatologists in identifying and screening patients with a history suggestive of a germline mutation. Objective: To describe 8 new families with germline mutations in BAP1 and provide a comprehensive review of reported cases...
August 9, 2017: JAMA Dermatology
https://www.readbyqxmd.com/read/28781790/somatic-brca1-associated-protein-1-bap1-loss-is-an-early-and-rare-event-in-esophageal-adenocarcinoma
#18
Heike Loeser, Dirk Waldschmidt, Fabian Kuetting, Simon Schallenberg, Thomas Zander, Elfriede Bollschweiler, Arnulf Hoelscher, Katharina Weckermann, Patrick Plum, Hakan Alakus, Reinhard Buettner, Alexander Quaas
Esophageal cancer is the eighth most common malignant tumor worldwide, and the number of incidences of esophageal adenocarcinoma is increasing in the Western world. Despite improvements in perioperative treatment, the overall survival rate of patients with esophageal adenocarcinoma remains poor. Breast cancer type 1 susceptibility protein (BRCA1)-associated protein (BAP1) is located on chromosome 3p21, and it is an enzyme with ubiquitin carboxyl hydrolase activity that regulates cell growth. It interacts with BRCA1, and the nuclear localization of BAP1 is required for its tumor suppressor function...
August 2017: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/28776573/pancreatic-intraductal-tubulopapillary-neoplasm-is-genetically-distinct-from-intraductal-papillary-mucinous-neoplasm-and-ductal-adenocarcinoma
#19
Olca Basturk, Michael F Berger, Hiroshi Yamaguchi, Volkan Adsay, Gokce Askan, Umesh K Bhanot, Ahmet Zehir, Fatima Carneiro, Seung-Mo Hong, Giuseppe Zamboni, Esra Dikoglu, Vaidehi Jobanputra, Kazimierz O Wrzeszczynski, Serdar Balci, Peter Allen, Naoki Ikari, Shoko Takeuchi, Hiroyuki Akagawa, Atsushi Kanno, Tooru Shimosegawa, Takanori Morikawa, Fuyuhiko Motoi, Michiaki Unno, Ryota Higuchi, Masakazu Yamamoto, Kyoko Shimizu, Toru Furukawa, David S Klimstra
Intraductal tubulopapillary neoplasm is a relatively recently described member of the pancreatic intraductal neoplasm family. The more common member of this family, intraductal papillary mucinous neoplasm, often carries genetic alterations typical of pancreatic infiltrating ductal adenocarcinoma (KRAS, TP53, and CDKN2A) but additionally has mutations in GNAS and RNF43 genes. However, the genetic characteristics of intraductal tubulopapillary neoplasm have not been well characterized. Twenty-two intraductal tubulopapillary neoplasms were analyzed by either targeted next-generation sequencing, which enabled the identification of sequence mutations, copy number alterations, and selected structural rearrangements involving all targeted (≥300) genes, or whole-exome sequencing...
August 4, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28765116/bap1-and-pbrm1-determinants-of-tumor-grade-and-mtor-activation-in-vhl-deficient-mouse-models-of-renal-cell-carcinoma
#20
Janet Y Leung, William Y Kim
Large genome sequencing efforts have identified frequent mutations in the histone-modifying and chromatin-remodeling genes BAP1 and PBRM1 in clear cell renal cell carcinoma (ccRCC). In this issue of Cancer Discovery, Gu and colleagues model these genetic events in mice and report that dual inactivation of Vhl with either Bap1 or Pbrm1 results in faithful genetically engineered murine models of ccRCC. Moreover, their work establishes that Bap1 and Pbrm1 are determinants of tumor grade and mTORC1 activation and provocatively suggests that the cell of origin of ccRCC may lie in PAX8-expressing Bowman capsule cells...
August 2017: Cancer Discovery
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