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https://www.readbyqxmd.com/read/29623743/immunoexpression-of-bap1-ros1-and-alk-in-spitzoid-melanocytic-tumors
#1
Leonardo Cardili, Cristiano Ribeiro Viana, Andressa Germano, Mariana Fernandes, Denise Barcellos, Gilles Landman
BACKGROUND: Spitzoid tumors are a heterogeneous group of melanocytic neoplasms that frequently imposes diagnostic difficulties. Lately, several advances in molecular biology afforded significant discoveries on the pathogenesis of these tumors. BAP1 (BRCA-1 associated protein-1) inactivation and anomalous expression of kinase translocation-related proteins are among the main criteria launched by new classification proposals. Our aim was to systematically assess the immunoexpression of BAP1, ROS1 (receptor tyrosine kinase c-Ros oncogene 1), and ALK (anaplastic lymphoma receptor tyrosine kinase) proteins in an unpublished series of spitzoid tumors...
April 1, 2018: International Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29617669/the-cancer-genome-atlas-comprehensive-molecular-characterization-of-renal-cell-carcinoma
#2
Christopher J Ricketts, Aguirre A De Cubas, Huihui Fan, Christof C Smith, Martin Lang, Ed Reznik, Reanne Bowlby, Ewan A Gibb, Rehan Akbani, Rameen Beroukhim, Donald P Bottaro, Toni K Choueiri, Richard A Gibbs, Andrew K Godwin, Scott Haake, A Ari Hakimi, Elizabeth P Henske, James J Hsieh, Thai H Ho, Rupa S Kanchi, Bhavani Krishnan, David J Kwaitkowski, Wembin Lui, Maria J Merino, Gordon B Mills, Jerome Myers, Michael L Nickerson, Victor E Reuter, Laura S Schmidt, C Simon Shelley, Hui Shen, Brian Shuch, Sabina Signoretti, Ramaprasad Srinivasan, Pheroze Tamboli, George Thomas, Benjamin G Vincent, Cathy D Vocke, David A Wheeler, Lixing Yang, William T Kim, A Gordon Robertson, Paul T Spellman, W Kimryn Rathmell, W Marston Linehan
Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers...
April 3, 2018: Cell Reports
https://www.readbyqxmd.com/read/29617666/systematic-analysis-of-splice-site-creating-mutations-in-cancer
#3
Reyka G Jayasinghe, Song Cao, Qingsong Gao, Michael C Wendl, Nam Sy Vo, Sheila M Reynolds, Yanyan Zhao, Héctor Climente-González, Shengjie Chai, Fang Wang, Rajees Varghese, Mo Huang, Wen-Wei Liang, Matthew A Wyczalkowski, Sohini Sengupta, Zhi Li, Samuel H Payne, David Fenyö, Jeffrey H Miner, Matthew J Walter, Benjamin Vincent, Eduardo Eyras, Ken Chen, Ilya Shmulevich, Feng Chen, Li Ding
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function...
April 3, 2018: Cell Reports
https://www.readbyqxmd.com/read/29610392/personalized-oncogenomic-analysis-of-metastatic-adenoid-cystic-carcinoma-using-whole-genome-sequencing-to-inform-clinical-decision-making
#4
Manik Chahal, Erin Pleasance, Jasleen Grewal, Eric Zhao, Tony Ng, Erin Chapman, Martin R Jones, Yaoqing Shen, Karen L Mungall, Melika Bonakdar, Gregory A Taylor, Yussanne Ma, Andrew J Mungall, Richard A Moore, Howard Lim, Daniel Renouf, Stephen Yip, Steven J M Jones, Marco A Marra, Janessa Laskin
Metastatic adenoid cystic carcinomas (ACCs) can cause significant morbidity and mortality. Because of their slow growth and relative rarity, there is limited evidence for systemic therapy regimens. Recently, molecular profiling studies have begun to reveal the genetic landscape of these poorly understood cancers, and new treatment possibilities are beginning to emerge. The objective is to use whole-genome and transcriptome sequencing and analysis to better understand the genetic alterations underlying the pathology of metastatic and rare ACCs and determine potentially actionable therapeutic targets...
April 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29606053/high-grade-meningiomas-biology-and-implications
#5
Wenya Linda Bi, Vikram C Prabhu, Ian F Dunn
The epochal developments in the treatment of meningioma-microsurgery, skull base techniques, and radiation therapy-will be appended to include the rational application of targeted and immune therapeutics, previously ill-fitting concepts for a tumor that has traditionally been a regarded as a surgical disease. The genomic and immunological architecture of these tumors continues to be defined in ever-greater detail. Grade I meningiomas are driven by NF2 alterations or mutations in AKT1, SMO, TRAF7, PIK3CA, KLF4, POLR2A, SUFU, and SMARCB1...
April 2018: Neurosurgical Focus
https://www.readbyqxmd.com/read/29573058/molecular-genomic-landscapes-of-hepatobiliary-cancer
#6
REVIEW
Tatsuhiro Shibata, Yasuhito Arai, Yasushi Totoki
Hepatocellular carcinoma (HCC) and biliary tract cancer (BTC) are more frequent in East Asia including Japan. Compiling 1,340 multi-ethnic HCC genomes, the largest cohort ever reported, identified comprehensive landscape of HCC driver genes, which constitutes three core drivers (TP53, TERT and WNT signaling) and combination of infrequent alterations in various cancer pathways. By contrast, five core driver genes (TP53, ARID1A, KRAS, SMAD4 and BAP1) with characteristic molecular alterations including fusion transcripts involving FGFR2 and the PKA pathway, and IDH1/2 mutation constituted the BTC genomes...
March 23, 2018: Cancer Science
https://www.readbyqxmd.com/read/29571968/ocular-treatment-of-choroidal-melanoma-in-relation-to-the-prevention-of-metastatic-death-a-personal-view
#7
REVIEW
Bertil Damato
About 50% of patients with choroidal melanoma develop metastatic disease, despite successful eradication of the primary tumor. Patient care is complicated by the fact that we do not know whether ocular treatment ever influences survival and if so in whom. Some authorities believe that metastatic spread is never preventable, because it has always occurred by the time the ocular tumor is detected. Others hold the view that metastatic spread can occur late, at least in some patients, in whom timely and successful treatment is life-saving...
March 20, 2018: Progress in Retinal and Eye Research
https://www.readbyqxmd.com/read/29565815/targeting-the-hippo-pathway-is-a-new-potential-therapeutic-modality-for-malignant-mesothelioma
#8
REVIEW
Yoshitaka Sekido
Malignant mesothelioma (MM) constitutes a very aggressive tumor that arises from the pleural or peritoneal cavities and is highly refractory to conventional therapies. Several key genetic alterations are associated with the development and progression of MM including mutations of the CDKN2A/ARF , NF2 , and BAP1 tumor-suppressor genes. Notably, activating oncogene mutations are very rare; thus, it is difficult to develop effective inhibitors to treat MM. The NF2 gene encodes merlin, a protein that regulates multiple cell-signaling cascades including the Hippo pathway...
March 22, 2018: Cancers
https://www.readbyqxmd.com/read/29558292/synergy-of-sex-differences-in-visceral-fat-measured-with-ct-and-tumor-metabolism-helps-predict-overall-survival-in-patients-with-renal-cell-carcinoma
#9
Gerard K Nguyen, Vincent M Mellnick, Aldrin Kay-Yuen Yim, Amber Salter, Joseph E Ippolito
Purpose To determine if sex differences in abdominal visceral fat composition, measured by using computed tomography (CT), and tumor glucose metabolism, measured by gene expression, can help predict outcomes in patients with clear cell renal cell carcinoma (RCC). Materials and Methods This retrospective cohort study included 222 patients with clear cell RCC from The Cancer Imaging Atlas. By using CT, body fat was segmented into subcutaneous fat and visceral fat areas (VFAs) and normalized to total fat to obtain the relative VFA (rVFA) and relative subcutaneous fat area...
March 20, 2018: Radiology
https://www.readbyqxmd.com/read/29554022/clinical-implications-of-real-time-integrative-sequencing-in-management-of-patients-with-suspected-germline-bap1-mutations
#10
Shayan Sengupta, Angela C Weyand, Santhosh A Upadhyaya, Yi-Mi Wu, Dan R Robinson, Rajen J Mody
Germline mutation of BRCA-associated protein-1 has been implicated in the development of tumor predisposition syndrome and high risk for malignant mesothelioma, lung adenocarcinoma, uveal melanoma, and cutaneous melanoma. Here, we present the case of a patient with recurrent metastatic melanoma who was found to have germline BAP1 and somatic BRAF mutation by clinical genomic sequencing. Detection of a germline mutation prompted screening for other cancers and surveillance in family members. Prospective integrative sequencing for pediatric cancer patients may identify pathogenic germline mutations and may improve outcomes and treatment-related morbidity by early diagnosis of malignancy...
March 16, 2018: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/29530782/correlation-of-immunocytochemistry-of-brca1-associated-protein-1-bap1-with-other-prognostic-markers-in-uveal-melanoma
#11
Ben J Glasgow, Tara A McCannel
PURPOSE: Prior studies have shown nuclear reactivity for BAP1 yields prognostic information for paraffin embedded uveal melanomas. Lacking are immunocytochemical studies of BAP1 on fine needle aspiration biopsies of uveal melanoma that correlate with prognosis or other markers of prognosis. Our purpose was to fill this gap. DESIGN: Experimental laboratory study METHODS: Fine needle aspiration biopsies were performed prospectively on 113 patients with uveal melanomas garnering limited subsets of cases for comparison...
March 9, 2018: American Journal of Ophthalmology
https://www.readbyqxmd.com/read/29528717/malignant-mesothelioma-in-individuals-with-nonmesothelial-neoplasms
#12
Kelly J Butnor, Elizabeth N Pavlisko, Thomas A Sporn, Victor L Roggli
CONTEXT: - Malignant mesothelioma (MM) is a component of the BAP1 tumor predisposition syndrome. Other than in BAP1 familial studies, nonmesothelial neoplasms in individuals with MM has not been comprehensively assessed. OBJECTIVE: - To assess the spectrum and prevalence of nonmesothelial neoplasms in individuals with MM. DESIGN: - Individuals with MM and second neoplasms were identified from a database of 3900 MM cases. The expected prevalence of each type of neoplasm was calculated and compared with the actual prevalence in the study population using available Surveillance, Epidemiology, and End Results data and other published data...
March 12, 2018: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29524617/state-of-the-art-advances-in-malignant-pleural-mesothelioma-in-2017
#13
REVIEW
Amanda J McCambridge, Andrea Napolitano, Aaron S Mansfield, Dean A Fennell, Yoshitaka Sekido, Anna K Nowak, Thanyanan Reungwetwattana, Weimin Mao, Harvey I Pass, Michele Carbone, Haining Yang, Tobias Peikert
Malignant pleural mesothelioma (MPM) is an uncommon, almost universally fatal, asbestos-induced malignancy. New and effective strategies for diagnosis, prognostication and treatment are urgently needed. Herein we review the advances in MPM achieved in 2017. While recent epidemiological data demonstrated that the incidence of MPM-related death continued to increase in United States between 2009 and 2015, new insight into the molecular pathogenesis and the immunological tumor microenvironment of MPM, for example, regarding the role of BRCA1 associated protein 1 (BAP1) and the expression programmed death receptor ligand 1 (PD-L1), are highlighting new potential therapeutic strategies...
March 7, 2018: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/29522175/rare-variant-gene-based-association-study-of-hereditary-melanoma-using-whole-exome-sequencing
#14
Mykyta Artomov, Alexander J Stratigos, Ivana Kim, Raj Kumar, Martin Lauss, Bobby Y Reddy, Benchun Miao, Carla Daniela Robles-Espinoza, Aravind Sankar, Ching-Ni Njauw, Kristen Shannon, Evangelos S Gragoudas, Anne Marie Lane, Vivek Iyer, Julia A Newton-Bishop, D Timothy Bishop, Elizabeth A Holland, Graham J Mann, Tarjinder Singh, Mark J Daly, Hensin Tsao
Background: Extraordinary progress has been made in our understanding of common variants in many diseases, including melanoma. Because the contribution of rare coding variants is not as well characterized, we performed an exome-wide, gene-based association study of familial cutaneous melanoma (CM) and ocular melanoma (OM). Methods: Using 11 990 jointly processed individual DNA samples, whole-exome sequencing was performed, followed by large-scale joint variant calling using GATK (Genome Analysis ToolKit)...
December 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29507804/molecular-markers-and-new-diagnostic-methods-to-differentiate-malignant-from-benign-mesothelial-pleural-proliferations-a-literature-review
#15
REVIEW
Rossella Bruno, Greta Alì, Gabriella Fontanini
Malignant pleural mesothelioma (MPM) is an aggressive tumor associated with asbestos exposure. Histopathological analysis of pleural tissues is the gold standard for diagnosis; however, it can be difficult to differentiate malignant from benign pleural lesions. The purpose of this review is to describe the most important biomarkers and new diagnostic tools suggested for this differential diagnosis. There are many studies concerning the separation between MPM and benign pleural proliferations from both pleural tissues or effusions; most of them are based on the evaluation of one or few biomarkers by immunohistochemistry (IHC) or enzyme-linked immunosorbent assays (ELISAs), whereas others focused on the identification of MPM signatures given by microRNA (miRNA) or gene expression profiles as well as on the combination of molecular data and classification algorithms...
January 2018: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29507796/the-pathological-and-molecular-diagnosis-of-malignant-pleural-mesothelioma-a-literature-review
#16
REVIEW
Greta Alì, Rossella Bruno, Gabriella Fontanini
Malignant pleural mesothelioma (MPM), an asbestos-induced tumor, represents significant diagnostic challenges for pathologists. Its histological diagnosis is stepwise and should be based on morphological assessment, supported by clinical and radiological findings, and supplemented with immunohistochemistry (IHC) and, more recently, molecular tests. The main diagnostic dilemmas are the differential diagnoses with benign mesothelial proliferations and other pleural malignant tumors. The present review is an update regarding the morphological, immunohistochemical, and molecular features with respect to MPM diagnosis...
January 2018: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29507792/the-genetic-susceptibility-in-the-development-of-malignant-pleural-mesothelioma
#17
REVIEW
Ombretta Melaiu, Federica Gemignani, Stefano Landi
Malignant pleural mesothelioma (MPM) is a cancer of the pleural cavity whose main risk factor is exposure to asbestos. However, it has been shown that only a minority of exposed people develops MPM. In fact, the incidence among professionally exposed workers was shown to vary between 0.5% and 18.0%. Various hints suggested that other important cofactors could play a role, in particular the genetic susceptibility. Impressive is the case of Cappadocians families exposed to erionite and affected by an "epidemic" of MPM with about half of the inhabitants dying for the disease...
January 2018: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29504908/exome-analysis-of-carotid-body-tumor
#18
Anastasiya V Snezhkina, Elena N Lukyanova, Dmitry V Kalinin, Anatoly V Pokrovsky, Alexey A Dmitriev, Nadezhda V Koroban, Elena A Pudova, Maria S Fedorova, Nadezhda N Volchenko, Oleg A Stepanov, Ekaterina A Zhevelyuk, Sergey L Kharitonov, Anastasiya V Lipatova, Ivan S Abramov, Alexander V Golovyuk, Yegor E Yegorov, Khava S Vishnyakova, Alexey A Moskalev, George S Krasnov, Nataliya V Melnikova, Dmitry S Shcherbo, Marina V Kiseleva, Andrey D Kaprin, Boris Y Alekseev, Andrew R Zaretsky, Anna V Kudryavtseva
BACKGROUND: Carotid body tumor (CBT) is a form of head and neck paragangliomas (HNPGLs) arising at the bifurcation of carotid arteries. Paragangliomas are commonly associated with germline and somatic mutations involving at least one of more than thirty causative genes. However, the specific functionality of a number of these genes involved in the formation of paragangliomas has not yet been fully investigated. METHODS: Exome library preparation was carried out using Nextera® Rapid Capture Exome Kit (Illumina, USA)...
February 13, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29490280/gna11-q209l-mouse-model-reveals-rasgrp3-as-an-essential-signaling-node-in-uveal-melanoma
#19
Amanda R Moore, Leili Ran, Youxin Guan, Jessica J Sher, Tyler D Hitchman, Jenny Q Zhang, Catalina Hwang, Edward G Walzak, Alexander N Shoushtari, Sébastien Monette, Rajmohan Murali, Thomas Wiesner, Klaus G Griewank, Ping Chi, Yu Chen
Uveal melanoma (UM) is characterized by mutually exclusive activating mutations in GNAQ, GNA11, CYSLTR2, and PLCB4, four genes in a linear pathway to activation of PLCβ in almost all tumors and loss of BAP1 in the aggressive subset. We generated mice with melanocyte-specific expression of GNA11Q209L with and without homozygous Bap1 loss. The GNA11Q209L mice recapitulated human Gq-associated melanomas, and they developed pigmented neoplastic lesions from melanocytes of the skin and non-cutaneous organs, including the eye and leptomeninges, as well as at atypical sites, including the lymph nodes and lungs...
February 27, 2018: Cell Reports
https://www.readbyqxmd.com/read/29483632/the-chejuenolide-biosynthetic-gene-cluster-harboring-an-iterative-trans-at-pks-system-in-hahella-chejuensis-strain-mb-1084
#20
Bee Gek Ng, Jae Woo Han, Dong Wan Lee, Gyung Ja Choi, Beom Seok Kim
Hahella chejuensis MB-1084 is a Gram-negative marine bacterial strain that produces unusual 17-membered carbocyclic tetraenes, chejuenolide A and B. Two fosmid clones responsible for chejuenolide production were identified from the genomic DNA library of the MB-1084 strain. Systematic inactivation of the open reading frames (ORFs) in the sequenced region defines the boundaries of the chejuenolide (che) biosynthetic gene cluster (24.9 kbp) that encodes one non-ribosomal peptide synthase (NRPS)-polyketide synthase (PKS) hybrid protein, three modular PKSs, two PKS domains, and an amine oxidase homolog...
February 26, 2018: Journal of Antibiotics
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