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ARID1A

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https://www.readbyqxmd.com/read/28062476/arid1a-deficiency-promotes-colorectal-cancer-via-enhancer-dysregulation
#1
(no author information available yet)
ARID1A loss disrupts SWI/SNF targeting to enhancers to alter gene expression and drive colorectal cancer.
January 6, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28049216/cancer-implications-for-patients-with-endometriosis
#2
Mary Ann Wilbur, Ie-Ming Shih, James H Segars, Amanda N Fader
Endometriosis is defined as the presence of viable endometrial glands and stroma outside of the uterus. It is a common disease, occurring in 5 to 15% of all women. Endometriosis is associated with chronic pelvic pain and infertility and often requires surgical intervention for definitive treatment. Although it is a benign gynecologic condition, endometriosis shares pathophysiologic features with cancer. In recent years, both histologic and epidemiologic evidence has accumulated, suggesting that ovarian endometriosis may give rise to malignant ovarian tumors, primarily those that are epithelial in origin, known as endometriosis-associated ovarian carcinoma (EAOC) including ovarian clear cell carcinoma, endometrioid carcinoma, and the least common, seromucinous tumors...
January 3, 2017: Seminars in Reproductive Medicine
https://www.readbyqxmd.com/read/28031120/-expression-and-clinical-significance-of-arid1a-in-gastric-cancer-and-paired-adjacent-noncancerous-tissues
#3
Xing Zhang, Shibo Wang, Na Liu
Objective To investigate the expression pattern and clinical significance of chromatin remodeling AT-rich interactive domain 1A (ARID1A) protein in gastric cancer and paired adjacent noncancerous tissue samples. Methods The expression of ARID1A protein was examined in 90 gastric cancer tissue samples and 90 paired adjacent noncancerous tissue samples by immunohistochemistry. The relationship of ARID1A protein expression with clinical-pathological characteristics was evaluated by Mann-Whitney test and Spearman correlation analysis...
January 2017: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/27994516/genes-involved-in-angiogenesis-and-mtor-pathways-are-frequently-mutated-in-asian-patients-with-pancreatic-neuroendocrine-tumors
#4
Wen-Chi Chou, Po-Han Lin, Yi-Chen Yeh, Yi-Ming Shyr, Wen-Liang Fang, Shin-E Wang, Chun-Yu Liu, Peter Mu-Hsin Chang, Ming-Han Chen, Yi-Ping Hung, Chung-Pin Li, Yee Chao, Ming-Huang Chen
Introduction: To address the issue of limited data on and inconsistent findings for genetic alterations in pancreatic neuroendocrine tumors (pNETs), we analyzed sequences of known pNET-associated genes for their impact on clinical outcomes in a Taiwanese cohort. Methods: Tissue samples from 40 patients with sporadic pNETs were sequenced using a customized sequencing panel that analyzed 43 genes with either an established or potential association with pNETs. Genetic mutations and clinical outcomes were analyzed for potential associations...
2016: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/27984237/rhabdoid-and-undifferentiated-phenotype-in-renal-cell-carcinoma-analysis-of-32-cases-indicating-a-distinctive-common-pathway-of-dedifferentiation-frequently-associated-with-swi-snf-complex-deficiency
#5
Abbas Agaimy, Liang Cheng, Lars Egevad, Bernd Feyerabend, Ondřej Hes, Bastian Keck, Stefano Pizzolitto, Stefano Sioletic, Bernd Wullich, Arndt Hartmann
Undifferentiated (anaplastic) and rhabdoid cell features are increasingly recognized as adverse prognostic findings in renal cell carcinoma (RCC), but their molecular pathogenesis has not been studied sufficiently. Recent studies identified alterations in the Switch Sucrose nonfermentable (SWI/SNF) chromatin remodeling complex as molecular mechanisms underlying dedifferentiation and rhabdoid features in carcinomas of different organs. We herein have analyzed 32 undifferentiated RCCs having in common an undifferentiated (anaplastic) phenotype, prominent rhabdoid features, or both, irrespective of the presence or absence of conventional RCC component...
December 14, 2016: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/27958275/atr-inhibitors-as-a-synthetic-lethal-therapy-for-tumours-deficient-in-arid1a
#6
Chris T Williamson, Rowan Miller, Helen N Pemberton, Samuel E Jones, James Campbell, Asha Konde, Nicholas Badham, Rumana Rafiq, Rachel Brough, Aditi Gulati, Colm J Ryan, Jeff Francis, Peter B Vermulen, Andrew R Reynolds, Philip M Reaper, John R Pollard, Alan Ashworth, Christopher J Lord
Identifying genetic biomarkers of synthetic lethal drug sensitivity effects provides one approach to the development of targeted cancer therapies. Mutations in ARID1A represent one of the most common molecular alterations in human cancer, but therapeutic approaches that target these defects are not yet clinically available. We demonstrate that defects in ARID1A sensitize tumour cells to clinical inhibitors of the DNA damage checkpoint kinase, ATR, both in vitro and in vivo. Mechanistically, ARID1A deficiency results in topoisomerase 2A and cell cycle defects, which cause an increased reliance on ATR checkpoint activity...
December 13, 2016: Nature Communications
https://www.readbyqxmd.com/read/27941798/arid1a-loss-impairs-enhancer-mediated-gene-regulation-and-drives-colon-cancer-in-mice
#7
Radhika Mathur, Burak H Alver, Adrianna K San Roman, Boris G Wilson, Xiaofeng Wang, Agoston T Agoston, Peter J Park, Ramesh A Shivdasani, Charles W M Roberts
Genes encoding subunits of SWI/SNF (BAF) chromatin-remodeling complexes are collectively mutated in ∼20% of all human cancers. Although ARID1A is the most frequent target of mutations, the mechanism by which its inactivation promotes tumorigenesis is unclear. Here we demonstrate that Arid1a functions as a tumor suppressor in the mouse colon, but not the small intestine, and that invasive ARID1A-deficient adenocarcinomas resemble human colorectal cancer (CRC). These tumors lack deregulation of APC/β-catenin signaling components, which are crucial gatekeepers in common forms of intestinal cancer...
December 12, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27939411/identification-of-novel-mutations-in-japanese-ovarian-clear-cell-carcinoma-patients-using-optimized-targeted-ngs-for-clinical-diagnosis
#8
Yoshiaki Maru, Naotake Tanaka, Miki Ohira, Makiko Itami, Yoshitaka Hippo, Hiroki Nagase
OBJECTIVE: Ovarian clear cell carcinoma (OCCC) is an aggressive ovarian cancer with a higher frequency in Japan and often becomes chemorefractory disease. Reliable genetic diagnosis is essential to affirm the success of precision medicine for OCCC treatment. The aim of this study is, therefore, to identify novel mutations in OCCCs and develop a feasible clinical next generation sequencing (NGS) approach using formalin-fixed paraffin-embedded (FFPE) rather than preferable but not always available fresh frozen (FF) samples...
December 8, 2016: Gynecologic Oncology
https://www.readbyqxmd.com/read/27925203/the-genetic-landscape-of-breast-carcinomas-with-neuroendocrine-differentiation
#9
Caterina Marchiò, Felipe C Geyer, Charlotte Ky Ng, Salvatore Piscuoglio, Maria R De Filippo, Marco Cupo, Anne M Schultheis, Raymond S Lim, Kathleen A Burke, Elena Guerini-Rocco, Mauro Papotti, Larry Norton, Anna Sapino, Britta Weigelt, Jorge S Reis-Filho
Neuroendocrine breast carcinomas (NBCs) account for 2-5% of all invasive breast cancers, and are histologically similar to neuroendocrine tumours from other sites. They typically express oestrogen receptor (ER), and are HER2-negative and of luminal 'intrinsic' subtype. Here, we sought to define the mutational profile of NBCs, and to investigate whether NBCs and common forms of luminal (ER(+) /HER2(-) ) breast carcinoma show distinct repertoires of somatic mutations. Eighteen ER(+) /HER2(-) NBCs, defined as harbouring >50% of tumour cells expressing chromogranin A and/or synaptophysin, and matched normal tissues were microdissected and subjected to massively parallel sequencing targeting all exons of 254 genes most frequently mutated in breast carcinomas and/or related to DNA repair...
December 7, 2016: Journal of Pathology
https://www.readbyqxmd.com/read/27910777/gastric-adenocarcinoma-biomarker-expression-profiles-and-their-prognostic-value
#10
Serkan Senol, Abdullah Aydin, Duygu Kosemetin, Dilek Ece, Ibrahim Akalin, Hasan Abuoglu, Esra Akdeniz Duran, Dincer Aydin, Burcak Erkol
Expression levels of several molecules implicated in carcinogenesis were examined by immunohistochemical staining, and the prognostic significance of their expression levels in gastric adenocarcinoma (GA) was evaluated. A total of 115 GA and 20 control gastric tissue samples were evaluated by immunohistochemistry using 33 antibodies targeting molecules known to play a part in the development of various tumors. Overexpression of carbonic anhydrase IX (CAIX) and loss of AT-rich interactive domain-containing protein 1A (ARID1A), aldehyde dehydrogenase 1 (ALDH1), and CD44 expression in GA patients were significantly correlated with lymph node (LN) metastasis, advanced tumor stage, and poor prognosis...
2016: Journal of Environmental Pathology, Toxicology and Oncology
https://www.readbyqxmd.com/read/27906199/microduplication-of-the-arid1a-gene-causes-intellectual-disability-with-recognizable-syndromic-features
#11
Marie Bidart, Michèle El Atifi, Sarra Miladi, John Rendu, Véronique Satre, Pierre F Ray, Caroline Bosson, Françoise Devillard, Daphné Lehalle, Valérie Malan, Jeanne Amiel, Maria Antonietta Mencarelli, Margherita Baldassarri, Alessandra Renieri, Jill Clayton-Smith, Gaëlle Vieville, Julien Thevenon, Florence Amblard, François Berger, Pierre-Simon Jouk, Charles Coutton
PURPOSE: To determine whether duplication of the ARID1A gene is responsible for a new recognizable syndrome. METHODS: We describe four patients with a 1p36.11 microduplication involving ARID1A as identified by array-comparative genomic hybridization . We performed comparative transcriptomic analysis of patient-derived fibroblasts using RNA sequencing and evaluated the impact of ARID1A duplication on the cell cycle using fluorescence-activated cell sorting. Functional relationships between differentially expressed genes were investigated with ingenuity pathway analysis (IPA)...
December 1, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/27873496/ovarian-clear-cell-carcinoma-sub-typing-by-arid1a-expression
#12
Jae Yoon Choi, Hyun Ho Han, Young Tae Kim, Joo Hyun Lee, Baek Gil Kim, Suki Kang, Nam Hoon Cho
PURPOSE: Loss of AT-rich DNA-interacting domain 1A (ARID1A) has been identified as a driving mutation of ovarian clear cell carcinoma (O-CCC), a triple-negative ovarian cancer that is intermediary between serous and endometrioid subtypes, in regards to molecular and clinical behaviors. However, about half of O-CCCs still express BAF250a, the protein encoded by ARID1A. Herein, we aimed to identify signatures of ARID1A-positive O-CCC in comparison with its ARID1A-negative counterpart. MATERIALS AND METHODS: Seventy cases of O-CCC were included in this study...
January 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/27872090/mutational-landscape-of-pediatric-acute-lymphoblastic-leukemia
#13
LingWen Ding, Qiao-Yang Sun, Kar-Tong Tan, Wenwen Chien, Anand Mayakonda Thippeswamy, Allen Yeoh Eng Juh, Norihiko Kawamata, Yasunobu Nagata, Jin-Fen Xiao, Xin-Yi Loh, De-Chen Lin, Manoj Garg, Su-Lin Lim, Li-Zhen Liu, Vikas Madan, Yan-Yi Jiang, Liang Xu, Masashi Sanada, Lucia Torres Fernández, Hema Preethi, Michael Lill, Hagop Kantarjian, S M Kornblau, Satoru Miyano, Seishi Ogawa, Der-Cherng Liang, Lee-Yung Shih, Henry Yang, H Phillip Koeffler
Current standard of care for patients with pediatric acute lymphoblastic leukemia (ALL) is mainly effective, with high remission rates after treatment. However, the genetic perturbations that give rise to this disease remain largely undefined, limiting the ability to address resistant tumors or develop less toxic targeted therapies. Here we report the use of next generation sequencing to interrogate the genetic and pathogenic mechanisms of 240 pediatric ALL cases with their matched remission samples. Commonly mutated genes fell into several categories, including RAS/receptor tyrosine kinases, epigenetic regulators, transcription factors involved in lineage commitment and the p53/cell cycle pathway...
November 21, 2016: Cancer Research
https://www.readbyqxmd.com/read/27767100/ccne1-copy-number-gain-and-overexpression-identify-ovarian-clear-cell-carcinoma-with-a-poor-prognosis
#14
Ayse Ayhan, Elisabetta Kuhn, Ren-Chin Wu, Hiroshi Ogawa, Asli Bahadirli-Talbott, Tsui-Lien Mao, Haruhiko Sugimura, Ie-Ming Shih, Tian-Li Wang
Ovarian clear cell carcinoma is a unique type of ovarian cancer, often derived from endometriosis, and advanced-stage disease has a dismal prognosis primarily due to the resistance to conventional chemotherapy. Previous studies have shown frequent somatic mutations in ARID1A, PIK3CA, hTERT promoter, and amplification of ZNF217; however, the molecular alterations that are associated with its aggressiveness remain largely unknown. This study examined and compared cyclin E1 expression in endometriosis-related ovarian tumors, with the aim of determining the relationship between hTERT mutations and ARID1A expression and evaluating the effects of these molecular alterations on patient survival...
October 21, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/27764136/immunohistochemistry-successfully-uncovers-intratumoral-heterogeneity-and-widespread-co-losses-of-chromatin-regulators-in-clear-cell-renal-cell-carcinoma
#15
Wei Jiang, Essel Dulaimi, Karthik Devarajan, Theodore Parsons, Qiong Wang, Lili Liao, Eun-Ah Cho, Raymond O'Neill, Charalambos Solomides, Stephen C Peiper, Joseph R Testa, Robert Uzzo, Haifeng Yang
Recent studies have shown that intratumoral heterogeneity (ITH) is prevalent in clear cell renal cell carcinoma (ccRCC), based on DNA sequencing and chromosome aberration analysis of multiple regions from the same tumor. VHL mutations were found to be universal throughout individual tumors when it occurred (ubiquitous), while the mutations in other tumor suppressor genes tended to be detected only in parts of the tumors (subclonal). ITH has been studied mostly by DNA sequencing in limited numbers of samples, either by whole genome sequencing or by targeted sequencing...
2016: PloS One
https://www.readbyqxmd.com/read/27756662/mutational-analysis-of-recurrent-meningioma-progressing-from-atypical-to-rhabdoid-subtype
#16
Mateusz Bujko, Marcin M Machnicki, Emilia Grecka, Natalia Rusetska, Ewa Matyja, Paulina Kober, Tomasz Mandat, Małgorzata Rydzanicz, Rafał Płoski, Romuald Krajewski, Wieslaw Bonicki, Tomasz Stokłosa, Janusz A Siedlecki
BACKGROUND: Rhabdoid meningioma is rare aggressive meningioma histological subtype, which develops predominantly through progression from less malignant tumors. Due to a low incidence the biological background is unknown. The aim of this study was to profile somatic mutations in four meningioma samples from the same patient, derived previously from four subsequent tumor resections. CASE DESCRIPTION: 58-year-old woman suffering from recurrent meningioma progressing from atypical to rhabdoid subtype...
October 15, 2016: World Neurosurgery
https://www.readbyqxmd.com/read/27729836/mutational-analysis-of-extranodal-nk-t-cell-lymphoma-using-targeted-sequencing-with-a-comprehensive-cancer-panel
#17
Seungkyu Choi, Jai Hyang Go, Eun Kyung Kim, Hojung Lee, Won Mi Lee, Chun-Sung Cho, Kyudong Han
Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples...
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27723760/the-genomic-landscape-of-schwannoma
#18
Sameer Agnihotri, Shahrzad Jalali, Mark R Wilson, Arnavaz Danesh, Mira Li, George Klironomos, Jonathan R Krieger, Alireza Mansouri, Osaama Khan, Yasin Mamatjan, Natalie Landon-Brace, Takyee Tung, Mark Dowar, Tiantian Li, Jeffrey P Bruce, Kelly E Burrell, Peter D Tonge, Amir Alamsahebpour, Boris Krischek, Pankaj Kumar Agarwalla, Wenya Linda Bi, Ian F Dunn, Rameen Beroukhim, Michael G Fehlings, Vera Bril, Stefano M Pagnotta, Antonio Iavarone, Trevor J Pugh, Kenneth D Aldape, Gelareh Zadeh
Schwannomas are common peripheral nerve sheath tumors that can cause debilitating morbidities. We performed an integrative analysis to determine genomic aberrations common to sporadic schwannomas. Exome sequence analysis with validation by targeted DNA sequencing of 125 samples uncovered, in addition to expected NF2 disruption, recurrent mutations in ARID1A, ARID1B and DDR1. RNA sequencing identified a recurrent in-frame SH3PXD2A-HTRA1 fusion in 12/125 (10%) cases, and genomic analysis demonstrated the mechanism as resulting from a balanced 19-Mb chromosomal inversion on chromosome 10q...
October 10, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27699033/effect-of-arid1a-baf250a-expression-on-carcinogenesis-and-clinicopathological-factors-in-pure-type-clear-cell-adenocarcinoma-of-the-ovary
#19
Masafumi Kato, Masashi Takano, Morikazu Miyamoto, Naoki Sasaki, Tomoko Goto, Ayako Suzuki, Junko Hirata, Hidenori Sasa, Hitoshi Tsuda, Kenichi Furuya
Frequent mutation of the ARID1A gene has been recently identified in ovarian clear-cell adenocarcinoma (CCA); however, the clinical significance of BAF250a expression encoded by the ARID1A gene remains to be determined. The aim of the present study was to assess whether BAF250a expression had an impact on the clinical features of CCA. A total of 97 cases of CCA treated at a single institution were enrolled in the present study. The tissue samples were evaluated by immunohistochemical staining. BAF250a-deficient expression was observed in 30% (29/97) of all CCA cases...
October 2016: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/27681437/loss-of-hdac-mediated-repression-and-gain-of-nf-%C3%AE%C2%BAb-activation-underlie-cytokine-induction-in-arid1a-and-pik3ca-mutation-driven-ovarian-cancer
#20
Minchul Kim, Falong Lu, Yi Zhang
ARID1A is frequently mutated in ovarian clear cell carcinoma (OCCC) and often co-exists with activating mutations of PIK3CA. Although induction of pro-inflammatory cytokines has been observed in this cancer, the mechanism by which the two mutations synergistically activate cytokine genes remains elusive. Here, we established an in vitro model of OCCC by introducing ARID1A knockdown and mutant PIK3CA into a normal human ovarian epithelial cell line, resulting in cell transformation and cytokine gene induction...
September 27, 2016: Cell Reports
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