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ARID1A

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https://www.readbyqxmd.com/read/28339163/next-generation-sequencing-of-urine-specimens-a-novel-platform-for-genomic-analysis-in-patients-with-non-muscle-invasive-urothelial-carcinoma-treated-with-bacille-calmette-gu%C3%A3-rin
#1
Sasinya N Scott, Irina Ostrovnaya, Caroline M Lin, Nancy Bouvier, Bernard H Bochner, Gopakumar Iyer, David Solit, Michael F Berger, Oscar Lin
BACKGROUND: Biopsies from patients with high-risk (HR) non-muscle-invasive urothelial carcinoma (NMIUC), especially flat urothelial carcinoma in situ, frequently contain scant diagnostic material or denuded mucosa only, and this precludes further extensive genomic analysis. This study evaluated the use of next-generation sequencing (NGS) analysis of urine cytology material from patients with HR NMIUC in an attempt to identify genetic alterations that might correlate with clinical features and responses to bacille Calmette-Guérin (BCG) treatment...
March 24, 2017: Cancer
https://www.readbyqxmd.com/read/28302680/genomic-and-epigenomic-heterogeneity-of-hepatocellular-carcinoma
#2
De-Chen Lin, Anand Mayakonda, Huy Q Dinh, Pinbo Huang, Lehang Lin, Xiaoping Liu, Ling-Wen Ding, Jie Wang, Benjamin Berman, Erwei Song, Dong Yin, H Phillip Koeffler
Understanding the intratumoral heterogeneity of hepatocellular carcinoma (HCC) is instructive for developing personalized therapy and identifying molecular biomarkers. Here we applied whole-exome sequencing to 69 samples from 11 patients to resolve the genetic architecture of subclonal diversification. Spatial genomic diversity was found in all 11 HCC cases, with 29% of driver mutations being heterogeneous, including TERT, ARID1A, NOTCH2, and STAG2. Similar with other cancer types, TP53 mutations were always shared between all tumor regions i...
February 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28297679/integrative-genomic-analysis-of-cholangiocarcinoma-identifies-distinct-idh-mutant-molecular-profiles
#3
Farshad Farshidfar, Siyuan Zheng, Marie-Claude Gingras, Yulia Newton, Juliann Shih, A Gordon Robertson, Toshinori Hinoue, Katherine A Hoadley, Ewan A Gibb, Jason Roszik, Kyle R Covington, Chia-Chin Wu, Eve Shinbrot, Nicolas Stransky, Apurva Hegde, Ju Dong Yang, Ed Reznik, Sara Sadeghi, Chandra Sekhar Pedamallu, Akinyemi I Ojesina, Julian M Hess, J Todd Auman, Suhn K Rhie, Reanne Bowlby, Mitesh J Borad, Andrew X Zhu, Josh M Stuart, Chris Sander, Rehan Akbani, Andrew D Cherniack, Vikram Deshpande, Taofic Mounajjed, Wai Chin Foo, Michael S Torbenson, David E Kleiner, Peter W Laird, David A Wheeler, Autumn J McRee, Oliver F Bathe, Jesper B Andersen, Nabeel Bardeesy, Lewis R Roberts, Lawrence N Kwong
Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number...
March 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28297605/identifying-cell-cycle-modulators-that-selectively-target-arid1a-deficiency-using-high-throughput-image-based-screening
#4
Lihong Zhang, Jianfeng Shen, Yuping Yin, Yang Peng, Lulu Wang, Hui-Ju Hsieh, Qian Shen, Powel H Brown, Kaixiong Tao, Ivan P Uray, Guang Peng
ARID1A, a component of the chromatin remodeling complex SWI/SNF, is an evolutionarily conserved complex that uses the energy of adenosine triphosphate hydrolysis to remodel chromatin structure and functions as a master regulator of gene transcription. Recent genomic studies have revealed that ARID1A is one of the most frequently mutated genes in human cancers. However, therapeutic approaches that selectively target ARID1A-mutant tumors are not yet clinically available. Our previous study showed that ARID1A facilitates chromatin response and cell cycle checkpoint activation after DNA damage...
March 1, 2017: SLAS Discov
https://www.readbyqxmd.com/read/28296015/constitutional-and-functional-genetics-of-human-alcohol-related-hepatocellular-carcinoma
#5
REVIEW
Pierre Nahon, Jean-Charles Nault
Exploration of the constitutional genetics of hepatocellular carcinoma (HCC) has identified numerous variants associated with a higher risk of liver cancer in alcoholic cirrhotic patients. Although Genome Wide Association studies have not been carried out in the field of alcohol-related HCC, common single nucleotide polymorphisms conferring a small increase in the risk of liver cancer risk been identified and been shown to modulate ethanol metabolism, inflammation, oxidative stress, iron or lipid metabolism...
March 14, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28294689/genomics-signaling-and-treatment-of-waldenstr%C3%A3-m-macroglobulinemia
#6
Zachary R Hunter, Guang Yang, Lian Xu, Xia Liu, Jorge J Castillo, Steven P Treon
Next-generation sequencing has revealed recurring somatic mutations in Waldenström macroglobulinemia (WM). Commonly recurring mutations include MYD88 (95% to 97%), CXCR4 (30% to 40%), ARID1A (17%), and CD79B (8% to 15%). Diagnostic discrimination of WM from overlapping B-cell malignancies is aided by MYD88 mutation status. Transcription is affected by MYD88 and CXCR4 mutations and includes overexpression of genes involved in VDJ recombination, CXCR4 pathway signaling, and BCL2 family members. Among patients with MYD88 mutations, those with CXCR4 mutations show transcriptional silencing of tumor suppressors associated with acquisition of mutated MYD88...
February 13, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28291122/smarcb1-ini-1-deficient-sinonasal-carcinoma-a-series-of-39-cases-expanding-the-morphologic-and-clinicopathologic-spectrum-of-a-recently-described-entity
#7
Abbas Agaimy, Arndt Hartmann, Cristina R Antonescu, Simion I Chiosea, Samir K El-Mofty, Helene Geddert, Heinrich Iro, James S Lewis, Bruno Märkl, Stacey E Mills, Marc-Oliver Riener, Thomas Robertson, Ann Sandison, Sabine Semrau, Roderick H W Simpson, Edward Stelow, William H Westra, Justin A Bishop
To more fully characterize the clinical and pathologic spectrum of a recently described tumor entity of the sinonasal tract characterized by loss of nuclear expression of SMARCB1 (INI1), we analyzed 39 SMARCB1-deficient sinonasal carcinomas collected from multiple medical centers. The tumors affected 23 males and 16 females with an age range of 19 to 89 years (median, 52). All patients presented with locally advanced disease (T3, n=5; T4, n=27) involving the sinuses (mainly ethmoid) with variable involvement of the nasal cavity...
April 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28271698/ovarian-cancer-in-endometriosis-clinical-and-molecular-aspects-an-update
#8
Rachel Ruderman, Mary E Pavone
While endometriosis is a benign condition, the presence of endometriosis has been associated with the development of several types of cancers, including ovarian. Endometriomas, or ovarian endometriotic cysts, are found in 17-44% of patients with endometriosis, and may be a common precursor lesions to ovarian cancer. Endometriosis associated ovarian cancer is especially prominent in endometrioid and clear cell ovarian tumor histological subtypes. Several common pathways linking endometriosis and ovarian cancer have been elucidated, including the dominance of certain cytokines, oxidative stress, and a hyper-estrogenic hormonal milieu, which propagate both endometriosis and endometriosis associated ovarian cancer...
March 7, 2017: Minerva Ginecologica
https://www.readbyqxmd.com/read/28253716/arid1a-gene-knockdown-promotes-neuroblastoma-migration-and-invasion
#9
C Li, Z Xu, Z Zhao, Q An, L Wang, Y Yu, D Piao
Neuroblastoma is the most common extracranial solid tumor in childhood which often acquires drug resistance and becomes aggressive phenotypes. The high-risk patients suffer from high mortality due to the limitation of the treatment strategies. ARID1A (AT-rich interactive domain-containing protein 1A), a subunit of SWI/SNF complexes, is considered as a tumor suppressor in many cancers. The aim of the present study was to investigate the effect of ARID1A on migration and invasion in neuroblastoma cells. The shRNA targeting ARID1A was designed and delivered into SK-N-SH cells to knock down ARID1A expression...
March 3, 2017: Neoplasma
https://www.readbyqxmd.com/read/28240000/endometriosis-and-ovarian-cancer-an-integrative-review-endometriosis-and-ovarian-cancer
#10
Aline Veras Morais Brilhante, Kathiane Lustosa Augusto, Manuela Cavalcante Portela, Luiz Carlos Gabriele Sucupira, Luiz Adriano Freitas Oliveira, Ana Juariana Magalhães Veríssimo Pouchaim, Lívia Rocha Mesquita Nóbrega, Thaís Fontes de Magalhães, Leonardo Robson Pinheiro Sobreira
Despite being initially considered a benign disease, it is widely thought nowadays that endometriosis and especially ovarian endometriomas are neoplastic conditions with the potential to become malignant. This review was conducted to summarize, in a concise and systematic manner, the available scientific data relating endometriosis to ovarian cancer, published in the past five years. After reading abstracts and applying our predefined inclusion and exclusion criteria, a final list of 11 scientific papers was obtained and subjected to review...
January 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28202515/systematic-in-vivo-inactivation-of-chromatin-regulating-enzymes-identifies-setd2-as-a-potent-tumor-suppressor-in-lung-adenocarcinoma
#11
David M Walter, Olivia S Venancio, Elizabeth L Buza, John W Tobias, Charuhas Deshpande, A Andrea Gudiel, Caroline Kim-Kiselak, Michelle Cicchini, Travis J Yates, David M Feldser
Chromatin modifying genes are frequently mutated in human lung adenocarcinoma, but the functional impact of these mutations on disease initiation and progression is not well understood. Using a CRISPR-based approach, we systematically inactivated three of the most commonly mutated chromatin regulatory genes in two KrasG12D-driven mouse models of lung adenocarcinoma to characterize the impact of their loss. Targeted inactivation of SWI/SNF nucleosome remodeling complex members Smarca4 (Brg1) or Arid1a had complex effects on lung adenocarcinoma initiation and progression...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28188630/genetic-analyses-of-isolated-high-grade-pancreatic-intraepithelial-neoplasia-hg-panin-reveal-paucity-of-alterations-in-tp53-and-smad4
#12
Waki Hosoda, Peter Chianchiano, James F Griffin, Meredith E Pittman, Lodewijk A A Brosens, Michaël Noë, Jun Yu, Koji Shindo, Masaya Suenaga, Neda Rezaee, Raluca Yonescu, Yi Ning, Jorge Albores-Saavedra, Naohiko Yoshizawa, Kenichi Harada, Akihiko Yoshizawa, Keiji Hanada, Shuji Yonehara, Michio Shimizu, Takeshi Uehara, Jaswinder S Samra, Anthony J Gill, Christopher L Wolfgang, Michael G Goggins, Ralph H Hruban, Laura D Wood
High-grade pancreatic intraepithelial neoplasia (HG-PanIN) is the major precursor of pancreatic ductal adenocarcinoma (PDAC) and is an ideal target for early detection. To characterize pure HG-PanIN, we analysed 23 isolated HG-PanIN lesions occurring in the absence of PDAC. Whole-exome sequencing of five of these HG-PanIN lesions revealed a median of 33 somatic mutations per lesion, with a total of 318 mutated genes. Targeted next-generation sequencing of 17 HG-PanIN lesions identified KRAS mutations in 94% of the lesions...
February 11, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28176137/smarca4-deficient-sinonasal-carcinoma
#13
Abbas Agaimy, Wilko Weichert
The term "sinonasal undifferentiated carcinoma (SNUC)" has been coined in 1986 for a highly aggressive sinonasal tract epithelial neoplasm showing distinctive morphology, but lacking any specific line of differentiation. Recent developments resulted in a dynamic splitting of new entities traditionally included in the spectrum of SNUC. Sinonasal NUT-midline carcinoma, adamantinoma-like Ewing family tumors and most recently, SMARCB1(INI1)-deficient sinonasal carcinoma are the main entities defined by specific genetic aberrations...
February 7, 2017: Head and Neck Pathology
https://www.readbyqxmd.com/read/28153863/the-landscape-of-somatic-genetic-alterations-in-metaplastic-breast-carcinomas
#14
Charlotte K Y Ng, Salvatore Piscuoglio, Felipe C Geyer, Kathleen A Burke, Fresia Pareja, Carey Eberle, Reymond Lim, Rachael Natrajan, Nadeem Riaz, Odette Mariani, Larry Norton, Anne Vincent-Salomon, Y Hannah Wen, Britta Weigelt, Jorge S Reis-Filho
PURPOSE: Metaplastic breast carcinoma (MBC) is a rare and aggressive histologic type of breast cancer predominantly of triple-negative phenotype, and characterized by the presence of malignant cells showing squamous and/or mesenchymal differentiation. We sought to define the repertoire of somatic genetic alterations and the mutational signatures of MBCs. EXPERIMENTAL DESIGN: Whole-exome sequencing was performed in 35 MBCs, with 16, ten and nine classified as harboring chondroid, spindle and squamous metaplasia as the predominant metaplastic component...
February 2, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28125452/morphologic-reproducibility-genotyping-and-immunohistochemical-profiling-do-not-support-a-category-of-seromucinous-carcinoma-of-the-ovary
#15
Peter F Rambau, John B McIntyre, Jennifer Taylor, Sandra Lee, Travis Ogilvie, Anna Sienko, Don Morris, Máire A Duggan, W Glenn McCluggage, Martin Köbel
The 2014 World Health Organization Classification of Tumors of Female Reproductive Organs endorsed the new category of seromucinous carcinoma, a neoplasm that exhibits morphologic and immunophenotypic overlap with other histotypes of ovarian carcinoma. The goal of this study was to determine whether seromucinous carcinoma was a distinct histotype by assessing its diagnostic reproducibility and comparing its molecular composition to the 5 major histotypes of ovarian carcinoma. Thirty-two tumors diagnosed as seromucinous carcinomas from 2 centers were studied...
January 25, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28124119/heterozygosity-for-arid2-loss-of-function-mutations-in-individuals-with-a-coffin-siris-syndrome-like-phenotype
#16
Nuria C Bramswig, O Caluseriu, H-J Lüdecke, F V Bolduc, N C L Noel, T Wieland, H M Surowy, H-J Christen, H Engels, T M Strom, D Wieczorek
Chromatin remodeling is a complex process shaping the nucleosome landscape, thereby regulating the accessibility of transcription factors to regulatory regions of target genes and ultimately managing gene expression. The SWI/SNF (switch/sucrose nonfermentable) complex remodels the nucleosome landscape in an ATP-dependent manner and is divided into the two major subclasses Brahma-associated factor (BAF) and Polybromo Brahma-associated factor (PBAF) complex. Somatic mutations in subunits of the SWI/SNF complex have been associated with different cancers, while germline mutations have been associated with autism spectrum disorder and the neurodevelopmental disorders Coffin-Siris (CSS) and Nicolaides-Baraitser syndromes (NCBRS)...
January 25, 2017: Human Genetics
https://www.readbyqxmd.com/read/28123592/downregulation-of-arid1a-a-component-of-the-swi-snf-chromatin-remodeling-complex-in-breast-cancer
#17
Chika Takao, Akemi Morikawa, Hiroshi Ohkubo, Yusuke Kito, Chiemi Saigo, Takuji Sakuratani, Manabu Futamura, Tamotsu Takeuchi, Kazuhiro Yoshida
Recent studies unraveled that AT-rich interactive domain-containing protein 1A (ARID1A), a subunit of the mammary SWI/SNF chromatin remodeling complex, acts as a tumor suppressor in various cancers. In this study, we first evaluated ARID1A expression by immunohistochemistry in invasive breast cancer tissue specimens and assessed the correlation with the prognosis of patients with breast cancer. Non-tumorous mammary duct epithelial cells exhibited strong nuclear ARID1A staining, whereas different degrees of loss in ARID1A immunoreactivity were observed in many invasive breast cancer cells...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28112728/integrated-genomic-and-molecular-characterization-of-cervical-cancer
#18
(no author information available yet)
Cervical cancer remains one of the leading causes of cancer-related deaths worldwide. Here we report the extensive molecular characterization of 228 primary cervical cancers, one of the largest comprehensive genomic studies of cervical cancer to date. We observed notable APOBEC mutagenesis patterns and identified SHKBP1, ERBB3, CASP8, HLA-A and TGFBR2 as novel significantly mutated genes in cervical cancer. We also discovered amplifications in immune targets CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2), and the BCAR4 long non-coding RNA, which has been associated with response to lapatinib...
March 16, 2017: Nature
https://www.readbyqxmd.com/read/28105136/arid1a-gene-silencing-reduces-the-sensitivity-of-ovarian-clear-cell-carcinoma-to-cisplatin
#19
Changshuai Lyu, Yinglan Zhang, Xingnan Zhou, Jinghe Lang
In ovarian clear cell carcinoma (OCCC), the mutation rate of the AT-rich interaction domain 1A (ARID1A) gene is 46-57%. However, the effects of ARID1A gene silencing by small interfering RNA (siRNA) on the sensitivity of OCCC to cisplatin have not been investigated. Thus, this study aimed to elucidate the association between ARID1A gene silencing and drug resistance in OCCC. Three pairs of ARID1A gene siRNA fragments (siRNA-1, siRNA-2 and siRNA-3) were designed and transiently transfected into ES2 OCCC cells using RNAi Max reagent...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28103826/tracking-the-origin-of-simultaneous-endometrial-and-ovarian-cancer-by-next-generation-sequencing-a-case-report
#20
Nadejda Valtcheva, Franziska M Lang, Aurelia Noske, Eleftherios P Samartzis, Anna-Maria Schmidt, Elisa Bellini, Daniel Fink, Holger Moch, Markus Rechsteiner, Konstantin J Dedes, Peter J Wild
BACKGROUND: Endometrioid adenocarcinoma of the uterus and ovarian endometrioid carcinoma share many morphological and molecular features. Differentiation between simultaneous primary carcinomas and ovarian metastases of an endometrial cancer may be very challenging but is essential for prognostic and therapeutic considerations. CASE PRESENTATION: In the present case study of a 33 year-old patient we used targeted amplicon next-generation re-sequencing for clarifying the origin of synchronous endometrioid cancer of the corpus uteri and the left ovary...
January 19, 2017: BMC Cancer
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