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https://www.readbyqxmd.com/read/28124119/heterozygosity-for-arid2-loss-of-function-mutations-in-individuals-with-a-coffin-siris-syndrome-like-phenotype
#1
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/28122867/the-genetic-basis-of-hepatosplenic-t-cell-lymphoma
#2
Matthew McKinney, Andrea B Moffitt, Philippe Gaulard, Marion Travert, Laurence De Leval, Alina Nicolae, Mark Raffeld, Elaine S Jaffe, Stefania Pittaluga, Liqiang Xi, Tayla Heavican, Javeed Iqbal, Karim Belhadj, Marie Helene Delfau-Larue, Virginie Fataccioli, Magdalena B Czader, Izidore S Lossos, Jennifer R Chapman-Fredricks, Kristy L Richards, Yuri Fedoriw, Sarah L Ondrejka, Eric D Hsi, Lawrence Low, Dennis Weisenburger, Wing C Chan, Neha Mehta-Shah, Steven Horwitz, Leon Bernal-Mizrachi, Christopher R Flowers, Anne W Beaven, Mayur Parihar, Lucile Baseggio, Marie Parrens, Anne Moreau, Pierre Sujobert, Monika Pilichowska, Andrew M Evens, Amy Chadburn, Rex K H Au-Yeung, Gopesh Srivastava, William W L Choi, John R Goodlad, Igor Aurer, Sandra Basic-Kinda, Randy D Gascoyne, Nicholas S Davis, Guojie Li, Jenny Zhang, Deepthi Rajagopalan, Anupama Reddy, Cassandra Love, Shawn Levy, Yuan Zhuang, Jyotishka Datta, David B Dunson, Sandeep S Dave
Hepatosplenic T cell lymphoma (HSTL) is a rare and lethal lymphoma; the genetic drivers of this disease are unknown.  Through whole exome sequencing of 68 HSTLs, we define recurrently mutated driver genes and copy number alterations in the disease. Chromatin modifying genes including SETD2, INO80 and ARID1B were commonly mutated in HSTL, affecting 62% of cases. HSTLs manifest frequent mutations in STAT5B (31%), STAT3 (9%), and PIK3CD (9%) for which there currently exist potential targeted therapies. In addition, we noted less frequent events in EZH2, KRAS and TP53...
January 25, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/27974047/fgfr1-and-ntrk3-actionable-alterations-in-wild-type-gastrointestinal-stromal-tumors
#3
Eileen Shi, Juliann Chmielecki, Chih-Min Tang, Kai Wang, Michael C Heinrich, Guhyun Kang, Christopher L Corless, David Hong, Katherine E Fero, James D Murphy, Paul T Fanta, Siraj M Ali, Martina De Siena, Adam M Burgoyne, Sujana Movva, Lisa Madlensky, Gregory M Heestand, Jonathan C Trent, Razelle Kurzrock, Deborah Morosini, Jeffrey S Ross, Olivier Harismendy, Jason K Sicklick
BACKGROUND: About 10-15% of adult, and most pediatric, gastrointestinal stromal tumors (GIST) lack mutations in KIT, PDGFRA, SDHx, or RAS pathway components (KRAS, BRAF, NF1). The identification of additional mutated genes in this rare subset of tumors can have important clinical benefit to identify altered biological pathways and select targeted therapies. METHODS: We performed comprehensive genomic profiling (CGP) for coding regions in more than 300 cancer-related genes of 186 GISTs to assess for their somatic alterations...
December 14, 2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27968834/methylation-loci-associated-with-body-mass-index-waist-circumference-and-waist-to-hip-ratio-in-chinese-adults-an-epigenome-wide-analysis
#4
Biqi Wang, Wenjing Gao, Jun Li, Canqing Yu, Weihua Cao, Jun Lv, Zengchang Pang, Liming Cong, Hua Wang, Xianping Wu, Liming Liang, Tangchun Wu, Liming Li
BACKGROUND: DNA methylation has been implicated in the pathology of obesity, but little is known about such epigenetic variants in Chinese people. We conducted an epigenome-wide analysis of methylation at CpG sites in relation to body mass index (BMI), waist circumference (WC) and waist-to-hip ratio (WHR) among Chinese adult populations. METHODS: 469 twins from the Chinese National Twin Registry were the discovery cohort. After quality control, methylation levels in whole blood leukocyte DNA were tested for association with BMI, WC, and WHR using mixed linear regressions, adjusting for demographics, lifestyle, and family structure...
October 2016: Lancet
https://www.readbyqxmd.com/read/27941798/arid1a-loss-impairs-enhancer-mediated-gene-regulation-and-drives-colon-cancer-in-mice
#5
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...
February 2017: Nature Genetics
https://www.readbyqxmd.com/read/27860230/cover-image-volume-170a-number-12-december-2016
#6
Toshiki Takenouchi, Hiroshi Yoshihashi, Yuri Sakaguchi, Tomoko Uehara, Masataka Honda, Takao Takahashi, Kenjiro Kosaki, Sahoko Miyama
The cover image, by Toshiki Takenouchi et al., is based on the Clinical Report Hirschsprung disease as a yet undescribed phenotype in a patient with ARID1B mutation, DOI: 10.1002/ajmg.a.37861.
December 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27737960/swi-snf-regulates-a-transcriptional-program-that-induces-senescence-to-prevent-liver-cancer
#7
Luca Tordella, Sadaf Khan, Anja Hohmeyer, Ana Banito, Sabrina Klotz, Selina Raguz, Nadine Martin, Gopuraja Dhamarlingam, Thomas Carroll, José Mario González Meljem, Sumit Deswal, Juan Pedro Martínez-Barbera, Ramón García-Escudero, Johannes Zuber, Lars Zender, Jesús Gil
Oncogene-induced senescence (OIS) is a potent tumor suppressor mechanism. To identify senescence regulators relevant to cancer, we screened an shRNA library targeting genes deleted in hepatocellular carcinoma (HCC). Here, we describe how knockdown of the SWI/SNF component ARID1B prevents OIS and cooperates with RAS to induce liver tumors. ARID1B controls p16(INK4a) and p21(CIP1a) transcription but also regulates DNA damage, oxidative stress, and p53 induction, suggesting that SWI/SNF uses additional mechanisms to regulate senescence...
October 1, 2016: Genes & Development
https://www.readbyqxmd.com/read/27723760/the-genomic-landscape-of-schwannoma
#8
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...
November 2016: Nature Genetics
https://www.readbyqxmd.com/read/27672547/coffin-siris-syndrome-with-caf%C3%A3-au-lait-spots-obesity-and-hyperinsulinism-caused-by-a-mutation-in-the-arid1b-gene
#9
Fatma Mujgan Sonmez, Eyyup Uctepe, Mehmet Gunduz, Zeliha Gormez, Seval Erpolat, Murat Oznur, Mahmut Samil Sagiroglu, Huseyin Demirci, Esra Gunduz
Coffin-Siris syndrome (CSS) (MIM 135900) is characterized by developmental delay, severe speech impairment, distinctive facial features, hypertrichosis, aplasia or hypoplasia of the distal phalanx or nail of the fifth digit and agenesis of the corpus callosum. Recently, it was shown that mutations in the ARID1B gene are the main cause of CSS, accounting for 76% of identified mutations. Here, we report a 15 year-old female patient who was admitted to our clinic with seizures, speech problems, dysmorphic features, bilaterally big, large thumb, café-au-lait (CAL) spots, obesity and hyperinsulinism...
August 2016: Intractable & Rare Diseases Research
https://www.readbyqxmd.com/read/27570168/a-novel-familial-autosomal-dominant-mutation-in-arid1b-causing-neurodevelopmental-delays-short-stature-and-dysmorphic-features
#10
Joshua A Smith, Kenton R Holden, Michael J Friez, Julie R Jones, Michael J Lyons
Recent studies have identified mutations in the ARID1B gene responsible for neurodevelopmental delays, intellectual disability, growth delay, and dysmorphic features. ARID1B encodes a subunit of the BAF chromatin-remodeling complex, and mutations in multiple components of the BAF complex have been implicated as causes of Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, and non-syndromic intellectual disability. The majority of documented pathogenic ARID1B mutations to date have arisen in a sporadic, de novo manner with no reports of inheritance of a pathogenic mutation from an affected parent...
August 29, 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27562491/concurrent-arid1a-and-arid1b-inactivation-in-endometrial-and-ovarian-dedifferentiated-carcinomas
#11
Mackenzie Coatham, Xiaodong Li, Anthony N Karnezis, Lien N Hoang, Basile Tessier-Cloutier, Bo Meng, Robert A Soslow, C Blake Gilks, David G Huntsman, Colin J R Stewart, Lynne M Postovit, Martin Köbel, Cheng-Han Lee
Dedifferentiated carcinoma of the endometrium or the ovary is an aggressive epithelial malignancy that comprises an endometrioid carcinoma together with an undifferentiated carcinoma. We recently reported that inactivation of BRG1 or INI1, core subunits of the switch/sucrose non-fermenting (SWI/SNF) complex, was the likely molecular event underlying dedifferentiation in about half of dedifferentiated carcinomas. In this study, we performed a genomic screen that included other members of the SWI/SNF complex to better delineate the molecular basis in the remainder of these tumours...
August 26, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/27511161/hirschsprung-disease-as-a-yet-undescribed-phenotype-in-a-patient-with-arid1b-mutation
#12
Toshiki Takenouchi, Hiroshi Yoshihashi, Yuri Sakaguchi, Tomoko Uehara, Masataka Honda, Takao Takahashi, Kenjiro Kosaki, Sahoko Miyama
Mutations in the BAF complex (mammalian SWI/SNF complex) are responsible for Coffin-Siris syndrome, which is characterized by developmental delay, distinctive facial features, hirsutism, and hypoplasia/aplasia of the fifth finger/fingernails. Hirschsprung disease is characterized by defective stem cells in the enteric neural system, and the involvement of multiple signaling cascades has been implicated. So far, the roles of the BAF complex in the genesis of Hirschsprung disease have remained unknown. Here, we document a patient with coarse facial features, postnatal growth failure, developmental delay, epilepsy, and hypoplasia of the corpus callosum and cerebellum but without a hypoplastic fifth finger/fingernail...
August 11, 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27431016/ibrutinib-downregulates-a-subset-of-mirna-leading-to-upregulation-of-tumor-suppressors-and-inhibition-of-cell-proliferation-in-chronic-lymphocytic-leukemia
#13
L M Saleh, W Wang, S E M Herman, N S Saba, V Anastas, E Barber, M Corrigan-Cummins, M Farooqui, C Sun, S M Sarasua, Z Zhao, N K Abousamra, O Elbaz, H A Abdelghaffar, A Wiestner, K R Calvo
The lymph node (LN) is the site of chronic lymphocytic leukemia (CLL) cell activation and proliferation. Aberrant microRNA (miRNA) expression has been shown to have a role in CLL pathogenesis; however, a comparison of miRNA expression between CLL cells in the LN and the peripheral blood (PB) has previously not been reported. On the basis of the analysis of 17 paired LN and PB samples from CLL patients, we identify a panel of miRNAs that are increased in LN CLL cells correlating with an activation phenotype...
February 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27392123/frequency-and-outcome-of-pediatric-acute-lymphoblastic-leukemia-with-znf384-gene-rearrangements-including-a-novel-translocation-resulting-in-an-arid1b-znf384-gene-fusion
#14
Mary Shago, Oussama Abla, Johann Hitzler, Sheila Weitzman, Mohamed Abdelhaleem
BACKGROUND: ZNF384 gene rearrangements with multiple partner genes are recurrent in acute leukemia and are most often associated with a precursor B cell immunophenotype. The overall incidence of this genetic category of leukemia is uncertain. PROCEDURE: Patients with ZNF384 gene rearrangements from a cohort of 240 precursor B cell acute lymphoblastic leukemia (ALL) pediatric patients over a 3.5-year time period were characterized with detailed cytogenetic, FISH, genomic, and clinical analyses...
November 2016: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/27264197/smarce1-a-rare-cause-of-coffin-siris-syndrome-clinical-description-of-three-additional-cases
#15
Yuri A Zarate, Elizabeth Bhoj, Julie Kaylor, Dong Li, Yoshinori Tsurusaki, Noriko Miyake, Naomichi Matsumoto, Shubha Phadke, Luis Escobar, Afifa Irani, Hakon Hakonarson, Samantha A Schrier Vergano
Coffin-Siris syndrome (CSS, MIM 135900), is a well-described, multiple congenital anomaly syndrome characterized by coarse facial features, hypertrichosis, sparse scalp hair, and hypo/aplastic digital nails and phalanges, typically of the 5th digits. Mutations in the BAF (SWI/SNF)-complex subunits (SMARCA4, SMARCE1, SMARCB1, SMARCA2, ARID1B, and ARID1A) have been shown to cause not only CSS, but also related disorders including Nicolaides-Baraitser (MIM 601358) syndrome and ARID1B-intellectual disability syndrome (MIM 614562)...
August 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27203213/genetic-landscape-of-t-and-nk-cell-post-transplant-lymphoproliferative-disorders
#16
Elizabeth Margolskee, Vaidehi Jobanputra, Preti Jain, Jinli Chen, Karthik Ganapathi, Odelia Nahum, Brynn Levy, Julie Morscio, Vundavalli Murty, Thomas Tousseyn, Bachir Alobeid, Mahesh Mansukhani, Govind Bhagat
Post-transplant lymphoproliferative disorders of T- or NK-cell origin (T/NK-PTLD) are rare entities and their genetic basis is unclear. We performed targeted sequencing of 465 cancer-related genes and high-resolution copy number analysis in 17 T-PTLD and 2 NK-PTLD cases. Overall, 377 variants were detected, with an average of 20 variants per case. Mutations of epigenetic modifier genes (TET2, KMT2C, KMT2D, DNMT3A, ARID1B, ARID2, KDM6B, n=11). and inactivation of TP53 by mutation and/or deletion(n=6) were the most frequent alterations, seen across disease subtypes, followed by mutations of JAK/STAT pathway genes (n=5)...
June 21, 2016: Oncotarget
https://www.readbyqxmd.com/read/27195705/analysis-of-paired-primary-metastatic-hormone-receptor-positive-breast-tumors-hrpbc-uncovers-potential-novel-drivers-of-hormonal-resistance
#17
Luis Manso, Silvana Mourón, Michael Tress, Gonzalo Gómez-López, Manuel Morente, Eva Ciruelos, Miriam Rubio-Camarillo, Jose Luis Rodriguez-Peralto, Miguel A Pujana, David G Pisano, Miguel Quintela-Fandino
We sought to identify genetic variants associated with disease relapse and failure to hormonal treatment in hormone-receptor positive breast cancer (HRPBC). We analyzed a series of HRPBC with distant relapse, by sequencing pairs (n = 11) of tumors (primary and metastases) at >800X. Comparative genomic hybridization was performed as well. Top hits, based on the frequency of alteration and severity of the changes, were tested in the TCGA series. Genes determining the most parsimonious prognostic signature were studied for their functional role in vitro, by performing cell growth assays in hormonal-deprivation conditions, a setting that mimics treatment with aromatase inhibitors...
2016: PloS One
https://www.readbyqxmd.com/read/27112773/the-role-of-objective-facial-analysis-using-fdna-in-making-diagnoses-following-whole-exome-analysis-report-of-two-patients-with-mutations-in-the-baf-complex-genes
#18
Karen W Gripp, Laura Baker, Aida Telegrafi, Kristin G Monaghan
The genetic basis of numerous intellectual disability (ID) syndromes has recently been identified by applying exome analysis on a research or clinical basis. There is significant clinical overlap of biologically related syndromes, as exemplified by Nicolaides-Baraitser (NCBRS) and Coffin-Siris (CSS) syndrome. Both result from mutations affecting the BAF (mSWI/SNF) complex and belong to the growing category of BAFopathies. In addition to the notable clinical overlap between these BAFopathies, heterogeneity exists for patients clinically diagnosed with one of these conditions...
July 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27063598/comprehensive-mutational-analysis-of-primary-and-relapse-acute-promyelocytic-leukemia
#19
V Madan, P Shyamsunder, L Han, A Mayakonda, Y Nagata, J Sundaresan, D Kanojia, K Yoshida, S Ganesan, N Hattori, N Fulton, K-T Tan, T Alpermann, M-C Kuo, S Rostami, J Matthews, M Sanada, L-Z Liu, Y Shiraishi, S Miyano, E Chendamarai, H-A Hou, G Malnassy, T Ma, M Garg, L-W Ding, Q-Y Sun, W Chien, T Ikezoe, M Lill, A Biondi, R A Larson, B L Powell, M Lübbert, W J Chng, H-F Tien, M Heuser, A Ganser, M Koren-Michowitz, S M Kornblau, H M Kantarjian, D Nowak, W-K Hofmann, H Yang, W Stock, A Ghavamzadeh, K Alimoghaddam, T Haferlach, S Ogawa, L-Y Shih, V Mathews, H P Koeffler
Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by differentiation block at the promyelocyte stage. Besides the presence of chromosomal rearrangement t(15;17), leading to the formation of PML-RARA (promyelocytic leukemia-retinoic acid receptor alpha) fusion, other genetic alterations have also been implicated in APL. Here, we performed comprehensive mutational analysis of primary and relapse APL to identify somatic alterations, which cooperate with PML-RARA in the pathogenesis of APL...
August 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/26937011/essential-roles-for-arid1b-in-dendritic-arborization-and-spine-morphology-of-developing-pyramidal-neurons
#20
Minhan Ka, Divyan A Chopra, Shashank M Dravid, Woo-Yang Kim
UNLABELLED: De novo truncating mutations in ARID1B, a chromatin-remodeling gene, cause Coffin-Siris syndrome, a developmental disorder characterized by intellectual disability and speech impairment; however, how the genetic elimination leads to cognitive dysfunction remains unknown. Thus, we investigated the neural functions of ARID1B during brain development. Here, we show that ARID1B regulates dendritic differentiation in the developing mouse brain. We knocked down ARID1B expression in mouse pyramidal neurons using in utero gene delivery methodologies...
March 2, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
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