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https://www.readbyqxmd.com/read/27860230/cover-image-volume-170a-number-12-december-2016
#1
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
#2
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
#3
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/27672547/coffin-siris-syndrome-with-caf%C3%A3-au-lait-spots-obesity-and-hyperinsulinism-caused-by-a-mutation-in-the-arid1b-gene
#4
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
#5
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
#6
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
#7
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
#8
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...
July 19, 2016: 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
#9
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
#10
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
#11
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)...
May 27, 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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/26920143/analysis-of-functional-germline-variants-in-apobec3-and-driver-genes-on-breast-cancer-risk-in-moroccan-study-population
#16
Chaymaa Marouf, Stella Göhler, Miguel Inacio Da Silva Filho, Omar Hajji, Kari Hemminki, Sellama Nadifi, Asta Försti
BACKGROUND: Breast cancer (BC) is the most prevalent cancer in women and a major public health problem in Morocco. Several Moroccan studies have focused on studying this disease, but more are needed, especially at the genetic and molecular levels. Therefore, we investigated the potential association of several functional germline variants in the genes commonly mutated in sporadic breast cancer. METHODS: In this case-control study, we examined 36 single nucleotide polymorphisms (SNPs) in 13 genes (APOBEC3A, APOBEC3B, ARID1B, ATR, MAP3K1, MLL2, MLL3, NCOR1, RUNX1, SF3B1, SMAD4, TBX3, TTN), which were located in the core promoter, 5'-and 3'UTR or which were nonsynonymous SNPs to assess their potential association with inherited predisposition to breast cancer development...
2016: BMC Cancer
https://www.readbyqxmd.com/read/26904939/insertional-mutagenesis-identifies-a-stat3-arid1b-%C3%AE-catenin-pathway-driving-neurofibroma-initiation
#17
Jianqiang Wu, Vincent W Keng, Deanna M Patmore, Jed J Kendall, Ami V Patel, Edwin Jousma, Walter J Jessen, Kwangmin Choi, Barbara R Tschida, Kevin A T Silverstein, Danhua Fan, Eric B Schwartz, James R Fuchs, Yuanshu Zou, Mi-Ok Kim, Eva Dombi, David E Levy, Gang Huang, Jose A Cancelas, Anat O Stemmer-Rachamimov, Robert J Spinner, David A Largaespada, Nancy Ratner
To identify genes and signaling pathways that initiate Neurofibromatosis type 1 (NF1) neurofibromas, we used unbiased insertional mutagenesis screening, mouse models, and molecular analyses. We mapped an Nf1-Stat3-Arid1b/β-catenin pathway that becomes active in the context of Nf1 loss. Genetic deletion of Stat3 in Schwann cell progenitors (SCPs) and Schwann cells (SCs) prevents neurofibroma formation, decreasing SCP self-renewal and β-catenin activity. β-catenin expression rescues effects of Stat3 loss in SCPs...
March 1, 2016: Cell Reports
https://www.readbyqxmd.com/read/26892443/the-landscape-of-fusion-transcripts-in-spitzoid-melanoma-and-biologically-indeterminate-spitzoid-tumors-by-rna-sequencing
#18
Gang Wu, Raymond L Barnhill, Seungjae Lee, Yongjin Li, Ying Shao, John Easton, James Dalton, Jinghui Zhang, Alberto Pappo, Armita Bahrami
Kinase activation by chromosomal translocations is a common mechanism that drives tumorigenesis in spitzoid neoplasms. To explore the landscape of fusion transcripts in these tumors, we performed whole-transcriptome sequencing using formalin-fixed, paraffin-embedded (FFPE) tissues in malignant or biologically indeterminate spitzoid tumors from 7 patients (age 2-14 years). RNA sequence libraries enriched for coding regions were prepared and the sequencing was analyzed by a novel assembly-based algorithm designed for detecting complex fusions...
April 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/26716708/genome-wide-transcriptional-regulation-mediated-by-biochemically-distinct-swi-snf-complexes
#19
Jesse R Raab, Samuel Resnick, Terry Magnuson
Multiple positions within the SWI/SNF chromatin remodeling complex can be filled by mutually exclusive subunits. Inclusion or exclusion of these proteins defines many unique forms of SWI/SNF and has profound functional consequences. Often this complex is studied as a single entity within a particular cell type and we understand little about the functional relationship between these biochemically distinct forms of the remodeling complex. Here we examine the functional relationships among three complex-specific ARID (AT-Rich Interacting Domain) subunits using genome-wide chromatin immunoprecipitation, transcriptome analysis, and transcription factor binding maps...
December 2015: PLoS Genetics
https://www.readbyqxmd.com/read/26546417/unique-dna-methylation-patterns-in-offspring-of-hypertensive-pregnancy
#20
Colleen G Julian, Brent S Pedersen, Carlos Salinas Salmon, Ivana V Yang, Marcelino Gonzales, Enrique Vargas, Lorna G Moore, David A Schwartz
Epigenomic processes are believed to play a pivotal role for the effect of environmental exposures in early life to modify disease risk throughout the lifespan. Offspring of women with hypertensive complications of pregnancy (HTNPREG ) have an increased risk of developing systemic and pulmonary vascular dysfunction in adulthood. In this preliminary report, we sought to determine whether epigenetic modifications of genes involved in the regulation of vascular function were present in HTNPREG offspring. We contrasted DNA methylation and gene expression patterns of peripheral blood mononuclear cells obtained from young male offspring of HTNPREG (n = 5) to those of normotensive controls (n = 19)...
December 2015: Clinical and Translational Science
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