Clonal Hematopoietic Mutations Linked to Platelet Traits and the Risk Of
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Genomic Profiling Reveals High Frequency of DNA Repair Genetic
www.nature.com/scientificreports OPEN Genomic profling reveals high frequency of DNA repair genetic aberrations in gallbladder cancer Reham Abdel‑Wahab1,9, Timothy A. Yap2, Russell Madison4, Shubham Pant1,2, Matthew Cooke4, Kai Wang4,5,7, Haitao Zhao8, Tanios Bekaii‑Saab6, Elif Karatas1, Lawrence N. Kwong3, Funda Meric‑Bernstam2, Mitesh Borad6 & Milind Javle1,10* DNA repair gene aberrations (GAs) occur in several cancers, may be prognostic and are actionable. We investigated the frequency of DNA repair GAs in gallbladder cancer (GBC), association with tumor mutational burden (TMB), microsatellite instability (MSI), programmed cell death protein 1 (PD‑1), and its ligand (PD‑L1) expression. Comprehensive genomic profling (CGP) of 760 GBC was performed. We investigated GAs in 19 DNA repair genes including direct DNA repair genes (ATM, ATR , BRCA1, BRCA2, FANCA, FANCD2, MLH1, MSH2, MSH6, PALB2, POLD1, POLE, PRKDC, and RAD50) and caretaker genes (BAP1, CDK12, MLL3, TP53, and BLM) and classifed patients into 3 groups based on TMB level: low (< 5.5 mutations/Mb), intermediate (5.5–19.5 mutations/Mb), and high (≥ 19.5 mutations/Mb). We assessed MSI status and PD‑1 & PD‑L1 expression. 658 (86.6%) had at least 1 actionable GA. Direct DNA repair gene GAs were identifed in 109 patients (14.2%), while 476 (62.6%) had GAs in caretaker genes. Both direct and caretaker DNA repair GAs were signifcantly associated with high TMB (P = 0.0005 and 0.0001, respectively). Tumor PD‑L1 expression was positive in 119 (15.6%), with 17 (2.2%) being moderate or high. DNA repair GAs are relatively frequent in GBC and associated with coexisting actionable mutations and a high TMB. -
Producing T Cells
Lnk/Sh2b3 Controls the Production and Function of Dendritic Cells and Regulates the Induction of IFN- −γ Producing T Cells This information is current as Taizo Mori, Yukiko Iwasaki, Yoichi Seki, Masanori Iseki, of September 28, 2021. Hiroko Katayama, Kazuhiko Yamamoto, Kiyoshi Takatsu and Satoshi Takaki J Immunol published online 14 July 2014 http://www.jimmunol.org/content/early/2014/07/13/jimmun ol.1303243 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2014/07/14/jimmunol.130324 Material 3.DCSupplemental http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 28, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2014 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published July 14, 2014, doi:10.4049/jimmunol.1303243 The Journal of Immunology Lnk/Sh2b3 Controls the Production and Function of Dendritic Cells and Regulates the Induction of IFN-g–Producing T Cells Taizo Mori,*,1 Yukiko Iwasaki,*,†,1 Yoichi Seki,* Masanori Iseki,* Hiroko Katayama,* Kazuhiko Yamamoto,† Kiyoshi Takatsu,‡,x and Satoshi Takaki* Dendritic cells (DCs) are proficient APCs that play crucial roles in the immune responses to various Ags and pathogens and polarize Th cell immune responses. -
Germline Risk of Clonal Haematopoiesis
REVIEWS Germline risk of clonal haematopoiesis Alexander J. Silver 1,2, Alexander G. Bick 1,3,4,5 and Michael R. Savona 1,2,4,5 ✉ Abstract | Clonal haematopoiesis (CH) is a common, age-related expansion of blood cells with somatic mutations that is associated with an increased risk of haematological malignancies, cardiovascular disease and all-cause mortality. CH may be caused by point mutations in genes associated with myeloid neoplasms, chromosomal copy number changes and loss of heterozygosity events. How inherited and environmental factors shape the incidence of CH is incompletely understood. Even though the several varieties of CH may have distinct phenotypic consequences, recent research points to an underlying genetic architecture that is highly overlapping. Moreover, there are numerous commonalities between the inherited variation associated with CH and that which has been linked to age-associated biomarkers and diseases. In this Review, we synthesize what is currently known about how inherited variation shapes the risk of CH and how this genetic architecture intersects with the biology of diseases that occur with ageing. Haematopoietic stem cells Haematopoiesis, the process by which blood cells are gen- First, advances in next-generation sequencing technolo- (HSCs). Cells that are erated, begins in embryogenesis and continues through- gies have enabled the identification of mutations with responsible for the creation of out an individual’s lifespan1. Haematopoietic stem cells high resolution (that is, single base-pair changes) even all blood cells in the human (HSCs) are responsible for the creation of all mature when these lesions are present in just a fraction of sampled body and are multipotent in blood cells, including red blood cells, platelets, and the cells. -
Intercellular Competition and the Inevitability of Multicellular Aging
Intercellular competition and the inevitability of multicellular aging Paul Nelsona,1 and Joanna Masela aDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 Edited by Raghavendra Gadagkar, Indian Institute of Science, Bangalore, India, and approved October 6, 2017 (received for review November 14, 2016) Current theories attribute aging to a failure of selection, due to Aging in multicellular organisms occurs at both the cellular either pleiotropic constraints or declining strength of selection and intercellular levels (17). Multicellular organisms, by definition, after the onset of reproduction. These theories implicitly leave require a high degree of intercellular cooperation to maintain open the possibility that if senescence-causing alleles could be homeostasis. Often, cellular traits required for producing a viable identified, or if antagonistic pleiotropy could be broken, the multicellular phenotype come at a steep cost to individual cells effects of aging might be ameliorated or delayed indefinitely. (14, 18, 19). Conversely, many mutant cells that do not invest in These theories are built on models of selection between multicel- holistic organismal fitness have a selective advantage over cells lular organisms, but a full understanding of aging also requires that do. If intercellular competition occurs, such “cheater” or examining the role of somatic selection within an organism. “defector” cells may proliferate and displace “cooperating” cells, Selection between somatic cells (i.e., intercellular competition) with detrimental consequences for the multicellular organism can delay aging by purging nonfunctioning cells. However, the (20, 21). Cancer, a leading cause of death in humans at rates that fitness of a multicellular organism depends not just on how increase with age, is one obvious manifestation of cheater pro- functional its individual cells are but also on how well cells work liferation (22–24). -
Crucial Role of the SH2B1 PH Domain for the Control of Energy Balance
Diabetes Page 2 of 46 1 Crucial Role of the SH2B1 PH Domain for the Control of 2 Energy Balance 3 4 Anabel Floresa, Lawrence S. Argetsingerb+, Lukas K. J. Stadlerc+, Alvaro E. Malagab, Paul B. 5 Vanderb, Lauren C. DeSantisb, Ray M. Joea,b, Joel M. Clineb, Julia M. Keoghc, Elana Henningc, 6 Ines Barrosod, Edson Mendes de Oliveirac, Gowri Chandrashekarb, Erik S. Clutterb, Yixin Hub, 7 Jeanne Stuckeyf, I. Sadaf Farooqic, Martin G. Myers Jr. a,b,e, Christin Carter-Sua,b,e, g * 8 aCell and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA 9 bDepartment of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA 10 cUniversity of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, 11 Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK 12 dMRC Epidemiology Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, 13 Cambridge, UK 14 eDepartment of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA 15 fLife Sciences Institute and Departments of Biological Chemistry and Biophysics, University of Michigan, Ann Arbor, 16 MI 48109, USA 17 +Authors contributed equally to this work 18 gLead contact 19 *Correspondence: [email protected] 20 21 Running title: Role of SH2B1 PH Domain in Energy Balance 22 23 24 25 26 27 28 1 Diabetes Publish Ahead of Print, published online August 22, 2019 Page 3 of 46 Diabetes 29 30 Abstract 31 Disruption of the adaptor protein SH2B1 is associated with severe obesity, insulin resistance and 32 neurobehavioral abnormalities in mice and humans. -
Germline and Somatic Mosaicism in a Family with Multiple Endocrine
2 180 H J B H Beijers and others Mosaicism in family with MEN1 180:2 K15–K19 Case Report syndrome Germline and somatic mosaicism in a family with multiple endocrine neoplasia type 1 (MEN1) syndrome Hanneke J B H Beijers1,2, Nike M L Stikkelbroeck2, Arjen R Mensenkamp3, Rolph Pfundt3, Rob B van der Luijt4, Henri J L M Timmers2, Ad R M M Hermus2 and Marlies J E Kempers3 Correspondence 1Department of Internal Medicine, Maasziekenhuis Pantein, Boxmeer, The Netherlands, 2Division of Endocrinology, should be addressed Department of Internal Medicine, 3Department of Human Genetics, Radboud University Nijmegen Medical Center, to M J E Kempers 4 Nijmegen, The Netherlands, and Department of Medical Genetics, University Medical Center Utrecht, Utrecht, Email The Netherlands Marlies.Kempers@ radboudumc.nl Abstract Context: Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disease caused by mutations in the tumor suppressor gene MEN1 and can be diagnosed based on clinical, familial and/or genetic criteria. We present a family in which we found both germline and somatic mosaicism for MEN1. Family description: In our proband, we diagnosed MEN1. The mutation was not detected in her parents (DNA extracted from leucocytes). When her brother was found to harbor the same MEN1 mutation as our proband and, around the same time, their father was diagnosed with a neuroendocrine carcinoma, this tumor was investigated for the MEN1 mutation as well. In the histologic biopsy of this tumor, the same MEN1 mutation was detected as previously found in his children. Re-analysis of his blood using multiplex ligation-dependent probe amplification (MLPA) showed a minimal, but consistently decreased signal for the MEN1-specific MLPA probes. -
Diagnostic Workflow for Hereditary Erythrocytosis and Thrombocytosis
Diagnostic workflow for hereditary erythrocytosis and thrombocytosis McMullin, M. F. (2019). Diagnostic workflow for hereditary erythrocytosis and thrombocytosis. Hematology (United States), 2019(1), 391-396. https://doi.org/10.1182/hematology.2019000047 Published in: Hematology (United States) Document Version: Peer reviewed version Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2019 American Society of Hematology. This work is made available online in accordance with the publisher’s policies. Please refer to any applicable terms of use of the publisher. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected]. Download date:29. Sep. 2021 Diagnostic workflow for hereditary erythrocytosis and thrombocytosis Mary Frances McMullin, Centre for Medical Education, Queen’s University Belfast, Belfast BT9 7AB, N. Ireland. Email [email protected] Abstract In the patient presenting with an elevated blood count who does not have an acquired clonal disorder causing a myeloproliferative neoplasm, hereditary erythrocytosis or hereditary thrombocytosis needs to be considered as a possible explanation. -
Clonality Identified by Targeted Sequencing
RESEARCH ARTICLE Idiopathic hypereosinophilia is clonal disorder? Clonality identified by targeted sequencing Jee-Soo Lee1¤, Heewon Seo2,3, Kyongok Im4, Si Nae Park4, Sung-Min Kim4, Eun Kyoung Lee4, Jung-Ah Kim1, Joon-hee Lee1, Sunghoon Kwon5, Miyoung Kim6, Insong Koh7, Seungwoo Hwang8, Heung-Woo Park9, Hye-Ryun Kang9, Kyoung Soo Park9, Ju Han Kim2,3, Dong Soon Lee1,4* 1 Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea, 2 Division of Biomedical Informatics, Seoul National University Biomedical Informatics (SNUBI), Seoul a1111111111 National University College of Medicine, Seoul, Republic of Korea, 3 Division of Biomedical Informatics, a1111111111 Systems Biomedical Informatics National Core Research Center, Seoul National University College of a1111111111 Medicine, Seoul, Republic of Korea, 4 Cancer Research Institute, Seoul National University College of a1111111111 Medicine, Seoul, Republic of Korea, 5 Department of Electrical Engineering, Seoul National University, a1111111111 Seoul, Republic of Korea, 6 Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea, 7 Department of Physiology, College of Medicine, Hanyang University, Seoul, Republic of Korea, 8 Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea, 9 Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea OPEN ACCESS ¤ Current address: Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea Citation: Lee J-S, Seo H, Im K, Park SN, Kim S-M, * [email protected] Lee EK, et al. (2017) Idiopathic hypereosinophilia is clonal disorder? Clonality identified by targeted sequencing. PLoS ONE 12(10): e0185602. -
Sex-Specific Association of SH2B3 and SMARCA4 Polymorphisms With
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 35), pp: 59397-59407 Research Paper Sex-specific association ofSH2B3 and SMARCA4 polymorphisms with coronary artery disease susceptibility Yuqiang Ji1,2,3,*, Yanbin Song1,2,4,*, Qingwen Wang5, Pengcheng Xu5, Zhao Zhao3, Xia Li3, Nan Wang3, Tianbo Jin1,2 and Chao Chen1,2 1Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, Xi’an, Shaanxi 710069, China 2School of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China 3Department of Cardiovascular Medicine, First Hospital of Xi’an, Xi’an 710002, China 4Department of Cardiovascular Medicine, Affiliated Hospital Yan’an University, Yan’an 716000, China 5Department of Hand Surgery, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, Cangzhou, Hebei 061001, China *These authors have contributed equally to this work Correspondence to: Tianbo Jin, email: [email protected] Chao Chen, email: [email protected] Keywords: coronary artery disease, SH2B3, SMARCA4, single nucleotide polymorphism, gene Received: February 06, 2017 Accepted: June 03, 2017 Published: July 31, 2017 Copyright: Ji et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT To determine whether sex differences affect the association between genetic polymorphisms and coronary artery disease (CAD) in the Chinese Han population, we conducted a study comparing the frequency of SH2B3 and SMARCA4 variants in 456 CAD patients (291 men, 165 women) and 685 age-matched controls (385 men, 300 women). -
Evolution and Genomic Signatures of Spontaneous Somatic Mutation in Drosophila Intestinal Stem Cells
Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells Nick Riddiford1, Katarzyna Siudeja1, Marius van den Beek1, Benjamin Boumard1, Allison J. Bardin1 * 1 Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France. * author for correspondence Abstract Spontaneous mutations can alter tissue dynamics and lead to cancer initiation. While large- scale sequencing projects have illuminated processes that influence somatic mutation and subsequent tumour evolution, the mutational dynamics operating in the very early stages of cancer development are currently not well understood. In order to explore mutational processes in the early stages of cancer evolution, we exploited neoplasia arising spontaneously in the Drosophila intestine. Analysing whole-genome sequencing data with a dedicated bioinformatic pipeline, we found neoplasia formation to be driven largely through the inactivation of Notch by structural variants, many of which involve highly complex genomic rearrangements. The genome-wide mutational burden in neoplasia was found to be similar to that of several human cancers. Finally, we identified genomic features associated with spontaneous mutation and defined the evolutionary dynamics and mutational landscape operating within intestinal neoplasia over the short lifespan of the adult fly. Our findings provide unique insight into mutational dynamics operating over a short time scale in the genetic model system, Drosophila melanogaster. 1 Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Introduction The accumulation of mutations in somatic tissues plays a major role in cancer and is proposed to contribute to ageing (Al Zouabi and Bardin 2020). -
Formal Discussion Of: Somatic Mutations and Carcinogenesis'
Formal Discussion of: Somatic Mutations and Carcinogenesis' HOWARD J. CURTIS Biology Department, Brookhaven National Laboratory, Upton, New York SUMMARY A great deal of evidence is now available indicating that mutations play a dominant role in the aging process. Because carcinogenesis is one facet of the aging process, mu tations must play a major role here also. However, carcinogenesis certainly does not consist of the simple induction of a mutation in one cell which confers the property of uncontrolled growth on that cell and its progeny. There must be some general condi tions, as well as a specific event, before carcinogenesis can take place. It is postulated that mutations in one form or another are responsible for both conditions. The mutation theory of carcinogenesis is old and well of the 1st generation (3). We then scored chromosome known to all workers in the field. It is an extremely aberrations in liver cells of mice by inducing cell division attractive theory, and there are many pieces of evidence by partial hepatectomy and examining anaphase figures which argue in its favor. Radiation, which is a very po (14). (Fig. 1). The percentage of cells containing aberra tent mutagenic agent, is also a very effective carcinogen. tions is taken as an index of the mutations present in these Most, if not all, of the chemical carcinogens are also muta cells. gens. The virus theory of carcinogenesis is well estab With the use of this technic a number of different situa lished in certain special cases, and in a very real sense it is tions have been investigated. -
The Somatic Mutation Landscape of the Human Body
bioRxiv preprint doi: https://doi.org/10.1101/668624; this version posted June 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. The somatic mutation landscape of the human body Pablo E. García-Nieto, Ashby J. Morrison, Hunter B. Fraser* Department of Biology, Stanford University, Stanford CA *Correspondence: [email protected] ABSTRACT Somatic mutations in healthy tissues contribute to aging, neurodegeneration, and cancer initiation, yet remain largely uncharacterized. To gain a better understanding of their distribution and functional impacts, we leveraged the genomic information contained in the transcriptome to uniformly call somatic mutations from over 7,500 tissue samples, representing 36 distinct tissues. This catalog, containing over 280,000 mutations, revealed a wide diversity of tissue- specific mutation profiles associated with gene expression levels and chromatin states. We found pervasive negative selection acting on missense and nonsense mutations, except for mutations previously observed in cancer samples, which were under positive selection and were highly enriched in many healthy tissues. These findings reveal fundamental patterns of tissue-specific somatic evolution and shed light on aging and the earliest stages of tumorigenesis. INTRODUCTION In humans, somatic mutations play a key role in senescence and tumorigenesis1. Pioneering work on somatic evolution in cancer has led to the characterization of cancer driver genes2 and mutation signatures3; the interplay between chromatin, nuclear architecture, carcinogens and the mutational landscape4–7; the evolutionary forces acting on somatic mutations8–11; and clinical implications of somatic mutations12.