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Eshel M, Milon B, Hertzano R, Elkon R. The cells of the sensory epithelium, and not the stria vascularis, are the main cochlear cells related to the genetic pathogenesis of age-related hearing loss. Am J Hum Genet 2024; 111:614-617. [PMID: 38330941 PMCID: PMC10940011 DOI: 10.1016/j.ajhg.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
Age-related hearing loss (ARHL) is a major health concern among the elderly population. It is hoped that increasing our understanding of its underlying pathophysiological processes will lead to the development of novel therapies. Recent genome-wide association studies (GWASs) discovered a few dozen genetic variants in association with elevated risk for ARHL. Integrated analysis of GWAS results and transcriptomics data is a powerful approach for elucidating specific cell types that are involved in disease pathogenesis. Intriguingly, recent studies that applied such bioinformatics approaches to ARHL resulted in disagreeing findings as for the key cell types that are most strongly linked to the genetic pathogenesis of ARHL. These conflicting studies pointed either to cochlear sensory epithelial or to stria vascularis cells as the cell types most prominently involved in the genetic basis of ARHL. Seeking to resolve this discrepancy, we integrated the analysis of four ARHL GWAS datasets with four independent inner-ear single-cell RNA-sequencing datasets. Our analysis clearly points to the cochlear sensory epithelial cells as the key cells for the genetic predisposition to ARHL. We also explain the limitation of the bioinformatics analysis performed by previous studies that led to missing the enrichment for ARHL GWAS signal in sensory epithelial cells. Collectively, we show that cochlear epithelial cells, not stria vascularis cells, are the main inner-ear cells related to the genetic pathogenesis of ARHL.
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Affiliation(s)
- Mai Eshel
- Department of Human Molecular Genetics and Biochemistry, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Beatrice Milon
- Neurotology Branch, NIDCD, National Institutes of Health, Bethesda, MD, USA
| | - Ronna Hertzano
- Neurotology Branch, NIDCD, National Institutes of Health, Bethesda, MD, USA.
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Levi H, Elkon R, Shamir R. The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population. Bioinformatics 2024; 40:btae036. [PMID: 38265251 PMCID: PMC10868313 DOI: 10.1093/bioinformatics/btae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/20/2023] [Accepted: 01/20/2024] [Indexed: 01/25/2024] Open
Abstract
MOTIVATION Polygenic risk scores (PRSs) predict individuals' genetic risk of developing complex diseases. They summarize the effect of many variants discovered in genome-wide association studies (GWASs). However, to date, large GWASs exist primarily for the European population and the quality of PRS prediction declines when applied to other ethnicities. Genetic profiling of individuals in the discovery set (on which the GWAS was performed) and target set (on which the PRS is applied) is typically done by SNP arrays that genotype a fraction of common SNPs. Therefore, a key step in GWAS analysis and PRS calculation is imputing untyped SNPs using a panel of fully sequenced individuals. The imputation results depend on the ethnic composition of the imputation panel. Imputing genotypes with a panel of individuals of the same ethnicity as the genotyped individuals typically improves imputation accuracy. However, there has been no systematic investigation into the influence of the ethnic composition of imputation panels on the accuracy of PRS predictions when applied to ethnic groups that differ from the population used in the GWAS. RESULTS We estimated the effect of imputation of the target set on prediction accuracy of PRS when the discovery and the target sets come from different ethnic groups. We analyzed binary phenotypes on ethnically distinct sets from the UK Biobank and other resources. We generated ethnically homogenous panels, imputed the target sets, and generated PRSs. Then, we assessed the prediction accuracy obtained from each imputation panel. Our analysis indicates that using an imputation panel matched to the ethnicity of the target population yields only a marginal improvement and only under specific conditions. AVAILABILITY AND IMPLEMENTATION The source code used for executing the analyses is this paper is available at https://github.com/Shamir-Lab/PRS-imputation-panels.
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Affiliation(s)
- Hagai Levi
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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3
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Levi H, Carmi S, Rosset S, Yerushalmi R, Zick A, Yablonski-Peretz T, Wang Q, Bolla MK, Dennis J, Michailidou K, Lush M, Ahearn T, Andrulis IL, Anton-Culver H, Antoniou AC, Arndt V, Augustinsson A, Auvinen P, Beane Freeman L, Beckmann M, Behrens S, Bermisheva M, Bodelon C, Bogdanova NV, Bojesen SE, Brenner H, Byers H, Camp N, Castelao J, Chang-Claude J, Chirlaque MD, Chung W, Clarke C, Collee MJ, Colonna S, Couch F, Cox A, Cross SS, Czene K, Daly M, Devilee P, Dork T, Dossus L, Eccles DM, Eliassen AH, Eriksson M, Evans G, Fasching P, Fletcher O, Flyger H, Fritschi L, Gabrielson M, Gago-Dominguez M, García-Closas M, Garcia-Saenz JA, Genkinger J, Giles GG, Goldberg M, Guénel P, Hall P, Hamann U, He W, Hillemanns P, Hollestelle A, Hoppe R, Hopper J, Jakovchevska S, Jakubowska A, Jernström H, John E, Johnson N, Jones M, Vijai J, Kaaks R, Khusnutdinova E, Kitahara C, Koutros S, Kristensen V, Kurian AW, Lacey J, Lambrechts D, Le Marchand L, Lejbkowicz F, Lindblom A, Loibl S, Lori A, Lubinski J, Mannermaa A, Manoochehri M, Mavroudis D, Menon U, Mulligan A, Murphy R, Nevelsteen I, Newman WG, Obi N, O'Brien K, Offit K, Olshan A, Plaseska-Karanfilska D, Olson J, Panico S, Park-Simon TW, Patel A, Peterlongo P, Rack B, Radice P, Rennert G, Rhenius V, Romero A, Saloustros E, Sandler D, Schmidt MK, Schwentner L, Shah M, Sharma P, Simard J, Southey M, Stone J, Tapper WJ, Taylor J, Teras L, Toland AE, Troester M, Truong T, van der Kolk LE, Weinberg C, Wendt C, Yang XR, Zheng W, Ziogas A, Dunning AM, Pharoah P, Easton DF, Ben-Sachar S, Elefant N, Shamir R, Elkon R. Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel. J Med Genet 2023; 60:1186-1197. [PMID: 37451831 PMCID: PMC10715538 DOI: 10.1136/jmg-2023-109185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/28/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Polygenic risk score (PRS), calculated based on genome-wide association studies (GWASs), can improve breast cancer (BC) risk assessment. To date, most BC GWASs have been performed in individuals of European (EUR) ancestry, and the generalisation of EUR-based PRS to other populations is a major challenge. In this study, we examined the performance of EUR-based BC PRS models in Ashkenazi Jewish (AJ) women. METHODS We generated PRSs based on data on EUR women from the Breast Cancer Association Consortium (BCAC). We tested the performance of the PRSs in a cohort of 2161 AJ women from Israel (1437 cases and 724 controls) from BCAC (BCAC cohort from Israel (BCAC-IL)). In addition, we tested the performance of these EUR-based BC PRSs, as well as the established 313-SNP EUR BC PRS, in an independent cohort of 181 AJ women from Hadassah Medical Center (HMC) in Israel. RESULTS In the BCAC-IL cohort, the highest OR per 1 SD was 1.56 (±0.09). The OR for AJ women at the top 10% of the PRS distribution compared with the middle quintile was 2.10 (±0.24). In the HMC cohort, the OR per 1 SD of the EUR-based PRS that performed best in the BCAC-IL cohort was 1.58±0.27. The OR per 1 SD of the commonly used 313-SNP BC PRS was 1.64 (±0.28). CONCLUSIONS Extant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC and therefore hold promise for improving BC risk assessment in AJ women.
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Grants
- R01 CA176785 NCI NIH HHS
- NU58DP006344 NCCDPHP CDC HHS
- R37 CA070867 NCI NIH HHS
- HHSN261201800015I NCI NIH HHS
- R01 CA064277 NCI NIH HHS
- P50 CA116201 NCI NIH HHS
- G1000143 Medical Research Council
- P30 CA062203 NCI NIH HHS
- HHSN261201800015C NCI NIH HHS
- R01 CA047305 NCI NIH HHS
- HHSN261201800009I NCI NIH HHS
- R01 CA163353 NCI NIH HHS
- UM1 CA164917 NCI NIH HHS
- U01 CA199277 NCI NIH HHS
- U01 CA179715 NCI NIH HHS
- HHSN261201800032C NCI NIH HHS
- U54 CA156733 NCI NIH HHS
- HHSN261201800009C NCI NIH HHS
- Z01 CP010119 Intramural NIH HHS
- UM1 CA164973 NCI NIH HHS
- P01 CA087969 NCI NIH HHS
- UM1 CA164920 NCI NIH HHS
- NU58DP006320 CDC HHS
- UM1 CA176726 NCI NIH HHS
- R01 CA092447 NCI NIH HHS
- Z01 ES049030 Intramural NIH HHS
- R01 CA058860 NCI NIH HHS
- K07 CA092044 NCI NIH HHS
- HHSN261201800016C NCI NIH HHS
- P50 CA058223 NCI NIH HHS
- R01 CA100374 NCI NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 CA128978 NCI NIH HHS
- R01 CA047147 NCI NIH HHS
- U19 CA148537 NCI NIH HHS
- R01 CA116167 NCI NIH HHS
- R01 CA148667 NCI NIH HHS
- R01 CA063464 NCI NIH HHS
- HHSN261201800016I NCI NIH HHS
- UM1 CA186107 NCI NIH HHS
- P30 CA023100 NCI NIH HHS
- U01 CA063464 NCI NIH HHS
- R01 CA077398 NCI NIH HHS
- R01 CA054281 NCI NIH HHS
- R01 CA132839 NCI NIH HHS
- P30 CA068485 NCI NIH HHS
- U01 CA058860 NCI NIH HHS
- U01 CA164920 NCI NIH HHS
- R35 CA253187 NCI NIH HHS
- 14136 Cancer Research UK
- U19 CA148112 NCI NIH HHS
- HHSN261201800032I NCI NIH HHS
- U01 CA098758 NCI NIH HHS
- Z01 ES044005 Intramural NIH HHS
- U19 CA148065 NCI NIH HHS
- P30 CA033572 NCI NIH HHS
- R01 CA069664 NCI NIH HHS
- Wellcome Trust
- 001 World Health Organization
- Z01 ES049033 Intramural NIH HHS
- R01 CA192393 NCI NIH HHS
- U01 CA164973 NCI NIH HHS
- R37 CA054281 NCI NIH HHS
- Consellería de Industria Programa Sectorial de Investigación Aplicada
- Statistics Netherlands
- South Eastern Norway Health Authority
- Lower Saxonian Cancer Society
- Lise Boserup Fund
- Heidelberger Zentrum für Personalisierte Onkologie Deutsches Krebsforschungszentrum In Der Helmholtz-Gemeinschaft
- Lon V. Smith Foundation
- Scottish Funding Council
- Komen Foundation
- Claudia von Schilling Foundation for Breast Cancer Research
- Russian Foundation for Basic Research
- Ligue Contre le Cancer
- Sigrid Juselius Foundation
- Kuopion Yliopistollinen Sairaala
- Sheffield Experimental Cancer Medicine Centre
- Stockholm läns landsting
- Department of Health and Human Services (USA)
- Department of Defence (USA)
- Stichting Tegen Kanker
- David F. and Margaret T. Grohne Family Foundation
- Sundhed og Sygdom, Det Frie Forskningsråd
- Stavros Niarchos Foundation
- Post-Cancer GWAS initiative
- Institute of the Ruhr University Bochum
- Instituto de Salud Carlos III
- Institute of Cancer Research
- Public Health Institute
- Fondation du cancer du sein du Québec
- Institut National de la Santé et de la Recherche Médicale
- Pink Ribbon
- Institute for Prevention and Occupational Medicine
- K.G. Jebsen Centre for Breast Cancer Research
- Research Centre for Genetic Engineering and Biotechnology
- Center of Excellence (Finland)
- Robert and Kate Niehaus Clinical Cancer Genetics Initiative
- Rudolf Bartling Foundation
- Center for Disease Control and Prevention (USA)
- Karolinska Institutet
- Norges Forskningsråd
- Robert Bosch Stiftung
- Intramural Research Funds of the National Cancer Institute (USA)
- Regional Governments of Andalucía, Asturias, Basque Country, Murcia and Navarra, ISCIII RETIC
- Intramural Research Program of the Division of Cancer Epidemiology and Genetics
- Centre International de Recherche sur le Cancer
- Queensland Cancer Fund
- Red Temática de Investigación Cooperativa en Cáncer
- Intramural Research Program of the National Institutes of Health
- National Health Service (UK)
- Ministerie van Volksgezondheid, Welzijn en Sport
- National cancer institute (USA)
- KWF Kankerbestrijding
- Märit and Hans Rausings Initiative Against Breast Cancer
- Associazione Italiana per la Ricerca sul Cancro
- Fundación Científica Asociación Española Contra el Cáncer
- ERC advanced grant
- Australian National Health and Medical Research Council
- Agence Nationale de la Recherche
- Dutch Prevention Funds,
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail
- American Cancer Society
- Dutch Zorg Onderzoek
- Alexander von Humboldt-Stiftung
- Ministerio de Economia y Competitividad (Spain)
- Ministère du Développement Économique, de l’Innovation et de l’Exportation
- Susan G. Komen for the Cure
- Minister of Science and Higher Education
- Medical Research Council UK
- Ministry of Science and Higher Education of the Russian Federation
- Ministry of Science and Higher Education (Sweden)
- Against Breast Cancer
- Mutuelle Générale de l’Education Nationale
- Academy of Finland
- Deutsche Krebshilfe e.V.
- Dietmar-Hopp Foundation,
- Division of Cancer Prevention, National Cancer Institute
- Deutsche Krebshilfe
- World Cancer Research Fund
- Genome Québec
- National Cancer Institute’s Surveillance, Epidemiology and End Results Program
- Breast Cancer Campaign
- National Cancer Research Network
- Berta Kamprad Foundation FBKS
- Bert von Kantzows foundation
- Biomedical Research Centre at Guy’s and St Thomas
- Genome Canada
- Freistaat Sachsen
- Biobanking and Biomolecular Resources Research Infrastructure
- Friends of Hannover Medical School
- Breast Cancer Research Foundation
- California Department of Public Health
- Government of Russian Federation
- Deutsche Forschungsgemeinschaft
- National Institute for Health and Care Research
- National Health and Medical Research Council (Australia)
- German Federal Ministry of Research and Education
- National Institute of Environmental Health Sciences
- Breast Cancer Now
- Seventh Framework Programme
- Transcan
- Centrum för idrottsforskning
- UK National Institute for Health Research Biomedical Research Centre
- University of Crete
- National Breast Cancer Foundation (Finland)
- European Regional Development Fund
- National Breast Cancer Foundation (Australia)
- United States Army Medical Research and Materiel Command
- EU Horizon 2020 Research and Innovation Programme
- Directorate-General XII, Science, Research, and Development
- Baden Württemberg Ministry of Science, Research and Arts
- VicHealth
- Fondo de Investigación Sanitario
- Victorian Breast Cancer Research Consortium.
- Finnish Cancer Foundation
- University of Southern California San Francisco
- Fomento de la Investigación Clínica Independiente
- the Cancer Biology Research Center (CBRC), Djerassi Oncology Center
- Bundesministerium für Bildung und Forschung
- Cancerfonden
- Tel Aviv University Center for AI and Data Science
- University of Oulu
- National Breast Cancer Foundation (JS)
- Safra Center for Bioinformatics
- Fondation de France, Institut National du Cancer
- Israeli Science Foundation
- University of Utah
- National Cancer Center Research and Development Fund (Japan)
- Chief Scientist Office, Scottish Government Health and Social Care Directorate
- Oak Foundation
- Health Research Fund (FIS)
- Ontario Familial Breast Cancer Registry
- New South Wales Cancer Council
- North Carolina University Cancer Research Fund
- Kreftforeningen
- Northern California Breast Cancer Family Registry
- Institut Gustave Roussy
- Huntsman Cancer Institute, University of Utah
- Ovarian Cancer Research Fund
- NIHR Oxford Biomedical Research Centre
- Hellenic Health Foundation
- Oulun Yliopistollinen Sairaala
- Helmholtz Society
- Herlev and Gentofte Hospital
- PSRSIIRI-701
- Helsinki University Hospital Research Fund
- Cancer Council Victoria
- National Research Council (Italy)
- Cancer Council Tasmania
- Cancer Council Western Australia
- Hamburger Krebsgesellschaft
- Gustav V Jubilee foundation
- National Program of Cancer Registries
- Canadian Cancer Society
- Cancer Council South Australia
- Canadian Institutes of Health Research
- Cancer Council NSW
- Guy's & St. Thomas' NHS Foundation Trust
- Netherlands Organisation of Scientific Research
- Cancer Institute NSW
- National Institutes of Health (USA)
- National Research Foundation of Korea
- Syöpäsäätiö
- Cancer Foundation of Western Australia
- Netherlands Cancer Registry (NKR),
- Cancer Fund of North Savo
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Affiliation(s)
- Hagai Levi
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Saharon Rosset
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
| | - Rinat Yerushalmi
- Institute of Oncology, Davidoff Cancer Center, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aviad Zick
- Department of oncology, Hadassah Medical Center, Jerusalem, Israel
- Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Yablonski-Peretz
- Department of oncology, Hadassah Medical Center, Jerusalem, Israel
- Hebrew University of Jerusalem, Jerusalem, Israel
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annelie Augustinsson
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Päivi Auvinen
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, Kuopio, Finland
- Department of Oncology, Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Laura Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthias Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Clara Bodelon
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hamburg, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Helen Byers
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Nicola Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt lake city, UT, USA
| | - Jose Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Christine Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Margriet J Collee
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Netherlands
| | - Sarah Colonna
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt lake city, UT, USA
| | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Department of Oncology and Metabolism, Sheffield Institute for Nucleic Acids (SInFoNiA), University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
- Department of Human Genetics, Leiden University Medical, Leiden, Netherlands
| | - Thilo Dork
- Gynaecology Research Unit, Hannover Medical School, Hamburg, Germany
| | - Laure Dossus
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Diana M Eccles
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gareth Evans
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Lin Fritschi
- School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Jeanine Genkinger
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, New York, New York, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Mark Goldberg
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, QU, Canada
| | - Pascal Guénel
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Hillemanns
- Gynaecology Research Unit, Hannover Medical School, Hamburg, Germany
| | | | - Reiner Hoppe
- Dr Margarete Fischer Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tubingen, Germany
| | - John Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Simona Jakovchevska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Skopje, North Macedonia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Helena Jernström
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Esther John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nichola Johnson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Michael Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Joseph Vijai
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Cari Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vessela Kristensen
- Institute of Clinical Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Allison W Kurian
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - James Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Flavio Lejbkowicz
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Annika Lindblom
- Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Usha Menon
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College, London, UK
| | - AnnaMarie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Rachel Murphy
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Ines Nevelsteen
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - William G Newman
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Nadia Obi
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katie O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Ken Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Olshan
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Janet Olson
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Salvatore Panico
- Dipertimento Di Medicina Clinca e Chirurgia, Federico II University, Naples, Italy
| | | | - Alpa Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Brigitte Rack
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Valerie Rhenius
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Atocha Romero
- Laboratorio de Oncología Molecular, Hospital Clínico San Carlos, Madrid, Spain
| | | | - Dale Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Lukas Schwentner
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, USA
| | - Jacques Simard
- Genomics Center, Molecular Medicine, Université Laval, Quebec, Quebec, Canada
| | - Melissa Southey
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia, Perth, Western Australia, Australia
| | - William J Tapper
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jack Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Lauren Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Melissa Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | | | - Clarice Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Camilla Wendt
- Department of Clinical Science and Education, Karolinska Institutet, Stockholm, Sweden
| | - Xiaohong Rose Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Argyrios Ziogas
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Shay Ben-Sachar
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Clalit Research Institute, Clalit Health Services, Ramat Gan, Israel
| | - Naama Elefant
- Clalit Research Institute, Clalit Health Services, Ramat Gan, Israel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
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4
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Kennedy CL, Shuster B, Amanipour R, Milon B, Patel P, Elkon R, Hertzano R. Metformin Protects Against Noise-Induced Hearing Loss in Male Mice. Otol Neurotol 2023; 44:956-963. [PMID: 37641232 PMCID: PMC10510802 DOI: 10.1097/mao.0000000000004002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
HYPOTHESIS Metformin treatment will protect mice from noise-induced hearing loss (NIHL). BACKGROUND We recently identified metformin as the top-ranking, Food and Drug Administration-approved drug to counter inner ear molecular changes induced by permanent threshold shift-inducing noise. This study is designed to functionally test metformin as a potential otoprotective drug against NIHL. METHODS Male and female B6CBAF1/J mice were obtained at 7 to 8 weeks of age. A cohort of the females underwent ovariectomy to simulate menopause and eliminate the effect of ovarian-derived estrogens. At 10 weeks of age, mice underwent a permanent threshold shift-inducing noise exposure (102.5 or 105 dB SPL, 8-16 kHz, 2 h). Auditory brainstem response (ABR) thresholds were obtained at baseline, 24 h after noise exposure, and 1 week after noise exposure. Mice were administered metformin (200 mg/kg/d) or a saline control in their drinking water after the baseline ABR and for the remainder of the study. After the 1-week ABR, mice were euthanized and cochlear tissue was analyzed. RESULTS Metformin treatment reduced the 1-week ABR threshold shift at 16 kHz ( p < 0.01; d = 1.20) and 24 kHz ( p < 0.01; d = 1.15) as well as outer hair cell loss in the 32-45.5 kHz range ( p < 0.0001; d = 2.37) in male mice. In contrast, metformin treatment did not prevent hearing loss or outer hair cell loss in the intact or ovariectomized female mice. CONCLUSIONS Metformin exhibits sex-dependent efficacy as a therapeutic for NIHL. These data compel continued investigation into metformin's protective effects and demonstrate the importance of evaluating the therapeutic efficacy of drugs in subjects of both sexes.
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Affiliation(s)
- Catherine L. Kennedy
- Department of Otorhinolaryngology–Head and Neck Surgery, University of Maryland School of Medicine, Baltimore
| | - Benjamin Shuster
- Neurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Reza Amanipour
- Neurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Beatrice Milon
- Neurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Priya Patel
- Department of Otorhinolaryngology–Head and Neck Surgery, University of Maryland School of Medicine, Baltimore
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronna Hertzano
- Department of Otorhinolaryngology–Head and Neck Surgery, University of Maryland School of Medicine, Baltimore
- Neurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
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5
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Ovadia S, Cui G, Elkon R, Cohen-Gulkar M, Zuk-Bar N, Tuoc T, Jing N, Ashery-Padan R. SWI/SNF complexes are required for retinal pigmented epithelium differentiation and for the inhibition of cell proliferation and neural differentiation programs. Development 2023; 150:dev201488. [PMID: 37522516 PMCID: PMC10482007 DOI: 10.1242/dev.201488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 07/14/2023] [Indexed: 08/01/2023]
Abstract
During embryonic development, tissue-specific transcription factors and chromatin remodelers function together to ensure gradual, coordinated differentiation of multiple lineages. Here, we define this regulatory interplay in the developing retinal pigmented epithelium (RPE), a neuroectodermal lineage essential for the development, function and maintenance of the adjacent retina. We present a high-resolution spatial transcriptomic atlas of the developing mouse RPE and the adjacent ocular mesenchyme obtained by geographical position sequencing (Geo-seq) of a single developmental stage of the eye that encompasses young and more mature ocular progenitors. These transcriptomic data, available online, reveal the key transcription factors and their gene regulatory networks during RPE and ocular mesenchyme differentiation. Moreover, conditional inactivation followed by Geo-seq revealed that this differentiation program is dependent on the activity of SWI/SNF complexes, shown here to control the expression and activity of RPE transcription factors and, at the same time, inhibit neural progenitor and cell proliferation genes. The findings reveal the roles of the SWI/SNF complexes in controlling the intersection between RPE and neural cell fates and the coupling of cell-cycle exit and differentiation.
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Affiliation(s)
- Shai Ovadia
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guizhong Cui
- Guangzhou National Laboratory, Department of Basic Research, Guangzhou 510005, China
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mazal Cohen-Gulkar
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nitay Zuk-Bar
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tran Tuoc
- Department of Human Genetics, Ruhr University of Bochum, 44791 Bochum, Germany
| | - Naihe Jing
- Guangzhou National Laboratory, Department of Basic Research, Guangzhou 510005, China
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
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6
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Haj M, Levon A, Frey Y, Hourvitz N, Campisi J, Tzfati Y, Elkon R, Ziv Y, Shiloh Y. Accelerated replicative senescence of ataxia-telangiectasia skin fibroblasts is retained at physiologic oxygen levels, with unique and common transcriptional patterns. Aging Cell 2023; 22:e13869. [PMID: 37254625 PMCID: PMC10410012 DOI: 10.1111/acel.13869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
The genetic disorder, ataxia-telangiectasia (A-T), is caused by loss of the homeostatic protein kinase, ATM, and combines genome instability, tissue degeneration, cancer predisposition, and premature aging. Primary fibroblasts from A-T patients exhibit premature senescence when grown at ambient oxygen concentration (21%). Here, we show that reducing oxygen concentration to a physiological level range (3%) dramatically extends the proliferative lifespan of human A-T skin fibroblasts. However, they still undergo senescence earlier than control cells grown under the same conditions and exhibit high genome instability. Comparative RNA-seq analysis of A-T and control fibroblasts cultured at 3% oxygen followed by cluster analysis of differentially expressed genes and functional enrichment analysis, revealed distinct transcriptional dynamics in A-T fibroblasts senescing in physiological oxygen concentration. While some transcriptional patterns were similar to those observed during replicative senescence of control cells, others were unique to the senescing A-T cells. We observed in them a robust activation of interferon-stimulated genes, with undetected expression the interferon genes themselves. This finding suggests an activation of a non-canonical cGAS-STING-mediated pathway, which presumably responds to cytosolic DNA emanating from extranuclear micronuclei detected in these cells. Senescing A-T fibroblasts also exhibited a marked, intriguely complex alteration in the expression of genes associated with extracellular matrix (ECM) remodeling. Notably, many of the induced ECM genes encode senescence-associated secretory phenotype (SASP) factors known for their paracrine pro-fibrotic effects. Our data provide a molecular dimension to the segmental premature aging observed in A-T patients and its associated symptoms, which develop as the patients advance in age.
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Affiliation(s)
- Majd Haj
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Amit Levon
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Yann Frey
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Noa Hourvitz
- The Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | | | - Yehuda Tzfati
- The Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Ran Elkon
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Yael Ziv
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Yosef Shiloh
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
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7
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Markovits E, Harush O, Baruch EN, Shulman ED, Debby A, Itzhaki O, Anafi L, Danilevsky A, Shomron N, Ben-Betzalel G, Asher N, Shapira-Frommer R, Schachter J, Barshack I, Geiger T, Elkon R, Besser MJ, Markel G. MYC Induces Immunotherapy and IFNγ Resistance Through Downregulation of JAK2. Cancer Immunol Res 2023; 11:909-924. [PMID: 37074069 DOI: 10.1158/2326-6066.cir-22-0184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 11/27/2022] [Accepted: 04/17/2023] [Indexed: 04/20/2023]
Abstract
Immunotherapy has revolutionized the treatment of advanced melanoma. Because the pathways mediating resistance to immunotherapy are largely unknown, we conducted transcriptome profiling of preimmunotherapy tumor biopsies from patients with melanoma that received PD-1 blockade or adoptive cell therapy with tumor-infiltrating lymphocytes. We identified two melanoma-intrinsic, mutually exclusive gene programs, which were controlled by IFNγ and MYC, and the association with immunotherapy outcome. MYC-overexpressing melanoma cells exhibited lower IFNγ responsiveness, which was linked with JAK2 downregulation. Luciferase activity assays, under the control of JAK2 promoter, demonstrated reduced activity in MYC-overexpressing cells, which was partly reversible upon mutagenesis of a MYC E-box binding site in the JAK2 promoter. Moreover, silencing of MYC or its cofactor MAX with siRNA increased JAK2 expression and IFNγ responsiveness of melanomas, while concomitantly enhancing the effector functions of T cells coincubated with MYC-overexpressing cells. Thus, we propose that MYC plays a pivotal role in immunotherapy resistance through downregulation of JAK2.
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Affiliation(s)
- Ettai Markovits
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Ortal Harush
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Erez N Baruch
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Eldad D Shulman
- Department of Human Molecular Genetics and Biochemistry, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Assaf Debby
- Institute of Pathology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel
| | - Orit Itzhaki
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Liat Anafi
- Institute of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - Artem Danilevsky
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Guy Ben-Betzalel
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Nethanel Asher
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Ronnie Shapira-Frommer
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Jacob Schachter
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Institute of Pathology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, Israel
- Felsenstein Medical Research Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, Israel
| | - Gal Markel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, Israel
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8
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Galves M, Sperber M, Amer-Sarsour F, Elkon R, Ashkenazi A. Transcriptional profiling of the response to starvation and fattening reveals differential regulation of autophagy genes in mammals. Proc Biol Sci 2023; 290:20230407. [PMID: 36987635 PMCID: PMC10050925 DOI: 10.1098/rspb.2023.0407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Nutrient deprivation (starvation) induced by fasting and hypercaloric regimens are stress factors that can influence cell and tissue homeostasis in mammals. One of the key cellular responses to changes in nutrient availability is the cell survival pathway autophagy. While there has been much research into the protein networks regulating autophagy, less is known about the gene expression networks involved in this fundamental process. Here, we applied a network algorithm designed to analyse omics datasets, to identify sub-networks that are enriched for induced genes in response to starvation. This enabled us to identify two prominent active modules, one composed of key stress-induced transcription factors, including members of the Jun, Fos and ATF families, and the other comprising autophagosome sub-network genes, including ULK1. The results were validated in the brain, liver and muscle of fasting mice. Moreover, differential expression analysis of autophagy genes in the brain, liver and muscle of high-fat diet-exposed mice showed significant suppression of GABARAPL1 in the liver. Finally, our data provide a resource that may facilitate the future identification of regulators of autophagy.
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Affiliation(s)
- Margarita Galves
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Michal Sperber
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Fatima Amer-Sarsour
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Avraham Ashkenazi
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, 6997801 Tel Aviv, Israel
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9
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Cohen-Gulkar M, David A, Messika-Gold N, Eshel M, Ovadia S, Zuk-Bar N, Idelson M, Cohen-Tayar Y, Reubinoff B, Ziv T, Shamay M, Elkon R, Ashery-Padan R. The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration. PLoS Biol 2023; 21:e3001924. [PMID: 36649236 PMCID: PMC9844853 DOI: 10.1371/journal.pbio.3001924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/16/2022] [Indexed: 01/18/2023] Open
Abstract
Tissue-specific transcription factors (TFs) control the transcriptome through an association with noncoding regulatory regions (cistromes). Identifying the combination of TFs that dictate specific cell fate, their specific cistromes and examining their involvement in complex human traits remain a major challenge. Here, we focus on the retinal pigmented epithelium (RPE), an essential lineage for retinal development and function and the primary tissue affected in age-related macular degeneration (AMD), a leading cause of blindness. By combining mechanistic findings in stem-cell-derived human RPE, in vivo functional studies in mice and global transcriptomic and proteomic analyses, we revealed that the key developmental TFs LHX2 and OTX2 function together in transcriptional module containing LDB1 and SWI/SNF (BAF) to regulate the RPE transcriptome. Importantly, the intersection between the identified LHX2-OTX2 cistrome with published expression quantitative trait loci, ATAC-seq data from human RPE, and AMD genome-wide association study (GWAS) data, followed by functional validation using a reporter assay, revealed a causal genetic variant that affects AMD risk by altering TRPM1 expression in the RPE through modulation of LHX2 transcriptional activity on its promoter. Taken together, the reported cistrome of LHX2 and OTX2, the identified downstream genes and interacting co-factors reveal the RPE transcription module and uncover a causal regulatory risk single-nucleotide polymorphism (SNP) in the multifactorial common blinding disease AMD.
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Affiliation(s)
- Mazal Cohen-Gulkar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Ahuvit David
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Naama Messika-Gold
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Mai Eshel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Shai Ovadia
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Nitay Zuk-Bar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Maria Idelson
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy and Department of Gynecology, Jerusalem, Israel
| | - Yamit Cohen-Tayar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Benjamin Reubinoff
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy and Department of Gynecology, Jerusalem, Israel
| | - Tamar Ziv
- Smoler Proteomics Center, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Meir Shamay
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (RE); (RAP)
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (RE); (RAP)
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10
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Bordeynik-Cohen M, Sperber M, Ebbers L, Messika-Gold N, Krohs C, Koffler-Brill T, Noy Y, Elkon R, Nothwang HG, Avraham KB. Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex. RNA Biol 2023; 20:629-640. [PMID: 37602850 PMCID: PMC10443965 DOI: 10.1080/15476286.2023.2247628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
The peripheral and central auditory subsystems together form a complex sensory network that allows an organism to hear. The genetic programs of the two subsystems must therefore be tightly coordinated during development. Yet, their interactions and common expression pathways have never been systematically explored. MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression and are essential for normal development of the auditory system. We performed mRNA and small-RNA sequencing of organs from both auditory subsystems at three critical developmental timepoints (E16, P0, P16) to obtain a comprehensive and unbiased insight of their expression profiles. Our analysis reveals common and organ-specific expression patterns for differentially regulated mRNAs and miRNAs, which could be clustered with a particular selection of functions such as inner ear development, Wnt signalling, K+ transport, and axon guidance, based on gene ontology. Bioinformatics detected enrichment of predicted targets of specific miRNAs in the clusters and predicted regulatory interactions by monitoring opposite trends of expression of miRNAs and their targets. This approach identified six miRNAs as strong regulatory candidates for both subsystems. Among them was miR-96, an established critical factor for proper development in both subsystems, demonstrating the strength of our approach. We suggest that other miRNAs identified by this analysis are also common effectors of proper hearing acquirement. This first combined comprehensive analysis of the developmental program of the peripheral and central auditory systems provides important data and bioinformatics insights into the shared genetic program of the two sensory subsystems and their regulation by miRNAs.
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Affiliation(s)
- Mor Bordeynik-Cohen
- Laboratory of Neural and Sensory Genomics, Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Michal Sperber
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lena Ebbers
- Neurogenetics group and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences and Research Center for Neurosensory Science, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Naama Messika-Gold
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Constanze Krohs
- Neurogenetics group and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences and Research Center for Neurosensory Science, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Tal Koffler-Brill
- Laboratory of Neural and Sensory Genomics, Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Yael Noy
- Laboratory of Neural and Sensory Genomics, Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hans Gerd Nothwang
- Neurogenetics group and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences and Research Center for Neurosensory Science, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Karen B. Avraham
- Laboratory of Neural and Sensory Genomics, Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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11
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Gulkar‐Cohen M, Messika N, David A, Idelson M, Cohen‐Tayar Y, Reubinoff B, Elkon R, Ashery‐Padan R. Retinal pigmented epithelium development from the perspective of transcription factors and cis‐regulatory elements. Acta Ophthalmol 2022. [DOI: 10.1111/j.1755-3768.2022.15476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mazal Gulkar‐Cohen
- Faculty of Medicine and Sagol School of Neuroscience Tel Aviv University Israel
| | - Naama Messika
- Faculty of Medicine and Sagol School of Neuroscience Tel Aviv University Israel
| | - Ahuvit David
- Faculty of Medicine and Sagol School of Neuroscience Tel Aviv University Israel
| | - Maria Idelson
- Faculty of Medicine and Sagol School of Neuroscience Tel Aviv University Israel
| | - Yamit Cohen‐Tayar
- Faculty of Medicine and Sagol School of Neuroscience Tel Aviv University Israel
| | - Benjamin Reubinoff
- Faculty of Medicine and Sagol School of Neuroscience Tel Aviv University Israel
| | - Ran Elkon
- Faculty of Medicine and Sagol School of Neuroscience Tel Aviv University Israel
| | - Ruth Ashery‐Padan
- Faculty of Medicine and Sagol School of Neuroscience Tel Aviv University Israel
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12
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Trpchevska N, Freidin MB, Broer L, Oosterloo BC, Yao S, Zhou Y, Vona B, Bishop C, Bizaki-Vallaskangas A, Canlon B, Castellana F, Chasman DI, Cherny S, Christensen K, Concas MP, Correa A, Elkon R, Mengel-From J, Gao Y, Giersch ABS, Girotto G, Gudjonsson A, Gudnason V, Heard-Costa NL, Hertzano R, Hjelmborg JVB, Hjerling-Leffler J, Hoffman HJ, Kaprio J, Kettunen J, Krebs K, Kähler AK, Lallemend F, Launer LJ, Lee IM, Leonard H, Li CM, Lowenheim H, Magnusson PKE, van Meurs J, Milani L, Morton CC, Mäkitie A, Nalls MA, Nardone GG, Nygaard M, Palviainen T, Pratt S, Quaranta N, Rämö J, Saarentaus E, Sardone R, Satizabal CL, Schweinfurth JM, Seshadri S, Shiroma E, Shulman E, Simonsick E, Spankovich C, Tropitzsch A, Lauschke VM, Sullivan PF, Goedegebure A, Cederroth CR, Williams FMK, Nagtegaal AP, Nelis M, Mägi R, Esko T. Genome-wide association meta-analysis identifies 48 risk variants and highlights the role of the stria vascularis in hearing loss. Am J Hum Genet 2022; 109:1077-1091. [PMID: 35580588 PMCID: PMC9247887 DOI: 10.1016/j.ajhg.2022.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/15/2022] [Indexed: 02/08/2023] Open
Abstract
Hearing loss is one of the top contributors to years lived with disability and is a risk factor for dementia. Molecular evidence on the cellular origins of hearing loss in humans is growing. Here, we performed a genome-wide association meta-analysis of clinically diagnosed and self-reported hearing impairment on 723,266 individuals and identified 48 significant loci, 10 of which are novel. A large proportion of associations comprised missense variants, half of which lie within known familial hearing loss loci. We used single-cell RNA-sequencing data from mouse cochlea and brain and mapped common-variant genomic results to spindle, root, and basal cells from the stria vascularis, a structure in the cochlea necessary for normal hearing. Our findings indicate the importance of the stria vascularis in the mechanism of hearing impairment, providing future paths for developing targets for therapeutic intervention in hearing loss.
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Affiliation(s)
- Natalia Trpchevska
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Maxim B Freidin
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Linda Broer
- Department of Internal Medicine, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Berthe C Oosterloo
- Department of Otorhinolaryngology, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany; Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany; Department of Otolaryngology-Head & Neck Surgery, University of Tübingen Medical Center, 72076 Tübingen, Germany
| | - Charles Bishop
- Department of Otolaryngology and Communicative Sciences, The University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Argyro Bizaki-Vallaskangas
- Department of Otolaryngology, University of Tampere, 33100 Tampere, Finland; Pirkanmaan Sairaanhoitopiiri, 33520 Tampere, Finland
| | - Barbara Canlon
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Fabio Castellana
- Unit of Data Sciences and Technology Innovation for Population Health, National Institute of Gastroenterology "Saverio de Bellis", Research Hospital, Castellana Grotte, 70124 Bari, Italy
| | - Daniel I Chasman
- Division of Preventative Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey Cherny
- Department of Anatomy and Anthropology and Department of Epidemiology and Preventive Medicine, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Kaare Christensen
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, 5000 Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark; Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense C, Denmark
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, 34127 Trieste, Italy
| | - Adolfo Correa
- Jackson Heart Study, The University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ran Elkon
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
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- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jonas Mengel-From
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, 5000 Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
| | - Yan Gao
- Jackson Heart Study, The University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Population Health Science, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Anne B S Giersch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Giorgia Girotto
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, 34127 Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, 34139 Trieste, Italy
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Nancy L Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA; Framingham Heart Study, Framingham, MA 01702, USA
| | - Ronna Hertzano
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland Baltimore, Baltimore, MD 21201, USA; Department of Anatomy and Neurobiology, University of Maryland Baltimore, Baltimore, MD 21201, USA; Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, MD 21201, USA
| | - Jacob V B Hjelmborg
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, 5000 Odense C, Denmark
| | - Jens Hjerling-Leffler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Howard J Hoffman
- Division of Scientific Programs, Epidemiology and Statistics Program, National Institute on Deafness and Other Communications Disorders (NIDCD), NIH, Bethesda, MD 20892, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland
| | - Johannes Kettunen
- Computational Medicine, Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90220 Oulu, Finland; Biocenter Oulu, University of Oulu, 90220 Oulu, Finland; Finnish Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Kristi Krebs
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anna K Kähler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Francois Lallemend
- Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program National Institute on Aging, Bethesda, MD 20892, USA
| | - I-Min Lee
- Division of Preventative Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hampton Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA
| | - Chuan-Ming Li
- Division of Scientific Programs, Epidemiology and Statistics Program, National Institute on Deafness and Other Communications Disorders (NIDCD), NIH, Bethesda, MD 20892, USA
| | - Hubert Lowenheim
- Department of Otolaryngology-Head & Neck Surgery, University of Tübingen Medical Center, 72076 Tübingen, Germany
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cynthia C Morton
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Manchester Centre for Audiology and Deafness, University of Manchester, Manchester M13 9PL, UK
| | - Antti Mäkitie
- Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA
| | | | - Marianne Nygaard
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, 5000 Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland
| | - Sheila Pratt
- Department of Communication Science & Disorders, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nicola Quaranta
- Otolaryngology Unit, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Joel Rämö
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland
| | - Rodolfo Sardone
- Unit of Data Sciences and Technology Innovation for Population Health, National Institute of Gastroenterology "Saverio de Bellis", Research Hospital, Castellana Grotte, 70124 Bari, Italy
| | - Claudia L Satizabal
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA; Framingham Heart Study, Framingham, MA 01702, USA; Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases and Department of Population Health Sciences, University of Texas Health Sciences Center, San Antonio, TX 78229, USA
| | - John M Schweinfurth
- Department of Otolaryngology and Communicative Sciences, The University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA; Framingham Heart Study, Framingham, MA 01702, USA; Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases and Department of Population Health Sciences, University of Texas Health Sciences Center, San Antonio, TX 78229, USA
| | - Eric Shiroma
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Baltimore, MD 21224, USA
| | - Eldad Shulman
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Eleanor Simonsick
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Christopher Spankovich
- Department of Otolaryngology and Communicative Sciences, The University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Anke Tropitzsch
- Department of Otolaryngology-Head & Neck Surgery, University of Tübingen Medical Center, 72076 Tübingen, Germany
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Genetics, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Andre Goedegebure
- Department of Otorhinolaryngology, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Christopher R Cederroth
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden; National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Ropewalk House, NG1 5DU Nottingham, UK; Hearing Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, NG7 2UH Nottingham, UK.
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Andries Paul Nagtegaal
- Department of Otorhinolaryngology, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
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13
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Groenewoud D, Shye A, Elkon R. Incorporating regulatory interactions into gene-set analyses for GWAS data: A controlled analysis with the MAGMA tool. PLoS Comput Biol 2022; 18:e1009908. [PMID: 35316269 PMCID: PMC8939811 DOI: 10.1371/journal.pcbi.1009908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/09/2022] [Indexed: 11/29/2022] Open
Abstract
To date, genome-wide association studies have identified thousands of statistically-significant associations between genetic variants, and phenotypes related to a myriad of traits and diseases. A key goal for human-genetics research is to translate these associations into functional mechanisms. Popular gene-set analysis tools, like MAGMA, map variants to genes they might affect, and then integrate genome-wide association study data (that is, variant-level associations for a phenotype) to score genes for association with a phenotype. Gene scores are subsequently used in competitive gene-set analyses to identify biological processes that are enriched for phenotype association. By default, variants are mapped to genes in their proximity. However, many variants that affect phenotypes are thought to act at regulatory elements, which can be hundreds of kilobases away from their target genes. Thus, we explored the idea of augmenting a proximity-based mapping scheme with publicly-available datasets of regulatory interactions. We used MAGMA to analyze genome-wide association study data for ten different phenotypes, and evaluated the effects of augmentation by comparing numbers, and identities, of genes and gene sets detected as statistically significant between mappings. We detected several pitfalls and confounders of such “augmented analyses”, and introduced ways to control for them. Using these controls, we demonstrated that augmentation with datasets of regulatory interactions only occasionally strengthened the enrichment for phenotype association amongst (biologically-relevant) gene sets for different phenotypes. Still, in such cases, genes and regulatory elements responsible for the improvement could be pinpointed. For instance, using brain regulatory-interactions for augmentation, we were able to implicate two acetylcholine receptor subunits involved in post-synaptic chemical transmission, namely CHRNB2 and CHRNE, in schizophrenia. Collectively, our study presents a critical approach for integrating regulatory interactions into gene-set analyses for genome-wide association study data, by introducing various controls to distinguish genuine results from spurious discoveries.
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Affiliation(s)
- David Groenewoud
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Avinoam Shye
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
- * E-mail:
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14
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Tammer L, Hameiri O, Keydar I, Roy VR, Ashkenazy-Titelman A, Custódio N, Sason I, Shayevitch R, Rodríguez-Vaello V, Rino J, Lev Maor G, Leader Y, Khair D, Aiden EL, Elkon R, Irimia M, Sharan R, Shav-Tal Y, Carmo-Fonseca M, Ast G. Gene architecture directs splicing outcome in separate nuclear spatial regions. Mol Cell 2022; 82:1021-1034.e8. [PMID: 35182478 DOI: 10.1016/j.molcel.2022.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
Abstract
How the splicing machinery defines exons or introns as the spliced unit has remained a puzzle for 30 years. Here, we demonstrate that peripheral and central regions of the nucleus harbor genes with two distinct exon-intron GC content architectures that differ in the splicing outcome. Genes with low GC content exons, flanked by long introns with lower GC content, are localized in the periphery, and the exons are defined as the spliced unit. Alternative splicing of these genes results in exon skipping. In contrast, the nuclear center contains genes with a high GC content in the exons and short flanking introns. Most splicing of these genes occurs via intron definition, and aberrant splicing leads to intron retention. We demonstrate that the nuclear periphery and center generate different environments for the regulation of alternative splicing and that two sets of splicing factors form discrete regulatory subnetworks for the two gene architectures. Our study connects 3D genome organization and splicing, thus demonstrating that exon and intron definition modes of splicing occur in different nuclear regions.
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Affiliation(s)
- Luna Tammer
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ofir Hameiri
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ifat Keydar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Vanessa Rachel Roy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Asaf Ashkenazy-Titelman
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Noélia Custódio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Itay Sason
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ronna Shayevitch
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Victoria Rodríguez-Vaello
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain, ICREA, Barcelona, Spain
| | - José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Galit Lev Maor
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Yodfat Leader
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Doha Khair
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain, ICREA, Barcelona, Spain
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel.
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15
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Levi H, Rahmanian N, Elkon R, Shamir R. The DOMINO web-server for active module identification analysis. Bioinformatics 2022; 38:2364-2366. [PMID: 35139202 PMCID: PMC9004647 DOI: 10.1093/bioinformatics/btac067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/06/2022] [Accepted: 02/01/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Active module identification (AMI) is an essential step in many omics analyses. Such algorithms receive a gene network and a gene activity profile as input and report subnetworks that show significant over-representation of accrued activity signal ('active modules'). Such modules can point out key molecular processes in the analyzed biological conditions. RESULTS We recently introduced a novel AMI algorithm called DOMINO and demonstrated that it detects active modules that capture biological signals with markedly improved rate of empirical validation. Here, we provide an online server that executes DOMINO, making it more accessible and user-friendly. To help the interpretation of solutions, the server provides GO enrichment analysis, module visualizations and accessible output formats for customized downstream analysis. It also enables running DOMINO with various gene identifiers of different organisms. AVAILABILITY AND IMPLEMENTATION The server is available at http://domino.cs.tau.ac.il. Its codebase is available at https://github.com/Shamir-Lab.
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Affiliation(s)
- Hagai Levi
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Ran Elkon
- To whom correspondence should be addressed. or
| | - Ron Shamir
- To whom correspondence should be addressed. or
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16
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Hait TA, Elkon R, Shamir R. CT-FOCS: a novel method for inferring cell type-specific enhancer–promoter maps. Nucleic Acids Res 2022; 50:e55. [PMID: 35100425 PMCID: PMC9178001 DOI: 10.1093/nar/gkac048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/09/2022] [Accepted: 01/15/2022] [Indexed: 11/13/2022] Open
Abstract
Spatiotemporal gene expression patterns are governed to a large extent by the activity of enhancer elements, which engage in physical contacts with their target genes. Identification of enhancer–promoter (EP) links that are functional only in a specific subset of cell types is a key challenge in understanding gene regulation. We introduce CT-FOCS (cell type FOCS), a statistical inference method that uses linear mixed effect models to infer EP links that show marked activity only in a single or a small subset of cell types out of a large panel of probed cell types. Analyzing 808 samples from FANTOM5, covering 472 cell lines, primary cells and tissues, CT-FOCS inferred such EP links more accurately than recent state-of-the-art methods. Furthermore, we show that strictly cell type-specific EP links are very uncommon in the human genome.
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Affiliation(s)
- Tom Aharon Hait
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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17
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Udagawa T, Atkinson PJ, Milon B, Abitbol JM, Song Y, Sperber M, Huarcaya Najarro E, Scheibinger M, Elkon R, Hertzano R, Cheng AG. Lineage-tracing and translatomic analysis of damage-inducible mitotic cochlear progenitors identifies candidate genes regulating regeneration. PLoS Biol 2021; 19:e3001445. [PMID: 34758021 PMCID: PMC8608324 DOI: 10.1371/journal.pbio.3001445] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 11/22/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
Cochlear supporting cells (SCs) are glia-like cells critical for hearing function. In the neonatal cochlea, the greater epithelial ridge (GER) is a mitotically quiescent and transient organ, which has been shown to nonmitotically regenerate SCs. Here, we ablated Lgr5+ SCs using Lgr5-DTR mice and found mitotic regeneration of SCs by GER cells in vivo. With lineage tracing, we show that the GER houses progenitor cells that robustly divide and migrate into the organ of Corti to replenish ablated SCs. Regenerated SCs display coordinated calcium transients, markers of the SC subtype inner phalangeal cells, and survive in the mature cochlea. Via RiboTag, RNA-sequencing, and gene clustering algorithms, we reveal 11 distinct gene clusters comprising markers of the quiescent and damaged GER, and damage-responsive genes driving cell migration and mitotic regeneration. Together, our study characterizes GER cells as mitotic progenitors with regenerative potential and unveils their quiescent and damaged translatomes.
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Affiliation(s)
- Tomokatsu Udagawa
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Otorhinolaryngology, The Jikei University School of Medicine, Tokyo, Japan
| | - Patrick J. Atkinson
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Beatrice Milon
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Julia M. Abitbol
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Michal Sperber
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elvis Huarcaya Najarro
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mirko Scheibinger
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronna Hertzano
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Alan G. Cheng
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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18
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Milon B, Shulman ED, So KS, Cederroth CR, Lipford EL, Sperber M, Sellon JB, Sarlus H, Pregernig G, Shuster B, Song Y, Mitra S, Orvis J, Margulies Z, Ogawa Y, Shults C, Depireux DA, Palermo AT, Canlon B, Burns J, Elkon R, Hertzano R. A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma. Cell Rep 2021; 36:109758. [PMID: 34592158 PMCID: PMC8709734 DOI: 10.1016/j.celrep.2021.109758] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/29/2021] [Accepted: 09/03/2021] [Indexed: 01/26/2023] Open
Abstract
Noise-induced hearing loss (NIHL) results from a complex interplay of damage to the sensory cells of the inner ear, dysfunction of its lateral wall, axonal retraction of type 1C spiral ganglion neurons, and activation of the immune response. We use RiboTag and single-cell RNA sequencing to survey the cell-type-specific molecular landscape of the mouse inner ear before and after noise trauma. We identify induction of the transcription factors STAT3 and IRF7 and immune-related genes across all cell-types. Yet, cell-type-specific transcriptomic changes dominate the response. The ATF3/ATF4 stress-response pathway is robustly induced in the type 1A noise-resilient neurons, potassium transport genes are downregulated in the lateral wall, mRNA metabolism genes are downregulated in outer hair cells, and deafness-associated genes are downregulated in most cell types. This transcriptomic resource is available via the Gene Expression Analysis Resource (gEAR; https://umgear.org/NIHL) and provides a blueprint for the rational development of drugs to prevent and treat NIHL.
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Affiliation(s)
- Beatrice Milon
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Eldad D Shulman
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kathy S So
- Decibel Therapeutics, Boston, MA 02215, USA
| | - Christopher R Cederroth
- Laboratory of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, 171 77 Stockholm, Sweden; Hearing Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Erika L Lipford
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michal Sperber
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Heela Sarlus
- Laboratory of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, 171 77 Stockholm, Sweden; Applied Immunology & Immunotherapy, Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, 171 77 Stockholm, Sweden
| | | | - Benjamin Shuster
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sunayana Mitra
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zachary Margulies
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yoko Ogawa
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Christopher Shults
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | | | - Barbara Canlon
- Laboratory of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Joe Burns
- Decibel Therapeutics, Boston, MA 02215, USA
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Margalit S, Abramson Y, Sharim H, Manber Z, Bhattacharya S, Chen YW, Vilain E, Barseghyan H, Elkon R, Sharan R, Ebenstein Y. Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution. Bioinformatics 2021; 37:i327-i333. [PMID: 34252972 PMCID: PMC8275347 DOI: 10.1093/bioinformatics/btab306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION While promoter methylation is associated with reinforcing fundamental tissue identities, the methylation status of distant enhancers was shown by genome-wide association studies to be a powerful determinant of cell-state and cancer. With recent availability of long reads that report on the methylation status of enhancer-promoter pairs on the same molecule, we hypothesized that probing these pairs on the single-molecule level may serve the basis for detection of rare cancerous transformations in a given cell population. We explore various analysis approaches for deconvolving cell-type mixtures based on their genome-wide enhancer-promoter methylation profiles. RESULTS To evaluate our hypothesis we examine long-read optical methylome data for the GM12878 cell line and myoblast cell lines from two donors. We identified over 100 000 enhancer-promoter pairs that co-exist on at least 30 individual DNA molecules. We developed a detailed methodology for mixture deconvolution and applied it to estimate the proportional cell compositions in synthetic mixtures. Analysis of promoter methylation, as well as enhancer-promoter pairwise methylation, resulted in very accurate estimates. In addition, we show that pairwise methylation analysis can be generalized from deconvolving different cell types to subtle scenarios where one wishes to resolve different cell populations of the same cell-type. AVAILABILITY AND IMPLEMENTATION The code used in this work to analyze single-molecule Bionano Genomics optical maps is available via the GitHub repository https://github.com/ebensteinLab/Single_molecule_methylation_in_EP.
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Affiliation(s)
- Sapir Margalit
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yotam Abramson
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Sharim
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Zohar Manber
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA
| | - Ran Elkon
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roded Sharan
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.,School of Computer Science, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Yuval Ebenstein
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
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20
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Shulman ED, Elkon R. Genetic mapping of developmental trajectories for complex traits and diseases. Comput Struct Biotechnol J 2021; 19:3458-3469. [PMID: 34194671 PMCID: PMC8220172 DOI: 10.1016/j.csbj.2021.05.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 11/04/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified numerous common genetic variants associated with complex human traits and diseases. However, the translation of GWAS discoveries into biological and clinical insights is highly challenging. In this study, we present a novel bioinformatics approach for enhancing the functional interpretation of GWAS signals, based on their integration with single-cell (sc)RNA-seq datasets that examine developmental processes. Our approach performs three tasks: (1) Identification of links between cell differentiation trajectories and traits; (2) Elucidation of biological processes and molecular pathways that underlie such trajectory-trait links; and (3) Prioritization of target genes that carry the links between trajectories, pathways and traits. We applied our method to a set of 11 traits of various pathologies, and 12 scRNA-seq datasets of diverse developmental processes, and it readily detected well-established biological connections, including those between the maturation of cortical inhibitory interneurons and schizophrenia, hepatocytes and cholesterol levels, and pancreatic beta-islet cells and type-2 diabetes. For each of these associations, our method pinpointed top candidate genes that are strongly associated with both the kinetics of the differentiation trajectory and the disease's genetic risk. By the identification of trajectory-disease links, molecular pathways that underlie them and prioritizing candidate risk genes, our method improves the understanding of the etiology of complex diseases, and thus holds promise for enhancing rational drug development that is aimed at targeting specific biological processes that mediate the genetic predisposition to diseases.
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Affiliation(s)
- Eldad David Shulman
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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21
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Krohs C, Bordeynik-Cohen M, Messika-Gold N, Elkon R, Avraham KB, Nothwang HG. Expression pattern of cochlear microRNAs in the mammalian auditory hindbrain. Cell Tissue Res 2021; 383:655-666. [PMID: 33156384 PMCID: PMC7904729 DOI: 10.1007/s00441-020-03290-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/24/2020] [Indexed: 12/28/2022]
Abstract
The auditory system comprises the auditory periphery, engaged in sound transduction and the central auditory system, implicated in auditory information processing and perception. Recently, evidence mounted that the mammalian peripheral and central auditory systems share a number of genes critical for proper development and function. This bears implication for auditory rehabilitation and evolution of the auditory system. To analyze to which extent microRNAs (miRNAs) belong to genes shared between both systems, we characterize the expression pattern of 12 cochlea-abundant miRNAs in the central auditory system. Quantitative real-time PCR (qRT-PCR) demonstrated expression of all 12 genes in the cochlea, the auditory hindbrain and the non-auditory prefrontal cortex (PFC) at embryonic stage (E)16 and postnatal stages (P)0 and P30. Eleven of them showed differences in expression between tissues and nine between the developmental time points. Hierarchical cluster analysis revealed that the temporal expression pattern in the auditory hindbrain was more similar to the PFC than to the cochlea. Spatiotemporal expression analysis by RNA in situ hybridization demonstrated widespread expression throughout the cochlear nucleus complex (CNC) and the superior olivary complex (SOC) during postnatal development. Altogether, our data indicate that miRNAs represent a relevant class of genetic factors functioning across the auditory system. Given the importance of gene regulatory network (GRN) components for development, physiology and evolution, the 12 miRNAs provide promising entry points to gain insights into their molecular underpinnings in the auditory system.
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Affiliation(s)
- Constanze Krohs
- Neurogenetics Group and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences, Carl Von Ossietzky University Oldenburg, 26111, Oldenburg, Germany
| | - Mor Bordeynik-Cohen
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Naama Messika-Gold
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Hans Gerd Nothwang
- Neurogenetics Group and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences, Carl Von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.
- Research Center for Neurosensory Science, Carl Von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.
- Department of Neuroscience, Center of Excellence Hearing4All, Carl Von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.
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22
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Li L, Ugalde AP, Scheele CLGJ, Dieter SM, Nagel R, Ma J, Pataskar A, Korkmaz G, Elkon R, Chien MP, You L, Su PR, Bleijerveld OB, Altelaar M, Momchev L, Manber Z, Han R, van Breugel PC, Lopes R, ten Dijke P, van Rheenen J, Agami R. A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis. Genome Biol 2021; 22:54. [PMID: 33514403 PMCID: PMC7845134 DOI: 10.1186/s13059-021-02272-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiveness. Although thousands of YAP/TEAD4 binding-sites are annotated, their functional importance is unknown. Here, we aim at further identification of enhancer elements that are required for YAP functions. RESULTS We first apply genome-wide ChIP profiling of YAP to systematically identify enhancers that are bound by YAP/TEAD4. Next, we implement a genetic approach to uncover functions of YAP/TEAD4-associated enhancers, demonstrate its robustness, and use it to reveal a network of enhancers required for YAP-mediated proliferation. We focus on EnhancerTRAM2, as its target gene TRAM2 shows the strongest expression-correlation with YAP activity in nearly all tumor types. Interestingly, TRAM2 phenocopies the YAP-induced cell proliferation, migration, and invasion phenotypes and correlates with poor patient survival. Mechanistically, we identify FSTL-1 as a major direct client of TRAM2 that is involved in these phenotypes. Thus, TRAM2 is a key novel mediator of YAP-induced oncogenic proliferation and cellular invasiveness. CONCLUSIONS YAP is a transcription co-factor that binds to thousands of enhancer loci and stimulates tumor aggressiveness. Using unbiased functional approaches, we dissect YAP enhancer network and characterize TRAM2 as a novel mediator of cellular proliferation, migration, and invasion. Our findings elucidate how YAP induces cancer aggressiveness and may assist diagnosis of cancer metastasis.
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Affiliation(s)
- Li Li
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Alejandro P. Ugalde
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Colinda L. G. J. Scheele
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Sebastian M. Dieter
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Remco Nagel
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Jin Ma
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
| | - Abhijeet Pataskar
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Gozde Korkmaz
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Miao-Ping Chien
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Li You
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pin-Rui Su
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Onno B. Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvt Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Lyubomir Momchev
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Zohar Manber
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ruiqi Han
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Pieter C. van Breugel
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Rui Lopes
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Peter ten Dijke
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
| | - Jacco van Rheenen
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
- Erasmus MC, Rotterdam University, Rotterdam, The Netherlands
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23
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Levi H, Elkon R, Shamir R. DOMINO: a network-based active module identification algorithm with reduced rate of false calls. Mol Syst Biol 2021; 17:e9593. [PMID: 33471440 PMCID: PMC7816759 DOI: 10.15252/msb.20209593] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 01/18/2023] Open
Abstract
Algorithms for active module identification (AMI) are central to analysis of omics data. Such algorithms receive a gene network and nodes' activity scores as input and report subnetworks that show significant over‐representation of accrued activity signal (“active modules”), thus representing biological processes that presumably play key roles in the analyzed conditions. Here, we systematically evaluated six popular AMI methods on gene expression and GWAS data. We observed that GO terms enriched in modules detected on the real data were often also enriched on modules found on randomly permuted data. This indicated that AMI methods frequently report modules that are not specific to the biological context measured by the analyzed omics dataset. To tackle this bias, we designed a permutation‐based method that empirically evaluates GO terms reported by AMI methods. We used the method to fashion five novel AMI performance criteria. Last, we developed DOMINO, a novel AMI algorithm, that outperformed the other six algorithms in extensive testing on GE and GWAS data. Software is available at https://github.com/Shamir‐Lab.
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Affiliation(s)
- Hagai Levi
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
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24
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Koffler-Brill T, Taiber S, Anaya A, Bordeynik-Cohen M, Rosen E, Kolla L, Messika-Gold N, Elkon R, Kelley MW, Ulitsky I, Avraham KB. Identification and characterization of key long non-coding RNAs in the mouse cochlea. RNA Biol 2020; 18:1160-1169. [PMID: 33131415 DOI: 10.1080/15476286.2020.1836456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The auditory system is a complex sensory network with an orchestrated multilayer regulatory programme governing its development and maintenance. Accumulating evidence has implicated long non-coding RNAs (lncRNAs) as important regulators in numerous systems, as well as in pathological pathways. However, their function in the auditory system has yet to be explored. Using a set of specific criteria, we selected four lncRNAs expressed in the mouse cochlea, which are conserved in the human transcriptome and are relevant for inner ear function. Bioinformatic characterization demonstrated a lack of coding potential and an absence of evolutionary conservation that represent properties commonly shared by their class members. RNAscope® analysis of the spatial and temporal expression profiles revealed specific localization to inner ear cells. Sub-cellular localization analysis presented a distinct pattern for each lncRNA and mouse tissue expression evaluation displayed a large variability in terms of level and location. Our findings establish the expression of specific lncRNAs in different cell types of the auditory system and present a potential pathway by which the lncRNA Gas5 acts in the inner ear. Studying lncRNAs and deciphering their functions may deepen our knowledge of inner ear physiology and morphology and may reveal the basis of as yet unresolved genetic hearing loss-related pathologies. Moreover, our experimental design may be employed as a reference for studying other inner ear-related lncRNAs, as well as lncRNAs expressed in other sensory systems.
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Affiliation(s)
- Tal Koffler-Brill
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Alejandro Anaya
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Mor Bordeynik-Cohen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Einat Rosen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Likhitha Kolla
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Naama Messika-Gold
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Matthew W Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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25
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Matern MS, Milon B, Lipford EL, McMurray M, Ogawa Y, Tkaczuk A, Song Y, Elkon R, Hertzano R. GFI1 functions to repress neuronal gene expression in the developing inner ear hair cells. Development 2020; 147:147/17/dev186015. [PMID: 32917668 PMCID: PMC7502595 DOI: 10.1242/dev.186015] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/24/2020] [Indexed: 01/24/2023]
Abstract
Despite the known importance of the transcription factors ATOH1, POU4F3 and GFI1 in hair cell development and regeneration, their downstream transcriptional cascades in the inner ear remain largely unknown. Here, we have used Gfi1cre;RiboTag mice to evaluate changes to the hair cell translatome in the absence of GFI1. We identify a systematic downregulation of hair cell differentiation genes, concomitant with robust upregulation of neuronal genes in the GFI1-deficient hair cells. This includes increased expression of neuronal-associated transcription factors (e.g. Pou4f1) as well as transcription factors that serve dual roles in hair cell and neuronal development (e.g. Neurod1, Atoh1 and Insm1). We further show that the upregulated genes are consistent with the NEUROD1 regulon and are normally expressed in hair cells prior to GFI1 onset. Additionally, minimal overlap of differentially expressed genes in auditory and vestibular hair cells suggests that GFI1 serves different roles in these systems. From these data, we propose a dual mechanism for GFI1 in promoting hair cell development, consisting of repression of neuronal-associated genes as well as activation of hair cell-specific genes required for normal functional maturation.
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Affiliation(s)
- Maggie S. Matern
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Beatrice Milon
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Erika L. Lipford
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Mark McMurray
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yoko Ogawa
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Andrew Tkaczuk
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA .,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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26
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Shulman ED, Elkon R. Systematic identification of functional SNPs interrupting 3'UTR polyadenylation signals. PLoS Genet 2020; 16:e1008977. [PMID: 32804959 PMCID: PMC7451987 DOI: 10.1371/journal.pgen.1008977] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 08/27/2020] [Accepted: 07/01/2020] [Indexed: 12/22/2022] Open
Abstract
Alternative polyadenylation (APA) is emerging as a widespread regulatory layer since the majority of human protein-coding genes contain several polyadenylation (p(A)) sites in their 3’UTRs. By generating isoforms with different 3’UTR length, APA potentially affects mRNA stability, translation efficiency, nuclear export, and cellular localization. Polyadenylation sites are regulated by adjacent RNA cis-regulatory elements, the principals among them are the polyadenylation signal (PAS) AAUAAA and its main variant AUUAAA, typically located ~20-nt upstream of the p(A) site. Mutations in PAS and other auxiliary poly(A) cis-elements in the 3’UTR of several genes have been shown to cause human Mendelian diseases, and to date, only a few common SNPs that regulate APA were associated with complex diseases. Here, we systematically searched for SNPs that affect gene expression and human traits by modulation of 3’UTR APA. First, focusing on the variants most likely to exert the strongest effect, we identified 2,305 SNPs that interrupt the canonical PAS or its main variant. Implementing pA-QTL tests using GTEx RNA-seq data, we identified 330 PAS SNPs (called PAS pA-QTLs) that were significantly associated with the usage of their p(A) site. As expected, PAS-interrupting alleles were mostly linked with decreased cleavage at their p(A) site and the consequential 3’UTR lengthening. However, interestingly, in ~10% of the cases, the PAS-interrupting allele was associated with increased usage of an upstream p(A) site and 3’UTR shortening. As an indication of the functional effects of these PAS pA-QTLs on gene expression and complex human traits, we observed for few dozens of them marked colocalization with eQTL and/or GWAS signals. The PAS-interrupting alleles linked with 3’UTR lengthening were also strongly associated with decreased gene expression, indicating that shorter isoforms generated by APA are generally more stable than longer ones. Last, we carried out an extended, genome-wide analysis of 3’UTR variants and detected thousands of additional pA-QTLs having weaker effects compared to the PAS pA-QTLs. mRNA molecules that encode for proteins end with a long stretch of adenosines, called poly(A) tail. The poly(A) tail contributes to the stability of the mRNA molecules, their translation to proteins and their import from the nucleus to the cytoplasm. The process of adding this tail to the mRNAs is called polyadenylation, and the termination site on the mRNAs at which the poly(A) tail is added is called the poly(A) site. In recent years it became evident that the vast majority of mRNAs of human genes contain several alternative poly(A) sites and their usage generates different mRNA isoforms that differ in their stability and translation efficiency. Therefore, alternative polyadenylation (APA) is emerging as a novel and important, yet underexplored, mechanism that regulate gene expression. The choice between alternative p(A) sites in an mRNA molecule is regulated by regulatory sequences located within a region in the mRNA called the 3’ untranslated region (3’UTR). A major challenge in present human genetics research is to understand how common genetic variants affect individuals’ health. In our study, we systematically identified dozens of genetic variants that affect the choice between alternative p(A) sites and demonstrated that by that, these variants influence the expression level of the target genes. Our results help to illuminate a novel mechanism by which genetic variants that are common in the population affect different traits including our risk for developing diseases.
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Affiliation(s)
- Eldad David Shulman
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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27
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Slobodin B, Bahat A, Sehrawat U, Becker-Herman S, Zuckerman B, Weiss AN, Han R, Elkon R, Agami R, Ulitsky I, Shachar I, Dikstein R. Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels. Mol Cell 2020; 78:434-444.e5. [PMID: 32294471 DOI: 10.1016/j.molcel.2020.03.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 02/02/2023]
Abstract
Gene expression is regulated by the rates of synthesis and degradation of mRNAs, but how these processes are coordinated is poorly understood. Here, we show that reduced transcription dynamics of specific genes leads to enhanced m6A deposition, preferential activity of the CCR4-Not complex, shortened poly(A) tails, and reduced stability of the respective mRNAs. These effects are also exerted by internal ribosome entry site (IRES) elements, which we found to be transcriptional pause sites. However, when transcription dynamics, and subsequently poly(A) tails, are globally altered, cells buffer mRNA levels by adjusting the expression of mRNA degradation machinery. Stress-provoked global impediment of transcription elongation leads to a dramatic inhibition of the mRNA degradation machinery and massive mRNA stabilization. Accordingly, globally enhanced transcription, such as following B cell activation or glucose stimulation, has the opposite effects. This study uncovers two molecular pathways that maintain balanced gene expression in mammalian cells by linking transcription to mRNA stability.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anat Bahat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Urmila Sehrawat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shirly Becker-Herman
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binyamin Zuckerman
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amanda N Weiss
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruiqi Han
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Igor Ulitsky
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idit Shachar
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
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28
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Shulman ED, Elkon R. Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data. Nucleic Acids Res 2019; 47:10027-10039. [PMID: 31501864 PMCID: PMC6821429 DOI: 10.1093/nar/gkz781] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 08/27/2019] [Accepted: 09/01/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative polyadenylation (APA) is emerging as an important layer of gene regulation because the majority of mammalian protein-coding genes contain multiple polyadenylation (pA) sites in their 3′ UTR. By alteration of 3′ UTR length, APA can considerably affect post-transcriptional gene regulation. Yet, our understanding of APA remains rudimentary. Novel single-cell RNA sequencing (scRNA-seq) techniques allow molecular characterization of different cell types to an unprecedented degree. Notably, the most popular scRNA-seq protocols specifically sequence the 3′ end of transcripts. Building on this property, we implemented a method for analysing patterns of APA regulation from such data. Analyzing multiple datasets from diverse tissues, we identified widespread modulation of APA in different cell types resulting in global 3′ UTR shortening/lengthening and enhanced cleavage at intronic pA sites. Our results provide a proof-of-concept demonstration that the huge volume of scRNA-seq data that accumulates in the public domain offers a unique resource for the exploration of APA based on a very broad collection of cell types and biological conditions.
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Affiliation(s)
- Eldad David Shulman
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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29
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Korkmaz G, Manber Z, Lopes R, Prekovic S, Schuurman K, Kim Y, Teunissen H, Flach K, Wit ED, Galli GG, Zwart W, Elkon R, Agami R. A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation. Nucleic Acids Res 2019; 47:9557-9572. [PMID: 31372638 PMCID: PMC6765117 DOI: 10.1093/nar/gkz675] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/11/2019] [Accepted: 07/24/2019] [Indexed: 01/07/2023] Open
Abstract
Estrogen receptor α (ERα) is an enhancer activating transcription factor, a key driver of breast cancer and a main target for cancer therapy. ERα-mediated gene regulation requires proper chromatin-conformation to facilitate interactions between ERα-bound enhancers and their target promoters. A major determinant of chromatin structure is the CCCTC-binding factor (CTCF), that dimerizes and together with cohesin stabilizes chromatin loops and forms the boundaries of topologically associated domains. However, whether CTCF-binding elements (CBEs) are essential for ERα-driven cell proliferation is unknown. To address this question in a global manner, we implemented a CRISPR-based functional genetic screen targeting CBEs located in the vicinity of ERα-bound enhancers. We identified four functional CBEs and demonstrated the role of one of them in inducing chromatin conformation changes in favor of activation of PREX1, a key ERα target gene in breast cancer. Indeed, high PREX1 expression is a bona-fide marker of ERα-dependency in cell lines, and is associated with good outcome after anti-hormonal treatment. Altogether, our data show that distinct CTCF-mediated chromatin structures are required for ERα- driven breast cancer cell proliferation.
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Affiliation(s)
- Gozde Korkmaz
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Zohar Manber
- Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rui Lopes
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Yongsoo Kim
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Koen Flach
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Giorgio G Galli
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands
| | - Ran Elkon
- Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Erasmus MC, Rotterdam University, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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30
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Mandelboum S, Manber Z, Elroy-Stein O, Elkon R. Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias. PLoS Biol 2019; 17:e3000481. [PMID: 31714939 PMCID: PMC6850523 DOI: 10.1371/journal.pbio.3000481] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/08/2019] [Indexed: 11/19/2022] Open
Abstract
Data normalization is a critical step in RNA sequencing (RNA-seq) analysis, aiming to remove systematic effects from the data to ensure that technical biases have minimal impact on the results. Analyzing numerous RNA-seq datasets, we detected a prevalent sample-specific length effect that leads to a strong association between gene length and fold-change estimates between samples. This stochastic sample-specific effect is not corrected by common normalization methods, including reads per kilobase of transcript length per million reads (RPKM), Trimmed Mean of M values (TMM), relative log expression (RLE), and quantile and upper-quartile normalization. Importantly, we demonstrate that this bias causes recurrent false positive calls by gene-set enrichment analysis (GSEA) methods, thereby leading to frequent functional misinterpretation of the data. Gene sets characterized by markedly short genes (e.g., ribosomal protein genes) or long genes (e.g., extracellular matrix genes) are particularly prone to such false calls. This sample-specific length bias is effectively removed by the conditional quantile normalization (cqn) and EDASeq methods, which allow the integration of gene length as a sample-specific covariate. Consequently, using these normalization methods led to substantial reduction in GSEA false results while retaining true ones. In addition, we found that application of gene-set tests that take into account gene–gene correlations attenuates false positive rates caused by the length bias, but statistical power is reduced as well. Our results advocate the inspection and correction of sample-specific length biases as default steps in RNA-seq analysis pipelines and reiterate the need to account for intergene correlations when performing gene-set enrichment tests to lessen false interpretation of transcriptomic data. Analysis of numerous RNA-seq datasets reveals a recurrent sample-specific length bias that causes frequent false positive calls by gene-set enrichment analyses, leading to functional misinterpretation of the data. Its removal requires methods that allow the integration of gene length as sample-specific covariate.
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Affiliation(s)
- Shir Mandelboum
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Zohar Manber
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Elroy-Stein
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (OE-S); (RE)
| | - Ran Elkon
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (OE-S); (RE)
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31
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Li L, van Breugel PC, Loayza-Puch F, Ugalde AP, Korkmaz G, Messika-Gold N, Han R, Lopes R, Barbera EP, Teunissen H, de Wit E, Soares RJ, Nielsen BS, Holmstrøm K, Martínez-Herrera DJ, Huarte M, Louloupi A, Drost J, Elkon R, Agami R. LncRNA-OIS1 regulates DPP4 activation to modulate senescence induced by RAS. Nucleic Acids Res 2019; 46:4213-4227. [PMID: 29481642 PMCID: PMC5934637 DOI: 10.1093/nar/gky087] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/29/2018] [Indexed: 12/15/2022] Open
Abstract
Oncogene-induced senescence (OIS), provoked in response to oncogenic activation, is considered an important tumor suppressor mechanism. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nt without a protein-coding capacity. Functional studies showed that deregulated lncRNA expression promote tumorigenesis and metastasis and that lncRNAs may exhibit tumor-suppressive and oncogenic function. Here, we first identified lncRNAs that were differentially expressed between senescent and non-senescent human fibroblast cells. Using RNA interference, we performed a loss-function screen targeting the differentially expressed lncRNAs, and identified lncRNA-OIS1 (lncRNA#32, AC008063.3 or ENSG00000233397) as a lncRNA required for OIS. Knockdown of lncRNA-OIS1 triggered bypass of senescence, higher proliferation rate, lower abundance of the cell-cycle inhibitor CDKN1A and high expression of cell-cycle-associated genes. Subcellular inspection of lncRNA-OIS1 indicated nuclear and cytosolic localization in both normal culture conditions as well as following oncogene induction. Interestingly, silencing lncRNA-OIS1 diminished the senescent-associated induction of a nearby gene (Dipeptidyl Peptidase 4, DPP4) with established role in tumor suppression. Intriguingly, similar to lncRNA-OIS1, silencing DPP4 caused senescence bypass, and ectopic expression of DPP4 in lncRNA-OIS1 knockdown cells restored the senescent phenotype. Thus, our data indicate that lncRNA-OIS1 links oncogenic induction and senescence with the activation of the tumor suppressor DPP4.
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Affiliation(s)
- Li Li
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Pieter C van Breugel
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Fabricio Loayza-Puch
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Alejandro Pineiro Ugalde
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Gozde Korkmaz
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Naama Messika-Gold
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, 69978, Tel Aviv University, Tel Aviv, Israel
| | - Ruiqi Han
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Rui Lopes
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Eric P Barbera
- Division of Molecular Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | | | | | - Kim Holmstrøm
- Bioneer A/S, Kogle Allé 2, DK-2970 Hørsholm, Denmark
| | | | - Maite Huarte
- Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Annita Louloupi
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Jarno Drost
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, 69978, Tel Aviv University, Tel Aviv, Israel
| | - Reuven Agami
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.,Erasmus MC, Rotterdam University, 3000 CA Rotterdam, The Netherlands.,Oncode institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
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32
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Gavish-Izakson M, Velpula BB, Elkon R, Prados-Carvajal R, Barnabas GD, Ugalde AP, Agami R, Geiger T, Huertas P, Ziv Y, Shiloh Y. Nuclear poly(A)-binding protein 1 is an ATM target and essential for DNA double-strand break repair. Nucleic Acids Res 2019; 46:730-747. [PMID: 29253183 PMCID: PMC5778506 DOI: 10.1093/nar/gkx1240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022] Open
Abstract
The DNA damage response (DDR) is an extensive signaling network that is robustly mobilized by DNA double-strand breaks (DSBs). The primary transducer of the DSB response is the protein kinase, ataxia-telangiectasia, mutated (ATM). Here, we establish nuclear poly(A)-binding protein 1 (PABPN1) as a novel target of ATM and a crucial player in the DSB response. PABPN1 usually functions in regulation of RNA processing and stability. We establish that PABPN1 is recruited to the DDR as a critical regulator of DSB repair. A portion of PABPN1 relocalizes to DSB sites and is phosphorylated on Ser95 in an ATM-dependent manner. PABPN1 depletion sensitizes cells to DSB-inducing agents and prolongs the DSB-induced G2/M cell-cycle arrest, and DSB repair is hampered by PABPN1 depletion or elimination of its phosphorylation site. PABPN1 is required for optimal DSB repair via both nonhomologous end-joining (NHEJ) and homologous recombination repair (HRR), and specifically is essential for efficient DNA-end resection, an initial, key step in HRR. Using mass spectrometry analysis, we capture DNA damage-induced interactions of phospho-PABPN1, including well-established DDR players as well as other RNA metabolizing proteins. Our results uncover a novel ATM-dependent axis in the rapidly growing interface between RNA metabolism and the DDR.
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Affiliation(s)
- Michal Gavish-Izakson
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bhagya Bhavana Velpula
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rosario Prados-Carvajal
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, Spain
| | - Georgina D Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alejandro Pineiro Ugalde
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, Spain
| | - Yael Ziv
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- To whom correspondence should be addressed. Tel: +972 3 6409760; . Correspondence may also be addressed to Yael Ziv. Tel: +972 3 6408584;
| | - Yosef Shiloh
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- To whom correspondence should be addressed. Tel: +972 3 6409760; . Correspondence may also be addressed to Yael Ziv. Tel: +972 3 6408584;
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Ziv Y, Rahamim N, Lezmy N, Even-Chen O, Shaham O, Malishkevich A, Giladi E, Elkon R, Gozes I, Barak S. Activity-dependent neuroprotective protein (ADNP) is an alcohol-responsive gene and negative regulator of alcohol consumption in female mice. Neuropsychopharmacology 2019; 44:415-424. [PMID: 30008470 PMCID: PMC6300527 DOI: 10.1038/s41386-018-0132-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 12/16/2022]
Abstract
Neuroadaptations in the brain reward system caused by excessive alcohol intake, lead to drinking escalation and alcohol use disorder phenotypes. Activity-dependent neuroprotective protein (ADNP) is crucial for brain development, and is implicated in neural plasticity in adulthood. Here, we discovered that alcohol exposure regulates Adnp expression in the mesolimbic system, and that Adnp keeps alcohol drinking in moderation, in a sex-dependent manner. Specifically, Sub-chronic alcohol treatment (2.5 g/kg/day for 7 days) increased Adnp mRNA levels in the dorsal hippocampus in both sexes, and in the nucleus accumbens of female mice, 24 h after the last alcohol injection. Long-term voluntary consumption of excessive alcohol quantities (~10-15 g/kg/24 h, 5 weeks) increased Adnp mRNA in the hippocampus of male mice immediately after an alcohol-drinking session, but the level returned to baseline after 24 h of withdrawal. In contrast, excessive alcohol consumption in females led to long-lasting reduction in hippocampal Adnp expression. We further tested the regulatory role of Adnp in alcohol consumption, using the Adnp haploinsufficient mouse model. We found that Adnp haploinsufficient female mice showed higher alcohol consumption and preference, compared to Adnp intact females, whereas no genotype difference was observed in males. Importantly, daily intranasal administration of the ADNP-snippet drug candidate NAP normalized alcohol consumption in Adnp haploinsufficient females. Finally, female Adnp haploinsufficient mice showed a sharp increase in alcohol intake after abstinence, suggesting that Adnp protects against relapse in females. The current data suggest that ADNP is a potential novel biomarker and negative regulator of alcohol-drinking behaviors.
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Affiliation(s)
- Yarden Ziv
- 0000 0004 1937 0546grid.12136.37Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel ,0000 0004 1937 0546grid.12136.37Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Nofar Rahamim
- 0000 0004 1937 0546grid.12136.37Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978 Tel Aviv, Israel ,0000 0004 1937 0546grid.12136.37School of Psychological Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Noa Lezmy
- 0000 0004 1937 0546grid.12136.37Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978 Tel Aviv, Israel ,0000 0004 1937 0546grid.12136.37School of Psychological Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Oren Even-Chen
- 0000 0004 1937 0546grid.12136.37School of Psychological Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ohad Shaham
- 0000 0004 1937 0546grid.12136.37School of Psychological Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Anna Malishkevich
- 0000 0004 1937 0546grid.12136.37Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Eliezer Giladi
- 0000 0004 1937 0546grid.12136.37Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ran Elkon
- 0000 0004 1937 0546grid.12136.37Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel ,0000 0004 1937 0546grid.12136.37Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Illana Gozes
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel. .,Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Segev Barak
- Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978, Tel Aviv, Israel. .,School of Psychological Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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Nurick I, Shamir R, Elkon R. Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions. Epigenetics Chromatin 2018; 11:49. [PMID: 30157915 PMCID: PMC6114837 DOI: 10.1186/s13072-018-0220-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
Background Our appreciation of the critical role of the genome’s 3D organization in gene regulation is steadily increasing. Recent 3C-based deep sequencing techniques elucidated a hierarchy of structures that underlie the spatial organization of the genome in the nucleus. At the top of this hierarchical organization are chromosomal territories and the megabase-scale A/B compartments that correlate with transcriptional activity within cells. Below them are the relatively cell-type-invariant topologically associated domains (TADs), characterized by high frequency of physical contacts between loci within the same TAD, and are assumed to function as regulatory units. Within TADs, chromatin loops bring enhancers and target promoters to close spatial proximity. Yet, we still have only rudimentary understanding how differences in chromatin organization between different cell types affect cell-type-specific gene expression programs that are executed under basal and challenged conditions. Results Here, we carried out a large-scale meta-analysis that integrated Hi–C data from thirteen different cell lines and dozens of ChIP-seq and RNA-seq datasets measured on these cells, either under basal conditions or after treatment. Pairwise comparisons between cell lines demonstrate a strong association between modulation of A/B compartmentalization, differential gene expression and transcription factor (TF) binding events. Furthermore, integrating the analysis of transcriptomes of different cell lines in response to various challenges, we show that A/B compartmentalization of cells under basal conditions significantly correlates not only with gene expression programs and TF binding profiles that are active under the basal condition but also with those induced in response to treatment. Yet, in pairwise comparisons between different cell lines, we find that a large portion of differential TF binding and gene induction events occur in genomic loci assigned to A compartment in both cell types, underscoring the role of additional critical factors in determining cell-type-specific transcriptional programs. Conclusions Our results further indicate the role of dynamic genome organization in regulation of differential gene expression between different cell types and the impact of intra-TAD enhancer–promoter interactions that are established under basal conditions on both the basal and treatment-induced gene expression programs. Electronic supplementary material The online version of this article (10.1186/s13072-018-0220-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Idan Nurick
- The Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.
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Han R, Li L, Ugalde AP, Tal A, Manber Z, Barbera EP, Chiara VD, Elkon R, Agami R. Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence. Genome Biol 2018; 19:118. [PMID: 30119690 PMCID: PMC6097335 DOI: 10.1186/s13059-018-1494-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/27/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncogene-induced senescence, a cellular state of irreversible proliferation arrest that is enforced following excessive oncogenic activity, is a major barrier against cancer transformation; therefore, bypassing oncogene-induced senescence is a critical step in tumorigenesis. Here, we aim at further identification of enhancer elements that are required for the establishment of this state. RESULTS We first apply genome-wide profiling of enhancer-RNAs (eRNAs) to systematically identify enhancers that are activated upon oncogenic stress. DNA motif analysis of these enhancers indicates AP-1 as a major regulator of the transcriptional program induced by oncogene-induced senescence. We thus constructed a CRISPR-Cas9 sgRNA library designed to target senescence-induced enhancers that are putatively regulated by AP-1 and used it in a functional screen. We identify a critical enhancer that we name EnhAP1-OIS1 and validate that mutating the AP-1 binding site within this element results in oncogene-induced senescence bypass. Furthermore, we identify FOXF1 as the gene regulated by this enhancer and demonstrate that FOXF1 mediates EnhAP1-OIS1 effect on the senescence phenotype. CONCLUSIONS Our study elucidates a novel cascade mediated by AP-1 and FOXF1 that regulates oncogene-induced senescence and further demonstrates the power of CRISPR-based functional genomic screens in deciphering the function of non-coding regulatory elements in the genome.
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Affiliation(s)
- Ruiqi Han
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Li Li
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Alejandro Piñeiro Ugalde
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Arieh Tal
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Zohar Manber
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Eric Pinto Barbera
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Veronica Della Chiara
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
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Cohen-Tayar Y, Cohen H, Mitiagin Y, Abravanel Z, Levy C, Idelson M, Reubinoff B, Itzkovitz S, Raviv S, Kaestner KH, Blinder P, Elkon R, Ashery-Padan R. Pax6 regulation of Sox9 in the mouse retinal pigmented epithelium controls its timely differentiation and choroid vasculature development. Development 2018; 145:dev.163691. [PMID: 29986868 DOI: 10.1242/dev.163691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/02/2018] [Indexed: 01/08/2023]
Abstract
The synchronized differentiation of neuronal and vascular tissues is crucial for normal organ development and function, although there is limited information about the mechanisms regulating the coordinated development of these tissues. The choroid vasculature of the eye serves as the main blood supply to the metabolically active photoreceptors, and develops together with the retinal pigmented epithelium (RPE). Here, we describe a novel regulatory relationship between the RPE transcription factors Pax6 and Sox9 that controls the timing of RPE differentiation and the adjacent choroid maturation. We used a novel machine learning algorithm tool to analyze high resolution imaging of the choroid in Pax6 and Sox9 conditional mutant mice. Additional unbiased transcriptomic analyses in mutant mice and RPE cells generated from human embryonic stem cells, as well as chromatin immunoprecipitation and high-throughput analyses, revealed secreted factors that are regulated by Pax6 and Sox9. These factors might be involved in choroid development and in the pathogenesis of the common blinding disease: age-related macular degeneration (AMD).
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Affiliation(s)
- Yamit Cohen-Tayar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hadar Cohen
- Department of Particle Physics, Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Yulia Mitiagin
- Department of Neurobiology, Biochemistry and Biophysics school, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Zohar Abravanel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carmit Levy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Masha Idelson
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy and The Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, 9112001 Jerusalem, Israel
| | - Benjamin Reubinoff
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy and The Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, 9112001 Jerusalem, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science 76100, Rehovot, Israel
| | - Shaul Raviv
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, 12-126 Smilow Center for Translational Research, 3400 Civic Center Blvd, Philadelphia, PA 19104-6145, USA
| | - Pablo Blinder
- Department of Neurobiology, Biochemistry and Biophysics school, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel.,Sagol School for Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel .,Sagol School for Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel .,Sagol School for Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
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Hait TA, Amar D, Shamir R, Elkon R. FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map. Genome Biol 2018; 19:56. [PMID: 29716618 PMCID: PMC5930446 DOI: 10.1186/s13059-018-1432-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/13/2018] [Indexed: 01/22/2023] Open
Abstract
Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer–promoter links. We show that current enhancer–promoter inference methods produce a high rate of false positive links. We introduce FOCS, a new inference method, and by benchmarking against ChIA-PET, HiChIP, and eQTL data show that it results in lower false discovery rates and at the same time higher inference power. By applying FOCS to 2630 samples taken from ENCODE, Roadmap Epigenomics, FANTOM5, and a new compendium of GRO-seq samples, we provide extensive enhancer–promotor maps (http://acgt.cs.tau.ac.il/focs). We illustrate the usability of our maps for deriving biological hypotheses.
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Affiliation(s)
- Tom Aharon Hait
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - David Amar
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Ran Elkon
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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Aviner R, Hofmann S, Elman T, Shenoy A, Geiger T, Elkon R, Ehrlich M, Elroy-Stein O. Proteomic analysis of polyribosomes identifies splicing factors as potential regulators of translation during mitosis. Nucleic Acids Res 2017; 45:5945-5957. [PMID: 28460002 PMCID: PMC5449605 DOI: 10.1093/nar/gkx326] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/16/2017] [Indexed: 12/16/2022] Open
Abstract
Precise regulation of mRNA translation is critical for proper cell division, but little is known about the factors that mediate it. To identify mRNA-binding proteins that regulate translation during mitosis, we analyzed the composition of polysomes from interphase and mitotic cells using unbiased quantitative mass-spectrometry (LC–MS/MS). We found that mitotic polysomes are enriched with a subset of proteins involved in RNA processing, including alternative splicing and RNA export. To demonstrate that these may indeed be regulators of translation, we focused on heterogeneous nuclear ribonucleoprotein C (hnRNP C) as a test case and confirmed that it is recruited to elongating ribosomes during mitosis. Then, using a combination of pulsed SILAC, metabolic labeling and ribosome profiling, we showed that knockdown of hnRNP C affects both global and transcript-specific translation rates and found that hnRNP C is specifically important for translation of mRNAs that encode ribosomal proteins and translation factors. Taken together, our results demonstrate how proteomic analysis of polysomes can provide insight into translation regulation under various cellular conditions of interest and suggest that hnRNP C facilitates production of translation machinery components during mitosis to provide daughter cells with the ability to efficiently synthesize proteins as they enter G1 phase.
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Affiliation(s)
- Ranen Aviner
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sarah Hofmann
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Elman
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anjana Shenoy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marcelo Ehrlich
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Orna Elroy-Stein
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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39
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Elkon R, Agami R. Characterization of noncoding regulatory DNA in the human genome. Nat Biotechnol 2017; 35:732-746. [DOI: 10.1038/nbt.3863] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/31/2017] [Indexed: 12/22/2022]
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40
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Slobodin B, Han R, Calderone V, Vrielink JAFO, Loayza-Puch F, Elkon R, Agami R. Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation. Cell 2017; 169:326-337.e12. [PMID: 28388414 PMCID: PMC5388891 DOI: 10.1016/j.cell.2017.03.031] [Citation(s) in RCA: 318] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 01/23/2017] [Accepted: 03/21/2017] [Indexed: 01/15/2023]
Abstract
Transcription and translation are two main pillars of gene expression. Due to the different timings, spots of action, and mechanisms of regulation, these processes are mainly regarded as distinct and generally uncoupled, despite serving a common purpose. Here, we sought for a possible connection between transcription and translation. Employing an unbiased screen of multiple human promoters, we identified a positive effect of TATA box on translation and a general coupling between mRNA expression and translational efficiency. Using a CRISPR-Cas9-mediated approach, genome-wide analyses, and in vitro experiments, we show that the rate of transcription regulates the efficiency of translation. Furthermore, we demonstrate that m6A modification of mRNAs is co-transcriptional and depends upon the dynamics of the transcribing RNAPII. Suboptimal transcription rates lead to elevated m6A content, which may result in reduced translation. This study uncovers a general and widespread link between transcription and translation that is governed by epigenetic modification of mRNAs. Transcription rates of mRNAs positively correlate with rates of their translation Dynamics of RNA polymerase II impact the deposition of m6A on mRNAs Suboptimal transcription enhances m6A modification of mRNAs Excessive m6A modification is detrimental for the translation process
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Affiliation(s)
- Boris Slobodin
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
| | - Ruiqi Han
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Vittorio Calderone
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joachim A F Oude Vrielink
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Fabricio Loayza-Puch
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Reuven Agami
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands.
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Drost R, Dhillon KK, van der Gulden H, van der Heijden I, Brandsma I, Cruz C, Chondronasiou D, Castroviejo-Bermejo M, Boon U, Schut E, van der Burg E, Wientjens E, Pieterse M, Klijn C, Klarenbeek S, Loayza-Puch F, Elkon R, van Deemter L, Rottenberg S, van de Ven M, Dekkers DHW, Demmers JAA, van Gent DC, Agami R, Balmaña J, Serra V, Taniguchi T, Bouwman P, Jonkers J. BRCA1185delAG tumors may acquire therapy resistance through expression of RING-less BRCA1. J Clin Invest 2016; 126:2903-18. [PMID: 27454287 DOI: 10.1172/jci70196] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/09/2016] [Indexed: 12/19/2022] Open
Abstract
Heterozygous germline mutations in breast cancer 1 (BRCA1) strongly predispose women to breast cancer. BRCA1 plays an important role in DNA double-strand break (DSB) repair via homologous recombination (HR), which is important for tumor suppression. Although BRCA1-deficient cells are highly sensitive to treatment with DSB-inducing agents through their HR deficiency (HRD), BRCA1-associated tumors display heterogeneous responses to platinum drugs and poly(ADP-ribose) polymerase (PARP) inhibitors in clinical trials. It is unclear whether all pathogenic BRCA1 mutations have similar effects on the response to therapy. Here, we have investigated mammary tumorigenesis and therapy sensitivity in mice carrying the Brca1185stop and Brca15382stop alleles, which respectively mimic the 2 most common BRCA1 founder mutations, BRCA1185delAG and BRCA15382insC. Both the Brca1185stop and Brca15382stop mutations predisposed animals to mammary tumors, but Brca1185stop tumors responded markedly worse to HRD-targeted therapy than did Brca15382stop tumors. Mice expressing Brca1185stop mutations also developed therapy resistance more rapidly than did mice expressing Brca15382stop. We determined that both murine Brca1185stop tumors and human BRCA1185delAG breast cancer cells expressed a really interesting new gene domain-less (RING-less) BRCA1 protein that mediated resistance to HRD-targeted therapies. Together, these results suggest that expression of RING-less BRCA1 may serve as a marker to predict poor response to DSB-inducing therapy in human cancer patients.
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42
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Hoffman Y, Bublik DR, P. Ugalde A, Elkon R, Biniashvili T, Agami R, Oren M, Pilpel Y. 3'UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells. PLoS Genet 2016; 12:e1005879. [PMID: 26908102 PMCID: PMC4764332 DOI: 10.1371/journal.pgen.1005879] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/27/2016] [Indexed: 11/29/2022] Open
Abstract
Most mammalian genes often feature alternative polyadenylation (APA) sites and hence diverse 3’UTR lengths. Proliferating cells were reported to favor APA sites that result in shorter 3’UTRs. One consequence of such shortening is escape of mRNAs from targeting by microRNAs (miRNAs) whose binding sites are eliminated. Such a mechanism might provide proliferation-related genes with an expression gain during normal or cancerous proliferation. Notably, miRNA sites tend to be more active when located near both ends of the 3’UTR compared to those located more centrally. Accordingly, miRNA sites located near the center of the full 3’UTR might become more active upon 3'UTR shortening. To address this conjecture we performed 3' sequencing to determine the 3' ends of all human UTRs in several cell lines. Remarkably, we found that conserved miRNA binding sites are preferentially enriched immediately upstream to APA sites, and this enrichment is more prominent in pro-differentiation/anti-proliferative genes. Binding sites of the miR17-92 cluster, upregulated in rapidly proliferating cells, are particularly enriched just upstream to APA sites, presumably conferring stronger inhibitory activity upon shortening. Thus 3’UTR shortening appears not only to enable escape from inhibition of growth promoting genes but also to potentiate repression of anti-proliferative genes. MicroRNAs (miRNAs) are regulators of gene expression. Typically they recognize a binding site in genes' sequences and exert a repressive effect. This scheme prescribes a regulatory network that determines which gene is regulated by which miRNA. Yet this is a static sequence-based scheme that might not support dynamic changes in network wiring. Can genes become subject to, or be released, from the regulation of a miRNA in a manner that depends on the physiological state of cells? Here we describe such a dynamic mechanism. It is established that miRNA regulation is often more effective when their binding sites reside near the end of the target mRNA or right after the coding sequence STOP codon. Thus, a site distant from the mRNA’s end might be latent as it will not bind efficiently its corresponding miRNA. Yet, in particular physiological states, e.g. cancer or rapidly proliferating cells, mRNA ends tend to become shortened. So far it was suggested that such shortening may serve to release proliferation-favoring genes from miRNA repression by eliminating their binding sites from the mRNA. We propose a mirror image, complementary mechanism that acts upon genes that need to be repressed during proliferation. Specifically, we propose that mRNA shortening can dynamically activate latent repressive miRNA binding sites by bringing the mRNA end close to them. We mapped the ends of all mRNAs in proliferating cells and found that cancer-enriched ends are strikingly positioned closely downstream to a high density of potentially latent binding sites, which are retained in the short mRNA but are now close to the new ends. This may enable such potentially latent miRNA sites to become dynamically activated upon proliferation. Remarkably, this mechanism targets preferentially pro-differentiation and antiproliferative genes, which are often repressed in cancer.
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Affiliation(s)
- Yonit Hoffman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Debora Rosa Bublik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alejandro P. Ugalde
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ran Elkon
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tammy Biniashvili
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (MO); (YP)
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (MO); (YP)
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43
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Creemers EE, Bawazeer A, Ugalde AP, van Deutekom HW, van der Made I, de Groot NE, Adriaens ME, Cook SA, Bezzina CR, Hubner N, van der Velden J, Elkon R, Agami R, Pinto YM. Genome-Wide Polyadenylation Maps Reveal Dynamic mRNA 3′-End Formation in the Failing Human Heart. Circ Res 2016; 118:433-8. [DOI: 10.1161/circresaha.115.307082] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/15/2015] [Indexed: 11/16/2022]
Abstract
Rationale:
Alternative cleavage and polyadenylation (APA) of mRNA represents a layer of gene regulation that to date has remained unexplored in the heart. This phenomenon may be relevant, as the positioning of the poly(A) tail in mRNAs influences the length of the 3′-untranslated region (UTR), a critical determinant of gene expression.
Objective:
To investigate whether the 3′UTR length is regulated by APA in the human heart and whether this changes in the failing heart.
Methods and Results:
We used 3′end RNA sequencing (e3′-Seq) to directly measure global patterns of APA in healthy and failing human heart specimens. By monitoring polyadenylation profiles in these hearts, we identified disease-specific APA signatures in numerous genes. Interestingly, many of the genes with shortened 3′UTRs in heart failure were enriched for functional groups such as RNA binding, whereas genes with longer 3′UTRs were enriched for cytoskeletal organization and actin binding. RNA sequencing in a larger series of human hearts revealed that these APA candidates are often differentially expressed in failing hearts, with an inverse correlation between 3′UTR length and the level of gene expression. Protein levels of the APA regulator, poly(A)-binding protein nuclear-1 were substantially downregulated in failing hearts.
Conclusions:
We provide genome-wide, high-resolution polyadenylation maps of the human heart and show that the 3′end formation of mRNA is dynamic in heart failure, suggesting that APA-mediated 3′UTR length modulation represents an additional layer of gene regulation in failing hearts.
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Affiliation(s)
- Esther E. Creemers
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Amira Bawazeer
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Alejandro P. Ugalde
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Hanneke W.M. van Deutekom
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Ingeborg van der Made
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Nina E. de Groot
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Michiel E. Adriaens
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Stuart A. Cook
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Connie R. Bezzina
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Norbert Hubner
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Jolanda van der Velden
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Ran Elkon
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Reuven Agami
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
| | - Yigal M. Pinto
- From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU
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44
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Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, Zwart W, Elkon R, Agami R. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat Biotechnol 2016; 34:192-8. [PMID: 26751173 DOI: 10.1038/nbt.3450] [Citation(s) in RCA: 289] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/08/2015] [Indexed: 01/03/2023]
Abstract
Systematic identification of noncoding regulatory elements has, to date, mainly relied on large-scale reporter assays that do not reproduce endogenous conditions. We present two distinct CRISPR-Cas9 genetic screens to identify and characterize functional enhancers in their native context. Our strategy is to target Cas9 to transcription factor binding sites in enhancer regions. We identified several functional enhancer elements and characterized the role of two of them in mediating p53 (TP53) and ERα (ESR1) gene regulation. Moreover, we show that a genomic CRISPR-Cas9 tiling screen can precisely map functional domains within enhancer elements. Our approach expands the utility of CRISPR-Cas9 to elucidate the functions of the noncoding genome.
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Affiliation(s)
- Gozde Korkmaz
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rui Lopes
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Alejandro P Ugalde
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ekaterina Nevedomskaya
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ruiqi Han
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ksenia Myacheva
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Wilbert Zwart
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ran Elkon
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands.,Erasmus MC, Rotterdam University, Rotterdam, the Netherlands
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45
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Elkon R, Loayza-Puch F, Korkmaz G, Lopes R, van Breugel PC, Bleijerveld OB, Altelaar AFM, Wolf E, Lorenzin F, Eilers M, Agami R. Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. EMBO Rep 2015; 16:1723-36. [PMID: 26538417 PMCID: PMC4687422 DOI: 10.15252/embr.201540717] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/21/2015] [Indexed: 12/15/2022] Open
Abstract
c‐Myc is one of the major human proto‐oncogenes and is often associated with tumor aggression and poor clinical outcome. Paradoxically, Myc was also reported as a suppressor of cell motility, invasiveness, and metastasis. Among the direct targets of Myc are many components of the protein synthesis machinery whose induction results in an overall increase in protein synthesis that empowers tumor cell growth. At present, it is largely unknown whether beyond the global enhancement of protein synthesis, Myc activation results in translation modulation of specific genes. Here, we measured Myc‐induced global changes in gene expression at the transcription, translation, and protein levels and uncovered extensive transcript‐specific regulation of protein translation. Particularly, we detected a broad coordination between regulation of transcription and translation upon modulation of Myc activity and showed the connection of these responses to mTOR signaling to enhance oncogenic transformation and to the TGFβ pathway to modulate cell migration and invasiveness. Our results elucidate novel facets of Myc‐induced cellular responses and provide a more comprehensive view of the consequences of its activation in cancer cells.
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Affiliation(s)
- Ran Elkon
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fabricio Loayza-Puch
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gozde Korkmaz
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rui Lopes
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pieter C van Breugel
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Onno B Bleijerveld
- Mass Spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - A F Maarten Altelaar
- Mass Spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Centre Cancer Genomics Centre, Utrecht, The Netherlands
| | - Elmar Wolf
- Biozentrum der Universität Würzburg Theodor Boveri Institut Am Hubland, Würzburg, Germany
| | - Francesca Lorenzin
- Biozentrum der Universität Würzburg Theodor Boveri Institut Am Hubland, Würzburg, Germany
| | - Martin Eilers
- Biozentrum der Universität Würzburg Theodor Boveri Institut Am Hubland, Würzburg, Germany
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands Erasmus MC, Rotterdam University, Rotterdam, The Netherlands
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46
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Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M, Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD, Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov GI, Strome SE, Durand B, Zaghloul NA, Jones SM, Reith W, Hertzano R. RFX transcription factors are essential for hearing in mice. Nat Commun 2015; 6:8549. [PMID: 26469318 PMCID: PMC4634137 DOI: 10.1038/ncomms9549] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/04/2015] [Indexed: 01/23/2023] Open
Abstract
Sensorineural hearing loss is a common and currently irreversible disorder, because mammalian hair cells (HCs) do not regenerate and current stem cell and gene delivery protocols result only in immature HC-like cells. Importantly, although the transcriptional regulators of embryonic HC development have been described, little is known about the postnatal regulators of maturating HCs. Here we apply a cell type-specific functional genomic analysis to the transcriptomes of auditory and vestibular sensory epithelia from early postnatal mice. We identify RFX transcription factors as essential and evolutionarily conserved regulators of the HC-specific transcriptomes, and detect Rfx1,2,3,5 and 7 in the developing HCs. To understand the role of RFX in hearing, we generate Rfx1/3 conditional knockout mice. We show that these mice are deaf secondary to rapid loss of initially well-formed outer HCs. These data identify an essential role for RFX in hearing and survival of the terminally differentiating outer HCs.
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Affiliation(s)
- Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Beatrice Milon
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Laura Morrison
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Manan Shah
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Sarath Vijayakumar
- Department of Special Education and Communication Disorders, University of Nebraska Lincoln, Lincoln, Nebraska 68583-0738, USA
| | - Manoj Racherla
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Carmen C. Leitch
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, USA
| | - Lorna Silipino
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Shadan Hadi
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536-0298, USA
| | - Michèle Weiss-Gayet
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, 69622 Villeurbanne, France
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Christoph D. Schmid
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, and University of Basel, 4051 Basel, Switzerland
| | - Aouatef Ait-Lounis
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Ashley Barnes
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - David J. Eisenman
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Efrat Eliyahu
- Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Gregory I. Frolenkov
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536-0298, USA
| | - Scott E. Strome
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Bénédicte Durand
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, 69622 Villeurbanne, France
| | - Norann A. Zaghloul
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, USA
| | - Sherri M. Jones
- Department of Special Education and Communication Disorders, University of Nebraska Lincoln, Lincoln, Nebraska 68583-0738, USA
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Ronna Hertzano
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA,
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47
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Rashi-Elkeles S, Warnatz HJ, Elkon R, Kupershtein A, Chobod Y, Paz A, Amstislavskiy V, Sultan M, Safer H, Nietfeld W, Lehrach H, Shamir R, Yaspo ML, Shiloh Y. Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation. Sci Signal 2014; 7:rs3. [PMID: 24825921 DOI: 10.1126/scisignal.2005032] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The DNA damage response (DDR) is a vast signaling network that is robustly activated by DNA double-strand breaks, the critical lesion induced by ionizing radiation (IR). Although much of this response operates at the protein level, a critical component of the network sustains many DDR branches by modulating the cellular transcriptome. Using deep sequencing, we delineated three layers in the transcriptional response to IR in human breast cancer cells: changes in the expression of genes encoding proteins or long noncoding RNAs, alterations in genomic binding by key transcription factors, and dynamics of epigenetic markers of active promoters and enhancers. We identified protein-coding and previously unidentified noncoding genes that were responsive to IR, and demonstrated that IR-induced transcriptional dynamics was mediated largely by the transcription factors p53 and nuclear factor κB (NF-κB) and was primarily dependent on the kinase ataxia-telangiectasia mutated (ATM). The resultant data set provides a rich resource for understanding a basic, underlying component of a critical cellular stress response.
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Affiliation(s)
- Sharon Rashi-Elkeles
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hans-Jörg Warnatz
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Ran Elkon
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ana Kupershtein
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yuliya Chobod
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Arnon Paz
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vyacheslav Amstislavskiy
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Marc Sultan
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Hershel Safer
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Wilfried Nietfeld
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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Abstract
The 3' end of most protein-coding genes and long non-coding RNAs is cleaved and polyadenylated. Recent discoveries have revealed that a large proportion of these genes contains more than one polyadenylation site. Therefore, alternative polyadenylation (APA) is a widespread phenomenon, generating mRNAs with alternative 3' ends. APA contributes to the complexity of the transcriptome by generating isoforms that differ either in their coding sequence or in their 3' untranslated regions (UTRs), thereby potentially regulating the function, stability, localization and translation efficiency of target RNAs. Here, we review our current understanding of the polyadenylation process and the latest progress in the identification of APA events, mechanisms that regulate poly(A) site selection, and biological processes and diseases resulting from APA.
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Affiliation(s)
- Ran Elkon
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Loayza-Puch F, Drost J, Rooijers K, Lopes R, Elkon R, Agami R. p53 induces transcriptional and translational programs to suppress cell proliferation and growth. Genome Biol 2013; 14:R32. [PMID: 23594524 PMCID: PMC4053767 DOI: 10.1186/gb-2013-14-4-r32] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 04/17/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Cell growth and proliferation are tightly connected to ensure that appropriately sized daughter cells are generated following mitosis. Energy stress blocks cell growth and proliferation, a critical response for survival under extreme conditions. Excessive oncogenic stress leads to p53 activation and the induction of senescence, an irreversible state of cell-cycle arrest and a critical component in the suppression of tumorigenesis. Nutrient-sensing and mitogenic cues converge on a major signaling node, which regulates the activity of the mTOR kinase. Although transcriptional responses to energy and oncogenic stresses have been examined by many gene-expression experiments, a global exploration of the modulation of mRNA translation in response to these conditions is lacking. RESULTS We combine RNA sequencing and ribosomal profiling analyses to systematically delineate modes of transcriptional and translational regulation induced in response to conditions of limited energy, oncogenic stress and cellular transformation. We detect a key role for mTOR and p53 in these distinct physiological states, and provide the first genome-wide demonstration that p53 activation results in mTOR inhibition and a consequent global repression of protein translation. We confirm the role of the direct p53 target genes Sestrin1 and Sestrin2 in this response, as part of the broad modulation of gene expression induced by p53 activation. CONCLUSIONS We delineate a bimodal tumor-suppressive regulatory program activated by p53, in which cell-cycle arrest is imposed mainly at the transcriptional level, whereas cell growth inhibition is enforced by global repression of the translation machinery.
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Morris AR, Bos A, Diosdado B, Rooijers K, Elkon R, Bolijn AS, Carvalho B, Meijer GA, Agami R. Alternative cleavage and polyadenylation during colorectal cancer development. Clin Cancer Res 2012; 18:5256-66. [PMID: 22874640 DOI: 10.1158/1078-0432.ccr-12-0543] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Alternative cleavage and polyadenylation (APA) of mRNAs is a phenomenon that alters 3'-untranslated region length leading to altered posttranscriptional regulation of gene expression. Changing APA patterns have been shown to result in misregulation of genes involved in carcinogenesis; therefore, we hypothesized that altered APA contributes to progression of colorectal cancer, and that measurement of APA may lead to discovery of novel biomarkers. EXPERIMENTAL DESIGN We used next-generation sequencing to directly measure global patterns of APA changes during colorectal carcinoma progression in 15 human patient samples. Results were validated in a larger cohort of 50 patients, including 5 normal/carcinoma pairs from individuals. RESULTS We discovered numerous genes presenting progressive changes in APA. Genes undergoing untranslated region (3'UTR) shortening were enriched for functional groups such as cell-cycle and nucleic acid-binding and processing factors, and those undergoing 3'UTR lengthening or alternative 3'UTR usage were enriched for categories such as cell-cell adhesion and extracellular matrix. We found indications that APA changes result from differential processing of transcripts because of increased expression of cleavage and polyadenylation factors. Quantitative PCR analysis in a larger series of human patient samples, including matched pairs, confirmed APA changes in DMKN, PDXK, and PPIE genes. CONCLUSIONS Our results suggest that genes undergoing altered APA during human cancer progression may be useful novel biomarkers and potentially targeted for disease prevention and treatment. We propose that the strategy presented here may be broadly useful in discovery of novel biomarkers for other types of cancer and human disease.
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