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Kiryluk K, Sanchez-Rodriguez E, Zhou XJ, Zanoni F, Liu L, Mladkova N, Khan A, Marasa M, Zhang JY, Balderes O, Sanna-Cherchi S, Bomback AS, Canetta PA, Appel GB, Radhakrishnan J, Trimarchi H, Sprangers B, Cattran DC, Reich H, Pei Y, Ravani P, Galesic K, Maixnerova D, Tesar V, Stengel B, Metzger M, Canaud G, Maillard N, Berthoux F, Berthelot L, Pillebout E, Monteiro R, Nelson R, Wyatt RJ, Smoyer W, Mahan J, Samhar AA, Hidalgo G, Quiroga A, Weng P, Sreedharan R, Selewski D, Davis K, Kallash M, Vasylyeva TL, Rheault M, Chishti A, Ranch D, Wenderfer SE, Samsonov D, Claes DJ, Akchurin O, Goumenos D, Stangou M, Nagy J, Kovacs T, Fiaccadori E, Amoroso A, Barlassina C, Cusi D, Del Vecchio L, Battaglia GG, Bodria M, Boer E, Bono L, Boscutti G, Caridi G, Lugani F, Ghiggeri G, Coppo R, Peruzzi L, Esposito V, Esposito C, Feriozzi S, Polci R, Frasca G, Galliani M, Garozzo M, Mitrotti A, Gesualdo L, Granata S, Zaza G, Londrino F, Magistroni R, Pisani I, Magnano A, Marcantoni C, Messa P, Mignani R, Pani A, Ponticelli C, Roccatello D, Salvadori M, Salvi E, Santoro D, Gembillo G, Savoldi S, Spotti D, Zamboli P, Izzi C, Alberici F, Delbarba E, Florczak M, Krata N, Mucha K, Pączek L, Niemczyk S, Moszczuk B, Pańczyk-Tomaszewska M, Mizerska-Wasiak M, Perkowska-Ptasińska A, Bączkowska T, Durlik M, Pawlaczyk K, Sikora P, Zaniew M, Kaminska D, Krajewska M, Kuzmiuk-Glembin I, Heleniak Z, Bullo-Piontecka B, Liberek T, Dębska-Slizien A, Hryszko T, Materna-Kiryluk A, Miklaszewska M, Szczepańska M, Dyga K, Machura E, Siniewicz-Luzeńczyk K, Pawlak-Bratkowska M, Tkaczyk M, Runowski D, Kwella N, Drożdż D, Habura I, Kronenberg F, Prikhodina L, van Heel D, Fontaine B, Cotsapas C, Wijmenga C, Franke A, Annese V, Gregersen PK, Parameswaran S, Weirauch M, Kottyan L, Harley JB, Suzuki H, Narita I, Goto S, Lee H, Kim DK, Kim YS, Park JH, Cho B, Choi M, Van Wijk A, Huerta A, Ars E, Ballarin J, Lundberg S, Vogt B, Mani LY, Caliskan Y, Barratt J, Abeygunaratne T, Kalra PA, Gale DP, Panzer U, Rauen T, Floege J, Schlosser P, Ekici AB, Eckardt KU, Chen N, Xie J, Lifton RP, Loos RJF, Kenny EE, Ionita-Laza I, Köttgen A, Julian BA, Novak J, Scolari F, Zhang H, Gharavi AG. Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy. Nat Genet 2023; 55:1091-1105. [PMID: 37337107 DOI: 10.1038/s41588-023-01422-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 12/06/2021] [Accepted: 05/05/2023] [Indexed: 06/21/2023]
Abstract
IgA nephropathy (IgAN) is a progressive form of kidney disease defined by glomerular deposition of IgA. Here we performed a genome-wide association study of 10,146 kidney-biopsy-diagnosed IgAN cases and 28,751 controls across 17 international cohorts. We defined 30 genome-wide significant risk loci explaining 11% of disease risk. A total of 16 loci were new, including TNFSF4/TNFSF18, REL, CD28, PF4V1, LY86, LYN, ANXA3, TNFSF8/TNFSF15, REEP3, ZMIZ1, OVOL1/RELA, ETS1, IGH, IRF8, TNFRSF13B and FCAR. The risk loci were enriched in gene orthologs causing abnormal IgA levels when genetically manipulated in mice. We also observed a positive genetic correlation between IgAN and serum IgA levels. High polygenic score for IgAN was associated with earlier onset of kidney failure. In a comprehensive functional annotation analysis of candidate causal genes, we observed convergence of biological candidates on a common set of inflammatory signaling pathways and cytokine ligand-receptor pairs, prioritizing potential new drug targets.
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Affiliation(s)
- Krzysztof Kiryluk
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York City, NY, USA.
| | - Elena Sanchez-Rodriguez
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Francesca Zanoni
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Lili Liu
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Nikol Mladkova
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Atlas Khan
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Maddalena Marasa
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Jun Y Zhang
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Olivia Balderes
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Simone Sanna-Cherchi
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
- Institute for Genomic Medicine, Columbia University, New York City, NY, USA
| | - Andrew S Bomback
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Pietro A Canetta
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Gerald B Appel
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Jai Radhakrishnan
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Hernan Trimarchi
- Nephrology Service, Hospital Británico de Buenos Aires, Buenos Aires, Argentina
| | - Ben Sprangers
- Department of Microbiology and Immunology, Laboratory of Molecular Immunology, KU Leuven, Leuven, Belgium
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Daniel C Cattran
- Department of Nephrology, University of Toronto, Toronto General Hospital, Toronto, Ontario, Canada
| | - Heather Reich
- Department of Nephrology, University of Toronto, Toronto General Hospital, Toronto, Ontario, Canada
| | - York Pei
- Department of Nephrology, University of Toronto, Toronto General Hospital, Toronto, Ontario, Canada
| | - Pietro Ravani
- Division of Nephrology, Department of Internal Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Dita Maixnerova
- 1st Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Vladimir Tesar
- 1st Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Benedicte Stengel
- Centre for Research in Epidemiology and Population Health (CESP), Paris-Saclay University, Versailles Saint Quentin University, INSERM Clinical Epidemiology Team, Villejuif, France
| | - Marie Metzger
- Centre for Research in Epidemiology and Population Health (CESP), Paris-Saclay University, Versailles Saint Quentin University, INSERM Clinical Epidemiology Team, Villejuif, France
| | - Guillaume Canaud
- Université de Paris, Hôpital Necker-Enfants Malades, Paris, France
| | - Nicolas Maillard
- Nephrology, Dialysis, and Renal Transplantation Department, University North Hospital, Saint Etienne, France
| | - Francois Berthoux
- Nephrology, Dialysis, and Renal Transplantation Department, University North Hospital, Saint Etienne, France
| | | | - Evangeline Pillebout
- Center for Research on Inflammation, University of Paris, INSERM and CNRS, Paris, France
| | - Renato Monteiro
- Center for Research on Inflammation, University of Paris, INSERM and CNRS, Paris, France
| | - Raoul Nelson
- Division of Pediatric Nephrology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Robert J Wyatt
- Division of Pediatric Nephrology, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Children's Foundation Research Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - William Smoyer
- Division of Pediatric Nephrology, Nationwide Children's Hospital, Columbus, OH, USA
| | - John Mahan
- Division of Pediatric Nephrology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Al-Akash Samhar
- Division of Pediatric Nephrology, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Guillermo Hidalgo
- Division of Pediatric Nephrology, Department of Pediatrics, HMH Hackensack University Medical Center, Hackensack, NJ, USA
| | - Alejandro Quiroga
- Division of Pediatric Nephrology, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Patricia Weng
- Division of Pediatric Nephrology, Mattel Children's Hospital, Los Angeles, CA, USA
| | - Raji Sreedharan
- Division of Pediatric Nephrology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - David Selewski
- Division of Pediatric Nephrology, Mott Children's Hospital, Ann Arbor, MI, USA
| | - Keefe Davis
- Division of Pediatric Nephrology, Department of Pediatrics, The Medical University of South Carolina (MUSC), Charleston, SC, USA
| | - Mahmoud Kallash
- Division of Pediatric Nephrology, SUNY Buffalo, Buffalo, NY, USA
| | - Tetyana L Vasylyeva
- Division of Pediatric Nephrology, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Michelle Rheault
- Division of Pediatric Nephrology, University of Minnesota, Minneapolis, MN, USA
| | - Aftab Chishti
- Division of Pediatric Nephrology, University of Kentucky, Lexington, KY, USA
| | - Daniel Ranch
- Division of Pediatric Nephrology, Department of Pediatrics, University of Kentucky, Lexington, KY, USA
| | - Scott E Wenderfer
- Division of Pediatric Nephrology, Baylor College of Medicine/Texas Children's Hospital, Houston, TX, USA
| | - Dmitry Samsonov
- Division of Pediatric Nephrology, Boston Children's Hospital, Boston, MA, USA
| | - Donna J Claes
- Division of Pediatric Nephrology, Department of Pediatrics, New York Medical College, New York City, NY, USA
| | - Oleh Akchurin
- Division of Pediatric Nephrology, Department of Pediatrics, Weill Cornell Medical College, New York City, NY, USA
| | | | - Maria Stangou
- The Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Judit Nagy
- 2nd Department of Internal Medicine, Nephrological and Diabetological Center, University of Pécs, Pécs, Hungary
| | - Tibor Kovacs
- 2nd Department of Internal Medicine, Nephrological and Diabetological Center, University of Pécs, Pécs, Hungary
| | - Enrico Fiaccadori
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Cristina Barlassina
- Renal Division, Dipartimento di Medicina, Chirurgia e Odontoiatria, San Paolo Hospital, School of Medicine, University of Milan, Milan, Italy
| | - Daniele Cusi
- Renal Division, Dipartimento di Medicina, Chirurgia e Odontoiatria, San Paolo Hospital, School of Medicine, University of Milan, Milan, Italy
| | | | | | | | - Emanuela Boer
- Division of Nephrology and Dialysis, Gorizia Hospital, Gorizia, Italy
| | - Luisa Bono
- Nephrology and Dialysis, A.R.N.A.S. Civico and Benfratelli, Palermo, Italy
| | - Giuliano Boscutti
- Nephrology, Dialysis and Renal Transplant Unit, S. Maria della Misericordia Hospital, ASUFC, Udine, Italy
| | - Gianluca Caridi
- Division of Nephrology, Dialysis and Transplantation, IRCCS Giannina Gaslini Institute, Genova, Italy
| | - Francesca Lugani
- Division of Nephrology, Dialysis and Transplantation, IRCCS Giannina Gaslini Institute, Genova, Italy
| | - GianMarco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, IRCCS Giannina Gaslini Institute, Genova, Italy
| | - Rosanna Coppo
- Regina Margherita Children's Hospital, Torino, Italy
| | - Licia Peruzzi
- Regina Margherita Children's Hospital, Torino, Italy
| | | | | | | | | | - Giovanni Frasca
- Division of Nephrology, Dialysis and Renal Transplantation, Riuniti Hospital, Ancona, Italy
| | | | - Maurizio Garozzo
- Unità Operativa di Nefrologia e Dialisi, Ospedale di Acireale, Acireale, Italy
| | - Adele Mitrotti
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Simona Granata
- Renal Unit, Department of Medicine, University of Verona, Verona, Italy
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University of Verona, Verona, Italy
| | | | - Riccardo Magistroni
- Department of Surgical, Medical, Dental, Oncologic and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Isabella Pisani
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Andrea Magnano
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | - Piergiorgio Messa
- Nephrology Dialysis and Kidney Transplant Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Renzo Mignani
- Azienda Unità Sanitaria Locale Rimini, Rimini, Italy
| | - Antonello Pani
- Department of Nephrology and Dialysis, G. Brotzu Hospital, Cagliari, Italy
| | | | - Dario Roccatello
- Nephrology and Dialysis Unit, G. Bosco Hub Hospital (ERK-net Member) and University of Torino, Torino, Italy
| | - Maurizio Salvadori
- Division of Nephrology and Renal Transplantation, Carreggi Hospital, Florence, Italy
| | - Erica Salvi
- Renal Division, DMCO (Dipartimento di Medicina, Chirurgia e Odontoiatria), San Paolo Hospital, School of Medicine, University of Milan, Milan, Italy
| | - Domenico Santoro
- Unit of Nephrology and Dialysis, AOU G Martino, University of Messina, Messina, Italy
| | - Guido Gembillo
- Unit of Nephrology and Dialysis, AOU G Martino, University of Messina, Messina, Italy
| | - Silvana Savoldi
- Unit of Nephrology and Dialysis, ASL TO4-Consultorio Cirié, Turin, Italy
| | | | | | - Claudia Izzi
- Department of Medical and Surgical Specialties and Nephrology Unit, University of Brescia-ASST Spedali Civili, Brescia, Italy
| | - Federico Alberici
- Department of Medical and Surgical Specialties and Nephrology Unit, University of Brescia-ASST Spedali Civili, Brescia, Italy
| | - Elisa Delbarba
- Department of Medical and Surgical Specialties and Nephrology Unit, University of Brescia-ASST Spedali Civili, Brescia, Italy
| | - Michał Florczak
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Natalia Krata
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Leszek Pączek
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Stanisław Niemczyk
- Department of Internal Disease, Nephrology and Dialysotherapy, Military Institute of Medicine, Warsaw, Poland
| | - Barbara Moszczuk
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | | | | | | | - Teresa Bączkowska
- Department of Transplantation Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Durlik
- Department of Transplantation Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Pawlaczyk
- Department of Nephrology, Transplantology and Internal Medicine, Poznan Medical University, Poznan, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Dorota Kaminska
- Clinical Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Magdalena Krajewska
- Clinical Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Izabella Kuzmiuk-Glembin
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Zbigniew Heleniak
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Barbara Bullo-Piontecka
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Tomasz Liberek
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Alicja Dębska-Slizien
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Tomasz Hryszko
- 2nd Department of Nephrology and Hypertension with Dialysis Unit, Medical University of Bialystok, Bialystok, Poland
| | | | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Szczepańska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Katarzyna Dyga
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Edyta Machura
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Katarzyna Siniewicz-Luzeńczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Monika Pawlak-Bratkowska
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Dariusz Runowski
- Department of Nephrology, Kidney Transplantation and Hypertension, Children's Memorial Health Institute, Warsaw, Poland
| | - Norbert Kwella
- Department of Nephrology, Hypertension and Internal Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Dorota Drożdż
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Ireneusz Habura
- Department of Nephrology, Karol Marcinkowski Hospital, Zielona Góra, Poland
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Larisa Prikhodina
- Division of Inherited and Acquired Kidney Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - David van Heel
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Bertrand Fontaine
- Sorbonne University, INSERM, Center of Research in Myology, Institute of Myology, University Hospital Pitie-Salpetriere, Paris, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Service of Neuro-Myology, University Hospital Pitie-Salpetriere, Paris, France
| | - Chris Cotsapas
- Departments of Neurology and Genetics, Yale University, New Haven, CT, USA
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Vito Annese
- CBP American Hospital, Dubai, United Arab Emirates
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, North Shore LIJ Health System, New York City, NY, USA
| | | | - Matthew Weirauch
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Leah Kottyan
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John B Harley
- US Department of Veterans Affairs Medical Center and Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, USA
| | - Hitoshi Suzuki
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shin Goto
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hajeong Lee
- Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong Ki Kim
- Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yon Su Kim
- Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jin-Ho Park
- Department of Family Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | - BeLong Cho
- Department of Family Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
- Institute on Aging, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Murim Choi
- Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ans Van Wijk
- Amsterdam University Medical Centre, VU University Medical Center (VUMC), Amsterdam, the Netherlands
| | - Ana Huerta
- Hospital Universitario Puerta del Hierro Majadahonda, REDINREN, IISCIII, Madrid, Spain
| | - Elisabet Ars
- Molecular Biology Laboratory and Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autònoma de Barcelona, REDINREN, IISCIII, Barcelona, Spain
| | - Jose Ballarin
- Molecular Biology Laboratory and Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autònoma de Barcelona, REDINREN, IISCIII, Barcelona, Spain
| | - Sigrid Lundberg
- Department of Nephrology, Danderyd University Hospital, and Department of Clinical Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Bruno Vogt
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Laila-Yasmin Mani
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yasar Caliskan
- Division of Nephrology, Saint Louis University, Saint Louis, MO, USA
| | - Jonathan Barratt
- John Walls Renal Unit, University Hospitals of Leicester, Leicester, UK
| | | | | | - Daniel P Gale
- Department of Renal Medicine, University College London, London, UK
| | | | - Thomas Rauen
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nan Chen
- Department of Nephrology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jingyuan Xie
- Department of Nephrology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York City, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eimear E Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York City, NY, USA
- Center for Population Genomic Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Bruce A Julian
- Departments of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jan Novak
- Departments of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Francesco Scolari
- Department of Medical and Surgical Specialties and Nephrology Unit, University of Brescia-ASST Spedali Civili, Brescia, Italy
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Ali G Gharavi
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York City, NY, USA.
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Burley K, Fitzgibbon L, van Heel D, Vuckovic D, Mumford AD. PIK3R3 is a candidate regulator of platelet count in people of Bangladeshi ancestry. Res Pract Thromb Haemost 2023; 7:100175. [PMID: 37538507 PMCID: PMC10394561 DOI: 10.1016/j.rpth.2023.100175] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 08/05/2023] Open
Abstract
Background Blood platelets are mediators of atherothrombotic disease and are regulated by complex sets of genes. Association studies in European ancestry populations have already detected informative platelet regulatory loci. Studies in other ancestries can potentially reveal new associations because of different allele frequencies, linkage structures, and variant effects. Objectives To reveal new regulatory genes for platelet count (PLT). Methods Genome-wide association studies (GWAS) were performed in 20,218 Bangladeshi and 9198 Pakistani individuals from the Genes & Health study. Loci significantly associated with PLT underwent fine-mapping to identify candidate genes. Results Of 1588 significantly associated variants (P < 5 × 10-8) at 20 loci in the Bangladeshi analysis, most replicated findings in prior transancestry GWAS and in the Pakistani analysis. However, the Bangladeshi locus defined by rs946528 (chr1:46019890) did not associate with PLT in the Pakistani analysis but was in the same linkage disequilibrium block (r2 ≥ 0.5) as PLT-associated variants in prior East Asian GWAS. The single independent association signal was refined to a 95% credible set of 343 variants spanning 8 coding genes. Functional annotation, mapping to megakaryocyte regulatory regions, and colocalization with blood expression quantitative trait loci identified the likely mediator of the PLT phenotype to be PIK3R3 encoding a regulator of phosphoinositol 3-kinase (PI3K). Conclusion Abnormal PI3K activity in the vessel wall is already implicated in the pathogenesis of atherothrombosis. Our identification of a new association between PIK3R3 and PLT provides further mechanistic insights into the contribution of the PI3K pathway to platelet biology.
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Affiliation(s)
- Kate Burley
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Lucy Fitzgibbon
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - David van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Dragana Vuckovic
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Andrew D. Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, 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C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, 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LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Cuvertino S, Hartill V, Colyer A, Garner T, Nair N, Al-Gazali L, Canham N, Faundes V, Flinter F, Hertecant J, Holder-Espinasse M, Jackson B, Lynch SA, Nadat F, Narasimhan VM, Peckham M, Sellers R, Seri M, Montanari F, Southgate L, Squeo GM, Trembath R, van Heel D, Venuto S, Weisberg D, Stals K, Ellard S, Barton A, Kimber SJ, Sheridan E, Merla G, Stevens A, Johnson CA, Banka S. Correction: A restricted spectrum of missense KMT2D variants cause a multiple malformations disorder distinct from Kabuki syndrome. Genet Med 2020; 22:980. [PMID: 32203228 PMCID: PMC7200592 DOI: 10.1038/s41436-020-0784-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Sara Cuvertino
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Verity Hartill
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Alice Colyer
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Terence Garner
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Nisha Nair
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine & Health Sciences, United Arab University, Al-Ain, UAE
| | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK.,North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Victor Faundes
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Frances Flinter
- Department of Clinical Genetics, Guy's & St Thomas NHS Foundation Trust, London, UK
| | | | | | - Brian Jackson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Sally Ann Lynch
- Temple street Children's University Hospital, Dublin, Ireland
| | - Fatima Nadat
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | | | - Michelle Peckham
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Robert Sellers
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Marco Seri
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Francesca Montanari
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Laura Southgate
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.,Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Gabriella Maria Squeo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Richard Trembath
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | | | - Santina Venuto
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Daniel Weisberg
- Clinical Psychology Department, Royal Manchester Children's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK
| | - Karen Stals
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | | | - Anne Barton
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Eamonn Sheridan
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Giuseppe Merla
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Adam Stevens
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Colin A Johnson
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK. .,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK.
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Cuvertino S, Hartill V, Colyer A, Garner T, Nair N, Al-Gazali L, Canham N, Faundes V, Flinter F, Hertecant J, Holder-Espinasse M, Jackson B, Lynch SA, Nadat F, Narasimhan VM, Peckham M, Sellers R, Seri M, Montanari F, Southgate L, Squeo GM, Trembath R, van Heel D, Venuto S, Weisberg D, Stals K, Ellard S, Barton A, Kimber SJ, Sheridan E, Merla G, Stevens A, Johnson CA, Banka S. A restricted spectrum of missense KMT2D variants cause a multiple malformations disorder distinct from Kabuki syndrome. Genet Med 2020; 22:867-877. [PMID: 31949313 PMCID: PMC7200597 DOI: 10.1038/s41436-019-0743-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 10/30/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose To investigate if specific exon 38 or 39 KMT2D missense variants (MVs) cause a condition distinct from
Kabuki syndrome type 1 (KS1). Methods Multiple individuals, with MVs in exons 38 or 39 of KMT2D that encode a highly conserved region of 54
amino acids flanked by Val3527 and Lys3583, were identified and phenotyped.
Functional tests were performed to study their pathogenicity and understand the
disease mechanism. Results The consistent clinical features of the affected individuals, from
seven unrelated families, included choanal atresia, athelia or hypoplastic
nipples, branchial sinus abnormalities, neck pits, lacrimal duct anomalies,
hearing loss, external ear malformations, and thyroid abnormalities. None of the
individuals had intellectual disability. The frequency of clinical features,
objective software-based facial analysis metrics, and genome-wide peripheral
blood DNA methylation patterns in these patients were significantly different
from that of KS1. Circular dichroism spectroscopy indicated that these MVs
perturb KMT2D secondary structure through an increased disordered to ɑ-helical
transition. Conclusion KMT2D MVs located in a specific
region spanning exons 38 and 39 and affecting highly conserved residues cause a
novel multiple malformations syndrome distinct from KS1. Unlike KMT2D haploinsufficiency in KS1, these MVs likely
result in disease through a dominant negative mechanism.
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Affiliation(s)
- Sara Cuvertino
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Verity Hartill
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Alice Colyer
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Terence Garner
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Nisha Nair
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine & Health Sciences, United Arab University, Al-Ain, UAE
| | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK.,North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Victor Faundes
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Frances Flinter
- Department of Clinical Genetics, Guy's & St Thomas NHS Foundation Trust, London, UK
| | | | | | - Brian Jackson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Sally Ann Lynch
- Temple street Children's University Hospital, Dublin, Ireland
| | - Fatima Nadat
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | | | - Michelle Peckham
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Robert Sellers
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Marco Seri
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Francesca Montanari
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Laura Southgate
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.,Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Gabriella Maria Squeo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Richard Trembath
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | | | - Santina Venuto
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Daniel Weisberg
- Clinical Psychology Department, Royal Manchester Children's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK
| | - Karen Stals
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | | | - Anne Barton
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Eamonn Sheridan
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Giuseppe Merla
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Adam Stevens
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Colin A Johnson
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK. .,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK.
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6
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Liu JZ, Hov JR, Folseraas T, Ellinghaus E, Rushbrook SM, Doncheva NT, Andreassen OA, Weersma RK, Weismüller TJ, Eksteen B, Invernizzi P, Hirschfield GM, Gotthardt DN, Pares A, Ellinghaus D, Shah T, Juran BD, Milkiewicz P, Rust C, Schramm C, Müller T, Srivastava B, Dalekos G, Nöthen MM, Herms S, Winkelmann J, Mitrovic M, Braun F, Ponsioen CY, Croucher PJP, Sterneck M, Teufel A, Mason AL, Saarela J, Leppa V, Dorfman R, Alvaro D, Floreani A, Onengut-Gumuscu S, Rich SS, Thompson WK, Schork AJ, Næss S, Thomsen I, Mayr G, König IR, Hveem K, Cleynen I, Gutierrez-Achury J, Ricaño-Ponce I, van Heel D, Björnsson E, Sandford RN, Durie PR, Melum E, Vatn MH, Silverberg MS, Duerr RH, Padyukov L, Brand S, Sans M, Annese V, Achkar JP, Boberg KM, Marschall HU, Chazouillères O, Bowlus CL, Wijmenga C, Schrumpf E, Vermeire S, Albrecht M, Rioux JD, Alexander G, Bergquist A, Cho J, Schreiber S, Manns MP, Färkkilä M, Dale AM, Chapman RW, Lazaridis KN, Franke A, Anderson CA, Karlsen TH. Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nat Genet 2013; 45:670-5. [PMID: 23603763 PMCID: PMC3667736 DOI: 10.1038/ng.2616] [Citation(s) in RCA: 277] [Impact Index Per Article: 25.2] [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: 10/09/2012] [Accepted: 03/29/2013] [Indexed: 12/14/2022]
Abstract
Primary sclerosing cholangitis (PSC) is a severe liver disease of unknown etiology leading to fibrotic destruction of the bile ducts and ultimately to the need for liver transplantation. We compared 3,789 PSC cases of European ancestry to 25,079 population controls across 130,422 SNPs genotyped using the Immunochip. We identified 12 genome-wide significant associations outside the human leukocyte antigen (HLA) complex, 9 of which were new, increasing the number of known PSC risk loci to 16. Despite comorbidity with inflammatory bowel disease (IBD) in 72% of the cases, 6 of the 12 loci showed significantly stronger association with PSC than with IBD, suggesting overlapping yet distinct genetic architectures for these two diseases. We incorporated association statistics from 7 diseases clinically occurring with PSC in the analysis and found suggestive evidence for 33 additional pleiotropic PSC risk loci. Together with network analyses, these findings add to the genetic risk map of PSC and expand on the relationship between PSC and other immune-mediated diseases.
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Affiliation(s)
- Jimmy Z. Liu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Johannes Roksund Hov
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Trine Folseraas
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Simon M. Rushbrook
- Department of Gastroenterology and Hepatology, Norfolk and Norwich, University Hospitals NHS Trust, Norwich, UK
| | | | - Ole A. Andreassen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, Ulleval, Oslo, Norway
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, the Netherlands
| | - Tobias J. Weismüller
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Integrated Research and Treatment Center-Transplantation (IFB-tx), Hannover Medical School, Hannover, Germany
- Current affiliation: Department of Internal Medicine 1, University Hospital of Bonn, Bonn, Germany
| | - Bertus Eksteen
- Snyder Institute of Chronic Diseases, Department of Medicine, University of Calgary, Calgary, Canada
| | - Pietro Invernizzi
- Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano (MI), Italy
| | - Gideon M. Hirschfield
- Division of Gastroenterology, Department of Medicine, University of Toronto, Toronto, Canada
- Centre for Liver Research, NIHR Biomedical Research Unit, Birmingham, UK
| | | | - Albert Pares
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tejas Shah
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Brian D. Juran
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic, College of Medicine, Rochester, Minnesota, USA
| | - Piotr Milkiewicz
- Liver Unit and Liver Research Laboratories, Pomeranian Medical University, Szczecin, Poland
| | - Christian Rust
- Department of Medicine 2, Grosshadern, University of Munich, Munich, Germany
| | - Christoph Schramm
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Müller
- Department of Internal Medicine, Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Brijesh Srivastava
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Georgios Dalekos
- Department of Medicine, Medical School, University of Thessaly, Larissa, Greece
- Research Laboratory of Internal Medicine, Medical School, University of Thessaly, Larissa, Greece
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Department of Neurology, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Mitja Mitrovic
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Felix Braun
- Department of General, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Medical Centre Schleswig-Holstein, Campus Kiel, Germany
| | - Cyriel Y. Ponsioen
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, the Netherlands
| | - Peter J. P. Croucher
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, United States of America
| | - Martina Sterneck
- Department of Hepatobiliary Surgery and Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas Teufel
- 1st Department of Medicine, University of Mainz, Mainz, Germany
| | - Andrew L. Mason
- Division of Gastroenterology and Hepatology, University of Alberta, Edmonton, Alberta, Canada
| | - Janna Saarela
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Virpi Leppa
- Public Health Genomics Unit, Institute for Molecular Medicine Finland FIMM, University of Helsinki and National Institute for Health and Welfare, Helsinki, Finland
| | - Ruslan Dorfman
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada
| | - Domenico Alvaro
- Department of Clinical Medicine, Division of Gastroenterology, Sapienza University of Rome, Rome, Italy
| | - Annarosa Floreani
- Dept. of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padova, Italy
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, Division of Endocrinology & Metabolism, University of Virginia, Charlottesville, USA
- Department of Internal Medicine, Division of Endocrinology & Metabolism, University of Virginia, Charlottesville, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, USA
| | - Wesley K. Thompson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Andrew J. Schork
- Graduate Program in Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Sigrid Næss
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingo Thomsen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Gabriele Mayr
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Inke R. König
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - Kristian Hveem
- Department of Public Health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Isabelle Cleynen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Clinical and Experimental Medicine, KU Leuven, Leuven, Belgium
| | - Javier Gutierrez-Achury
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Isis Ricaño-Ponce
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - David van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Einar Björnsson
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Landspitali University Hospital, Reykjavik, Iceland
| | - Richard N. Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Peter R. Durie
- Physiology and Experimental Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Espen Melum
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- EpiGen, Campus AHUS, Akershus University Hospital, Nordbyhagen, Norway
| | - Mark S. Silverberg
- Inflammatory Bowel Disease (IBD) Group, Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Toronto, Ontario, Canada
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Stephan Brand
- Department of Medicine II, University Hospital Munich-Grosshadern, Ludwig-Maximilians-University Munich, Germany
| | - Miquel Sans
- Department of Digestive Diseases, Centro Médico Teknon, Barcelona, Spain
| | - Vito Annese
- Division of Gastroenterology, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievodella Sofferenza Hospital, San Giovanni Rotondo, Italy
- Unit of Gastroenterology SOD2, Azienda Ospedaliero Universitaria Careggi, Florence, Italy
| | - Jean-Paul Achkar
- Department of Gastroenterology and Hepatology, Digestive Disease Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kirsten Muri Boberg
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Hanns-Ulrich Marschall
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy and University Hospital, Gothenburg, Sweden
| | - Olivier Chazouillères
- AP-HP, Hôpital Saint Antoine, Department of Hepatology, UPMC Univ Paris 06, Paris, France
| | - Christopher L. Bowlus
- Division of Gastroenterology and Hepatology, University of California Davis, Davis, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Erik Schrumpf
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Severine Vermeire
- Department of Clinical and Experimental Medicine, KU Leuven, Leuven, Belgium
- Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
| | - Mario Albrecht
- Max Planck Institute for Informatics, Saarbrücken, Germany
- Department of Bioinformatics, Institute of Biometrics and Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | | | | | - John D. Rioux
- Université de Montréal, Research Center, Montreal, Quebec, Canada
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | - Graeme Alexander
- Department of Medicine, Division of Hepatology, University of Cambridge, Cambridge, UK
| | - Annika Bergquist
- Department of Gastroenterology and Hepatology, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Judy Cho
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, USA
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Department for General Internal Medicine, Christian-Albrechts-University, Kiel, Germany
- Popgen Biobank, University Hospital Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Michael P. Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Integrated Research and Treatment Center-Transplantation (IFB-tx), Hannover Medical School, Hannover, Germany
| | - Martti Färkkilä
- Division of Gastroenterology, Department of Medicine, Helsinki University Hospital, Finland
| | - Anders M. Dale
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Roger W. Chapman
- Department of Hepatology, John Radcliffe University Hospitals NHS Trust, Oxford, UK
| | - Konstantinos N. Lazaridis
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic, College of Medicine, Rochester, Minnesota, USA
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Carl A. Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Tom H. Karlsen
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Division of Gastroenterology, Institute of Medicine, University of Bergen, Bergen, Norway
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7
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Fu J, Wolfs MGM, Deelen P, Westra HJ, Fehrmann RSN, te Meerman GJ, Buurman WA, Rensen SSM, Groen HJM, Weersma RK, van den Berg LH, Veldink J, Ophoff RA, Snieder H, van Heel D, Jansen RC, Hofker MH, Wijmenga C, Franke L. Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS Genet 2012; 8:e1002431. [PMID: 22275870 PMCID: PMC3261927 DOI: 10.1371/journal.pgen.1002431] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [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: 07/19/2011] [Accepted: 11/08/2011] [Indexed: 01/17/2023] Open
Abstract
It is known that genetic variants can affect gene expression, but it is not yet completely clear through what mechanisms genetic variation mediate this expression. We therefore compared the cis-effect of single nucleotide polymorphisms (SNPs) on gene expression between blood samples from 1,240 human subjects and four primary non-blood tissues (liver, subcutaneous, and visceral adipose tissue and skeletal muscle) from 85 subjects. We characterized four different mechanisms for 2,072 probes that show tissue-dependent genetic regulation between blood and non-blood tissues: on average 33.2% only showed cis-regulation in non-blood tissues; 14.5% of the eQTL probes were regulated by different, independent SNPs depending on the tissue of investigation. 47.9% showed a different effect size although they were regulated by the same SNPs. Surprisingly, we observed that 4.4% were regulated by the same SNP but with opposite allelic direction. We show here that SNPs that are located in transcriptional regulatory elements are enriched for tissue-dependent regulation, including SNPs at 3' and 5' untranslated regions (P = 1.84×10(-5) and 4.7×10(-4), respectively) and SNPs that are synonymous-coding (P = 9.9×10(-4)). SNPs that are associated with complex traits more often exert a tissue-dependent effect on gene expression (P = 2.6×10(-10)). Our study yields new insights into the genetic basis of tissue-dependent expression and suggests that complex trait associated genetic variants have even more complex regulatory effects than previously anticipated.
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Affiliation(s)
- Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail: (JF); (LF)
| | - Marcel G. M. Wolfs
- Department of Pathology and Medical Biology, Molecular Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rudolf S. N. Fehrmann
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerard J. te Meerman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wim A. Buurman
- Department of Surgery, University Hospital Maastricht and Nutrition and Toxicology Research Institute (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Sander S. M. Rensen
- Department of Surgery, University Hospital Maastricht and Nutrition and Toxicology Research Institute (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Harry J. M. Groen
- Department of Pulmonology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Leonard H. van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roel A. Ophoff
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - David van Heel
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Marten H. Hofker
- Department of Pathology and Medical Biology, Molecular Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail: (JF); (LF)
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8
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Westra HJ, Jansen RC, Fehrmann RSN, te Meerman GJ, van Heel D, Wijmenga C, Franke L. MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. ACTA ACUST UNITED AC 2011; 27:2104-11. [PMID: 21653519 DOI: 10.1093/bioinformatics/btr323] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Sample mix-ups can arise during sample collection, handling, genotyping or data management. It is unclear how often sample mix-ups occur in genome-wide studies, as there currently are no post hoc methods that can identify these mix-ups in unrelated samples. We have therefore developed an algorithm (MixupMapper) that can both detect and correct sample mix-ups in genome-wide studies that study gene expression levels. RESULTS We applied MixupMapper to five publicly available human genetical genomics datasets. On average, 3% of all analyzed samples had been assigned incorrect expression phenotypes: in one of the datasets 23% of the samples had incorrect expression phenotypes. The consequences of sample mix-ups are substantial: when we corrected these sample mix-ups, we identified on average 15% more significant cis-expression quantitative trait loci (cis-eQTLs). In one dataset, we identified three times as many significant cis-eQTLs after correction. Furthermore, we show through simulations that sample mix-ups can lead to an underestimation of the explained heritability of complex traits in genome-wide association datasets. AVAILABILITY AND IMPLEMENTATION MixupMapper is freely available at http://www.genenetwork.nl/mixupmapper/
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Affiliation(s)
- Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
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9
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Billmann-Born S, Till A, Arlt A, Lipinski S, Sina C, Latiano A, Annese V, Häsler R, Kerick M, Manke T, Seegert D, Hanidu A, Schäfer H, van Heel D, Li J, Schreiber S, Rosenstiel P. Genome-wide expression profiling identifies an impairment of negative feedback signals in the Crohn's disease-associated NOD2 variant L1007fsinsC. J Immunol 2011; 186:4027-38. [PMID: 21335489 DOI: 10.4049/jimmunol.1000085] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
NOD2 is an intracellular receptor for the bacterial cell wall component muramyl dipeptide (MDP), and variants of NOD2 are associated with chronic inflammatory diseases of barrier organs (e.g., Crohn's disease, asthma, and atopic eczema). It is known that activation of NOD2 induces a variety of inflammatory and antibacterial factors. The exact transcriptomal signatures that define the cellular programs downstream of NOD2 activation and the influence of the Crohn-associated variant L1007fsinsC are yet to be defined. To describe the MDP-induced activation program, we analyzed the transcriptomal reactions of isogenic HEK293 cells expressing NOD2(wt) or NOD2(L1007fsinsC) to stimulation with MDP. Importantly, a clear loss of function could be observed in the cells carrying the Crohn-associated variant L1007fsinsC, whereas the NOD2(wt) cells showed differential regulation of growth factors, chemokines, and several antagonists of NF-κB (e.g., TNFAIP3 [A20] and IER3). This genotype-dependent regulation pattern was confirmed in primary human myelomonocytic cells. The influence of TNFAIP3 and IER3 in the context of NOD2 signaling was characterized, and we could validate the predicted role as inhibitors of NOD2-induced NF-κB activation. We show that IER3 impairs the protective effect of NOD2(wt) against bacterial cytoinvasion. These results further our understanding of NOD2 as a first-line defense molecule and emphasize the importance of simultaneous upregulation of counterregulatory anti-inflammatory factors as an integral part of the NOD2-induced cellular program. Lack of these regulatory events due to the L1007fsinsC variant may pivotally contribute to the induction and perpetuation of chronic inflammation.
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Affiliation(s)
- Susanne Billmann-Born
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
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