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Ideozu JE, Liu M, Riley-Gillis BM, Paladugu SR, Rahimov F, Krishnan P, Tripathi R, Dorr P, Levy H, Singh A, Waring JF, Vasanthakumar A. Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences. Genome Med 2024; 16:43. [PMID: 38515211 PMCID: PMC10956269 DOI: 10.1186/s13073-024-01316-5] [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: 08/11/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Limited understanding of the diversity of variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene across ancestries hampers efforts to advance molecular diagnosis of cystic fibrosis (CF). The consequences pose a risk of delayed diagnoses and subsequently worsened health outcomes for patients. Therefore, characterizing the spectrum of CFTR variants across ancestries is critical for revolutionizing molecular diagnoses of CF. METHODS We analyzed 454,727 UK Biobank (UKBB) whole-exome sequences to characterize the diversity of CFTR variants across ancestries. Using the PanUKBB classification, the participants were assigned into six major groups: African (AFR), American/American Admixed (AMR), Central South Asia (CSA), East Asian (EAS), European (EUR), and Middle East (MID). We segregated ancestry-specific CFTR variants, including those that are CF-causing or clinically relevant. The ages of certain CF-causing variants were determined and analyzed for selective pressure effects, and curated phenotype analysis was performed for participants with clinically relevant CFTR genotypes. RESULTS We detected over 4000 CFTR variants, including novel ancestry-specific variants, across six ancestries. Europeans had the most unique CFTR variants [n = 2212], while the American group had the least unique variants [n = 23]. F508del was the most prevalent CF-causing variant found in all ancestries, except in EAS, where V520F was the most prevalent. Common EAS variants such as 3600G > A, V456A, and V520, which appeared approximately 270, 215, and 338 generations ago, respectively, did not show evidence of selective pressure. Sixteen participants had two CF-causing variants, with two being diagnosed with CF. We found 154 participants harboring a CF-causing and varying clinical consequences (VCC) variant. Phenotype analysis performed for participants with multiple clinically relevant variants returned significant associations with CF and its pulmonary phenotypes [Bonferroni-adjusted p < 0.05]. CONCLUSIONS We leveraged the UKBB database to comprehensively characterize the broad spectrum of CFTR variants across ancestries. The detection of over 4000 CFTR variants, including several ancestry-specific and uncharacterized CFTR variants, warrants the need for further characterization of their functional and clinical relevance. Overall, the presentation of classical CF phenotypes seen in non-CF diagnosed participants with more than one CF-causing variant indicates that they may benefit from current CFTR modulator therapies.
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Affiliation(s)
- Justin E Ideozu
- Genomic Medicine, Genomics Research Center, AbbVie, Chicago, IL, USA.
| | - Mengzhen Liu
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | | | - Sri R Paladugu
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | - Fedik Rahimov
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | | | | | | | - Hara Levy
- Department of Pediatrics, Division of Pulmonology and Sleep Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Jeffrey F Waring
- Genomic Medicine, Genomics Research Center, AbbVie, Chicago, IL, USA
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
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2
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Stolzenburg LR, Esmaeeli S, Kulkarni AS, Murphy E, Kwon T, Preiss C, Bahnassawy L, Stender JD, Manos JD, Reinhardt P, Rahimov F, Waring JF, Ramathal CY. Functional characterization of a single nucleotide polymorphism associated with Alzheimer's disease in a hiPSC-based neuron model. PLoS One 2023; 18:e0291029. [PMID: 37751459 PMCID: PMC10521995 DOI: 10.1371/journal.pone.0291029] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/20/2023] [Indexed: 09/28/2023] Open
Abstract
Neurodegenerative diseases encompass a group of debilitating conditions resulting from progressive nerve cell death. Of these, Alzheimer's disease (AD) occurs most frequently, but is currently incurable and has limited treatment success. Late onset AD, the most common form, is highly heritable but is caused by a combination of non-genetic risk factors and many low-effect genetic variants whose disease-causing mechanisms remain unclear. By mining the FinnGen study database of phenome-wide association studies, we identified a rare variant, rs148726219, enriched in the Finnish population that is associated with AD risk and dementia, and appears to have arisen on a common haplotype with older AD-associated variants such as rs429358. The rs148726219 variant lies in an overlapping intron of the FosB proto-oncogene (FOSB) and ERCC excision repair 1 (ERCC1) genes. To understand the impact of this SNP on disease phenotypes, we performed CRISPR/Cas9 editing in a human induced pluripotent stem cell (hiPSC) line to generate isogenic clones harboring heterozygous and homozygous alleles of rs148726219. hiPSC clones differentiated into induced excitatory neurons (iNs) did not exhibit detectable molecular or morphological variation in differentiation potential compared to isogenic controls. However, global transcriptome analysis showed differential regulation of nearby genes and upregulation of several biological pathways related to neuronal function, particularly synaptogenesis and calcium signaling, specifically in mature iNs harboring rs148726219 homozygous and heterozygous alleles. Functional differences in iN circuit maturation as measured by calcium imaging were observed across genotypes. Edited mature iNs also displayed downregulation of unfolded protein response and cell death pathways. This study implicates a phenotypic impact of rs148726219 in the context of mature neurons, consistent with its identification in late onset AD, and underscores a hiPSC-based experimental model to functionalize GWAS-identified variants.
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Affiliation(s)
| | - Sahar Esmaeeli
- AbbVie Inc., North Chicago, Illinois, United States of America
| | | | - Erin Murphy
- AbbVie Inc., North Chicago, Illinois, United States of America
| | - Taekyung Kwon
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, United States of America
| | - Christina Preiss
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, United States of America
| | - Lamiaa Bahnassawy
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, Ludwigshafen, Germany
| | | | - Justine D. Manos
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, United States of America
| | - Peter Reinhardt
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, Ludwigshafen, Germany
| | - Fedik Rahimov
- AbbVie Inc., North Chicago, Illinois, United States of America
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3
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Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H, Aavikko M, Kaunisto MA, Loukola A, Lahtela E, Mattsson H, Laiho P, Della Briotta Parolo P, Lehisto AA, Kanai M, Mars N, Rämö J, Kiiskinen T, Heyne HO, Veerapen K, Rüeger S, Lemmelä S, Zhou W, Ruotsalainen S, Pärn K, Hiekkalinna T, Koskelainen S, Paajanen T, Llorens V, Gracia-Tabuenca J, Siirtola H, Reis K, Elnahas AG, Sun B, Foley CN, Aalto-Setälä K, Alasoo K, Arvas M, Auro K, Biswas S, Bizaki-Vallaskangas A, Carpen O, Chen CY, Dada OA, Ding Z, Ehm MG, Eklund K, Färkkilä M, Finucane H, Ganna A, Ghazal A, Graham RR, Green EM, Hakanen A, Hautalahti M, Hedman ÅK, Hiltunen M, Hinttala R, Hovatta I, Hu X, Huertas-Vazquez A, Huilaja L, Hunkapiller J, Jacob H, Jensen JN, Joensuu H, John S, Julkunen V, Jung M, Junttila J, Kaarniranta K, Kähönen M, Kajanne R, Kallio L, Kälviäinen R, Kaprio J, Kerimov N, Kettunen J, Kilpeläinen E, Kilpi T, Klinger K, Kosma VM, Kuopio T, Kurra V, Laisk T, Laukkanen J, Lawless N, Liu A, Longerich S, Mägi R, Mäkelä J, Mäkitie A, Malarstig A, Mannermaa A, Maranville J, Matakidou A, Meretoja T, Mozaffari SV, Niemi MEK, Niemi M, Niiranen T, O Donnell CJ, Obeidat ME, Okafo G, Ollila HM, Palomäki A, Palotie T, Partanen J, Paul DS, Pelkonen M, Pendergrass RK, Petrovski S, Pitkäranta A, Platt A, Pulford D, Punkka E, Pussinen P, Raghavan N, Rahimov F, Rajpal D, Renaud NA, Riley-Gillis B, Rodosthenous R, Saarentaus E, Salminen A, Salminen E, Salomaa V, Schleutker J, Serpi R, Shen HY, Siegel R, Silander K, Siltanen S, Soini S, Soininen H, Sul JH, Tachmazidou I, Tasanen K, Tienari P, Toppila-Salmi S, Tukiainen T, Tuomi T, Turunen JA, Ulirsch JC, Vaura F, Virolainen P, Waring J, Waterworth D, Yang R, Nelis M, Reigo A, Metspalu A, Milani L, Esko T, Fox C, Havulinna AS, Perola M, Ripatti S, Jalanko A, Laitinen T, Mäkelä TP, Plenge R, McCarthy M, Runz H, Daly MJ, Palotie A. FinnGen provides genetic insights from a well-phenotyped isolated population. Nature 2023; 613:508-518. [PMID: 36653562 PMCID: PMC9849126 DOI: 10.1038/s41586-022-05473-8] [Citation(s) in RCA: 505] [Impact Index Per Article: 505.0] [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: 01/10/2022] [Accepted: 10/21/2022] [Indexed: 01/20/2023]
Abstract
Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored1,2. FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10-11) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of <5% in non-Finnish European individuals, of which 62 (32 PWS) were enriched by more than twofold in Finland. These findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.
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Affiliation(s)
- Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Kati M Donner
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mary P Reeve
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland.,Faculty of Medicine and Health Technology, Center for Child, Adolescent and Maternal Health, University of Tampere, Tampere, Finland
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mari A Kaunisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Loukola
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Elisa Lahtela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Mattsson
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Päivi Laiho
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Pietro Della Briotta Parolo
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Arto A Lehisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Masahiro Kanai
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Joel Rämö
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Henrike O Heyne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Digital Health Center, Hasso Plattner Institute for Digital Engineering, University of Potsdam Potsdam, Potsdam, Germany.,Hasso Plattner Institute for Digital Health at Mount Sinai, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kumar Veerapen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sina Rüeger
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Susanna Lemmelä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Kalle Pärn
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tero Hiekkalinna
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sami Koskelainen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Teemu Paajanen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Vincent Llorens
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Javier Gracia-Tabuenca
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Harri Siirtola
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Kadri Reis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Benjamin Sun
- Translational Biology, Research and Development, Biogen, Cambridge, MA, USA.,BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Christopher N Foley
- Optima Partners, Edinburgh, UK.,MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Mikko Arvas
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | | | | | - Olli Carpen
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | | | - Oluwaseun A Dada
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Zhihao Ding
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | | | - Kari Eklund
- Division of Rheumatology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland.,Orton Orthopedic Hospital, Helsinki, Finland
| | - Martti Färkkilä
- Abdominal Center, Helsinki University Hospital, Helsinki University, Helsinki, Finland
| | - Hilary Finucane
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | - Antti Hakanen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | - Åsa K Hedman
- Pfizer, New York, NY, USA.,Department of Medicine, Karolinska Institute, Solna, Sweden
| | - Mikko Hiltunen
- Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Reetta Hinttala
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Oulu University Hospital, Oulu, Finland
| | - Iiris Hovatta
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | - Laura Huilaja
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | | | | | | | - Heikki Joensuu
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Valtteri Julkunen
- Neuro Center, Neurology, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Marc Jung
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Juhani Junttila
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Kuopio University Hospital, Kuopio, Finland.,Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mika Kähönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Risto Kajanne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Lila Kallio
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Reetta Kälviäinen
- Epilepsy Center, Kuopio University Hospital, Kuopio, Finland.,Department of Neurology, University of Eastern Finland, Kuopio, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | | | - Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Johannes Kettunen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Computational Medicine, Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Terhi Kilpi
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | | | - Veli-Matti Kosma
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland.,Kuopio University Hospital, Kuopio, Finland
| | - Teijo Kuopio
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland
| | - Venla Kurra
- Department of Clinical Genetics, Tampere University Hospital, Tampere, Finland.,Department of Clinical Genetics, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jari Laukkanen
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland.,Department of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Antti Mäkitie
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital, Helsinki, Finland
| | - Anders Malarstig
- Pfizer, Cambridge, MA, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Solna, Sweden
| | - Arto Mannermaa
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland.,Kuopio University Hospital, Kuopio, Finland
| | | | - Athena Matakidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Tuomo Meretoja
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Mari E K Niemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Marianna Niemi
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,TAUCHI Research Center & Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland.,Turku University Hospital and University of Turku, Turku, Finland
| | | | - Ma En Obeidat
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - George Okafo
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Antti Palomäki
- Turku University Hospital and University of Turku, Turku, Finland
| | - Tuula Palotie
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital, Helsinki, Finland.,Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Helsinki, Finland.,Finnish Hematological Biobank, Helsinki, Finland
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Margit Pelkonen
- Department of Pulmonary Diseases, Kuopio University Hospital, Kuopio, Finland
| | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Anne Pitkäranta
- Department of Otorhinolaryngology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Adam Platt
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Eero Punkka
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Pirkko Pussinen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | | | | | - Deepak Rajpal
- Translational Sciences, Sanofi R&D, Framingham, MA, USA
| | - Nicole A Renaud
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Rodosthenis Rodosthenous
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Aino Salminen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Eveliina Salminen
- Helsinki University Hospital, Helsinki, Finland.,Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki, Helsinki, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Johanna Schleutker
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Raisa Serpi
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Huei-Yi Shen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Richard Siegel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Kaisa Silander
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sanna Siltanen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Sirpa Soini
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Hilkka Soininen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Ioanna Tachmazidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Kaisa Tasanen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Pentti Tienari
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland.,Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Sanna Toppila-Salmi
- Department of Allergy, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Abdominal Center, Endocrinology, Helsinki University Hospital, Helsinki, Finland.,Folkhalsan Research Center, Helsinki, Finland.,Research Program of Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Joni A Turunen
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland.,Eye Genetics Group, Folkhälsan Research Center, Helsinki, Finland
| | - Jacob C Ulirsch
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Felix Vaura
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland.,University of Turku, Turku, Finland
| | - Petri Virolainen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | | | | | - Mari Nelis
- Genomics Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Reigo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Markus Perola
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Jalanko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tarja Laitinen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Tomi P Mäkelä
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | | | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland. .,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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4
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Karczewski KJ, Solomonson M, Chao KR, Goodrich JK, Tiao G, Lu W, Riley-Gillis BM, Tsai EA, Kim HI, Zheng X, Rahimov F, Esmaeeli S, Grundstad AJ, Reppell M, Waring J, Jacob H, Sexton D, Bronson PG, Chen X, Hu X, Goldstein JI, King D, Vittal C, Poterba T, Palmer DS, Churchhouse C, Howrigan DP, Zhou W, Watts NA, Nguyen K, Nguyen H, Mason C, Farnham C, Tolonen C, Gauthier LD, Gupta N, MacArthur DG, Rehm HL, Seed C, Philippakis AA, Daly MJ, Davis JW, Runz H, Miller MR, Neale BM. Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes. Cell Genom 2022; 2:100168. [PMID: 36778668 PMCID: PMC9903662 DOI: 10.1016/j.xgen.2022.100168] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 07/16/2022] [Indexed: 01/20/2023]
Abstract
Genome-wide association studies have successfully discovered thousands of common variants associated with human diseases and traits, but the landscape of rare variations in human disease has not been explored at scale. Exome-sequencing studies of population biobanks provide an opportunity to systematically evaluate the impact of rare coding variations across a wide range of phenotypes to discover genes and allelic series relevant to human health and disease. Here, we present results from systematic association analyses of 4,529 phenotypes using single-variant and gene tests of 394,841 individuals in the UK Biobank with exome-sequence data. We find that the discovery of genetic associations is tightly linked to frequency and is correlated with metrics of deleteriousness and natural selection. We highlight biological findings elucidated by these data and release the dataset as a public resource alongside the Genebass browser for rapidly exploring rare-variant association results.
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Affiliation(s)
- Konrad J. Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia K. Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wenhan Lu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Hye In Kim
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xiuwen Zheng
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Fedik Rahimov
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Sahar Esmaeeli
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Mark Reppell
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Jeff Waring
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Howard Jacob
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | | | - Xing Chen
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xinli Hu
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Jacqueline I. Goldstein
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel King
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Vittal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Duncan S. Palmer
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claire Churchhouse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel P. Howrigan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas A. Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Huy Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cara Mason
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Farnham
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Charlotte Tolonen
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Laura D. Gauthier
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Namrata Gupta
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cotton Seed
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - J. Wade Davis
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Melissa R. Miller
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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5
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Palmer NP, Silvester JA, Lee JJ, Beam AL, Fried I, Valtchinov VI, Rahimov F, Kong SW, Ghodoussipour S, Hood HC, Bousvaros A, Grand RJ, Kunkel LM, Kohane IS. Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease. PLoS One 2019; 14:e0222952. [PMID: 31618209 PMCID: PMC6795427 DOI: 10.1371/journal.pone.0222952] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 04/10/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
Background Presenting features of inflammatory bowel disease (IBD) are non-specific. We hypothesized that mRNA profiles could (1) identify genes and pathways involved in disease pathogenesis; (2) identify a molecular signature that differentiates IBD from other conditions; (3) provide insight into systemic and colon-specific dysregulation through study of the concordance of the gene expression. Methods Children (8–18 years) were prospectively recruited at the time of diagnostic colonoscopy for possible IBD. We used transcriptome-wide mRNA profiling to study gene expression in colon biopsies and paired whole blood samples. Using blood mRNA measurements, we fit a regression model for disease state prediction that was validated in an independent test set of adult subjects (GSE3365). Results Ninety-eight children were recruited [39 Crohn’s disease, 18 ulcerative colitis, 2 IBDU, 39 non-IBD]. There were 1,118 significantly differentially (IBD vs non-IBD) expressed genes in colon tissue, and 880 in blood. The direction of relative change in expression was concordant for 106/112 genes differentially expressed in both tissue types. The regression model from the blood mRNA measurements distinguished IBD vs non-IBD disease status in the independent test set with 80% accuracy using only 6 genes. The overlap of 5 immune and metabolic pathways in the two tissue types was significant (p<0.001). Conclusions Blood and colon tissue from patients with IBD share a common transcriptional profile dominated by immune and metabolic pathways. Our results suggest that peripheral blood expression levels of as few as 6 genes (IL7R, UBB, TXNIP, S100A8, ALAS2, and SLC2A3) may distinguish patients with IBD from non-IBD.
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Affiliation(s)
- Nathan P. Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jocelyn A. Silvester
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| | - Jessica J. Lee
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew L. Beam
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Inbar Fried
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vladimir I. Valtchinov
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Evidence Based Imaging, Brigham and Women’s Hospital, Harvard Medical School, Massachusetts, United States of America
| | - Fedik Rahimov
- Division of Genetics and Genomics, Boston Children’s Hospital, Departments of Genetics and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Saum Ghodoussipour
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Helen C. Hood
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Athos Bousvaros
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard J. Grand
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Louis M. Kunkel
- Division of Genetics and Genomics, Boston Children’s Hospital, Departments of Genetics and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
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6
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Pakula A, Lek A, Widrick J, Mitsuhashi H, Bugda Gwilt KM, Gupta VA, Rahimov F, Criscione J, Zhang Y, Gibbs D, Murphy Q, Manglik A, Mead L, Kunkel L. Transgenic zebrafish model of DUX4 misexpression reveals a developmental role in FSHD pathogenesis. Hum Mol Genet 2019; 28:320-331. [PMID: 30307508 DOI: 10.1093/hmg/ddy348] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/21/2018] [Indexed: 11/13/2022] Open
Abstract
Facioscapulohumeral dystrophy type 1 (FSHD-1) is the most common autosomal dominant form of muscular dystrophy with a prevalence of ∼1 in 8000 individuals. It is considered a late-onset form of muscular dystrophy and leads to asymmetric muscle weakness in the facial, scapular, trunk and lower extremities. The prevalent hypothesis on disease pathogenesis is explained by misexpression of a germ line, primate-specific transcription factor DUX4-fl (double homeobox 4, full-length isoform) linked to the chromosome 4q35. In vitro and in vivo studies have demonstrated that very low levels of DUX4-fl expression are sufficient to induce an apoptotic and/or lethal phenotype, and therefore modeling of the disease has proved challenging. In this study, we expand upon our previously established injection model of DUX4 misexpression in zebrafish and describe a DUX4-inducible transgenic zebrafish model that better recapitulates the expression pattern and late onset phenotype characteristic of FSHD patients. We show that an induced burst of DUX4 expression during early development results in the onset of FSHD-like phenotypes in adulthood, even when DUX4 is no longer detectable. We also utilize our injection model to study long-term consequences of DUX4 expression in those that fail to show a developmental phenotype. Herein, we introduce a hypothesis that DUX4 expression during developmental stages is sufficient to induce FSHD-like phenotypes in later adulthood. Our findings point to a developmental role of DUX4 misexpression in the pathogenesis of FSHD and should be factored into the design of future therapies.
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Affiliation(s)
- Anna Pakula
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Angela Lek
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA.,Australian Regenerative Medicine Institute, Monash University, Clayton, Vic, Australia
| | - Jeffrey Widrick
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Hiroaki Mitsuhashi
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Katlynn M Bugda Gwilt
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vandana A Gupta
- Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA.,Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fedik Rahimov
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - June Criscione
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Yuanfan Zhang
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Devin Gibbs
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Quinn Murphy
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Anusha Manglik
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Lillian Mead
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Louis Kunkel
- Division of Genetics and Genomics,Boston Children's Hospital, Boston, MA, USA.,Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
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7
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Heeney MM, Guo D, De Falco L, Campagna DR, Olbina G, Kao PPC, Schmitz-Abe K, Rahimov F, Gutschow P, Westerman K, Ostland V, Jackson T, Klaassen RJ, Markianos K, Finberg KE, Iolascon A, Westerman M, London WB, Fleming MD. Normalizing hepcidin predicts TMPRSS6 mutation status in patients with chronic iron deficiency. Blood 2018; 132:448-452. [PMID: 29895660 PMCID: PMC6071554 DOI: 10.1182/blood-2017-03-773028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/06/2018] [Indexed: 12/30/2022] Open
Affiliation(s)
- Matthew M Heeney
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Dongjing Guo
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Luigia De Falco
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University Medical School, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Dean R Campagna
- Department of Pathology, Boston Children's Hospital, Boston, MA
| | | | - Paige P-C Kao
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | | | - Fedik Rahimov
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA
| | | | | | | | - Tracy Jackson
- Division of Pediatric Hematology-Oncology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada; and
| | - Robert J Klaassen
- Division of Pediatric Hematology-Oncology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada; and
| | | | | | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University Medical School, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Wendy B London
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA
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8
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Alexander MS, Rozkalne A, Colletta A, Spinazzola JM, Johnson S, Rahimov F, Meng H, Lawlor MW, Estrella E, Kunkel LM, Gussoni E. CD82 Is a Marker for Prospective Isolation of Human Muscle Satellite Cells and Is Linked to Muscular Dystrophies. Cell Stem Cell 2016; 19:800-807. [PMID: 27641304 DOI: 10.1016/j.stem.2016.08.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 05/17/2016] [Accepted: 08/05/2016] [Indexed: 12/23/2022]
Abstract
Cell-surface markers for prospective isolation of stem cells from human skeletal muscle have been difficult to identify. Such markers would be powerful tools for studying satellite cell function during homeostasis and in pathogenesis of diseases such as muscular dystrophies. In this study, we show that the tetraspanin KAI/CD82 is an excellent marker for prospectively isolating stem cells from human fetal and adult skeletal muscle. Human CD82+ muscle cells robustly engraft into a mouse model of muscular dystrophy. shRNA knockdown of CD82 in myogenic cells reduces myoblast proliferation, suggesting it is functionally involved in muscle homeostasis. CD82 physically interacts with alpha7beta1 integrin (α7β1-ITG) and with α-sarcoglycan, a member of the Dystrophin-Associated Glycoprotein Complex (DAPC), both of which have been linked to muscular dystrophies. Consistently, CD82 expression is decreased in Duchenne muscular dystrophy patients. Together, these findings suggest that CD82 function may be important for muscle stem cell function in muscular disorders.
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Affiliation(s)
- Matthew S Alexander
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Stem Cell Program at Boston Children's Hospital, Boston, MA 02115, USA
| | - Anete Rozkalne
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alessandro Colletta
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Boston University School of Medicine, Boston, MA 02215, USA
| | - Janelle M Spinazzola
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Stem Cell Program at Boston Children's Hospital, Boston, MA 02115, USA
| | - Samuel Johnson
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Fedik Rahimov
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Stem Cell Program at Boston Children's Hospital, Boston, MA 02115, USA
| | - Hui Meng
- Division of Pediatric Pathology, Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael W Lawlor
- Division of Pediatric Pathology, Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Elicia Estrella
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Louis M Kunkel
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Stem Cell Program at Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Emanuela Gussoni
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Stem Cell Program at Boston Children's Hospital, Boston, MA 02115, USA.
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9
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Lek A, Rahimov F, Jones PL, Kunkel LM. Emerging preclinical animal models for FSHD. Trends Mol Med 2015; 21:295-306. [PMID: 25801126 DOI: 10.1016/j.molmed.2015.02.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [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: 01/19/2015] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 12/18/2022]
Abstract
Facioscapulohumeral dystrophy (FSHD) is a unique and complex genetic disease that is not entirely solved. Recent advances in the field have led to a consensus genetic premise for the disorder, enabling researchers to now pursue the design of preclinical models. In this review we explore all available FSHD models (DUX4-dependent and -independent) for their utility in therapeutic discovery and potential to yield novel disease insights. Owing to the complex nature of FSHD, there is currently no single model that accurately recapitulates the genetic and pathophysiological spectrum of the disorder. Existing models emphasize only specific aspects of the disease, highlighting the need for more collaborative research and novel paradigms to advance the translational research space of FSHD.
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Affiliation(s)
- Angela Lek
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; The Wellstone Program, Departments of Neurology and Cell and Developmental Biology, University of Massachusetts Medical School (UMMS), Worcester, MA 01655, USA.
| | - Fedik Rahimov
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; The Wellstone Program, Departments of Neurology and Cell and Developmental Biology, University of Massachusetts Medical School (UMMS), Worcester, MA 01655, USA
| | - Peter L Jones
- The Wellstone Program, Departments of Neurology and Cell and Developmental Biology, University of Massachusetts Medical School (UMMS), Worcester, MA 01655, USA; The Eunice Kennedy Shriver National Institute of Child Health and Human Development (NIHCD) Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Louis M Kunkel
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; The Wellstone Program, Departments of Neurology and Cell and Developmental Biology, University of Massachusetts Medical School (UMMS), Worcester, MA 01655, USA
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10
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Alexander MS, Casar JC, Motohashi N, Vieira NM, Eisenberg I, Marshall JL, Gasperini MJ, Lek A, Myers JA, Estrella EA, Kang PB, Shapiro F, Rahimov F, Kawahara G, Widrick JJ, Kunkel LM. MicroRNA-486-dependent modulation of DOCK3/PTEN/AKT signaling pathways improves muscular dystrophy-associated symptoms. J Clin Invest 2014; 124:2651-67. [PMID: 24789910 DOI: 10.1172/jci73579] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is caused by mutations in the gene encoding dystrophin, which results in dysfunctional signaling pathways within muscle. Previously, we identified microRNA-486 (miR-486) as a muscle-enriched microRNA that is markedly reduced in the muscles of dystrophin-deficient mice (Dmdmdx-5Cv mice) and in DMD patient muscles. Here, we determined that muscle-specific transgenic overexpression of miR-486 in muscle of Dmdmdx-5Cv mice results in reduced serum creatine kinase levels, improved sarcolemmal integrity, fewer centralized myonuclei, increased myofiber size, and improved muscle physiology and performance. Additionally, we identified dedicator of cytokinesis 3 (DOCK3) as a miR-486 target in skeletal muscle and determined that DOCK3 expression is induced in dystrophic muscles. DOCK3 overexpression in human myotubes modulated PTEN/AKT signaling, which regulates muscle hypertrophy and growth, and induced apoptosis. Furthermore, several components of the PTEN/AKT pathway were markedly modulated by miR-486 in dystrophin-deficient muscle. Skeletal muscle-specific miR-486 overexpression in Dmdmdx-5Cv animals decreased levels of DOCK3, reduced PTEN expression, and subsequently increased levels of phosphorylated AKT, which resulted in an overall beneficial effect. Together, these studies demonstrate that stable overexpression of miR-486 ameliorates the disease progression of dystrophin-deficient skeletal muscle.
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MESH Headings
- Animals
- Base Sequence
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Line
- Guanine Nucleotide Exchange Factors/genetics
- Guanine Nucleotide Exchange Factors/metabolism
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred mdx
- Mice, Transgenic
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Muscle Fibers, Skeletal/metabolism
- Muscle Fibers, Skeletal/pathology
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Animal/genetics
- Muscular Dystrophy, Animal/metabolism
- Muscular Dystrophy, Animal/pathology
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/pathology
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- PTEN Phosphohydrolase/metabolism
- Proto-Oncogene Proteins c-akt/metabolism
- Sequence Homology, Nucleic Acid
- Signal Transduction
- Up-Regulation
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11
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Zhang Y, King OD, Rahimov F, Jones TI, Ward CW, Kerr JP, Liu N, Emerson CP, Kunkel LM, Partridge TA, Wagner KR. Human skeletal muscle xenograft as a new preclinical model for muscle disorders. Hum Mol Genet 2014; 23:3180-8. [PMID: 24452336 DOI: 10.1093/hmg/ddu028] [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: 11/14/2022] Open
Abstract
Development of novel therapeutics requires good animal models of disease. Disorders for which good animal models do not exist have very few drugs in development or clinical trial. Even where there are accepted, albeit imperfect models, the leap from promising preclinical drug results to positive clinical trials commonly fails, including in disorders of skeletal muscle. The main alternative model for early drug development, tissue culture, lacks both the architecture and, usually, the metabolic fidelity of the normal tissue in vivo. Herein, we demonstrate the feasibility and validity of human to mouse xenografts as a preclinical model of myopathy. Human skeletal muscle biopsies transplanted into the anterior tibial compartment of the hindlimbs of NOD-Rag1(null) IL2rγ(null) immunodeficient host mice regenerate new vascularized and innervated myofibers from human myogenic precursor cells. The grafts exhibit contractile and calcium release behavior, characteristic of functional muscle tissue. The validity of the human graft as a model of facioscapulohumeral muscular dystrophy is demonstrated in disease biomarker studies, showing that gene expression profiles of xenografts mirror those of the fresh donor biopsies. These findings illustrate the value of a new experimental model of muscle disease, the human muscle xenograft in mice, as a feasible and valid preclinical tool to better investigate the pathogenesis of human genetic myopathies and to more accurately predict their response to novel therapeutics.
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Affiliation(s)
- Yuanfan Zhang
- The Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205, USA Graduate Program in Cellular and Molecular Medicine and
| | - Oliver D King
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - Takako I Jones
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - Jaclyn P Kerr
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and
| | - Naili Liu
- The Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Charles P Emerson
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Louis M Kunkel
- Program in Genomics, Division of Genetics, and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Terence A Partridge
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Kathryn R Wagner
- The Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205, USA Graduate Program in Cellular and Molecular Medicine and Departments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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12
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Fakhouri WD, Rahimov F, Attanasio C, Kouwenhoven EN, Ferreira De Lima RL, Felix TM, Nitschke L, Huver D, Barrons J, Kousa YA, Leslie E, Pennacchio LA, Van Bokhoven H, Visel A, Zhou H, Murray JC, Schutte BC. An etiologic regulatory mutation in IRF6 with loss- and gain-of-function effects. Hum Mol Genet 2014; 23:2711-20. [PMID: 24442519 DOI: 10.1093/hmg/ddt664] [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: 02/04/2023] Open
Abstract
DNA variation in Interferon Regulatory Factor 6 (IRF6) causes Van der Woude syndrome (VWS), the most common syndromic form of cleft lip and palate (CLP). However, an etiologic variant in IRF6 has been found in only 70% of VWS families. To test whether DNA variants in regulatory elements cause VWS, we sequenced three conserved elements near IRF6 in 70 VWS families that lack an etiologic mutation within IRF6 exons. A rare mutation (350dupA) was found in a conserved IRF6 enhancer element (MCS9.7) in a Brazilian family. The 350dupA mutation abrogated the binding of p63 and E47 transcription factors to cis-overlapping motifs, and significantly disrupted enhancer activity in human cell cultures. Moreover, using a transgenic assay in mice, the 350dupA mutation disrupted the activation of MCS9.7 enhancer element and led to failure of lacZ expression in all head and neck pharyngeal arches. Interestingly, disruption of the p63 Motif1 and/or E47 binding sites by nucleotide substitution did not fully recapitulate the effect of the 350dupA mutation. Rather, we recognized that the 350dupA created a CAAAGT motif, a binding site for Lef1 protein. We showed that Lef1 binds to the mutated site and that overexpression of Lef1/β-Catenin chimeric protein repressed MCS9.7-350dupA enhancer activity. In conclusion, our data strongly suggest that 350dupA variant is an etiologic mutation in VWS patients and disrupts enhancer activity by a loss- and gain-of-function mechanism, and thus support the rationale for additional screening for regulatory mutations in patients with CLP.
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13
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Eran A, Li JB, Vatalaro K, McCarthy J, Rahimov F, Collins C, Markianos K, Margulies DM, Brown EN, Calvo SE, Kohane IS, Kunkel LM. Comparative RNA editing in autistic and neurotypical cerebella. Mol Psychiatry 2013; 18:1041-8. [PMID: 22869036 PMCID: PMC3494744 DOI: 10.1038/mp.2012.118] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/29/2012] [Accepted: 06/29/2012] [Indexed: 01/03/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a neurodevelopmentally regulated epigenetic modification shown to modulate complex behavior in animals. Little is known about human A-to-I editing, but it is thought to constitute one of many molecular mechanisms connecting environmental stimuli and behavioral outputs. Thus, comprehensive exploration of A-to-I RNA editing in human brains may shed light on gene-environment interactions underlying complex behavior in health and disease. Synaptic function is a main target of A-to-I editing, which can selectively recode key amino acids in synaptic genes, directly altering synaptic strength and duration in response to environmental signals. Here, we performed a high-resolution survey of synaptic A-to-I RNA editing in a human population, and examined how it varies in autism, a neurodevelopmental disorder in which synaptic abnormalities are a common finding. Using ultra-deep (>1000 × ) sequencing, we quantified the levels of A-to-I editing of 10 synaptic genes in postmortem cerebella from 14 neurotypical and 11 autistic individuals. A high dynamic range of editing levels was detected across individuals and editing sites, from 99.6% to below detection limits. In most sites, the extreme ends of the population editing distributions were individuals with autism. Editing was correlated with isoform usage, clusters of correlated sites were identified, and differential editing patterns examined. Finally, a dysfunctional form of the editing enzyme adenosine deaminase acting on RNA B1 was found more commonly in postmortem cerebella from individuals with autism. These results provide a population-level, high-resolution view of A-to-I RNA editing in human cerebella and suggest that A-to-I editing of synaptic genes may be informative for assessing the epigenetic risk for autism.
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Affiliation(s)
- Alal Eran
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA,Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kayla Vatalaro
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jillian McCarthy
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Fedik Rahimov
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christin Collins
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kyriacos Markianos
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - David M. Margulies
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA,Correlagen Diagnostics, Waltham, MA 02452, USA,Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Emery N. Brown
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA,Neuroscience Statistics Research Laboratory, Department of Anesthesia and Critical Care, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Sarah E. Calvo
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Isaac S. Kohane
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA,Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA,Correspondence: Louis Kunkel, Program in Genomics, Department of Genetics, Boston Children’s Hospital, 3 Blackfan Circle, CLS 15027.1, Boston, MA 02115, USA. Telephone: (617) 355-6279, fax: (617) 730-0253, , Isaac Kohane, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave., Enders 144, Boston, MA 02115, USA. Telephone: (617) 919-2182, fax: (617) 730-0921,
| | - Louis M. Kunkel
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA,The Manton Center for Orphan Disease Research, Boston, MA 02115, USA,Correspondence: Louis Kunkel, Program in Genomics, Department of Genetics, Boston Children’s Hospital, 3 Blackfan Circle, CLS 15027.1, Boston, MA 02115, USA. Telephone: (617) 355-6279, fax: (617) 730-0253, , Isaac Kohane, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave., Enders 144, Boston, MA 02115, USA. Telephone: (617) 919-2182, fax: (617) 730-0921,
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14
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Mitsuhashi S, Boyden SE, Estrella EA, Jones TI, Rahimov F, Yu TW, Darras BT, Amato AA, Folkerth RD, Jones PL, Kunkel LM, Kang PB. Exome sequencing identifies a novel SMCHD1 mutation in facioscapulohumeral muscular dystrophy 2. Neuromuscul Disord 2013; 23:975-80. [PMID: 24128691 DOI: 10.1016/j.nmd.2013.08.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [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: 04/29/2013] [Revised: 07/24/2013] [Accepted: 08/19/2013] [Indexed: 12/16/2022]
Abstract
FSHD2 is a rare form of facioscapulohumeral muscular dystrophy (FSHD) characterized by the absence of a contraction in the D4Z4 macrosatellite repeat region on chromosome 4q35 that is the hallmark of FSHD1. However, hypomethylation of this region is common to both subtypes. Recently, mutations in SMCHD1 combined with a permissive 4q35 allele were reported to cause FSHD2. We identified a novel p.Lys275del SMCHD1 mutation in a family affected with FSHD2 using whole-exome sequencing and linkage analysis. This mutation alters a highly conserved amino acid in the ATPase domain of SMCHD1. Subject III-11 is a male who developed asymmetrical muscle weakness characteristic of FSHD at 13 years. Physical examination revealed marked bilateral atrophy at biceps brachii, bilateral scapular winging, some asymmetrical weakness at tibialis anterior and peroneal muscles, and mild lower facial weakness. Biopsy of biceps brachii in subject II-5, the father of III-11, demonstrated lobulated fibers and dystrophic changes. Endomysial and perivascular inflammation was found, which has been reported in FSHD1 but not FSHD2. Given the previous report of SMCHD1 mutations in FSHD2 and the clinical presentations consistent with the FSHD phenotype, we conclude that the SMCHD1 mutation is the likely cause of the disease in this family.
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Affiliation(s)
- Satomi Mitsuhashi
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
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15
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Abstract
The muscular dystrophies are a group of heterogeneous genetic diseases characterized by progressive degeneration and weakness of skeletal muscle. Since the discovery of the first muscular dystrophy gene encoding dystrophin, a large number of genes have been identified that are involved in various muscle-wasting and neuromuscular disorders. Human genetic studies complemented by animal model systems have substantially contributed to our understanding of the molecular pathomechanisms underlying muscle degeneration. Moreover, these studies have revealed distinct molecular and cellular mechanisms that link genetic mutations to diverse muscle wasting phenotypes.
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Affiliation(s)
- Fedik Rahimov
- Program in Genomics, Division of Genetics, Boston Children's Hospital, and 2 Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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16
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Stadler G, Rahimov F, King OD, Chen JCJ, Robin JD, Wagner KR, Shay JW, Emerson CP, Wright WE. Telomere position effect regulates DUX4 in human facioscapulohumeral muscular dystrophy. Nat Struct Mol Biol 2013; 20:671-8. [PMID: 23644600 PMCID: PMC3711615 DOI: 10.1038/nsmb.2571] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/19/2013] [Indexed: 11/09/2022]
Abstract
Telomeres may regulate human disease by at least two independent mechanisms. First, replicative senescence occurs once short telomeres generate DNA-damage signals that produce a barrier to tumor progression. Second, telomere position effects (TPE) could change gene expression at intermediate telomere lengths in cultured human cells. Here we report that telomere length may contribute to the pathogenesis of facioscapulohumeral muscular dystrophy (FSHD). FSHD is a late-onset disease genetically residing only 25-60 kilobases from the end of chromosome 4q. We used a floxable telomerase to generate isogenic clones with different telomere lengths from affected patients and their unaffected siblings. DUX4, the primary candidate for FSHD pathogenesis, is upregulated over ten-fold in FSHD myoblasts and myotubes with short telomeres, and its expression is inversely proportional to telomere length. FSHD may be the first known human disease in which TPE contributes to age-related phenotype.
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Affiliation(s)
- Guido Stadler
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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17
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Windelborn J, Rahimov F, Emerson CP. Dux4 target gene expression in mouse muscle transplanted with muscle cells from FSHD patients. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.751.6] [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: 11/11/2022]
Affiliation(s)
| | - Fedik Rahimov
- Division of Genetics, Program in GenomicsChildren's Hospital BostonBostonMA
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18
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Rahimov F, King OD, Leung DG, Bibat GM, Emerson CP, Kunkel LM, Wagner KR. Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers. Proc Natl Acad Sci U S A 2012; 109:16234-9. [PMID: 22988124 PMCID: PMC3479603 DOI: 10.1073/pnas.1209508109] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [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: 01/06/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a progressive neuromuscular disorder caused by contractions of repetitive elements within the macrosatellite D4Z4 on chromosome 4q35. The pathophysiology of FSHD is unknown and, as a result, there is currently no effective treatment available for this disease. To better understand the pathophysiology of FSHD and develop mRNA-based biomarkers of affected muscles, we compared global analysis of gene expression in two distinct muscles obtained from a large number of FSHD subjects and their unaffected first-degree relatives. Gene expression in two muscle types was analyzed using GeneChip Gene 1.0 ST arrays: biceps, which typically shows an early and severe disease involvement; and deltoid, which is relatively uninvolved. For both muscle types, the expression differences were mild: using relaxed cutoffs for differential expression (fold change ≥1.2; nominal P value <0.01), we identified 191 and 110 genes differentially expressed between affected and control samples of biceps and deltoid muscle tissues, respectively, with 29 genes in common. Controlling for a false-discovery rate of <0.25 reduced the number of differentially expressed genes in biceps to 188 and in deltoid to 7. Expression levels of 15 genes altered in this study were used as a "molecular signature" in a validation study of an additional 26 subjects and predicted them as FSHD or control with 90% accuracy based on biceps and 80% accuracy based on deltoids.
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Affiliation(s)
- Fedik Rahimov
- Program in Genomics, Division of Genetics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and
| | - Oliver D. King
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and
- Boston Biomedical Research Institute, Watertown, MA 02472
| | - Doris G. Leung
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205; Departments of
- Neurology and
| | - Genila M. Bibat
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205; Departments of
| | - Charles P. Emerson
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and
- Boston Biomedical Research Institute, Watertown, MA 02472
| | - Louis M. Kunkel
- Program in Genomics, Division of Genetics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115
| | - Kathryn R. Wagner
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205; Departments of
- Neurology and
- Neuroscience, The Johns Hopkins School of Medicine, Baltimore, MD 21205; and
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19
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Jones TI, Chen JCJ, Rahimov F, Homma S, Arashiro P, Beermann ML, King OD, Miller JB, Kunkel LM, Emerson CP, Wagner KR, Jones PL. Facioscapulohumeral muscular dystrophy family studies of DUX4 expression: evidence for disease modifiers and a quantitative model of pathogenesis. Hum Mol Genet 2012; 21:4419-30. [PMID: 22798623 DOI: 10.1093/hmg/dds284] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), the most prevalent myopathy afflicting both children and adults, is predominantly associated with contractions in the 4q35-localized macrosatellite D4Z4 repeat array. Recent studies have proposed that FSHD pathology is caused by the misexpression of the DUX4 (double homeobox 4) gene resulting in production of a pathogenic protein, DUX4-FL, which has been detected in FSHD, but not in unaffected control myogenic cells and muscle tissue. Here, we report the analysis of DUX4 mRNA and protein expression in a much larger collection of myogenic cells and muscle biopsies derived from biceps and deltoid muscles of FSHD affected subjects and their unaffected first-degree relatives. We confirmed that stable DUX4-fl mRNA and protein were expressed in myogenic cells and muscle tissues derived from FSHD affected subjects, including several genetically diagnosed adult FSHD subjects yet to show clinical manifestations of the disease in the assayed muscles. In addition, we report DUX4-fl mRNA and protein expression in muscle biopsies and myogenic cells from genetically unaffected relatives of the FSHD subjects, although at a significantly lower frequency. These results establish that DUX4-fl expression per se is not sufficient for FSHD muscle pathology and indicate that quantitative modifiers of DUX4-fl expression and/or function and family genetic background are determinants of FSHD muscle disease progression.
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20
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Abstract
With an average worldwide prevalence of approximately 1.2/1000 live births, orofacial clefts are the most common craniofacial birth defects in humans. Like other complex disorders, these birth defects are thought to result from the complex interplay of multiple genes and environmental factors. Significant progress in the identification of underlying genes and pathways has benefited from large populations available for study, increased international collaboration, rapid advances in genotyping technology, and major improvements in analytic approaches. Here we review recent advances in genetic epidemiological approaches to complex traits and their applications to studies of nonsyndromic orofacial clefts. Our main aim is to bring together a discussion of new and previously identified candidate genes to create a more cohesive picture of interacting pathways that shape the human craniofacial region. In future directions, we highlight the need to search for copy number variants that affect gene dosage and rare variants that are possibly associated with a higher disease penetrance. In addition, sequencing of protein-coding regions in candidate genes and screening for genetic variation in noncoding regulatory elements will help advance this important area of research.
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Affiliation(s)
- Fedik Rahimov
- Interdisciplinary Ph.D. Program in Genetics, Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
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21
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Rahimov F, King OD, Warsing LC, Powell RE, Emerson CP, Kunkel LM, Wagner KR. Gene expression profiling of skeletal muscles treated with a soluble activin type IIB receptor. Physiol Genomics 2011; 43:398-407. [PMID: 21266502 DOI: 10.1152/physiolgenomics.00223.2010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Inhibition of the myostatin signaling pathway is emerging as a promising therapeutic means to treat muscle wasting and degenerative disorders. Activin type IIB receptor (ActRIIB) is the putative myostatin receptor, and a soluble activin receptor (ActRIIB-Fc) has been demonstrated to potently inhibit a subset of transforming growth factor (TGF)-β family members including myostatin. To determine reliable and valid biomarkers for ActRIIB-Fc treatment, we assessed gene expression profiles for quadriceps muscles from mice treated with ActRIIB-Fc compared with mice genetically lacking myostatin and control mice. Expression of 134 genes was significantly altered in mice treated with ActRIIB-Fc over a 2-wk period relative to control mice (fold change > 1.5, P < 0.001), whereas the number of significantly altered genes in mice treated for 2 days was 38, demonstrating a time-dependent response to ActRIIB-Fc in overall muscle gene expression. The number of significantly altered genes in Mstn(-/-) mice relative to control mice was substantially higher (360), but for most of these genes the expression levels in the 2-wk treated mice were closer to the levels in the Mstn(-/-) mice than in control mice (P < 10⁻³⁰). Expression levels of 30 selected genes were further validated with quantitative real-time polymerase chain reaction (qPCR), and a correlation of ≥ 0.89 was observed between the fold changes from the microarray analysis and the qPCR analysis. These data suggest that treatment with ActRIIB-Fc results in overlapping but distinct gene expression signatures compared with myostatin genetic mutation. Differentially expressed genes identified in this study can be used as potential biomarkers for ActRIIB-Fc treatment, which is currently in clinical trials as a therapeutic agent for muscle wasting and degenerative disorders.
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Affiliation(s)
- Fedik Rahimov
- Program in Genomics, Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, USA
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Rahimov F, Marazita ML, Visel A, Cooper ME, Hitchler MJ, Rubini M, Domann FE, Govil M, Christensen K, Bille C, Melbye M, Jugessur A, Lie RT, Wilcox AJ, Fitzpatrick DR, Green ED, Mossey PA, Little J, Steegers-Theunissen RP, Pennacchio LA, Schutte BC, Murray JC. Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nat Genet 2008; 40:1341-7. [PMID: 18836445 PMCID: PMC2691688 DOI: 10.1038/ng.242] [Citation(s) in RCA: 341] [Impact Index Per Article: 21.3] [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: 12/05/2007] [Accepted: 08/18/2008] [Indexed: 11/09/2022]
Abstract
Previously we have shown that nonsyndromic cleft lip with or without cleft palate (NSCL/P) is strongly associated with SNPs in IRF6 (interferon regulatory factor 6). Here, we use multispecies sequence comparisons to identify a common SNP (rs642961, G>A) in a newly identified IRF6 enhancer. The A allele is significantly overtransmitted (P = 1 x 10(-11)) in families with NSCL/P, in particular those with cleft lip but not cleft palate. Further, there is a dosage effect of the A allele, with a relative risk for cleft lip of 1.68 for the AG genotype and 2.40 for the AA genotype. EMSA and ChIP assays demonstrate that the risk allele disrupts the binding site of transcription factor AP-2alpha and expression analysis in the mouse localizes the enhancer activity to craniofacial and limb structures. Our findings place IRF6 and AP-2alpha in the same developmental pathway and identify a high-frequency variant in a regulatory element contributing substantially to a common, complex disorder.
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Affiliation(s)
- Fedik Rahimov
- Department of Pediatrics, University of Iowa, 2182 ML, S Grand Ave, Iowa City, Iowa 52242, USA
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23
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Jugessur A, Rahimov F, Lie RT, Wilcox AJ, Gjessing HK, Nilsen RM, Nguyen TT, Murray JC. Genetic variants in IRF6 and the risk of facial clefts: single-marker and haplotype-based analyses in a population-based case-control study of facial clefts in Norway. Genet Epidemiol 2008; 32:413-24. [PMID: 18278815 DOI: 10.1002/gepi.20314] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mutations in the gene encoding interferon regulatory factor 6 (IRF6) underlie a common form of syndromic clefting known as Van der Woude syndrome. Lip pits and missing teeth are the only additional features distinguishing the syndrome from isolated clefts. Van der Woude syndrome, therefore, provides an excellent model for studying the isolated forms of clefting. From a population-based case-control study of facial clefts in Norway (1996-2001), we selected 377 cleft lip with or without cleft palate (CL/P), 196 cleft palate only (CPO), and 763 control infant-parent triads for analysis. We genotyped six single nucleotide polymorphisms within the IRF6 locus and estimated the relative risks (RR) conferred on the child by alleles and haplotypes of the child and of the mother. On the whole, there were strong statistical associations with CL/P but not CPO in our data. In single-marker analyses, mothers with a double-dose of the 'a'-allele at rs4844880 had an increased risk of having a child with CL/P (RR=1.85, 95% confidence interval: 1.04-3.25; P=0.036). An RR of 0.38 (95% confidence interval: 0.16-0.92; P=0.031) was obtained when the child carried a single-dose of the 'a'-allele at rs2235371 (the p.V274I polymorphism). The P-value for the overall test was <0.001. In haplotype analyses, several of the fetal and maternal haplotype relative risks were statistically significant individually but were not strong enough to show up on the overall test (P=0.113). Taken together, these findings further support a role for IRF6 variants in clefting of the lip and provide specific risk estimates in a Norwegian population.
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Affiliation(s)
- Astanand Jugessur
- Section for Epidemiology and Medical Statistics, Department of Public Health and Primary Health Care, University of Bergen, Bergen, Norway.
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Rahimov F, Ribeiro LA, de Miranda E, Richieri-Costa A, Murray JC. GLI2 mutations in four Brazilian patients: how wide is the phenotypic spectrum? Am J Med Genet A 2007; 140:2571-6. [PMID: 17096318 DOI: 10.1002/ajmg.a.31370] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [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] [Indexed: 11/05/2022]
Abstract
We report four patients with GLI2 mutations together with their associated phenotypes: (1) holoprosencephaly-like phenotype, (2) anophthalmia, branchial arch anomalies, and CNS abnormalities, (3) heminasal aplasia and orbital anomalies, and (4) lobar holoprosencephaly. This diversity of phenotypes expands our understanding. Findings include not only (1) holoprosencephaly or a holoprosencephaly-like phenotype, but also (2) heminasal aplasia with orbital anomalies, and (3) branchial arch anomalies of the type seen in hemifacial microsomia with anophthalmia and in oculoauriculofrontonasal syndrome. Finally, this is the first report of a double mutation involving GLI2 and PTCH in the same patient.
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Affiliation(s)
- Fedik Rahimov
- Department of Pediatrics, University of Iowa, Iowa, USA
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25
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Vieira AR, Avila JR, Daack-Hirsch S, Dragan E, Félix TM, Rahimov F, Harrington J, Schultz RR, Watanabe Y, Johnson M, Fang J, O'Brien SE, Orioli IM, Castilla EE, FitzPatrick DR, Jiang R, Marazita ML, Murray JC. Medical sequencing of candidate genes for nonsyndromic cleft lip and palate. PLoS Genet 2005; 1:e64. [PMID: 16327884 PMCID: PMC1298935 DOI: 10.1371/journal.pgen.0010064] [Citation(s) in RCA: 184] [Impact Index Per Article: 9.7] [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: 03/03/2005] [Accepted: 10/17/2005] [Indexed: 11/26/2022] Open
Abstract
Nonsyndromic or isolated cleft lip with or without cleft palate (CL/P) occurs in wide geographic distribution with an average birth prevalence of 1/700. We used direct sequencing as an approach to study candidate genes for CL/P. We report here the results of sequencing on 20 candidate genes for clefts in 184 cases with CL/P selected with an emphasis on severity and positive family history. Genes were selected based on expression patterns, animal models, and/or role in known human clefting syndromes. For seven genes with identified coding mutations that are potentially etiologic, we performed linkage disequilibrium studies as well in 501 family triads (affected child/mother/father). The recently reported MSX1 P147Q mutation was also studied in an additional 1,098 cleft cases. Selected missense mutations were screened in 1,064 controls from unrelated individuals on the Centre d'Étude du Polymorphisme Humain (CEPH) diversity cell line panel. Our aggregate data suggest that point mutations in these candidate genes are likely to contribute to 6% of isolated clefts, particularly those with more severe phenotypes (bilateral cleft of the lip with cleft palate). Additional cases, possibly due to microdeletions or isodisomy, were also detected and may contribute to clefts as well. Sequence analysis alone suggests that point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated cleft lip with or without cleft palate, and the linkage disequilibrium data support a larger, as yet unspecified, role for variants in or near MSX2, JAG2, and SKI. This study also illustrates the need to test large numbers of controls to distinguish rare polymorphic variants and prioritize functional studies for rare point mutations. Nonsyndromic or isolated cleft lip with or without cleft palate (CL/P) is a birth defect with wide geographic distribution, occurring with an average frequency of 1/700 live births. Treatment can be provided, but it will involve medical, surgical, dental, and psychological personnel. Several different genes have been implicated in different cases. Here the researchers report the results of sequencing 20 different genes in 184 CL/P cases selected with an emphasis on more severe cases and cases with a positive family history for CL/P. Genes were selected based on previous work done by others and by the researchers' group. The authors' results suggest that point mutations in these candidate genes are likely to contribute to about 5% of CL/P, and particularly those with more severe phenotypes (bilateral cleft of the lip with cleft palate). This study also illustrates the need to test large numbers of controls to distinguish rare polymorphic variants and allow investigators to focus functional studies on the rare point mutations that seem to be disease-causing, so that researchers might better understand the mechanisms that play a role in CL/P.
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Affiliation(s)
- Alexandre R Vieira
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Joseph R Avila
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Sandra Daack-Hirsch
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Ecaterina Dragan
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Têmis M Félix
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Fedik Rahimov
- Interdisciplinary Genetics PhD Program, University of Iowa, Iowa City, Iowa, United States of America
| | - Jill Harrington
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Rebecca R Schultz
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Yoriko Watanabe
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Marla Johnson
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Jennifer Fang
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Sarah E O'Brien
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Iêda M Orioli
- Latin American Collaborative Study of Congenital Malformations, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo E Castilla
- Latin American Collaborative Study of Congenital Malformations, Department of Genetics, Fiocruz, Rio de Janeiro, Brazil
- Center for Medical Education and Investigation, Buenos Aires, Argentina
| | - David R FitzPatrick
- Cell and Molecular Genetics, Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Rulang Jiang
- Center for Oral Biology and Department of Biomedical Genetics, University of Rochester, Rochester, New York, United States of America
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
- * To whom correspondence should be addressed. E-mail:
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26
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Ober C, Aldrich CL, Chervoneva I, Billstrand C, Rahimov F, Gray HL, Hyslop T. Variation in the HLA-G promoter region influences miscarriage rates. Am J Hum Genet 2003; 72:1425-35. [PMID: 12721954 PMCID: PMC1180303 DOI: 10.1086/375501] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.4] [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: 01/24/2003] [Accepted: 03/14/2003] [Indexed: 01/08/2023] Open
Abstract
The HLA-G gene is primarily expressed in placental cells that invade the maternal decidua during pregnancy. This gene encodes multiple isoforms that fulfill a variety of functions at the maternal-fetal interface throughout gestation. Recently, a null allele for the most abundant HLA-G isoform was associated with recurrent miscarriage in two independent studies, suggesting that reduced levels of the HLA-G1 protein may compromise successful pregnancy. We initiated the present study to determine whether other polymorphisms that could affect expression levels of HLA-G were associated with fetal loss in women participating in a 15-year prospective study of pregnancy outcome. We genotyped these subjects for 18 single-nucleotide polymorphisms in the 1,300 bp upstream of exon 1, 13 of which were identified as part of this study, as well as for an insertion/deletion (in/del) polymorphism in the 3' untranslated region. The 18 SNPs defined eight unique haplotypes. One polymorphism, -725C/G, was associated with fetal loss, with an increased risk for miscarriage in couples in which both partners carried the -725G allele, compared with couples not carrying this allele (odds ratio 2.76, 95% confidence interval 1.08-7.09; P=.035). Further, the G at nucleotide -725 creates a CpG dinucleotide, and we demonstrate that this CpG site is methylated on -725G alleles. Overall, this study identified extraordinary levels of variation in the 5'-upstream regulatory region of HLA-G and provides evidence for an association between a promoter-region SNP and fetal loss rates, further attesting to the novel features and critical role of this gene in pregnancy.
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Affiliation(s)
- Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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