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De Jonge CJ, Barratt CLR, Aitken RJ, Anderson RA, Baker P, Chan DYL, Connolly MP, Eisenberg ML, Garrido N, Jørgensen N, Kimmins S, Krausz C, McLachlan RI, Niederberger C, O’Bryan MK, Pacey A, Priskorn L, Rautakallio-Hokkanen S, Serour G, Veltman JA, Vogel DL, Vazquez-Levin MH. Current global status of male reproductive health. Hum Reprod Open 2024; 2024:hoae017. [PMID: 38699533 PMCID: PMC11065475 DOI: 10.1093/hropen/hoae017] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/22/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND The widespread interest in male reproductive health (MRH), fueled by emerging evidence, such as the global decline in sperm counts, has intensified concerns about the status of MRH. Consequently, there is a pressing requirement for a strategic, systematic approach to identifying critical questions, collecting pertinent information, and utilizing these data to develop evidence-based strategies. The methods for addressing these questions and the pathways toward their answers will inevitably vary based on the variations in cultural, geopolitical, and health-related contexts. To address these issues, a conjoint ESHRE and Male Reproductive Health Initiative (MRHI) Campus workshop was convened. OBJECTIVE AND RATIONALE The three objectives were: first, to assess the current state of MRH around the world; second, to identify some of the key gaps in knowledge; and, third, to examine how MRH stakeholders can collaboratively generate intelligent and effective paths forward. SEARCH METHODS Each expert reviewed and summarized the current literature that was subsequently used to provide a comprehensive overview of challenges related to MRH. OUTCOMES This narrative report is an overview of the data, opinions, and arguments presented during the workshop. A number of outcomes are presented and can be summarized by the following overarching themes: MRH is a serious global issue and there is a plethora of gaps in our understanding; there is a need for widespread international collaborative networks to undertake multidisciplinary research into fundamental issues, such as lifestyle/environmental exposure studies, and high-quality clinical trials; and there is an urgent requirement for effective strategies to educate young people and the general public to safeguard and improve MRH across diverse population demographics and resources. LIMITATIONS REASONS FOR CAUTION This was a workshop where worldwide leading experts from a wide range of disciplines presented and discussed the evidence regarding challenges related to MRH. While each expert summarized the current literature and placed it in context, the data in a number of areas are limited and/or sparse. Equally, important areas for consideration may have been missed. Moreover, there are clear gaps in our knowledge base, which makes some conclusions necessarily speculative and warranting of further study. WIDER IMPLICATIONS Poor MRH is a global issue that suffers from low awareness among the public, patients, and heathcare professionals. Addressing this will require a coordinated multidisciplinary approach. Addressing the significant number of knowledge gaps will require policy makers prioritizing MRH and its funding. STUDY FUNDING/COMPETING INTERESTS The authors would like to extend their gratitude to ESHRE for providing financial support for the Budapest Campus Workshop, as well as to Microptic S.L. (Barcelona) for kindly sponsoring the workshop. P.B. is the Director of the not-for-profit organization Global Action on Men's Health and receives fees and expenses for his work, (which includes the preparation of this manuscript). Conflicts of interest: C.J.D.J., C.L.R.B., R.A.A., P.B., M.P.C., M.L.E., N.G., N.J., C.K., AAP, M.K.O., S.R.-H., M.H.V.-L.: ESHRE Campus Workshop 2022 (Travel support-personal). C.J.D.J.: Cambridge University Press (book royalties-personal). ESHRE Annual Meeting 2022 and Yale University Panel Meeting 2023 (Travel support-personal). C.L.R.B.: Ferring and IBSA (Lecture), RBMO editor (Honorarium to support travel, etc.), ExSeed and ExScentia (University of Dundee), Bill & Melinda Gates Foundation (for research on contraception). M.P.C.: Previously received funding from pharmaceutical companies for health economic research. The funding was not in relation to this work and had no bearing on the contents of this work. No funding from other sources has been provided in relation to this work (funding was provided to his company Global Market Access Solutions). M.L.E.: Advisor to Ro, Doveras, Next, Hannah, Sandstone. C.K.: European Academy of Andrology (Past president UNPAID), S.K.: CEO of His Turn, a male fertility Diagnostic and Therapeutic company (No payments or profits to date). R.I.M.: www.healthymale.org.au (Australian Government funded not for profit in men's health sector (Employed as Medical Director 0.2 FET), Monash IVF Pty Ltd (Equity holder)). N.J.: Merck (consulting fees), Gedeon Richter (honoraria). S.R.-H.: ESHRE (Travel reimbursements). C.N.: LLC (Nursing educator); COMMIT (Core Outcomes Measures for Infertility Trials) Advisor, meeting attendee, and co-author; COMMA (Core Outcomes in Menopause) Meeting attendee, and co-author; International Federation of Gynecology and Obstetrics (FIGO) Delegate Letters and Sciences; ReproNovo, Advisory board; American Board of Urology Examiner; American Urological Association Journal subsection editor, committee member, guidelines co-author Ferring Scientific trial NexHand Chief Technology Officer, stock ownership Posterity Health Board member, stock ownership. A.P.: Economic and Social Research Council (A collaborator on research grant number ES/W001381/1). Member of an advisory committee for Merck Serono (November 2022), Member of an advisory board for Exceed Health, Speaker fees for educational events organized by Mealis Group; Chairman of the Cryos External Scientific Advisory Committee: All fees associated with this are paid to his former employer The University of Sheffield. Trustee of the Progress Educational Trust (Unpaid). M.K.O.: National Health and Medical Research Council and Australian Research Council (Funding for research of the topic of male fertility), Bill and Melinda Gates Foundation (Funding aimed at the development of male gamete-based contraception), Medical Research Future Fund (Funding aimed at defining the long-term consequences of male infertility). M.H.V.-L.: Department of Sexual and Reproductive Health and Research (SRH)/Human Reproduction Programme (HRP) Research Project Panel RP2/WHO Review Member; MRHI (Core Group Member), COMMIT (member), EGOI (Member); Human Reproduction (Associate Editor), Fertility and Sterility (Editor), AndroLATAM (Founder and Coordinator).
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Affiliation(s)
- Christopher J De Jonge
- Department of Urology, University of Minnesota Medical Center, University of Minnesota, Minneapolis, MN, USA
| | - Christopher L R Barratt
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - R John Aitken
- Discipline of Biological Sciences, School of Environment and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Newcastle, Australia
| | - Richard A Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | | | - David Y L Chan
- Assisted Reproductive Technology Unit, Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, China
| | - Mark P Connolly
- Health Economics, Global Market Access Solutions LLC, Mooresville, NC, USA
- University Medical Center Groningen, Groningen, The Netherlands
| | - Michael L Eisenberg
- Department of Urology and Obstetrics & Gynecology, Stanford University, Stanford, CA, USA
| | - Nicolas Garrido
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Niels Jørgensen
- Department of Growth and Reproduction and International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, QC, Canada
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, QC, Canada
| | - Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences, ‘Mario Serio’, University of Florence, University Hospital of Careggi (AOUC), Florence, Italy
| | - Robert I McLachlan
- Hudson Institute of Medical Research, Monash University, Melbourne, Australia
- Monash IVF Group, Cremorne, Australia
| | - Craig Niederberger
- Clarence C. Department of Urology, University of Illinois Chicago (UIC), College of Medicine, Department of Bioengineering, UIC College of Engineering, Chicago, IL,USA
| | - Moira K O’Bryan
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - Allan Pacey
- Faculty of Biology, Medicine and Health, Core Technology Facility, University of Manchester, Manchester, UK
| | - Lærke Priskorn
- Department of Growth and Reproduction and International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Gamal Serour
- The International Islamic Center for Population Studies and Research, Al-Azhar University, Maadi, Cairo, Egypt
- Egyptian IVF Center, Maadi, Cairo, Egypt
| | - Joris A Veltman
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Donna L Vogel
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Mónica H Vazquez-Levin
- Instituto de Biología y Medicina Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina—Fundación IBYME, Buenos Aires, Argentina
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2
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Kimmins S, Anderson RA, Barratt CLR, Behre HM, Catford SR, De Jonge CJ, Delbes G, Eisenberg ML, Garrido N, Houston BJ, Jørgensen N, Krausz C, Lismer A, McLachlan RI, Minhas S, Moss T, Pacey A, Priskorn L, Schlatt S, Trasler J, Trasande L, Tüttelmann F, Vazquez-Levin MH, Veltman JA, Zhang F, O'Bryan MK. Frequency, morbidity and equity - the case for increased research on male fertility. Nat Rev Urol 2024; 21:102-124. [PMID: 37828407 DOI: 10.1038/s41585-023-00820-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 10/14/2023]
Abstract
Currently, most men with infertility cannot be given an aetiology, which reflects a lack of knowledge around gamete production and how it is affected by genetics and the environment. A failure to recognize the burden of male infertility and its potential as a biomarker for systemic illness exists. The absence of such knowledge results in patients generally being treated as a uniform group, for whom the strategy is to bypass the causality using medically assisted reproduction (MAR) techniques. In doing so, opportunities to prevent co-morbidity are missed and the burden of MAR is shifted to the woman. To advance understanding of men's reproductive health, longitudinal and multi-national centres for data and sample collection are essential. Such programmes must enable an integrated view of the consequences of genetics, epigenetics and environmental factors on fertility and offspring health. Definition and possible amelioration of the consequences of MAR for conceived children are needed. Inherent in this statement is the necessity to promote fertility restoration and/or use the least invasive MAR strategy available. To achieve this aim, protocols must be rigorously tested and the move towards personalized medicine encouraged. Equally, education of the public, governments and clinicians on the frequency and consequences of infertility is needed. Health options, including male contraceptives, must be expanded, and the opportunities encompassed in such investment understood. The pressing questions related to male reproductive health, spanning the spectrum of andrology are identified in the Expert Recommendation.
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Affiliation(s)
- Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- The Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- The Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Richard A Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - Christopher L R Barratt
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Hermann M Behre
- Center for Reproductive Medicine and Andrology, University Hospital, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Sarah R Catford
- Hudson Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Obstetrics and Gynaecology, The Royal Women's Hospital, Melbourne, Victoria, Australia
| | | | - Geraldine Delbes
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Sante Biotechnologie, Laval, Quebec, Canada
| | - Michael L Eisenberg
- Department of Urology and Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
| | - Nicolas Garrido
- IVI Foundation, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Brendan J Houston
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Melbourne, Australia
| | - Niels Jørgensen
- Department of Growth and Reproduction, International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences, 'Mario Serio', University of Florence, University Hospital of Careggi Florence, Florence, Italy
| | - Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Robert I McLachlan
- Hudson Institute of Medical Research and the Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
- Monash IVF Group, Richmond, Victoria, Australia
| | - Suks Minhas
- Department of Surgery and Cancer Imperial, London, UK
| | - Tim Moss
- Healthy Male and the Department of Obstetrics and Gynaecology, Monash University, Melbourne, Victoria, Australia
| | - Allan Pacey
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Lærke Priskorn
- Department of Growth and Reproduction, International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Stefan Schlatt
- Centre for Reproductive Medicine and Andrology, University of Münster, Münster, Germany
| | - Jacquetta Trasler
- Departments of Paediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Leonardo Trasande
- Center for the Investigation of Environmental Hazards, Department of Paediatrics, NYU Grossman School of Medicine, New York, NY, USA
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Mónica Hebe Vazquez-Levin
- Instituto de Biología y Medicina Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Fundación IBYME, Buenos Aires, Argentina
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Moira K O'Bryan
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Melbourne, Australia.
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Wyrwoll MJ, van der Heijden GW, Krausz C, Aston KI, Kliesch S, McLachlan R, Ramos L, Conrad DF, O'Bryan MK, Veltman JA, Tüttelmann F. Improved phenotypic classification of male infertility to promote discovery of genetic causes. Nat Rev Urol 2024; 21:91-101. [PMID: 37723288 DOI: 10.1038/s41585-023-00816-0] [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] [Accepted: 08/16/2023] [Indexed: 09/20/2023]
Abstract
An increasing number of genes are being described in the context of non-syndromic male infertility. Linking the underlying genetic causes of non-syndromic male infertility with clinical data from patients is important to establish new genotype-phenotype correlations. This process can be facilitated by using universal nomenclature, but no standardized vocabulary is available in the field of non-syndromic male infertility. The International Male Infertility Genomics Consortium aimed at filling this gap, providing a standardized vocabulary containing nomenclature based on the Human Phenotype Ontology (HPO). The "HPO tree" was substantially revised compared with the previous version and is based on the clinical work-up of infertile men, including physical examination and hormonal assessment. Some causes of male infertility can already be suspected based on the patient's clinical history, whereas in other instances, a testicular biopsy is needed for diagnosis. We assembled 49 HPO terms that are linked in a logical hierarchy and showed examples of morphological features of spermatozoa and testicular histology of infertile men with identified genetic diagnoses to describe the phenotypes. This work will help to record patients' phenotypes systematically and facilitate communication between geneticists and andrologists. Collaboration across institutions will improve the identification of patients with the same phenotypes, which will promote the discovery of novel genetic causes for non-syndromic male infertility.
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Affiliation(s)
- Margot J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | | | - Csilla Krausz
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, University Hospital of Careggi (AOUC), Florence, Italy
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah, Salt Lake City, UT, USA
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University of Münster, Münster, Germany
| | - Robert McLachlan
- Department of Clinical Research, Hudson Institute of Medical Research, Melbourne, Victoria, Australia
| | - Liliana Ramos
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Donald F Conrad
- Department of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Moira K O'Bryan
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany.
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4
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Wiel L, Hampstead JE, Venselaar H, Vissers LE, Brunner HG, Pfundt R, Vriend G, Veltman JA, Gilissen C. De novo mutation hotspots in homologous protein domains identify function-altering mutations in neurodevelopmental disorders. Am J Hum Genet 2023; 110:92-104. [PMID: 36563679 PMCID: PMC9892778 DOI: 10.1016/j.ajhg.2022.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Variant interpretation remains a major challenge in medical genetics. We developed Meta-Domain HotSpot (MDHS) to identify mutational hotspots across homologous protein domains. We applied MDHS to a dataset of 45,221 de novo mutations (DNMs) from 31,058 individuals with neurodevelopmental disorders (NDDs) and identified three significantly enriched missense DNM hotspots in the ion transport protein domain family (PF00520). The 37 unique missense DNMs that drive enrichment affect 25 genes, 19 of which were previously associated with NDDs. 3D protein structure modeling supports the hypothesis of function-altering effects of these mutations. Hotspot genes have a unique expression pattern in tissue, and we used this pattern alongside in silico predictors and population constraint information to identify candidate NDD-associated genes. We also propose a lenient version of our method, which identifies 32 hotspot positions across 16 different protein domains. These positions are enriched for likely pathogenic variation in clinical databases and DNMs in other genetic disorders.
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands,Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Juliet E. Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Han G. Brunner
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Gerrit Vriend
- Baco Institute of Protein Science, Baco, 5201 Mindoro, Philippines
| | - Joris A. Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands,Corresponding author
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5
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Nagirnaja L, Lopes AM, Charng WL, Miller B, Stakaitis R, Golubickaite I, Stendahl A, Luan T, Friedrich C, Mahyari E, Fadial E, Kasak L, Vigh-Conrad K, Oud MS, Xavier MJ, Cheers SR, James ER, Guo J, Jenkins TG, Riera-Escamilla A, Barros A, Carvalho F, Fernandes S, Gonçalves J, Gurnett CA, Jørgensen N, Jezek D, Jungheim ES, Kliesch S, McLachlan RI, Omurtag KR, Pilatz A, Sandlow JI, Smith J, Eisenberg ML, Hotaling JM, Jarvi KA, Punab M, Rajpert-De Meyts E, Carrell DT, Krausz C, Laan M, O’Bryan MK, Schlegel PN, Tüttelmann F, Veltman JA, Almstrup K, Aston KI, Conrad DF. Diverse monogenic subforms of human spermatogenic failure. Nat Commun 2022; 13:7953. [PMID: 36572685 PMCID: PMC9792524 DOI: 10.1038/s41467-022-35661-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022] Open
Abstract
Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human "knockouts", and, for the most part, have yet to be linked to a Mendelian trait. Integration with single-cell RNA sequencing data shows that azoospermia genes can be grouped into molecular subforms with synchronized expression patterns, and analogs of these subforms exist in mice. This analysis framework identifies groups of genes with known roles in spermatogenesis but also reveals unrecognized subforms, such as a set of genes expressed across mitotic divisions of differentiating spermatogonia. Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may provide a rational basis for disease classification.
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Affiliation(s)
- Liina Nagirnaja
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Alexandra M. Lopes
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Wu-Lin Charng
- grid.4367.60000 0001 2355 7002Department of Neurology, Washington University, St. Louis, MO USA
| | - Brian Miller
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Rytis Stakaitis
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.45083.3a0000 0004 0432 6841Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ieva Golubickaite
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.45083.3a0000 0004 0432 6841Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexandra Stendahl
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Tianpengcheng Luan
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - Corinna Friedrich
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Eisa Mahyari
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Eloise Fadial
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Laura Kasak
- grid.10939.320000 0001 0943 7661Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Katinka Vigh-Conrad
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Manon S. Oud
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Miguel J. Xavier
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Samuel R. Cheers
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - Emma R. James
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Jingtao Guo
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Timothy G. Jenkins
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Antoni Riera-Escamilla
- grid.418813.70000 0004 1767 1951Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia Spain ,grid.7080.f0000 0001 2296 0625Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Catalonia 08025 Spain
| | - Alberto Barros
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Filipa Carvalho
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Susana Fernandes
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - João Gonçalves
- grid.422270.10000 0001 2287 695XDepartamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal ,grid.10772.330000000121511713Centre for Toxicogenomics and Human Health, Nova Medical School, Lisbon, Portugal
| | - Christina A. Gurnett
- grid.4367.60000 0001 2355 7002Department of Neurology, Washington University, St. Louis, MO USA
| | - Niels Jørgensen
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Davor Jezek
- grid.4808.40000 0001 0657 4636Department of Histology and Embryology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Emily S. Jungheim
- grid.16753.360000 0001 2299 3507Department of Obstetrics and Gynecology at Northwestern University, Division of Reproductive Endocrinology, Chicago, IL USA
| | - Sabine Kliesch
- grid.16149.3b0000 0004 0551 4246Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Robert I. McLachlan
- grid.1002.30000 0004 1936 7857Hudson Institute of Medical Research and the Department of Obstetrics and Gynecology, Monash University, Clayton, VIC Australia
| | - Kenan R. Omurtag
- grid.34477.330000000122986657Department of Obstetrics and Gynecology at Washington University, Division of Reproductive Endocrinology, St. Louis, MO USA
| | - Adrian Pilatz
- grid.8664.c0000 0001 2165 8627Clinic for Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
| | - Jay I. Sandlow
- grid.30760.320000 0001 2111 8460Department of Urology, Medical College of Wisconsin, Milwaukee, WI USA
| | - James Smith
- grid.266102.10000 0001 2297 6811Department of Urology, University California San Francisco, San Francisco, CA USA
| | - Michael L. Eisenberg
- grid.168010.e0000000419368956Department of Urology, Stanford University School of Medicine, Stanford, CA USA
| | - James M. Hotaling
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Keith A. Jarvi
- grid.17063.330000 0001 2157 2938Division of Urology, Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, ON Canada
| | - Margus Punab
- grid.412269.a0000 0001 0585 7044Andrology Center, Tartu University Hospital, Tartu, Estonia ,grid.10939.320000 0001 0943 7661Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ewa Rajpert-De Meyts
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Douglas T. Carrell
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Csilla Krausz
- grid.8404.80000 0004 1757 2304Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Maris Laan
- grid.10939.320000 0001 0943 7661Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Moira K. O’Bryan
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia ,grid.1002.30000 0004 1936 7857School of Biological Sciences, Monash University, Clayton, VIC Australia
| | - Peter N. Schlegel
- grid.5386.8000000041936877XDepartment of Urology, Weill Cornell Medicine, New York, NY USA
| | - Frank Tüttelmann
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Joris A. Veltman
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Kristian Almstrup
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Kenneth I. Aston
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Donald F. Conrad
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
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6
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Holt GS, Batty LE, Alobaidi BKS, Smith HE, Oud MS, Ramos L, Xavier MJ, Veltman JA. Phasing of de novo mutations using a scaled-up multiple amplicon long-read sequencing approach. Hum Mutat 2022; 43:1545-1556. [PMID: 36047340 PMCID: PMC9826063 DOI: 10.1002/humu.24450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/11/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023]
Abstract
De novo mutations (DNMs) play an important role in severe genetic disorders that reduce fitness. To better understand their role in disease, it is important to determine the parent-of-origin and timing of mutational events that give rise to these mutations, especially in sex-specific developmental disorders such as male infertility. However, currently available short-read sequencing approaches are not ideally suited for phasing, as this requires long continuous DNA strands that span both the DNM and one or more informative single-nucleotide polymorphisms. To overcome these challenges, we optimized and implemented a multiplexed long-read sequencing approach using Oxford Nanopore technologies MinION platform. We focused on improving target amplification, integrating long-read sequenced data with high-quality short-read sequence data, and developing an anchored phasing computational method. This approach handled the inherent phasing challenges of long-range target amplification and the normal accumulation of sequencing error associated with long-read sequencing. In total, 77 of 109 DNMs (71%) were successfully phased and parent-of-origin identified. The majority of phased DNMs were prezygotic (90%), the accuracy of which is highlighted by an average mutant allele frequency of 49.6% and standard error of 0.84%. This study demonstrates the benefits of employing an integrated short-read and long-read sequencing approach for large-scale DNM phasing.
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Affiliation(s)
- Giles S. Holt
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Lois E. Batty
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Bilal K. S. Alobaidi
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Hannah E. Smith
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Manon S. Oud
- Department of Human Genetics, Donders Institute for BrainCognition and Behaviour, RadboudumcNijmegenThe Netherlands
| | - Liliana Ramos
- Department of Obstetrics and Gynecology, Division of Reproductive MedicineRadboudumcNijmegenThe Netherlands
| | - Miguel J. Xavier
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Joris A. Veltman
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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7
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Wyrwoll MJ, Gaasbeek CM, Golubickaite I, Stakaitis R, Oud MS, Nagirnaja L, Dion C, Sindi EB, Leitch HG, Jayasena CN, Sironen A, Dicke AK, Rotte N, Stallmeyer B, Kliesch S, Grangeiro CHP, Araujo TF, Lasko P, D'Hauwers K, Smits RM, Ramos L, Xavier MJ, Conrad DF, Almstrup K, Veltman JA, Tüttelmann F, van der Heijden GW. The piRNA-pathway factor FKBP6 is essential for spermatogenesis but dispensable for control of meiotic LINE-1 expression in humans. Am J Hum Genet 2022; 109:1850-1866. [PMID: 36150389 PMCID: PMC9606565 DOI: 10.1016/j.ajhg.2022.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 05/15/2022] [Accepted: 09/01/2022] [Indexed: 01/25/2023] Open
Abstract
Infertility affects around 7% of the male population and can be due to severe spermatogenic failure (SPGF), resulting in no or very few sperm in the ejaculate. We initially identified a homozygous frameshift variant in FKBP6 in a man with extreme oligozoospermia. Subsequently, we screened a total of 2,699 men with SPGF and detected rare bi-allelic loss-of-function variants in FKBP6 in five additional persons. All six individuals had no or extremely few sperm in the ejaculate, which were not suitable for medically assisted reproduction. Evaluation of testicular tissue revealed an arrest at the stage of round spermatids. Lack of FKBP6 expression in the testis was confirmed by RT-qPCR and immunofluorescence staining. In mice, Fkbp6 is essential for spermatogenesis and has been described as being involved in piRNA biogenesis and formation of the synaptonemal complex (SC). We did not detect FKBP6 as part of the SC in normal human spermatocytes, but small RNA sequencing revealed that loss of FKBP6 severely impacted piRNA levels, supporting a role for FKBP6 in piRNA biogenesis in humans. In contrast to findings in piRNA-pathway mouse models, we did not detect an increase in LINE-1 expression in men with pathogenic FKBP6 variants. Based on our findings, FKBP6 reaches a "strong" level of evidence for being associated with male infertility according to the ClinGen criteria, making it directly applicable for clinical diagnostics. This will improve patient care by providing a causal diagnosis and will help to predict chances for successful surgical sperm retrieval.
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Affiliation(s)
- Margot J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Channah M Gaasbeek
- Department of Human Genetics, Radboudumc, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ieva Golubickaite
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA; Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark; Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rytis Stakaitis
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA; Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark; Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Manon S Oud
- Department of Human Genetics, Radboudumc, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Camille Dion
- MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK
| | - Emad B Sindi
- Section of Investigative Medicine, Imperial College London, London, UK
| | - Harry G Leitch
- MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Channa N Jayasena
- Section of Investigative Medicine, Imperial College London, London, UK
| | - Anu Sironen
- Natural Resources Institute Finland, Production Systems, Jokioinen, Finland; Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ann-Kristin Dicke
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Nadja Rotte
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Birgit Stallmeyer
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, Münster, Germany
| | | | - Thaís F Araujo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Paul Lasko
- Department of Human Genetics, Radboudumc, Nijmegen, the Netherlands; Department of Biology, McGill University, Montréal, QC, Canada
| | | | - Roos M Smits
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Liliana Ramos
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Miguel J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Don F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Kristian Almstrup
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark; Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
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8
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Riera-Escamilla A, Vockel M, Nagirnaja L, Xavier MJ, Carbonell A, Moreno-Mendoza D, Pybus M, Farnetani G, Rosta V, Cioppi F, Friedrich C, Oud MS, van der Heijden GW, Soave A, Diemer T, Ars E, Sánchez-Curbelo J, Kliesch S, O’Bryan MK, Ruiz-Castañe E, Azorín F, Veltman JA, Aston KI, Conrad DF, Tüttelmann F, Krausz C. Large-scale analyses of the X chromosome in 2,354 infertile men discover recurrently affected genes associated with spermatogenic failure. Am J Hum Genet 2022; 109:1458-1471. [PMID: 35809576 PMCID: PMC9388793 DOI: 10.1016/j.ajhg.2022.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 03/24/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
Although the evolutionary history of the X chromosome indicates its specialization in male fitness, its role in spermatogenesis has largely been unexplored. Currently only three X chromosome genes are considered of moderate-definitive diagnostic value. We aimed to provide a comprehensive analysis of all X chromosome-linked protein-coding genes in 2,354 azoospermic/cryptozoospermic men from four independent cohorts. Genomic data were analyzed and compared with data in normozoospermic control individuals and gnomAD. While updating the clinical significance of known genes, we propose 21 recurrently mutated genes strongly associated with and 34 moderately associated with azoospermia/cryptozoospermia not previously linked to male infertility (novel). The most frequently affected prioritized gene, RBBP7, was found mutated in ten men across all cohorts, and our functional studies in Drosophila support its role in germ stem cell maintenance. Collectively, our study represents a significant step towards the definition of the missing genetic etiology in idiopathic severe spermatogenic failure and significantly reduces the knowledge gap of X-linked genetic causes of azoospermia/cryptozoospermia contributing to the development of future diagnostic gene panels.
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Affiliation(s)
- Antoni Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau, Barcelona, 08025 Catalonia, Spain
| | - Matthias Vockel
- Institute of Human Genetics, University of Münster, Vesaliusweg 12-14, 48149 Münster, Germany
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Miguel J. Xavier
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Albert Carbonell
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, Barcelona, 08028 Catalonia, Spain,Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10, Barcelona, 08028 Catalonia, Spain
| | - Daniel Moreno-Mendoza
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau, Barcelona, 08025 Catalonia, Spain,Department of Urology, Hospital del Oriente de Asturias, Arriondas, 33540 Asturias, Spain
| | - Marc Pybus
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autònoma de Barcelona, Barcelona, 08025 Catalonia, Spain
| | - Ginevra Farnetani
- Department of Biomedical, Experimental and Clinical Sciences Mario Serio, University of Florence, Florence 50139, Italy
| | - Viktoria Rosta
- Department of Biomedical, Experimental and Clinical Sciences Mario Serio, University of Florence, Florence 50139, Italy
| | - Francesca Cioppi
- Department of Biomedical, Experimental and Clinical Sciences Mario Serio, University of Florence, Florence 50139, Italy
| | - Corinna Friedrich
- Institute of Reproductive Genetics, University of Münster, Vesaliusweg 12-14, 48149 Münster, Germany
| | - Manon S. Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen 6525, the Netherlands
| | | | - Armin Soave
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Thorsten Diemer
- Clinic for Urology, Paediatric Urology and Andrology, Justus Liebig University, Gießen 35392, Germany
| | - Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autònoma de Barcelona, Barcelona, 08025 Catalonia, Spain
| | - Josvany Sánchez-Curbelo
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau, Barcelona, 08025 Catalonia, Spain
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster 48149, Germany
| | - Moira K. O’Bryan
- The School of BioScience that the Bio21 Institute, The Faculty of Science, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Eduard Ruiz-Castañe
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau, Barcelona, 08025 Catalonia, Spain
| | | | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, Barcelona, 08028 Catalonia, Spain,Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10, Barcelona, 08028 Catalonia, Spain
| | - Joris A. Veltman
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kenneth I. Aston
- Andrology and IVF Laboratories, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Donald F. Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA,Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Vesaliusweg 12-14, 48149 Münster, Germany
| | - Csilla Krausz
- Department of Biomedical, Experimental and Clinical Sciences Mario Serio, University of Florence, Florence 50139, Italy,Corresponding author
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9
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Smits RM, Xavier MJ, Oud MS, Astuti GDN, Meijerink AM, de Vries PF, Holt GS, Alobaidi BKS, Batty LE, Khazeeva G, Sablauskas K, Vissers LELM, Gilissen C, Fleischer K, Braat DDM, Ramos L, Veltman JA. De novo mutations in children born after medical assisted reproduction. Hum Reprod 2022; 37:1360-1369. [PMID: 35413117 PMCID: PMC9156847 DOI: 10.1093/humrep/deac068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/08/2022] [Indexed: 01/23/2023] Open
Abstract
STUDY QUESTION Are there more de novo mutations (DNMs) present in the genomes of children born through medical assisted reproduction (MAR) compared to spontaneously conceived children? SUMMARY ANSWER In this pilot study, no statistically significant difference was observed in the number of DNMs observed in the genomes of MAR children versus spontaneously conceived children. WHAT IS KNOWN ALREADY DNMs are known to play a major role in sporadic disorders with reduced fitness such as severe developmental disorders, including intellectual disability and epilepsy. Advanced paternal age is known to place offspring at increased disease risk, amongst others by increasing the number of DNMs in their genome. There are very few studies reporting on the effect of MAR on the number of DNMs in the offspring, especially when male infertility is known to be affecting the potential fathers. With delayed parenthood an ongoing epidemiological trend in the 21st century, there are more children born from fathers of advanced age and more children born through MAR every day. STUDY DESIGN, SIZE, DURATION This observational pilot study was conducted from January 2015 to March 2019 in the tertiary care centre at Radboud University Medical Center. We included a total of 53 children and their respective parents, forming 49 trios (mother, father and child) and two quartets (mother, father and two siblings). One group of children was born after spontaneous conception (n = 18); a second group of children born after IVF (n = 17) and a third group of children born after ICSI combined with testicular sperm extraction (ICSI-TESE) (n = 18). In this pilot study, we also subdivided each group by paternal age, resulting in a subgroup of children born to younger fathers (<35 years of age at conception) and older fathers (>45 years of age at conception). PARTICIPANTS/MATERIALS, SETTING, METHODS Whole-genome sequencing (WGS) was performed on all parent-offspring trios to identify DNMs. For 34 of 53 trios/quartets, WGS was performed twice to independently detect and validate the presence of DNMs. Quality of WGS-based DNM calling was independently assessed by targeted Sanger sequencing. MAIN RESULTS AND THE ROLE OF CHANCE No significant differences were observed in the number of DNMs per child for the different methods of conception, independent of parental age at conception (multi-factorial ANOVA, f(2) = 0.17, P-value = 0.85). As expected, a clear paternal age effect was observed after adjusting for method of conception and maternal age at conception (multiple regression model, t = 5.636, P-value = 8.97 × 10-7), with on average 71 DNMs in the genomes of children born to young fathers (<35 years of age) and an average of 94 DNMs in the genomes of children born to older fathers (>45 years of age). LIMITATIONS, REASONS FOR CAUTION This is a pilot study and other small-scale studies have recently reported contrasting results. Larger unbiased studies are required to confirm or falsify these results. WIDER IMPLICATIONS OF THE FINDINGS This pilot study did not show an effect for the method of conception on the number of DNMs per genome in offspring. Given the role that DNMs play in disease risk, this negative result is good news for IVF and ICSI-TESE born children, if replicated in a larger cohort. STUDY FUNDING/COMPETING INTEREST(S) This research was funded by the Netherlands Organisation for Scientific Research (918-15-667) and by an Investigator Award in Science from the Wellcome Trust (209451). The authors have no conflicts of interest to declare. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- R M Smits
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - M J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - G D N Astuti
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - A M Meijerink
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - P F de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - G S Holt
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - B K S Alobaidi
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - L E Batty
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - G Khazeeva
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - K Sablauskas
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - L E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - K Fleischer
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - D D M Braat
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - L Ramos
- Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, the Netherlands
| | - J A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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10
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Houston BJ, Riera-Escamilla A, Wyrwoll MJ, Salas-Huetos A, Xavier MJ, Nagirnaja L, Friedrich C, Conrad DF, Aston KI, Krausz C, Tüttelmann F, O’Bryan MK, Veltman JA, Oud MS. A systematic review of the validated monogenic causes of human male infertility: 2020 update and a discussion of emerging gene-disease relationships. Hum Reprod Update 2021; 28:15-29. [PMID: 34498060 PMCID: PMC8730311 DOI: 10.1093/humupd/dmab030] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/05/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human male infertility has a notable genetic component, including well-established diagnoses such as Klinefelter syndrome, Y-chromosome microdeletions and monogenic causes. Approximately 4% of all infertile men are now diagnosed with a genetic cause, but a majority (60-70%) remain without a clear diagnosis and are classified as unexplained. This is likely in large part due to a delay in the field adopting next-generation sequencing (NGS) technologies, and the absence of clear statements from field leaders as to what constitutes a validated cause of human male infertility (the current paper aims to address this). Fortunately, there has been a significant increase in the number of male infertility NGS studies. These have revealed a considerable number of novel gene-disease relationships (GDRs), which each require stringent assessment to validate the strength of genotype-phenotype associations. To definitively assess which of these GDRs are clinically relevant, the International Male Infertility Genomics Consortium (IMIGC) has identified the need for a systematic review and a comprehensive overview of known male infertility genes and an assessment of the evidence for reported GDRs. OBJECTIVE AND RATIONALE In 2019, the first standardised clinical validity assessment of monogenic causes of male infertility was published. Here, we provide a comprehensive update of the subsequent 1.5 years, employing the joint expertise of the IMIGC to systematically evaluate all available evidence (as of 1 July 2020) for monogenic causes of isolated or syndromic male infertility, endocrine disorders or reproductive system abnormalities affecting the male sex organs. In addition, we systematically assessed the evidence for all previously reported possible monogenic causes of male infertility, using a framework designed for a more appropriate clinical interpretation of disease genes. SEARCH METHODS We performed a literature search according to the PRISMA guidelines up until 1 July 2020 for publications in English, using search terms related to 'male infertility' in combination with the word 'genetics' in PubMed. Next, the quality and the extent of all evidence supporting selected genes were assessed using an established and standardised scoring method. We assessed the experimental quality, patient phenotype assessment and functional evidence based on gene expression, mutant in-vitro cell and in-vivo animal model phenotypes. A final score was used to determine the clinical validity of each GDR, across the following five categories: no evidence, limited, moderate, strong or definitive. Variants were also reclassified according to the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines and were recorded in spreadsheets for each GDR, which are available at imigc.org. OUTCOMES The primary outcome of this review was an overview of all known GDRs for monogenic causes of human male infertility and their clinical validity. We identified a total of 120 genes that were moderately, strongly or definitively linked to 104 infertility phenotypes. WIDER IMPLICATIONS Our systematic review curates all currently available evidence to reveal the strength of GDRs in male infertility. The existing guidelines for genetic testing in male infertility cases are based on studies published 25 years ago, and an update is far overdue. The identification of 104 high-probability 'human male infertility genes' is a 33% increase from the number identified in 2019. The insights generated in the current review will provide the impetus for an update of existing guidelines, will inform novel evidence-based genetic testing strategies used in clinics, and will identify gaps in our knowledge of male infertility genetics. We discuss the relevant international guidelines regarding research related to gene discovery and provide specific recommendations to the field of male infertility. Based on our findings, the IMIGC consortium recommend several updates to the genetic testing standards currently employed in the field of human male infertility, most important being the adoption of exome sequencing, or at least sequencing of the genes validated in this study, and expanding the patient groups for which genetic testing is recommended.
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Affiliation(s)
- Brendan J Houston
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Antoni Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia, Spain
| | - Margot J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Albert Salas-Huetos
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Miguel J Xavier
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
- Genetics of Male Infertility Initiative (GEMINI)
| | - Corinna Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Don F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
- Genetics of Male Infertility Initiative (GEMINI)
- International Male Infertility Genomics Consortium (IMIGC)
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
- Genetics of Male Infertility Initiative (GEMINI)
- International Male Infertility Genomics Consortium (IMIGC)
| | - Csilla Krausz
- Genetics of Male Infertility Initiative (GEMINI)
- International Male Infertility Genomics Consortium (IMIGC)
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
- International Male Infertility Genomics Consortium (IMIGC)
| | - Moira K O’Bryan
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, VIC, Australia
- Genetics of Male Infertility Initiative (GEMINI)
- International Male Infertility Genomics Consortium (IMIGC)
| | - Joris A Veltman
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- International Male Infertility Genomics Consortium (IMIGC)
| | - Manon S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
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Nagirnaja L, Mørup N, Nielsen JE, Stakaitis R, Golubickaite I, Oud MS, Winge SB, Carvalho F, Aston KI, Khani F, van der Heijden GW, Marques CJ, Skakkebaek NE, Rajpert-De Meyts E, Schlegel PN, Jørgensen N, Veltman JA, Lopes AM, Conrad DF, Almstrup K. Variant PNLDC1, Defective piRNA Processing, and Azoospermia. N Engl J Med 2021; 385:707-719. [PMID: 34347949 PMCID: PMC7615015 DOI: 10.1056/nejmoa2028973] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are short (21 to 35 nucleotides in length) and noncoding and are found almost exclusively in germ cells, where they regulate aberrant expression of transposable elements and postmeiotic gene expression. Critical to the processing of piRNAs is the protein poly(A)-specific RNase-like domain containing 1 (PNLDC1), which trims their 3' ends and, when disrupted in mice, causes azoospermia and male infertility. METHODS We performed exome sequencing on DNA samples from 924 men who had received a diagnosis of nonobstructive azoospermia. Testicular-biopsy samples were analyzed by means of histologic and immunohistochemical tests, in situ hybridization, reverse-transcriptase-quantitative-polymerase-chain-reaction assay, and small-RNA sequencing. RESULTS Four unrelated men of Middle Eastern descent who had nonobstructive azoospermia were found to carry mutations in PNLDC1: the first patient had a biallelic stop-gain mutation, p.R452Ter (rs200629089; minor allele frequency, 0.00004); the second, a novel biallelic missense variant, p.P84S; the third, two compound heterozygous mutations consisting of p.M259T (rs141903829; minor allele frequency, 0.0007) and p.L35PfsTer3 (rs754159168; minor allele frequency, 0.00004); and the fourth, a novel biallelic canonical splice acceptor site variant, c.607-2A→T. Testicular histologic findings consistently showed error-prone meiosis and spermatogenic arrest with round spermatids of type Sa as the most advanced population of germ cells. Gene and protein expression of PNLDC1, as well as the piRNA-processing proteins PIWIL1, PIWIL4, MYBL1, and TDRKH, were greatly diminished in cells of the testes. Furthermore, the length distribution of piRNAs and the number of pachytene piRNAs was significantly altered in men carrying PNLDC1 mutations. CONCLUSIONS Our results suggest a direct mechanistic effect of faulty piRNA processing on meiosis and spermatogenesis in men, ultimately leading to male infertility. (Funded by Innovation Fund Denmark and others.).
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Affiliation(s)
- Liina Nagirnaja
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Nina Mørup
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - John E Nielsen
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Rytis Stakaitis
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Ieva Golubickaite
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Manon S Oud
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Sofia B Winge
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Filipa Carvalho
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Kenneth I Aston
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Francesca Khani
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Godfried W van der Heijden
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - C Joana Marques
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Niels E Skakkebaek
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Ewa Rajpert-De Meyts
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Peter N Schlegel
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Niels Jørgensen
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Joris A Veltman
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Alexandra M Lopes
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Donald F Conrad
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
| | - Kristian Almstrup
- From the Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton (L.N., D.F.C.); the Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland (D.F.C.); the Department of Growth and Reproduction (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.) and the International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (N.M., J.E.N., R.S., I.G., S.B.W., N.E.S., E.R.-D.M., N.J., K.A.), Rigshospitalet, and the Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences (K.A.), University of Copenhagen, Copenhagen; the Laboratory of Molecular Neurooncology, Neuroscience Institute (R.S.), and the Institute of Biology Systems and Genetic Research (I.G.), Lithuanian University of Health Sciences, Kaunas, Lithuania; the Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior (M.S.O., G.W.H.), and the Department of Obstetrics and Gynecology (G.W.H.), Radboud University Medical Center, Nijmegen, the Netherlands; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto (F.C., C.J.M.), Instituto de Investigação e Inovação em Saúde, Universidade do Porto (F.C., C.J.M., A.M.L.), and the Institute of Molecular Pathology and Immunology of the University of Porto (A.M.L.) - all in Porto, Portugal; the Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City (K.I.A.); the Departments of Pathology and Laboratory Medicine (F.K.) and Urology (P.N.S.), Weill Cornell Medicine, New York; and the Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom (J.A.V.)
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Goldmann JM, Seplyarskiy VB, Wong WSW, Vilboux T, Neerincx PB, Bodian DL, Solomon BD, Veltman JA, Deeken JF, Gilissen C, Niederhuber JE. Publisher Correction: Germline de novo mutation clusters arise during oocyte aging in genomic regions with high double-strand-break incidence. Nat Genet 2021; 53:1270. [PMID: 34302146 DOI: 10.1038/s41588-021-00905-z] [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: 11/09/2022]
Affiliation(s)
- Jakob M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vladimir B Seplyarskiy
- Division of Genetics, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.,Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia
| | - Wendy S W Wong
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA
| | - Thierry Vilboux
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA
| | - Pieter B Neerincx
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dale L Bodian
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA
| | - Benjamin D Solomon
- Department of Pediatrics, Inova Children's Hospital, Inova Health System, Falls Church, VA, USA.,Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - John F Deeken
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - John E Niederhuber
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA. .,Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Goldmann JM, Hampstead JE, Wong WSW, Wilfert AB, Turner TN, Jonker MA, Bernier R, Huynen MA, Eichler EE, Veltman JA, Maxwell GL, Gilissen C. Differences in the number of de novo mutations between individuals are due to small family-specific effects and stochasticity. Genome Res 2021; 31:1513-1518. [PMID: 34301630 PMCID: PMC8415378 DOI: 10.1101/gr.271809.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 07/14/2021] [Indexed: 11/24/2022]
Abstract
The number of de novo mutations (DNMs) in the human germline is correlated with parental age at conception, but this explains only part of the observed variation. We investigated whether there is a family-specific contribution to the number of DNMs in offspring. The analysis of DNMs in 111 dizygotic twin pairs did not identify a substantial family-specific contribution. This result was corroborated by comparing DNMs of 1669 siblings to those of age-matched unrelated offspring following correction for parental age. In addition, by modeling DNM data from 1714 multi-offspring families, we estimated that the family-specific contribution explains ∼5.2% of the variation in DNM number. Furthermore, we found no substantial difference between the observed number of DNMs and those predicted by a stochastic Poisson process. We conclude that there is a small family-specific contribution to DNM number and that stochasticity explains a large proportion of variation in DNM counts.
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Affiliation(s)
- Jakob M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.,Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Juliet E Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.,Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Wendy S W Wong
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia 22042, USA
| | - Amy B Wilfert
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Tychele N Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Marianne A Jonker
- Department for Health Evidence, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen 6525 GA, The Netherlands
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - George L Maxwell
- Department of Obstetrics and Gynecology, Inova Fairfax Department and Inova Schar Cancer Institute, Falls Church, Virginia 22042, USA
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.,Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
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Oud MS, Houston BJ, Volozonoka L, Mastrorosa FK, Holt GS, Alobaidi BKS, deVries PF, Astuti G, Ramos L, Mclachlan RI, O’Bryan MK, Veltman JA, Chemes HE, Sheth H. Exome sequencing reveals variants in known and novel candidate genes for severe sperm motility disorders. Hum Reprod 2021; 36:2597-2611. [PMID: 34089056 PMCID: PMC8373475 DOI: 10.1093/humrep/deab099] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
STUDY QUESTION What are the causative genetic variants in patients with male infertility due to severe sperm motility disorders? SUMMARY ANSWER We identified high confidence disease-causing variants in multiple genes previously associated with severe sperm motility disorders in 10 out of 21 patients (48%) and variants in novel candidate genes in seven additional patients (33%). WHAT IS KNOWN ALREADY Severe sperm motility disorders are a form of male infertility characterised by immotile sperm often in combination with a spectrum of structural abnormalities of the sperm flagellum that do not affect viability. Currently, depending on the clinical sub-categorisation, up to 50% of causality in patients with severe sperm motility disorders can be explained by pathogenic variants in at least 22 genes. STUDY DESIGN, SIZE, DURATION We performed exome sequencing in 21 patients with severe sperm motility disorders from two different clinics. PARTICIPANTS/MATERIALS, SETTING, METHOD Two groups of infertile men, one from Argentina (n = 9) and one from Australia (n = 12), with clinically defined severe sperm motility disorders (motility <5%) and normal morphology values of 0–4%, were included. All patients in the Argentine cohort were diagnosed with DFS-MMAF, based on light and transmission electron microscopy. Sperm ultrastructural information was not available for the Australian cohort. Exome sequencing was performed in all 21 patients and variants with an allele frequency of <1% in the gnomAD population were prioritised and interpreted. MAIN RESULTS AND ROLE OF CHANCE In 10 of 21 patients (48%), we identified pathogenic variants in known sperm assembly genes: CFAP43 (3 patients); CFAP44 (2 patients), CFAP58 (1 patient), QRICH2 (2 patients), DNAH1 (1 patient) and DNAH6 (1 patient). The diagnostic rate did not differ markedly between the Argentinian and the Australian cohort (55% and 42%, respectively). Furthermore, we identified patients with variants in the novel human candidate sperm motility genes: DNAH12, DRC1, MDC1, PACRG, SSPL2C and TPTE2. One patient presented with variants in four candidate genes and it remains unclear which variants were responsible for the severe sperm motility defect in this patient. LARGE SCALE DATA N/A LIMITATIONS, REASONS FOR CAUTION In this study, we described patients with either a homozygous or two heterozygous candidate pathogenic variants in genes linked to sperm motility disorders. Due to unavailability of parental DNA, we have not assessed the frequency of de novo or maternally inherited dominant variants and could not determine the parental origin of the mutations to establish in all cases that the mutations are present on both alleles. WIDER IMPLICATIONS OF THE FINDINGS Our results confirm the likely causal role of variants in six known genes for sperm motility and we demonstrate that exome sequencing is an effective method to diagnose patients with severe sperm motility disorders (10/21 diagnosed; 48%). Furthermore, our analysis revealed six novel candidate genes for severe sperm motility disorders. Genome-wide sequencing of additional patient cohorts and re-analysis of exome data of currently unsolved cases may reveal additional variants in these novel candidate genes. STUDY FUNDING/COMPETING INTEREST(S) This project was supported in part by funding from the Australian National Health and Medical Research Council (APP1120356) to M.K.O.B., J.A.V. and R.I.M.L., The Netherlands Organisation for Scientific Research (918-15-667) to J.A.V., the Royal Society and Wolfson Foundation (WM160091) to J.A.V., as well as an Investigator Award in Science from the Wellcome Trust (209451) to J.A.V. and Grants from the National Research Council of Argentina (PIP 0900 and 4584) and ANPCyT (PICT 9591) to H.E.C. and a UUKi Rutherford Fund Fellowship awarded to B.J.H.
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Affiliation(s)
- M S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - B J Houston
- School of Biological Sciences, Monash University, Monash, Australia
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - L Volozonoka
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - F K Mastrorosa
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - G S Holt
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - B K S Alobaidi
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - P F deVries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G Astuti
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L Ramos
- Department of Gynaecology and Obstetrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R I Mclachlan
- Hudson Institute of Medical Research, Monash University, Clayton, Melbourne, Australia
| | - M K O’Bryan
- School of Biological Sciences, Monash University, Monash, Australia
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - J A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Correspondence address. Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 4EP, UK. E-mail:
| | - H E Chemes
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CEDIE-CONICET-FEI, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - H Sheth
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Foundation for Research in Genetics and Endocrinology, Institute of Human Genetics, Ahmedabad, India
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15
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Oud MS, Okutman Ö, Hendricks LAJ, de Vries PF, Houston BJ, Vissers LELM, O'Bryan MK, Ramos L, Chemes HE, Viville S, Veltman JA. Exome sequencing reveals novel causes as well as new candidate genes for human globozoospermia. Hum Reprod 2021; 35:240-252. [PMID: 31985809 PMCID: PMC6993856 DOI: 10.1093/humrep/dez246] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/08/2019] [Indexed: 12/11/2022] Open
Abstract
STUDY QUESTION Can exome sequencing identify new genetic causes of globozoospermia? SUMMARY ANSWER Exome sequencing in 15 cases of unexplained globozoospermia revealed deleterious mutations in seven new genes, of which two have been validated as causing globozoospermia when knocked out in mouse models. WHAT IS KNOWN ALREADY Globozoospermia is a rare form of male infertility characterised by round-headed sperm and malformation of the acrosome. Although pathogenic variants in DPY19L2 and SPATA16 are known causes of globozoospermia and explain up to 70% of all cases, genetic causality remains unexplained in the remaining patients. STUDY DESIGN, SIZE, DURATION After pre-screening 16 men for mutations in known globozoospermia genes DPY19L2 and SPATA16, exome sequencing was performed in 15 males with globozoospermia or acrosomal hypoplasia of unknown aetiology. PARTICIPANTS/MATERIALS, SETTING, METHOD Targeted next-generation sequencing and Sanger sequencing was performed for all 16 patients to screen for single-nucleotide variants and copy number variations in DPY19L2 and SPATA16. After exclusion of one patient with DPY19L2 mutations, we performed exome sequencing for the 15 remaining subjects. We prioritised recessive and X-linked protein-altering variants with an allele frequency of <0.5% in the population database GnomAD in genes with an enhanced expression in the testis. All identified candidate variants were confirmed in patients and, where possible, in family members using Sanger sequencing. Ultrastructural examination of semen from one of the patients allowed for a precise phenotypic characterisation of abnormal spermatozoa. MAIN RESULTS AND ROLE OF CHANCE After prioritisation and validation, we identified possibly causative variants in eight of 15 patients investigated by exome sequencing. The analysis revealed homozygous nonsense mutations in ZPBP and CCDC62 in two unrelated patients, as well as rare missense mutations in C2CD6 (also known as ALS2CR11), CCIN, C7orf61 and DHNA17 and a frameshift mutation in GGN in six other patients. All variants identified through exome sequencing, except for the variants in DNAH17, were located in a region of homozygosity. Familial segregation of the nonsense variant in ZPBP revealed two fertile brothers and the patient’s mother to be heterozygous carriers. Paternal DNA was unavailable. Immunohistochemistry confirmed that ZPBP localises to the acrosome in human spermatozoa. Ultrastructural analysis of spermatozoa in the patient with the C7orf61 mutation revealed a mixture of round heads with no acrosomes (globozoospermia) and ovoid or irregular heads with small acrosomes frequently detached from the sperm head (acrosomal hypoplasia). LIMITATIONS, REASONS FOR CAUTION Stringent filtering criteria were used in the exome data analysis which could result in possible pathogenic variants remaining undetected. Additionally, functional follow-up is needed for several candidate genes to confirm the impact of these mutations on normal spermatogenesis. WIDER IMPLICATIONS OF THE FINDINGS Our study revealed an important role for mutations in ZPBP and CCDC62 in human globozoospermia as well as five new candidate genes. These findings provide a more comprehensive understanding of the genetics of male infertility and bring us closer to a complete molecular diagnosis for globozoospermia patients which would help to predict the success of reproductive treatments. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by The Netherlands Organisation for Scientific Research (918–15-667); National Health and Medical Research Council of Australia (APP1120356) and the National Council for Scientific Research (CONICET), Argentina, PIP grant 11220120100279CO. The authors have nothing to disclose.
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Affiliation(s)
- M S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboudumc, Nijmegen, The Netherlands
| | - Ö Okutman
- Laboratoire de Diagnostic Génétique, UF3472-génétique de l'infertilité, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France.,Institut de Parasitologie et Pathologie Tropicale, EA 7292, Université de Strasbourg, 3 rue Koeberlé, 67000 Strasbourg, France
| | - L A J Hendricks
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboudumc, Nijmegen, The Netherlands
| | - P F de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboudumc, Nijmegen, The Netherlands
| | - B J Houston
- School of Biological Sciences, Monash University, Clayton, Australia
| | - L E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboudumc, Nijmegen, The Netherlands
| | - M K O'Bryan
- School of Biological Sciences, Monash University, Clayton, Australia
| | - L Ramos
- Department of Gynaecology and Obstetrics, Radboudumc, Nijmegen, The Netherlands
| | - H E Chemes
- Center for Research in Endocrinology (CEDIE), National Research Council, Department of Endocrinology, Buenos Aires Children's Hospital, Argentina
| | - S Viville
- Laboratoire de Diagnostic Génétique, UF3472-génétique de l'infertilité, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France.,Institut de Parasitologie et Pathologie Tropicale, EA 7292, Université de Strasbourg, 3 rue Koeberlé, 67000 Strasbourg, France
| | - J A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboudumc, Nijmegen, The Netherlands.,Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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16
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Oud MS, Volozonoka L, Friedrich C, Kliesch S, Nagirnaja L, Gilissen C, O'Bryan MK, McLachlan RI, Aston KI, Tüttelmann F, Conrad DF, Veltman JA. Lack of evidence for a role of PIWIL1 variants in human male infertility. Cell 2021; 184:1941-1942. [PMID: 33861957 PMCID: PMC7614813 DOI: 10.1016/j.cell.2021.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/09/2021] [Accepted: 03/01/2021] [Indexed: 11/18/2022]
Affiliation(s)
- M S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - L Volozonoka
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, LV-1007, Riga, Latvia
| | - C Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - S Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - L Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - C Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - M K O'Bryan
- School of Biological Sciences, Monash University, Clayton, Melbourne, Australia; School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, Melbourne, Australia
| | - R I McLachlan
- Hudson Institute of Medical Research, Clayton, Melbourne, Australia; Department of Obstetrics and Gynecology, Monash University, Clayton, Melbourne, Australia
| | - K I Aston
- Division of Urology, Department of Surgery, University of Utah, Salt Lake City, UT, USA
| | - F Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - D F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - J A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
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17
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Barratt CLR, De Jonge CJ, Anderson RA, Eisenberg ML, Garrido N, Rautakallio Hokkanen S, Krausz C, Kimmins S, O’Bryan MK, Pacey AA, Tüttelmann F, Veltman JA. A global approach to addressing the policy, research and social challenges of male reproductive health. Hum Reprod Open 2021; 2021:hoab009. [PMID: 33768166 PMCID: PMC7982782 DOI: 10.1093/hropen/hoab009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/30/2021] [Indexed: 01/19/2023] Open
Abstract
Male infertility is a global health issue; yet to a large extent, our knowledge of its causes, impact and consequence is largely unknown. Recent data indicate that infertile men have an increased risk of somatic disorders such as cancer and die younger compared to fertile men. Moreover, several studies point to a significant adverse effect on the health of the offspring. From the startling lack of progress in male contraception combined with the paucity of improvements in the diagnosis of male infertility, we conclude there is a crisis in male reproductive health. The Male Reproductive Health Initiative has been organized to directly address these issues (www.eshre.eu/Specialty-groups/Special-Interest-Groups/Andrology/MRHI). The Working Group will formulate an evidence-based strategic road map outlining the ways forward. This is an open consortium desiring to engage with all stakeholders and governments.
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Affiliation(s)
- Christopher L R Barratt
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK,Correspondence address. Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD19SY, UK; E-mail: https://orcid.org/0000-0003-0062-9979; Department of Urology, University of Minnesota Medical Center, University of Minnesota, Minneapolis, MN, 55454, USA; E-mail: https://orcid.org/0000-0002-4083-5833
| | - Christopher J De Jonge
- Department of Urology, University of Minnesota Medical Center, University of Minnesota, Minneapolis, MN, USA,Correspondence address. Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD19SY, UK; E-mail: https://orcid.org/0000-0003-0062-9979; Department of Urology, University of Minnesota Medical Center, University of Minnesota, Minneapolis, MN, 55454, USA; E-mail: https://orcid.org/0000-0002-4083-5833
| | - Richard A Anderson
- Section of Obstetrics and Gynaecology, MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - Michael L Eisenberg
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolás Garrido
- IVI Foundation, Health Research Institute La Fe, Valencia, Spain
| | | | - Csilla Krausz
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, and Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - Moira K O’Bryan
- Department of Anatomy and Developmental Biology, School of BioSciences, Faculty of Science, University of Melbourne, Parkville, Australia
| | - Allan A Pacey
- Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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18
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Liu C, Tu C, Wang L, Wu H, Houston BJ, Mastrorosa FK, Zhang W, Shen Y, Wang J, Tian S, Meng L, Cong J, Yang S, Jiang Y, Tang S, Zeng Y, Lv M, Lin G, Li J, Saiyin H, He X, Jin L, Touré A, Ray PF, Veltman JA, Shi Q, O'Bryan MK, Cao Y, Tan YQ, Zhang F. Deleterious variants in X-linked CFAP47 induce asthenoteratozoospermia and primary male infertility. Am J Hum Genet 2021; 108:309-323. [PMID: 33472045 PMCID: PMC7895902 DOI: 10.1016/j.ajhg.2021.01.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [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: 09/30/2020] [Accepted: 12/29/2020] [Indexed: 02/04/2023] Open
Abstract
Asthenoteratozoospermia characterized by multiple morphological abnormalities of the flagella (MMAF) has been identified as a sub-type of male infertility. Recent progress has identified several MMAF-associated genes with an autosomal recessive inheritance in human affected individuals, but the etiology in approximately 40% of affected individuals remains unknown. Here, we conducted whole-exome sequencing (WES) and identified hemizygous missense variants in the X-linked CFAP47 in three unrelated Chinese individuals with MMAF. These three CFAP47 variants were absent in human control population genome databases and were predicted to be deleterious by multiple bioinformatic tools. CFAP47 encodes a cilia- and flagella-associated protein that is highly expressed in testis. Immunoblotting and immunofluorescence assays revealed obviously reduced levels of CFAP47 in spermatozoa from all three men harboring deleterious missense variants of CFAP47. Furthermore, WES data from an additional cohort of severe asthenoteratozoospermic men originating from Australia permitted the identification of a hemizygous Xp21.1 deletion removing the entire CFAP47 gene. All men harboring hemizygous CFAP47 variants displayed typical MMAF phenotypes. We also generated a Cfap47-mutated mouse model, the adult males of which were sterile and presented with reduced sperm motility and abnormal flagellar morphology and movement. However, fertility could be rescued by the use of intra-cytoplasmic sperm injections (ICSIs). Altogether, our experimental observations in humans and mice demonstrate that hemizygous mutations in CFAP47 can induce X-linked MMAF and asthenoteratozoospermia, for which good ICSI prognosis is suggested. These findings will provide important guidance for genetic counseling and assisted reproduction treatments.
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Affiliation(s)
- Chunyu Liu
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Chaofeng Tu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha 410000, China; Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, China; Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, China
| | - Lingbo Wang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China; State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Huan Wu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei 230032, China
| | - Brendan J Houston
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Francesco K Mastrorosa
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Wen Zhang
- Fudan University Pudong Medical Center, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ying Shen
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Jiaxiong Wang
- State Key Laboratory of Reproductive Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China; Suzhou Municipal Hospital, Suzhou 215002, China
| | - Shixiong Tian
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Lanlan Meng
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, China
| | - Jiangshan Cong
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Shenmin Yang
- State Key Laboratory of Reproductive Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China; Suzhou Municipal Hospital, Suzhou 215002, China
| | - Yiwen Jiang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China
| | - Shuyan Tang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Yuyan Zeng
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China
| | - Mingrong Lv
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei 230032, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha 410000, China; Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, China; Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hexige Saiyin
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China
| | - Xiaojin He
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei 230032, China
| | - Li Jin
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China
| | - Aminata Touré
- Team Genetics Epigenetics and Therapies of Infertility, Institute for Advance Biosciences, Grenoble Alpes University, INSERM U1209, Centre National de la Recherche Scientifique UMR 5309, Grenoble 38000, France
| | - Pierre F Ray
- Team Genetics Epigenetics and Therapies of Infertility, Institute for Advance Biosciences, Grenoble Alpes University, INSERM U1209, Centre National de la Recherche Scientifique UMR 5309, Grenoble 38000, France; UM de genetique de l'infertilite et de diagnostic pre-implantatoire, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble 38000, France
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Qinghua Shi
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China
| | - Moira K O'Bryan
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei 230032, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha 410000, China; Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, China; Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, China.
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China.
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19
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Veltman JA. Big data and innovative bioinformatics approaches in personalized genomic medicine. BIO Web Conf 2021. [DOI: 10.1051/bioconf/20214101003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The field of human genetics has been radically changed by the introduction of massive parallel sequencing, also called next generation sequencing, approaches. Instead of studying a single gene or a few genetic variants, nowadays we can study genetic variation present in all genes and even throughout the entire human genome. For the first time in history, we can really study what makes us unique and use that to explain differences in for example disease susceptibility or response to treatment. In rare disease, genetics research is essential to identify the molecular diagnosis that provides the basis for a personalized patient management approach. It allows for more precise answers about the underlying cause and family recurrence risk, but also aids in optimizing treatment plans aimed at reducing co-morbidities and providing information about potential drugs or participation in drug trials, with an increasing number focused on gene therapy. These high-throughput sequencing technologies generate enormous amounts of data in order to assemble a genome and identify all of the variation present at different levels, from single nucleotide variations to chromosomal abnormalities. In addition, a genome sequence of a person in itself is not very useful. Value is derived from annotation of all the variation, and integration of the genome sequence with information about the patient involved (clinical information, disease-specific information, family history) as well as biological information (gene as well as variant-specific information, including population variation frequency, pathogenicity predictions, gene-expression information, etc). In this presentation, I will give an overview of the impact of genomics on the diagnosis of patients with rare developmental disorders and fertility disorders. I will highlight the importance of innovative bioinformatics approaches to detect and interpret genetic variation in a clinical context. Also, I will highlight some of the challenges that individual research and diagnostics units face in dealing with the data generated, discuss some of the ethical/privacy issues related to these approaches and discuss some of the latest genomics technologies being developed and validated.
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20
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Abstract
Identifying the genes causing male infertility is important to increase our biological understanding as well as the diagnostic yield and clinical relevance of genetic testing in this disorder. While significant progress has been made in some areas, mainly in our knowledge of the genes underlying rare qualitative sperm defects, the same cannot be said for the genetics of quantitative sperm defects. Technological advances and approaches in genomics are critical for the process of disease gene identification. In this review we highlight the impact of various technological developments on male infertility gene discovery as well as functional validation, going from the past to the present and the future. In particular, we draw attention to the use of unbiased genomics approaches, the development of increasingly relevant functional assays and the importance of large-scale international collaboration to advance disease gene identification in male infertility.
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Affiliation(s)
- M J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - A Salas-Huetos
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah, Salt Lake City, USA
| | - M S Oud
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - K I Aston
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah, Salt Lake City, USA.
| | - J A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK.
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21
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Cannata Serio M, Graham LA, Ashikov A, Larsen LE, Raymond K, Timal S, Le Meur G, Ryan M, Czarnowska E, Jansen JC, He M, Ficicioglu C, Pichurin P, Hasadsri L, Minassian B, Rugierri A, Kalimo H, Ríos‐Ocampo WA, Gilissen C, Rodenburg R, Jonker JW, Holleboom AG, Morava E, Veltman JA, Socha P, Stevens TH, Simons M, Lefeber DJ. Mutations in the V-ATPase Assembly Factor VMA21 Cause a Congenital Disorder of Glycosylation With Autophagic Liver Disease. Hepatology 2020; 72:1968-1986. [PMID: 32145091 PMCID: PMC7483274 DOI: 10.1002/hep.31218] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Vacuolar H+-ATP complex (V-ATPase) is a multisubunit protein complex required for acidification of intracellular compartments. At least five different factors are known to be essential for its assembly in the endoplasmic reticulum (ER). Genetic defects in four of these V-ATPase assembly factors show overlapping clinical features, including steatotic liver disease and mild hypercholesterolemia. An exception is the assembly factor vacuolar ATPase assembly integral membrane protein (VMA21), whose X-linked mutations lead to autophagic myopathy. APPROACH AND RESULTS Here, we report pathogenic variants in VMA21 in male patients with abnormal protein glycosylation that result in mild cholestasis, chronic elevation of aminotransferases, elevation of (low-density lipoprotein) cholesterol and steatosis in hepatocytes. We also show that the VMA21 variants lead to V-ATPase misassembly and dysfunction. As a consequence, lysosomal acidification and degradation of phagocytosed materials are impaired, causing lipid droplet (LD) accumulation in autolysosomes. Moreover, VMA21 deficiency triggers ER stress and sequestration of unesterified cholesterol in lysosomes, thereby activating the sterol response element-binding protein-mediated cholesterol synthesis pathways. CONCLUSIONS Together, our data suggest that impaired lipophagy, ER stress, and increased cholesterol synthesis lead to LD accumulation and hepatic steatosis. V-ATPase assembly defects are thus a form of hereditary liver disease with implications for the pathogenesis of nonalcoholic fatty liver disease.
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Affiliation(s)
- Magda Cannata Serio
- Laboratory of Epithelial Biology and DiseaseImagine InstituteUniversité Paris Descartes‐Sorbonne Paris CitéParisFrance,RBIV RNA Biology of Influenza Viruses UnitInstitut PasteurCNRS, UMR3569ParisFrance
| | - Laurie A. Graham
- Department of Chemistry and BiochemistryInstitute of Molecular BiologyUniversity of OregonEugeneOR
| | - Angel Ashikov
- Department of NeurologyDonders Institute for BrainCognition and BehaviourRadboud University Medical CenterNijmegenthe Netherlands,Department of Laboratory MedicineTranslational Metabolic LaboratoryRadboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenthe Netherlands
| | - Lars Elmann Larsen
- Department of Laboratory Medicine and PathologyMayo College of MedicineRochesterMN,Department of Chemistry and BiochemistryInstitute of Molecular BiologyUniversity of OregonEugeneOR
| | - Kimiyo Raymond
- Department of PathologyThe Children’s Memorial Health InstituteWarsawPoland
| | - Sharita Timal
- Department of NeurologyDonders Institute for BrainCognition and BehaviourRadboud University Medical CenterNijmegenthe Netherlands,Department of Laboratory MedicineTranslational Metabolic LaboratoryRadboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenthe Netherlands
| | - Gwenn Le Meur
- Laboratory of Epithelial Biology and DiseaseImagine InstituteUniversité Paris Descartes‐Sorbonne Paris CitéParisFrance
| | - Margret Ryan
- Department of Gastroenterology and HepatologyTranslational Metabolic LaboratoryRadboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenthe Netherlands
| | - Elzbieta Czarnowska
- Department of Pathology and Laboratory MedicineUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA
| | - Jos C. Jansen
- Division of Laboratory MedicineThe Children’s Hospital of PhiladelphiaPhiladelphiaPA
| | - Miao He
- Division of Human GeneticsDepartment of PediatricsThe Children’s Hospital of PhiladelphiaPhiladelphiaPA,Department of Clinical GenomicsCollege of MedicineMayo ClinicRochesterMN
| | - Can Ficicioglu
- Division of Laboratory GeneticsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMN
| | - Pavel Pichurin
- Department of Human GeneticsRadboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenthe Netherlands
| | - Linda Hasadsri
- Department of PediatricsRadboudumc Amalia Childrens HospitalRadboud Center for Mitochondrial MedicineNijmegenthe Netherlands
| | - Berge Minassian
- Department of PediatricsUniversity of Texas SouthwesternDallasTXUSA
| | - Alessandra Rugierri
- Department of Neuroimmunology and Neuromuscular DiseasesFondazione IRCCS Neurological Institute Carlo BestaMilanItaly,Department of Molecular and Translation MedicineUnit of Biology and Genetics, University of BresciaBresciaItaly
| | - Hannu Kalimo
- Department of Pathology, Haartman InstituteUniversity of Helsinki, FIN–00014HelsinkiFinland
| | | | | | - Richard Rodenburg
- Department of Human GeneticsDonders Centre for NeuroscienceRadboud University Medical CenterNijmegenthe Netherlands
| | - Johan W. Jonker
- Department of Laboratory Medicine and PathologyMayo College of MedicineRochesterMN
| | - Adriaan G. Holleboom
- Department of Chemistry and BiochemistryInstitute of Molecular BiologyUniversity of OregonEugeneOR
| | - Eva Morava
- Institute of Genetic MedicineInternational Centre for LifeNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Joris A. Veltman
- Department of GastroenterologyFeeding Disorders and PediatricsChildren’s Memorial Health InstituteWarsawPoland,Section of Molecular Metabolism and NutritionDepartment of PediatricsUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Piotr Socha
- Department of Experimental Vascular MedicineAmsterdam University Medical CentersLocation AMCAmsterdamthe Netherlands
| | - Tom H. Stevens
- Department of Gastroenterology and HepatologyTranslational Metabolic LaboratoryRadboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenthe Netherlands
| | - Matias Simons
- Laboratory of Epithelial Biology and DiseaseImagine InstituteUniversité Paris Descartes‐Sorbonne Paris CitéParisFrance,Institute of Human GeneticsUniversity Hospital HeidelbergHeidelbergGermany
| | - Dirk J. Lefeber
- Department of NeurologyDonders Institute for BrainCognition and BehaviourRadboud University Medical CenterNijmegenthe Netherlands,Department of Laboratory MedicineTranslational Metabolic LaboratoryRadboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenthe Netherlands
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22
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Wilkins-Haug L, Veltman JA, Hui L. Opportunities and challenges for international societies in the COVID-19 era. Prenat Diagn 2020; 40:1753-1754. [PMID: 33067852 DOI: 10.1002/pd.5843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/11/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Louise Wilkins-Haug
- Gynecology and Reproductive Biologyl, Brigham and Women's Hospita, Harvard Medical School, Boston, Massachusetts, USA
| | - Joris A Veltman
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
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23
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Wyrwoll MJ, Temel ŞG, Nagirnaja L, Oud MS, Lopes AM, van der Heijden GW, Heald JS, Rotte N, Wistuba J, Wöste M, Ledig S, Krenz H, Smits RM, Carvalho F, Gonçalves J, Fietz D, Türkgenç B, Ergören MC, Çetinkaya M, Başar M, Kahraman S, McEleny K, Xavier MJ, Turner H, Pilatz A, Röpke A, Dugas M, Kliesch S, Neuhaus N, Aston KI, Conrad DF, Veltman JA, Friedrich C, Tüttelmann F. Bi-allelic Mutations in M1AP Are a Frequent Cause of Meiotic Arrest and Severely Impaired Spermatogenesis Leading to Male Infertility. Am J Hum Genet 2020; 107:342-351. [PMID: 32673564 PMCID: PMC7413853 DOI: 10.1016/j.ajhg.2020.06.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 10/12/2019] [Accepted: 06/12/2020] [Indexed: 01/08/2023] Open
Abstract
Male infertility affects ∼7% of men, but its causes remain poorly understood. The most severe form is non-obstructive azoospermia (NOA), which is, in part, caused by an arrest at meiosis. So far, only a few validated disease-associated genes have been reported. To address this gap, we performed whole-exome sequencing in 58 men with unexplained meiotic arrest and identified the same homozygous frameshift variant c.676dup (p.Trp226LeufsTer4) in M1AP, encoding meiosis 1 associated protein, in three unrelated men. This variant most likely results in a truncated protein as shown in vitro by heterologous expression of mutant M1AP. Next, we screened four large cohorts of infertile men and identified three additional individuals carrying homozygous c.676dup and three carrying combinations of this and other likely causal variants in M1AP. Moreover, a homozygous missense variant, c.1166C>T (p.Pro389Leu), segregated with infertility in five men from a consanguineous Turkish family. The common phenotype between all affected men was NOA, but occasionally spermatids and rarely a few spermatozoa in the semen were observed. A similar phenotype has been described for mice with disruption of M1ap. Collectively, these findings demonstrate that mutations in M1AP are a relatively frequent cause of autosomal recessive severe spermatogenic failure and male infertility with strong clinical validity.
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Affiliation(s)
- Margot J Wyrwoll
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - Şehime G Temel
- Bursa Uludag University, Faculty of Medicine, Department of Medical Genetics & Department of Histology & Embryology & Health Sciences Institute, Department of Translational Medicine, 16059 Bursa, Turkey
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Manon S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Alexandra M Lopes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), 4200-804 Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, 4099-002 Porto, Portugal
| | - Godfried W van der Heijden
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 Nijmegen, the Netherlands; Department of Obstetrics and Gynecology, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - James S Heald
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Nadja Rotte
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany; Centre of Reproductive Medicine and Andrology, Institute of Reproductive Medicine, University of Münster, 48149 Münster, Germany
| | - Joachim Wistuba
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive Medicine, University of Münster, 48149 Münster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - Susanne Ledig
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - Henrike Krenz
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - Roos M Smits
- Department of Obstetrics and Gynecology, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Filipa Carvalho
- Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, 4099-002 Porto, Portugal; Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, 4099-002 Porto, Portugal
| | - João Gonçalves
- Departmento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal; ToxOmics - Centro de Toxicogenómica e Saúde Humana, Nova Medical School, 1169-056 Lisboa, Portugal
| | - Daniela Fietz
- Institute of Veterinary Anatomy, Histology and Embryology, Justus Liebig University, 35392 Gießen, Germany
| | - Burcu Türkgenç
- University of Acibadem, Acibadem Genetic Diagnostic Centre, 34662 Istanbul, Turkey
| | - Mahmut C Ergören
- Near East University, Faculty of Medicine, Department of Medical Biology, 99138 Nicosia, Cyprus
| | - Murat Çetinkaya
- Istanbul Memorial Hospital, Assisted Reproductive Technologies and Reproductive Genetics Centre, 34385 Istanbul, Turkey
| | - Murad Başar
- Istanbul Memorial Hospital, Department of Urology & Andrology, 34385 Istanbul, Turkey
| | - Semra Kahraman
- Istanbul Memorial Hospital, Assisted Reproductive Technologies and Reproductive Genetics, 34385 Istanbul, Turkey
| | - Kevin McEleny
- Newcastle Fertility Centre, The Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4EP Newcastle upon Tyne, UK
| | - Miguel J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Helen Turner
- Department of Cellular Pathology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | - Adrian Pilatz
- Clinic for Urology, Pediatric Urology and Andrology, Justus Liebig University, 35392 Gießen, Germany
| | - Albrecht Röpke
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, 48149 Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive Medicine, University of Münster, 48149 Münster, Germany
| | - Kenneth I Aston
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 Nijmegen, the Netherlands; Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Corinna Friedrich
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - Frank Tüttelmann
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany.
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24
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Jaeger M, Pinelli M, Borghi M, Constantini C, Dindo M, van Emst L, Puccetti M, Pariano M, Ricaño-Ponce I, Büll C, Gresnigt MS, Wang X, Gutierrez Achury J, Jacobs CWM, Xu N, Oosting M, Arts P, Joosten LAB, van de Veerdonk FL, Veltman JA, Ten Oever J, Kullberg BJ, Feng M, Adema GJ, Wijmenga C, Kumar V, Sobel J, Gilissen C, Romani L, Netea MG. A systems genomics approach identifies SIGLEC15 as a susceptibility factor in recurrent vulvovaginal candidiasis. Sci Transl Med 2020; 11:11/496/eaar3558. [PMID: 31189718 DOI: 10.1126/scitranslmed.aar3558] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 08/13/2018] [Accepted: 05/14/2019] [Indexed: 12/30/2022]
Abstract
Candida vaginitis is a frequent clinical diagnosis with up to 8% of women experiencing recurrent vulvovaginal candidiasis (RVVC) globally. RVVC is characterized by at least three episodes per year. Most patients with RVVC lack known risk factors, suggesting a role for genetic risk factors in this condition. Through integration of genomic approaches and immunological studies in two independent cohorts of patients with RVVC and healthy individuals, we identified genes and cellular processes that contribute to the pathogenesis of RVVC, including cellular morphogenesis and metabolism, and cellular adhesion. We further identified SIGLEC15, a lectin expressed by various immune cells that binds sialic acid-containing structures, as a candidate gene involved in RVVC susceptibility. Candida stimulation induced SIGLEC15 expression in human peripheral blood mononuclear cells (PBMCs) and a polymorphism in the SIGLEC15 gene that was associated with RVVC in the patient cohorts led to an altered cytokine profile after PBMC stimulation. The same polymorphism led to an increase in IL1B and NLRP3 expression after Candida stimulation in HeLa cells in vitro. Last, Siglec15 expression was induced by Candida at the vaginal surface of mice, where in vivo silencing of Siglec15 led to an increase in the fungal burden. Siglec15 silencing was additionally accompanied by an increase in polymorphonuclear leukocytes during the course of infection. Identification of these pathways and cellular processes contributes to a better understanding of RVVC and may open new therapeutic avenues.
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Affiliation(s)
- M Jaeger
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands.,Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, 6525GA, Netherlands
| | - M Pinelli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, 80078, Italy.,Department of Human Genetics, Donders Center for Neuroscience, Radboud University Medical Center, Nijmegen, 6525HR, Netherlands
| | - M Borghi
- Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, Perugia, 06123, Italy
| | - C Constantini
- Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, Perugia, 06123, Italy
| | - M Dindo
- Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, Perugia, 06123, Italy
| | - L van Emst
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands
| | - M Puccetti
- Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, Perugia, 06123, Italy
| | - M Pariano
- Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, Perugia, 06123, Italy
| | - I Ricaño-Ponce
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, 9713GZ, Netherlands
| | - C Büll
- Department of Radiation Oncology, Radiotherapy & OncoImmunology Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, Nijmegen, 6525GA, Netherlands
| | - M S Gresnigt
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands.,Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, 6525GA, Netherlands.,Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, Jena, 07745, Germany
| | - X Wang
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands.,College of Computer, Qinghai Normal University, 810008 Xining, China
| | - J Gutierrez Achury
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, 9713GZ, Netherlands
| | - C W M Jacobs
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands
| | - N Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - M Oosting
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands
| | - P Arts
- Department of Human Genetics, Donders Center for Neuroscience, Radboud University Medical Center, Nijmegen, 6525HR, Netherlands
| | - L A B Joosten
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands
| | - F L van de Veerdonk
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands
| | - J A Veltman
- Department of Human Genetics, Donders Center for Neuroscience, Radboud University Medical Center, Nijmegen, 6525HR, Netherlands.,Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, 6229HX, Netherlands
| | - J Ten Oever
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands
| | - B J Kullberg
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands
| | - M Feng
- BGI-Shenzhen, Shenzhen 518083, China
| | - G J Adema
- Department of Radiation Oncology, Radiotherapy & OncoImmunology Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, Nijmegen, 6525GA, Netherlands
| | - C Wijmenga
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, 9713GZ, Netherlands
| | - V Kumar
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, 9713GZ, Netherlands
| | - J Sobel
- Infectious Diseases, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - C Gilissen
- Department of Human Genetics, Donders Center for Neuroscience, Radboud University Medical Center, Nijmegen, 6525HR, Netherlands
| | - L Romani
- Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, Perugia, 06123, Italy
| | - M G Netea
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525GA, Netherlands. .,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, 200349
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25
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Gunadi, Kalim AS, Budi NYP, Hafiq HM, Maharani A, Febrianti M, Ryantono F, Yulianda D, Iskandar K, Veltman JA. Aberrant Expressions and Variant Screening of SEMA3D in Indonesian Hirschsprung Patients. Front Pediatr 2020; 8:60. [PMID: 32219083 PMCID: PMC7078240 DOI: 10.3389/fped.2020.00060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 11/28/2019] [Accepted: 02/07/2020] [Indexed: 12/28/2022] Open
Abstract
Background: The semaphorin 3D (SEMA3D) gene has been implicated in the pathogenesis of Hirschsprung disease (HSCR), a complex genetic disorder characterized by the loss of ganglion cells in varying lengths of gastrointestinal tract. We wished to investigate the role of SEMA3D variants, both rare and common variants, as well as its mRNA expression in Indonesian HSCR patients. Methods: Sanger sequencing was performed in 54 HSCR patients to find a pathogenic variant in SEMA3D. Next, we determined SEMA3D expression in 18 HSCR patients and 13 anorectal malformation colons as controls by quantitative real-time polymerase chain reaction (qPCR). Results: No rare variant was found in the SEMA3D gene, except one common variant in exon 17, p.Lys701Gln (rs7800072). The risk allele (C) frequency at rs7800072 among HSCR patients (23%) was similar to those reported for the 1,000 Genomes (27%) and ExAC (28%) East Asian ancestry controls (p = 0.49 and 0.41, respectively). A significant difference in SEMA3D expression was observed between groups (p = 0.04). Furthermore, qPCR revealed that SEMA3D expression was strongly up-regulated (5.5-fold) in the ganglionic colon of HSCR patients compared to control colon (ΔCT 10.8 ± 2.1 vs. 13.3 ± 3.9; p = 0.025). Conclusions: We report the first study of aberrant SEMA3D expressions in HSCR patients and suggest further understanding into the contribution of aberrant SEMA3D expression in the development of HSCR. In addition, this study is the first comprehensive analysis of SEMA3D variants in the Asian ancestry.
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Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Alvin Santoso Kalim
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Nova Yuli Prasetyo Budi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Hamzah Muhammad Hafiq
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Annisa Maharani
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Maharani Febrianti
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Fiko Ryantono
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Dicky Yulianda
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Joris A Veltman
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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26
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Goldmann JM, Veltman JA, Gilissen C. De Novo Mutations Reflect Development and Aging of the Human Germline. Trends Genet 2019; 35:828-839. [PMID: 31610893 DOI: 10.1016/j.tig.2019.08.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/15/2019] [Accepted: 08/28/2019] [Indexed: 01/19/2023]
Abstract
Human germline de novo mutations (DNMs) are both a driver of evolution and an important cause of genetic diseases. In the past few years, whole-genome sequencing (WGS) of parent-offspring trios has facilitated the large-scale detection and study of human DNMs, which has led to exciting discoveries. The overarching theme of all of these studies is that the DNMs of an individual are a complex mixture of mutations that arise through different biological processes acting at different times during human development and life.
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Affiliation(s)
- J M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - J A Veltman
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK; Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands.
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27
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
| | - Coos Baakman
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
| | - Daan Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
- Bio-informatica; HAN University of Applied Sciences; Nijmegen The Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour; Radboud University Medical Center; Nijmegen The Netherlands
- Institute of Genetic Medicine, International Centre for Life; Newcastle University; Newcastle upon Tyne United Kingdom
| | - Gerrit Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
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28
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Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat 2019; 40:1030-1038. [PMID: 31116477 PMCID: PMC6772141 DOI: 10.1002/humu.23798] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/21/2019] [Accepted: 05/15/2019] [Indexed: 01/19/2023]
Abstract
The growing availability of human genetic variation has given rise to novel methods of measuring genetic tolerance that better interpret variants of unknown significance. We recently developed a concept based on protein domain homology in the human genome to improve variant interpretation. For this purpose, we mapped population variation from the Exome Aggregation Consortium (ExAC) and pathogenic mutations from the Human Gene Mutation Database (HGMD) onto Pfam protein domains. The aggregation of these variation data across homologous domains into meta-domains allowed us to generate amino acid resolution of genetic intolerance profiles for human protein domains. Here, we developed MetaDome, a fast and easy-to-use web server that visualizes meta-domain information and gene-wide profiles of genetic tolerance. We updated the underlying data of MetaDome to contain information from 56,319 human transcripts, 71,419 protein domains, 12,164,292 genetic variants from gnomAD, and 34,076 pathogenic mutations from ClinVar. MetaDome allows researchers to easily investigate their variants of interest for the presence or absence of variation at corresponding positions within homologous domains. We illustrate the added value of MetaDome by an example that highlights how it may help in the interpretation of variants of unknown significance. The MetaDome web server is freely accessible at https://stuart.radboudumc.nl/metadome.
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Coos Baakman
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Daan Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Bio‐informaticaHAN University of Applied SciencesNijmegenThe Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
- Institute of Genetic Medicine, International Centre for LifeNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Gerrit Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
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29
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Oud MS, Volozonoka L, Smits RM, Vissers LELM, Ramos L, Veltman JA. A systematic review and standardized clinical validity assessment of male infertility genes. Hum Reprod 2019; 34:932-941. [PMID: 30865283 PMCID: PMC6505449 DOI: 10.1093/humrep/dez022] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/14/2018] [Accepted: 02/11/2019] [Indexed: 02/06/2023] Open
Abstract
STUDY QUESTION Which genes are confidently linked to human monogenic male infertility? SUMMARY ANSWER Our systematic literature search and clinical validity assessment reveals that a total of 78 genes are currently confidently linked to 92 human male infertility phenotypes. WHAT IS KNOWN ALREADY The discovery of novel male infertility genes is rapidly accelerating with the availability of next-generating sequencing methods, but the quality of evidence for gene-disease relationships varies greatly. In order to improve genetic research, diagnostics and counseling, there is a need for an evidence-based overview of the currently known genes. STUDY DESIGN, SIZE, DURATION We performed a systematic literature search and evidence assessment for all publications in Pubmed until December 2018 covering genetic causes of male infertility and/or defective male genitourinary development. PARTICIPANTS/MATERIALS, SETTING, METHODS Two independent reviewers conducted the literature search and included papers on the monogenic causes of human male infertility and excluded papers on genetic association or risk factors, karyotype anomalies and/or copy number variations affecting multiple genes. Next, the quality and the extent of all evidence supporting selected genes was weighed by a standardized scoring method and used to determine the clinical validity of each gene-disease relationship as expressed by the following six categories: no evidence, limited, moderate, strong, definitive or unable to classify. MAIN RESULTS AND THE ROLE OF CHANCE From a total of 23 526 records, we included 1337 publications about monogenic causes of male infertility leading to a list of 521 gene-disease relationships. The clinical validity of these gene-disease relationships varied widely and ranged from definitive (n = 38) to strong (n = 22), moderate (n = 32), limited (n = 93) or no evidence (n = 160). A total of 176 gene-disease relationships could not be classified because our scoring method was not suitable. LARGE SCALE DATA Not applicable. LIMITATIONS, REASONS FOR CAUTION Our literature search was limited to Pubmed. WIDER IMPLICATIONS OF THE FINDINGS The comprehensive overview will aid researchers and clinicians in the field to establish gene lists for diagnostic screening using validated gene-disease criteria and help to identify gaps in our knowledge of male infertility. For future studies, the authors discuss the relevant and important international guidelines regarding research related to gene discovery and provide specific recommendations for the field of male infertility. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by a VICI grant from The Netherlands Organization for Scientific Research (918-15-667 to J.A.V.), the Royal Society, and Wolfson Foundation (WM160091 to J.A.V.) as well as an investigator award in science from the Wellcome Trust (209451 to J.A.V.). PROSPERO REGISTRATION NUMBER None.
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Affiliation(s)
- Manon S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Ludmila Volozonoka
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Roos M Smits
- Department of Obstetrics and Gynecology, Division of Reproductive Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Liliana Ramos
- Department of Obstetrics and Gynecology, Division of Reproductive Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Nijmegen, The Netherlands
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
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30
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Lipinski S, Petersen BS, Barann M, Piecyk A, Tran F, Mayr G, Jentzsch M, Aden K, Stengel ST, Klostermeier UC, Sheth V, Ellinghaus D, Rausch T, Korbel JO, Nothnagel M, Krawczak M, Gilissen C, Veltman JA, Forster M, Forster P, Lee CC, Fritscher-Ravens A, Schreiber S, Franke A, Rosenstiel P. Missense variants in NOX1 and p22phox in a case of very-early-onset inflammatory bowel disease are functionally linked to NOD2. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a002428. [PMID: 30709874 PMCID: PMC6371741 DOI: 10.1101/mcs.a002428] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 10/29/2018] [Indexed: 02/07/2023] Open
Abstract
Whole-genome and whole-exome sequencing of individual patients allow the study of rare and potentially causative genetic variation. In this study, we sequenced DNA of a trio comprising a boy with very-early-onset inflammatory bowel disease (veoIBD) and his unaffected parents. We identified a rare, X-linked missense variant in the NAPDH oxidase NOX1 gene (c.C721T, p.R241C) in heterozygous state in the mother and in hemizygous state in the patient. We discovered that, in addition, the patient was homozygous for a common missense variant in the CYBA gene (c.T214C, p.Y72H). CYBA encodes the p22phox protein, a cofactor for NOX1. Functional assays revealed reduced cellular ROS generation and antibacterial capacity of NOX1 and p22phox variants in intestinal epithelial cells. Moreover, the identified NADPH oxidase complex variants affected NOD2-mediated immune responses, and p22phox was identified as a novel NOD2 interactor. In conclusion, we detected missense variants in a veoIBD patient that disrupt the host response to bacterial challenges and reduce protective innate immune signaling via NOD2. We assume that the patient's individual genetic makeup favored disturbed intestinal mucosal barrier function.
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Affiliation(s)
- Simone Lipinski
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Matthias Barann
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Agnes Piecyk
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany.,Department of General Internal Medicine, Christian-Albrechts-University, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Marlene Jentzsch
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany.,Department of General Internal Medicine, Christian-Albrechts-University, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Stephanie T Stengel
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Ulrich C Klostermeier
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Vrunda Sheth
- Life Technologies, Beverly, Massachusetts 01915, USA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Michael Nothnagel
- Institute of Medical Informatics and Statistics (IMIS), Christian-Albrechts University, 24105 Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics (IMIS), Christian-Albrechts University, 24105 Kiel, Germany
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen 6525, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen 6525, The Netherlands.,Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Michael Forster
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Peter Forster
- Murray Edwards College, University of Cambridge, Cambridge CB3 0DF, United Kingdom
| | - Clarence C Lee
- Department of General Internal Medicine, Christian-Albrechts-University, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Annette Fritscher-Ravens
- Department of General Internal Medicine, Christian-Albrechts-University, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany.,Department of General Internal Medicine, Christian-Albrechts-University, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University, 24105 Kiel, Germany
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31
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Nicolas G, Veltman JA. The role of de novo mutations in adult-onset neurodegenerative disorders. Acta Neuropathol 2019; 137:183-207. [PMID: 30478624 PMCID: PMC6513904 DOI: 10.1007/s00401-018-1939-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022]
Abstract
The genetic underpinnings of the most common adult-onset neurodegenerative disorders (AOND) are complex in majority of the cases. In some families, however, the disease can be inherited in a Mendelian fashion as an autosomal-dominant trait. Next to that, patients carrying mutations in the same disease genes have been reported despite a negative family history. Although challenging to demonstrate due to the late onset of the disease in most cases, the occurrence of de novo mutations can explain this sporadic presentation, as demonstrated for severe neurodevelopmental disorders. Exome or genome sequencing of patient-parent trios allows a hypothesis-free study of the role of de novo mutations in AOND and the discovery of novel disease genes. Another hypothesis that may explain a proportion of sporadic AOND cases is the occurrence of a de novo mutation after the fertilization of the oocyte (post-zygotic mutation) or even as a late-somatic mutation, restricted to the brain. Such somatic mutation hypothesis, that can be tested with the use of novel sequencing technologies, is fully compatible with the seeding and spreading mechanisms of the pathological proteins identified in most of these disorders. We review here the current knowledge and future perspectives on de novo mutations in known and novel candidate genes identified in the most common AONDs such as Alzheimer's disease, Parkinson's disease, the frontotemporal lobar degeneration spectrum and Prion disorders. Also, we review the first lessons learned from recent genomic studies of control and diseased brains and the challenges which remain to be addressed.
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Affiliation(s)
- Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, 22, Boulevard Gambetta, 76000, 76031, Rouen Cedex, France.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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32
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Jansen S, van der Werf IM, Innes AM, Afenjar A, Agrawal PB, Anderson IJ, Atwal PS, van Binsbergen E, van den Boogaard MJ, Castiglia L, Coban-Akdemir ZH, van Dijck A, Doummar D, van Eerde AM, van Essen AJ, van Gassen KL, Guillen Sacoto MJ, van Haelst MM, Iossifov I, Jackson JL, Judd E, Kaiwar C, Keren B, Klee EW, Klein Wassink-Ruiter JS, Meuwissen ME, Monaghan KG, de Munnik SA, Nava C, Ockeloen CW, Pettinato R, Racher H, Rinne T, Romano C, Sanders VR, Schnur RE, Smeets EJ, Stegmann APA, Stray-Pedersen A, Sweetser DA, Terhal PA, Tveten K, VanNoy GE, de Vries PF, Waxler JL, Willing M, Pfundt R, Veltman JA, Kooy RF, Vissers LELM, de Vries BBA. De novo variants in FBXO11 cause a syndromic form of intellectual disability with behavioral problems and dysmorphisms. Eur J Hum Genet 2019; 27:738-746. [PMID: 30679813 DOI: 10.1038/s41431-018-0292-2] [Citation(s) in RCA: 22] [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] [Received: 02/20/2018] [Revised: 09/07/2018] [Accepted: 09/25/2018] [Indexed: 01/15/2023] Open
Abstract
Determining pathogenicity of genomic variation identified by next-generation sequencing techniques can be supported by recurrent disruptive variants in the same gene in phenotypically similar individuals. However, interpretation of novel variants in a specific gene in individuals with mild-moderate intellectual disability (ID) without recognizable syndromic features can be challenging and reverse phenotyping is often required. We describe 24 individuals with a de novo disease-causing variant in, or partial deletion of, the F-box only protein 11 gene (FBXO11, also known as VIT1 and PRMT9). FBXO11 is part of the SCF (SKP1-cullin-F-box) complex, a multi-protein E3 ubiquitin-ligase complex catalyzing the ubiquitination of proteins destined for proteasomal degradation. Twenty-two variants were identified by next-generation sequencing, comprising 2 in-frame deletions, 11 missense variants, 1 canonical splice site variant, and 8 nonsense or frameshift variants leading to a truncated protein or degraded transcript. The remaining two variants were identified by array-comparative genomic hybridization and consisted of a partial deletion of FBXO11. All individuals had borderline to severe ID and behavioral problems (autism spectrum disorder, attention-deficit/hyperactivity disorder, anxiety, aggression) were observed in most of them. The most relevant common facial features included a thin upper lip and a broad prominent space between the paramedian peaks of the upper lip. Other features were hypotonia and hyperlaxity of the joints. We show that de novo variants in FBXO11 cause a syndromic form of ID. The current series show the power of reverse phenotyping in the interpretation of novel genetic variances in individuals who initially did not appear to have a clear recognizable phenotype.
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Affiliation(s)
- Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ilse M van der Werf
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, 2888 Shaganappi Trail NW, Calgary, AB, T3B 6A8, Canada
| | - Alexandra Afenjar
- Centre de Référence Déficiences Intellectuelles de Causes Rares, 75013, Paris, France.,APHP, GHUEP, Hôpital Armand Trousseau, Centre de Référence 'Malformations et maladies congénitales du cervelet', 75012, Paris, France
| | - Pankaj B Agrawal
- Divisions of Genetics and Genomics and Newborn Medicine, Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Ilse J Anderson
- The University of Tennessee Genetics Center, Knoxville, TN, 37920, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Marie-José van den Boogaard
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Lucia Castiglia
- Laboratory of Medical Genetics, Oasi Research Institute, 94018, Troina, Italy
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anke van Dijck
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Diane Doummar
- APHP, Service de Neurologie pédiatrique, Hôpital Armand Trousseau, Paris, France.,Sorbonne Université,GRC ConCer-LD, AP-HP, Hôpital Trousseau, Paris, France.,Service de neuropediatrie, Hôpital Trousseau, 26 avenue du dr Arnold Netter, 75012, Paris, France
| | - Albertien M van Eerde
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Anthonie J van Essen
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), 9700 RB, Groningen, The Netherlands
| | - Koen L van Gassen
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | | | - Mieke M van Haelst
- Department of Clinical Genetics, VU University Medical Center, 1081 HV, Amsterdam, The Netherlands
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.,New York Genome Center, New York, NY, 10013, USA
| | - Jessica L Jackson
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Elizabeth Judd
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA.,Invitae, 1400 16th Street, San Francisco, CA, 94103, USA
| | - Boris Keren
- Département de Génétique, APHP, GH Pitié-Salpêtrière, Paris, 75013, France
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jolien S Klein Wassink-Ruiter
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), 9700 RB, Groningen, The Netherlands
| | - Marije E Meuwissen
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | | | - Sonja A de Munnik
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Caroline Nava
- Département de Génétique, APHP, GH Pitié-Salpêtrière, Paris, 75013, France.,INSERM, U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Sorbonne Universités, UPMC Université de Paris 06, 75013, Paris, France
| | - Charlotte W Ockeloen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Rosa Pettinato
- Pediatrics and Medical Genetics, Oasi Research Institute - IRCCS, 94018, Troina, Italy
| | - Hilary Racher
- Alberta Children's Hospital Research Institute and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, 2888 Shaganappi Trail NW, Calgary, AB, T3B 6A8, Canada.,Impact Genetics, 1100 Bennett Road, Bowmanville, ON, L1C 3K5, Canada
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Corrado Romano
- Pediatrics and Medical Genetics, Oasi Research Institute - IRCCS, 94018, Troina, Italy
| | - Victoria R Sanders
- Department of Pediatrics, Division of Genetics, Birth Defects and Metabolism, Ann and Robert H Lurie Children's Hospital of Chicago, 225 East Chicago Avenue, Chicago, IL, 60611, USA
| | | | - Eric J Smeets
- Department of Clinical Genetics, Maastricht University Medical Centre, Universiteitssingel 50, 9229 ER, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Centre, Universiteitssingel 50, 9229 ER, Maastricht, The Netherlands
| | - Asbjørg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, 77030, USA.,Norwegian National Unit for Newborn Screening, Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Pb 4950 Nydalen, 0424, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway
| | - David A Sweetser
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, MA, 02114, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710, Skien, Norway
| | - Grace E VanNoy
- Divisions of Genetics and Genomics and Newborn Medicine, Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Petra F de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Jessica L Waxler
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, MA, 02114, USA
| | - Marcia Willing
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, UK
| | - R Frank Kooy
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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33
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Goldmann JM, Wong WSW, Pinelli M, Farrah T, Bodian D, Stittrich AB, Glusman G, Vissers LELM, Hoischen A, Roach JC, Vockley JG, Veltman JA, Solomon BD, Gilissen C, Niederhuber JE. Author Correction: Parent-of-origin-specific signatures of de novo mutations. Nat Genet 2018; 50:1615. [PMID: 30291356 DOI: 10.1038/s41588-018-0226-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article published, the P values for the enrichment of single mutation categories were inadvertently not corrected for multiple testing. After multiple-testing correction, only two of the six mutation categories mentioned are still statistically significant. To reflect this, the text "More specifically, paternally derived DNMs are enriched in transitions in A[.]G contexts, especially ACG>ATG and ATG>ACG (Bonferroni-corrected P = 1.3 × 10-2 and P = 1 × 10-3, respectively). Additionally, we observed overrepresentation of ATA>ACA mutations (Bonferroni-corrected P = 4.28 × 10-2) for DNMs of paternal origin. Among maternally derived DNMs, CCA>CTA, GCA>GTA and TCT>TGT mutations were significantly overrepresented (Bonferroni-corrected P = 4 × 10-4, P = 5 × 10-4, P = 1 × 10-3, respectively)" should read "More specifically, CCA>CTA and GCA>GTA mutations were significantly overenriched on the maternal allele (Bonferroni-corrected P = 0.0192 and P = 0.048, respectively)." Additionally, the last sentence to the legend for Fig. 3b should read "Green boxes highlight the mutation categories that differ significantly" instead of "Green boxes highlight the mutation categories that differ more than 1% of mutation load with a bootstrapping P value <0.05." Corrected versions of Fig. 3b and Supplementary Table 25 appear with the Author Correction.
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Affiliation(s)
- Jakob M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wendy S W Wong
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Terry Farrah
- Institute for Systems Biology, Seattle, Washington, USA
| | - Dale Bodian
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA
| | | | | | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jared C Roach
- Institute for Systems Biology, Seattle, Washington, USA
| | - Joseph G Vockley
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA.,Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Benjamin D Solomon
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA.,Department of Pediatrics, Inova Children's Hospital, Inova Health System, Falls Church, Virginia, USA.,Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - John E Niederhuber
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA. .,Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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34
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Friederich MW, Timal S, Powell CA, Dallabona C, Kurolap A, Palacios-Zambrano S, Bratkovic D, Derks TGJ, Bick D, Bouman K, Chatfield KC, Damouny-Naoum N, Dishop MK, Falik-Zaccai TC, Fares F, Fedida A, Ferrero I, Gallagher RC, Garesse R, Gilberti M, González C, Gowan K, Habib C, Halligan RK, Kalfon L, Knight K, Lefeber D, Mamblona L, Mandel H, Mory A, Ottoson J, Paperna T, Pruijn GJM, Rebelo-Guiomar PF, Saada A, Sainz B, Salvemini H, Schoots MH, Smeitink JA, Szukszto MJ, Ter Horst HJ, van den Brandt F, van Spronsen FJ, Veltman JA, Wartchow E, Wintjes LT, Zohar Y, Fernández-Moreno MA, Baris HN, Donnini C, Minczuk M, Rodenburg RJ, Van Hove JLK. Pathogenic variants in glutamyl-tRNA Gln amidotransferase subunits cause a lethal mitochondrial cardiomyopathy disorder. Nat Commun 2018; 9:4065. [PMID: 30283131 PMCID: PMC6170436 DOI: 10.1038/s41467-018-06250-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 02/09/2018] [Accepted: 08/23/2018] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial protein synthesis requires charging a mitochondrial tRNA with its amino acid. Here, the authors describe pathogenic variants in the GatCAB protein complex genes required for the generation of glutaminyl-mt-tRNAGln, that impairs mitochondrial translation and presents with cardiomyopathy. Mitochondrial protein synthesis requires charging mt-tRNAs with their cognate amino acids by mitochondrial aminoacyl-tRNA synthetases, with the exception of glutaminyl mt-tRNA (mt-tRNAGln). mt-tRNAGln is indirectly charged by a transamidation reaction involving the GatCAB aminoacyl-tRNA amidotransferase complex. Defects involving the mitochondrial protein synthesis machinery cause a broad spectrum of disorders, with often fatal outcome. Here, we describe nine patients from five families with genetic defects in a GatCAB complex subunit, including QRSL1, GATB, and GATC, each showing a lethal metabolic cardiomyopathy syndrome. Functional studies reveal combined respiratory chain enzyme deficiencies and mitochondrial dysfunction. Aminoacylation of mt-tRNAGln and mitochondrial protein translation are deficient in patients’ fibroblasts cultured in the absence of glutamine but restore in high glutamine. Lentiviral rescue experiments and modeling in S. cerevisiae homologs confirm pathogenicity. Our study completes a decade of investigations on mitochondrial aminoacylation disorders, starting with DARS2 and ending with the GatCAB complex.
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Affiliation(s)
- Marisa W Friederich
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, 80045, CO, USA
| | - Sharita Timal
- Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Christopher A Powell
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 OXY, United Kingdom
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Alina Kurolap
- The Genetics Institute, Rambam Health Care Campus, Haifa, 3109601, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3109601, Israel
| | - Sara Palacios-Zambrano
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER). Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, 28029, Spain.,Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, 28041, Spain
| | - Drago Bratkovic
- SA Pathology, Women and Children's Hospital Adelaide, Adelaide, 5006, Australia
| | - Terry G J Derks
- Division of Metabolic Diseases, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, 9700 RB, The Netherlands
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Katelijne Bouman
- Department of Genetics, University Medical Center of Groningen, University of Groningen, Groningen, 9700 RB, The Netherlands
| | - Kathryn C Chatfield
- Department of Pediatrics, Section of Pediatric Cardiology, Children's Hospital Colorado, University of Colorado, Aurora, CO, 80045, USA
| | - Nadine Damouny-Naoum
- The Genetics Institute, Rambam Health Care Campus, Haifa, 3109601, Israel.,Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Megan K Dishop
- Department of Pathology, Children's Hospital Colorado, University of Colorado, Aurora, 80045, CO, USA
| | - Tzipora C Falik-Zaccai
- Institute of Human Genetics, Galilee Medical Center, Nahariya, 22100, Israel.,The Azrieli Faculty of Medicine in the Galilee, Bar Ilan University, Safed, 1311502, Israel
| | - Fuad Fares
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Ayalla Fedida
- Institute of Human Genetics, Galilee Medical Center, Nahariya, 22100, Israel.,The Azrieli Faculty of Medicine in the Galilee, Bar Ilan University, Safed, 1311502, Israel
| | - Ileana Ferrero
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Renata C Gallagher
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, 80045, CO, USA
| | - Rafael Garesse
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER). Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, 28029, Spain.,Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, 28041, Spain
| | - Micol Gilberti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Cristina González
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER). Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, 28029, Spain.,Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, 28041, Spain
| | - Katherine Gowan
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, 80045, USA
| | - Clair Habib
- Department of Pediatrics, Bnai Zion Medical Center, Haifa, 3339419, Israel
| | - Rebecca K Halligan
- SA Pathology, Women and Children's Hospital Adelaide, Adelaide, 5006, Australia
| | - Limor Kalfon
- Institute of Human Genetics, Galilee Medical Center, Nahariya, 22100, Israel
| | - Kaz Knight
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, 80045, CO, USA
| | - Dirk Lefeber
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Laura Mamblona
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER). Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, 28029, Spain.,Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, 28041, Spain
| | - Hanna Mandel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3109601, Israel.,Institute of Human Genetics, Galilee Medical Center, Nahariya, 22100, Israel.,Metabolic Unit, Rambam Health Care Campus, Haifa, 3109601, Israel
| | - Adi Mory
- The Genetics Institute, Rambam Health Care Campus, Haifa, 3109601, Israel
| | - John Ottoson
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, 80045, CO, USA
| | - Tamar Paperna
- The Genetics Institute, Rambam Health Care Campus, Haifa, 3109601, Israel
| | - Ger J M Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, 6500 HB, The Netherlands
| | - Pedro F Rebelo-Guiomar
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 OXY, United Kingdom.,Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto, 4200-135, Portugal
| | - Ann Saada
- Monique and Jacques Roboh Department of Genetic Research and the Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, 91120, Israel
| | - Bruno Sainz
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER). Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, 28029, Spain.,Enfermedades Crónicas y Cáncer Area, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, 28034, Spain
| | - Hayley Salvemini
- SA Pathology, Women and Children's Hospital Adelaide, Adelaide, 5006, Australia
| | - Mirthe H Schoots
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB, Groningen, The Netherlands
| | - Jan A Smeitink
- Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Maciej J Szukszto
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 OXY, United Kingdom
| | - Hendrik J Ter Horst
- Division of Neonatology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, 9700 RB, The Netherlands
| | - Frans van den Brandt
- Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Francjan J van Spronsen
- Division of Metabolic Diseases, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, 9700 RB, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands.,Institute of Genetic Medicine, Newcastle University, Newcastle, NE1 3BZ, United Kingdom
| | - Eric Wartchow
- Department of Pathology, Children's Hospital Colorado, University of Colorado, Aurora, 80045, CO, USA
| | - Liesbeth T Wintjes
- Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Yaniv Zohar
- Institute of Pathology, Rambam Health Care Campus, 3109601, Haifa, Israel
| | - Miguel A Fernández-Moreno
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER). Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, 28029, Spain.,Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, 28041, Spain
| | - Hagit N Baris
- The Genetics Institute, Rambam Health Care Campus, Haifa, 3109601, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3109601, Israel
| | - Claudia Donnini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Michal Minczuk
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 OXY, United Kingdom
| | - Richard J Rodenburg
- Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Johan L K Van Hove
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, 80045, CO, USA.
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35
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Nicolas G, Charbonnier C, Campion D, Veltman JA. Estimation of minimal disease prevalence from population genomic data: Application to primary familial brain calcification. Am J Med Genet B Neuropsychiatr Genet 2018; 177:68-74. [PMID: 29152850 DOI: 10.1002/ajmg.b.32605] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/22/2017] [Indexed: 12/13/2022]
Abstract
Primary Familial Brain Calcification (PFBC) is a rare calcifying disorder of the brain with autosomal dominant inheritance, of unknown prevalence. Four causal genes have been identified so far: SLC20A2, PDGFB, PDGFRB, and XPR1, with pathogenic, probably pathogenic or missense variants of unknown significance found in 27.7% probands in the French PFBC series. Estimating PFBC prevalence from a clinical input is arduous due to a large diversity of symptoms and ages of onset and to incomplete clinical penetrance. Abnormal calcifications on CT scan can be used as a reliable diagnostic biomarker whatever the clinical status, but differential diagnoses should be ruled out including the challenging exclusion of common basal ganglia calcifications. Our primary aim was to estimate the minimal prevalence of PFBC due to a variant in one of the known genes. We extracted variants from the four known genes present in the gnomAD database gathering genomic data from 138,632 individuals. We interpreted all variants based on their predicted effect, their frequency, and previous studies on PFBC patients. Using the most conservative estimate, the minimal prevalence of PFBC related to a variant in one of the four known genes was 4.5 p. 10,000 (95%CI [3.4-5.5] p. 10,000). We then used variant detection rates in patients to extrapolate an overall minimal prevalence of PFBC to 2.1 p. 1,000 (95%CI [1.9-2.4] p. 1,000). The population-based genomic analysis indicates that PFBC is not an exceptionally rare disorder, still underestimated and underdiagnosed.
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Affiliation(s)
- Gaël Nicolas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Genetics and CNR-MAJ, F 76000, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Camille Charbonnier
- Department of Genetics and CNR-MAJ, F 76000, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Dominique Campion
- Department of Genetics and CNR-MAJ, F 76000, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France.,Department of Research, Rouvray Psychiatric Hospital, Sotteville-lès-Rouen, France
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
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36
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Bouwkamp CG, Kievit AJA, Markx S, Friedman JI, van Zutven L, van Minkelen R, Vrijenhoek T, Xu B, Sterrenburg-van de Nieuwegiessen I, Veltman JA, Bonifati V, Kushner SA. Copy Number Variation in Syndromic Forms of Psychiatric Illness: The Emerging Value of Clinical Genetic Testing in Psychiatry. Am J Psychiatry 2017; 174:1036-1050. [PMID: 29088930 DOI: 10.1176/appi.ajp.2017.16080946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian G Bouwkamp
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Anneke J A Kievit
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Sander Markx
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Joseph I Friedman
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Laura van Zutven
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rick van Minkelen
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Terry Vrijenhoek
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Bin Xu
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Ineke Sterrenburg-van de Nieuwegiessen
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Joris A Veltman
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Vincenzo Bonifati
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Steven A Kushner
- From the Department of Psychiatry and the Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands; the Department of Psychiatry and the Center for Precision Neuropsychiatry, Columbia University, New York; New York State Psychiatric Institute, New York; the Departments of Psychiatry, Neuroscience, and Human Genetics, Mount Sinai School of Medicine, New York; the Clinical Neuroscience Center, Pilgrim Psychiatric Center, West Brentwood, N.Y.; the Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Delta Psychiatric Center, Portugaal, the Netherlands; the Department of Human Genetics, Donders Center for Neuroscience, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; and the Department of Clinical Genetics, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
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37
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Wortmann SB, Timal S, Venselaar H, Wintjes LT, Kopajtich R, Feichtinger RG, Onnekink C, Mühlmeister M, Brandt U, Smeitink JA, Veltman JA, Sperl W, Lefeber D, Pruijn G, Stojanovic V, Freisinger P, V Spronsen F, Derks TG, Veenstra-Knol HE, Mayr JA, Rötig A, Tarnopolsky M, Prokisch H, Rodenburg RJ. Biallelic variants in WARS2 encoding mitochondrial tryptophanyl-tRNA synthase in six individuals with mitochondrial encephalopathy. Hum Mutat 2017; 38:1786-1795. [PMID: 28905505 DOI: 10.1002/humu.23340] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 07/19/2017] [Revised: 09/07/2017] [Accepted: 09/10/2017] [Indexed: 12/12/2022]
Abstract
Mitochondrial protein synthesis involves an intricate interplay between mitochondrial DNA encoded RNAs and nuclear DNA encoded proteins, such as ribosomal proteins and aminoacyl-tRNA synthases. Eukaryotic cells contain 17 mitochondria-specific aminoacyl-tRNA synthases. WARS2 encodes mitochondrial tryptophanyl-tRNA synthase (mtTrpRS), a homodimeric class Ic enzyme (mitochondrial tryptophan-tRNA ligase; EC 6.1.1.2). Here, we report six individuals from five families presenting with either severe neonatal onset lactic acidosis, encephalomyopathy and early death or a later onset, more attenuated course of disease with predominating intellectual disability. Respiratory chain enzymes were usually normal in muscle and fibroblasts, while a severe combined respiratory chain deficiency was found in the liver of a severely affected individual. Exome sequencing revealed rare biallelic variants in WARS2 in all affected individuals. An increase of uncharged mitochondrial tRNATrp and a decrease of mtTrpRS protein content were found in fibroblasts of affected individuals. We hereby define the clinical, neuroradiological, and metabolic phenotype of WARS2 defects. This confidently implicates that mutations in WARS2 cause mitochondrial disease with a broad spectrum of clinical presentation.
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Affiliation(s)
- Saskia B Wortmann
- Department of Pediatrics, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Sharita Timal
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Neurology, Donders Center for Brain, Cognition, and Behavior, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hanka Venselaar
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Liesbeth T Wintjes
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert Kopajtich
- Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - René G Feichtinger
- Department of Pediatrics, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Carla Onnekink
- Department of Biomolecular Chemistry, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mareike Mühlmeister
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ulrich Brandt
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan A Smeitink
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wolfgang Sperl
- Department of Pediatrics, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Dirk Lefeber
- Department of Neurology, Donders Center for Brain, Cognition, and Behavior, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ger Pruijn
- Department of Biomolecular Chemistry, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vesna Stojanovic
- School of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute for Child and Youth Health Care of Vojvodina, Intensive Care Unit, Novi Sad, Serbia
| | - Peter Freisinger
- Children's Hospital, Klinikum am Steinenberg, Reutlingen, Germany
| | - Francjan V Spronsen
- Division of Metabolic Diseases, Beatrix Children's Hospital, University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands
| | - Terry Gj Derks
- Division of Metabolic Diseases, Beatrix Children's Hospital, University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands
| | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Agnes Rötig
- INSERM U1163, Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - Mark Tarnopolsky
- Department of Pediatrics, Division of Neuromuscular and Neurometabolic Diseases, McMaster University Medical Center, Hamilton, Ontario, Canada
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Richard J Rodenburg
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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38
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Paciejewska MM, Maijenburg MW, Gilissen C, Kleijer M, Vermeul K, Weijer K, Veltman JA, von Lindern M, van der Schoot CE, Voermans C. Different Balance of Wnt Signaling in Adult and Fetal Bone Marrow-Derived Mesenchymal Stromal Cells. Stem Cells Dev 2017; 25:934-47. [PMID: 27154244 DOI: 10.1089/scd.2015.0263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) are applied as novel therapeutics for their regenerative and immune-suppressive capacities. Clinical applications, however, require extensive expansion of MSCs. Fetal bone marrow-derived MSCs (FBMSCs) proliferate faster than adult bone marrow-derived MSC (ABMSCs). To optimize expansion and function of MSC in general, we explored the differences between ABMSC and FBMSC. Gene expression profiling implicated differential expression of genes encoding proteins in the Wnt signaling pathway, including excreted inhibitors of Wnt signaling, particularly by ABMSC. Both MSC types had a similar basal level of canonical Wnt signaling. Abrogation of autocrine Wnt production by inhibitor of Wnt production-2 (IWP2) reduced canonical Wnt signaling and cell proliferation of FBMSCs, but hardly affected ABMSC. Addition of exogenous Wnt3a, however, induced expression of the target genes lymphocyte enhancer-binding factor (LEF) and T-cell factor (TCF) faster and at lower Wnt3a levels in ABMSC compared to FBMSC. Medium replacement experiments indicated that ABMSC produce an inhibitor of Wnt signaling that is effective on ABMSC itself but not on FBMSC, whereas FBMSC excrete (Wnt) factors that stimulate proliferation of ABMSC. In contrast, FBMSC were not able to support hematopoiesis, whereas ABMSC displayed hematopoietic support sensitive to IWP2, the inhibitor of Wnt factor excretion. In conclusion, ABMSC and FBMSC differ in their Wnt signature. While FBMSC produced factors, including Wnt signals, that enhanced MSC proliferation, ABMSC produced Wnt factors in a setting that enhanced hematopoietic support. Thus, further unraveling the molecular basis of this phenomenon may lead to improvement of clinical expansion protocols of ABMSCs.
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Affiliation(s)
- Maja M Paciejewska
- 1 Department of Hematopoiesis, Sanquin Research, Amsterdam, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Marijke W Maijenburg
- 1 Department of Hematopoiesis, Sanquin Research, Amsterdam, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands .,2 Department of Experimental Immunohematology, Sanquin Research, Amsterdam, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Christian Gilissen
- 3 Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Marion Kleijer
- 1 Department of Hematopoiesis, Sanquin Research, Amsterdam, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Kim Vermeul
- 1 Department of Hematopoiesis, Sanquin Research, Amsterdam, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Kees Weijer
- 4 Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Joris A Veltman
- 3 Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Marieke von Lindern
- 1 Department of Hematopoiesis, Sanquin Research, Amsterdam, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands .,5 Department of Hematology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - C Ellen van der Schoot
- 2 Department of Experimental Immunohematology, Sanquin Research, Amsterdam, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands .,5 Department of Hematology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Carlijn Voermans
- 1 Department of Hematopoiesis, Sanquin Research, Amsterdam, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands .,2 Department of Experimental Immunohematology, Sanquin Research, Amsterdam, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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39
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Lelieveld SH, Wiel L, Venselaar H, Pfundt R, Vriend G, Veltman JA, Brunner HG, Vissers LE, Gilissen C. Spatial Clustering of de Novo Missense Mutations Identifies Candidate Neurodevelopmental Disorder-Associated Genes. Am J Hum Genet 2017; 101:478-484. [PMID: 28867141 DOI: 10.1016/j.ajhg.2017.08.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/04/2017] [Indexed: 10/19/2022] Open
Abstract
Haploinsufficiency (HI) is the best characterized mechanism through which dominant mutations exert their effect and cause disease. Non-haploinsufficiency (NHI) mechanisms, such as gain-of-function and dominant-negative mechanisms, are often characterized by the spatial clustering of mutations, thereby affecting only particular regions or base pairs of a gene. Variants leading to haploinsufficency might occasionally cluster as well, for example in critical domains, but such clustering is on the whole less pronounced with mutations often spread throughout the gene. Here we exploit this property and develop a method to specifically identify genes with significant spatial clustering patterns of de novo mutations in large cohorts. We apply our method to a dataset of 4,061 de novo missense mutations from published exome studies of trios with intellectual disability and developmental disorders (ID/DD) and successfully identify 15 genes with clustering mutations, including 12 genes for which mutations are known to cause neurodevelopmental disorders. For 11 out of these 12, NHI mutation mechanisms have been reported. Additionally, we identify three candidate ID/DD-associated genes of which two have an established role in neuronal processes. We further observe a higher intolerance to normal genetic variation of the identified genes compared to known genes for which mutations lead to HI. Finally, 3D modeling of these mutations on their protein structures shows that 81% of the observed mutations are unlikely to affect the overall structural integrity and that they therefore most likely act through a mechanism other than HI.
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40
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Oud MS, Ramos L, O'Bryan MK, McLachlan RI, Okutman Ö, Viville S, Vries PF, Smeets DF, Lugtenberg D, Hehir‐Kwa JY, Gilissen C, de Vorst M, Vissers LE, Hoischen A, Meijerink AM, Fleischer K, Veltman JA, Noordam MJ. Validation and application of a novel integrated genetic screening method to a cohort of 1,112 men with idiopathic azoospermia or severe oligozoospermia. Hum Mutat 2017; 38:1592-1605. [DOI: 10.1002/humu.23312] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Manon S. Oud
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
| | - Liliana Ramos
- Department of Gynaecology and Obstetrics Radboudumc Nijmegen The Netherlands
| | - Moira K. O'Bryan
- The Development and Stem Cells Program of Monash Biomedicine Discovery Institute Monash University Clayton Australia
- Department of Anatomy and Developmental Biology Monash University Clayton Australia
| | | | - Özlem Okutman
- Laboratory of Genetic Diagnostics UF3472‐Genetics of Infertility University Hospital Strasbourg Strasbourg France
| | - Stephane Viville
- Laboratory of Genetic Diagnostics UF3472‐Genetics of Infertility University Hospital Strasbourg Strasbourg France
| | - Petra F. Vries
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
| | - Dominique F.C.M. Smeets
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
| | - Jayne Y. Hehir‐Kwa
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
| | - Christian Gilissen
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
| | - Maartje de Vorst
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI) Radboudumc Nijmegen The Netherlands
| | - Aukje M. Meijerink
- Department of Gynaecology and Obstetrics Radboudumc Nijmegen The Netherlands
| | - Kathrin Fleischer
- Department of Gynaecology and Obstetrics Radboudumc Nijmegen The Netherlands
| | - Joris A. Veltman
- Department of Human Genetics Donders Institute for Brain Cognition and Behavior Radboudumc Nijmegen The Netherlands
- Institute of Genetic Medicine Newcastle University Newcastle upon Tyne United Kingdom
- Department of Genetics and Cell Biology Maastricht UMC+ Maastricht The Netherlands
| | - Michiel J. Noordam
- Department of Genetics and Cell Biology Maastricht UMC+ Maastricht The Netherlands
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41
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Wiel L, Venselaar H, Veltman JA, Vriend G, Gilissen C. Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. Hum Mutat 2017; 38:1454-1463. [PMID: 28815929 PMCID: PMC5656839 DOI: 10.1002/humu.23313] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 12/11/2022]
Abstract
Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population‐based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease‐causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 “meta‐domains.” These meta‐domains consist of 30,853 homologous Pfam protein domain instances that cover 36% of all human protein coding sequences. We find that genetic tolerance is consistent across protein domain homologues, and that patterns of genetic tolerance faithfully mimic patterns of evolutionary conservation. Furthermore, for a significant fraction (68%) of the meta‐domains high‐frequency population variation re‐occurs at the same positions across domain homologues more often than expected. In addition, we observe that the presence of pathogenic missense variants at an aligned homologous domain position is often paired with the absence of population variation and vice versa. The use of these meta‐domains can improve the interpretation of genetic variation.
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
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42
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Plantinga TS, Arts P, Knarren GH, Mulder AH, Wakelkamp IM, Hermus AR, Joosten LA, Netea MG, Bisschop PH, de Herder WW, Beijers HJ, de Bruin IJ, Gilissen C, Veltman JA, Hoischen A, Smit JW, Netea-Maier RT. Rare NOX3 Variants Confer Susceptibility to Agranulocytosis During Thyrostatic Treatment of Graves' Disease. Clin Pharmacol Ther 2017; 102:1017-1024. [PMID: 28486791 DOI: 10.1002/cpt.733] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/12/2017] [Accepted: 05/01/2017] [Indexed: 01/12/2023]
Abstract
Agranulocytosis is a rare and serious adverse effect of antithyroid drugs, with unknown etiology. The present study aimed to uncover genetic susceptibility and underlying mechanisms of antithyroid drug-induced agranulocytosis (ATDAC). We studied two independent families with familial Graves' disease, of which several members developed ATDAC. In addition, six sporadic ATDAC patients with Graves' disease were investigated. Whole exome sequencing analysis of affected and unaffected family members was performed to identify genetic susceptibility variants for ATDAC, followed by functional characterization of primary granulocytes from patients and unrelated healthy controls. Whole exome sequencing, cosegregation analysis, and stringent selection criteria of candidate gene variants identified NOX3 as a genetic factor related to ATDAC. Functional studies revealed increased apoptosis of methimazole-treated granulocytes from patients carrying NOX3 variants. In conclusion, genetic variants in NOX3 may confer susceptibility to antithyroid drug-induced apoptosis of granulocytes. These findings contribute to the understanding of the mechanisms underlying ATDAC.
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Affiliation(s)
- T S Plantinga
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - P Arts
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G H Knarren
- Department of Internal Medicine, Slingeland Hospital, Doetinchem, The Netherlands
| | - A H Mulder
- Department of Internal Medicine, Slingeland Hospital, Doetinchem, The Netherlands
| | - I M Wakelkamp
- Department of Internal Medicine, St Antonius Hospital, Nieuwegein, The Netherlands
| | - A R Hermus
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L A Joosten
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M G Netea
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - P H Bisschop
- Department of Endocrinology and Metabolism, Academic Medical Centre, Amsterdam, The Netherlands
| | - W W de Herder
- Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - H J Beijers
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - I J de Bruin
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J W Smit
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R T Netea-Maier
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
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43
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Chen XS, Reader RH, Hoischen A, Veltman JA, Simpson NH, Francks C, Newbury DF, Fisher SE. Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. Sci Rep 2017; 7:46105. [PMID: 28440294 PMCID: PMC5404330 DOI: 10.1038/srep46105] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/08/2017] [Indexed: 12/22/2022] Open
Abstract
A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential “multiple-hit” cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affecting STARD9, while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation.
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Affiliation(s)
- Xiaowei Sylvia Chen
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Rose H Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Clinical Genetics, University of Maastricht, Maastricht, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
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Acuna-Hidalgo R, Deriziotis P, Steehouwer M, Gilissen C, Graham SA, van Dam S, Hoover-Fong J, Telegrafi AB, Destree A, Smigiel R, Lambie LA, Kayserili H, Altunoglu U, Lapi E, Uzielli ML, Aracena M, Nur BG, Mihci E, Moreira LMA, Borges Ferreira V, Horovitz DDG, da Rocha KM, Jezela-Stanek A, Brooks AS, Reutter H, Cohen JS, Fatemi A, Smitka M, Grebe TA, Di Donato N, Deshpande C, Vandersteen A, Marques Lourenço C, Dufke A, Rossier E, Andre G, Baumer A, Spencer C, McGaughran J, Franke L, Veltman JA, De Vries BBA, Schinzel A, Fisher SE, Hoischen A, van Bon BW. Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies. PLoS Genet 2017; 13:e1006683. [PMID: 28346496 PMCID: PMC5386295 DOI: 10.1371/journal.pgen.1006683] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 04/10/2017] [Accepted: 03/10/2017] [Indexed: 11/18/2022] Open
Abstract
Schinzel-Giedion syndrome (SGS) is a rare developmental disorder characterized by multiple malformations, severe neurological alterations and increased risk of malignancy. SGS is caused by de novo germline mutations clustering to a 12bp hotspot in exon 4 of SETBP1. Mutations in this hotspot disrupt a degron, a signal for the regulation of protein degradation, and lead to the accumulation of SETBP1 protein. Overlapping SETBP1 hotspot mutations have been observed recurrently as somatic events in leukemia. We collected clinical information of 47 SGS patients (including 26 novel cases) with germline SETBP1 mutations and of four individuals with a milder phenotype caused by de novo germline mutations adjacent to the SETBP1 hotspot. Different mutations within and around the SETBP1 hotspot have varying effects on SETBP1 stability and protein levels in vitro and in in silico modeling. Substitutions in SETBP1 residue I871 result in a weak increase in protein levels and mutations affecting this residue are significantly more frequent in SGS than in leukemia. On the other hand, substitutions in residue D868 lead to the largest increase in protein levels. Individuals with germline mutations affecting D868 have enhanced cell proliferation in vitro and higher incidence of cancer compared to patients with other germline SETBP1 mutations. Our findings substantiate that, despite their overlap, somatic SETBP1 mutations driving malignancy are more disruptive to the degron than germline SETBP1 mutations causing SGS. Additionally, this suggests that the functional threshold for the development of cancer driven by the disruption of the SETBP1 degron is higher than for the alteration in prenatal development in SGS. Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype.
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MESH Headings
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Abnormalities, Multiple/pathology
- Blotting, Western
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Line
- Cell Proliferation/genetics
- Cell Transformation, Neoplastic/genetics
- Child
- Child, Preschool
- Craniofacial Abnormalities/genetics
- Craniofacial Abnormalities/metabolism
- Craniofacial Abnormalities/pathology
- Female
- Gene Expression Profiling
- Genetic Association Studies
- Genetic Predisposition to Disease/genetics
- Germ-Line Mutation
- HEK293 Cells
- Hand Deformities, Congenital/genetics
- Hand Deformities, Congenital/metabolism
- Hand Deformities, Congenital/pathology
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/metabolism
- Hematologic Neoplasms/pathology
- Humans
- Infant
- Infant, Newborn
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Male
- Mutation
- Nails, Malformed/genetics
- Nails, Malformed/metabolism
- Nails, Malformed/pathology
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phenotype
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Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pelagia Deriziotis
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah A. Graham
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Sipko van Dam
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Julie Hoover-Fong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | - Anne Destree
- Institute of Pathology and Genetics (IPG), Gosselies, Belgium
| | - Robert Smigiel
- Department of Pediatrics and Rare Disorders, Medical University, Wroclaw, Poland
| | - Lindsday A. Lambie
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine (KUSOM), İstanbul, Turkey
| | - Umut Altunoglu
- Medical Genetics Department, İstanbul Medical Faculty, İstanbul University, İstanbul, Turkey
| | - Elisabetta Lapi
- Medical Genetics Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | | | - Mariana Aracena
- División de Pediatría, Pontificia Universidad Católica de Chile and Unidad de Genética, Hospital Dr. Luis Calvo Mackenna, Santiago Chile
| | - Banu G. Nur
- Department of Pediatric Genetics, Akdeniz University Medical School, Antalya, Turkey
| | - Ercan Mihci
- Department of Pediatric Genetics, Akdeniz University Medical School, Antalya, Turkey
| | - Lilia M. A. Moreira
- Laboratory of Human Genetics, Biology Institute, Federal University of Bahia (UFBA), Bahia, Brazil
| | | | - Dafne D. G. Horovitz
- CERES-Genetica Reference Center and Studies in Medical Genetics and Instituto Fernandes Figueira / Fiocruz, Rio de Janeiro, Brazil
| | - Katia M. da Rocha
- Center for Human Genome Studies, Institute of Biosciences, USP, Sao Paulo, Brazil
| | | | - Alice S. Brooks
- Department of Clinical Genetics, Sophia Children's Hospital, Erasmus MC, Rotterdam, The Netherlands
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany and Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Julie S. Cohen
- Division of Neurogenetics, Kennedy Krieger Institute, Departments of Neurology and Pediatrics, The Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Ali Fatemi
- Division of Neurogenetics, Kennedy Krieger Institute, Departments of Neurology and Pediatrics, The Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Martin Smitka
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Theresa A. Grebe
- Division of Genetics & Metabolism, Phoenix Children’s Hospital, Phoenix, Arizona, United States of America
| | | | - Charu Deshpande
- Department of Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Anthony Vandersteen
- North West Thames Regional Genetics Unit, Kennedy Galton Centre, North West London Hospitals NHS Trust, Northwick Park & St Marks Hospital, Harrow, Middlesex, United Kingdom
| | - Charles Marques Lourenço
- Neurogenetics Unit, Department of Medical Genetics School of Medicine of Ribeirao Preto, University of Sao Paulo, Sao Paulo, Brazil
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Eva Rossier
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Gwenaelle Andre
- Unité de foetopathologie, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Careni Spencer
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland and School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bert B. A. De Vries
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail: (BWvB); (AH)
| | - Bregje W. van Bon
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail: (BWvB); (AH)
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45
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Becker KL, Arts P, Jaeger M, Plantinga TS, Gilissen C, van Laarhoven A, van Ingen J, Veltman JA, Joosten LAB, Hoischen A, Netea MG, Iseman MD, Chan ED, van de Veerdonk FL. MST1R mutation as a genetic cause of Lady Windermere syndrome. Eur Respir J 2017; 49:13993003.01478-2016. [PMID: 28100548 DOI: 10.1183/13993003.01478-2016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/19/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Katharina L Becker
- Dept of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Both authors contributed equally
| | - Peer Arts
- Dept of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.,Both authors contributed equally
| | - Martin Jaeger
- Dept of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Theodorus S Plantinga
- Dept of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Dept of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjan van Laarhoven
- Dept of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jakko van Ingen
- Dept of Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joris A Veltman
- Dept of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.,Dept of Clinical Genetics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Leo A B Joosten
- Dept of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Dept of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Dept of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael D Iseman
- Dept of Medicine and Academic Affairs, National Jewish Health, Denver, CO, USA
| | - Edward D Chan
- Dept of Medicine and Academic Affairs, National Jewish Health, Denver, CO, USA.,Dept of Medicine, Denver Veterans Affairs Medical Center, Denver, CO, USA.,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Frank L van de Veerdonk
- Dept of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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46
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Abstract
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.
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Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
- Department of Clinical Genetics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Alexander Hoischen
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
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47
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van Nimwegen KJM, van Soest RA, Veltman JA, Nelen MR, van der Wilt GJ, Vissers LELM, Grutters JPC. Is the $1000 Genome as Near as We Think? A Cost Analysis of Next-Generation Sequencing. Clin Chem 2016; 62:1458-1464. [DOI: 10.1373/clinchem.2016.258632] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
Abstract
BACKGROUND
The substantial technological advancements in next-generation sequencing (NGS), combined with dropping costs, have allowed for a swift diffusion of NGS applications in clinical settings. Although several commercial parties report to have broken the $1000 barrier for sequencing an entire human genome, a valid cost overview for NGS is currently lacking. This study provides a complete, transparent and up-to-date overview of the total costs of different NGS applications.
METHODS
Cost calculations for targeted gene panels (TGP), whole exome sequencing (WES) and whole genome sequencing (WGS) were based on the Illumina NextSeq500, HiSeq4000, and HiSeqX5 platforms, respectively. To anticipate future developments, sensitivity analyses are performed.
RESULTS
Per-sample costs were €1669 for WGS, € 792 for WES and €333 for TGP. To reach the coveted $1000 genome, not only is the long-term and efficient use of the sequencing equipment needed, but also large reductions in capital costs and especially consumable costs are also required.
CONCLUSIONS
WES and TGP are considerably lower-cost alternatives to WGS. However, this does not imply that these NGS approaches should be preferred in clinical practice, since this should be based on the tradeoff between costs and the expected clinical utility of the approach chosen. The results of the present study contribute to the evaluation of such tradeoffs.
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Affiliation(s)
- Kirsten J M van Nimwegen
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center
| | | | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, and
- Department of Clinical Genetics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Marcel R Nelen
- Department of Human Genetics, Donders Centre for Neuroscience, and
| | - Gert Jan van der Wilt
- Department for Health Evidence, Donders Centre for Neuroscience, Radboud university medical center, Nijmegen, the Netherlands
| | | | - Janneke P C Grutters
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center
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48
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Abstract
With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Department of Clinical Genetics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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49
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Jansen EJR, Timal S, Ryan M, Ashikov A, van Scherpenzeel M, Graham LA, Mandel H, Hoischen A, Iancu TC, Raymond K, Steenbergen G, Gilissen C, Huijben K, van Bakel NHM, Maeda Y, Rodenburg RJ, Adamowicz M, Crushell E, Koenen H, Adams D, Vodopiutz J, Greber-Platzer S, Müller T, Dueckers G, Morava E, Sykut-Cegielska J, Martens GJM, Wevers RA, Niehues T, Huynen MA, Veltman JA, Stevens TH, Lefeber DJ. ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation. Nat Commun 2016; 7:11600. [PMID: 27231034 PMCID: PMC4894975 DOI: 10.1038/ncomms11600] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 04/12/2016] [Indexed: 02/07/2023] Open
Abstract
The V-ATPase is the main regulator of intra-organellar acidification. Assembly of this complex has extensively been studied in yeast, while limited knowledge exists for man. We identified 11 male patients with hemizygous missense mutations in ATP6AP1, encoding accessory protein Ac45 of the V-ATPase. Homology detection at the level of sequence profiles indicated Ac45 as the long-sought human homologue of yeast V-ATPase assembly factor Voa1. Processed wild-type Ac45, but not its disease mutants, restored V-ATPase-dependent growth in Voa1 mutant yeast. Patients display an immunodeficiency phenotype associated with hypogammaglobulinemia, hepatopathy and a spectrum of neurocognitive abnormalities. Ac45 in human brain is present as the common, processed ∼40-kDa form, while liver shows a 62-kDa intact protein, and B-cells a 50-kDa isoform. Our work unmasks Ac45 as the functional ortholog of yeast V-ATPase assembly factor Voa1 and reveals a novel link of tissue-specific V-ATPase assembly with immunoglobulin production and cognitive function.
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Affiliation(s)
- Eric J. R. Jansen
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Centre for Neuroscience and Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Sharita Timal
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Margret Ryan
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Angel Ashikov
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Monique van Scherpenzeel
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Laurie A. Graham
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Hanna Mandel
- Metabolic Unit, Rambam Health Care Center, Rappaport School of Medicine, Technion, 3109601 Haifa, Israel
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Theodore C. Iancu
- The Milman-David Biomedical Research Unit, 24 Hazevi Avenue, 34355 Haifa, Israel
| | - Kimiyo Raymond
- Department of Laboratory Medicine and Pathology, Mayo College of Medicine, Rochester, Minnesota 55905, USA
| | - Gerry Steenbergen
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Karin Huijben
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nick H. M. van Bakel
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Centre for Neuroscience and Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Yusuke Maeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Richard J. Rodenburg
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders (NCMD), Radboud university medical center, 6525 GA Nijmegen, The Netherlands
| | - Maciej Adamowicz
- Protein Laboratory, Children's Memorial Health Institute, 04730 Warsaw, Poland
| | - Ellen Crushell
- Temple Street Children's University Hospital, Temple Street, Dublin 1, DC01 YC67, Ireland
| | - Hans Koenen
- Department of Laboratory Medicine, Medical Immunology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Darius Adams
- Personalized Genomic Medicine Pediatric Genetics and Metabolism Goryeb Children's Hospital, Morristown, New Jersey 07960, USA
| | - Julia Vodopiutz
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Susanne Greber-Platzer
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Müller
- Department of Pediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Gregor Dueckers
- HELIOS Kliniken Krefeld, Children's Hospital, Lutherplatz 40, 47805 Krefeld, Germany
| | - Eva Morava
- Department of Pediatrics, Tulane University Medical School, New Orleans, Los Angeles 70112, USA
- Department of Pediatrics, University Medical School of Leuven, 3000 Leuven, Belgium
- Department of Pediatrics, Radboudumc, 6525GA, Nijmegen, The Netherlands
| | | | - Gerard J. M. Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Centre for Neuroscience and Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Tim Niehues
- HELIOS Kliniken Krefeld, Children's Hospital, Lutherplatz 40, 47805 Krefeld, Germany
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands
| | - Tom H. Stevens
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Dirk J. Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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Krabbenborg L, Vissers LELM, Schieving J, Kleefstra T, Kamsteeg EJ, Veltman JA, Willemsen MA, Van der Burg S. Understanding the Psychosocial Effects of WES Test Results on Parents of Children with Rare Diseases. J Genet Couns 2016; 25:1207-1214. [PMID: 27098417 PMCID: PMC5114322 DOI: 10.1007/s10897-016-9958-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 04/06/2016] [Indexed: 01/02/2023]
Abstract
The use of whole exome sequencing (WES) for diagnostics of children with rare genetic diseases raises questions about best practices in genetic counselling. While a lot of attention is now given to pre-test counselling procedures for WES, little is known about how parents experience the (positive, negative, or inconclusive) WES results in daily life. To fill this knowledge gap, data were gathered through in-depth interviews with parents of 15 children who underwent WES analysis. WES test results, like results from other genetic tests, evoked relief as well as worries, irrespective of the type of result. Advantages of obtaining a conclusive diagnosis included becoming more accepting towards the situation, being enabled to attune care to the needs of the child, and better coping with feelings of guilt. Disadvantages experienced included a loss of hope for recovery, and a loss by parents of their social network of peers and the effort necessary to re-establish that social network. While parents with conclusive diagnoses were able to re-establish a peer community with the help of social media, parents receiving a possible diagnosis experienced hurdles in seeking peer support, as peers still needed to be identified. These types of psychosocial effects of WES test results for parents are important to take into account for the development of successful genetic counselling strategies.
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Affiliation(s)
- Lotte Krabbenborg
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands. .,Institute for Science, Innovation and Society (ISIS), Radboud University, P.O. Box 9010, 6500, Nijmegen, the Netherlands.
| | - L E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525, Nijmegen, the Netherlands
| | - J Schieving
- Department of Paediatric Neurology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - T Kleefstra
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525, Nijmegen, the Netherlands
| | - E J Kamsteeg
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525, Nijmegen, the Netherlands
| | - J A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525, Nijmegen, the Netherlands.,Department of Clinical Genetics, Maastricht University Medical Centre, Universiteitssingel 50, 6229, Maastricht, the Netherlands
| | - M A Willemsen
- Department of Paediatric Neurology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - S Van der Burg
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
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