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Robevska G, van den Bergen JA, Ohnesorg T, Eggers S, Hanna C, Hersmus R, Thompson EM, Baxendale A, Verge CF, Lafferty AR, Marzuki NS, Santosa A, Listyasari NA, Riedl S, Warne G, Looijenga L, Faradz S, Ayers KL, Sinclair AH. Functional characterization of novel NR5A1 variants reveals multiple complex roles in disorders of sex development. Hum Mutat 2017; 39:124-139. [PMID: 29027299 PMCID: PMC5765430 DOI: 10.1002/humu.23354] [Citation(s) in RCA: 33] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 12/23/2022]
Abstract
Variants in the NR5A1 gene encoding SF1 have been described in a diverse spectrum of disorders of sex development (DSD). Recently, we reported the use of a targeted gene panel for DSD where we identified 15 individuals with a variant in NR5A1, nine of which are novel. Here, we examine the functional effect of these changes in relation to the patient phenotype. All novel variants tested had reduced trans‐activational activity, while several had altered protein level, localization, or conformation. In addition, we found evidence of new roles for SF1 protein domains including a region within the ligand binding domain that appears to contribute to SF1 regulation of Müllerian development. There was little correlation between the severity of the phenotype and the nature of the NR5A1 variant. We report two familial cases of NR5A1 deficiency with evidence of variable expressivity; we also report on individuals with oligogenic inheritance. Finally, we found that the nature of the NR5A1 variant does not inform patient outcomes (including pubertal androgenization and malignancy risk). This study adds nine novel pathogenic NR5A1 variants to the pool of diagnostic variants. It highlights a greater need for understanding the complexity of SF1 function and the additional factors that contribute.
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Affiliation(s)
| | | | | | | | - Chloe Hanna
- Murdoch Children's Research Institute, Melbourne, Australia.,Royal Children's Hospital, Melbourne, Australia
| | - Remko Hersmus
- Department of Pathology, Josephine Nefkens Institute, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Elizabeth M Thompson
- SA Clinical Genetics Service, SA Pathology at the Women's and Children's Hospital, Adelaide, Australia.,School of Medicine, University of Adelaide, Adelaide, Australia
| | - Anne Baxendale
- SA Clinical Genetics Service, SA Pathology at the Women's and Children's Hospital, Adelaide, Australia
| | - Charles F Verge
- Sydney Children's Hospital, Sydney, Australia.,School of Women's and Children's Health, UNSW, Sydney, Australia
| | - Antony R Lafferty
- Centenary Hospital for Women and Children, Canberra, Australia.,ANU Medical School, Canberra, Australia
| | | | - Ardy Santosa
- Division of Urology, Department of Surgery, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Nurin A Listyasari
- Division of Human Genetics, Centre for Biomedical Research Faculty of Medicine Diponegoro University (FMDU), Semarang, Indonesia
| | - Stefan Riedl
- St Anna Children's Hospital, Department of Paediatrics, Medical University of Vienna, Wien, Austria.,Division of Paediatric Pulmology, Allergology, and Endocrinology, Department of Paediatrics, Medical University of Vienna, Wien, Austria
| | - Garry Warne
- Murdoch Children's Research Institute, Melbourne, Australia.,Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Leendert Looijenga
- Department of Pathology, Josephine Nefkens Institute, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Sultana Faradz
- Division of Human Genetics, Centre for Biomedical Research Faculty of Medicine Diponegoro University (FMDU), Semarang, Indonesia
| | - Katie L Ayers
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Andrew H Sinclair
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
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2
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Eggers S, Sadedin S, van den Bergen JA, Robevska G, Ohnesorg T, Hewitt J, Lambeth L, Bouty A, Knarston IM, Tan TY, Cameron F, Werther G, Hutson J, O'Connell M, Grover SR, Heloury Y, Zacharin M, Bergman P, Kimber C, Brown J, Webb N, Hunter MF, Srinivasan S, Titmuss A, Verge CF, Mowat D, Smith G, Smith J, Ewans L, Shalhoub C, Crock P, Cowell C, Leong GM, Ono M, Lafferty AR, Huynh T, Visser U, Choong CS, McKenzie F, Pachter N, Thompson EM, Couper J, Baxendale A, Gecz J, Wheeler BJ, Jefferies C, MacKenzie K, Hofman P, Carter P, King RI, Krausz C, van Ravenswaaij-Arts CMA, Looijenga L, Drop S, Riedl S, Cools M, Dawson A, Juniarto AZ, Khadilkar V, Khadilkar A, Bhatia V, Dũng VC, Atta I, Raza J, Thi Diem Chi N, Hao TK, Harley V, Koopman P, Warne G, Faradz S, Oshlack A, Ayers KL, Sinclair AH. Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort. Genome Biol 2016; 17:243. [PMID: 27899157 PMCID: PMC5126855 DOI: 10.1186/s13059-016-1105-y] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/10/2016] [Indexed: 01/20/2023] Open
Abstract
Background Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients receive an accurate clinical genetic diagnosis. To address this we have developed a massively parallel sequencing targeted DSD gene panel which allows us to sequence all 64 known diagnostic DSD genes and candidate genes simultaneously. Results We analyzed DNA from the largest reported international cohort of patients with DSD (278 patients with 46,XY DSD and 48 with 46,XX DSD). Our targeted gene panel compares favorably with other sequencing platforms. We found a total of 28 diagnostic genes that are implicated in DSD, highlighting the genetic spectrum of this disorder. Sequencing revealed 93 previously unreported DSD gene variants. Overall, we identified a likely genetic diagnosis in 43% of patients with 46,XY DSD. In patients with 46,XY disorders of androgen synthesis and action the genetic diagnosis rate reached 60%. Surprisingly, little difference in diagnostic rate was observed between singletons and trios. In many cases our findings are informative as to the likely cause of the DSD, which will facilitate clinical management. Conclusions Our massively parallel sequencing targeted DSD gene panel represents an economical means of improving the genetic diagnostic capability for patients affected by DSD. Implementation of this panel in a large cohort of patients has expanded our understanding of the underlying genetic etiology of DSD. The inclusion of research candidate genes also provides an invaluable resource for future identification of novel genes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1105-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefanie Eggers
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,Victorian Clinical Genetic Services, Melbourne, VIC, Australia
| | - Simon Sadedin
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | | | | | - Thomas Ohnesorg
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia
| | - Jacqueline Hewitt
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,University of Melbourne, School of Bioscience, Melbourne, VIC, Australia.,Department Of Paediatric Urology, Monash Children's Hospital, Clayton, VIC, Australia
| | - Luke Lambeth
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia
| | - Aurore Bouty
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,The Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - Ingrid M Knarston
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiong Yang Tan
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,The Royal Children's Hospital Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetic Services, Melbourne, VIC, Australia
| | - Fergus Cameron
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,The Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - George Werther
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,The Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - John Hutson
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Michele O'Connell
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,The Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - Sonia R Grover
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,The Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - Yves Heloury
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,The Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - Margaret Zacharin
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,The Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - Philip Bergman
- Department of Paediatric Endocrinology and Diabetes, Monash Children's Hospital, Clayton, VIC, Australia.,Monash Medical Centre, Clayton, VIC, Australia
| | - Chris Kimber
- Monash Children's Hospital, Clayton, VIC, Australia
| | - Justin Brown
- Department of Paediatric Endocrinology and Diabetes, Monash Children's Hospital, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Nathalie Webb
- Department Of Paediatric Urology, Monash Children's Hospital, Clayton, VIC, Australia
| | - Matthew F Hunter
- Department of Paediatrics, Monash University, Clayton, VIC, Australia.,Monash Genetics, Monash Health, Clayton, VIC, Australia
| | - Shubha Srinivasan
- The Children's Hospital at Westmead, Institute of Endocrinology and Diabetes, Westmead, NSW, Australia
| | - Angela Titmuss
- The Children's Hospital at Westmead, Institute of Endocrinology and Diabetes, Westmead, NSW, Australia
| | - Charles F Verge
- Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, UNSW, Sydney, NSW, Australia
| | - David Mowat
- Department of Medical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Grahame Smith
- Urology and Clinical Programs, The Children's Hospital at Westmead, Westmead, NSW, Australia.,The University of Sydney, Westmead, NSW, Australia
| | - Janine Smith
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Lisa Ewans
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Carolyn Shalhoub
- Department of Medical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Patricia Crock
- John Hunter Children's Hospital, New Lambton Heights, NSW, Australia
| | - Chris Cowell
- The Children's Hospital at Westmead, Institute of Endocrinology and Diabetes, Westmead, NSW, Australia
| | - Gary M Leong
- Department of Paediatric Endocrinology and Diabetes, Lady Cilento Children's Hospital, Brisbane, QLD, Australia
| | - Makato Ono
- Department of Paediatrics, Tokyo Bay Medical Centre, Tokyo, Chiba, Japan
| | - Antony R Lafferty
- Centenary Hospital for Women and Children, Canberra, ACT, Australia.,ANU Medical School, Canberra, ACT, Australia
| | - Tony Huynh
- Department of Paediatric Endocrinology and Diabetes, Lady Cilento Children's Hospital, Brisbane, QLD, Australia
| | - Uma Visser
- Sydney Children's Hospital, Randwick, NSW, Australia
| | - Catherine S Choong
- Department of Endocrinology and Diabetes, Princess Margaret Hospital, Subiaco, WA, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Crawley, WA, Australia
| | - Fiona McKenzie
- School of Paediatrics and Child Health, The University of Western Australia, Crawley, WA, Australia.,Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Nicholas Pachter
- School of Paediatrics and Child Health, The University of Western Australia, Crawley, WA, Australia.,Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Elizabeth M Thompson
- SA Clinical Genetics Service, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA, Australia.,School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Jennifer Couper
- Women's and Children's Hospital and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Anne Baxendale
- SA Clinical Genetics Service, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Jozef Gecz
- School of Medicine and The Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Benjamin J Wheeler
- Department of Women's and Children's Health, University of Otago, Dunedin, New Zealand
| | - Craig Jefferies
- Diabetes and Endocrinology, Auckland District Health Board, Auckland, New Zealand
| | | | - Paul Hofman
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Philippa Carter
- Starship Paediatric Diabetes and Endocrinology, Auckland, New Zealand
| | - Richard I King
- Canterbury Health Laboratories, Christchurch, Canterbury, New Zealand
| | - Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | | | - Leendert Looijenga
- Department of Pathology, Josephine Nefkens Institute, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Sten Drop
- Department of Paediatrics, Division of Endocrinology, Sophia Children's Hospital, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Stefan Riedl
- St Anna Children's Hospital, Vienna, Austria.,Paediatric Department, Medical University of Vienna, Vienna, Austria
| | - Martine Cools
- Department of Paediatric Endocrinology, Ghent University Hospital, Ghent, Belgium
| | - Angelika Dawson
- Genomic Laboratory, Diagnostic Services of Manitoba and Genetics & Metabolism Program, WRHA, Winnipeg, MB, Canada.,Department Biochemistry & Medical Genetics and Paediatrics & Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Achmad Zulfa Juniarto
- Division of Human Genetics, Centre for Biomedical Research Faculty of Medicine Diponegoro University (FMDU), Semarang, Indonesia
| | - Vaman Khadilkar
- Growth and Pediatric Endocrine Clinic, Hirabai Cowasji Jehangir Medical Research Institute, Pune, India.,Hirabai Cowasji Jehangir Medical Research Institute, Pune, India
| | - Anuradha Khadilkar
- Growth and Pediatric Endocrine Clinic, Hirabai Cowasji Jehangir Medical Research Institute, Pune, India.,Hirabai Cowasji Jehangir Medical Research Institute, Pune, India
| | | | - Vũ Chí Dũng
- Department of Endocrinology, Metabolism and Genetics National Children's Hospital, Hanoi, Vietnam
| | - Irum Atta
- National Institute of Child Health, Karachi, Pakistan
| | - Jamal Raza
- National Institute of Child Health, Karachi, Pakistan
| | | | - Tran Kiem Hao
- Paediatric Centre, Hue Central Hospital, Hue city, Vietnam
| | - Vincent Harley
- Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Garry Warne
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,The Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - Sultana Faradz
- Division of Human Genetics, Centre for Biomedical Research Faculty of Medicine Diponegoro University (FMDU), Semarang, Indonesia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,University of Melbourne, School of Bioscience, Melbourne, VIC, Australia
| | - Katie L Ayers
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew H Sinclair
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia. .,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
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6
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White S, Ohnesorg T, Notini A, Roeszler K, Hewitt J, Daggag H, Smith C, Turbitt E, Gustin S, van den Bergen J, Miles D, Western P, Arboleda V, Schumacher V, Gordon L, Bell K, Bengtsson H, Speed T, Hutson J, Warne G, Harley V, Koopman P, Vilain E, Sinclair A. Copy number variation in patients with disorders of sex development due to 46,XY gonadal dysgenesis. PLoS One 2011; 6:e17793. [PMID: 21408189 PMCID: PMC3049794 DOI: 10.1371/journal.pone.0017793] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [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: 10/27/2010] [Accepted: 02/14/2011] [Indexed: 01/07/2023] Open
Abstract
Disorders of sex development (DSD), ranging in severity from mild genital abnormalities to complete sex reversal, represent a major concern for patients and their families. DSD are often due to disruption of the genetic programs that regulate gonad development. Although some genes have been identified in these developmental pathways, the causative mutations have not been identified in more than 50% 46,XY DSD cases. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to analyse copy number variation in 23 individuals with unexplained 46,XY DSD due to gonadal dysgenesis (GD). Here we describe three discrete changes in copy number that are the likely cause of the GD. Firstly, we identified a large duplication on the X chromosome that included DAX1 (NR0B1). Secondly, we identified a rearrangement that appears to affect a novel gonad-specific regulatory region in a known testis gene, SOX9. Surprisingly this patient lacked any signs of campomelic dysplasia, suggesting that the deletion affected expression of SOX9 only in the gonad. Functional analysis of potential SRY binding sites within this deleted region identified five putative enhancers, suggesting that sequences additional to the known SRY-binding TES enhancer influence human testis-specific SOX9 expression. Thirdly, we identified a small deletion immediately downstream of GATA4, supporting a role for GATA4 in gonad development in humans. These CNV analyses give new insights into the pathways involved in human gonad development and dysfunction, and suggest that rearrangements of non-coding sequences disturbing gene regulation may account for significant proportion of DSD cases.
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Affiliation(s)
- Stefan White
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas Ohnesorg
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Amanda Notini
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Kelly Roeszler
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Jacqueline Hewitt
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hinda Daggag
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Craig Smith
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Erin Turbitt
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Sonja Gustin
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Jocelyn van den Bergen
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Denise Miles
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Patrick Western
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Valerie Arboleda
- Department of Medical Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Valerie Schumacher
- Pediatrics Department, Children's Hospital, Boston, Massachusetts, United States of America
| | - Lavinia Gordon
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Katrina Bell
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | | | - Terry Speed
- Walter and Eliza Hall Institute, Melbourne, Victoria, Australia
| | - John Hutson
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Garry Warne
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Vincent Harley
- Prince Henry's Institute of Medical Research, Melbourne, Victoria, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Eric Vilain
- Department of Medical Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Andrew Sinclair
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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