1
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Cheng YHH, Bohaczuk SC, Stergachis AB. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum Genet 2024; 143:559-605. [PMID: 38436667 PMCID: PMC11078748 DOI: 10.1007/s00439-023-02639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.
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Affiliation(s)
- Y H Hank Cheng
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C Bohaczuk
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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2
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Belyaeva EO, Lebedev IN. Interloci CNV Interactions in Variability of the Phenotypes of Neurodevelopmental Disorders. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422100027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Liu X, Wang J, Yang M, Tian T, Hu T. Case report: Cystic hygroma accompanied with campomelic dysplasia in the first trimester caused by haploinsufficiency with SOX9 deletion. Front Genet 2022; 13:950271. [PMID: 36105084 PMCID: PMC9465627 DOI: 10.3389/fgene.2022.950271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: Campomelic dysplasia (CD) is a rare autosomal dominant skeletal malformation syndrome characterized by shortness and bowing of the lower extremities with or without XY sex reversal. Diagnosis using ultrasonography is most often made in the latter half of pregnancy. Intragenic heterozygous mutations in SOX9 are responsible for most cases of CD. CD caused by SOX9 deletion is a rare condition.Case presentation: We present a single case report of an individual with cystic hygroma accompanied by CD, which was detected by ultrasound in the first trimester. Chromosomal microarray analysis (CMA) was performed to determine copy number variants, whereas whole exome sequencing (WES) was performed to elucidate single-nucleotide variants. Chorionic villus sampling was performed to enable such analyses. Ultimately, CMA detected a 606 kb deletion in the 17q24.3 region with only one protein-coding gene (SOX9). However, no mutation in the SOX9 protein-coding sequence was detected by WES.Conclusion: When cystic hygroma is detected, prenatal diagnoses for skeletal dysplasia by ultrasound are likely to be confirmed in the first trimester. We propose a comprehensive prenatal diagnostic strategy that combines CMA and WES to diagnose fetuses with cystic hygroma accompanied by skeletal dysplasia.
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Affiliation(s)
- Xijing Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jianmin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Mei Yang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Tian Tian
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Diagnostic Ultrasound, West China Second University Hospital, Sichuan University, Chengdu, China
- *Correspondence: Tian Tian, ; Ting Hu,
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- *Correspondence: Tian Tian, ; Ting Hu,
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4
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Sreenivasan R, Gonen N, Sinclair A. SOX Genes and Their Role in Disorders of Sex Development. Sex Dev 2022; 16:80-91. [PMID: 35760052 DOI: 10.1159/000524453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 03/29/2022] [Indexed: 11/19/2022] Open
Abstract
SOX genesare master regulatory genes controlling development and are fundamental to the establishment of sex determination in a multitude of organisms. The discovery of the master sex-determining gene SRY in 1990 was pivotal for the understanding of how testis development is initiated in mammals. With this discovery, an entire family of SOX factors were uncovered that play crucial roles in cell fate decisions during development. The importance of SOX genes in human reproductive development is evident from the various disorders of sex development (DSD) upon loss or overexpression of SOX gene function. Here, we review the roles that SOX genes play in gonad development and their involvement in DSD. We start with an overview of sex determination and differentiation, DSDs, and the SOX gene family and function. We then provide detailed information and discussion on SOX genes that have been implicated in DSDs, both at the gene and regulatory level. These include SRY, SOX9, SOX3, SOX8, and SOX10. This review provides insights on the crucial balance of SOX gene expression levels needed for gonad development and maintenance and how changes in these levels can lead to DSDs.
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Affiliation(s)
- Rajini Sreenivasan
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Andrew Sinclair
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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5
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Qiao X, Wu L, Tang J, Xiang R, Fan L, Huang H, Chen Y. Case report: A de novo Non-sense SOX9 mutation (p.Q417*) located in transactivation domain is Responsible for Campomelic Dysplasia. Front Pediatr 2022; 10:1089194. [PMID: 36741086 PMCID: PMC9890166 DOI: 10.3389/fped.2022.1089194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Campomelic dysplasia (CD) is an autosomal dominant skeletal dysplasia syndrome characterized by shortness and bowing of lower extremities, and often accompanied by XY sex reversal. Heterozygous pathogenic variants of SOX9 or rearrangement involving the long arm of chromosome 17 are the causes of disease. However, evidence for pathogenesis of SOX9 haploinsufficiency is insufficient. METHODS We enrolled a Chinese family where the fetus was diagnosed with CD. The affected fetus was selected for whole-exome sequencing to identify the pathogenic mutations in this family. RESULTS After data filtering, a novel non-sense SOX9 variant (NM_000346.3; c.1249C > T; p.Q417*) was identified as the pathogenic lesion in the fetus. Further co-segregation analysis using Sanger sequencing confirmed that this novel SOX9 mutation (c.1249C > T; p.Q417*) was a de novo mutation in the affected fetus. This terminated codon mutation identified by bioinformatics was located at an evolutionarily conserved site of SOX9. The bioinformatics-based analysis predicted this variant was pathogenic and affected SOX9 transactivation activity. CONCLUSION CD is a rare condition, which connected with SOX9 tightly. We identified a novel heterozygous SOX9 variant (p.Q417*) in a Chinese CD family. Our study supports the putative reduced transactivation of SOX9 variants in the pathogenicity of CD.
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Affiliation(s)
- Xingxing Qiao
- Department of Cardiology, Second Xiangya Hospital Central South University, Changsha, China
| | - Liping Wu
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China.,Obstetric Inpatient Department, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Jianjun Tang
- Department of Cardiology, Second Xiangya Hospital Central South University, Changsha, China
| | - Rong Xiang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Liangliang Fan
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Hao Huang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Yaqin Chen
- Department of Cardiology, Second Xiangya Hospital Central South University, Changsha, China
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6
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Atlas G, Sreenivasan R, Sinclair A. Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development. Sex Dev 2021; 15:392-410. [PMID: 34634785 DOI: 10.1159/000519238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 11/19/2022] Open
Abstract
Disorders of sex development (DSD) are a complex group of conditions with highly variable clinical phenotypes, most often caused by failure of gonadal development. DSD are estimated to occur in around 1.7% of all live births. Whilst the understanding of genes involved in gonad development has increased exponentially, approximately 50% of patients with a DSD remain without a genetic diagnosis, possibly implicating non-coding genomic regions instead. Here, we review how variants in the non-coding genome of DSD patients can be identified using techniques such as array comparative genomic hybridization (CGH) to detect copy number variants (CNVs), and more recently, whole genome sequencing (WGS). Once a CNV in a patient's non-coding genome is identified, putative regulatory elements such as enhancers need to be determined within these vast genomic regions. We will review the available online tools and databases that can be used to refine regions with potential enhancer activity based on chromosomal accessibility, histone modifications, transcription factor binding site analysis, chromatin conformation, and disease association. We will also review the current in vitro and in vivo techniques available to demonstrate the functionality of the identified enhancers. The review concludes with a clinical update on the enhancers linked to DSD.
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Affiliation(s)
- Gabby Atlas
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia, .,Department of Endocrinology and Diabetes, Royal Children's Hospital, Melbourne, Victoria, Australia, .,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia,
| | - Rajini Sreenivasan
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Sinclair
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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7
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Kayhan G, Calis P, Karcaaltincaba D, Tug E. Prenatal diagnosis of campomelic dysplasia due to SOX9 deletion. J OBSTET GYNAECOL 2019; 39:1175-1176. [PMID: 31234679 DOI: 10.1080/01443615.2019.1601165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Gulsum Kayhan
- Department of Medical Genetics, Faculty of Medicine, Gazi University , Ankara , Turkey
| | - Pınar Calis
- Department of Obstetrics and Gynecology, Faculty of Medicine, Gazi University , Ankara , Turkey
| | - Deniz Karcaaltincaba
- Department of Obstetrics and Gynecology, Faculty of Medicine, Gazi University , Ankara , Turkey
| | - Esra Tug
- Department of Medical Genetics, Faculty of Medicine, Gazi University , Ankara , Turkey
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8
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Yip RK, Chan D, Cheah KS. Mechanistic insights into skeletal development gained from genetic disorders. Curr Top Dev Biol 2019; 133:343-385. [DOI: 10.1016/bs.ctdb.2019.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Abstract
PURPOSE OF REVIEW The current review focuses on the neonatal presentation of disorders of sex development, summarize the current approach to the evaluation of newborns and describes recent advances in understanding of underlying genetic aetiology of these conditions. RECENT FINDINGS Several possible candidate genes as well as other adverse environmental factors have been described as contributing to several clinical subgroups of 46,XY DSDs. Moreover, registry-based studies showed that infants with suspected DSD may have extragenital anomalies and in 46,XY cases, being small for gestational age (SGA), cardiac and neurological malformations are the commonest concomitant conditions. SUMMARY Considering that children and adults with DSD may be at risk of several comorbidities a clear aetiological diagnosis will guide further management. To date, a firm diagnosis is not reached in over half of the cases of 46,XY DSD. Whilst it is likely that improved diagnostic resources will bridge this gap in the future, the next challenge to the clinical community will be to show that such advances will result in an improvement in clinical care.
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10
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Harel T, Lupski JR. Genomic disorders 20 years on-mechanisms for clinical manifestations. Clin Genet 2017; 93:439-449. [PMID: 28950406 DOI: 10.1111/cge.13146] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/01/2017] [Accepted: 09/21/2017] [Indexed: 12/18/2022]
Abstract
Genomic disorders result from copy-number variants (CNVs) or submicroscopic rearrangements of the genome rather than from single nucleotide variants (SNVs). Diverse technologies, including array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) microarrays, and more recently, whole genome sequencing and whole-exome sequencing, have enabled robust genome-wide unbiased detection of CNVs in affected individuals and in reportedly healthy controls. Sequencing of breakpoint junctions has allowed for elucidation of upstream mechanisms leading to genomic instability and resultant structural variation, whereas studies of the association between CNVs and specific diseases or susceptibility to morbid traits have enhanced our understanding of the downstream effects. In this review, we discuss the hallmarks of genomic disorders as they were defined during the first decade of the field, including genomic instability and the mechanism for rearrangement defined as nonallelic homologous recombination (NAHR); recurrent vs nonrecurrent rearrangements; and gene dosage sensitivity. Moreover, we highlight the exciting advances of the second decade of this field, including a deeper understanding of genomic instability and the mechanisms underlying complex rearrangements, mechanisms for constitutional and somatic chromosomal rearrangements, structural intra-species polymorphisms and susceptibility to NAHR, the role of CNVs in the context of genome-wide copy number and single nucleotide variation, and the contribution of noncoding CNVs to human disease.
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Affiliation(s)
- T Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - J R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
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11
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Baetens D, Mendonça BB, Verdin H, Cools M, De Baere E. Non-coding variation in disorders of sex development. Clin Genet 2017; 91:163-172. [PMID: 27801941 DOI: 10.1111/cge.12911] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/26/2023]
Abstract
Genetic studies in Disorders of Sex Development (DSD), representing a wide spectrum of developmental or functional conditions of the gonad, have mainly been oriented towards the coding genome. Application of genomic technologies, such as whole-exome sequencing, result in a molecular genetic diagnosis in ∼50% of cases with DSD. Many of the genes mutated in DSD encode transcription factors such as SRY, SOX9, NR5A1, and FOXL2, characterized by a strictly regulated spatiotemporal expression. Hence, it can be hypothesized that at least part of the missing genetic variation in DSD can be explained by non-coding mutations in regulatory elements that alter gene expression, either by reduced, mis- or overexpression of their target genes. In addition, structural variations such as translocations, deletions, duplications or inversions can affect the normal chromatin conformation by different mechanisms. Here, we review non-coding defects in human DSD phenotypes and in animal models. The wide variety of non-coding defects found in DSD emphasizes that the regulatory landscape of known and to be discovered DSD genes has to be taken into consideration when investigating the molecular pathogenesis of DSD.
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Affiliation(s)
- D Baetens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - B B Mendonça
- Laboratório de Hormônios e Genética Molecular, LIM/42, Unidade de Adrenal, Disc. de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - H Verdin
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - M Cools
- Department of Pediatrics, Division of Pediatric Endocrinology, Ghent University Hospital and Ghent University, Ghent, Belgium
| | - E De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
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12
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Sreenivasan R, Gordon CT, Benko S, de Iongh R, Bagheri-Fam S, Lyonnet S, Harley V. Altered SOX9 genital tubercle enhancer region in hypospadias. J Steroid Biochem Mol Biol 2017; 170:28-38. [PMID: 27989796 DOI: 10.1016/j.jsbmb.2016.10.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/17/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022]
Abstract
Human mutations in the SOX9 gene or its regulatory region can disrupt testicular development, leading to disorders of sex development (DSDs). Our previous work involving the genomic analysis of isolated DSD patients revealed a 78kb minimal sex determining region (RevSex) far upstream of SOX9 that was duplicated in 46,XX and deleted in 46,XY DSDs. It was postulated that RevSex contains a gonadal enhancer. However, the most highly conserved sub-region within RevSex, called SR4, was neither responsive to sex determining factors in vitro nor active in the gonads of transgenic mice, suggesting that SR4 may not be functioning as a testicular enhancer. Interestingly, SR4 transgenic mice showed reporter activity in the genital tubercle, the primordium of the penis and clitoris, a previously unreported domain of Sox9 expression. SOX9 protein was detected in the genital tubercle, notably in the urethral plate epithelium, preputial glands, ventral surface ectoderm and corpus cavernosa. SR4 may therefore function as a Sox9 genital tubercle enhancer, mutations of which could possibly lead to hypospadias, a birth defect seen in the DSD patients in the RevSex study. SR4 activity and the observed SOX9 expression pattern suggest that SR4 may function as a Sox9 genital tubercle enhancer. However, conditional ablation of Sox9 in the genital tubercle using Shh-Cre/+;Sox9flox/flox mice revealed no genital tubercle abnormalities, possibly due to compensation by similar Sox factors. To conclude, we have identified a novel regulatory enhancer driving Sox9 expression during external genitalia development.
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Affiliation(s)
- Rajini Sreenivasan
- Molecular Genetics and Development, Hudson Institute of Medical Research, Melbourne, Victoria, Australia; Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, Australia; Monash University, Melbourne, Victoria, Australia
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Sabina Benko
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Robb de Iongh
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, Australia
| | - Stefan Bagheri-Fam
- Molecular Genetics and Development, Hudson Institute of Medical Research, Melbourne, Victoria, Australia; Monash University, Melbourne, Victoria, Australia
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Vincent Harley
- Molecular Genetics and Development, Hudson Institute of Medical Research, Melbourne, Victoria, Australia; Monash University, Melbourne, Victoria, Australia.
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13
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Smyk M, Akdemir KC, Stankiewicz P. SOX9 chromatin folding domains correlate with its real and putative distant cis-regulatory elements. Nucleus 2017; 8:182-187. [PMID: 28085555 DOI: 10.1080/19491034.2017.1279776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Evolutionary conserved transcription factor SOX9, encoded by the dosage sensitive SOX9 gene on chromosome 17q24.3, plays an important role in development of multiple organs, including bones and testes. Heterozygous point mutations and genomic copy-number variant (CNV) deletions involving SOX9 have been reported in patients with campomelic dysplasia (CD), a skeletal malformation syndrome often associated with male-to-female sex reversal. Balanced and unbalanced structural genomic variants with breakpoints mapping up to 1.3 Mb up- and downstream to SOX9 have been described in patients with milder phenotypes, including acampomelic campomelic dysplasia, sex reversal, and Pierre Robin sequence. Based on the localization of breakpoints of genomic rearrangements causing different phenotypes, 5 genomic intervals mapping upstream to SOX9 have been defined. We have analyzed the publically available database of high-throughput chromosome conformation capture (Hi-C) in multiple cell lines in the genomic regions flanking SOX9. Consistent with the literature data, chromatin domain boundaries in the SOX9 locus exhibit conservation across species and remain largely constant across multiple cell types. Interestingly, we have found that chromatin folding domains in the SOX9 locus associate with the genomic intervals harboring real and putative regulatory elements of SOX9, implicating that variation in intra-domain interactions may be critical for dynamic regulation of SOX9 expression in a cell type-specific fashion. We propose that tissue-specific enhancers for other transcription factor genes may similarly utilize chromatin folding sub-domains in gene regulation.
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Affiliation(s)
- Marta Smyk
- a Department of Medical Genetics , Institute of Mother and Child , Warsaw , Poland
| | - Kadir Caner Akdemir
- b Genomic Medicine Department , MD Anderson Cancer Center , Houston , TX , USA
| | - Paweł Stankiewicz
- c Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
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14
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Spielmann M, Mundlos S. Looking beyond the genes: the role of non-coding variants in human disease. Hum Mol Genet 2016; 25:R157-R165. [PMID: 27354350 DOI: 10.1093/hmg/ddw205] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/23/2016] [Indexed: 12/20/2022] Open
Abstract
Over the past decades the search for disease causing variants has been focusing exclusively on the coding genome. This highly selective approach has been extremely successful resulting in the identification of thousands of disease genes, but ignores the functional and therefore disease relevance of the rest of the genome. Dropping sequencing costs and new high-throughput technologies such as ChIP-seq and chromosome conformation capture have opened new possibilities for the systematic investigation of the non-coding genome. These data have revealed the importance of non-coding DNA in fundamental processes such as gene regulation and 3D chromatin folding. Research into the principles of chromatin folding has revealed a domain structure of the genome, called topologically associated domains that provide a scaffold for enhancer promoter contacts. Non-coding mutations that affect regulatory elements can affect gene regulation by a loss of function, resulting in reduced gene expression, or a gain of function resulting in gene mis- or overexpression. Structural variations such as deletions, inversions or duplications have the potential to disturb normal chromatin folding. This may lead to the repositioning or disruption of topological associating domains and the relocation of enhancer elements with consecutive gene misexpression. Several recent studies highlight this as important disease mechanisms in developmental disorders and cancer. Therefore, the regulatory landscape of the genome has to be taken into consideration when investigating the pathology of human disease. In this review, we will discuss the recent discoveries in the field of non-coding variation, gene regulation, 3D genome architecture, and their implications for human genetics.
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Affiliation(s)
- Malte Spielmann
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
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15
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Castori M, Bottillo I, Morlino S, Barone C, Cascone P, Grammatico P, Laino L. Variability in a three-generation family with Pierre Robin sequence, acampomelic campomelic dysplasia, and intellectual disability due to a novel ∼1 Mb deletion upstream of SOX9, and including KCNJ2 and KCNJ16. ACTA ACUST UNITED AC 2015; 106:61-8. [PMID: 26663529 DOI: 10.1002/bdra.23463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Campomelic dysplasia and acampomelic campomelic dysplasia (ACD) are allelic disorders due to heterozygous mutations in or around SOX9. Translocations and deletions involving the SOX9 5' regulatory region are rare causes of these disorders, as well as Pierre Robin sequence (PRS) and 46,XY gonadal dysgenesis. Genotype-phenotype correlations are not straightforward due to the complex epigenetic regulation of SOX9 expression during development. METHODS We report a three-generation pedigree with a novel ∼1 Mb deletion upstream of SOX9 and including KCNJ2 and KCNJ16, and ascertained for dominant transmission of PRS. RESULTS Further characterization of the family identified subtle appendicular anomalies and a variable constellation of axial skeletal features evocative of ACD in several members. Affected males showed learning disability. CONCLUSION The identified deletion was smaller than all other chromosome rearrangements associated with ACD. Comparison with other reported translocations and deletions involving this region allowed further refining of genotype-phenotype correlations and an update of the smallest regions of overlap associated with the different phenotypes. Intrafamilial variability in this pedigree suggests a phenotypic continuity between ACD and PRS in patients carrying mutations in the SOX9 5' regulatory region.
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Affiliation(s)
- Marco Castori
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Irene Bottillo
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Silvia Morlino
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Chiara Barone
- Center for Genetic Counseling and Reproductive Teratology, Maternal and Child Health Department, Garibaldi Nesima Hospital, Catania, Italy
| | - Piero Cascone
- Division of Maxillo-Facial Surgery, Sapienza University, Policlinico Umberto I Hospital, Rome, Italy
| | | | - Paola Grammatico
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Luigi Laino
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
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16
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Polla DL, Cardoso MTO, Silva MCB, Cardoso ICC, Medina CTN, Araujo R, Fernandes CC, Reis AMM, de Andrade RV, Pereira RW, Pogue R. Use of Targeted Exome Sequencing for Molecular Diagnosis of Skeletal Disorders. PLoS One 2015; 10:e0138314. [PMID: 26380986 PMCID: PMC4575211 DOI: 10.1371/journal.pone.0138314] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/28/2015] [Indexed: 01/19/2023] Open
Abstract
Genetic disorders of the skeleton comprise a large group of more than 450 clinically distinct and genetically heterogeneous diseases associated with mutations in more than 300 genes. Achieving a definitive diagnosis is complicated due to the genetic heterogeneity of these disorders, their individual rarity and their diverse radiographic presentations. We used targeted exome sequencing and designed a 1.4Mb panel for simultaneous testing of more than 4,800 exons in 309 genes involved in skeletal disorders. DNA from 69 individuals from 66 families with a known or suspected clinical diagnosis of a skeletal disorder was analyzed. Of 36 cases with a specific clinical hypothesis with a known genetic basis, mutations were identified for eight cases (22%). Of 20 cases with a suspected skeletal disorder but without a specific diagnosis, four causative mutations were identified. Also included were 11 cases with a specific skeletal disorder but for which there was at the time no known associated gene. For these cases, one mutation was identified in a known skeletal disease genes, and re-evaluation of the clinical phenotype in this case changed the diagnoses from osteodysplasia syndrome to Apert syndrome. These results suggest that the NGS panel provides a fast, accurate and cost-effective molecular diagnostic tool for identifying mutations in a highly genetically heterogeneous set of disorders such as genetic skeletal disorders. The data also stress the importance of a thorough clinical evaluation before DNA sequencing. The strategy should be applicable to other groups of disorders in which the molecular basis is largely known.
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Affiliation(s)
- Daniel L. Polla
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Maria T. O. Cardoso
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
- Curso de Medicina, Universidade Católica de Brasília, Taguatinga, Distrito Federal, Brazil
| | - Mayara C. B. Silva
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Isabela C. C. Cardoso
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Cristina T. N. Medina
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
| | - Rosenelle Araujo
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
| | - Camila C. Fernandes
- Departamento de Tecnologia, Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Campus Jaboticabal, Jaboticabal, São Paulo, Brazil
| | - Alessandra M. M. Reis
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Rosangela V. de Andrade
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Rinaldo W. Pereira
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Robert Pogue
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- * E-mail:
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17
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Katoh-Fukui Y, Igarashi M, Nagasaki K, Horikawa R, Nagai T, Tsuchiya T, Suzuki E, Miyado M, Hata K, Nakabayashi K, Hayashi K, Matsubara Y, Baba T, Morohashi KI, Igarashi A, Ogata T, Takada S, Fukami M. Testicular dysgenesis/regression without campomelic dysplasia in patients carrying missense mutations and upstream deletion of SOX9. Mol Genet Genomic Med 2015; 3:550-7. [PMID: 26740947 PMCID: PMC4694128 DOI: 10.1002/mgg3.165] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 11/28/2022] Open
Abstract
SOX9 haploinsufficiency underlies campomelic dysplasia (CD) with or without testicular dysgenesis. Current understanding of the phenotypic variability and mutation spectrum of SOX9 abnormalities remains fragmentary. Here, we report three patients with hitherto unreported SOX9 abnormalities. These patients were identified through molecular analysis of 33 patients with 46,XY disorders of sex development (DSD). Patients 1–3 manifested testicular dysgenesis or regression without CD. Patients 1 and 2 carried probable damaging mutations p.Arg394Gly and p.Arg437Cys, respectively, in the SOX9 C‐terminal domain but not in other known 46,XY DSD causative genes. These substitutions were absent from ~120,000 alleles in the exome database. These mutations retained normal transactivating activity for the Col2a1 enhancer, but showed impaired activity for the Amh promoter. Patient 3 harbored a maternally inherited ~491 kb SOX9 upstream deletion that encompassed the known 32.5 kb XY sex reversal region. Breakpoints of the deletion resided within nonrepeat sequences and were accompanied by a short‐nucleotide insertion. The results imply that testicular dysgenesis and regression without skeletal dysplasia may be rare manifestations of SOX9 abnormalities. Furthermore, our data broaden pathogenic SOX9 abnormalities to include C‐terminal missense substitutions which lead to target‐gene‐specific protein dysfunction, and enhancer‐containing upstream microdeletions mediated by nonhomologous end‐joining.
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Affiliation(s)
- Yuko Katoh-Fukui
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Maki Igarashi
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Keisuke Nagasaki
- Division of Pediatrics Department of Homeostatic Regulation and Development Niigata University Graduate School of Medical and Dental Sciences Niigata Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism National Center for Child Health and Development Tokyo Japan
| | - Toshiro Nagai
- Department of Pediatrics Dokkyo Medical University Koshigaya Hospital Koshigaya Japan
| | - Takayoshi Tsuchiya
- Department of Pediatrics Dokkyo Medical University Koshigaya Hospital Koshigaya Japan
| | - Erina Suzuki
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Mami Miyado
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology National Research Institute for Child Health and Development Tokyo Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology National Research Institute for Child Health and Development Tokyo Japan
| | - Keiko Hayashi
- Department of Maternal-Fetal Biology National Research Institute for Child Health and Development Tokyo Japan
| | - Yoichi Matsubara
- National Research Institute for Child Health and Development Tokyo Japan
| | - Takashi Baba
- Department of Molecular Biology Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Ken-Ichirou Morohashi
- Department of Molecular Biology Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Arisa Igarashi
- Department of Systems BioMedicine National Research Institute for Child Health and Development Tokyo Japan
| | - Tsutomu Ogata
- Department of Molecular EndocrinologyNational Research Institute for Child Health and DevelopmentTokyoJapan; Department of PediatricsHamamatsu University School of MedicineHamamatsuJapan
| | - Shuji Takada
- Department of Systems BioMedicine National Research Institute for Child Health and Development Tokyo Japan
| | - Maki Fukami
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
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18
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Zhang F, Lupski JR. Non-coding genetic variants in human disease. Hum Mol Genet 2015; 24:R102-10. [PMID: 26152199 DOI: 10.1093/hmg/ddv259] [Citation(s) in RCA: 356] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/03/2015] [Indexed: 01/16/2023] Open
Abstract
Genetic variants, including single-nucleotide variants (SNVs) and copy number variants (CNVs), in the non-coding regions of the human genome can play an important role in human traits and complex diseases. Most of the genome-wide association study (GWAS) signals map to non-coding regions and potentially point to non-coding variants, whereas their functional interpretation is challenging. In this review, we discuss the human non-coding variants and their contributions to human diseases in the following four parts. (i) Functional annotations of non-coding SNPs mapped by GWAS: we discuss recent progress revealing some of the molecular mechanisms for GWAS signals affecting gene function. (ii) Technical progress in interpretation of non-coding variants: we briefly describe some of the technologies for functional annotations of non-coding variants, including the methods for genome-wide mapping of chromatin interaction, computational tools for functional predictions and the new genome editing technologies useful for dissecting potential functional consequences of non-coding variants. (iii) Non-coding CNVs in human diseases: we review our emerging understanding the role of non-coding CNVs in human disease. (iv) Compound inheritance of large genomic deletions and non-coding variants: compound inheritance at a locus consisting of coding variants plus non-coding ones is described.
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Affiliation(s)
- Feng Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA and Texas Children's Hospital, Houston, TX 77030, USA
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19
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Smyk M, Roeder E, Cheung SW, Szafranski P, Stankiewicz P. A de novo 1.58 Mb deletion, including MAP2K6 and mapping 1.28 Mb upstream to SOX9, identified in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Am J Med Genet A 2015; 167A:1842-50. [PMID: 26059046 DOI: 10.1002/ajmg.a.37057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/23/2015] [Indexed: 12/18/2022]
Abstract
Defects of long-range regulatory elements of dosage-sensitive genes represent an under-recognized mechanism underlying genetic diseases. Haploinsufficiency of SOX9, the gene essential for development of testes and differentiation of chondrocytes, results in campomelic dysplasia, a skeletal malformation syndrome often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.6 Mb up- and downstream to SOX9, and disrupting its distant cis-regulatory elements, have been described in patients with milder forms of campomelic dysplasia, Pierre Robin sequence, and sex reversal. We present an ∼1.58 Mb deletion mapping ∼1.28 Mb upstream to SOX9 that encompasses its putative long-range cis-regulatory element(s) and MAP2K6 in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Low bone mass panel testing using massively parallel sequencing of 23 nuclear genes, including COL1A1 and COL1A2 was negative. Based on the previous mouse model of Map2k6, suggesting that Sox9 is likely a downstream target of the p38 MAPK pathway, and our previous chromosome conformation capture-on-chip (4C) data showing potential interactions between SOX9 promoter and MAP2K6, we hypothesize that deletion of MAP2K6 might have affected SOX9 expression and contributed to our patient's phenotype.
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Affiliation(s)
- Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Elizabeth Roeder
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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20
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Kim GJ, Sock E, Buchberger A, Just W, Denzer F, Hoepffner W, German J, Cole T, Mann J, Seguin JH, Zipf W, Costigan C, Schmiady H, Rostásy M, Kramer M, Kaltenbach S, Rösler B, Georg I, Troppmann E, Teichmann AC, Salfelder A, Widholz SA, Wieacker P, Hiort O, Camerino G, Radi O, Wegner M, Arnold HH, Scherer G. Copy number variation of two separate regulatory regions upstream ofSOX9causes isolated 46,XY or 46,XX disorder of sex development. J Med Genet 2015; 52:240-7. [DOI: 10.1136/jmedgenet-2014-102864] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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21
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Vetro A, Dehghani MR, Kraoua L, Giorda R, Beri S, Cardarelli L, Merico M, Manolakos E, Parada-Bustamante A, Castro A, Radi O, Camerino G, Brusco A, Sabaghian M, Sofocleous C, Forzano F, Palumbo P, Palumbo O, Calvano S, Zelante L, Grammatico P, Giglio S, Basly M, Chaabouni M, Carella M, Russo G, Bonaglia MC, Zuffardi O. Testis development in the absence of SRY: chromosomal rearrangements at SOX9 and SOX3. Eur J Hum Genet 2014; 23:1025-32. [PMID: 25351776 DOI: 10.1038/ejhg.2014.237] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/02/2014] [Accepted: 09/30/2014] [Indexed: 02/01/2023] Open
Abstract
Duplications in the ~2 Mb desert region upstream of SOX9 at 17q24.3 may result in familial 46,XX disorders of sex development (DSD) without any effects on the XY background. A balanced translocation with its breakpoint falling within the same region has also been described in one XX DSD subject. We analyzed, by conventional and molecular cytogenetics, 19 novel SRY-negative unrelated 46,XX subjects both familial and sporadic, with isolated DSD. One of them had a de novo reciprocal t(11;17) translocation. Two cases carried partially overlapping 17q24.3 duplications ~500 kb upstream of SOX9, both inherited from their normal fathers. Breakpoints cloning showed that both duplications were in tandem, whereas the 17q in the reciprocal translocation was broken at ~800 kb upstream of SOX9, which is not only close to a previously described 46,XX DSD translocation, but also to translocations without any effects on the gonadal development. A further XX male, ascertained because of intellectual disability, carried a de novo cryptic duplication at Xq27.1, involving SOX3. CNVs involving SOX3 or its flanking regions have been reported in four XX DSD subjects. Collectively in our cohort of 19 novel cases of SRY-negative 46,XX DSD, the duplications upstream of SOX9 account for ~10.5% of the cases, and are responsible for the disease phenotype, even when inherited from a normal father. Translocations interrupting this region may also affect the gonadal development, possibly depending on the chromatin context of the recipient chromosome. SOX3 duplications may substitute SRY in some XX subjects.
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Affiliation(s)
- Annalisa Vetro
- Biotechnology Research Laboratories, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mohammad Reza Dehghani
- 1] Department of Molecular Medicine, University of Pavia, Pavia, Italy [2] Reproductive Science Institute, Yazd University of Medical Sciences, Yazd, Iran
| | - Lilia Kraoua
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Roberto Giorda
- Molecular Biology Laboratory, Scientific Institute Eugenio Medea, IRCCS, Bosisio Parini (LC), Italy
| | - Silvana Beri
- Molecular Biology Laboratory, Scientific Institute Eugenio Medea, IRCCS, Bosisio Parini (LC), Italy
| | - Laura Cardarelli
- Laboratorio Analisi CITOTEST, Consorzio GENiMED, Sarmeola di Rubano (PD), Italy
| | - Maurizio Merico
- Endocrinologic Unit, San Giacomo Hospital, Castelfranco Veneto (TV), Italy
| | | | - Alexis Parada-Bustamante
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
| | - Andrea Castro
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
| | - Orietta Radi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Marjan Sabaghian
- Department of Andrology at Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, Tehran, Iran
| | | | | | - Pietro Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Savino Calvano
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Leopoldo Zelante
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Paola Grammatico
- Department of Molecular Medicine, Medical Genetics, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Sabrina Giglio
- Medical Genetics Section, Department of Clinical Pathophysiology, University of Florence, Florence, Italy
| | - Mohamed Basly
- Department of Obstetrics and Gynecology, Military Hospital, Tunis, Tunisia
| | - Myriam Chaabouni
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Gianni Russo
- Department of Pediatrics, Endocrine Unit, University Vita-Salute, San Raffaele Hospital, Milano, Italy
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute Eugenio Medea, IRCCS, Bosisio Parini (LC), Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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22
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Bhagavath B, Layman LC, Ullmann R, Shen Y, Ha K, Rehman K, Looney S, McDonough PG, Kim HG, Carr BR. Familial 46,XY sex reversal without campomelic dysplasia caused by a deletion upstream of the SOX9 gene. Mol Cell Endocrinol 2014; 393:1-7. [PMID: 24907458 PMCID: PMC4332518 DOI: 10.1016/j.mce.2014.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 04/26/2014] [Accepted: 05/09/2014] [Indexed: 01/10/2023]
Abstract
BACKGROUND 46,XY sex reversal is a rare disorder and familial cases are even more rare. The purpose of the present study was to determine the molecular basis for a family with three affected siblings who had 46,XY sex reversal. METHODS DNA was extracted from three females with 46,XY sex reversal, two normal sisters, and both unaffected parents. All protein coding exons of the SRY and NR5A1 genes were subjected to PCR-based DNA sequencing. In addition, array comparative genomic hybridization was performed on DNA from all seven family members. A deletion was confirmed using quantitative polymerase chain reaction. Expression of SOX9 gene was quantified using reverse transcriptase polymerase chain reaction. RESULTS A 349kb heterozygous deletion located 353kb upstream of the SOX9 gene on the long arm of chromosome 17 was discovered in the father and three affected siblings, but not in the mother. The expression of SOX9 was significantly decreased in the affected siblings. Two of three affected sisters had gonadoblastomas. CONCLUSION This is the first report of 46,XY sex reversal in three siblings who have a paternally inherited deletion upstream of SOX9 associated with reduced SOX9 mRNA expression.
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Affiliation(s)
- Bala Bhagavath
- Division of Reproductive Endocrinology and Infertility, Department of OB/GYN, University of Rochester Medical Center, Rochester, NY 14642, United States.
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of OB/GYN, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States
| | - Reinhard Ullmann
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Yiping Shen
- Department of Pathology, Children's Hospital Boston, Boston, MA 02115, United States; Department of Laboratory Medicine, Children's Hospital Boston, Boston, MA 02115, United States; Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, China
| | - Kyungsoo Ha
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of OB/GYN, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States
| | - Khurram Rehman
- Overlake Reproductive Health, 11232 NE 15th Street Suite 201, Bellevue, WA 98004, United States
| | - Stephen Looney
- Dept. of Biostatistics and Epidemiology, Georgia Regents University, 1120 15th Street, AE-1014, Augusta, GA 30912-4900, United States; Dept. of Oral Health and Diagnostic Sciences, Georgia Regents University, 1120 15th Street, AE-1014, Augusta, GA 30912-4900, United States
| | - Paul G McDonough
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of OB/GYN, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States
| | - Hyung-Goo Kim
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of OB/GYN, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States
| | - Bruce R Carr
- Division of Reproductive Endocrinology and Infertility, Department of OB/GYN, University of Texas Southwestern Medical Center, Dallas, TX 75235, United States
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23
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Mattos EP, Sanseverino MTV, Magalhães JAA, Leite JCL, Félix TM, Todeschini LA, Cavalcanti DP, Schüler-Faccini L. Clinical and molecular characterization of a Brazilian cohort of campomelic dysplasia patients, and identification of seven new SOX9 mutations. Genet Mol Biol 2014; 38:14-20. [PMID: 25983619 PMCID: PMC4415563 DOI: 10.1590/s1415-475738120140147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/19/2014] [Indexed: 11/21/2022] Open
Abstract
Campomelic dysplasia (CD) is an autosomal, dominantly inherited, skeletal abnormality
belonging to the subgroup of bent bone dysplasias. In addition to bowed lower limbs,
CD typically includes the following: disproportionate short stature, flat face,
micrognathia, cleft palate, bell-shaped thorax, and club feet. Up to three quarters
of 46, XY individuals may be sex-reversed. Radiological signs include scapular and
pubic hypoplasia, narrow iliac wings, spaced ischia, and bowed femora and tibiae.
Lethal CD is usually due to heterozygous mutations in SOX9, a major regulator of
chondrocytic development. We present a detailed clinical and molecular
characterization of nine Brazilian CD patients. Infants were either stillborn (n = 2)
or died shortly after birth and presented similar phenotypes. Sex-reversal was
observed in one of three chromosomally male patients. Sequencing of SOX9 revealed new
heterozygous mutations in seven individuals. Six patients had mutations that resulted
in premature transcriptional termination, while one infant had a single-nucleotide
substitution at the conserved splice-site acceptor of intron 1. No clear
genotype-phenotype correlations were observed. This study highlights the diversity of
SOX9 mutations leading to lethal CD, and expands the group of known genetic
alterations associated with this skeletal dysplasia.
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Affiliation(s)
- Eduardo P Mattos
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil . ; Departamento de Genética, Universidade Federal de Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | | | - Júlio César L Leite
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Temis Maria Félix
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | | | - Denise P Cavalcanti
- Grupo de Displasias Esqueléticas, Departamento de Genética Médica, Faculdade de Medicina, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Lavinia Schüler-Faccini
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil . ; Departamento de Genética, Universidade Federal de Rio Grande do Sul, Porto Alegre, RS, Brazil
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Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
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Lybæk H, de Bruijn D, den Engelsman-van Dijk AHA, Vanichkina D, Nepal C, Brendehaug A, Houge G. RevSex duplication-induced and sex-related differences in the SOX9 regulatory region chromatin landscape in human fibroblasts. Epigenetics 2013; 9:416-27. [PMID: 24351654 PMCID: PMC4053460 DOI: 10.4161/epi.27474] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
It was recently shown that duplications of the RevSex element, located 0.5 Mb upstream of SOX9, cause XX-disorder of sex development (DSD), and that deletions cause XY-DSD. To explore how a 148 kb RevSex duplication could have turned on gonadal SOX9 expression in the absence of SRY in an XX-male, we examined the chromatin landscape in primary skin fibroblast cultures from the index, his RevSex duplication-carrier father and six controls. The ENCODE project supports the notion that chromatin state maps show overlap between different cell types, i.e., that our study of fibroblasts could be of biological relevance. We examined the SOX9 regulatory region by high-resolution ChIP-on-chip experiments (a kind of “chromatin-CGH”) and DNA methylation investigations. The RevSex duplication was associated with chromatin changes predicting better accessibility of the SRY-responsive TESCO enhancer region 14–15 kb upstream of SOX9. Four kb downstream of the TESCO evolutionary conserved region, a peak of the enhancer/promoter-associated H3K4me3 mark was found together with a major dip of the repressive H3K9me3 chromatin mark. Similar differences were also found when three control males were compared with three control females. A marked male/female difference was a more open chromatin signature in males starting ~400 kb upstream of SOX9 and increasing toward the SOX9 promoter. In the RevSex duplication-carrier father, two positions of DNA hypomethylation were also found, one corresponding to the H3K4me3 peak mentioned above. Our results suggest that the RevSex duplication could operate by inducing long-range epigenetic changes. Furthermore, the differences in chromatin state maps between males and females suggest that the Y chromosome or X chromosome dosage may affect chromatin conformation, i.e., that sex-dependent gene regulation may take place by chromatin modification.
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Affiliation(s)
- Helle Lybæk
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen, Norway
| | - Diederik de Bruijn
- Department of Human Genetics; Radboud University Nijmegen Medical Centre; Nijmegen, the Netherlands
| | | | - Darya Vanichkina
- Institute for Molecular Bioscience; University of Queensland; Brisbane, QLD Australia
| | - Chirag Nepal
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen, Norway
| | - Atle Brendehaug
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen, Norway
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen, Norway
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A rare case of 46, XX SRY-negative male with a ∼74-kb duplication in a region upstream of SOX9. Eur J Med Genet 2013; 56:695-8. [DOI: 10.1016/j.ejmg.2013.10.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/02/2013] [Indexed: 11/23/2022]
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Smyk M, Szafranski P, Startek M, Gambin A, Stankiewicz P. Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter. Chromosome Res 2013; 21:781-8. [PMID: 24254229 DOI: 10.1007/s10577-013-9386-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/04/2013] [Accepted: 10/08/2013] [Indexed: 12/27/2022]
Abstract
Evolutionarily conserved transcription factor SOX9 is essential for the differentiation of chondrocytes and the development of testes. Heterozygous point mutations and genomic deletions involving SOX9 lead to campomelic dysplasia (CD), a skeletal malformation syndrome often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.6 Mb up- and downstream to SOX9, and likely disrupting its distant cis-regulatory elements, have been described in patients with milder forms of CD. Based on the location of these aberration breakpoints, four clusters upstream of SOX9 have been defined. Interestingly, we found that each of these intervals overlaps a gene encoding long noncoding RNA (lncRNA), suggesting that lncRNAs may contribute to long-range regulation of SOX9 expression. One of the four upstream regions, RevSex (517-595 kb 5' to SOX9), is associated with sex reversal, and was suggested to harbor a testis-specific and sex-determining enhancer. Another sex-determining interval was mapped to a gene desert >1.3 Mb downstream of SOX9. We have performed chromosome conformation capture-on-chip (4C) analysis in Sertoli cells and lymphoblasts to verify the proposed long-range interactions of the SOX9 promoter and to identify potential novel regulatory elements that might be responsible for sex reversal in patients with CD. We identified several novel potentially cis-interacting regions both up- and downstream to SOX9, with some of them overlapping lncRNA genes. Our data point to lncRNAs as likely mediators of some of these regulatory interactions.
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Affiliation(s)
- Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
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Fonseca ACS, Bonaldi A, Bertola DR, Kim CA, Otto PA, Vianna-Morgante AM. The clinical impact of chromosomal rearrangements with breakpoints upstream of the SOX9 gene: two novel de novo balanced translocations associated with acampomelic campomelic dysplasia. BMC MEDICAL GENETICS 2013; 14:50. [PMID: 23648064 PMCID: PMC3658899 DOI: 10.1186/1471-2350-14-50] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 04/23/2013] [Indexed: 12/31/2022]
Abstract
BACKGROUND The association of balanced rearrangements with breakpoints near SOX9 [SRY (sex determining region Y)-box 9] with skeletal abnormalities has been ascribed to the presumptive altering of SOX9 expression by the direct disruption of regulatory elements, their separation from SOX9 or the effect of juxtaposed sequences. CASE PRESENTATION We report on two sporadic apparently balanced translocations, t(7;17)(p13;q24) and t(17;20)(q24.3;q11.2), whose carriers have skeletal abnormalities that led to the diagnosis of acampomelic campomelic dysplasia (ACD; MIM 114290). No pathogenic chromosomal imbalances were detected by a-CGH. The chromosome 17 breakpoints were mapped, respectively, 917-855 kb and 601-585 kb upstream of the SOX9 gene. A distal cluster of balanced rearrangements breakpoints on chromosome 17 associated with SOX9-related skeletal disorders has been mapped to a segment 932-789 kb upstream of SOX9. In this cluster, the breakpoint of the herein described t(17;20) is the most telomeric to SOX9, thus allowing the redefining of the telomeric boundary of the distal breakpoint cluster region related to skeletal disorders to 601-585 kb upstream of SOX9. Although both patients have skeletal abnormalities, the t(7;17) carrier presents with relatively mild clinical features, whereas the t(17;20) was detected in a boy with severe broncheomalacia, depending on mechanical ventilation. Balanced and unbalanced rearrangements associated with disorders of sex determination led to the mapping of a regulatory region of SOX9 function on testicular differentiation to a 517-595 kb interval upstream of SOX9, in addition to TESCO (Testis-specific enhancer of SOX9 core). As the carrier of t(17;20) has an XY sex-chromosome constitution and normal male development for his age, the segment of chromosome 17 distal to the translocation breakpoint should contain the regulatory elements for normal testis development. CONCLUSIONS These two novel translocations illustrate the clinical variability in carriers of balanced translocations with breakpoints near SOX9. The translocation t(17;20) breakpoint provides further evidence for an additional testis-specific SOX9 enhancer 517 to 595 kb upstream of the SOX9 gene.
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Affiliation(s)
- Ana Carolina S Fonseca
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, Brazil
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29
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Amarillo IE, Dipple KM, Quintero-Rivera F. Familial microdeletion of 17q24.3 upstream of SOX9 is associated with isolated Pierre Robin sequence due to position effect. Am J Med Genet A 2013; 161A:1167-72. [PMID: 23532965 DOI: 10.1002/ajmg.a.35847] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/13/2012] [Indexed: 11/12/2022]
Abstract
Pierre Robin sequence (PRS) is a malformation pattern characterized by the core triad of retrognathia, glossoptosis, and cleft palate that causes difficulty in glossopharyngeal-laryngeal-vagal functions. The etiology of PRS remains largely unknown; previous reports have suggested that it is caused by intrauterine constriction or external conditions such as oligohydramnios, breech position, or abnormal uterine anatomy. Genetic causes include occurrence as a manifestation of many single gene conditions and chromosomal rearrangements. Positional effect on some loci or genes, including SOX9 has also been posited as a cause. Here, we report on an 18-month-old girl born with isolated PRS. Clinical chromosome microarray analysis (CMA) revealed a maternally inherited ~623 kb microdeletion that is -725 kb upstream of 5' SOX9 at chromosome locus 17q24.3. Her mother had cleft palate. This region, although devoid of any genes, is known to have a position effect on SOX9 due to elimination of highly conserved non-coding cis-regulatory elements. This report supports the evidence that deregulation of an intact SOX9 coding region is a cause of or associated with isolated PRS, and provides further evidence that CMA in the clinical setting is a powerful tool in detecting microdeletions in gene "desert" regions that have pathogenic position effect on specific genes.
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Affiliation(s)
- Ina E Amarillo
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90024, USA
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30
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Scherer G, Zabel B, Nishimura G. Clinical Utility Gene Card for: campomelic dysplasia. Eur J Hum Genet 2012; 21:ejhg2012228. [PMID: 23047745 DOI: 10.1038/ejhg.2012.228] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Gerd Scherer
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany.
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31
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Verhagen JM, Diderich KE, Oudesluijs G, Mancini GM, Eggink AJ, Verkleij-Hagoort AC, Groenenberg IA, Willems PJ, du Plessis FA, de Man SA, Srebniak MI, van Opstal D, Hulsman LO, van Zutven LJ, Wessels MW. Phenotypic variability of atypical 22q11.2 deletions not includingTBX1. Am J Med Genet A 2012; 158A:2412-20. [DOI: 10.1002/ajmg.a.35517] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/10/2012] [Indexed: 11/09/2022]
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Abstract
Disorders of sex development (DSD) are congenital conditions in which the development of chromosomal, gonadal, or anatomical sex is atypical. Many of the genes required for gonad development have been identified by analysis of DSD patients. However, the use of knockout and transgenic mouse strains have contributed enormously to the study of gonad gene function and interactions within the development network. Although the genetic basis of mammalian sex determination and differentiation has advanced considerably in recent years, a majority of 46,XY gonadal dysgenesis patients still cannot be provided with an accurate diagnosis. Some of these unexplained DSD cases may be due to mutations in novel DSD genes or genomic rearrangements affecting regulatory regions that lead to atypical gene expression. Here, we review our current knowledge of mammalian sex determination drawing on insights from human DSD patients and mouse models.
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Affiliation(s)
- Stefanie Eggers
- Murdoch Children’s Research Institute, Royal Children’s Hospital and Department of Paediatrics, The University of Melbourne, Melbourne, VIC Australia
| | - Andrew Sinclair
- Murdoch Children’s Research Institute, Royal Children’s Hospital and Department of Paediatrics, The University of Melbourne, Melbourne, VIC Australia
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Fukami M, Tsuchiya T, Takada S, Kanbara A, Asahara H, Igarashi A, Kamiyama Y, Nishimura G, Ogata T. Complex genomic rearrangement in theSOX95′ region in a patient with Pierre Robin sequence and hypoplastic left scapula. Am J Med Genet A 2012; 158A:1529-34. [DOI: 10.1002/ajmg.a.35308] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 02/03/2012] [Indexed: 11/09/2022]
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34
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Abstract
During the past decade, widespread use of microarray-based technologies, including oligonucleotide array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) genotyping arrays have dramatically changed our perspective on genome-wide structural variation. Submicroscopic genomic rearrangements or copy-number variation (CNV) have proven to be an important factor responsible for primate evolution, phenotypic differences between individuals and populations, and susceptibility to many diseases. The number of diseases caused by chromosomal microdeletions and microduplications, also referred to as genomic disorders, has been increasing at a rapid pace. Microdeletions and microduplications are found in patients with a wide variety of phenotypes, including Mendelian diseases as well as common complex traits, such as developmental delay/intellectual disability, autism, schizophrenia, obesity, and epilepsy. This chapter provides an overview of common microdeletion and microduplication syndromes and their clinical phenotypes, and discusses the genomic structures and molecular mechanisms of formation. In addition, an explanation for how these genomic rearrangements convey abnormal phenotypes is provided.
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Affiliation(s)
- Lisenka E L M Vissers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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35
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Klopocki E, Mundlos S. Copy-number variations, noncoding sequences, and human phenotypes. Annu Rev Genomics Hum Genet 2011; 12:53-72. [PMID: 21756107 DOI: 10.1146/annurev-genom-082410-101404] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Whereas single-nucleotide polymorphisms and their role in predisposition to disease have been studied extensively, the analysis of structural variants--genomic changes such as insertions, deletions, inversions, duplications, and translocations--is still in its infancy. Changes in copy number, also known as copy-number variations (CNVs), constitute one such group of these structural variants. CNVs are structural genomic variants that arise from deletions (loss) or duplications (gain), and as a consequence result in a copy-number change of the respective genomic region. CNVs may include entire genes or regions of transcribed sequence, or, indeed, comprise only nontranscribed sequences. Whereas the duplication or deletion of a gene can be expected to have an effect on gene dosage, the consequences of CNVs in nontranscribed sequences are less obvious. Here we review CNVs that involve regulatory nontranscribed regions of the genome, describe the associated human phenotypes, and discuss possible disease mechanisms.
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Affiliation(s)
- Eva Klopocki
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany.
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36
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Benko S, Gordon CT, Amiel J, Lyonnet S. [Cis-ruptions of highly conserved non-coding genomic elements distant from the SOX9 gene in the Pierre Robin sequence]. Biol Aujourdhui 2011; 205:111-124. [PMID: 21831342 DOI: 10.1051/jbio/2011010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Indexed: 05/31/2023]
Abstract
Major developmental genes, exhibiting complex expression patterns, are often embedded within a genic desert particularly rich in regions, which though non-coding are highly conserved. The developmental expression of these genes in many areas requires coordinated regulation in time and space, which is orchestrated by some of these conserved non-coding regions, acting as transcriptional regulators. SOX9 is an essential gene for many developmental processes, such as chondrogenesis, migration and differentiation of neural crest cells and testis development. In agreement with these major expression areas, SOX9 haploinsufficiency, linked to alterations in coding sequence, leads to a polymorphic malformation syndrome - campomelic dysplasia - whose major symptoms are a bone anomaly, a Pierre Robin sequence, and a sexual differentiation anomaly (Disorder of Sex Development, DSD). SOX9 is located in a ~2.5 Mb gene desert extremely rich in conserved sequences. We have used the SOX9 locus and campomelic dysplasia as a model to show that one or several endophenotypes within a complex syndrome may arise from a tissue-specific deregulation of a major developmental gene transcription. Our work has focused on one of these endophenotypes, SPR, characterized by the triad micro- and/or retrognathy, glossoptosis and cleft palate. Here we report in detail how we identified alterations (translocations, deletions, point mutations) in non-coding regions, located far away (more than 1.2 Mb) upstream and downstream of SOX9, in clustered or sporadic SPR cases.
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Affiliation(s)
- Sabina Benko
- Département de génétique, Université Paris Descartes et Inserm U-781, Hôpital Necker-Enfants Malades, Paris Cedex, France
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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] [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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38
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Zarate YA, Dwivedi A, Bartel FO, Corning K, Dupont BR. 47, XY, +der(Y),t(X;Y)(p21.1;p11.2): a unique case of XY sex reversal. Am J Med Genet A 2010; 155A:386-91. [PMID: 21271659 DOI: 10.1002/ajmg.a.33799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 10/18/2010] [Indexed: 11/06/2022]
Abstract
Translocations involving the short arms of the X and Y chromosomes are rare and can result in a functional disomy of the short arm of the X chromosome, including the dosage-sensitive sex reversal (DSS) locus. A result of such imbalance may be sex reversal with multiple congenital anomalies. We present the clinical and cytogenetic evaluation of a newborn infant with DSS and additional clinical findings of minor facial anomalies, left abdominal mass, 5th finger clinodactyly, and mild hypotonia. The external genitalia appeared to be normal female. The infant had bilateral corneal opacities and findings suggestive of anterior segment dysgenesis. Ultrasonography showed a small uterus with undetectable ovaries, and a left multicystic dysplastic kidney. High-resolution chromosome analysis identified the presence of a derivative Y chromosome, 47,XY, +der(Y)t(X;Y)(p21.1;p11.2), which was confirmed by fluorescence in situ hybridization studies. Array CGH showed a 35.1 Mb copy number gain of chromosome region Xp22.33-p21.1 and a 52.2 Mb copy number gain of Yp11.2-qter, in addition to the intact X and Y chromosomes. Previously reported patients with XY sex reversal have not had DSS with corneal opacities, dysgenesis of the anterior segment of the eye, and unilateral multicystic dysplastic kidney. These findings represent a new form of XY sex reversal due to an Xp duplication.
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Affiliation(s)
- Yuri A Zarate
- Greenwood Genetic Center, Greenwood, South Carolina, USA.
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39
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Ledig S, Hiort O, Scherer G, Hoffmann M, Wolff G, Morlot S, Kuechler A, Wieacker P. Array-CGH analysis in patients with syndromic and non-syndromic XY gonadal dysgenesis: evaluation of array CGH as diagnostic tool and search for new candidate loci. Hum Reprod 2010; 25:2637-46. [PMID: 20685758 DOI: 10.1093/humrep/deq167] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND XY gonadal dysgenesis (XY-GD) is a heterogeneous disorder characterized by failure of testicular development despite a normal male karyotype. Non-syndromic and syndromic forms can be delineated. Currently, only a minority of cases can be explained by gene mutations. METHODS The aim of this study was to detect microdeletions and duplications by using high-resolution Agilent oligonucleotide arrays in a cohort of 87 patients with syndromic or non-syndromic 46,XY-GD. RESULTS In 26 patients, we identified gains or losses in regions including genes involved in XY-GD (DMRT1, SOX9, DAX1) or in regions, which have not been described as polymorphic copy number variants (CNVs). CONCLUSIONS This study shows that array comparative genomic hybridization (CGH) analysis is a useful tool for the molecular diagnosis of XY-GD as well as for the identification of potential candidate genes involved in male sexual development.
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Affiliation(s)
- S Ledig
- Institute of Human Genetics, Westfälische Wilhelms Universität Münster, Vesaliusweg 12-14, 48149 Münster, Germany
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40
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Stankiewicz P, Pursley AN, Cheung SW. Challenges in clinical interpretation of microduplications detected by array CGH analysis. Am J Med Genet A 2010; 152A:1089-100. [DOI: 10.1002/ajmg.a.33216] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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41
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Refai O, Friedman A, Terry L, Jewett T, Pearlman A, Perle MA, Ostrer H. De novo 12;17 translocation upstream ofSOX9resulting in 46,XX testicular disorder of sex development. Am J Med Genet A 2010; 152A:422-6. [DOI: 10.1002/ajmg.a.33201] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Wada Y, Nishimura G, Nagai T, Sawai H, Yoshikata M, Miyagawa S, Hanita T, Sato S, Hasegawa T, Ishikawa S, Ogata T. Mutation analysis ofSOX9and single copy number variant analysis of the upstream region in eight patients with campomelic dysplasia and acampomelic campomelic dysplasia. Am J Med Genet A 2009; 149A:2882-5. [DOI: 10.1002/ajmg.a.33107] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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43
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Lecointre C, Pichon O, Hamel A, Heloury Y, Michel-Calemard L, Morel Y, David A, Le Caignec C. Familial acampomelic form of campomelic dysplasia caused by a 960 kb deletion upstream of SOX9. Am J Med Genet A 2009; 149A:1183-9. [PMID: 19449405 DOI: 10.1002/ajmg.a.32830] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Campomelic dysplasia (CD) is a rare autosomal dominant osteochondrodysplasia with or without XY disorders of sexual development (DSD). Campomelia is absent in about 10% of the cases, referred to as the acampomelic form of CD (ACD). Most CDs are caused by mutations within the SOX9 coding region. Several CD patients with balanced chromosome rearrangements involving the 17q24 region have been reported suggesting the presence of cis-regulatory elements upstream and/or downstream of the gene. Deletions upstream of SOX9 represent a third mechanism of mutation. To date, a 1.5 Mb de novo deletion in the SOX9 upstream region has been identified in a single 46,XY patient with ACD and DSD. We report here for the first time on a familial ACD caused by an inherited deletion mapping upstream of the SOX9 gene. Using high-density oligoarray comparative genomic hybridization (CGH), we showed that the size of the deletion was 960 kb in the XY-DSD child and her mother, both affected. The deletion lying from 517 kb to 1.477 Mb upstream of SOX9 remove several highly conserved elements and reduce the minimum critical size and therefore the number of highly conserved sequence elements responsible for ACD.
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Kleinjan DA, Lettice LA. Long-range gene control and genetic disease. ADVANCES IN GENETICS 2008; 61:339-88. [PMID: 18282513 DOI: 10.1016/s0065-2660(07)00013-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past two decades have seen great progress in the elucidation of the genetic basis of human genetic disease. Many clinical phenotypes have been linked with mutations or deletions in specific causative genes. However, it is often less recognized that in addition to the integrity of the protein-coding sequences, human health critically also depends on the spatially, temporally, and quantitatively correct expression of those genes. Genetic disease can therefore equally be caused by disruption of the regulatory mechanisms that ensure proper gene expression. The term "position effect" is used in those situations where the expression level of a gene is deleteriously affected by an alteration in its chromosomal environment, while maintaining an intact transcription unit. Here, we review recent advances in our understanding of the possible mechanisms of a number of "position effect" disease cases and discuss the findings with respect to current models for genome organization and long-range control of gene expression.
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Affiliation(s)
- Dirk A Kleinjan
- MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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Izumi K, Nakano M, Kosaki K, Kosaki R, Hosogai N, Matsumoto H, Hasegawa T, Takahashi T, Kosaki K. Two distinctive mechanisms leading to disruption of the SHOX transcription unit in a single family. Am J Med Genet A 2007; 143A:2838-42. [PMID: 17994568 DOI: 10.1002/ajmg.a.31870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kosuke Izumi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
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Jakobsen LP, Ullmann R, Christensen SB, Jensen KE, Mølsted K, Henriksen KF, Hansen C, Knudsen MA, Larsen LA, Tommerup N, Tümer Z. Pierre Robin sequence may be caused by dysregulation of SOX9 and KCNJ2. J Med Genet 2007; 44:381-6. [PMID: 17551083 PMCID: PMC2740883 DOI: 10.1136/jmg.2006.046177] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND The Pierre Robin sequence (PRS), consisting of cleft palate, micrognathia and glossoptosis, can be seen as part of the phenotype in other Mendelian syndromes--for instance, campomelic dysplasia (CD) which is caused by SOX9 mutations--but the aetiology of non-syndromic PRS has not yet been unravelled. OBJECTIVE To gain more insight into the aetiology of PRS by studying patients with PRS using genetic and cytogenetic methods. METHODS 10 unrelated patients with PRS were investigated by chromosome analyses and bacterial artificial chromosome arrays. A balanced translocation was found in one patient, and the breakpoints were mapped with fluorescence in situ hybridisation and Southern blot analysis. All patients were screened for SOX9 and KCNJ2 mutations, and in five of the patients expression analysis of SOX9 and KCNJ2 was carried out by quantitative real-time PCR. RESULTS An abnormal balanced karyotype 46,XX, t(2;17)(q23.3;q24.3) was identified in one patient with PRS and the 17q breakpoint was mapped to 1.13 Mb upstream of the transcription factor SOX9 and 800 kb downstream of the gene KCNJ2. Furthermore, a significantly reduced SOX9 and KCNJ2 mRNA expression was observed in patients with PRS. CONCLUSION Our findings suggest that non-syndromic PRS may be caused by both SOX9 and KCNJ2 dysregulation.
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MESH Headings
- Adolescent
- Base Pairing/genetics
- Child
- Child, Preschool
- Chromosome Breakage
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 2/genetics
- Female
- Gene Expression Regulation
- High Mobility Group Proteins/genetics
- High Mobility Group Proteins/metabolism
- Humans
- In Situ Hybridization, Fluorescence
- Lymphocytes/metabolism
- Male
- Pierre Robin Syndrome/genetics
- Potassium Channels, Inwardly Rectifying/genetics
- Potassium Channels, Inwardly Rectifying/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- SOX9 Transcription Factor
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Translocation, Genetic
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Smyk M, Berg JS, Pursley A, Curtis FK, Fernandez BA, Bien-Willner GA, Lupski JR, Cheung SW, Stankiewicz P. Male-to-female sex reversal associated with an ∼250 kb deletion upstream of NR0B1 (DAX1). Hum Genet 2007; 122:63-70. [PMID: 17503084 DOI: 10.1007/s00439-007-0373-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Accepted: 04/24/2007] [Indexed: 10/23/2022]
Abstract
Deletion of the dosage sensitive gene NR0B1 encoding DAX1 on chromosome Xp21.2 results in congenital adrenal hypoplasia (AHC), whereas NR0B1 duplication in 46,XY individuals leads to gonadal dysgenesis and a female phenotype. We describe a 21-year-old 46,XY female manifesting primary amenorrhea, a small immature uterus, gonadal dysgenesis, and notably absent adrenal insufficiency with a submicroscopic (257 kb) deletion upstream of NR0B1. We hypothesize that loss of regulatory sequences may have resulted in position effect up-regulation of DAX1 expression, consistent with phenotypic consequences of NR0B1 duplication. We propose that this genomic region and by extension those surrounding the dosage sensitive SRY, SOX9, SF1, and WNT-4 genes, should be examined for copy-number variation in patients with sex reversal.
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Affiliation(s)
- Marta Smyk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Bien-Willner GA, Stankiewicz P, Lupski JR. SOX9cre1, a cis-acting regulatory element located 1.1 Mb upstream of SOX9, mediates its enhancement through the SHH pathway. Hum Mol Genet 2007; 16:1143-56. [PMID: 17409199 DOI: 10.1093/hmg/ddm061] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SOX9 is a temporal and tissue-specific transcription factor involved in male sexual development and bone formation. Haploinsufficiency of SOX9 is known to cause campomelic dysplasia (CD). CD cases without SOX9 coding region mutations have been described in association with translocations that have breakpoints mapping as far as 932 kb upstream from the gene. These rearrangements suggest that position effects acting from a great distance regulate SOX9 gene expression. Studies of one such case (900 kb upstream to SOX9) have led to the delineation of a potential 2.1 kb cis-acting regulatory element 1.1 Mb upstream of SOX9, termed SOX9cre1. We investigated the role of this putative regulator in SOX9 expression. SOX9cre1 increases the activity of a minimal SOX9 promoter in reporter constructs in a dose-dependent and tissue-specific manner, consistent with an enhancer role. In silico studies identify a putative binding site within SOX9cre1 for GLI1, a downstream mediator of sonic hedgehog (SHH). Furthermore, the stimulation of primary human chondrocyte cells in culture with SHH increases endogenous SOX9 expression 3-fold. Electrophoresis mobility shift assay (EMSA) studies that demonstrate physical interactions between the GLI1 transcription factor and a putative binding site within SOX9cre1, as well as experiments in which reporter constructs are co-transfected with GLI1, suggest a direct interaction between GLI1 and SOX9cre1. GLI1-SOX9cre1 interactions are verified in chromatin immunoprecipitation experiments. These data support a direct molecular link between the Hh signaling pathway and SOX9 regulation, wherein SHH stimulates SOX9 through its mediator GLI1, and are consistent with a mechanism of SOX9 regulation through distal chromatin interactions.
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Affiliation(s)
- Gabriel A Bien-Willner
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Leipoldt M, Erdel M, Bien-Willner GA, Smyk M, Theurl M, Yatsenko SA, Lupski JR, Lane AH, Shanske AL, Stankiewicz P, Scherer G. Two novel translocation breakpoints upstream of SOX9 define borders of the proximal and distal breakpoint cluster region in campomelic dysplasia. Clin Genet 2007; 71:67-75. [PMID: 17204049 DOI: 10.1111/j.1399-0004.2007.00736.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The semilethal skeletal malformation syndrome campomelic dysplasia (CD) with or without XY sex reversal is caused by mutations within the SOX9 gene on 17q24.3 or by chromosomal aberrations (translocations, inversions or deletions) with breakpoints outside the SOX9 coding region. The previously published CD translocation breakpoints upstream of SOX9 fall into two clusters: a proximal cluster with breakpoints between 50-300 kb and a distal cluster with breakpoints between 899-932 kb. Here, we present clinical, cytogenetic and molecular data from two novel CD translocation cases. Case 1 with karyotype 46,XY,t(1;17)(q42.1;q24.3) has characteristic symptoms of CD, including mild tibial bowing, cryptorchidism and hypospadias. By standard fluorescence in situ hybridization (FISH) and by high-resolution fiber FISH, the 17q breakpoint was mapped 375 kb from SOX9, defining the centromeric border of the proximal breakpoint cluster region. Case 2 with karyotype 46,X,t(Y;17)(q11.2;q24.3) has the acampomelic form of CD and complete XY sex reversal. By FISH and somatic cell hybrid analysis, the 17q breakpoint was mapped 789 kb from SOX9, defining the telomeric border of the distal breakpoint cluster region. We discuss the structure of the 1 Mb cis-control region upstream of SOX9 and the correlation between the position of the 14 mapped translocation breakpoints with respect to disease severity and XY sex reversal.
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Affiliation(s)
- M Leipoldt
- Institute of Human Genetics and Anthropology, University of Freiburg, Freiburg, Germany
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Smyk M, Obersztyn E, Nowakowska B, Bocian E, Cheung SW, Mazurczak T, Stankiewicz P. RecurrentSOX9 deletion campomelic dysplasia due to somatic mosaicism in the father. Am J Med Genet A 2007; 143A:866-70. [PMID: 17352389 DOI: 10.1002/ajmg.a.31631] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Haploinsufficiency of SOX9, a master gene in chondrogenesis and testis development, leads to the semi-lethal skeletal malformation syndrome campomelic dysplasia (CD), with or without XY sex reversal. We report on two children with CD and a phenotypically normal father, a carrier of a somatic mosaic SOX9 deletion. This is the first report of a mosaic deletion of SOX9; few familial CD cases with germline and somatic mutation mosaicism have been described. Our findings confirm the utility of aCGH and indicate that for a more accurate estimate of the recurrence risk for a completely penetrant autosomal dominant disorder, parental somatic mosaicism should be considered in healthy parents.
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Affiliation(s)
- M Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
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