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Fonova EA, Tolmacheva EN, Kashevarova AA, Sazhenova EA, Nikitina TV, Lopatkina ME, Vasilyeva OY, Zarubin AА, Aleksandrova TN, Yuriev SY, Skryabin NA, Stepanov VA, Lebedev IN. Skewed X-Chromosome Inactivation as a Possible Marker of X-Linked CNV in Women with Pregnancy Loss. Cytogenet Genome Res 2022; 162:97-108. [PMID: 35636401 DOI: 10.1159/000524342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
Skewed X-chromosome inactivation (sXCI) can be a marker of lethal genetic variants on the X chromosome in a woman since sXCI modifies the pathological phenotype. The aim of this study was to search for CNVs in women with miscarriages and sXCI. XCI was assayed using the classical method based on the amplification of highly polymorphic exon 1 of the androgen receptor (AR) gene. The XCI status was analysed in 313 women with pregnancy loss and in 87 spontaneously aborted embryos with 46,XX karyotype, as well as in control groups of 135 women without pregnancy loss and 64 embryos with 46,XX karyotype from induced abortions in women who terminated a normal pregnancy. The frequency of sXCI differed significantly between women with miscarriages and women without pregnancy losses (6.3% and 2.2%, respectively; p = 0.019). To exclude primary causes of sXCI, sequencing of the XIST and XACT genes was performed. The XIST and XACT gene sequencing revealed no known pathogenic variants that could lead to sXCI. Molecular karyotyping was performed using aCGH, followed by verification of X-linked CNVs by RT-PCR and MLPA. Microdeletions at Xp11.23 and Xq24 as well as gains of Xq28 were detected in women with sXCI and pregnancy loss.
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Affiliation(s)
- Elizaveta A Fonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Anna A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Elena A Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Tatyana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Maria E Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Oksana Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Aleksei А Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Tatyana N Aleksandrova
- Department of Obstetrics and Gynecology, Siberian State Medical University, Tomsk, Russian Federation
| | - Sergey Yu Yuriev
- Department of Obstetrics and Gynecology, Siberian State Medical University, Tomsk, Russian Federation
| | - Nikolay A Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Vadim A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
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Moosmann J, Uebe S, Dittrich S, Rüffer A, Ekici AB, Toka O. Novel loci for non-syndromic coarctation of the aorta in sporadic and familial cases. PLoS One 2015; 10:e0126873. [PMID: 25984793 PMCID: PMC4436177 DOI: 10.1371/journal.pone.0126873] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/08/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Coarctation of the aorta (CoA) accounts for 5-8% of all congenital heart defects. CoA can be detected in up to 20% of patients with Ullrich-Turner syndrome (UTS), in which a part or all of one of the X chromosomes is absent. The etiology of non-syndromic CoA is poorly understood. In the present work, we test the hypothesis that rare copy number variation (CNV) especially on the gonosomes, contribute to the etiology of non-syndromic CoA. METHODS We performed high-resolution genome-wide CNV analysis using the Affymetrix SNP 6.0 microarray platform for 70 individuals with sporadic CoA, 3 families with inherited CoA (n=13) and 605 controls. Our analysis comprised genome wide association, CNV burden and linkage. CNV was validated by multiplex ligation-dependent probe amplification. RESULTS We identified a significant abundance of large (>100 kb) CNVs on the X chromosome in males with CoA (p=0.005). 11 out of 51 (~ 22%) male cases had these large CNVs. Association analysis in the sporadic cohort revealed 14 novel loci for CoA. The locus on 21q22.3 in the sporadic CoA cohort overlapped with a gene locus identified in all familial cases of CoA (candidate gene TRPM2). We identified one CNV locus within a locus with high multipoint LOD score from a linkage analysis of the familial cases (SEPT9); another locus overlapped with a region implicated in Kabuki syndrome. In the familial cases, we identified a total of 7 CNV loci that were exclusively present in cases but not in unaffected family members. CONCLUSION Of all candidate loci identified, the TRPM2 locus was the most frequently implicated autosomal locus in sporadic and familial cases. However, the abundance of large CNVs on the X chromosome of affected males suggests that gonosomal aberrations are not only responsible for syndromic CoA but also involved in the development of sporadic and non-syndromic CoA and their male dominance.
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Affiliation(s)
- Julia Moosmann
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Pediatric Cardiology, Loschgestraße 15, 91054 Erlangen, Germany
| | - Steffen Uebe
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Sven Dittrich
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Pediatric Cardiology, Loschgestraße 15, 91054 Erlangen, Germany
| | - André Rüffer
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Pediatric Cardiac Surgery, Loschgestraße 15, 91054 Erlangen, Germany
| | - Arif B. Ekici
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Okan Toka
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Pediatric Cardiology, Loschgestraße 15, 91054 Erlangen, Germany
- * E-mail:
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Lopes AM, Aston KI, Thompson E, Carvalho F, Gonçalves J, Huang N, Matthiesen R, Noordam MJ, Quintela I, Ramu A, Seabra C, Wilfert AB, Dai J, Downie JM, Fernandes S, Guo X, Sha J, Amorim A, Barros A, Carracedo A, Hu Z, Hurles ME, Moskovtsev S, Ober C, Paduch DA, Schiffman JD, Schlegel PN, Sousa M, Carrell DT, Conrad DF. Human spermatogenic failure purges deleterious mutation load from the autosomes and both sex chromosomes, including the gene DMRT1. PLoS Genet 2013; 9:e1003349. [PMID: 23555275 PMCID: PMC3605256 DOI: 10.1371/journal.pgen.1003349] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 01/17/2013] [Indexed: 01/17/2023] Open
Abstract
Gonadal failure, along with early pregnancy loss and perinatal death, may be an important filter that limits the propagation of harmful mutations in the human population. We hypothesized that men with spermatogenic impairment, a disease with unknown genetic architecture and a common cause of male infertility, are enriched for rare deleterious mutations compared to men with normal spermatogenesis. After assaying genomewide SNPs and CNVs in 323 Caucasian men with idiopathic spermatogenic impairment and more than 1,100 controls, we estimate that each rare autosomal deletion detected in our study multiplicatively changes a man's risk of disease by 10% (OR 1.10 [1.04–1.16], p<2×10−3), rare X-linked CNVs by 29%, (OR 1.29 [1.11–1.50], p<1×10−3), and rare Y-linked duplications by 88% (OR 1.88 [1.13–3.13], p<0.03). By contrasting the properties of our case-specific CNVs with those of CNV callsets from cases of autism, schizophrenia, bipolar disorder, and intellectual disability, we propose that the CNV burden in spermatogenic impairment is distinct from the burden of large, dominant mutations described for neurodevelopmental disorders. We identified two patients with deletions of DMRT1, a gene on chromosome 9p24.3 orthologous to the putative sex determination locus of the avian ZW chromosome system. In an independent sample of Han Chinese men, we identified 3 more DMRT1 deletions in 979 cases of idiopathic azoospermia and none in 1,734 controls, and found none in an additional 4,519 controls from public databases. The combined results indicate that DMRT1 loss-of-function mutations are a risk factor and potential genetic cause of human spermatogenic failure (frequency of 0.38% in 1306 cases and 0% in 7,754 controls, p = 6.2×10−5). Our study identifies other recurrent CNVs as potential causes of idiopathic azoospermia and generates hypotheses for directing future studies on the genetic basis of male infertility and IVF outcomes. Infertility is a disease that prevents the transmission of DNA from one generation to the next, and consequently it has been difficult to study the genetics of infertility using classical human genetics methods. Now, new technologies for screening entire genomes for rare and patient-specific mutations are revolutionizing our understanding of reproductively lethal diseases. Here, we apply techniques for variation discovery to study a condition called azoospermia, the failure to produce sperm. Large deletions of the Y chromosome are the primary known genetic risk factor for azoospermia, and genetic testing for these deletions is part of the standard treatment for this condition. We have screened over 300 men with azoospermia for rare deletions and duplications, and find an enrichment of these mutations throughout the genome compared to unaffected men. Our results indicate that sperm production is affected by mutations beyond the Y chromosome and will motivate whole-genome analyses of larger numbers of men with impaired spermatogenesis. Our finding of an enrichment of rare deleterious mutations in men with poor sperm production also raises the possibility that the slightly increased rate of birth defects reported in children conceived by in vitro fertilization may have a genetic basis.
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Affiliation(s)
- Alexandra M. Lopes
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- * E-mail: (AML); (DFC)
| | - Kenneth I. Aston
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Emma Thompson
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Filipa Carvalho
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
| | - João Gonçalves
- Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Ni Huang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rune Matthiesen
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Michiel J. Noordam
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Inés Quintela
- Genomics Medicine Group, National Genotyping Center, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catarina Seabra
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Amy B. Wilfert
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jonathan M. Downie
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Susana Fernandes
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - António Amorim
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Alberto Barros
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
- Centre for Reproductive Genetics Alberto Barros, Porto, Portugal
| | - Angel Carracedo
- Genomics Medicine Group, National Genotyping Center, University of Santiago de Compostela, Santiago de Compostela, Spain
- Galician Foundation of Genomic Medicine and University of Santiago de Compostela, CIBERER, Santiago de Compostela, Spain
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Matthew E. Hurles
- Genome Mutation and Genetic Disease Group, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Sergey Moskovtsev
- CReATe Fertility Center, University of Toronto, Toronto, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Canada
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, Illinois, United States of America
| | - Darius A. Paduch
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, New York, United States of America
| | - Joshua D. Schiffman
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Center for Children's Cancer Research (C3R), Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Division of Pediatric Hematology/Oncology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Peter N. Schlegel
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, New York, United States of America
| | - Mário Sousa
- Laboratory of Cell Biology, UMIB, ICBAS, University of Porto, Porto, Portugal
| | - Douglas T. Carrell
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Physiology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Donald F. Conrad
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: (AML); (DFC)
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