1
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Rypdal KB, Olav Melleby A, Robinson EL, Li J, Palmero S, Seifert DE, Martin D, Clark C, López B, Andreassen K, Dahl CP, Sjaastad I, Tønnessen T, Stokke MK, Louch WE, González A, Heymans S, Christensen G, Apte SS, Lunde IG. ADAMTSL3 knock-out mice develop cardiac dysfunction and dilatation with increased TGFβ signalling after pressure overload. Commun Biol 2022; 5:1392. [PMID: 36539599 PMCID: PMC9767913 DOI: 10.1038/s42003-022-04361-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Heart failure is a major cause of morbidity and mortality worldwide, and can result from pressure overload, where cardiac remodelling is characterized by cardiomyocyte hypertrophy and death, fibrosis, and inflammation. In failing hearts, transforming growth factor (TGF)β drives cardiac fibroblast (CFB) to myofibroblast differentiation causing excessive extracellular matrix production and cardiac remodelling. New strategies to target pathological TGFβ signalling in heart failure are needed. Here we show that the secreted glycoprotein ADAMTSL3 regulates TGFβ in the heart. We found that Adamtsl3 knock-out mice develop exacerbated cardiac dysfunction and dilatation with increased mortality, and hearts show increased TGFβ activity and CFB activation after pressure overload by aortic banding. Further, ADAMTSL3 overexpression in cultured CFBs inhibits TGFβ signalling, myofibroblast differentiation and collagen synthesis, suggesting a cardioprotective role for ADAMTSL3 by regulating TGFβ activity and CFB phenotype. These results warrant future investigation of the potential beneficial effects of ADAMTSL3 in heart failure.
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Affiliation(s)
- Karoline B Rypdal
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway. .,Division of Diagnostics and Technology, Akershus University Hospital, Lørenskog, Norway. .,K.G. Jebsen Center for Cardiac Biomarkers, University of Oslo, Oslo, Norway.
| | - A Olav Melleby
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Emma L Robinson
- Department of Cardiology, Maastricht University, CARIM School for Cardiovascular Diseases, Maastricht, Netherlands
| | - Jia Li
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Sheryl Palmero
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Deborah E Seifert
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Daniel Martin
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Catelyn Clark
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Begoña López
- Program of Cardiovascular Diseases, CIMA Universidad de Navarra and IdiSNA, Pamplona, Spain.,CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | - Kristine Andreassen
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Christen P Dahl
- Department of Cardiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Ivar Sjaastad
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Theis Tønnessen
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,Department of Cardiothoracic Surgery, Oslo University Hospital Ullevål, Oslo, Norway
| | - Mathis K Stokke
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - William E Louch
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Arantxa González
- Program of Cardiovascular Diseases, CIMA Universidad de Navarra and IdiSNA, Pamplona, Spain.,CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | - Stephane Heymans
- Department of Cardiology, Maastricht University, CARIM School for Cardiovascular Diseases, Maastricht, Netherlands.,Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, Leuven, Belgium
| | - Geir Christensen
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Ida G Lunde
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,Division of Diagnostics and Technology, Akershus University Hospital, Lørenskog, Norway.,K.G. Jebsen Center for Cardiac Biomarkers, University of Oslo, Oslo, Norway
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2
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Mahjani B, Birnbaum R, Buxbaum Grice A, Cappi C, Jung S, Avila MN, Reichenberg A, Sandin S, Hultman CM, Buxbaum JD, Grice DE. Phenotypic Impact of Rare Potentially Damaging Copy Number Variation in Obsessive-Compulsive Disorder and Chronic Tic Disorders. Genes (Basel) 2022; 13:1796. [PMID: 36292681 PMCID: PMC9601402 DOI: 10.3390/genes13101796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Recent studies report an important-and previously underestimated-role of rare variation in risk of obsessive-compulsive disorder (OCD) and chronic tic disorders (CTD). Using data from a large epidemiological study, we evaluate the distribution of potentially damaging copy number variation (pdCNV) in OCD and CTD, examining associations between pdCNV and the phenotypes of probands, including a consideration of early- vs. late-diagnoses. METHOD The Obsessive-Compulsive Inventory-Revised (OCI-R) questionnaire was used to ascertain psychometric profiles of OCD probands. CNV were identified genome-wide using chromosomal microarray data. RESULTS For 993 OCD cases, 86 (9%) were identified as pdCNV carriers. The most frequent pdCNV found was at the 16p13.11 region. There was no significant association between pdCNV and the OCI-R total score. However, pdCNV was associated with Obsessing and Checking subscores. There was no significant difference in pdCNV frequency between early- vs. late-diagnosed OCD probands. Of the 217 CTD cases, 18 (8%) were identified as pdCNV carriers. CTD probands with pdCNV were significantly more likely to have co-occurring autism spectrum disorder (ASD). CONCLUSIONS pdCNV represents part of the risk architecture for OCD and CTD. If replicated, our findings suggest pdCNV impact some OCD symptoms. Genes within the 16p13.11 region are potential OCD risk genes.
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Affiliation(s)
- Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Tics, OCD and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rebecca Birnbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ariela Buxbaum Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seulgi Jung
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Natividad Avila
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sven Sandin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dorothy E. Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Tics, OCD and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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3
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Molecular Mechanisms Contributing to the Etiology of Congenital Diaphragmatic Hernia: A Review and Novel Cases. J Pediatr 2022; 246:251-265.e2. [PMID: 35314152 DOI: 10.1016/j.jpeds.2022.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 12/25/2022]
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Scott DA, Gofin Y, Berry AM, Adams AD. Underlying genetic etiologies of congenital diaphragmatic hernia. Prenat Diagn 2022; 42:373-386. [PMID: 35037267 PMCID: PMC8924940 DOI: 10.1002/pd.6099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/09/2022]
Abstract
Congenital diaphragmatic hernia (CDH) is often detectable prenatally. Advances in genetic testing have made it possible to obtain a molecular diagnosis in many fetuses with CDH. Here, we review the aneuploidies, copy number variants (CNVs), and single genes that have been clearly associated with CDH. We suggest that array-based CNV analysis, with or without a chromosome analysis, is the optimal test for identifying chromosomal abnormalities and CNVs in fetuses with CDH. To identify causative sequence variants, whole exome sequencing (WES) is the most comprehensive strategy currently available. Whole genome sequencing (WGS) with CNV analysis has the potential to become the most efficient and effective means of identifying an underlying diagnosis but is not yet routinely available for prenatal diagnosis. We describe how to overcome and address the diagnostic and clinical uncertainty that may remain after genetic testing, and review how a molecular diagnosis may impact recurrence risk estimations, mortality rates, and the availability and outcomes of fetal therapy. We conclude that after the prenatal detection of CDH, patients should be counseled about the possible genetic causes of the CDH, and the genetic testing modalities available to them, in accordance with generally accepted guidelines for pretest counseling in the prenatal setting.
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Affiliation(s)
- Daryl A. Scott
- Texas Children’s Hospital, Houston, TX, 77030,
USA,Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA,Department of Molecular Physiology and Biophysics, Baylor
College of Medicine, Houston, TX, 77030, USA,Correspondence: Daryl A. Scott, R813, One Baylor
Plaza. BCM225, Houston, TX 77030, USA, Phone: +1 713-203-7242,
| | - Yoel Gofin
- Texas Children’s Hospital, Houston, TX, 77030,
USA,Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA
| | - Aliska M. Berry
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA
| | - April D. Adams
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA,Department of Obstetrics and Gynecology, Division of
Maternal Fetal Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
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5
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Schilders KAA, Edel GG, Eenjes E, Oresta B, Birkhoff J, Boerema-de Munck A, Buscop-van Kempen M, Liakopoulos P, Kolovos P, Demmers JAA, Poot R, Wijnen RMH, Tibboel D, Rottier RJ. Identification of SOX2 Interacting Proteins in the Developing Mouse Lung With Potential Implications for Congenital Diaphragmatic Hernia. Front Pediatr 2022; 10:881287. [PMID: 35615634 PMCID: PMC9124971 DOI: 10.3389/fped.2022.881287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/04/2022] [Indexed: 12/02/2022] Open
Abstract
Congenital diaphragmatic hernia is a structural birth defect of the diaphragm, with lung hypoplasia and persistent pulmonary hypertension. Aside from vascular defects, the lungs show a disturbed balance of differentiated airway epithelial cells. The Sry related HMG box protein SOX2 is an important transcription factor for proper differentiation of the lung epithelium. The transcriptional activity of SOX2 depends on interaction with other proteins and the identification of SOX2-associating factors may reveal important complexes involved in the disturbed differentiation in CDH. To identify SOX2-associating proteins, we purified SOX2 complexes from embryonic mouse lungs at 18.5 days of gestation. Mass spectrometry analysis of SOX2-associated proteins identified several potential candidates, among which were the Chromodomain Helicase DNA binding protein 4 (CHD4), Cut-Like Homeobox1 (CUX1), and the Forkhead box proteins FOXP2 and FOXP4. We analyzed the expression patterns of FOXP2, FOXP4, CHD4, and CUX1 in lung during development and showed co-localization with SOX2. Co-immunoprecipitations validated the interactions of these four transcription factors with SOX2, and large-scale chromatin immunoprecipitation (ChIP) data indicated that SOX2 and CHD4 bound to unique sites in the genome, but also co-occupied identical regions, suggesting that these complexes could be involved in co-regulation of genes involved in the respiratory system.
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Affiliation(s)
- Kim A A Schilders
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Gabriëla G Edel
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Evelien Eenjes
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Bianca Oresta
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Judith Birkhoff
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Anne Boerema-de Munck
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Marjon Buscop-van Kempen
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Panagiotis Liakopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Raymond Poot
- Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands
| | - Rene M H Wijnen
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Robbert J Rottier
- Department of Pediatric Surgery, Erasmus Medical Center (MC)-Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands
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6
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Chen CP, Chan CH, Chern SR, Wu PS, Chen SW, Wu FT, Town DD, Lee MS, Wang W. Prenatal diagnosis and molecular cytogenetic characterization of a small supernumerary marker chromosome derived from chromosome 15 in a pregnancy associated with recurrent Down syndrome. Taiwan J Obstet Gynecol 2021; 60:152-156. [PMID: 33494992 DOI: 10.1016/j.tjog.2020.11.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis and molecular cytogenetic characterization of a small supernumerary marker chromosome (sSMC) derived from chromosome 15 in a pregnancy associated with recurrent Down syndrome. CASE REPORT A 33-year-old, gravida 4, para 2, woman underwent amniocentesis at 16 weeks of gestation because of a previous child with Down syndrome and a karyotype of 46,XY,der(14;21)(q10; q10),+21. In this pregnancy, amniocentesis revealed a karyotype of 47,XX,+21[12]/48,XX,+21,+mar[3]. The parental karyotypes were normal. The pregnancy was terminated, and a malformed fetus was delivered with characteristic craniofacial appearance of Down syndrome and hypoplastic middle phalanx of the fifth fingers. The placenta had a karyotype of 47,XX,+21[37]/48,XX,+21,+mar[3]. The umbilical cord had a karyotype of 47,XX,+21[38]/48,XX,+21,+mar[2]. In addition to trisomy 21, array comparative genomic hybridization (aCGH) on the DNA extracted from umbilical cord revealed 40∼50% mosaicism for a 2.604-Mb duplication of 15q25.2-q25.3, or arr 15q25.2q25.3 (83,229,665-85,834,131) × 2.4 [GRCh37 (hg19)] encompassing 19 Online Mendelian Inheritance in Man (OMIM) genes. Quantitative fluorescent polymerase chain reaction (QF-PCR) using the DNAs extracted from cultured amniocytes and parental bloods revealed maternal origin of the sSMC(15) and the extra chromosome 21. CONCLUSION aCGH is useful for identification of the nature of sSMC, and QF-PCR is useful for determination of the parental origin of the aberrant chromosomes.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan.
| | - Chia-Hao Chan
- Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Dai-Dyi Town
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Meng-Shan Lee
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
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7
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Beneventi G, Munita R, Cao Thi Ngoc P, Madej M, Cieśla M, Muthukumar S, Krogh N, Nielsen H, Swaminathan V, Bellodi C. The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells. NAR Cancer 2021; 3:zcab026. [PMID: 34316713 PMCID: PMC8271217 DOI: 10.1093/narcan/zcab026] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/19/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023] Open
Abstract
Small Cajal body-specific RNAs (scaRNAs) guide post-transcriptional modification of spliceosomal RNA and, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here, we uncover that SCARNA15 directs alternative splicing (AS) and stress adaptation in cancer cells. Specifically, we find that SCARNA15 guides critical pseudouridylation (Ψ) of U2 spliceosomal RNA to fine-tune AS of distinct transcripts enriched for chromatin and transcriptional regulators in malignant cells. This critically impacts the expression and function of the key tumor suppressors ATRX and p53. Significantly, SCARNA15 loss impairs p53-mediated redox homeostasis and hampers cancer cell survival, motility and anchorage-independent growth. In sum, these findings highlight an unanticipated role for SCARNA15 and Ψ in directing cancer-associated splicing programs.
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Affiliation(s)
- Giulia Beneventi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Magdalena Madej
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Maciej Cieśla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Vinay Swaminathan
- Division of Oncology, Department of Clinical Sciences, Lund University, 22184, Lund, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
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8
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Joseph S, Mahale SD. Male Infertility Knowledgebase: decoding the genetic and disease landscape. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6344845. [PMID: 34363073 PMCID: PMC8346693 DOI: 10.1093/database/baab049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/01/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022]
Abstract
Male infertility is a multifactorial condition that contributes to around one-third of cases of infertility worldwide. Several chromosomal aberrations, single-gene and polygenic associations with male factor defects have been reported. These defects manifest as sperm number or sperm quality defects leading to infertility. However, in almost 40% of cases, the genetic etiology of male infertility remains unexplained. Understanding the causal genetic factors is crucial for effective patient management and counseling. Integrating the vast amount of available omics data on male infertility is a first step towards understanding, delineating and prioritizing genes associated with the different male reproductive disorders. The Male Infertility Knowledgebase (MIK) is a manually curated repository developed to boost research on the elusive genetic etiology of male infertility. It integrates information on ∼17 000 genes, their associated pathways, gene ontology, diseases and gene and sequence-based analysis tools. In addition, it also incorporates information on reported chromosomal aberrations and syndromic associations with male infertility. Disease enrichment of genes in MIK indicate a shared genetic etiology between cancer, male and female infertility disorders. While the genes involved in cancer pathways were found to be common causal factors for sperm number and sperm quality defects, the interleukin pathways were found to be shared and enriched between male factor defects and non-reproductive conditions like cardiovascular diseases, metabolic diseases, etc. Disease information in MIK can be explored further to identify high-risk conditions associated with male infertility and delineate shared genetic etiology. Utility of the knowledgebase in predicting novel genes is illustrated by identification of 149 novel candidates for cryptorchidism using gene prioritization and network analysis. MIK will serve as a platform for review of genetic information on male infertility, identification pleiotropic genes, prediction of novel candidate genes for the different male infertility diseases and for portending future high-risk diseases associated with male infertility. Database URL: http://mik.bicnirrh.res.in/
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Affiliation(s)
- Shaini Joseph
- Genetic Research Center, ICMR-National Institute for Research in Reproductive Health, J.M. Street, Parel, Mumbai 400012, India
| | - Smita D Mahale
- Emeritus Scientist, ICMR-National Institute for Research in Reproductive Health, J.M. Street, Parel, Mumbai 400012, India
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9
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A 15q25.2 microdeletion phenotype for premature ovarian failure in a Chinese girl: a case report and review of literature. BMC Med Genomics 2020; 13:126. [PMID: 32894148 PMCID: PMC7487592 DOI: 10.1186/s12920-020-00787-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 08/31/2020] [Indexed: 11/29/2022] Open
Abstract
Background Proximal microdeletions on chromosome 15q25.2 are very rare, and are associated with neurodevelopmental delay, inguinal hernia, chest deformities, and anemia. The minimum length missed so far is 1.4 Mb. However, there were no cases reported till date on microdeletions at position q25.2 on chromosome 15 with premature ovarian failure (POF). Case presentation We herein reported a POF case characterized by short stature with only 0.447 Mb deletion on chromosome 15q25.2. The clinical and molecular characteristics in our patient showed the slightest clinical manifestations, with no clinical signs of neurodevelopmental delay, inguinal hernia, chest deformities, and anemia when compared to the previously reported cases. The microdeletions in our case included only 7 genes (HOMER2, FAM103A1, C15orf40, BTBD1, TM6SF1, HDGFRP3 and BNC1), and excluded the CPEB1 gene. Among these, the BNC1 gene is the only one that is known to be involved in reproduction. We hypothesized that the deletion of BNC1 gene in this patient led to haploinsufficiency, and consequently to POF. Conclusions The study of this case increased the knowledge on the molecular and phenotypic consequences of interstitial 15q25.2 deletion, emphasizing that BNC1 gene deletion in this region might contribute to POF.
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10
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Yoo YS, Lee NH, Choi YB. Bochdalek hernia with Diamond-Blackfan anemia associated with RPS19 gene mutation: A case report. Medicine (Baltimore) 2019; 98:e17337. [PMID: 31574871 PMCID: PMC6775407 DOI: 10.1097/md.0000000000017337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
RATIONALE Diamond-Blackfan anemia (DBA) is a rare inherited marrow disorder, characterized by erythrocyte aplasia and is associated with congenital anomalies and a susceptibility to cancer. Although congenital abnormalities have been observed in ∼50% of DBA patients, the occurrence of an associated congenital diaphragmatic hernia (CDH) has rarely been reported. PATIENT CONCERNS A 19-month-old male child was referred to our pediatric hematology-oncology outpatient clinic with anemic appearance. He presented to us with recurrent anemia, short stature, and developmental delay. DIAGNOSIS On bone marrow examination, only erythropoietic cells were markedly decreased in number, whereas other cell lines were unaffected. An abdominal computed tomography scan revealed a Bochdalek type of CDH. A genetic analysis revealed heterozygous mutation of RPS19; therefore, he was diagnosed as having DBA with CDH. INTERVENTIONS The patient received an initial packed red blood cell transfusion, followed by an administration of oral prednisone. OUTCOMES The patient is maintained on oral prednisone administered at a dose of 0.3 mg/kg every alternate day and has since a hemoglobin level of >9.0 g/dL without further RBC transfusions. LESSONS We learned that a Bochdalek type of CDH can manifest in a DBA patient with RPS19 gene mutation. Therefore, patients diagnosed with the latter disorder should also be screened for an early detection of potential CDHs.
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Affiliation(s)
- Ye Seul Yoo
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju
| | - Na Hee Lee
- Department of Pediatrics, Cha Bundang Medical Center, Cha University, Seongnam, Korea
| | - Young Bae Choi
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju
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11
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Maggiolini FAM, Cantsilieris S, D’Addabbo P, Manganelli M, Coe BP, Dumont BL, Sanders AD, Pang AWC, Vollger MR, Palumbo O, Palumbo P, Accadia M, Carella M, Eichler EE, Antonacci F. Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus. PLoS Genet 2019; 15:e1008075. [PMID: 30917130 PMCID: PMC6436712 DOI: 10.1371/journal.pgen.1008075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
Human chromosome 15q25 is involved in several disease-associated structural rearrangements, including microdeletions and chromosomal markers with inverted duplications. Using comparative fluorescence in situ hybridization, strand-sequencing, single-molecule, real-time sequencing and Bionano optical mapping analyses, we investigated the organization of the 15q25 region in human and nonhuman primates. We found that two independent inversions occurred in this region after the fission event that gave rise to phylogenetic chromosomes XIV and XV in humans and great apes. One of these inversions is still polymorphic in the human population today and may confer differential susceptibility to 15q25 microdeletions and inverted duplications. The inversion breakpoints map within segmental duplications containing core duplicons of the GOLGA gene family and correspond to the site of an ancestral centromere, which became inactivated about 25 million years ago. The inactivation of this centromere likely released segmental duplications from recombination repression typical of centromeric regions. We hypothesize that this increased the frequency of ectopic recombination creating a hotspot of hominid inversions where dispersed GOLGA core elements now predispose this region to recurrent genomic rearrangements associated with disease.
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Affiliation(s)
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Pietro D’Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Michele Manganelli
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Ashley D. Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Pietro Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital “Cardinale G. Panico”, Via San Pio X n°4, Tricase, LE, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States of America
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
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12
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Jordan VK, Beck TF, Hernandez-Garcia A, Kundert PN, Kim BJ, Jhangiani SN, Gambin T, Starkovich M, Punetha J, Paine IS, Posey JE, Li AH, Muzny D, Hsu CW, Lashua AJ, Sun X, Fernandes CJ, Dickinson ME, Lally KP, Gibbs RA, Boerwinkle E, Lupski JR, Scott DA. The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia. Hum Mol Genet 2019; 27:2064-2075. [PMID: 29618029 DOI: 10.1093/hmg/ddy110] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/26/2018] [Indexed: 11/13/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) has been reported twice in individuals with a clinical diagnosis of Fraser syndrome, a genetic disorder that can be caused by recessive mutations affecting FREM2 and FRAS1. In the extracellular matrix, FREM2 and FRAS1 form a self-stabilizing complex with FREM1, a protein whose deficiency causes sac CDH in humans and mice. By sequencing FREM2 and FRAS1 in a CDH cohort, and searching online databases, we identified five individuals who carried recessive or double heterozygous, putatively deleterious variants in these genes which may represent susceptibility alleles. Three of these alleles were significantly enriched in our CDH cohort compared with ethnically matched controls. We subsequently demonstrated that 8% of Frem2ne/ne and 1% of Fras1Q1263*/Q1263* mice develop the same type of anterior sac CDH seen in FREM1-deficient mice. We went on to show that development of sac hernias in FREM1-deficient mice is preceded by failure of anterior mesothelial fold progression resulting in the persistence of an amuscular, poorly vascularized anterior diaphragm that is abnormally adherent to the underlying liver. Herniation occurs in the perinatal period when the expanding liver protrudes through this amuscular region of the anterior diaphragm that is juxtaposed to areas of muscular diaphragm. Based on these data, we conclude that deficiency of FREM2, and possibly FRAS1, are associated with an increased risk of developing CDH and that loss of the FREM1/FREM2/FRAS1 complex, or its function, leads to anterior sac CDH development through its effects on mesothelial fold progression.
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Affiliation(s)
- Valerie K Jordan
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tyler F Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter N Kundert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bum-Jun Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Molly Starkovich
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ingrid S Paine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander H Li
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amber J Lashua
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xin Sun
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin P Lally
- Department of Pediatric Surgery, McGovern Medical School at UT Health, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daryl A Scott
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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13
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Monzani A, Babu D, Mellone S, Genoni G, Fanelli A, Prodam F, Bellone S, Giordano M. Co-occurrence of genomic imbalances on Xp22.1 in the SHOX region and 15q25.2 in a girl with short stature, precocious puberty, urogenital malformations and bone anomalies. BMC Med Genomics 2019; 12:5. [PMID: 30626445 PMCID: PMC6327496 DOI: 10.1186/s12920-018-0445-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 12/06/2018] [Indexed: 11/30/2022] Open
Abstract
Background Mutations of SHOX represent the most frequent monogenic cause of short stature and related syndromes. The genetic alterations include point mutations and deletions/duplications spanning both SHOX and its regulatory regions, although microrearrangements are confined to either the downstream or upstream enhancers in many patients. Mutations in the heterozygous state have been identified in up to 60–80% of Leri-Weill Dyschondrosteosis (LWD; MIM #127300) and approximately 4–5% of Idiopathic Short Stature (ISS; MIM#300582) patients. Homozygous or compound heterozygous mutations as well as biallelic deletions of SHOX and/or the enhancer regions result in a more severe phenotype, which is known as Langer Mesomelic Dysplasia (LMD; MIM #249700). Case presentation A 17 year old girl, presented with severe short stature, growth hormone deficiency (GHD), precocious puberty, dorsal scoliosis, dysmorphisms and urogenital malformations. She was born with agenesis of the right tibia and fibula, as well as with a supernumerary digit on the left foot. Array comparative genomic hybridization (aCGH) analysis detected the presence of two distinct duplications on Xp22.1 flanking the SHOX coding sequence and involving its regulatory regions. An additional duplication of 1.6–2.5 Mb on 15q25.2 that included 13 genes was also identified. The girl was adopted and the parent’s DNA was not available to establish the origin of the chromosome imbalances. Conclusions The complex phenotype observed in our patient is probably the result of the co-occurrence of rearrangements on chromosomes Xp22.1 and 15q25.2. The duplicated region on 15q25.2 region is likely to contain dosage-sensitive genes responsible for some of the clinical features observed in this patient, whereas the extreme short stature and the skeletal anomalies are likely attributable to the comorbidity of GHD and copy number variants in the SHOX region. Electronic supplementary material The online version of this article (10.1186/s12920-018-0445-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alice Monzani
- Division of Pediatrics, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Deepak Babu
- Laboratory of Human Genetics, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Simona Mellone
- Laboratory of Human Genetics, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Giulia Genoni
- Division of Pediatrics, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Antonella Fanelli
- Laboratory of Human Genetics, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Flavia Prodam
- Division of Pediatrics, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Simonetta Bellone
- Division of Pediatrics, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Mara Giordano
- Laboratory of Human Genetics, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy.
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14
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Ulirsch JC, Verboon JM, Kazerounian S, Guo MH, Yuan D, Ludwig LS, Handsaker RE, Abdulhay NJ, Fiorini C, Genovese G, Lim ET, Cheng A, Cummings BB, Chao KR, Beggs AH, Genetti CA, Sieff CA, Newburger PE, Niewiadomska E, Matysiak M, Vlachos A, Lipton JM, Atsidaftos E, Glader B, Narla A, Gleizes PE, O'Donohue MF, Montel-Lehry N, Amor DJ, McCarroll SA, O'Donnell-Luria AH, Gupta N, Gabriel SB, MacArthur DG, Lander ES, Lek M, Da Costa L, Nathan DG, Korostelev AA, Do R, Sankaran VG, Gazda HT. The Genetic Landscape of Diamond-Blackfan Anemia. Am J Hum Genet 2018; 103:930-947. [PMID: 30503522 PMCID: PMC6288280 DOI: 10.1016/j.ajhg.2018.10.027] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/29/2018] [Indexed: 01/19/2023] Open
Abstract
Diamond-Blackfan anemia (DBA) is a rare bone marrow failure disorder that affects 7 out of 1,000,000 live births and has been associated with mutations in components of the ribosome. In order to characterize the genetic landscape of this heterogeneous disorder, we recruited a cohort of 472 individuals with a clinical diagnosis of DBA and performed whole-exome sequencing (WES). We identified relevant rare and predicted damaging mutations for 78% of individuals. The majority of mutations were singletons, absent from population databases, predicted to cause loss of function, and located in 1 of 19 previously reported ribosomal protein (RP)-encoding genes. Using exon coverage estimates, we identified and validated 31 deletions in RP genes. We also observed an enrichment for extended splice site mutations and validated their diverse effects using RNA sequencing in cell lines obtained from individuals with DBA. Leveraging the size of our cohort, we observed robust genotype-phenotype associations with congenital abnormalities and treatment outcomes. We further identified rare mutations in seven previously unreported RP genes that may cause DBA, as well as several distinct disorders that appear to phenocopy DBA, including nine individuals with biallelic CECR1 mutations that result in deficiency of ADA2. However, no new genes were identified at exome-wide significance, suggesting that there are no unidentified genes containing mutations readily identified by WES that explain >5% of DBA-affected case subjects. Overall, this report should inform not only clinical practice for DBA-affected individuals, but also the design and analysis of rare variant studies for heterogeneous Mendelian disorders.
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Affiliation(s)
- Jacob C Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shideh Kazerounian
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Guo
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Yuan
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Leif S Ludwig
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nour J Abdulhay
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elaine T Lim
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron Cheng
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beryl B Cummings
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine R Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Colin A Sieff
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Peter E Newburger
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Edyta Niewiadomska
- Department of Pediatric Hematology/Oncology, Medical University of Warsaw, Warsaw, Poland
| | - Michal Matysiak
- Department of Pediatric Hematology/Oncology, Medical University of Warsaw, Warsaw, Poland
| | - Adrianna Vlachos
- Feinstein Institute for Medical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children's Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA
| | - Jeffrey M Lipton
- Feinstein Institute for Medical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children's Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA
| | - Eva Atsidaftos
- Feinstein Institute for Medical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children's Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA
| | - Bertil Glader
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 02114, USA
| | - Anupama Narla
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 02114, USA
| | - Pierre-Emmanuel Gleizes
- Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Nathalie Montel-Lehry
- Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey B Gabriel
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eric S Lander
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lydie Da Costa
- University Paris VII Denis DIDEROT, Faculté de Médecine Xavier Bichat, 75019 Paris, France; Laboratory of Excellence for Red Cell, LABEX GR-Ex, 75015 Paris, France
| | - David G Nathan
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ron Do
- Department of Genetics and Genomic Sciences and The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Hanna T Gazda
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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15
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Urh K, Kolenc Ž, Hrovat M, Svet L, Dovč P, Kunej T. Molecular Mechanisms of Syndromic Cryptorchidism: Data Synthesis of 50 Studies and Visualization of Gene-Disease Network. Front Endocrinol (Lausanne) 2018; 9:425. [PMID: 30093884 PMCID: PMC6070605 DOI: 10.3389/fendo.2018.00425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/09/2018] [Indexed: 12/17/2022] Open
Abstract
Background: Cryptorchidism is one of the most frequent congenital birth defects in male children and is present in 2-4% of full-term male births. It has several possible health effects including reduced fertility, increased risk for testicular neoplasia, testicular torsion, and psychological consequences. Cryptorchidism is often diagnosed as comorbid; copresent with other diseases. It is also present in clinical picture of several syndromes. However, this field has not been systematically studied. The aim of the present study was to catalog published cases of syndromes which include cryptorchidism in the clinical picture and associated genomic information. Methods: The literature was extracted from Public/Publisher MEDLINE and Web of Science databases, using the keywords including: syndrome, cryptorchidism, undescended testes, loci, and gene. The obtained data was organized in a table according to the previously proposed standardized data format. The results of the study were visually represented using Gephi and karyotype view. Results: Fifty publications had sufficient data for analysis. Literature analysis resulted in 60 genomic loci, associated with 44 syndromes that have cryptorchidism in clinical picture. Genomic loci included 38 protein-coding genes and 22 structural variations containing microdeletions and microduplications. Loci, associated with syndromic cryptorchidism are located on 16 chromosomes. Visualization of retrieved data is presented in a gene-disease network. Conclusions: The study is ongoing and further studies will be needed to develop a complete catalog with the data from upcoming publications. Additional studies will also be needed for revealing of molecular mechanisms associated with syndromic cryptorchidism and revealing complete diseasome network.
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Affiliation(s)
| | | | | | | | | | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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16
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Urh K, Kunej T. Genome-wide screening for smallest regions of overlaps in cryptorchidism. Reprod Biomed Online 2018; 37:85-99. [PMID: 29631949 DOI: 10.1016/j.rbmo.2018.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 01/01/2023]
Abstract
Cryptorchidism is a urogenital abnormality associated with increased rates of testicular neoplasia and impaired spermatogenesis. The field is facing expansion of genomics data; however, it lacks protocols for biomarker prioritization. Identification of smallest regions of overlap (SRO) presents an approach for candidate gene identification but has not yet been systematically conducted in cryptorchidism. The aim of this study was to conduct a genome-wide screening for SRO (GW-SRO) associated with cryptorchidism development. We updated the Cryptorchidism Gene Database to version 3, remapped genomic coordinates of loci from older assemblies to the GRCh38 and performed genome-wide screening for overlapping regions associated with cryptorchidism risk. A total of 73 chromosomal loci (68 involved in chromosomal mutations and five copy number variations) described in 37 studies associated with cryptorchidism risk in humans were used for SRO identification. Analysis resulted in 18 SRO, based on deletions, duplications, inversions, derivations and copy number variations. Screening for SRO was challenging owing to heterogeneous reporting of genomic locations. To our knowledge, this is the first GW-SRO study for cryptorchidism and it presents the basis for further narrowing of critical regions for cryptorchidism and planning functional experiments. The developed protocol could also be applied to other multifactorial diseases.
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Affiliation(s)
- Kristian Urh
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, Slovenia.
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17
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Monkam CY, Kemeny S, Miret A, Pebrel-Richard C, Sarret C. A case which further refines the critical region for 15q25.2 microduplication phenotypes. Acta Neurol Belg 2016; 116:683-685. [PMID: 26927603 DOI: 10.1007/s13760-016-0620-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 02/13/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Cécile Yossa Monkam
- Génétique médicale, Université d'Auvergne, Centre hospitalo-universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Stéphan Kemeny
- Cytogénétique médicale, Université d'Auvergne, Centre hospitalo-universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Anne Miret
- Génétique médicale, Université d'Auvergne, Centre hospitalo-universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Céline Pebrel-Richard
- Cytogénétique médicale, Université d'Auvergne, Centre hospitalo-universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Catherine Sarret
- Génétique médicale, Université d'Auvergne, Centre hospitalo-universitaire de Clermont-Ferrand, Clermont-Ferrand, France.
- IGCNC, EA7282, Université d'Auvergne, Clermont-Ferrand, France.
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18
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Starkovich M, Lalani SR, Mercer CL, Scott DA. Chromosome 5q33 deletions associated with congenital heart defects. Am J Med Genet A 2016; 170:3338-3342. [PMID: 27589475 DOI: 10.1002/ajmg.a.37957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/15/2016] [Indexed: 02/04/2023]
Abstract
Congenital heart defects (CHD) are present in over 1% of all newborns and are the leading cause of birth-defect-related deaths in the United States. We describe two male subjects with CHD, one with an atrial septal defect, a ventricular septal defect, and pulmonary artery stenosis; and the other with tetralogy of Fallot and a right aortic arch, who carry partially overlapping, de novo deletions of chromosome 5q33. The maximum region of overlap between these deletions encompasses HAND1 and SAP30L, two genes that have previously been shown to play a role in cardiac development. HAND1 encodes a basic helix-loop-helix transcription factor. Cardiac-specific ablation of Hand1 in mice causes septal, valvular, and outflow tract defects. SAP30L, its paralog SAP30, and other SAP proteins form part of a multi-subunit complex involved in transcriptional regulation via histone deacetylation. Morpholino knockdown of sap30L in zebrafish, which do not have a distinct sap30 gene, leads to cardiac hypoplasia and cardiac insufficiency. We subsequently identified two other individuals with chromosomal deletions involving HAND1 and SAP30L in whom cardiac-related medical problems were not described. These observations suggest that haploinsufficiency of HAND1 and/or SAP30L may contribute to the development of CHD, although the contribution of other genes on chromosome 5q33 cannot be excluded. Our findings also suggest that the penetrance of CHD associated with 5q33 deletions is incomplete and may be influenced by other genetic, environmental or stochastic factors. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Molly Starkovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Catherine L Mercer
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton, United Kingdom
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
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19
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Yuan H, Meng Z, Zhang L, Luo X, Liu L, Chen M, Li X, Zhao W, Liang L. A rare de novo interstitial duplication of 15q15.3q21.2 in a boy with severe short stature, hypogonadism, global developmental delay and intellectual disability. Mol Cytogenet 2016; 9:2. [PMID: 26759605 PMCID: PMC4710046 DOI: 10.1186/s13039-016-0214-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Interstitial duplications distal to 15q13 are very rare. CASE PRESENTATION Here, we reported a 14-year-old boy with severe short stature, delayed bone age, hypogonadism, global developmental delay and intellectual disability. His had distinctive facial features including macrocephaly, broad forehead, deep-set and widely spaced eyes, broad nose bridge, shallow philtrum and thick lips. A de novo 6.4 Mb interstitial duplication of 15q15.3q21.2 was detected by chromosomal microarray analysis. We compared our patient's clinical phenotypes with those of several individuals with overlapping duplications and several candidate genes responsible for the phenotypes were identified as well. CONCLUSION The results suggest a novel contiguous gene duplication syndrome characterized with shared features including short stature, hypogonadism, global developmental delay and other congenital anomalies.
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Affiliation(s)
- Haiming Yuan
- Guangzhou kingmed center for clinical laboratory Co.,Ltd., Guangzhou, 510330 Guangdong China ; KingMed School of Laboratory Medicine Guangzhou Medical University, Guangzhou, 510330 Guangdong China
| | - Zhe Meng
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 Guangdong China
| | - Lina Zhang
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 Guangdong China
| | - Xiangyang Luo
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 Guangdong China
| | - Liping Liu
- Department of Obstetrics and Gynecology, Wuhan women and children medical healthcare center, Wuhan, 430016 China
| | - Mengfan Chen
- Guangzhou kingmed center for clinical laboratory Co.,Ltd., Guangzhou, 510330 Guangdong China
| | - Xinwei Li
- Guangzhou kingmed center for clinical laboratory Co.,Ltd., Guangzhou, 510330 Guangdong China
| | - Weiwei Zhao
- Guangzhou kingmed center for clinical laboratory Co.,Ltd., Guangzhou, 510330 Guangdong China ; KingMed School of Laboratory Medicine Guangzhou Medical University, Guangzhou, 510330 Guangdong China
| | - Liyang Liang
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 Guangdong China
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20
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Stark Z, Behrsin J, Burgess T, Ritchie A, Yeung A, Tan TY, Brown NJ, Savarirayan R, Patel N. SNP microarray abnormalities in a cohort of 28 infants with congenital diaphragmatic hernia. Am J Med Genet A 2015; 167A:2319-26. [DOI: 10.1002/ajmg.a.37177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 05/10/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Zornitza Stark
- VictorianClinicalGenetics Service and Murdoch Children Institute; Melbourne Australia
| | - Joanna Behrsin
- Newborn Intensive Care Unit; Royal Children's Hospital; Melbourne Australia
| | - Trent Burgess
- VictorianClinicalGenetics Service and Murdoch Children Institute; Melbourne Australia
- University of Melbourne Department of Paediatrics; Melbourne Australia
| | - Anna Ritchie
- VictorianClinicalGenetics Service and Murdoch Children Institute; Melbourne Australia
| | - Alison Yeung
- VictorianClinicalGenetics Service and Murdoch Children Institute; Melbourne Australia
| | - Tiong Y. Tan
- VictorianClinicalGenetics Service and Murdoch Children Institute; Melbourne Australia
- University of Melbourne Department of Paediatrics; Melbourne Australia
| | - Natasha J. Brown
- VictorianClinicalGenetics Service and Murdoch Children Institute; Melbourne Australia
- University of Melbourne Department of Paediatrics; Melbourne Australia
| | - Ravi Savarirayan
- VictorianClinicalGenetics Service and Murdoch Children Institute; Melbourne Australia
- University of Melbourne Department of Paediatrics; Melbourne Australia
| | - Neil Patel
- Newborn Intensive Care Unit; Royal Children's Hospital; Melbourne Australia
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21
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Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Nat Genet 2014; 46:1293-302. [PMID: 25326701 PMCID: PMC4244265 DOI: 10.1038/ng.3120] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 09/25/2014] [Indexed: 12/14/2022]
Abstract
Recurrent deletions of chromosome 15q13.3 associate with intellectual disability, schizophrenia, autism and epilepsy. To gain insight into its instability, we sequenced the region in patients, normal individuals and nonhuman primates. We discovered five structural configurations of the human chromosome 15q13.3 region ranging in size from 2 to 3 Mbp. These configurations arose recently (~0.5–0.9 million years ago) as a result of human-specific expansions of segmental duplications and two independent inversion events. All inversion breakpoints map near GOLGA8 core duplicons—a ~14 kbp primate-specific chromosome 15 repeat that became organized into larger palindromic structures. GOLGA8-flanked palindromes also demarcate the breakpoints of recurrent 15q13.3 microdeletions, the expansion of chromosome 15 segmental duplications in the human lineage, and independent structural changes in apes. The significant clustering (p=0.002) of breakpoints provides mechanistic evidence for the role of this core duplicon and its palindromic architecture in promoting evolutionary and disease-related instability of chromosome 15.
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22
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Watson CT, Marques-Bonet T, Sharp AJ, Mefford HC. The genetics of microdeletion and microduplication syndromes: an update. Annu Rev Genomics Hum Genet 2014; 15:215-244. [PMID: 24773319 DOI: 10.1146/annurev-genom-091212-153408] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chromosomal abnormalities, including microdeletions and microduplications, have long been associated with abnormal developmental outcomes. Early discoveries relied on a common clinical presentation and the ability to detect chromosomal abnormalities by standard karyotype analysis or specific assays such as fluorescence in situ hybridization. Over the past decade, the development of novel genomic technologies has allowed more comprehensive, unbiased discovery of microdeletions and microduplications throughout the human genome. The ability to quickly interrogate large cohorts using chromosome microarrays and, more recently, next-generation sequencing has led to the rapid discovery of novel microdeletions and microduplications associated with disease, including very rare but clinically significant rearrangements. In addition, the observation that some microdeletions are associated with risk for several neurodevelopmental disorders contributes to our understanding of shared genetic susceptibility for such disorders. Here, we review current knowledge of microdeletion/duplication syndromes, with a particular focus on recurrent rearrangement syndromes.
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Affiliation(s)
- Corey T Watson
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra/CSIC, 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.,Centro Nacional de Análisis Genómico, 08023 Barcelona, Spain
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Heather C Mefford
- Department of Pediatrics, University of Washington, Seattle, Washington 98195
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23
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Burgess T, Brown NJ, Stark Z, Bruno DL, Oertel R, Chong B, Calabro V, Kornberg A, Sanderson C, Kelly J, Howell KB, Savarirayan R, Hinds R, Greenway A, Slater HR, White SM. Characterization of core clinical phenotypes associated with recurrent proximal 15q25.2 microdeletions. Am J Med Genet A 2013; 164A:77-86. [DOI: 10.1002/ajmg.a.36203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 07/28/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Trent Burgess
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
| | - Natasha J. Brown
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
- Department of Paediatrics; Royal Children's Hospital; University of Melbourne; Parkville Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
| | - Damien L. Bruno
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
| | - Ralph Oertel
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
| | - Belinda Chong
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
| | - Vanessa Calabro
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
| | - Andrew Kornberg
- Department of Paediatrics; Royal Children's Hospital; University of Melbourne; Parkville Australia
- Department of Neurology; Royal Children's Hospital; Parkville Australia
| | | | - Julian Kelly
- Department of Paediatrics; Royal Children's Hospital; University of Melbourne; Parkville Australia
- Department of General Medicine; Royal Children's Hospital; Parkville Australia
| | | | - Ravi Savarirayan
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
- Department of Paediatrics; Royal Children's Hospital; University of Melbourne; Parkville Australia
| | - Rupert Hinds
- Department of Paediatrics; Monash Children's; Medical Centre; Clayton Australia
| | - Anthea Greenway
- Department of Clinical Haematology; Royal Children's Hospital; Parkville Australia
| | - Howard R. Slater
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
| | - Susan M. White
- Victorian Clinical Genetics Service; MCRI, Royal Children's Hospital; Parkville Australia
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24
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Brady PD, DeKoninck P, Fryns JP, Devriendt K, Deprest JA, Vermeesch JR. Identification of dosage-sensitive genes in fetuses referred with severe isolated congenital diaphragmatic hernia. Prenat Diagn 2013; 33:1283-92. [PMID: 24122781 DOI: 10.1002/pd.4244] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/09/2013] [Accepted: 09/21/2013] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Congenital diaphragmatic hernia (CDH) is a fetal abnormality affecting diaphragm and lung development with a high mortality rate despite advances in fetal and neonatal therapy. CDH may occur either as an isolated defect or in syndromic form for which the prognosis is worse. Although conventional karyotyping and, more recently, chromosomal microarrays support a substantial role for genetic factors, causal genes responsible for isolated CDH remain elusive. We propose that chromosomal microarray analysis will identify copy number variations (CNVs) associated with isolated CDH. METHODS We perform a prospective genome-wide screen for CNVs using chromosomal microarrays on 75 fetuses referred with apparently isolated CDH, six of which were later reclassified as non-isolated CDH. RESULTS The results pinpoint haploinsufficiency of NR2F2 as a cause of CDH and cardiovascular malformations. In addition, the 15q25.2 and 16p11.2 recurrent microdeletions are associated with isolated CDH. By using gene prioritisation and network analysis, we provide strong evidence for several novel dosage-sensitive candidate genes associated with CDH. CONCLUSIONS Chromosomal microarray analysis detects submicroscopic CNVs associated with isolated CDH or CDH with cardiovascular malformations.
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Affiliation(s)
- P D Brady
- Centre for Human Genetics, KU Leuven/University Hospital Leuven, Leuven, Belgium
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25
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Yu L, Wynn J, Ma L, Guha S, Mychaliska GB, Crombleholme TM, Azarow KS, Lim FY, Chung DH, Potoka D, Warner BW, Bucher B, LeDuc CA, Costa K, Stolar C, Aspelund G, Arkovitz MS, Chung WK. De novo copy number variants are associated with congenital diaphragmatic hernia. J Med Genet 2013; 49:650-9. [PMID: 23054247 DOI: 10.1136/jmedgenet-2012-101135] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Congenital diaphragmatic hernia (CDH) is a common birth defect with significant morbidity and mortality. Although the aetiology of CDH remains poorly understood, studies from animal models and patients with CDH suggest that genetic factors play an important role in the development of CDH. Chromosomal anomalies have been reported in CDH. METHODS In this study, the authors investigated the frequency of chromosomal anomalies and copy number variants (CNVs) in 256 parent-child trios of CDH using clinical conventional cytogenetic and microarray analysis. The authors also selected a set of CDH related training genes to prioritise the genes in those segmental aneuploidies and identified the genes and gene sets that may contribute to the aetiology of CDH. RESULTS The authors identified chromosomal anomalies in 16 patients (6.3%) of the series including three aneuploidies, two unbalanced translocation, and 11 patients with de novo CNVs ranging in size from 95 kb to 104.6 Mb. The authors prioritised the genes in the CNV segments and identified KCNA2, LMNA, CACNA1S, MYOG, HLX, LBR, AGT, GATA4, SOX7, HYLS1, FOXC1, FOXF2, PDGFA, FGF6, COL4A1, COL4A2, HOMER2, BNC1, BID, and TBX1 as genes that may be involved in diaphragm development. Gene enrichment analysis identified the most relevant gene ontology categories as those involved in tissue development (p=4.4×10(-11)) or regulation of multicellular organismal processes (p=2.8×10(-10)) and 'receptor binding' (p=8.7×10(-14)) and 'DNA binding transcription factor activity' (p=4.4×10(-10)). CONCLUSIONS The present findings support the role of chromosomal anomalies in CDH and provide a set of candidate genes including FOXC1, FOXF2, PDGFA, FGF6, COL4A1, COL4A2, SOX7, BNC1, BID, and TBX1 for further analysis in CDH.
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Affiliation(s)
- Lan Yu
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
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26
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O’Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O’Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Eichler EE, Shendure J. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 2012; 338:1619-22. [PMID: 23160955 PMCID: PMC3528801 DOI: 10.1126/science.1227764] [Citation(s) in RCA: 943] [Impact Index Per Article: 78.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Exome sequencing studies of autism spectrum disorders (ASDs) have identified many de novo mutations but few recurrently disrupted genes. We therefore developed a modified molecular inversion probe method enabling ultra-low-cost candidate gene resequencing in very large cohorts. To demonstrate the power of this approach, we captured and sequenced 44 candidate genes in 2446 ASD probands. We discovered 27 de novo events in 16 genes, 59% of which are predicted to truncate proteins or disrupt splicing. We estimate that recurrent disruptive mutations in six genes-CHD8, DYRK1A, GRIN2B, TBR1, PTEN, and TBL1XR1-may contribute to 1% of sporadic ASDs. Our data support associations between specific genes and reciprocal subphenotypes (CHD8-macrocephaly and DYRK1A-microcephaly) and replicate the importance of a β-catenin-chromatin-remodeling network to ASD etiology.
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Affiliation(s)
- Brian J. O’Roak
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wenqing Fu
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jarrett D. Egertson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian B. Stanaway
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian G. Phelps
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Gemma Carvill
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Akash Kumar
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katy Ankenman
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jeff Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joseph B. Hiatt
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily H. Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Roie Levy
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Diana R. O’Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Heather C. Mefford
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
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27
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Doelken SC, Seeger K, Hundsdoerfer P, Weber-Ferro W, Klopocki E, Graul-Neumann L. Proximal and distal 15q25.2 microdeletions-genotype-phenotype delineation of two neurodevelopmental susceptibility loci. Am J Med Genet A 2012; 161A:218-24. [DOI: 10.1002/ajmg.a.35695] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 09/09/2012] [Indexed: 11/09/2022]
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28
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Palumbo O, Palumbo P, Palladino T, Stallone R, Miroballo M, Piemontese MR, Zelante L, Carella M. An emerging phenotype of interstitial 15q25.2 microdeletions: Clinical report and review. Am J Med Genet A 2012; 158A:3182-9. [DOI: 10.1002/ajmg.a.35631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/26/2012] [Indexed: 11/09/2022]
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29
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Wat MJ, Beck TF, Hernández-García A, Yu Z, Veenma D, Garcia M, Holder AM, Wat JJ, Chen Y, Mohila CA, Lally KP, Dickinson M, Tibboel D, de Klein A, Lee B, Scott DA. Mouse model reveals the role of SOX7 in the development of congenital diaphragmatic hernia associated with recurrent deletions of 8p23.1. Hum Mol Genet 2012; 21:4115-25. [PMID: 22723016 DOI: 10.1093/hmg/dds241] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recurrent microdeletions of 8p23.1 that include GATA4 and SOX7 confer a high risk of both congenital diaphragmatic hernia (CDH) and cardiac defects. Although GATA4-deficient mice have both CDH and cardiac defects, no humans with cardiac defects attributed to GATA4 mutations have been reported to have CDH. We were also unable to identify deleterious GATA4 sequence changes in a CDH cohort. This suggested that haploinsufficiency of another 8p23.1 gene may contribute, along with GATA4, to the development of CDH. To determine if haploinsufficiency of SOX7-another transcription factor encoding gene-contributes to the development of CDH, we generated mice with a deletion of the second exon of Sox7. A portion of these Sox7(Δex2/+) mice developed retrosternal diaphragmatic hernias located in the anterior muscular portion of the diaphragm. Anterior CDH is also seen in Gata4(+/-) mice and has been described in association with 8p23.1 deletions in humans. Immunohistochemistry revealed that SOX7 is expressed in the vascular endothelial cells of the developing diaphragm and may be weakly expressed in some diaphragmatic muscle cells. Sox7(Δex2/Δex2) embryos die prior to diaphragm development with dilated pericardial sacs and failure of yolk sac remodeling suggestive of cardiovascular failure. Similar to our experience screening GATA4, no clearly deleterious SOX7 sequence changes were identified in our CDH cohort. We conclude that haploinsufficiency of Sox7 or Gata4 is sufficient to produce anterior CDH in mice and that haploinsufficiency of SOX7 and GATA4 may each contribute to the development of CDH in individuals with 8p23.1 deletions.
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Affiliation(s)
- Margaret J Wat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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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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Abstract
Diamond-Blackfan anemia (DBA) is a congenital BM failure syndrome characterized by hypoproliferative anemia, associated physical abnormalities, and a predisposition to cancer. Perturbations of the ribosome appear to be critically important in DBA; alterations in 9 different ribosomal protein genes have been identified in multiple unrelated families, along with rarer abnormalities of additional ribosomal proteins. However, at present, only 50% to 60% of patients have an identifiable genetic lesion by ribosomal protein gene sequencing. Using genome-wide single-nucleotide polymorphism array to evaluate for regions of recurrent copy variation, we identified deletions at known DBA-related ribosomal protein gene loci in 17% (9 of 51) of patients without an identifiable mutation, including RPS19, RPS17, RPS26, and RPL35A. No recurrent regions of copy variation at novel loci were identified. Because RPS17 is a duplicated gene with 4 copies in a diploid genome, we demonstrate haploinsufficient RPS17 expression and a small subunit ribosomal RNA processing abnormality in patients harboring RPS17 deletions. Finally, we report the novel identification of variable mosaic loss involving known DBA gene regions in 3 patients from 2 kindreds. These data suggest that ribosomal protein gene deletion is more common than previously suspected and should be considered a component of the initial genetic evaluation in cases of suspected DBA.
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Kariminejad R, Lind-Thomsen A, Tümer Z, Erdogan F, Ropers HH, Tommerup N, Ullmann R, Møller RS. High frequency of rare copy number variants affecting functionally related genes in patients with structural brain malformations. Hum Mutat 2011; 32:1427-35. [DOI: 10.1002/humu.21585] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 07/26/2011] [Indexed: 01/20/2023]
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Wat MJ, Veenma D, Hogue J, Holder AM, Yu Z, Wat JJ, Hanchard N, Shchelochkov OA, Fernandes CJ, Johnson A, Lally KP, Slavotinek A, Danhaive O, Schaible T, Cheung SW, Rauen KA, Tonk VS, Tibboel D, de Klein A, Scott DA. Genomic alterations that contribute to the development of isolated and non-isolated congenital diaphragmatic hernia. J Med Genet 2011; 48:299-307. [PMID: 21525063 DOI: 10.1136/jmg.2011.089680] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Congenital diaphragmatic hernia (CDH) is a life threatening birth defect. Most of the genetic factors that contribute to the development of CDH remain unidentified. OBJECTIVE To identify genomic alterations that contribute to the development of diaphragmatic defects. METHODS A cohort of 45 unrelated patients with CDH or diaphragmatic eventrations was screened for genomic alterations by array comparative genomic hybridisation or single nucleotide polymorphism based copy number analysis. RESULTS Genomic alterations that were likely to have contributed to the development of CDH were identified in 8 patients. Inherited deletions of ZFPM2 were identified in 2 patients with isolated diaphragmatic defects and a large de novo 8q deletion overlapping the same gene was found in a patient with non-isolated CDH. A de novo microdeletion of chromosome 1q41q42 and two de novo microdeletions on chromosome 16p11.2 were identified in patients with non-isolated CDH. Duplications of distal 11q and proximal 13q were found in a patient with non-isolated CDH and a de novo single gene deletion of FZD2 was identified in a patient with a partial pentalogy of Cantrell phenotype. CONCLUSIONS Haploinsufficiency of ZFPM2 can cause dominantly inherited isolated diaphragmatic defects with incomplete penetrance. These data define a new minimal deleted region for CDH on 1q41q42, provide evidence for the existence of CDH related genes on chromosomes 16p11.2, 11q23-24 and 13q12, and suggest a possible role for FZD2 and Wnt signalling in pentalogy of Cantrell phenotypes. These results demonstrate the clinical utility of screening for genomic alterations in individuals with both isolated and non-isolated diaphragmatic defects.
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Affiliation(s)
- Margaret J Wat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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