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Baird DA, Mubeen H, Doganli C, Miltenburg JB, Thomsen OK, Ali Z, Naveed T, Rehman AU, Baig SM, Christensen ST, Farooq M, Larsen LA. Rare homozygous cilia gene variants identified in consanguineous congenital heart disease patients. Hum Genet 2024:10.1007/s00439-024-02703-z. [PMID: 39347817 DOI: 10.1007/s00439-024-02703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 09/09/2024] [Indexed: 10/01/2024]
Abstract
Congenital heart defects (CHD) appear in almost one percent of live births. Asian countries have the highest birth prevalence of CHD in the world. Recessive genotypes may represent a CHD risk factor in Asian populations with a high degree of consanguineous marriages. Genetic analysis of consanguineous families may represent a relatively unexplored source for investigating CHD etiology. To obtain insight into the contribution of recessive genotypes in CHD we analysed a cohort of forty-nine Pakistani CHD probands, originating from consanguineous unions. The majority (82%) of patient's malformations were septal defects. We identified protein altering, rare homozygous variants (RHVs) in the patient's coding genome by whole exome sequencing. The patients had a median of seven damaging RHVs each, and our analysis revealed a total of 758 RHVs in 693 different genes. By prioritizing these genes based on variant severity, loss-of-function intolerance and specific expression in the developing heart, we identified a set of 23 candidate disease genes. These candidate genes were significantly enriched for genes known to cause heart defects in recessive mouse models (P < 2.4e-06). In addition, we found a significant enrichment of cilia genes in both the initial set of 693 genes (P < 5.4e-04) and the 23 candidate disease genes (P < 5.2e-04). Functional investigation of ADCY6 in cell- and zebrafish-models verified its role in heart development. Our results confirm a significant role for cilia genes in recessive forms of CHD and suggest important functions of cilia genes in cardiac septation.
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Affiliation(s)
- Daniel A Baird
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - Hira Mubeen
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Allama Iqbal Road, Faisalabad, 38000, Pakistan
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Canan Doganli
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - Jasmijn B Miltenburg
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | | | - Zafar Ali
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Tahir Naveed
- Rawalpindi Institute of Cardiology, Rawalpindi, Pakistan
| | | | - Shahid Mahmood Baig
- Faculty of Life Sciences, Health Services Academy, Islamabad, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | | | - Muhammad Farooq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Allama Iqbal Road, Faisalabad, 38000, Pakistan.
| | - Lars Allan Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark.
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2
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Blackburn PR, Ebstein F, Hsieh TC, Motta M, Radio FC, Herkert JC, Rinne T, Thiffault I, Rapp M, Alders M, Maas S, Gerard B, Smol T, Vincent-Delorme C, Cogné B, Isidor B, Vincent M, Bachmann-Gagescu R, Rauch A, Joset P, Ferrero GB, Ciolfi A, Husson T, Guerrot AM, Bacino C, Macmurdo C, Thompson SS, Rosenfeld JA, Faivre L, Mau-Them FT, Deb W, Vignard V, Agrawal PB, Madden JA, Goldenberg A, Lecoquierre F, Zech M, Prokisch H, Necpál J, Jech R, Winkelmann J, Koprušáková MT, Konstantopoulou V, Younce JR, Shinawi M, Mighton C, Fung C, Morel CF, Lerner-Ellis J, DiTroia S, Barth M, Bonneau D, Krapels I, Stegmann APA, van der Schoot V, Brunet T, Bußmann C, Mignot C, Zampino G, Wortmann SB, Mayr JA, Feichtinger RG, Courtin T, Ravelli C, Keren B, Ziegler A, Hasadsri L, Pichurin PN, Klee EW, Grand K, Sanchez-Lara PA, Krüger E, Bézieau S, Klinkhammer H, Krawitz PM, Eichler EE, Tartaglia M, Küry S, Wang T. Loss-of-Function Variants in CUL3 Cause a Syndromic Neurodevelopmental Disorder. Ann Neurol 2024. [PMID: 39301775 DOI: 10.1002/ana.27077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/22/2024]
Abstract
OBJECTIVE De novo variants in cullin-3 ubiquitin ligase (CUL3) have been strongly associated with neurodevelopmental disorders (NDDs), but no large case series have been reported so far. Here, we aimed to collect sporadic cases carrying rare variants in CUL3, describe the genotype-phenotype correlation, and investigate the underlying pathogenic mechanism. METHODS Genetic data and detailed clinical records were collected via multicenter collaboration. Dysmorphic facial features were analyzed using GestaltMatcher. Variant effects on CUL3 protein stability were assessed using patient-derived T-cells. RESULTS We assembled a cohort of 37 individuals with heterozygous CUL3 variants presenting a syndromic NDD characterized by intellectual disability with or without autistic features. Of these, 35 have loss-of-function (LoF) and 2 have missense variants. CUL3 LoF variants in patients may affect protein stability leading to perturbations in protein homeostasis, as evidenced by decreased ubiquitin-protein conjugates in vitro. Notably, we show that 4E-BP1 (EIF4EBP1), a prominent substrate of CUL3, fails to be targeted for proteasomal degradation in patient-derived cells. INTERPRETATION Our study further refines the clinical and mutational spectrum of CUL3-associated NDDs, expands the spectrum of cullin RING E3 ligase-associated neuropsychiatric disorders, and suggests haploinsufficiency via LoF variants is the predominant pathogenic mechanism. ANN NEUROL 2024.
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Affiliation(s)
- Patrick R Blackburn
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
| | - Tzung-Chien Hsieh
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Marialetizia Motta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Johanna C Herkert
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, USA
| | - Michele Rapp
- Department of Pediatrics-Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, CO, USA
| | - Mariel Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam, The Netherlands
| | - Saskia Maas
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam, The Netherlands
| | - Bénédicte Gerard
- Unité de Biologie et de Génétique Moléculaire, Center Hospitalier Universitaire de Strasbourg, Strasbourg, France
| | - Thomas Smol
- Univ Lille, CHU Lille, RADEME Team, Institut de Génétique Médicale, Lille, France
| | | | - Benjamin Cogné
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Marie Vincent
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Pascal Joset
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Giovanni Battista Ferrero
- Department of Clinical and Biological Sciences, San Luigi Gonzaga University Hospital, University of Torino, Turin, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Thomas Husson
- Department of Research, Center Hospitalier du Rouvray, Rouen, France
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France
| | - Anne-Marie Guerrot
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France
| | - Carlos Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Colleen Macmurdo
- Division of Medical Genetics, Department of Internal Medicine, Baylor Scott and White Medical Center, Temple, TX, USA
| | - Stephanie S Thompson
- Division of Medical Genetics, Department of Internal Medicine, Baylor Scott and White Medical Center, Temple, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD CHU, Dijon, France
- INSERM UMR1231, équipe GAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Frederic Tran Mau-Them
- INSERM UMR1231, équipe GAD, Université de Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Wallid Deb
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Virginie Vignard
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston, MA, USA
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL, USA
| | - Jill A Madden
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston, MA, USA
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL, USA
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Ján Necpál
- Department of Neurology, Zvolen Hospital, Zvolen, Slovakia
- Department of Neurology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Robert Jech
- Department of Neurology, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Neurogenetics, Technische Universitaet Muenchen, Munich, Germany
- Institute of Human Genetics, Klinikum rechts der Isar der TUM, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | | | - John R Younce
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, St. Louis Children's Hospital, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Charlotte Fung
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Sinai Health System, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Chantal F Morel
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Sinai Health System, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Canada
| | - Stephanie DiTroia
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Magalie Barth
- Department of Biochemistry and Genetics, University Hospital of Angers, Angers, France
- Mitovasc Unit, UMR CNRS 6015-INSERM 1083, Angers, France
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital of Angers, Angers, France
| | - Ingrid Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Vyne van der Schoot
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Dr. v. Hauner Children's Hospital, Department of Pediatric Neurology and Developmental Medicine, LMU-University of Munich, Munich, Germany
| | - Cornelia Bußmann
- Department of Neuropediatrics, ATOS Klinik Heidelberg, Heidelberg, Germany
| | - Cyril Mignot
- Département de Génétique, AP-HP-Sorbonne Université, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Giuseppe Zampino
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Saskia B Wortmann
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Johannes A Mayr
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - René G Feichtinger
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Thomas Courtin
- Center for Molecular and Chromosomal Genetics, AP-HP-Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Claudia Ravelli
- Department of Pediatric Neurology and Neurogenetic Referral Center, AP-HP-Sorbonne Université, Armand Trousseau Hospital, Paris, France
| | - Boris Keren
- Département de Génétique, AP-HP-Sorbonne Université, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Alban Ziegler
- Mitovasc Unit, UMR CNRS 6015-INSERM 1083, Angers, France
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS, Angers, France
| | - Linda Hasadsri
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Katheryn Grand
- Department of Pediatrics, Guerin Children's at Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Pedro A Sanchez-Lara
- Department of Pediatrics, Guerin Children's at Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Stéphane Bézieau
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Hannah Klinkhammer
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Peter Michael Krawitz
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Sébastien Küry
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique Médicale, Nantes, France
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
- Neuroscience Research Institute, Peking University, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, China
- Autism Research Center, Peking University Health Science Center, Beijing, China
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Barakat AJ, Butler MG. Genetics of anomalies of the kidney and urinary tract with congenital heart disease: A review. Clin Genet 2024. [PMID: 39289831 DOI: 10.1111/cge.14615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/19/2024]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) and congenital heart disease (CHD) are the most common congenital defects and constitute a major cause of morbidity in children. Anomalies of both systems may be isolated or associated with congenital anomalies of other organ systems. Various reports support the co-occurrence of CAKUT and CHD, although the prevalence can vary. Cardiovascular anomalies occur in 11.2% to 34% of patients with CAKUT, and CAKUT occur in 5.3% to 35.8% of those with CHD. The co-occurrence of genetic factors in both CAKUT and CHD would raise common etiologies including genetics, genetic-environmental interactions, or shared molecular mechanisms and pathways such as NODAL, NOTCH, BMP, WNT, and VEGF. Studies in animal models and humans have indicated a genetic etiology for CHD and CAKUT with hundreds of genes recognized and thousands of entries, found in a catalog of human genetic disorders. There are over 80 CAKUT genes and over 100 CHD genes available for clinical testing. For example, the HNFIB gene accounts for 5% to 31% of reported cases of CAKUT. In view of the association between CAKUT and CHD, a thorough cardiac examination should be performed in patients with CAKUT, and a similar evaluation for CAKUT in the presence of CHD. This will allow early diagnosis and therapeutic intervention to improve the long- term outcome of patients affected, and test for at-risk family members. We present here evidence for an association of anomalies involving the two organ systems, and discuss possible etiologies of targeted genes, their functions, biological processes and interactions on embryogenesis.
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Affiliation(s)
- Amin J Barakat
- Department of Pediatrics, Georgetown University Medical Center, Washington, DC, USA
| | - Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, USA
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Wang F, Chen F, Song W, Li Y, Wu H, Tian T, Tian M, Tang D, Liu Y. Sodium Fluoride Exposure Induces Developmental Toxicity and Cardiotoxicity in Zebrafish Embryos. Biol Trace Elem Res 2024:10.1007/s12011-024-04381-4. [PMID: 39287768 DOI: 10.1007/s12011-024-04381-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 09/14/2024] [Indexed: 09/19/2024]
Abstract
Fluorosis is a worldwide public health problem, in which the heart is an important target organ. However, studies on its toxicological mechanism in embryonic development are limited. This study assessed the toxicity of sodium fluoride (NaF) toward zebrafish embryos. We determined the mortality, hatching rate, phenotypic malformation, heart function, and morphology of zebrafish embryos after exposure to NaF. Subsequently, the molecular mechanism was revealed using high-throughput RNA sequencing analysis. The expression levels of key genes for heart development were detected using quantitative real-time reverse transcription PCR. The 50% lethal concentration (LC50) value of NaF toward zebrafish embryos at 96 h post-fertilization was 335.75 mg/L. When the concentration of NaF was higher than 200 mg/L, severe deformities, such as pericardial edema, yolk sac edema, spine curvature, shortened body length, reduced head area, and eye area, were observed. The heart rate of the embryos exposed to NaF decreased in a dose-dependent fashion. The distance between the sinus venosus and bulbus arteriosus was significantly increased in the NaF-exposed group compared with that in the control group. The stroke volume and cardiac output decreased significantly in the NaF groups. Compared with the control group, the expression levels of Gata4, Tbx5a, Hand2, Tnnt2c, Nppa, and Myh6 were significantly increased in the NaF-treated group. Through transcriptome sequencing, 1354 differentially expressed genes (DEGs) were detected in the NaF (200 mg/L) treated groups, including 1253 upregulated genes and 101 downregulated genes. Gene ontology functional analysis and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the DEGs showed that cardiac-related pathways, such as actin cytoskeleton regulation, Jak-Stat, PI3k-Akt, and Ras, were activated in the NaF-exposed group. This study revealed the underlying mechanism of fluoride-induced cardiac morphological and functional abnormalities and provides clues for the clinical prevention and treatment of fluorosis.
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Affiliation(s)
- Feiqing Wang
- Clinical Research Center, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 71 Bao Shan North Road, Yunyan District, Guiyang, 550001, Guizhou Province, China
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin City, 300072, China
| | - Fa Chen
- Clinical Research Center, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 71 Bao Shan North Road, Yunyan District, Guiyang, 550001, Guizhou Province, China
| | - Wen Song
- Clinical Research Center, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 71 Bao Shan North Road, Yunyan District, Guiyang, 550001, Guizhou Province, China
| | - Yanju Li
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
| | - Haiyan Wu
- Clinical Research Center, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 71 Bao Shan North Road, Yunyan District, Guiyang, 550001, Guizhou Province, China
| | - Tingting Tian
- Clinical Research Center, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 71 Bao Shan North Road, Yunyan District, Guiyang, 550001, Guizhou Province, China
| | - Mengxian Tian
- Clinical Research Center, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 71 Bao Shan North Road, Yunyan District, Guiyang, 550001, Guizhou Province, China
| | - Dongxin Tang
- Clinical Research Center, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 71 Bao Shan North Road, Yunyan District, Guiyang, 550001, Guizhou Province, China.
| | - Yang Liu
- Clinical Research Center, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 71 Bao Shan North Road, Yunyan District, Guiyang, 550001, Guizhou Province, China.
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Gao R, Yang H, Wang Y. SETD3 functions beyond histidine methylation. Life Sci 2024; 357:123064. [PMID: 39299385 DOI: 10.1016/j.lfs.2024.123064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/02/2024] [Accepted: 09/14/2024] [Indexed: 09/22/2024]
Abstract
SETD3 is a member of SET domain-containing proteins. It has been discovered as the first metazoan protein (actin) histidine methyltransferase. In addition to this well-characterized molecular function of SETD3, it has been clearly shown to be involved in multiple biological processes, such as cell differentiation, tumorigenesis and viral infection. Here, we summarize the current knowledge on the roles of SETD3 beyond its histidine methyltransferase activity, and outline its cellular and molecular modes of action, as well as the upstream regulation on SETD3, therefore providing insights for the molecular basis of how SETD3 fine regulates multiple physiological and pathological processes.
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Affiliation(s)
- Rui Gao
- Institute of Cardiovascular Diseases, Xiamen Cardiovascular Hospital, School of medicine, Xiamen University, Xiamen 361000, China.
| | - Hao Yang
- Institute of Cardiovascular Diseases, Xiamen Cardiovascular Hospital, School of medicine, Xiamen University, Xiamen 361000, China
| | - Yan Wang
- Institute of Cardiovascular Diseases, Xiamen Cardiovascular Hospital, School of medicine, Xiamen University, Xiamen 361000, China
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Huang Y, Dong X, Sun SY, Lim TK, Lin Q, He CY. ARL3 GTPases facilitate ODA16 unloading from IFT in motile cilia. SCIENCE ADVANCES 2024; 10:eadq2950. [PMID: 39231220 PMCID: PMC11373600 DOI: 10.1126/sciadv.adq2950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/30/2024] [Indexed: 09/06/2024]
Abstract
Eukaryotic cilia and flagella are essential for cell motility and sensory functions. Their biogenesis and maintenance rely on the intraflagellar transport (IFT). Several cargo adapters have been identified to aid IFT cargo transport, but how ciliary cargos are discharged from the IFT remains largely unknown. During our explorations of small GTPases ARL13 and ARL3 in Trypanosoma brucei, we found that ODA16, a known IFT cargo adapter present exclusively in motile cilia, is a specific effector of ARL3. In the cilia, active ARL3 GTPases bind to ODA16 and dissociate ODA16 from the IFT complex. Depletion of ARL3 GTPases stabilizes ODA16 interaction with the IFT, leading to ODA16 accumulation in cilia and defects in axonemal assembly. The interactions between human ODA16 homolog HsDAW1 and ARL GTPases are conserved, and these interactions are altered in HsDAW1 disease variants. These findings revealed a conserved function of ARL GTPases in IFT transport of motile ciliary components, and a mechanism of cargo unloading from the IFT.
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Affiliation(s)
- Yameng Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Xiaoduo Dong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Stella Y Sun
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Teck-Kwang Lim
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cynthia Y He
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- The Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
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7
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Monaghan RM, Naylor RW, Flatman D, Kasher PR, Williams SG, Keavney BD. FLT4 causes developmental disorders of the cardiovascular and lymphovascular systems via pleiotropic molecular mechanisms. Cardiovasc Res 2024; 120:1164-1176. [PMID: 38713105 PMCID: PMC11368125 DOI: 10.1093/cvr/cvae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 05/08/2024] Open
Abstract
AIMS Rare, deleterious genetic variants in FLT4 are associated with Tetralogy of Fallot (TOF), the most common cyanotic congenital heart disease. The distinct genetic variants in FLT4 are also an established cause of Milroy disease, the most prevalent form of primary hereditary lymphoedema. The phenotypic features of these two conditions are non-overlapping, implying pleiotropic cellular mechanisms during development. METHODS AND RESULTS In this study, we show that FLT4 variants identified in patients with TOF, when expressed in primary human endothelial cells, cause aggregation of FLT4 protein in the perinuclear endoplasmic reticulum, activating proteostatic and metabolic signalling, whereas lymphoedema-associated FLT4 variants and wild-type (WT) FLT4 do not. FLT4 TOF variants display characteristic gene expression profiles in key developmental signalling pathways, revealing a role for FLT4 in cardiogenesis distinct from its role in lymphatic development. Inhibition of proteostatic signalling abrogates these effects, identifying potential avenues for therapeutic intervention. Depletion of flt4 in zebrafish caused cardiac phenotypes of reduced heart size and altered heart looping. These phenotypes were rescued with coinjection of WT human FLT4 mRNA, but incompletely or not at all by mRNA harbouring FLT4 TOF variants. CONCLUSION Taken together, we identify a pathogenic mechanism for FLT4 variants predisposing to TOF that is distinct from the known dominant negative mechanism of Milroy-causative variants. FLT4 variants give rise to conditions of the two circulatory subdivisions of the vascular system via distinct developmental pleiotropic molecular mechanisms.
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Affiliation(s)
- Richard M Monaghan
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, 5th Floor, AV Hill Building, Oxford Road, Manchester, M13 9NT, UK
| | - Richard W Naylor
- Wellcome Centre for Cell Matrix Research, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, M13 9PN, UK
| | - Daisy Flatman
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Paul R Kasher
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Simon G Williams
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, 5th Floor, AV Hill Building, Oxford Road, Manchester, M13 9NT, UK
| | - Bernard D Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, 5th Floor, AV Hill Building, Oxford Road, Manchester, M13 9NT, UK
- Manchester Heart Institute, Manchester University NHS Foundation Trust, Oxford Road, M13 9WL, UK
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8
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Nawaz K, Alifah N, Hussain T, Hameed H, Ali H, Hamayun S, Mir A, Wahab A, Naeem M, Zakria M, Pakki E, Hasan N. From genes to therapy: A comprehensive exploration of congenital heart disease through the lens of genetics and emerging technologies. Curr Probl Cardiol 2024; 49:102726. [PMID: 38944223 DOI: 10.1016/j.cpcardiol.2024.102726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Congenital heart disease (CHD) affects approximately 1 % of live births worldwide, making it the most common congenital anomaly in newborns. Recent advancements in genetics and genomics have significantly deepened our understanding of the genetics of CHDs. While the majority of CHD etiology remains unclear, evidence consistently indicates that genetics play a significant role in its development. CHD etiology holds promise for enhancing diagnosis and developing novel therapies to improve patient outcomes. In this review, we explore the contributions of both monogenic and polygenic factors of CHDs and highlight the transformative impact of emerging technologies on these fields. We also summarized the state-of-the-art techniques, including targeted next-generation sequencing (NGS), whole genome and whole exome sequencing (WGS, WES), single-cell RNA sequencing (scRNA-seq), human induced pluripotent stem cells (hiPSCs) and others, that have revolutionized our understanding of cardiovascular disease genetics both from diagnosis perspective and from disease mechanism perspective in children and young adults. These molecular diagnostic techniques have identified new genes and chromosomal regions involved in syndromic and non-syndromic CHD, enabling a more defined explanation of the underlying pathogenetic mechanisms. As our knowledge and technologies continue to evolve, they promise to enhance clinical outcomes and reduce the CHD burden worldwide.
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Affiliation(s)
- Khalid Nawaz
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Nur Alifah
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Talib Hussain
- Women Dental College, Khyber Medical University, Abbottabad, 22080, Khyber Pakhtunkhwa, Pakistan
| | - Hamza Hameed
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Haider Ali
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shah Hamayun
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Awal Mir
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Mohammad Zakria
- Advanced Center for Genomic Technologies, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Ermina Pakki
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia.
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9
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Kalisch-Smith JI, Ehtisham-Uddin N, Rodriguez-Caro H. Feto-placental and coronary endothelial genes implicated in miscarriage, congenital heart disease and stillbirth, a systematic review and meta-analysis. Placenta 2024; 156:55-66. [PMID: 39276426 DOI: 10.1016/j.placenta.2024.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/12/2024] [Accepted: 08/27/2024] [Indexed: 09/17/2024]
Abstract
The first trimester placenta is very rarely investigated for placental vascular formation in developmental or diseased contexts. Defects in placental formation can cause heart defects in the fetus, and vice versa. Determining the causality is therefore difficult as both organs develop concurrently and express many of the same genes. Here, we performed a systematic review to determine feto-placental and coronary endothelial genes implicated in miscarriages, stillbirth and congenital heart defects (CHD) from human genome wide screening studies. 4 single cell RNAseq datasets from human first/early second trimester cardiac and placental samples were queried to generate a list of 1187 endothelial genes. This broad list was cross-referenced with genes implicated in the pregnancy disorders above. 39 papers reported feto-placental and cardiac coronary endothelial genes, totalling 612 variants. Vascular gene variants were attributed to the incidence of miscarriage (8 %), CHD (4 %) and stillbirth (3 %). The most common genes for CHD (NOTCH, DST, FBN1, JAG1, CHD4), miscarriage (COL1A1, HERC1), and stillbirth (AKAP9, MYLK), were involved in blood vessel and cardiac valve formation, with roles in endothelial differentiation, angiogenesis, extracellular matrix signaling, growth factor binding and cell adhesion. NOTCH1, AKAP12, CHD4, LAMC1 and SOS1 showed greater relative risk ratios with CHD. Many of the vascular genes identified were expressed highly in both placental and heart EC populations. Both feto-placental and cardiac vascular genes are likely to result in poor endothelial cell development and function during human pregnancy that leads to higher risk of miscarriage, congenital heart disease and stillbirth.
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Affiliation(s)
- Jacinta I Kalisch-Smith
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX3 7TY, UK.
| | - Nusaybah Ehtisham-Uddin
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX3 7TY, UK
| | - Helena Rodriguez-Caro
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX3 7TY, UK; Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research, Lausanne, Switzerland
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10
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Liang J, He X, Wang Y. Cardiomyocyte proliferation and regeneration in congenital heart disease. PEDIATRIC DISCOVERY 2024; 2:e2501. [PMID: 39308981 PMCID: PMC11412308 DOI: 10.1002/pdi3.2501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/25/2024] [Indexed: 09/25/2024]
Abstract
Despite advances in prenatal screening and a notable decrease in mortality rates, congenital heart disease (CHD) remains the most prevalent congenital disorder in newborns globally. Current therapeutic surgical approaches face challenges due to the significant rise in complications and disabilities. Emerging cardiac regenerative therapies offer promising adjuncts for CHD treatment. One novel avenue involves investigating methods to stimulate cardiomyocyte proliferation. However, the mechanism of altered cardiomyocyte proliferation in CHD is not fully understood, and there are few feasible approaches to stimulate cardiomyocyte cell cycling for optimal healing in CHD patients. In this review, we explore recent progress in understanding genetic and epigenetic mechanisms underlying defective cardiomyocyte proliferation in CHD from development through birth. Targeting cell cycle pathways shows promise for enhancing cardiomyocyte cytokinesis, division, and regeneration to repair heart defects. Advancements in human disease modeling techniques, CRISPR-based genome and epigenome editing, and next-generation sequencing technologies will expedite the exploration of abnormal machinery governing cardiomyocyte differentiation, proliferation, and maturation across diverse genetic backgrounds of CHD. Ongoing studies on screening drugs that regulate cell cycling are poised to translate this nascent technology of enhancing cardiomyocyte proliferation into a new therapeutic paradigm for CHD surgical interventions.
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Affiliation(s)
- Jialiang Liang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Xingyu He
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
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11
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Li L, Lu L, Xiao Z, Lv J, Huang H, Wu B, Zhao T, Li C, Wang W, Wang H. Deamidation enables pathogenic SMAD6 variants to activate the BMP signaling pathway. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1915-1927. [PMID: 38913236 DOI: 10.1007/s11427-023-2532-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 01/23/2024] [Indexed: 06/25/2024]
Abstract
The BMP signaling pathway plays a crucial role in regulating early embryonic development and tissue homeostasis. SMAD6 encodes a negative regulator of BMP, and rare variants of SMAD6 are recurrently found in individuals with birth defects. However, we observed that a subset of rare pathogenic variants of SMAD6 consistently exhibited positive regulatory effects instead of the initial negative effects on the BMP signaling pathway. We sought to determine whether these SMAD6 variants have common pathogenic mechanisms. Here, we showed that pathogenic SMAD6 variants accompanying this functional reversal exhibit similar increases in deamidation. Mechanistically, increased deamidation of SMAD6 variants promotes the accumulation of the BMP receptor BMPR1A and the formation of new complexes, both of which lead to BMP signaling pathway activation. Specifically, two residues, N262 and N404, in SMAD6 were identified as the crucial sites of deamidation, which was catalyzed primarily by glutamine-fructose-6-phosphate transaminase 2 (GFPT2). Additionally, treatment of cells harboring SMAD6 variants with a deamidase inhibitor restored the inhibitory effect of SMAD6 on the BMP signaling pathway. Conversely, when wild-type SMAD6 was manually simulated to mimic the deamidated state, the reversed function of activating BMP signaling was reproduced. Taken together, these findings show that deamidation of SMAD6 plays a crucial role in the functional reversal of BMP signaling activity, which can be induced by a subset of various SMAD6 variants. Our study reveals a common pathogenic mechanism shared by these variants and provides a potential strategy for preventing birth defects through deamidation regulation, which might prevent the off-target effects of gene editing.
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Affiliation(s)
- Ling Li
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, and Children's Hospital, Fudan University, Shanghai, 200090, China
| | - Lei Lu
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China.
| | - Ziqi Xiao
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China
| | - Jingyi Lv
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, and Children's Hospital, Fudan University, Shanghai, 200090, China
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, and Children's Hospital, Fudan University, Shanghai, 200090, China
| | - Bo Wu
- Prenatal Diagnosis Center of Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, 518028, China
| | - Tongjin Zhao
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China
| | - Chengtao Li
- Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Weimin Wang
- Department of Pharmacy, College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, and Children's Hospital, Fudan University, Shanghai, 200090, China.
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China.
- Prenatal Diagnosis Center of Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, 518028, China.
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12
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Mansoorshahi S, Yetman AT, Bissell MM, Kim YY, Michelena HI, De Backer J, Mosquera LM, Hui DS, Caffarelli A, Andreassi MG, Foffa I, Guo D, Citro R, De Marco M, Tretter JT, Morris SA, Body SC, Chong JX, Bamshad MJ, Milewicz DM, Prakash SK. Whole-exome sequencing uncovers the genetic complexity of bicuspid aortic valve in families with early-onset complications. Am J Hum Genet 2024:S0002-9297(24)00287-8. [PMID: 39226896 DOI: 10.1016/j.ajhg.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 09/05/2024] Open
Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart lesion with an estimated population prevalence of 1%. We hypothesize that specific gene variants predispose to early-onset complications of BAV (EBAV). We analyzed whole-exome sequences (WESs) to identify rare coding variants that contribute to BAV disease in 215 EBAV-affected families. Predicted damaging variants in candidate genes with moderate or strong supportive evidence to cause developmental cardiac phenotypes were present in 107 EBAV-affected families (50% of total), including genes that cause BAV (9%) or heritable thoracic aortic disease (HTAD, 19%). After appropriate filtration, we also identified 129 variants in 54 candidate genes that are associated with autosomal-dominant congenital heart phenotypes, including recurrent deleterious variation of FBN2, MYH6, channelopathy genes, and type 1 and 5 collagen genes. These findings confirm our hypothesis that unique rare genetic variants drive early-onset presentations of BAV disease.
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Affiliation(s)
- Sara Mansoorshahi
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Anji T Yetman
- Children's Hospital and Medical Center, University of Nebraska, Omaha, NE, USA
| | - Malenka M Bissell
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Yuli Y Kim
- Division of Cardiovascular Medicine, The Hospital of the University of Pennsylvania, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | - Julie De Backer
- Department of Cardiology and Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Laura Muiño Mosquera
- Department of Cardiology and Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Dawn S Hui
- Department of Cardiothoracic Surgery, University of Texas Health Science Center, San Antonio, TX, USA
| | - Anthony Caffarelli
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Maria G Andreassi
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Ilenia Foffa
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Dongchuan Guo
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rodolfo Citro
- Cardiothoracic and Vascular Department, University Hospital "San Giovanni di Dio e Ruggi d'Aragona," Salerno, Italy
| | - Margot De Marco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy
| | | | - Shaine A Morris
- Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Simon C Body
- Department of Anesthesiology, Boston University School of Medicine, Boston, MA, USA
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Dianna M Milewicz
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Siddharth K Prakash
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.
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13
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Seeler S, Arnarsson K, Dreßen M, Krane M, Doppler SA. Beyond the Heartbeat: Single-Cell Omics Redefining Cardiovascular Research. Curr Cardiol Rep 2024:10.1007/s11886-024-02117-3. [PMID: 39158785 DOI: 10.1007/s11886-024-02117-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/07/2024] [Indexed: 08/20/2024]
Abstract
PURPOSE OF REVIEW This review aims to explore recent advances in single-cell omics techniques as applied to various regions of the human heart, illuminating cellular diversity, regulatory networks, and disease mechanisms. We examine the contributions of single-cell transcriptomics, genomics, proteomics, epigenomics, and spatial transcriptomics in unraveling the complexity of cardiac tissues. RECENT FINDINGS Recent strides in single-cell omics technologies have revolutionized our understanding of the heart's cellular composition, cell type heterogeneity, and molecular dynamics. These advancements have elucidated pathological conditions as well as the cellular landscape in heart development. We highlight emerging applications of integrated single-cell omics, particularly for cardiac regeneration, disease modeling, and precision medicine, and emphasize the transformative potential of these technologies to advance cardiovascular research and clinical practice.
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Affiliation(s)
- Sabine Seeler
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
| | - Kristjan Arnarsson
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
| | - Martina Dreßen
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Division of Cardiac Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Stefanie A Doppler
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany.
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany.
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14
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Vandewouw MM, Norris-Brilliant A, Rahman A, Assimopoulos S, Morton SU, Kushki A, Cunningham S, King E, Goldmuntz E, Miller TA, Thomas NH, Adams HR, Cleveland J, Cnota JF, Ellen Grant P, Goldberg CS, Huang H, Li JS, McQuillen P, Porter GA, Roberts AE, Russell MW, Seidman CE, Tivarus ME, Chung WK, Hagler DJ, Newburger JW, Panigrahy A, Lerch JP, Gelb BD, Anagnostou E. Identifying novel data-driven subgroups in congenital heart disease using multi-modal measures of brain structure. Neuroimage 2024; 297:120721. [PMID: 38968977 DOI: 10.1016/j.neuroimage.2024.120721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/18/2024] [Accepted: 07/03/2024] [Indexed: 07/07/2024] Open
Abstract
Individuals with congenital heart disease (CHD) have an increased risk of neurodevelopmental impairments. Given the hypothesized complexity linking genomics, atypical brain structure, cardiac diagnoses and their management, and neurodevelopmental outcomes, unsupervised methods may provide unique insight into neurodevelopmental variability in CHD. Using data from the Pediatric Cardiac Genomics Consortium Brain and Genes study, we identified data-driven subgroups of individuals with CHD from measures of brain structure. Using structural magnetic resonance imaging (MRI; N = 93; cortical thickness, cortical volume, and subcortical volume), we identified subgroups that differed primarily on cardiac anatomic lesion and language ability. In contrast, using diffusion MRI (N = 88; white matter connectivity strength), we identified subgroups that were characterized by differences in associations with rare genetic variants and visual-motor function. This work provides insight into the differential impacts of cardiac lesions and genomic variation on brain growth and architecture in patients with CHD, with potentially distinct effects on neurodevelopmental outcomes.
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Affiliation(s)
- Marlee M Vandewouw
- Autism Research Centre, Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
| | | | - Anum Rahman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada; Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Stephania Assimopoulos
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Sarah U Morton
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Azadeh Kushki
- Autism Research Centre, Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Sean Cunningham
- Department of Pediatrics, Division of General Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Eileen King
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA; Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Centre, Cincinnati, OH, USA
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas A Miller
- Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Nina H Thomas
- Department of Child and Adolescent Psychiatry and Behavioral Sciences and Center for Human Phenomic Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Heather R Adams
- Departments of Neurology and Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - John Cleveland
- Departments of Surgery and Pediatrics, Keck School of Medicine, University of Southern California, LA, USA
| | - James F Cnota
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA; Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - P Ellen Grant
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Department of Radiology, Boston Children's Hospital, Boston, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Caren S Goldberg
- Department of Pediatrics, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI, USA
| | - Hao Huang
- Department of Radiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer S Li
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Patrick McQuillen
- Departments of Pediatrics and Neurology, University of California San Francisco, San Francisco, CA, USA
| | - George A Porter
- Departments of Neurology and Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Amy E Roberts
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Department of Cardiology, Boston Children's Hospital, Boston, MA USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Mark W Russell
- Department of Pediatrics, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Madalina E Tivarus
- Department of Imaging Sciences and Department of Neuroscience, University of Rochester Medical Center, Rochester, NY, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Donald J Hagler
- Center for Multimodal Imaging and Genetics, University of California San Diego, USA; Department of Radiology, School of Medicine, University of California San Diego, USA; Departments of Cognitive Science and Neuroscience, University of California San Diego, USA
| | - Jane W Newburger
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Department of Cardiology, Boston Children's Hospital, Boston, MA USA
| | - Ashok Panigrahy
- Department of Pediatric Radiology, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA USA
| | - Jason P Lerch
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Program in Neurosciences & Mental Health, The Hospital for Sick Children, Toronto, ON, Canada; Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Evdokia Anagnostou
- Autism Research Centre, Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada; Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
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15
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Sun S, Ji Y, Shao D, Xu Y, Yang X, Sun L, Li N, Huang H, Wu Q. Genomic insights into prenatal diagnosis of congenital heart defects: value of CNV-seq and WES in clinical practice. Front Genet 2024; 15:1448383. [PMID: 39205944 PMCID: PMC11349688 DOI: 10.3389/fgene.2024.1448383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
This study aimed to assess the efficiency of CNV-seq and WES in detecting genetic cause of congenital heart disease (CHDs) in prenatal diagnoses and to compare CNV detection rate between isolated and non-isolated CHD cases. We conducted a retrospective study of 118 Chinese fetuses diagnosed with CHD by prenatal ultrasound. Participants underwent CNV-seq and, if necessary, WES to detect chromosomal and single nucleotide variations. The overall detection rate for pathogenic or likely pathogenic chromosomal abnormalities was 16.9%, including 7.6% aneuploidies and 9.3% pathogenic/likely pathogenic copy number variations (CNVs), predominantly 22q11.2 deletion syndrome (54.4%). The sensitivity and specificity of CNV-Seq for detecting P/Lp CNVs were 95% and 100%, respectively. CNV-Seq offered a 6.7% improvement in detecting chromosomal abnormalities over karyotyping. WES further identified significant single nucleotide and small indel variations contributing to CHD in genes such as TMEM67, PLD1, ANKRD11, and PNKP, enhancing diagnostic yield by 14.8% in cases negative for CNVs. Non-isolated CHD cases exhibited higher rates of detectable chromosomal abnormalities compared to isolated cases (32.4% vs. 9.9%, p = 0.005), underlining the genetic complexity of these conditions. The combined use of CNV-seq and WES provides a comprehensive approach to prenatal genetic testing for CHDs, unveiling significant genetic cause that could impact clinical management and parental decision-making. This study supports the integration of these advanced genomic technologies in routine prenatal diagnostics to increase detection diagnostic yields of causal genetic variants associated with CHDs.
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Affiliation(s)
- Shiyu Sun
- Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yizhen Ji
- Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Di Shao
- BGI Genomics, Shenzhen, China
| | - Yasong Xu
- Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Xiaomei Yang
- Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Li Sun
- Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Nan Li
- BGI Genomics, Shenzhen, China
| | | | - Qichang Wu
- Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
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16
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Nadimpalli Kobren S, Moldovan MA, Reimers R, Traviglia D, Li X, Barnum D, Veit A, Willett J, Berselli M, Ronchetti W, Sherwood R, Krier J, Kohane IS, Sunyaev SR. Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580158. [PMID: 38405764 PMCID: PMC10888768 DOI: 10.1101/2024.02.13.580158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development.1,2 The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale N-of-1 analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser (https://dbmi-bgm.github.io/udn-browser/). These results show that N-of-1 efforts should be supplemented by a joint genomic analysis across cohorts.
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Affiliation(s)
| | | | | | - Daniel Traviglia
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Xinyun Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| | | | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Julian Willett
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Michele Berselli
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - William Ronchetti
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Richard Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joel Krier
- Department of Genetics, Atrius Health, Boston, MA
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | | | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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17
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Luo X, Liu L, Rong H, Liu X, Yang L, Li N, Shi H. ENU-based dominant genetic screen identifies contractile and neuronal gene mutations in congenital heart disease. Genome Med 2024; 16:97. [PMID: 39135118 PMCID: PMC11318149 DOI: 10.1186/s13073-024-01372-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is the most prevalent congenital anomaly, but its underlying causes are still not fully understood. It is believed that multiple rare genetic mutations may contribute to the development of CHD. METHODS In this study, we aimed to identify novel genetic risk factors for CHD using an ENU-based dominant genetic screen in mice. We analyzed fetuses with malformed hearts and compared them to control littermates by whole exome or whole genome sequencing (WES/WGS). The differences in mutation rates between observed and expected values were tested using the Poisson and Binomial distribution. Additionally, we compared WES data from human CHD probands obtained from the Pediatric Cardiac Genomics Consortium with control subjects from the 1000 Genomes Project using Fisher's exact test to evaluate the burden of rare inherited damaging mutations in patients. RESULTS By screening 10,285 fetuses, we identified 1109 cases with various heart defects, with ventricular septal defects and bicuspid aortic valves being the most common types. WES/WGS analysis of 598 cases and 532 control littermates revealed a higher number of ENU-induced damaging mutations in cases compared to controls. GO term and KEGG pathway enrichment analysis showed that pathways related to cardiac contraction and neuronal development and functions were enriched in cases. Further analysis of 1457 human CHD probands and 2675 control subjects also revealed an enrichment of genes associated with muscle and nervous system development in patients. By combining the mice and human data, we identified a list of 101 candidate digenic genesets, from which each geneset was co-mutated in at least one mouse and two human probands with CHD but not in control mouse and control human subjects. CONCLUSIONS Our findings suggest that gene mutations affecting early hemodynamic perturbations in the developing heart may play a significant role as a genetic risk factor for CHD. Further validation of the candidate gene set identified in this study could enhance our understanding of the complex genetics underlying CHD and potentially lead to the development of new diagnostic and therapeutic approaches.
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Affiliation(s)
- Xiaoxi Luo
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- School of Medicine, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lifeng Liu
- School of Medicine, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Haowei Rong
- School of Medicine, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xiangyang Liu
- School of Medicine, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Ling Yang
- Westlake University High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Nan Li
- Westlake University High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Hongjun Shi
- School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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18
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Bhattacharya R, Ward T, Kalejaiye TD, Mishra A, Leeman S, Arzaghi H, Seidman JG, Seidman CE, Musah S. Engineered human iPS cell models reveal altered podocytogenesis and glomerular capillary wall in CHD-associated SMAD2 mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606108. [PMID: 39211233 PMCID: PMC11360959 DOI: 10.1101/2024.08.02.606108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Early developmental programming involves extensive cell lineage diversification through shared molecular signaling networks. Clinical observations of congenital heart disease (CHD) patients carrying SMAD2 genetic variants revealed correlations with multi-organ impairments at the developmental and functional levels. For example, many CHD patients present with glomerulosclerosis, periglomerular fibrosis, and albuminuria. Still, it remains largely unknown whether SMAD2 variants associated with CHD can directly alter kidney cell fate, tissue patterning, and organ-level function. To address this question, we engineered human iPS cells (iPSCs) and organ-on-a-chip systems to uncover the role of pathogenic SMAD2 variants in kidney podocytogenesis. Our results show that abrogation of SMAD2 causes altered patterning of the mesoderm and intermediate mesoderm (IM) cell lineages, which give rise to nearly all kidney cell types. Upon further differentiation of IM cells, the mutant podocytes failed to develop arborizations and interdigitations. A reconstituted glomerulus-on-a-chip platform exhibited significant proteinuria as clinically observed in glomerulopathies. This study implicates CHD-associated SMAD2 mutations in kidney tissue malformation and provides opportunities for therapeutic discovery in the future.
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19
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Gabriel GC, Ganapathiraju M, Lo CW. The Role of Cilia and the Complex Genetics of Congenital Heart Disease. Annu Rev Genomics Hum Genet 2024; 25:309-327. [PMID: 38724024 DOI: 10.1146/annurev-genom-121222-105345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Congenital heart disease (CHD) can affect up to 1% of live births, and despite abundant evidence of a genetic etiology, the genetic landscape of CHD is still not well understood. A large-scale mouse chemical mutagenesis screen for mutations causing CHD yielded a preponderance of cilia-related genes, pointing to a central role for cilia in CHD pathogenesis. The genes uncovered by the screen included genes that regulate ciliogenesis and cilia-transduced cell signaling as well as many that mediate endocytic trafficking, a cell process critical for both ciliogenesis and cell signaling. The clinical relevance of these findings is supported by whole-exome sequencing analysis of CHD patients that showed enrichment for pathogenic variants in ciliome genes. Surprisingly, among the ciliome CHD genes recovered were many that encoded direct protein-protein interactors. Assembly of the CHD genes into a protein-protein interaction network yielded a tight interactome that suggested this protein-protein interaction may have functional importance and that its disruption could contribute to the pathogenesis of CHD. In light of these and other findings, we propose that an interactome enriched for ciliome genes may provide the genomic context for the complex genetics of CHD and its often-observed incomplete penetrance and variable expressivity.
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Affiliation(s)
- George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; ,
| | - Madhavi Ganapathiraju
- Carnegie Mellon University in Qatar, Doha, Qatar
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA;
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; ,
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20
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Song Z, Bian W, Lin J, Guo Y, Shi W, Meng H, Chen Y, Zhang M, Liu Z, Lin Z, Ma K, Li L. Heart proteomic profiling discovers MYH6 and COX5B as biomarkers for sudden unexplained death. Forensic Sci Int 2024; 361:112121. [PMID: 38971138 DOI: 10.1016/j.forsciint.2024.112121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/03/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Sudden unexplained death (SUD) is not uncommon in forensic pathology. Yet, diagnosis of SUD remains challenging due to lack of specific biomarkers. This study aimed to screen differentially expressed proteins (DEPs) and validate their usefulness as diagnostic biomarkers for SUD cases. We designed a three-phase investigation, where in the discovery phase, formalin-fixed paraffin-embedded (FFPE) heart specimens were screened through label-free proteomic analysis of cases dying from SUD, mechanical injury and carbon monoxide (CO) intoxication. A total of 26 proteins were identified to be DEPs for the SUD cases after rigorous criterion. Bioinformatics and Adaboost-recursive feature elimination (RFE) analysis further revealed that three of the 26 proteins (MYH6, COX5B and TNNT2) were potential discriminative biomarkers. In the training phase, MYH6 and COX5B were verified to be true DEPs in cardiac tissues from 29 independent SUD cases as compared with a serial of control cases (n = 42). Receiver operating characteristic (ROC) analysis illustrated that combination of MYH6 and COX5B achieved optimal diagnostic sensitivity (89.7 %) and specificity (84.4 %), with area under the curve (AUC) being 0.91. A diagnostic software based on the logistic regression formula derived from the training phase was then constructed. In the validation phase, the diagnostic software was applied to eight authentic SUD cases, seven (87.5 %) of which were accurately recognized. Our study provides a valid strategy towards practical diagnosis of SUD by integrating cardiac MYH6 and COX5B as dual diagnostic biomarkers.
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Affiliation(s)
- Ziyan Song
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Wensi Bian
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Junyi Lin
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Yadong Guo
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, PR China.
| | - Weibo Shi
- Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, Hebei 050017, PR China.
| | - Hang Meng
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Public Security, Bureau, Shanghai 200083, PR China.
| | - Yuanyuan Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, Jiangxi 341000, PR China.
| | - Molin Zhang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Zheng Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Zijie Lin
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Kaijun Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Public Security, Bureau, Shanghai 200083, PR China.
| | - Liliang Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China; Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, Hebei 050017, PR China; Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Public Security, Bureau, Shanghai 200083, PR China.
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21
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Teerikorpi N, Lasser MC, Wang S, Kostyanovskaya E, Bader E, Sun N, Dea J, Nowakowski TJ, Willsey AJ, Willsey HR. Ciliary biology intersects autism and congenital heart disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.602578. [PMID: 39131273 PMCID: PMC11312554 DOI: 10.1101/2024.07.30.602578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Autism spectrum disorder (ASD) commonly co-occurs with congenital heart disease (CHD), but the molecular mechanisms underlying this comorbidity remain unknown. Given that children with CHD come to clinical attention by the newborn period, understanding which CHD variants carry ASD risk could provide an opportunity to identify and treat individuals at high risk for developing ASD far before the typical age of diagnosis. Therefore, it is critical to delineate the subset of CHD genes most likely to increase the risk of ASD. However, to date there is relatively limited overlap between high confidence ASD and CHD genes, suggesting that alternative strategies for prioritizing CHD genes are necessary. Recent studies have shown that ASD gene perturbations commonly dysregulate neural progenitor cell (NPC) biology. Thus, we hypothesized that CHD genes that disrupt neurogenesis are more likely to carry risk for ASD. Hence, we performed an in vitro pooled CRISPR interference (CRISPRi) screen to identify CHD genes that disrupt NPC biology similarly to ASD genes. Overall, we identified 45 CHD genes that strongly impact proliferation and/or survival of NPCs. Moreover, we observed that a cluster of physically interacting ASD and CHD genes are enriched for ciliary biology. Studying seven of these genes with evidence of shared risk (CEP290, CHD4, KMT2E, NSD1, OFD1, RFX3, TAOK1), we observe that perturbation significantly impacts primary cilia formation in vitro. While in vivo investigation of TAOK1 reveals a previously unappreciated role for the gene in motile cilia formation and heart development, supporting its prediction as a CHD risk gene. Together, our findings highlight a set of CHD risk genes that may carry risk for ASD and underscore the role of cilia in shared ASD and CHD biology.
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Affiliation(s)
- Nia Teerikorpi
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Micaela C. Lasser
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sheng Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elina Kostyanovskaya
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ethel Bader
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J. Nowakowski
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco CA 94158, USA
- Department of Anatomy, University of California, San Francisco, San Francisco CA 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research University of California, San Francisco, San Francisco CA 94158, USA
| | - A. Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA 94158, USA
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22
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Viswanathan S, Sandeep Oza P, Bellad A, Uttarilli A. Conotruncal Heart Defects: A Narrative Review of Molecular Genetics, Genomics Research and Innovation. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:324-346. [PMID: 38986083 DOI: 10.1089/omi.2024.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Congenital heart defects (CHDs) are most prevalent cardiac defects that occur at birth, leading to significant neonatal mortality and morbidity, especially in the developing nations. Among the CHDs, conotruncal heart defects (CTDs) are particularly noteworthy, comprising a significant portion of congenital cardiac anomalies. While advances in imaging and surgical techniques have improved the diagnosis, prognosis, and management of CTDs, their molecular genetics and genomic substrates remain incompletely understood. This expert review covers the recent advances from January 2016 onward and examines the complexities surrounding the genetic etiologies, prevalence, embryology, diagnosis, and clinical management of CTDs. We also emphasize the known copy number variants and single nucleotide variants associated with CTDs, along with the current planetary health research efforts aimed at CTDs in large cohort studies. In all, this comprehensive narrative review of molecular genetics and genomics research and innovation on CTDs draws from and highlights selected works from around the world and offers new ideas for advances in CTD diagnosis, precision medicine interventions, and accurate assessment of prognosis and recurrence risks.
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Affiliation(s)
- Sruthi Viswanathan
- Institute of Bioinformatics, Bengaluru, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prachi Sandeep Oza
- Institute of Bioinformatics, Bengaluru, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anikha Bellad
- Institute of Bioinformatics, Bengaluru, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anusha Uttarilli
- Institute of Bioinformatics, Bengaluru, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
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23
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Kibalnyk Y, Afanasiev E, Noble RMN, Watson AES, Poverennaya I, Dittmann NL, Alexiou M, Goodkey K, Greenwell AA, Ussher JR, Adameyko I, Massey J, Graf D, Bourque SL, Stratton JA, Voronova A. The chromatin regulator Ankrd11 controls cardiac neural crest cell-mediated outflow tract remodeling and heart function. Nat Commun 2024; 15:4632. [PMID: 38951500 PMCID: PMC11217281 DOI: 10.1038/s41467-024-48955-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/17/2024] [Indexed: 07/03/2024] Open
Abstract
ANKRD11 (Ankyrin Repeat Domain 11) is a chromatin regulator and a causative gene for KBG syndrome, a rare developmental disorder characterized by multiple organ abnormalities, including cardiac defects. However, the role of ANKRD11 in heart development is unknown. The neural crest plays a leading role in embryonic heart development, and its dysfunction is implicated in congenital heart defects. We demonstrate that conditional knockout of Ankrd11 in the murine embryonic neural crest results in persistent truncus arteriosus, ventricular dilation, and impaired ventricular contractility. We further show these defects occur due to aberrant cardiac neural crest cell organization leading to outflow tract septation failure. Lastly, knockout of Ankrd11 in the neural crest leads to impaired expression of various transcription factors, chromatin remodelers and signaling pathways, including mTOR, BMP and TGF-β in the cardiac neural crest cells. In this work, we identify Ankrd11 as a regulator of neural crest-mediated heart development and function.
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Affiliation(s)
- Yana Kibalnyk
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- Women and Children's Health Research Institute, 5-083 Edmonton Clinic Health Academy, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
| | - Elia Afanasiev
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Ronan M N Noble
- Women and Children's Health Research Institute, 5-083 Edmonton Clinic Health Academy, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - Adrianne E S Watson
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- Women and Children's Health Research Institute, 5-083 Edmonton Clinic Health Academy, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
| | - Irina Poverennaya
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, 1090, Vienna, Austria
| | - Nicole L Dittmann
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- Neuroscience and Mental Health Institute, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Maria Alexiou
- Department of Dentistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Kara Goodkey
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- Women and Children's Health Research Institute, 5-083 Edmonton Clinic Health Academy, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
| | - Amanda A Greenwell
- Women and Children's Health Research Institute, 5-083 Edmonton Clinic Health Academy, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
- Faculty of Pharmacy & Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Edmonton, AB, T6G 2H1, Canada
| | - John R Ussher
- Women and Children's Health Research Institute, 5-083 Edmonton Clinic Health Academy, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
- Faculty of Pharmacy & Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Edmonton, AB, T6G 2H1, Canada
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, 1090, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177, Stockholm, Sweden
| | | | - Daniel Graf
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- Women and Children's Health Research Institute, 5-083 Edmonton Clinic Health Academy, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
- Department of Dentistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Stephane L Bourque
- Women and Children's Health Research Institute, 5-083 Edmonton Clinic Health Academy, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada
- Department of Anesthesiology & Pain Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - Jo Anne Stratton
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Anastassia Voronova
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
- Women and Children's Health Research Institute, 5-083 Edmonton Clinic Health Academy, University of Alberta, 11405 87 Avenue NW, Edmonton, AB, T6G 1C9, Canada.
- Neuroscience and Mental Health Institute, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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Waheed‐Ullah Q, Wilsdon A, Abbad A, Rochette S, Bu'Lock F, Hitz M, Dombrowsky G, Cuello F, Brook JD, Loughna S. Effect of deletion of the protein kinase PRKD1 on development of the mouse embryonic heart. J Anat 2024; 245:70-83. [PMID: 38419169 PMCID: PMC11161829 DOI: 10.1111/joa.14033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Congenital heart disease (CHD) is the most common congenital anomaly, with an overall incidence of approximately 1% in the United Kingdom. Exome sequencing in large CHD cohorts has been performed to provide insights into the genetic aetiology of CHD. This includes a study of 1891 probands by our group in collaboration with others, which identified three novel genes-CDK13, PRKD1, and CHD4, in patients with syndromic CHD. PRKD1 encodes a serine/threonine protein kinase, which is important in a variety of fundamental cellular functions. Individuals with a heterozygous mutation in PRKD1 may have facial dysmorphism, ectodermal dysplasia and may have CHDs such as pulmonary stenosis, atrioventricular septal defects, coarctation of the aorta and bicuspid aortic valve. To obtain a greater appreciation for the role that this essential protein kinase plays in cardiogenesis and CHD, we have analysed a Prkd1 transgenic mouse model (Prkd1em1) carrying deletion of exon 2, causing loss of function. High-resolution episcopic microscopy affords detailed morphological 3D analysis of the developing heart and provides evidence for an essential role of Prkd1 in both normal cardiac development and CHD. We show that homozygous deletion of Prkd1 is associated with complex forms of CHD such as atrioventricular septal defects, and bicuspid aortic and pulmonary valves, and is lethal. Even in heterozygotes, cardiac differences occur. However, given that 97% of Prkd1 heterozygous mice display normal heart development, it is likely that one normal allele is sufficient, with the defects seen most likely to represent sporadic events. Moreover, mRNA and protein expression levels were investigated by RT-qPCR and western immunoblotting, respectively. A significant reduction in Prkd1 mRNA levels was seen in homozygotes, but not heterozygotes, compared to WT littermates. While a trend towards lower PRKD1 protein expression was seen in the heterozygotes, the difference was only significant in the homozygotes. There was no compensation by the related Prkd2 and Prkd3 at transcript level, as evidenced by RT-qPCR. Overall, we demonstrate a vital role of Prkd1 in heart development and the aetiology of CHD.
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Affiliation(s)
- Qazi Waheed‐Ullah
- School of Life Sciences, Faculty of Medicine and Health SciencesUniversity of NottinghamNottinghamUK
| | - Anna Wilsdon
- School of Life Sciences, Faculty of Medicine and Health SciencesUniversity of NottinghamNottinghamUK
| | - Aseel Abbad
- School of Life Sciences, Faculty of Medicine and Health SciencesUniversity of NottinghamNottinghamUK
| | - Sophie Rochette
- School of Life Sciences, Faculty of Medicine and Health SciencesUniversity of NottinghamNottinghamUK
| | - Frances Bu'Lock
- East Midlands Congenital Heart CentreUniversity Hospitals of Leicester NHS TrustLeicesterUK
| | - Marc‐Phillip Hitz
- Institute of Medical GeneticsCarl von Ossietzky University OldenburgOldenburgGermany
| | - Gregor Dombrowsky
- Institute of Medical GeneticsCarl von Ossietzky University OldenburgOldenburgGermany
| | - Friederike Cuello
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research CenterUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- DZHK (German Center for Cardiovascular Research), partner site Hamburg/Kiel/LübeckUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - J. David Brook
- School of Life Sciences, Faculty of Medicine and Health SciencesUniversity of NottinghamNottinghamUK
| | - Siobhan Loughna
- School of Life Sciences, Faculty of Medicine and Health SciencesUniversity of NottinghamNottinghamUK
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25
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Zuo JY, Chen HX, Yang Q, Liu ZG, He GW. Tetralogy of Fallot: variants of MYH6 gene promoter and cellular functional analyses. Pediatr Res 2024; 96:338-346. [PMID: 38135727 DOI: 10.1038/s41390-023-02955-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/10/2023] [Accepted: 11/18/2023] [Indexed: 12/24/2023]
Abstract
BACKGROUND Tetralogy of Fallot (TOF) is a common form of congenital heart disease. The MYH6 gene has important effects on cardiovascular growth and development. METHODS In 608 subjects, including 315 TOF patients, we investigated the MYH6 gene promoter variants and verified the effect on gene expression by using cellular functional experiments with three cell lines (HEK-293, HL-1, and H9C2 cells) and bioinformatics analysis. RESULTS In the MYH6 gene promoter, 12 variants were identified from 608 subjects. Five variants were found only in patients with TOF and two of them (g.3384G>T and g.4518T>C) were novel. Electrophoretic mobility shift assay with three cell lines (HEK-293, HL-1, and H9C2) showed significant changes in the transcription factors bound by the promoter variants compared to the wild-type. Dual luciferase reporter showed that four of the five variants reduced the transcriptional activity of the MYH6 gene promoter (p < 0.05). CONCLUSIONS This study is the first to test the cellular function of variants in the promoter region of the MYH6 gene in patients with TOF, which provides new insights into the genetic basis of TOF and provides a basis for further study of the mechanism of TOF formation. IMPACT DNA from 608 human subjects was sequenced for MYH6 gene promoter region variants with five variants found only in TOF patients and two were novel. EMSA and dual luciferase reporter experiments in three cell lines found these variants pathological. Prediction by JASPAR database indicated that these variants alter the transcription factor binding sites. The study, for the first time, confirmed that there are variants at the MYH6 gene promoter region and these variants alter the cellular function. The variants found in this study suggest the possible pathological role in the formation of TOF.
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Affiliation(s)
- Ji-Yang Zuo
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, 300457, China
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational Medicine, Tianjin, 300457, China
- Clinical School of Cardiovascular Disease, Tianjin Medical University, Tianjin, China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, 300457, China
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational Medicine, Tianjin, 300457, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, 300457, China
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational Medicine, Tianjin, 300457, China
| | - Zhi-Gang Liu
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, 300457, China.
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational Medicine, Tianjin, 300457, China.
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, 300457, China.
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational Medicine, Tianjin, 300457, China.
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26
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Leduc F, Smol T, Catteau B, Boute O, Petit F. PRKD1-related telangiectasia-ectodermal dysplasia-brachydactyly-cardiac anomaly syndrome: Case report and review of the literature. Eur J Med Genet 2024; 69:104942. [PMID: 38677542 DOI: 10.1016/j.ejmg.2024.104942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/18/2023] [Accepted: 04/25/2024] [Indexed: 04/29/2024]
Abstract
Telangiectasia-ectodermal dysplasia-brachydactyly-cardiac anomaly (TEBC) syndrome is a rare autosomal dominant condition, recently linked to the protein kinase D1 (PRKD1) gene. The phenotype of TEBC remains incomplete at this point. Our aim is to improve the characterization of the clinical and molecular aspects of the TEBC syndrome. We report on the 8th patient carrying a heterozygous de novo variation of PRKD1 c.2134G > A, p. (Val712Met) identified by trio exome sequencing. The proband presents with partial atrioventricular septal defect, brachydactyly, ectodermal dysplasia, telangiectasia that developed in childhood, intellectual disability with microcephaly, multicystic renal dysplasia and moderate hormonal resistance. In view of this 8th description and review of the literature, it appears that neurodevelopmental disorders and microcephaly are frequently associated with PRKD1 missense variants, adding to the four main clinical signs described initially in the TEBC syndrome. Further descriptions are required to confirm the observed endocrine and kidney abnormalities. This should contribute to a more comprehensive understanding of the phenotypic spectrum and may help establish genotype-phenotype correlations. In the context of genotype-first strategy, accurate patient descriptions are fundamental. Characterization of specific syndromic associations is essential for variant interpretation support and patient follow-up, even in very rare diseases, such as the TEBC syndrome.
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Affiliation(s)
- Fiona Leduc
- CHU Lille, Univ. Lille, Clinique de génétique « Guy Fontaine », ULR7364 RADEME, F-59000, Lille, France.
| | - Thomas Smol
- CHU Lille, Univ. Lille, Institut de Génétique médicale, ULR7364 RADEME, F-59000, Lille, France
| | - Benoit Catteau
- CHU Lille, Service de dermatologie, F-59000, Lille, France
| | - Odile Boute
- CHU Lille, Univ. Lille, Clinique de génétique « Guy Fontaine », ULR7364 RADEME, F-59000, Lille, France
| | - Florence Petit
- CHU Lille, Univ. Lille, Clinique de génétique « Guy Fontaine », ULR7364 RADEME, F-59000, Lille, France
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27
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Sessa F, Chisari M, Salerno M, Esposito M, Zuccarello P, Capasso E, Scoto E, Cocimano G. Congenital heart diseases (CHDs) and forensic investigations: Searching for the cause of death. Exp Mol Pathol 2024; 137:104907. [PMID: 38820762 DOI: 10.1016/j.yexmp.2024.104907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
Congenital Heart Diseases (CHDs) are a group of structural abnormalities or defects of the heart that are present at birth. CHDs could be connected to sudden death (SD), defined by the WHO (World Health Organization) as "death occurring within 24 h after the onset of the symptoms" in an apparently "healthy" subject. These conditions can range from relatively mild defects to severe, life-threatening anomalies. The prevalence of CHDs varies across populations, but they affect millions of individuals worldwide. This article aims to discuss the post-mortem investigation of death related to CHDs, exploring the forensic approach, current methodologies, challenges, and potential advancements in this challenging field. A further goal of this article is to provide a guide for understanding these complex diseases, highlighting the pivotal role of autopsy, histopathology, and genetic investigations in defining the cause of death, and providing evidence about the translational use of autopsy reports. Forensic investigations play a crucial role in understanding the complexities of CHDs and determining the cause of death accurately. Through collaboration between medical professionals and forensic experts, meticulous examinations, and analysis of evidence, valuable insights can be gained. These insights not only provide closure to the families affected but also contribute to the prevention of future tragedies.
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Affiliation(s)
- Francesco Sessa
- Department of Medical, Surgical and Advanced Technologies "G.F. Ingrassia", University of Catania, 95121 Catania, Italy.
| | - Mario Chisari
- "Rodolico-San Marco" Hospital, Santa Sofia Street, 87, Catania 95121, Italy.
| | - Monica Salerno
- Department of Medical, Surgical and Advanced Technologies "G.F. Ingrassia", University of Catania, 95121 Catania, Italy.
| | | | - Pietro Zuccarello
- Department of Medical, Surgical and Advanced Technologies "G.F. Ingrassia", University of Catania, 95121 Catania, Italy.
| | - Emanuele Capasso
- Department of Advanced Biomedical Science-Legal Medicine Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Edmondo Scoto
- Department of Medical, Surgical and Advanced Technologies "G.F. Ingrassia", University of Catania, 95121 Catania, Italy
| | - Giuseppe Cocimano
- Department of Mental and Physical Health and Preventive Medicine, University of Campania "Vanvitelli", 80121 Napoli, Italy.
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28
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Shorbaji A, Pushparaj PN, Bakhashab S, Al-Ghafari AB, Al-Rasheed RR, Siraj Mira L, Basabrain MA, Alsulami M, Abu Zeid IM, Naseer MI, Rasool M. Current genetic models for studying congenital heart diseases: Advantages and disadvantages. Bioinformation 2024; 20:415-429. [PMID: 39132229 PMCID: PMC11309114 DOI: 10.6026/973206300200415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 08/13/2024] Open
Abstract
Congenital heart disease (CHD) encompasses a diverse range of structural and functional anomalies that affect the heart and the major blood vessels. Epidemiological studies have documented a global increase in CHD prevalence, which can be attributed to advancements in diagnostic technologies. Extensive research has identified a plethora of CHD-related genes, providing insights into the biochemical pathways and molecular mechanisms underlying this pathological state. In this review, we discuss the advantages and challenges of various In vitro and in vivo CHD models, including primates, canines, Xenopus frogs, rabbits, chicks, mice, Drosophila, zebrafish, and induced pluripotent stem cells (iPSCs). Primates are closely related to humans but are rare and expensive. Canine models are costly but structurally comparable to humans. Xenopus frogs are advantageous because of their generation of many embryos, ease of genetic modification, and cardiac similarity. Rabbits mimic human physiology but are challenging to genetically control. Chicks are inexpensive and simple to handle; however, cardiac events can vary among humans. Mice differ physiologically, while being evolutionarily close and well-resourced. Drosophila has genes similar to those of humans but different heart structures. Zebrafish have several advantages, including high gene conservation in humans and physiological cardiac similarities but limitations in cross-reactivity with mammalian antibodies, gene duplication, and limited embryonic stem cells for reverse genetic methods. iPSCs have the potential for gene editing, but face challenges in terms of 2D structure and genomic stability. CRISPR-Cas9 allows for genetic correction but requires high technical skills and resources. These models have provided valuable knowledge regarding cardiac development, disease simulation, and the verification of genetic factors. This review highlights the distinct features of various models with respect to their biological characteristics, vulnerability to developing specific heart diseases, approaches employed to induce particular conditions, and the comparability of these species to humans. Therefore, the selection of appropriate models is based on research objectives, ultimately leading to an enhanced comprehension of disease pathology and therapy.
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Affiliation(s)
- Ayat Shorbaji
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Peter Natesan Pushparaj
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherin Bakhashab
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ayat B Al-Ghafari
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
- Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rana R Al-Rasheed
- Experimental Biochemistry Unit, King Fahad research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Loubna Siraj Mira
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Abdullah Basabrain
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majed Alsulami
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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29
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Ohanele C, Peoples JN, Karlstaedt A, Geiger JT, Gayle AD, Ghazal N, Sohani F, Brown ME, Davis ME, Porter GA, Faundez V, Kwong JQ. Mitochondrial citrate carrier SLC25A1 is a dosage-dependent regulator of metabolic reprogramming and morphogenesis in the developing heart. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.22.541833. [PMID: 37292906 PMCID: PMC10245819 DOI: 10.1101/2023.05.22.541833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The developing mammalian heart undergoes an important metabolic shift from glycolysis toward mitochondrial oxidation, such that oxidative phosphorylation defects may present with cardiac abnormalities. Here, we describe a new mechanistic link between mitochondria and cardiac morphogenesis, uncovered by studying mice with systemic loss of the mitochondrial citrate carrier SLC25A1. Slc25a1 null embryos displayed impaired growth, cardiac malformations, and aberrant mitochondrial function. Importantly, Slc25a1 heterozygous embryos, which are overtly indistinguishable from wild type, exhibited an increased frequency of these defects, suggesting Slc25a1 haploinsuffiency and dose-dependent effects. Supporting clinical relevance, we found a near-significant association between ultrarare human pathogenic SLC25A1 variants and pediatric congenital heart disease. Mechanistically, SLC25A1 may link mitochondria to transcriptional regulation of metabolism through epigenetic control of gene expression to promote metabolic remodeling in the developing heart. Collectively, this work positions SLC25A1 as a novel mitochondrial regulator of ventricular morphogenesis and cardiac metabolic maturation and suggests a role in congenital heart disease.
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30
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Watkins WS, Hernandez EJ, Miller TA, Blue NR, Zimmerman R, Griffiths ER, Frise E, Bernstein D, Boskovski MT, Brueckner M, Chung WK, Gaynor JW, Gelb BD, Goldmuntz E, Gruber PJ, Newburger JW, Roberts AE, Morton SU, Mayer JE, Seidman CE, Seidman JG, Shen Y, Wagner M, Yost HJ, Yandell M, Tristani-Firouzi M. Genome Sequencing is Critical for Forecasting Outcomes following Congenital Cardiac Surgery. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24306784. [PMID: 38746151 PMCID: PMC11092705 DOI: 10.1101/2024.05.03.24306784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
While genome sequencing has transformed medicine by elucidating the genetic underpinnings of both rare and common complex disorders, its utility to predict clinical outcomes remains understudied. Here, we used artificial intelligence (AI) technologies to explore the predictive value of genome sequencing in forecasting clinical outcomes following surgery for congenital heart defects (CHD). We report results for a cohort of 2,253 CHD patients from the Pediatric Cardiac Genomics Consortium with a broad range of complex heart defects, pre- and post-operative clinical variables and exome sequencing. Damaging genotypes in chromatin-modifying and cilia-related genes were associated with an elevated risk of adverse post-operative outcomes, including mortality, cardiac arrest and prolonged mechanical ventilation. The impact of damaging genotypes was further amplified in the context of specific CHD phenotypes, surgical complexity and extra-cardiac anomalies. The absence of a damaging genotype in chromatin-modifying and cilia-related genes was also informative, reducing the risk for adverse postoperative outcomes. Thus, genome sequencing enriches the ability to forecast outcomes following congenital cardiac surgery.
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31
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Zuo JY, Chen HX, Yang Q, He GW. Variants of the promoter of MYH6 gene in congenital isolated and sporadic patent ductus arteriosus: case-control study and cellular functional analyses. Hum Mol Genet 2024; 33:884-893. [PMID: 38340456 DOI: 10.1093/hmg/ddae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/25/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Patent ductus arteriosus (PDA) is a common form of congenital heart disease. The MYH6 gene has important effects on cardiovascular growth and development, but the effect of variants in the MYH6 gene promoter on ductus arteriosus is unknown. DNA was extracted from blood samples of 721 subjects (428 patients with isolated and sporadic PDA and 293 healthy controls) and analyzed by sequencing for MYH6 gene promoter region variants. Cellular function experiments with three cell lines (HEK-293, HL-1, and H9C2 cells) and bioinformatics analyses were performed to verify their effects on gene expression. In the MYH6 gene promoter, 11 variants were identified. Four variants were found only in patients with PDA and 2 of them (g.3434G>C and g.4524C>T) were novel. Electrophoretic mobility shift assay showed that the transcription factors bound by the promoter variants were significantly altered in comparison to the wild-type in all three cell lines. Dual luciferase reporter showed that all the 4 variants reduced the transcriptional activity of the MYH6 gene promoter (P < 0.05). Prediction of transcription factors bound by the variants indicated that these variants alter the transcription factor binding sites. These pathological alterations most likely affect the contraction of the smooth muscle of ductus arteriosus, leading to PDA. This study is the first to focus on variants at the promoter region of the MYH6 gene in PDA patients with cellular function tests. Therefore, this study provides new insights to understand the genetic basis and facilitates further studies on the mechanism of PDA formation.
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Affiliation(s)
- Ji-Yang Zuo
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational Medicine, No. 61, the 3rd Ave, TEDA, Tianjin 300457, China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational Medicine, No. 61, the 3rd Ave, TEDA, Tianjin 300457, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational Medicine, No. 61, the 3rd Ave, TEDA, Tianjin 300457, China
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Molecular Regulation of Cardiovascular Diseases and Translational Medicine, No. 61, the 3rd Ave, TEDA, Tianjin 300457, China
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32
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Chao KR, Wang L, Panchal R, Liao C, Abderrazzaq H, Ye R, Schultz P, Compitello J, Grant RH, Kosmicki JA, Weisburd B, Phu W, Wilson MW, Laricchia KM, Goodrich JK, Goldstein D, Goldstein JI, Vittal C, Poterba T, Baxter S, Watts NA, Solomonson M, Tiao G, Rehm HL, Neale BM, Talkowski ME, MacArthur DG, O'Donnell-Luria A, Karczewski KJ, Radivojac P, Daly MJ, Samocha KE. The landscape of regional missense mutational intolerance quantified from 125,748 exomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.588920. [PMID: 38645134 PMCID: PMC11030311 DOI: 10.1101/2024.04.11.588920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Missense variants can have a range of functional impacts depending on factors such as the specific amino acid substitution and location within the gene. To interpret their deleteriousness, studies have sought to identify regions within genes that are specifically intolerant of missense variation 1-12 . Here, we leverage the patterns of rare missense variation in 125,748 individuals in the Genome Aggregation Database (gnomAD) 13 against a null mutational model to identify transcripts that display regional differences in missense constraint. Missense-depleted regions are enriched for ClinVar 14 pathogenic variants, de novo missense variants from individuals with neurodevelopmental disorders (NDDs) 15,16 , and complex trait heritability. Following ClinGen calibration recommendations for the ACMG/AMP guidelines, we establish that regions with less than 20% of their expected missense variation achieve moderate support for pathogenicity. We create a missense deleteriousness metric (MPC) that incorporates regional constraint and outperforms other deleteriousness scores at stratifying case and control de novo missense variation, with a strong enrichment in NDDs. These results provide additional tools to aid in missense variant interpretation.
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Zhong G, Zhao Y, Zhuang D, Chung WK, Shen Y. PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581321. [PMID: 38746140 PMCID: PMC11092447 DOI: 10.1101/2024.02.20.581321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Accurate prediction of the functional impact of missense variants is important for disease gene discovery, clinical genetic diagnostics, therapeutic strategies, and protein engineering. Previous efforts have focused on predicting a binary pathogenicity classification, but the functional impact of missense variants is multi-dimensional. Pathogenic missense variants in the same gene may act through different modes of action (i.e., gain/loss-of-function) by affecting different aspects of protein function. They may result in distinct clinical conditions that require different treatments. We developed a new method, PreMode, to perform gene-specific mode-of-action predictions. PreMode models effects of coding sequence variants using SE(3)-equivariant graph neural networks on protein sequences and structures. Using the largest-to-date set of missense variants with known modes of action, we showed that PreMode reached state-of-the-art performance in multiple types of mode-of-action predictions by efficient transfer-learning. Additionally, PreMode's prediction of G/LoF variants in a kinase is consistent with inactive-active conformation transition energy changes. Finally, we show that PreMode enables efficient study design of deep mutational scans and optimization in protein engineering.
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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Becerir C, Tayman C, Kurt A, Çakır U, Koyuncu İ, Ceran B, Toprak K, Kızılgün M. Serum ADAMTS-9 Level in Newborn Babies with Congenital Heart Disease. Am J Perinatol 2024; 41:e2555-e2561. [PMID: 37419139 DOI: 10.1055/a-2125-1330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
OBJECTIVE A Disintegrin and Metalloproteinase with Thrombospondin-9 (ADAMTS-9), one of the ADAMTS enzymes, is expressed in all fetal tissues, unlike other ADAMTS enzymes, and is thus thought to play a role in fetal development. In this context, the objective of this study is to investigate the relationship between ADAMTS-9 activity and the development of congenital heart diseases (CHD) with a view to using ADAMTS-9 level as a biomarker for CHDs. STUDY DESIGN Newborns diagnosed with CHD and healthy newborns were included in the study as the CHD and control groups, respectively. Gestational age, maternal age, and mode of delivery information pertaining to the mothers and Apgar score and birthweight information pertaining to the newborns were recorded. Blood samples were taken from all newborns to determine their ADAMTS-9 levels in the first 24 hours of life. RESULTS Fifty-eight newborns with CHD and 46 healthy newborns were included in the study. Median ADAMTS-9 levels were 46.57 (interquartile range [IQR]: 33.31 [min: 26.92, max: 124.25]) and 23.36 (IQR: 5.48 [min: 11.7, max: 37.71]) ng/mL in the CHD and control groups, respectively. ADAMTS-9 levels in the CHD group were statistically significantly higher than in the control group (p = 0.000). ADAMTS-9 levels of the CHD and control groups were analyzed by the receiver operating characteristics curve. The area under the curve value for ADAMTS-9 levels of >27.86 ng/mL as the cut-off value for predicting the development of CHD in newborns was 0.836 (95% confidence interval [CI]: 0.753-0.900, p = 0.0001). ADAMTS-9 levels of >27.86 ng/mL were determined to predict the development of CHD in newborns with a sensitivity of 77.78% (95% CI: 65.5-87.38) and a specificity of 84.78% (95% CI: 71.1-93.60). CONCLUSION In conclusion, it was found that the serum ADAMTS-9 levels were significantly higher in newborns with CHD than in healthy newborns. In parallel, ADAMTS-9 levels above a certain cut-off value were associated with CHD. KEY POINTS · ADAMTS-9 is expressed in fetal tissues.. · Its level increases in congenital heart diseases.. · It can be used as a biochemical marker in diagnosis..
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Affiliation(s)
- Cem Becerir
- Department of Neonatology, Ankara City Hospital, Neonatal Intensive Care Unit, University of Health Sciences, Ankara, Turkey
| | - Cüneyt Tayman
- Department of Neonatology, Ankara City Hospital, Neonatal Intensive Care Unit, University of Health Sciences, Ankara, Turkey
| | - Abdullah Kurt
- Department of Neonatology, Yildirim Beyazit University Faculty of Medicine, Ankara Turkey
| | - Ufuk Çakır
- Department of Neonatology, Ankara City Hospital, Neonatal Intensive Care Unit, University of Health Sciences, Ankara, Turkey
| | - İsmail Koyuncu
- Department of Medical Biochemistry, Harran University, Urfa, Turkey
| | - Burak Ceran
- Department of Neonatology, Ankara City Hospital, Neonatal Intensive Care Unit, University of Health Sciences, Ankara, Turkey
| | - Kenan Toprak
- Cardiology Department, Faculty of Medicine, Harran University, Şanlıurfa, Turkey
| | - Murat Kızılgün
- Department of Medical Biochemistry, Sağlık Bilimleri Üniversitesi Gülhane Tıp Fakültesi, Health Science University Ankara, Turkey
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Inoue T, Takase R, Uchida K, Kodo K, Suda K, Watanabe Y, Yoshiura KI, Kunimatsu M, Ishizaki R, Azuma K, Inai K, Muneuchi J, Furutani Y, Akagawa H, Yamagishi H. The c.1617del variant of TMEM260 is identified as the most frequent single gene determinant for Japanese patients with a specific type of congenital heart disease. J Hum Genet 2024; 69:215-222. [PMID: 38409496 PMCID: PMC11043032 DOI: 10.1038/s10038-024-01225-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
Although the molecular mechanisms underlying congenital heart disease (CHD) remain poorly understood, recent advances in genetic analysis have facilitated the exploration of causative genes for CHD. We reported that the pathogenic variant c.1617del of TMEM260, which encodes a transmembrane protein, is highly associated with CHD, specifically persistent truncus arteriosus (PTA), the most severe cardiac outflow tract (OFT) defect. Using whole-exome sequencing, the c.1617del variant was identified in two siblings with PTA in a Japanese family and in three of the 26 DNAs obtained from Japanese individuals with PTA. The c.1617del of TMEM260 has been found only in East Asians, especially Japanese and Korean populations, and the frequency of this variant in PTA is estimated to be next to that of the 22q11.2 deletion, the most well-known genetic cause of PTA. Phenotype of patients with c.1617del appears to be predominantly in the heart, although TMEM260 is responsible for structural heart defects and renal anomalies syndrome (SHDRA). The mouse TMEM260 variant (p.W535Cfs*56), synonymous with the human variant (p.W539Cfs*9), exhibited truncation and downregulation by western blotting, and aggregation by immunocytochemistry. In situ hybridization demonstrated that Tmem260 is expressed ubiquitously during embryogenesis, including in the development of cardiac OFT implicated in PTA. This expression may be regulated by a ~ 0.8 kb genomic region in intron 3 of Tmem260 that includes multiple highly conserved binding sites for essential cardiac transcription factors, thus revealing that the c.1617del variant of TMEM260 is the major single-gene variant responsible for PTA in the Japanese population.
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Affiliation(s)
- Tadashi Inoue
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
| | - Ryuta Takase
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
| | - Keiko Uchida
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.
- Keio University Health Center, Tokyo, Japan.
| | - Kazuki Kodo
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenji Suda
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
| | - Yoriko Watanabe
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
- Research Institute of Medical Mass Spectrometry, Kurume University School of Medicine, Fukuoka, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Division of Advanced Preventive Medical Sciences, Leading Medical Research Core Unit, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masaya Kunimatsu
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Reina Ishizaki
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenko Azuma
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Kei Inai
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Jun Muneuchi
- Department of Pediatrics, Kyushu Hospital, Japan Community Healthcare Organization, Kitakyushu, Japan
| | - Yoshiyuki Furutani
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Akagawa
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Yamagishi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Center for Preventive Medicine, Keio University School of Medicine, Tokyo, Japan
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Helm BM, Ware SM. Clinical Decision Analysis of Genetic Evaluation and Testing in 1013 Intensive Care Unit Infants with Congenital Heart Defects Supports Universal Genetic Testing. Genes (Basel) 2024; 15:505. [PMID: 38674439 PMCID: PMC11050575 DOI: 10.3390/genes15040505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Extracardiac anomalies (ECAs) are strong predictors of genetic disorders in infants with congenital heart disease (CHD), but there are no prior studies assessing performance of ECA status as a screen for genetic diagnoses in CHD patients. This retrospective cohort study assessed this in our comprehensive inpatient CHD genetics service focusing on neonates and infants admitted to the intensive care unit (ICU). The performance and diagnostic utility of using ECA status to screen for genetic disorders was assessed using decision curve analysis, a statistical tool to assess clinical utility, determining the threshold of phenotypic screening by ECA versus a Test-All approach. Over 24% of infants had genetic diagnoses identified (n = 244/1013), and ECA-positive status indicated a 4-fold increased risk of having a genetic disorder. However, ECA status had low-moderate screening performance based on predictive summary index, a compositive measure of positive and negative predictive values. For those with genetic diagnoses, nearly one-third (32%, 78/244) were ECA-negative but had cytogenetic and/or monogenic disorders identified by genetic testing. Thus, if the presence of multiple congenital anomalies is the phenotypic driver to initiate genetic testing, 13.4% (78/580) of infants with isolated CHD with identifiable genetic causes will be missed. Given the prevalence of genetic disorders and limited screening performance of ECA status, this analysis supports genetic testing in all CHD infants in intensive care settings rather than screening based on ECA.
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Affiliation(s)
- Benjamin M. Helm
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202, USA
| | - Stephanie M. Ware
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Liu ZY, Wang QQ, Pang XY, Huang XB, Yang GM, Zhao S. Association of congenital heart disease and neurodevelopmental disorders: an observational and Mendelian randomization study. Ital J Pediatr 2024; 50:63. [PMID: 38589916 PMCID: PMC11003105 DOI: 10.1186/s13052-024-01610-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/23/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND This study aims to thoroughly study the connection between congenital heart disease (CHD) and neurodevelopmental disorders (NDDs) through observational and Mendelian randomization (MR) designs. METHODS This observational study uses data from the National Survey of Children's Health (2020-2021). Multivariable logistic regression and propensity score matching (PSM) were performed to analyze the association. PSM was used to minimize bias for covariates such as age, race, gender, maternal age, birth weight, concussion or brain injury, preterm birth, cerebral palsy, Down syndrome, and other inherited conditions. In MR analyses, inverse variance-weighted measures, weighted median, and MR-Egger were employed to calculate causal effects. RESULTS A total of 85,314 children aged 0-17 were analyzed in this study. In regression analysis, CHD (p = 0.04), the current heart condition (p = 0.03), and the severity of current heart condition (p < 0.05) had a suggestive association with speech or language disorders. The severity of current heart condition (p = 0.08) has a potential statistically significant association with attention deficit hyperactivity disorder(ADHD). In PSM samples, ADHD(p = 0.003), intellectual disability(p = 0.012), and speech or language disorders(p < 0.001) were all significantly associated with CHD. The severity of current heart condition (p < 0.001) also had a significant association with autism. MR analysis did not find causality between genetically proxied congenital cardiac malformations and the risk of NDDs. CONCLUSIONS Our study shows that children with CHD have an increased risk of developing NDDs. Heart conditions currently and severity of current heart conditions were also significantly associated with these NDDs. In the future, we need to try more methods to clarify the causal relationship between CHD and NDDs.
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Affiliation(s)
- Zhi-Yuan Liu
- Department of Cardiology, Anhui Provincial Children's Hospital, Hefei, Anhui, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Qiong-Qiong Wang
- Department of Cardiology, Anhui Provincial Children's Hospital, Hefei, Anhui, China
| | - Xian-Yong Pang
- Department of Cardiology, Anhui Provincial Children's Hospital, Hefei, Anhui, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Bi Huang
- Department of Cardiology, Anhui Provincial Children's Hospital, Hefei, Anhui, China
| | - Gui-Ming Yang
- Department of Cardiology, Anhui Provincial Children's Hospital, Hefei, Anhui, China
| | - Sheng Zhao
- Department of Cardiology, Anhui Provincial Children's Hospital, Hefei, Anhui, China.
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China.
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Wang L, Kranzler HR, Gelernter J, Zhou H. Multi-ancestry Whole-exome Sequencing Study of Alcohol Use Disorder in Two Cohorts. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305412. [PMID: 38645055 PMCID: PMC11030482 DOI: 10.1101/2024.04.05.24305412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Alcohol use disorder (AUD) is a leading cause of death and disability worldwide. There has been substantial progress in identifying genetic variants underlying AUD. However, there are few whole-exome sequencing (WES) studies of AUD. We analyzed WES of 4,530 samples from the Yale-Penn cohort and 469,835 samples from the UK Biobank (UKB). After quality control, 1,420 AUD cases and 619 controls of European ancestry (EUR) and 1,142 cases and 608 controls of African ancestry (AFR) from Yale-Penn were retained for subsequent analyses. WES data from 415,617 EUR samples (12,861 cases), 6,142 AFR samples (130 cases) and 4,607 South Asian (SAS) samples (130 cases) from UKB were also analyzed. Single-variant association analysis identified the well-known functional variant rs1229984 in ADH1B ( P =4.88×10 -31 ) and several other common variants in ADH1C . Gene-based tests identified ADH1B ( P =1.00×10 -31 ), ADH1C ( P =5.23×10 -7 ), CNST ( P =1.19×10 -6 ), and IFIT5 (3.74×10 -6 ). This study extends our understanding of the genetic basis of AUD.
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Jin Y, Zhao M, Guo Q, Zhao W, Lei M, Zhang Y, Zhang Y, Shen Y, Lin K, Yang Z, Chu J, Sun H, Luo Z. Association study of FLT4 and HYDIN single nucleotide polymorphisms with atrial septal defect susceptibility in the Han Chinese population of Southwest China. Ital J Pediatr 2024; 50:62. [PMID: 38581027 PMCID: PMC10998412 DOI: 10.1186/s13052-024-01630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Atrial septal defect (ASD) is a common form of congenital heart disease. Although several genes related to ASD have been found, the genetic factors of ASD remain unclear. This study aimed to evaluate the correlation between 10 candidate single nucleotide polymorphisms (SNPs) and sporadic atrial septal defects. METHODS Based on the results of 34 individual whole exome sequences, 10 candidate SNPs were selected. In total, 489 ASD samples and 420 normal samples were collected. The 10 SNPs in the case group and the control group were identified through Snapshot genotyping technology. The χ2-test and unconditional regression model were used to evaluate the relationship between ASD and each candidate SNP. Haploview software was used to perform linkage disequilibrium and haplotype analysis. RESULTS The χ2 results showed that the FLT4 rs383985 (P = 0.003, OR = 1.115-1.773), HYDIN rs7198975 (P = 0.04621, OR = 1.003-1.461), and HYDIN rs1774266 (P = 0.04621, OR = 1.003-1.461) alleles were significantly different between the control group and the case group (P < 0.05). Only the association with the FLT4 polymorphism was statistically significant after adjustment for multiple comparisons. CONCLUSION These findings suggest that a possible molecular pathogenesis associated with sporadic ASD is worth exploring in future studies.
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Affiliation(s)
- Ye Jin
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Miao Zhao
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Qiuzhe Guo
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Wanyu Zhao
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Min Lei
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Yifei Zhang
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Yunhan Zhang
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Yan Shen
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Keqin Lin
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiao ling Road, 650118, Kunming, Yunnan, China
| | - Zhaoqing Yang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiao ling Road, 650118, Kunming, Yunnan, China
| | - Jiayou Chu
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiao ling Road, 650118, Kunming, Yunnan, China
| | - Hao Sun
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiao ling Road, 650118, Kunming, Yunnan, China.
| | - Zhiling Luo
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China.
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Dardas Z, Fatih JM, Jolly A, Dawood M, Du H, Grochowski CM, Jones EG, Jhangiani SN, Wehrens XHT, Liu P, Bi W, Boerwinkle E, Posey JE, Muzny DM, Gibbs RA, Lupski JR, Coban-Akdemir Z, Morris SA. NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy. Genome Med 2024; 16:53. [PMID: 38570875 PMCID: PMC10988827 DOI: 10.1186/s13073-024-01312-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND NODAL signaling plays a critical role in embryonic patterning and heart development in vertebrates. Genetic variants resulting in perturbations of the TGF-β/NODAL signaling pathway have reproducibly been shown to cause laterality defects in humans. To further explore this association and improve genetic diagnosis, the study aims to identify and characterize a broader range of NODAL variants in a large number of individuals with laterality defects. METHODS We re-analyzed a cohort of 321 proband-only exomes of individuals with clinically diagnosed laterality congenital heart disease (CHD) using family-based, rare variant genomic analyses. To this cohort we added 12 affected subjects with known NODAL variants and CHD from institutional research and clinical cohorts to investigate an allelic series. For those with candidate contributory variants, variant allele confirmation and segregation analysis were studied by Sanger sequencing in available family members. Array comparative genomic hybridization and droplet digital PCR were utilized for copy number variants (CNV) validation and characterization. We performed Human Phenotype Ontology (HPO)-based quantitative phenotypic analyses to dissect allele-specific phenotypic differences. RESULTS Missense, nonsense, splice site, indels, and/or structural variants of NODAL were identified as potential causes of heterotaxy and other laterality defects in 33 CHD cases. We describe a recurrent complex indel variant for which the nucleic acid secondary structure predictions implicate secondary structure mutagenesis as a possible mechanism for formation. We identified two CNV deletion alleles spanning NODAL in two unrelated CHD cases. Furthermore, 17 CHD individuals were found (16/17 with known Hispanic ancestry) to have the c.778G > A:p.G260R NODAL missense variant which we propose reclassification from variant of uncertain significance (VUS) to likely pathogenic. Quantitative HPO-based analyses of the observed clinical phenotype for all cases with p.G260R variation, including heterozygous, homozygous, and compound heterozygous cases, reveal clustering of individuals with biallelic variation. This finding provides evidence for a genotypic-phenotypic correlation and an allele-specific gene dosage model. CONCLUSION Our data further support a role for rare deleterious variants in NODAL as a cause for sporadic human laterality defects, expand the repertoire of observed anatomical complexity of potential cardiovascular anomalies, and implicate an allele specific gene dosage model.
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Affiliation(s)
- Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Moez Dawood
- 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
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Edward G Jones
- Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and 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
| | - Xander H T Wehrens
- Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M 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
| | - 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
| | - 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
- Texas Children's Hospital, Houston, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Shaine A Morris
- Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA.
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Baker EK, Shikany A, Winlaw DS, Weaver KN. Phenotypes and genotypes in a cohort of children with single-ventricle CHD. Cardiol Young 2024; 34:815-821. [PMID: 37850440 DOI: 10.1017/s1047951123003505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
OBJECTIVE CHD is known to be associated with increased risk for neurodevelopmental disorders. The combination of CHD with neurodevelopmental disorders and/or extra-cardiac anomalies increases the chance for an underlying genetic diagnosis. Over the last 15 years, there has been a dramatic increase in the use of broad-scale genetic testing. We sought to determine if neurodevelopmental disorders in children with single-ventricle CHD born prior to the genetic testing revolution are associated with genetic diagnosis. METHODS We identified 74 5-12-year-old patients with single-ventricle CHD post-Fontan procedure. We retrospectively evaluated genetic testing performed and neurodevelopmental status of these patients. RESULTS In this cohort, there was an overall higher rate of neurodevelopmental disorders (80%) compared to the literature (50%). More of the younger (5-7-year-old) patients were seen by genetic counsellors compared to the older (8-12-year-old) cohort (46% versus 19% p value = 0.01). In the younger cohort, the average age of initial consultation was 7.7 days compared to 251 days in the older cohort. The overall rate of achieving a molecular diagnosis was 12% and 8% in the younger and older cohorts, respectively; however, the vast majority of did not have broad genetic testing. CONCLUSION The minority of patients in our cohort achieved a genetic diagnosis. Given a large increase in the number of genes associated with monogenic CHD and neurodevelopmental disorders in the last decade, comprehensive testing and consultation with clinical genetics should be considered in this age range, since current testing standards did not exist during their infancy.
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Affiliation(s)
- Elizabeth K Baker
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Amy Shikany
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - David S Winlaw
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Heart Institute, Cardiothoracic Surgery, Cincinnati Children's Hospital Medicine, Cincinnati, OH, USA
| | - K Nicole Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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43
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Sood E, Newburger JW, Anixt JS, Cassidy AR, Jackson JL, Jonas RA, Lisanti AJ, Lopez KN, Peyvandi S, Marino BS. Neurodevelopmental Outcomes for Individuals With Congenital Heart Disease: Updates in Neuroprotection, Risk-Stratification, Evaluation, and Management: A Scientific Statement From the American Heart Association. Circulation 2024; 149:e997-e1022. [PMID: 38385268 DOI: 10.1161/cir.0000000000001211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Over the past decade, new research has advanced scientific knowledge of neurodevelopmental trajectories, factors that increase neurodevelopmental risk, and neuroprotective strategies for individuals with congenital heart disease. In addition, best practices for evaluation and management of developmental delays and disorders in this high-risk patient population have been formulated based on literature review and expert consensus. This American Heart Association scientific statement serves as an update to the 2012 statement on the evaluation and management of neurodevelopmental outcomes in children with congenital heart disease. It includes revised risk categories for developmental delay or disorder and an updated list of factors that increase neurodevelopmental risk in individuals with congenital heart disease according to current evidence, including genetic predisposition, fetal and perinatal factors, surgical and perioperative factors, socioeconomic disadvantage, and parental psychological distress. It also includes an updated algorithm for referral, evaluation, and management of individuals at high risk. Risk stratification of individuals with congenital heart disease with the updated categories and risk factors will identify a large and growing population of survivors at high risk for developmental delay or disorder and associated impacts across the life span. Critical next steps must include efforts to prevent and mitigate developmental delays and disorders. The goal of this scientific statement is to inform health care professionals caring for patients with congenital heart disease and other key stakeholders about the current state of knowledge of neurodevelopmental outcomes for individuals with congenital heart disease and best practices for neuroprotection, risk stratification, evaluation, and management.
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Luyckx I, Walton IS, Boeckx N, Van Schil K, Pang C, De Praeter M, Lord H, Watson CM, Bonthron DT, Van Laer L, Wilkie AOM, Loeys B. Homozygous SMAD6 variants in two unrelated patients with craniosynostosis and radioulnar synostosis. J Med Genet 2024; 61:363-368. [PMID: 38290823 PMCID: PMC10982635 DOI: 10.1136/jmg-2023-109151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 11/29/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND SMAD6 encodes an intracellular inhibitor of the bone morphogenetic protein (BMP) signalling pathway. Until now, rare heterozygous loss-of-function variants in SMAD6 were demonstrated to increase the risk of disparate clinical disorders including cardiovascular disease, craniosynostosis and radioulnar synostosis. Only two unrelated patients harbouring biallelic SMAD6 variants presenting a complex cardiovascular phenotype and facial dysmorphism have been described. CASES Here, we present the first two patients with craniosynostosis harbouring homozygous SMAD6 variants. The male probands, both born to healthy consanguineous parents, were diagnosed with metopic synostosis and bilateral or unilateral radioulnar synostosis. Additionally, one proband had global developmental delay. Echocardiographic evaluation did not reveal cardiac or outflow tract abnormalities. MOLECULAR ANALYSES The novel missense (c.[584T>G];[584T>G], p.[(Val195Gly)];[(Val195Gly)]) and missense/splice-site variant (c.[817G>A];[817G>A], r.[(817g>a,817delins[a;817+2_817+228])];[(817g>a,817delins[a;817+2_817+228])], p.[(Glu273Lys,Glu273Serfs*72)];[(Glu273Lys,Glu273Serfs*72)]) both locate in the functional MH1 domain of the protein and have not been reported in gnomAD database. Functional analyses of the variants showed reduced inhibition of BMP signalling or abnormal splicing, respectively, consistent with a hypomorphic mechanism of action. CONCLUSION Our data expand the spectrum of variants and phenotypic spectrum associated with homozygous variants of SMAD6 to include craniosynostosis.
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Affiliation(s)
- Ilse Luyckx
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
- Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Isaac Scott Walton
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nele Boeckx
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Kristof Van Schil
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Chingyiu Pang
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Mania De Praeter
- Department of Paediatric Neurosurgery, University Hospital Antwerp, Antwerp, Belgium
| | - Helen Lord
- Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Christopher Mark Watson
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - David T Bonthron
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Lut Van Laer
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Andrew O M Wilkie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Bart Loeys
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
- Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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Xie Y, Wu R, Li H, Dong W, Zhou G, Zhao H. Statistical methods for assessing the effects of de novo variants on birth defects. Hum Genomics 2024; 18:25. [PMID: 38486307 PMCID: PMC10938830 DOI: 10.1186/s40246-024-00590-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
With the development of next-generation sequencing technology, de novo variants (DNVs) with deleterious effects can be identified and investigated for their effects on birth defects such as congenital heart disease (CHD). However, statistical power is still limited for such studies because of the small sample size due to the high cost of recruiting and sequencing samples and the low occurrence of DNVs. DNV analysis is further complicated by genetic heterogeneity across diseased individuals. Therefore, it is critical to jointly analyze DNVs with other types of genomic/biological information to improve statistical power to identify genes associated with birth defects. In this review, we discuss the general workflow, recent developments in statistical methods, and future directions for DNV analysis.
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Affiliation(s)
- Yuhan Xie
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Ruoxuan Wu
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Hongyu Li
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Geyu Zhou
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA.
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46
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Broberg M, Ampuja M, Jones S, Ojala T, Rahkonen O, Kivelä R, Priest J, Palotie A, Ollila HM, Helle E. Genome-wide association studies highlight novel risk loci for septal defects and left-sided congenital heart defects. BMC Genomics 2024; 25:256. [PMID: 38454350 PMCID: PMC10918883 DOI: 10.1186/s12864-024-10172-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/28/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Congenital heart defects (CHD) are structural defects of the heart affecting approximately 1% of newborns. They exhibit low penetrance and non-Mendelian patterns of inheritance as varied and complex traits. While genetic factors are known to play an important role in the development of CHD, the specific genetics remain unknown for the majority of patients. To elucidate the underlying genetic risk, we performed a genome wide association study (GWAS) of CHDs in general and specific CHD subgroups using the FinnGen Release 10 (R10) (N > 393,000), followed by functional fine-mapping through eQTL and co-localization analyses using the GTEx database. RESULTS We discovered three genome-wide significant loci associated with general CHD. Two of them were located in chromosome 17: 17q21.32 (rs2316327, intronic: LRRC37A2, Odds ratio (OR) [95% Confidence Interval (CI)] = 1.17[1.12-1.23], p = 1.5 × 10-9) and 17q25.3 (rs1293973611, nearest: BAHCC1, OR[95%CI] = 4.48[2.80-7.17], p = 7.0 × 10-10), respectively, and in addition to general CHD, the rs1293973611 locus was associated with the septal defect subtype. The third locus was in band 1p21.2 (rs35046143, nearest: PALMD, OR[95%CI] = 1.15[1.09-1.21], p = 7.1 × 10-9), and it was associated with general CHD and left-sided lesions. In the subgroup analysis, two additional loci were associated with septal defects (rs75230966 and rs6824295), and one with left-sided lesions (rs1305393195). In the eQTL analysis the variants rs2316327 (general CHD), and rs75230966 (septal defects) both located in 17q21.32 (with a LD r2 of 0.41) were both predicted to significantly associate with the expression of WNT9B in the atrial appendage tissue category. This effect was further confirmed by co-localization analysis, which also implicated WNT3 expression in the atrial appendage. A meta-analysis of general CHD together with the UK Biobank (combined N = 881,678) provided a different genome-wide significant locus in LRRC37A2; rs16941382 (OR[95%CI] = 1.15[1.11-1.20], p = 1.5 × 10-9) which is in significant LD with rs2316327. CONCLUSIONS Our results of general CHD and different CHD subcategories identified a complex risk locus on chromosome 17 near BAHCC1 and LRRC37A2, interacting with the genes WNT9B, WNT3 and MYL4, may constitute potential novel CHD risk associated loci, warranting future experimental tests to determine their role.
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Affiliation(s)
- Martin Broberg
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Minna Ampuja
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Samuel Jones
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Tiina Ojala
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Otto Rahkonen
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Riikka Kivelä
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Wihuri Research Institute, 00290, Helsinki, Finland
- Faculty of Sport and Health Sciences, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - James Priest
- School of Medicine, Stanford University, Stanford University, Stanford, CA, 94305, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Emmi Helle
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland.
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland.
- , Haartmaninkatu 8, Helsinki, 00014, Finland.
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, 00271, Finland.
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47
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Maddhesiya J, Mohapatra B. Understanding the Genetic and Non-genetic Interconnections in the Aetiology of Isolated Congenital Heart Disease: An Updated Review: Part 1. Curr Cardiol Rep 2024; 26:147-165. [PMID: 38546930 DOI: 10.1007/s11886-024-02022-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/15/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE OF REVIEW Congenital heart disease (CHD) is the most frequently occurring birth defect. Majority of the earlier reviews focussed on the association of genetic factors with CHD. A few epidemiological studies provide convincing evidence for environmental factors in the causation of CHD. Although the multifactorial theory of gene-environment interaction is the prevailing explanation, explicit understanding of the biological mechanism(s) involved, remains obscure. Nonetheless, integration of all the information into one platform would enable us to better understand the collective risk implicated in CHD development. RECENT FINDINGS Great strides in novel genomic technologies namely, massive parallel sequencing, whole exome sequencing, multiomics studies supported by system-biology have greatly improved our understanding of the aetiology of CHD. Molecular genetic studies reveal that cardiac specific gene variants in transcription factors or signalling molecules, or structural proteins could cause CHD. Additionally, non-hereditary contributors such as exposure to teratogens, maternal nutrition, parental age and lifestyle factors also contribute to induce CHD. Moreover, DNA methylation and non-coding RNA are also correlated with CHD. Here, we inform that a complex combination of genetic, environmental and epigenetic factors interact to interfere with morphogenetic processes of cardiac development leading to CHD. It is important, not only to identify individual genetic and non-inherited risk factors but also to recognize which factors interact mutually, causing cardiac defects.
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Affiliation(s)
- Jyoti Maddhesiya
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi, 221005, India
| | - Bhagyalaxmi Mohapatra
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi, 221005, India.
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48
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Maddhesiya J, Mohapatra B. Understanding the Genetic and Non-Genetic Interconnections in the Aetiology of Syndromic Congenital Heart Disease: An Updated Review: Part 2. Curr Cardiol Rep 2024; 26:167-178. [PMID: 38358608 DOI: 10.1007/s11886-024-02020-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
PURPOSE OF REVIEW Approximately 30% of syndromic cases diagnosed with CHD, which lure us to further investigate the molecular and clinical challenges behind syndromic CHD (sCHD). The aetiology of sCHD in a majority of cases remains enigmatic due to involvement of multiple factors, namely genetic, epigenetic and environmental modifiable risk factors for the development of the disease. Here, we aim to update the role of genetic contributors including chromosomal abnormalities, copy number variations (CNVs) and single gene mutations in cardiac specific genes, maternal lifestyle conditions, environmental exposures and epigenetic modifiers in causing CHD in different genetic syndromes. RECENT FINDINGS The exact aetiology of sCHD is still unknown. With the advancement of next-generation technologies including WGS, WES, transcriptome, proteome and methylome study, numerous novel genes and pathways have been identified. Moreover, our recent knowledge regarding epigenetic and environmental regulation during cardiogenesis is still evolving and may solve some of the mystery behind complex sCHD. Here, we focus to understand how the complex combination of genetic, environmental and epigenetic factors interact to interfere with developmental pathways, culminating into cardiac and extracardiac defects in sCHD.
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Affiliation(s)
- Jyoti Maddhesiya
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Bhagyalaxmi Mohapatra
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India.
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49
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Xiao F, Zhang X, Morton SU, Kim SW, Fan Y, Gorham JM, Zhang H, Berkson PJ, Mazumdar N, Cao Y, Chen J, Hagen J, Liu X, Zhou P, Richter F, Shen Y, Ward T, Gelb BD, Seidman JG, Seidman CE, Pu WT. Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nat Genet 2024; 56:420-430. [PMID: 38378865 PMCID: PMC11218660 DOI: 10.1038/s41588-024-01669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Rare coding mutations cause ∼45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases, but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity, often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context, four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing, we used the MPRA data to develop a regression model, EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together, we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD.
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Affiliation(s)
- Feng Xiao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Youfei Fan
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Huan Zhang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul J Berkson
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Neil Mazumdar
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jian Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Jacob Hagen
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Xujie Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Felix Richter
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York City, NY, USA
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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50
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Padmanabhan A, de Soysa TY, Pelonero A, Sapp V, Shah PP, Wang Q, Li L, Lee CY, Sadagopan N, Nishino T, Ye L, Yang R, Karnay A, Poleshko A, Bolar N, Linares-Saldana R, Ranade SS, Alexanian M, Morton SU, Jain M, Haldar SM, Srivastava D, Jain R. A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation. NATURE CARDIOVASCULAR RESEARCH 2024; 3:317-331. [PMID: 39196112 PMCID: PMC11361716 DOI: 10.1038/s44161-024-00431-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/19/2024] [Indexed: 08/29/2024]
Abstract
Human induced pluripotent stem cell (hiPSC) to cardiomyocyte (CM) differentiation has reshaped approaches to studying cardiac development and disease. In this study, we employed a genome-wide CRISPR screen in a hiPSC to CM differentiation system and reveal here that BRD4, a member of the bromodomain and extraterminal (BET) family, regulates CM differentiation. Chemical inhibition of BET proteins in mouse embryonic stem cell (mESC)-derived or hiPSC-derived cardiac progenitor cells (CPCs) results in decreased CM differentiation and persistence of cells expressing progenitor markers. In vivo, BRD4 deletion in second heart field (SHF) CPCs results in embryonic or early postnatal lethality, with mutants demonstrating myocardial hypoplasia and an increase in CPCs. Single-cell transcriptomics identified a subpopulation of SHF CPCs that is sensitive to BRD4 loss and associated with attenuated CM lineage-specific gene programs. These results highlight a previously unrecognized role for BRD4 in CM fate determination during development and a heterogenous requirement for BRD4 among SHF CPCs.
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Affiliation(s)
- Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | | | | | - Valerie Sapp
- Department of Medicine, University of California, San Diego, School of Medicine, San Diego, CA, USA
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
| | - Parisha P Shah
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Qiaohong Wang
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Li Li
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Clara Youngna Lee
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | - Nandhini Sadagopan
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | | | - Lin Ye
- Gladstone Institutes, San Francisco, CA, USA
| | - Rachel Yang
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ashley Karnay
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikhita Bolar
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ricardo Linares-Saldana
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Michael Alexanian
- Gladstone Institutes, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | - Sarah U Morton
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Mohit Jain
- Department of Medicine, University of California, San Diego, School of Medicine, San Diego, CA, USA
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
| | - Saptarsi M Haldar
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
- Amgen Research, Cardiometabolic Disorders, South San Francisco, CA, USA
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Pediatrics, University of California, San Francisco, School of Medicine, San Francisco, CA, USA.
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone Institutes, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
| | - Rajan Jain
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
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