1
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Qiao L, Welch CL, Hernan R, Wynn J, Krishnan US, Zalieckas JM, Buchmiller T, Khlevner J, De A, Farkouh-Karoleski C, Wagner AJ, Heydweiller A, Mueller AC, de Klein A, Warner BW, Maj C, Chung D, McCulley DJ, Schindel D, Potoka D, Fialkowski E, Schulz F, Kipfmuller F, Lim FY, Magielsen F, Mychaliska GB, Aspelund G, Reutter HM, Needelman H, Schnater JM, Fisher JC, Azarow K, Elfiky M, Nöthen MM, Danko ME, Li M, Kosiński P, Wijnen RMH, Cusick RA, Soffer SZ, Cochius-Den Otter SCM, Schaible T, Crombleholme T, Duron VP, Donahoe PK, Sun X, High FA, Bendixen C, Brosens E, Shen Y, Chung WK. Common variants increase risk for congenital diaphragmatic hernia within the context of de novo variants. Am J Hum Genet 2024; 111:2362-2381. [PMID: 39332409 PMCID: PMC11568762 DOI: 10.1016/j.ajhg.2024.08.024] [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: 04/23/2024] [Revised: 08/24/2024] [Accepted: 08/30/2024] [Indexed: 09/29/2024] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly often accompanied by other structural anomalies and/or neurobehavioral manifestations. Rare de novo protein-coding variants and copy-number variations contribute to CDH in the population. However, most individuals with CDH remain genetically undiagnosed. Here, we perform integrated de novo and common-variant analyses using 1,469 CDH individuals, including 1,064 child-parent trios and 6,133 ancestry-matched, unaffected controls for the genome-wide association study. We identify candidate CDH variants in 15 genes, including eight novel genes, through deleterious de novo variants. We further identify two genomic loci contributing to CDH risk through common variants with similar effect sizes among Europeans and Latinx. Both loci are in putative transcriptional regulatory regions of developmental patterning genes. Estimated heritability in common variants is ∼19%. Strikingly, there is no significant difference in estimated polygenic risk scores between isolated and complex CDH or between individuals harboring deleterious de novo variants and individuals without these variants. The data support a polygenic model as part of the CDH genetic architecture.
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Affiliation(s)
- Lu Qiao
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Carrie L Welch
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rebecca Hernan
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Usha S Krishnan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jill M Zalieckas
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Terry Buchmiller
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Julie Khlevner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aliva De
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Amy J Wagner
- Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Andreas Heydweiller
- Department of General, Visceral, Vascular, and Thoracic Surgery, Unit of Pediatric Surgery, University Hospital Bonn, Bonn, Germany
| | - Andreas C Mueller
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Brad W Warner
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - David J McCulley
- Department of Pediatrics, San Diego Medical School, University of California, San Diego, San Diego, CA 92092, USA
| | | | | | | | - Felicitas Schulz
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Florian Kipfmuller
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Foong-Yen Lim
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Frank Magielsen
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | | | - Gudrun Aspelund
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Heiko Martin Reutter
- Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Howard Needelman
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | - J Marco Schnater
- Department of Pediatric Surgery, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Jason C Fisher
- New York University Grossman School of Medicine, Hassenfeld Children's Hospital at NYU Langone, New York, NY 10016, USA
| | - Kenneth Azarow
- Oregon Health and Science University, Portland, OR 97239, USA
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - Mindy Li
- Rush University Medical Center, Chicago, IL 60612, USA
| | - Przemyslaw Kosiński
- Department of Obstetrics, Perinatology and Gynecology, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Rene M H Wijnen
- Department of Pediatric Surgery, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Robert A Cusick
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | | | - Suzan C M Cochius-Den Otter
- Department of Neonatology and Pediatric Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Thomas Schaible
- Department of Neonatology, University Children's Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | | | - Vincent P Duron
- Department of Surgery (Pediatrics), Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Xin Sun
- Department of Pediatrics, San Diego Medical School, University of California, San Diego, San Diego, CA 92092, USA
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Charlotte Bendixen
- Department of General, Visceral, Vascular, and Thoracic Surgery, Unit of Pediatric Surgery, University Hospital Bonn, Bonn, Germany
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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2
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Liu S, Yu L. Role of genetics and the environment in the etiology of congenital diaphragmatic hernia. WORLD JOURNAL OF PEDIATRIC SURGERY 2024; 7:e000884. [PMID: 39183805 PMCID: PMC11340715 DOI: 10.1136/wjps-2024-000884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 07/22/2024] [Indexed: 08/27/2024] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a congenital malformation characterized by failure of diaphragm closure during embryonic development, leading to pulmonary hypoplasia and pulmonary hypertension, which contribute significantly to morbidity and mortality. The occurrence of CDH and pulmonary hypoplasia is theorized to result from both abnormalities in signaling pathways of smooth muscle cells in pleuroperitoneal folds and mechanical compression by abdominal organs within the chest cavity on the developing lungs. Although, the precise etiology of diaphragm maldevelopment in CDH is not fully understood, it is believed that interplay between genes and the environment contributes to its onset. Approximately 30% of patients with CDH possess chromosomal or single gene defects and these patients tend to have inferior outcomes compared with those without genetic associations. At present, approximately 150 gene variants have been linked to the occurrence of CDH. The variable expression of the CDH phenotype in the presence of a recognized genetic predisposition can be explained by an environmental effect on gene penetrance and expression. The retinoic acid pathway is thought to play an essential role in the interactions of genes and environment in CDH. However, apart from the gradually maturing retinol hypothesis, there is limited evidence implicating other environmental factors in CDH occurrence. This review aims to describe the pathogenesis of CDH by summarizing the genetic defects and potential environmental influences on CDH development.
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Affiliation(s)
- Siyuan Liu
- Department of Cardiac & Thoracic Surgery, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Lan Yu
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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3
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Rivas JFG, Clugston RD. The etiology of congenital diaphragmatic hernia: the retinoid hypothesis 20 years later. Pediatr Res 2024; 95:912-921. [PMID: 37990078 PMCID: PMC10920205 DOI: 10.1038/s41390-023-02905-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023]
Abstract
Congenital diaphragmatic hernia (CDH) is a severe birth defect and a major cause of neonatal respiratory distress. Impacting ~2-3 in 10,000 births, CDH is associated with a high mortality rate, and long-term morbidity in survivors. Despite the significant impact of CDH, its etiology remains incompletely understood. In 2003, Greer et al. proposed the Retinoid Hypothesis, stating that the underlying cause of abnormal diaphragm development in CDH was related to altered retinoid signaling. In this review, we provide a comprehensive update to the Retinoid Hypothesis, discussing work published in support of this hypothesis from the past 20 years. This includes reviewing teratogenic and genetic models of CDH, lessons from the human genetics of CDH and epidemiological studies, as well as current gaps in the literature and important areas for future research. The Retinoid Hypothesis is one of the leading hypotheses to explain the etiology of CDH, as we continue to better understand the role of retinoid signaling in diaphragm development, we hope that this information can be used to improve CDH outcomes. IMPACT: This review provides a comprehensive update on the Retinoid Hypothesis, which links abnormal retinoic acid signaling to the etiology of congenital diaphragmatic hernia. The Retinoid Hypothesis was formulated in 2003. Twenty years later, we extensively review the literature in support of this hypothesis from both animal models and humans.
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Affiliation(s)
- Juan F Garcia Rivas
- Department of Physiology, University of Alberta, Edmonton, AB, Canada
- Women and Children's Health Research Institute, Edmonton, AB, Canada
| | - Robin D Clugston
- Department of Physiology, University of Alberta, Edmonton, AB, Canada.
- Women and Children's Health Research Institute, Edmonton, AB, Canada.
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Petit F, Longoni M, Wells J, Maser RS, Bogenschutz EL, Dysart MJ, Contreras HTM, Frénois F, Pober BR, Clark RD, Giampietro PF, Ropers HH, Hu H, Loscertales M, Wagner R, Ai X, Brand H, Jourdain AS, Delrue MA, Gilbert-Dussardier B, Devisme L, Keren B, McCulley DJ, Qiao L, Hernan R, Wynn J, Scott TM, Calame DG, Coban-Akdemir Z, Hernandez P, Hernandez-Garcia A, Yonath H, Lupski JR, Shen Y, Chung WK, Scott DA, Bult CJ, Donahoe PK, High FA. PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects. Am J Hum Genet 2023; 110:1787-1803. [PMID: 37751738 PMCID: PMC10577083 DOI: 10.1016/j.ajhg.2023.09.002] [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: 12/22/2021] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/28/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a relatively common and genetically heterogeneous structural birth defect associated with high mortality and morbidity. We describe eight unrelated families with an X-linked condition characterized by diaphragm defects, variable anterior body-wall anomalies, and/or facial dysmorphism. Using linkage analysis and exome or genome sequencing, we found that missense variants in plastin 3 (PLS3), a gene encoding an actin bundling protein, co-segregate with disease in all families. Loss-of-function variants in PLS3 have been previously associated with X-linked osteoporosis (MIM: 300910), so we used in silico protein modeling and a mouse model to address these seemingly disparate clinical phenotypes. The missense variants in individuals with CDH are located within the actin-binding domains of the protein but are not predicted to affect protein structure, whereas the variants in individuals with osteoporosis are predicted to result in loss of function. A mouse knockin model of a variant identified in one of the CDH-affected families, c.1497G>C (p.Trp499Cys), shows partial perinatal lethality and recapitulates the key findings of the human phenotype, including diaphragm and abdominal-wall defects. Both the mouse model and one adult human male with a CDH-associated PLS3 variant were observed to have increased rather than decreased bone mineral density. Together, these clinical and functional data in humans and mice reveal that specific missense variants affecting the actin-binding domains of PLS3 might have a gain-of-function effect and cause a Mendelian congenital disorder.
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Affiliation(s)
- Florence Petit
- Clinique de Génétique, CHU de Lille, Lille, France; EA7364 RADEME, Université de Lille, Lille, France
| | - Mauro Longoni
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Matthew J Dysart
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | - Hannah T M Contreras
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | | | - Barbara R Pober
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
| | - Robin D Clark
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | | | - Hilger H Ropers
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hao Hu
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maria Loscertales
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Richard Wagner
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA; Department of Pediatric Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Xingbin Ai
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison Brand
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Boris Keren
- Département de Génétique, Hôpital Pitié Salpétrière, CHU de Paris, Paris, France
| | - David J McCulley
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Lu Qiao
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Rebecca Hernan
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Tiana M Scott
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 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, USA
| | - Patricia Hernandez
- IDDRC/TCC, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Hagith Yonath
- Internal Medicine A and Genetics Institute, Sheba Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | | | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Frances A High
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Boston Children's Hospital, Boston, MA, USA.
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5
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Schreiner Y, Stoll T, Nowak O, Weis M, Hetjens S, Steck E, Perez Ortiz A, Rafat N. aCGH Analysis Reveals Novel Mutations Associated with Congenital Diaphragmatic Hernia Plus (CDH+). J Clin Med 2023; 12:6111. [PMID: 37834755 PMCID: PMC10573849 DOI: 10.3390/jcm12196111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a major birth anomaly that often occurs with additional non-hernia-related malformations, and is then referred to as CDH+. While the impact of genetic alterations does not play a major role in isolated CDH, patients with CDH+ display mutations that are usually determined via array-based comparative genomic hybridization (aCGH). We analyzed 43 patients with CDH+ between 2012 and 2021 to identify novel specific mutations via aCGH associated with CDH+ and its outcome. Deletions (n = 32) and duplications (n = 29) classified as either pathological or variants of unknown significance (VUS) could be detected. We determined a heterozygous deletion of approximately 3.75 Mb located at 8p23.1 involving several genes including GATA4, NEIL2, SOX7, and MSRA, which was consequently evaluated as pathological. Another heterozygous deletion within the region of 9p23 (9,972,017-10,034,230 kb) encompassing the Protein Tyrosine Phosphatase Receptor Type Delta gene (PTPRD) was identified in 2 patients. This work expands the knowledge of genetic alterations associated with CDH+ and proposes two novel candidate genes discovered via aCGH.
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Affiliation(s)
- Yannick Schreiner
- Department of Neonatology, University Children’s Hospital Mannheim, University of Heidelberg, 69117 Mannheim, Germany; (Y.S.); (T.S.); (A.P.O.)
| | - Teresa Stoll
- Department of Neonatology, University Children’s Hospital Mannheim, University of Heidelberg, 69117 Mannheim, Germany; (Y.S.); (T.S.); (A.P.O.)
| | - Oliver Nowak
- Department of Gynecology and Obstetrics, University Hospital Mannheim, University of Heidelberg, 68167 Mannheim, Germany;
| | - Meike Weis
- Department of Clinical Radiology and Nuclear Medicine, University Medical Center Mannheim, University of Heidelberg, 69117 Mannheim, Germany;
| | - Svetlana Hetjens
- Department of Medical Statistics and Biomathematics, Medical Faculty Mannheim, University of Heidelberg, 69117 Mannheim, Germany;
| | - Eric Steck
- SYNLAB Centre for Human Genetics, 68163 Mannheim, Germany;
| | - Alba Perez Ortiz
- Department of Neonatology, University Children’s Hospital Mannheim, University of Heidelberg, 69117 Mannheim, Germany; (Y.S.); (T.S.); (A.P.O.)
| | - Neysan Rafat
- Department of Neonatology, University Children’s Hospital Mannheim, University of Heidelberg, 69117 Mannheim, Germany; (Y.S.); (T.S.); (A.P.O.)
- Department of Neonatology, Center for Children, Adolescent and Women’s Medicine, Olgahospital, Klinikum Stuttgart, 70174 Stuttgart, Germany
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6
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Gilbert RM, Gleghorn JP. Connecting clinical, environmental, and genetic factors point to an essential role for vitamin A signaling in the pathogenesis of congenital diaphragmatic hernia. Am J Physiol Lung Cell Mol Physiol 2023; 324:L456-L467. [PMID: 36749917 PMCID: PMC10042603 DOI: 10.1152/ajplung.00349.2022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/09/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a developmental disorder that results in incomplete diaphragm formation, pulmonary hypoplasia, and pulmonary hypertension. Although a variety of genes have been linked to its etiology, CDH is not a monogenetic disease, and the cause of the condition is still unclear in the vast majority of clinical cases. By comparing human clinical data and experimental rodent data from the literature, we present clear support demonstrating the importance of vitamin A (vitA) during the early window of pregnancy when the diaphragm and lung are forming. Alteration of vitA signaling via dietary and genetic perturbations can create diaphragmatic defects. Unfortunately, vitA deficiency is chronic among people of child-bearing age, and this early window of diaphragm development occurs before many might be aware of pregnancy. Furthermore, there is an increased demand for vitA during this critical period, which exacerbates the likelihood of deficiency. It would be beneficial for the field to further investigate the connections between maternal vitA and CDH incidence, with the goal of determining vitA status as a CDH risk factor. Regular clinical monitoring of vitA levels in child-bearing years is a tractable method by which CDH outcomes could be prevented or improved.
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Affiliation(s)
- Rachel M Gilbert
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, United States
| | - Jason P Gleghorn
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, United States
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States
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7
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De Leon N, Tse WH, Ameis D, Keijzer R. Embryology and anatomy of congenital diaphragmatic hernia. Semin Pediatr Surg 2022; 31:151229. [PMID: 36446305 DOI: 10.1016/j.sempedsurg.2022.151229] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Prenatal and postnatal treatment modalities for congenital diaphragmatic hernia (CDH) continue to improve, however patients still face high rates of morbidity and mortality caused by severe underlying persistent pulmonary hypertension and pulmonary hypoplasia. Though the majority of CDH cases are idiopathic, it is believed that CDH is a polygenic developmental defect caused by interactions between candidate genes, as well as environmental and epigenetic factors. However, the origin and pathogenesis of these developmental insults are poorly understood. Further, connections between disrupted lung development and the failure of diaphragmatic closure during embryogenesis have not been fully elucidated. Though several animal models have been useful in identifying candidate genes and disrupted signalling pathways, more studies are required to understand the pathogenesis and to develop effective preventative care. In this article, we summarize the most recent litterature on disrupted embryological lung and diaphragmatic development associated with CDH.
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Affiliation(s)
- Nolan De Leon
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology and Pathophysiology, University of Manitoba and Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Wai Hei Tse
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology and Pathophysiology, University of Manitoba and Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Dustin Ameis
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology and Pathophysiology, University of Manitoba and Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard Keijzer
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology and Pathophysiology, University of Manitoba and Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
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8
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Burns NG, Kardon G. The role of genes and environment in the etiology of congenital diaphragmatic hernias. Curr Top Dev Biol 2022; 152:115-138. [PMID: 36707209 PMCID: PMC10923182 DOI: 10.1016/bs.ctdb.2022.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Structural birth defects are a common cause of abnormalities in newborns. While there are cases of structural birth defects arising due to monogenic defects or environmental exposures, many birth defects are likely caused by a complex interaction between genes and the environment. A structural birth defect with complex etiology is congenital diaphragmatic hernias (CDH), a common and often lethal disruption in diaphragm development. Mutations in more than 150 genes have been implicated in CDH pathogenesis. Although there is generally less evidence for a role for environmental factors in the etiology of CDH, deficiencies in maternal vitamin A and its derivative embryonic retinoic acid are strongly associated with CDH. However, the incomplete penetrance of CDH-implicated genes and environmental factors such as vitamin A deficiency suggest that interactions between genes and environment may be necessary to cause CDH. In this review, we examine the genetic and environmental factors implicated in diaphragm and CDH development. In addition, we evaluate the potential for gene-environment interactions in CDH etiology, focusing on the potential interactions between the CDH-implicated gene, Gata4, and maternal vitamin A deficiency.
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Affiliation(s)
- Nathan G Burns
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States
| | - Gabrielle Kardon
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States.
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9
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Hardcastle A, Berry AM, Campbell IM, Zhao X, Liu P, Gerard AE, Rosenfeld JA, Sisoudiya SD, Hernandez-Garcia A, Loddo S, Di Tommaso S, Novelli A, Dentici ML, Capolino R, Digilio MC, Graziani L, Rustad CF, Neas K, Ferrero GB, Brusco A, Di Gregorio E, Wellesley D, Beneteau C, Joubert M, Van Den Bogaert K, Boogaerts A, McMullan DJ, Dean J, Giuffrida MG, Bernardini L, Varghese V, Shannon NL, Harrison RE, Lam WWK, McKee S, Turnpenny PD, Cole T, Morton J, Eason J, Jones MC, Hall R, Wright M, Horridge K, Shaw CA, Chung WK, Scott DA. Identifying phenotypic expansions for congenital diaphragmatic hernia plus (CDH+) using DECIPHER data. Am J Med Genet A 2022; 188:2958-2968. [PMID: 35904974 PMCID: PMC9474674 DOI: 10.1002/ajmg.a.62919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/28/2022] [Accepted: 07/10/2022] [Indexed: 01/31/2023]
Abstract
Congenital diaphragmatic hernia (CDH) can occur in isolation or in conjunction with other birth defects (CDH+). A molecular etiology can only be identified in a subset of CDH cases. This is due, in part, to an incomplete understanding of the genes that contribute to diaphragm development. Here, we used clinical and molecular data from 36 individuals with CDH+ who are cataloged in the DECIPHER database to identify genes that may play a role in diaphragm development and to discover new phenotypic expansions. Among this group, we identified individuals who carried putatively deleterious sequence or copy number variants affecting CREBBP, SMARCA4, UBA2, and USP9X. The role of these genes in diaphragm development was supported by their expression in the developing mouse diaphragm, their similarity to known CDH genes using data from a previously published and validated machine learning algorithm, and/or the presence of CDH in other individuals with their associated genetic disorders. Our results demonstrate how data from DECIPHER, and other public databases, can be used to identify new phenotypic expansions and suggest that CREBBP, SMARCA4, UBA2, and USP9X play a role in diaphragm development.
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Affiliation(s)
- Amy Hardcastle
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Aliska M. Berry
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ian M. Campbell
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Amanda E. Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Saumya D. Sisoudiya
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Sara Loddo
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Silvia Di Tommaso
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maria L. Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Maria C. Digilio
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ludovico Graziani
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
- Medical Genetics Unit, Tor Vergata Hospital, Rome, Italy
| | - Cecilie F. Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Giovanni B. Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | - Diana Wellesley
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, Hampshire, UK
- University Hospital Southampton, Southampton, Hampshire, UK
| | - Claire Beneteau
- Nantes Université, CHU de Nantes, UF 9321 de Fœtopathologie et Génétique, Nantes, France
| | - Madeleine Joubert
- Nantes Université, CHU de Nantes, UF 9321 de Fœtopathologie et Génétique, Nantes, France
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven–KU Leuven, Leuven, Belgium
| | - Anneleen Boogaerts
- Center for Human Genetics, University Hospitals Leuven–KU Leuven, Leuven, Belgium
| | - Dominic J. McMullan
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s NHS Foundation Trust, UK
| | - John Dean
- Clinical Genetics Service, Ashgrove House, NHS Grampian, Aberdeen, UK
| | - Maria G. Giuffrida
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Laura Bernardini
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Nora L Shannon
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rachel E. Harrison
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Wayne W. K. Lam
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, Scotland
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Peter D. Turnpenny
- Clinical Genetics Department, Royal Devon and Exeter Hospital, Exeter, UK
| | - Trevor Cole
- Clinical Genetics Unit, Birmingham Women’s Hospital, Birmingham, UK
| | - Jenny Morton
- Clinical Genetics Unit, Birmingham Women’s Hospital, Birmingham, UK
| | - Jacqueline Eason
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Marilyn C. Jones
- University of California, San Diego and Rady Children’s Hospital, San Diego, CA, USA
| | - Rebecca Hall
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michael Wright
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Karen Horridge
- South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
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10
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Campbell M, Wei J, Attaar M, Wu H, Wong HJ, Ujiki MB, Xu J. Identification of 14 novel susceptibility loci for diaphragmatic hernia development and their biological and clinical implications: results from the UK Biobank. Surg Endosc 2022; 36:7647-7651. [PMID: 36076102 DOI: 10.1007/s00464-022-09064-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/17/2022] [Indexed: 10/14/2022]
Abstract
INTRODUCTION Genetic contributions to hernia development are incompletely understood. This study performed the first comprehensive genome-wide association study (GWAS) for diaphragmatic hernia using a large population-based cohort in the UK Biobank (UKB). METHODS AND PROCEDURES Two-stage GWAS (discovery and confirmation) was performed for diaphragmatic hernia in the UKB. Briefly, 275,549 and 91,850 subjects were randomly selected for association tests in Stages 1 and 2, respectively. Association tests between 8,568,156 SNPs (genotyped or imputed with MAF > 0.01) in the autosomal genome and diaphragmatic hernia were performed in Stage 1. SNPs with P < 1 × 10-5 were selected for confirmation in Stage 2, and those with P < 0.05 and the same direction of association as Stage 1 were selected for combined association testing; SNPs with combined P < 5 × 10-8 were considered GWAS-significant. LD clumping analysis identified genetically independent chromosomal regions (loci). A genetic risk score (GRS) measured the cumulative risk of independent SNPs in 91,849 additional subjects using odds ratios (ORs) from Stages 1 and 2. RESULTS 36,351 patients were identified with diaphragmatic hernia (ICD-10 K44). In Stage 1 analysis, 2654 SNPs were associated (P < 1 × 10-5) with diaphragmatic hernia. Stage 2 analysis confirmed 338 SNPs (P < 0.05). In combined analysis, 245 SNPs reached GWAS significance (P < 5 × 10-8). LD clumping analysis revealed 14 independent loci associated with diaphragmatic hernia. Two loci have been previously associated with inguinal hernia at 2p16 (rs181661155) and 11p13 (rs5030123). eQTL analysis suggested genes CRLF1, UBA52, and CALD1 are also significantly associated with these loci. GRS showed significant increase in cases compared to controls (P < 1 × 10-16) and is associated with increased risk of diaphragmatic hernia (P < 1 × 10-7). CONCLUSIONS We identified 245 SNPs at 14 susceptibility loci associated with diaphragmatic hernia in a large population-based cohort. These results offer insight into pathogenetic mechanisms of diaphragmatic hernia development and may be used in genetic risk scores for pre-operative risk-stratification and clinical prediction models.
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Affiliation(s)
- Michelle Campbell
- Department of Surgery, University of Chicago Medical Center, Chicago, IL, USA.
- Department of Surgery, Northshore University HealthSystem, 2650 Ridge Ave, GCSI Suite B665, Evanston, IL, 60201, USA.
| | - Jun Wei
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Mikhail Attaar
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
- Department of Surgery, University of Chicago Medical Center, Chicago, IL, USA
| | - Hoover Wu
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
- Department of Surgery, University of Chicago Medical Center, Chicago, IL, USA
| | - Harry J Wong
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
- Department of Surgery, University of Chicago Medical Center, Chicago, IL, USA
| | - Michael B Ujiki
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
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11
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Pechriggl E, Blumer M, Tubbs RS, Olewnik Ł, Konschake M, Fortélny R, Stofferin H, Honis HR, Quinones S, Maranillo E, Sanudo J. Embryology of the Abdominal Wall and Associated Malformations—A Review. Front Surg 2022; 9:891896. [PMID: 35874129 PMCID: PMC9300894 DOI: 10.3389/fsurg.2022.891896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/10/2022] [Indexed: 12/12/2022] Open
Abstract
In humans, the incidence of congenital defects of the intraembryonic celom and its associated structures has increased over recent decades. Surgical treatment of abdominal and diaphragmatic malformations resulting in congenital hernia requires deep knowledge of ventral body closure and the separation of the primary body cavities during embryogenesis. The correct development of both structures requires the coordinated and fine-tuned synergy of different anlagen, including a set of molecules governing those processes. They have mainly been investigated in a range of vertebrate species (e.g., mouse, birds, and fish), but studies of embryogenesis in humans are rather rare because samples are seldom available. Therefore, we have to deal with a large body of conflicting data concerning the formation of the abdominal wall and the etiology of diaphragmatic defects. This review summarizes the current state of knowledge and focuses on the histological and molecular events leading to the establishment of the abdominal and thoracic cavities in several vertebrate species. In chronological order, we start with the onset of gastrulation, continue with the establishment of the three-dimensional body shape, and end with the partition of body cavities. We also discuss well-known human etiologies.
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Affiliation(s)
- Elisabeth Pechriggl
- Institute of Clinical and Functional Anatomy, Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Michael Blumer
- Institute of Clinical and Functional Anatomy, Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - R. Shane Tubbs
- Department of Neurosurgery, Tulane Center for Clinical Neurosciences, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Neurology, Tulane Center for Clinical Neurosciences, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Anatomical Sciences, St. George’s University, St. George’s, Grenada, West Indies
- Department of Structural & Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Surgery, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Neurosurgery and Ochsner Neuroscience Institute, Ochsner Health System, New Orleans, LA, United States
- University of Queensland, Brisbane, Australia
| | - Łukasz Olewnik
- Department of Anatomical Dissection and Donation, Medical University of Lodz, Lodz, Poland
| | - Marko Konschake
- Institute of Clinical and Functional Anatomy, Medical University of Innsbruck (MUI), Innsbruck, Austria
- Correspondence: Marko Konschake
| | - René Fortélny
- Department of General, Visceral, and Oncological Surgery, Wilhelminenspital, Vienna, Austria
| | - Hannes Stofferin
- Institute of Clinical and Functional Anatomy, Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Hanne Rose Honis
- Institute of Clinical and Functional Anatomy, Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Sara Quinones
- Department of Anatomy and Embryology, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Eva Maranillo
- Department of Anatomy and Embryology, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - José Sanudo
- Department of Anatomy and Embryology, School of Medicine, Complutense University of Madrid, Madrid, Spain
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12
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Molecular Mechanisms Contributing to the Etiology of Congenital Diaphragmatic Hernia: A Review and Novel Cases. J Pediatr 2022; 246:251-265.e2. [PMID: 35314152 DOI: 10.1016/j.jpeds.2022.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 12/25/2022]
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13
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Zani A, Chung WK, Deprest J, Harting MT, Jancelewicz T, Kunisaki SM, Patel N, Antounians L, Puligandla PS, Keijzer R. Congenital diaphragmatic hernia. Nat Rev Dis Primers 2022; 8:37. [PMID: 35650272 DOI: 10.1038/s41572-022-00362-w] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/22/2022] [Indexed: 11/09/2022]
Abstract
Congenital diaphragmatic hernia (CDH) is a rare birth defect characterized by incomplete closure of the diaphragm and herniation of fetal abdominal organs into the chest that results in pulmonary hypoplasia, postnatal pulmonary hypertension owing to vascular remodelling and cardiac dysfunction. The high mortality and morbidity rates associated with CDH are directly related to the severity of cardiopulmonary pathophysiology. Although the aetiology remains unknown, CDH has a polygenic origin in approximately one-third of cases. CDH is typically diagnosed with antenatal ultrasonography, which also aids in risk stratification, alongside fetal MRI and echocardiography. At specialized centres, prenatal management includes fetal endoscopic tracheal occlusion, which is a surgical intervention aimed at promoting lung growth in utero. Postnatal management focuses on cardiopulmonary stabilization and, in severe cases, can involve extracorporeal life support. Clinical practice guidelines continue to evolve owing to the rapidly changing landscape of therapeutic options, which include pulmonary hypertension management, ventilation strategies and surgical approaches. Survivors often have long-term, multisystem morbidities, including pulmonary dysfunction, gastroesophageal reflux, musculoskeletal deformities and neurodevelopmental impairment. Emerging research focuses on small RNA species as biomarkers of severity and regenerative medicine approaches to improve fetal lung development.
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Affiliation(s)
- Augusto Zani
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Department of Surgery, University of Toronto, Toronto, Ontario, Canada. .,Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada.
| | - Wendy K Chung
- Department of Paediatrics, Columbia University, New York, NY, USA
| | - Jan Deprest
- Department of Development and Regeneration, Cluster Woman and Child and Clinical Department of Obstetrics and Gynaecology, University Hospitals, KU Leuven, Leuven, Belgium.,Institute for Women's Health, UCL, London, UK
| | - Matthew T Harting
- Department of Paediatric Surgery, McGovern Medical School at the University of Texas Health Science Center, Houston, TX, USA.,The Comprehensive Center for CDH Care, Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Tim Jancelewicz
- Division of Pediatric Surgery, Le Bonheur Children's Hospital, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Shaun M Kunisaki
- Division of General Paediatric Surgery, Johns Hopkins Children's Center, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neil Patel
- Department of Neonatology, Royal Hospital for Children, Glasgow, UK
| | - Lina Antounians
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Department of Surgery, University of Toronto, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pramod S Puligandla
- Department of Paediatric Surgery, Harvey E. Beardmore Division of Paediatric Surgery, Montreal Children's Hospital of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Richard Keijzer
- Department of Surgery, Division of Paediatric Surgery, Paediatrics & Child Health, Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
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14
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Nicholas TJ, Al‐Sweel N, Farrell A, Mao R, Bayrak‐Toydemir P, Miller CE, Bentley D, Palmquist R, Moore B, Hernandez EJ, Cormier MJ, Fredrickson E, Noble K, Rynearson S, Holt C, Karren M, Bonkowsky JL, Tristani‐Firouzi M, Yandell M, Marth G, Quinlan AR, Brunelli L, Toydemir R, Shayota BJ, Carey JC, Boyden SE, Malone Jenkins S. Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Mol Genet Genomic Med 2022; 10:e1888. [PMID: 35119225 PMCID: PMC9000945 DOI: 10.1002/mgg3.1888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Genetic disorders contribute to significant morbidity and mortality in critically ill newborns. Despite advances in genome sequencing technologies, a majority of neonatal cases remain unsolved. Complex structural variants (SVs) often elude conventional genome sequencing variant calling pipelines and will explain a portion of these unsolved cases. METHODS As part of the Utah NeoSeq project, we used a research-based, rapid whole-genome sequencing (WGS) protocol to investigate the genomic etiology for a newborn with a left-sided congenital diaphragmatic hernia (CDH) and cardiac malformations, whose mother also had a history of CDH and atrial septal defect. RESULTS Using both a novel, alignment-free and traditional alignment-based variant callers, we identified a maternally inherited complex SV on chromosome 8, consisting of an inversion flanked by deletions. This complex inversion, further confirmed using orthogonal molecular techniques, disrupts the ZFPM2 gene, which is associated with both CDH and various congenital heart defects. CONCLUSIONS Our results demonstrate that complex structural events, which often are unidentifiable or not reported by clinically validated testing procedures, can be discovered and accurately characterized with conventional, short-read sequencing and underscore the utility of WGS as a first-line diagnostic tool.
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Affiliation(s)
- Thomas J. Nicholas
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Najla Al‐Sweel
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | - Andrew Farrell
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Rong Mao
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | - Pinar Bayrak‐Toydemir
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | | | - Dawn Bentley
- Division of Neonatology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Rachel Palmquist
- Division of Pediatric Neurology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
- Primary Children's Center for Personalized MedicineSalt Lake CityUSA
| | - Barry Moore
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Edgar J. Hernandez
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Michael J. Cormier
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | | | | | - Shawn Rynearson
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Carson Holt
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Mary Anne Karren
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Joshua L. Bonkowsky
- Division of Pediatric Neurology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
- Primary Children's Center for Personalized MedicineSalt Lake CityUSA
| | - Martin Tristani‐Firouzi
- Division of Pediatric Cardiology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Mark Yandell
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Gabor Marth
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Aaron R. Quinlan
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
- Department of Biomedical InformaticsUniversity of UtahSalt Lake CityUSA
| | - Luca Brunelli
- Division of Neonatology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Reha M. Toydemir
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | - Brian J. Shayota
- Division of Medical Genetics, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - John C. Carey
- Division of Medical Genetics, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Steven E. Boyden
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
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15
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Scott DA, Gofin Y, Berry AM, Adams AD. Underlying genetic etiologies of congenital diaphragmatic hernia. Prenat Diagn 2022; 42:373-386. [PMID: 35037267 PMCID: PMC8924940 DOI: 10.1002/pd.6099] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/09/2022]
Abstract
Congenital diaphragmatic hernia (CDH) is often detectable prenatally. Advances in genetic testing have made it possible to obtain a molecular diagnosis in many fetuses with CDH. Here, we review the aneuploidies, copy number variants (CNVs), and single genes that have been clearly associated with CDH. We suggest that array-based CNV analysis, with or without a chromosome analysis, is the optimal test for identifying chromosomal abnormalities and CNVs in fetuses with CDH. To identify causative sequence variants, whole exome sequencing (WES) is the most comprehensive strategy currently available. Whole genome sequencing (WGS) with CNV analysis has the potential to become the most efficient and effective means of identifying an underlying diagnosis but is not yet routinely available for prenatal diagnosis. We describe how to overcome and address the diagnostic and clinical uncertainty that may remain after genetic testing, and review how a molecular diagnosis may impact recurrence risk estimations, mortality rates, and the availability and outcomes of fetal therapy. We conclude that after the prenatal detection of CDH, patients should be counseled about the possible genetic causes of the CDH, and the genetic testing modalities available to them, in accordance with generally accepted guidelines for pretest counseling in the prenatal setting.
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Affiliation(s)
- Daryl A. Scott
- Texas Children’s Hospital, Houston, TX, 77030,
USA,Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA,Department of Molecular Physiology and Biophysics, Baylor
College of Medicine, Houston, TX, 77030, USA,Correspondence: Daryl A. Scott, R813, One Baylor
Plaza. BCM225, Houston, TX 77030, USA, Phone: +1 713-203-7242,
| | - Yoel Gofin
- Texas Children’s Hospital, Houston, TX, 77030,
USA,Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA
| | - Aliska M. Berry
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA
| | - April D. Adams
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA,Department of Obstetrics and Gynecology, Division of
Maternal Fetal Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
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16
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Bendixen C, Brosens E, Chung WK. Genetic Diagnostic Strategies and Counseling for Families Affected by Congenital Diaphragmatic Hernia. Eur J Pediatr Surg 2021; 31:472-481. [PMID: 34911129 DOI: 10.1055/s-0041-1740337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Congenital diaphragmatic hernia (CDH) is a relatively common and severe birth defect with variable clinical outcome and associated malformations in up to 60% of patients. Mortality and morbidity remain high despite advances in pre-, intra-, and postnatal management. We review the current literature and give an overview about the genetics of CDH to provide guidelines for clinicians with respect to genetic diagnostics and counseling for families. Until recently, the common practice was (molecular) karyotyping or chromosome microarray if the CDH diagnosis is made prenatally with a 10% diagnostic yield. Undiagnosed patients can be reflexed to trio exome/genome sequencing with an additional diagnostic yield of 10 to 20%. Even with a genetic diagnosis, there can be a range of clinical outcomes. All families with a child with CDH with or without additional malformations should be offered genetic counseling and testing in a family-based trio approach.
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Affiliation(s)
- Charlotte Bendixen
- Department of General, Visceral, Vascular and Thoracic Surgery, Unit of Pediatric Surgery, Universitätsklinikum Bonn, Bonn, Germany
| | - Erwin Brosens
- Department of Pediatric Surgery, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Wendy Kay Chung
- Department of Medicine, Columbia University Irving Medical Center, New York, United States.,Department of Pediatrics, Columbia University Irving Medical Center, New York, United States
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17
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Genetics of diaphragmatic hernia. Eur J Hum Genet 2021; 29:1729-1733. [PMID: 34621023 PMCID: PMC8632982 DOI: 10.1038/s41431-021-00972-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 01/14/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a life-threatening malformation characterised by failure of diaphragmatic development with lung hypoplasia and persistent pulmonary hypertension of the newborn (PPHN). The incidence is 1:2000 corresponding to 8% of all major congenital malformations. Morbidity and mortality in affected newborns are very high and at present, there is no precise prenatal or early postnatal prognostication parameter to predict clinical outcome in CDH patients. Most cases occur sporadically, however, genetic causes have long been discussed to explain a proportion of cases. These range from aneuploidy to complex chromosomal aberrations and specific mutations often causing a complex phenotype exhibiting multiple malformations along with CDH. This review summarises the genetic variations which have been observed in syndromic and isolated cases of congenital diaphragmatic hernia.
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18
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Qiao L, Xu L, Yu L, Wynn J, Hernan R, Zhou X, Farkouh-Karoleski C, Krishnan US, Khlevner J, De A, Zygmunt A, Crombleholme T, Lim FY, Needelman H, Cusick RA, Mychaliska GB, Warner BW, Wagner AJ, Danko ME, Chung D, Potoka D, Kosiński P, McCulley DJ, Elfiky M, Azarow K, Fialkowski E, Schindel D, Soffer SZ, Lyon JB, Zalieckas JM, Vardarajan BN, Aspelund G, Duron VP, High FA, Sun X, Donahoe PK, Shen Y, Chung WK. Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene. Am J Hum Genet 2021; 108:1964-1980. [PMID: 34547244 PMCID: PMC8546037 DOI: 10.1016/j.ajhg.2021.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease-associated genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (lon peptidase 1, mitochondrial) and ALYREF (Aly/REF export factor) as candidate CDH-associated genes on the basis of de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 affected individuals and 11,220 ancestry-matched population control individuals and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in affected familial individuals. Approximately 3% of our CDH cohort who are heterozygous with ultra-rare predicted damaging variants in LONP1 have a range of clinical phenotypes, including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium-specific deletion of Lonp1 die immediately after birth, most likely because of the observed severe reduction of lung growth, a known contributor to the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.
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Affiliation(s)
- Lu Qiao
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Le Xu
- Department of Pediatrics, University of California, San Diego Medical School, San Diego, CA 92093, USA
| | - Lan Yu
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rebecca Hernan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xueya Zhou
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Usha S Krishnan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julie Khlevner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aliva De
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Annette Zygmunt
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Foong-Yen Lim
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Howard Needelman
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | - Robert A Cusick
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | | | - Brad W Warner
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amy J Wagner
- Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | | | | | - David J McCulley
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 52726, USA
| | | | - Kenneth Azarow
- Oregon Health & Science University, Portland, OR 97239, USA
| | | | | | | | - Jane B Lyon
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Jill M Zalieckas
- Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Badri N Vardarajan
- Department of Neurology, Taub Institute for Research on Alzheimer Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University, New York, NY 10032, USA
| | - Gudrun Aspelund
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vincent P Duron
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xin Sun
- Department of Pediatrics, University of California, San Diego Medical School, San Diego, CA 92093, USA
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.
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19
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Bendixen C, Reutter H. The Role of De Novo Variants in Patients with Congenital Diaphragmatic Hernia. Genes (Basel) 2021; 12:genes12091405. [PMID: 34573387 PMCID: PMC8466043 DOI: 10.3390/genes12091405] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 01/21/2023] Open
Abstract
The genetic etiology of congenital diaphragmatic hernia (CDH), a common and severe birth defect, is still incompletely understood. Chromosomal aneuploidies, copy number variations (CNVs), and variants in a large panel of CDH-associated genes, both de novo and inherited, have been described. Due to impaired reproductive fitness, especially of syndromic CDH patients, and still significant mortality rates, the contribution of de novo variants to the genetic background of CDH is assumed to be high. This assumption is supported by the relatively low recurrence rate among siblings. Advantages in high-throughput genome-wide genotyping and sequencing methods have recently facilitated the detection of de novo variants in CDH. This review gives an overview of the known de novo disease-causing variants in CDH patients.
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Affiliation(s)
- Charlotte Bendixen
- Unit of Paediatric Surgery, Department of General, Visceral, Vascular and Thoracic Surgery, University Hospital Bonn, 53127 Bonn, Germany
- Correspondence:
| | - Heiko Reutter
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany;
- Division of Neonatology and Paediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
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20
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Cannata G, Caporilli C, Grassi F, Perrone S, Esposito S. Management of Congenital Diaphragmatic Hernia (CDH): Role of Molecular Genetics. Int J Mol Sci 2021; 22:ijms22126353. [PMID: 34198563 PMCID: PMC8231903 DOI: 10.3390/ijms22126353] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a relatively common major life-threatening birth defect that results in significant mortality and morbidity depending primarily on lung hypoplasia, persistent pulmonary hypertension, and cardiac dysfunction. Despite its clinical relevance, CDH multifactorial etiology is still not completely understood. We reviewed current knowledge on normal diaphragm development and summarized genetic mutations and related pathways as well as cellular mechanisms involved in CDH. Our literature analysis showed that the discovery of harmful de novo variants in the fetus could constitute an important tool for the medical team during pregnancy, counselling, and childbirth. A better insight into the mechanisms regulating diaphragm development and genetic causes leading to CDH appeared essential to the development of new therapeutic strategies and evidence-based genetic counselling to parents. Integrated sequencing, development, and bioinformatics strategies could direct future functional studies on CDH; could be applied to cohorts and consortia for CDH and other birth defects; and could pave the way for potential therapies by providing molecular targets for drug discovery.
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Affiliation(s)
- Giulia Cannata
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
| | - Chiara Caporilli
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
| | - Federica Grassi
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
| | - Serafina Perrone
- Neonatology Unit, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy;
| | - Susanna Esposito
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
- Correspondence: ; Tel.: +39-0521-7047
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21
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Abstract
The term "Autism spectrum disorder" (ASD), in vogue at present, has evolved after continual substantial developments taking place over more than a century. ASD is a heterogeneous, multi-factorial, developmental disability in which an unusual pattern of development takes place during infant and toddler years. As per DSM-5, Autism spectrum disorder is a combined phrase for a family of complex developmental disabilities inclusive of "Autistic Disorder, Pervasive Developmental Disorder not Otherwise Specified (PDD-NOS), and Asperger's Disorder". "ASD is characterized not only by persistent impairments in reciprocal social communication and social interactions, but is also manifested by restricted, repetitive patterns of behavior, interests, or activities". The classical clinical signs that exist in two major domains, viz. the 'social domain' and the 'behavioral domain' for the precise diagnosis of ASD have been tabulated and major differences between DSM-5 and DSM-4 are depicted with the help of a figure in this basic review article. A sharp rise in the incidence of ASD cases has been observed worldwide owing to various risk factors such as genetic predisposition coupled with adverse environmental conditions, gynecological interventions, etc. Two official manuals viz. the "Diagnostic and Statistical Manual of Mental Disorders" (DSM) (published by the American Psychiatric Association), and the "International Classification of Diseases" (ICD) (published by the World Health Organization) is being regularly updated to facilitate diagnosis of ASD. ICD-11 guidelines being prospectively implemented with effect from January 2022 have attracted global attention.
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22
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Brosens E, Peters NCJ, van Weelden KS, Bendixen C, Brouwer RWW, Sleutels F, Bruggenwirth HT, van Ijcken WFJ, Veenma DCM, Otter SCMCD, Wijnen RMH, Eggink AJ, van Dooren MF, Reutter HM, Rottier RJ, Schnater JM, Tibboel D, de Klein A. Unraveling the Genetics of Congenital Diaphragmatic Hernia: An Ongoing Challenge. Front Pediatr 2021; 9:800915. [PMID: 35186825 PMCID: PMC8852845 DOI: 10.3389/fped.2021.800915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/28/2021] [Indexed: 12/16/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a congenital structural anomaly in which the diaphragm has not developed properly. It may occur either as an isolated anomaly or with additional anomalies. It is thought to be a multifactorial disease in which genetic factors could either substantially contribute to or directly result in the developmental defect. Patients with aneuploidies, pathogenic variants or de novo Copy Number Variations (CNVs) impacting specific genes and loci develop CDH typically in the form of a monogenetic syndrome. These patients often have other associated anatomical malformations. In patients without a known monogenetic syndrome, an increased genetic burden of de novo coding variants contributes to disease development. In early years, genetic evaluation was based on karyotyping and SNP-array. Today, genomes are commonly analyzed with next generation sequencing (NGS) based approaches. While more potential pathogenic variants are being detected, analysis of the data presents a bottleneck-largely due to the lack of full appreciation of the functional consequence and/or relevance of the detected variant. The exact heritability of CDH is still unknown. Damaging de novo alterations are associated with the more severe and complex phenotypes and worse clinical outcome. Phenotypic, genetic-and likely mechanistic-variability hampers individual patient diagnosis, short and long-term morbidity prediction and subsequent care strategies. Detailed phenotyping, clinical follow-up at regular intervals and detailed registries are needed to find associations between long-term morbidity, genetic alterations, and clinical parameters. Since CDH is a relatively rare disorder with only a few recurrent changes large cohorts of patients are needed to identify genetic associations. Retrospective whole genome sequencing of historical patient cohorts using will yield valuable data from which today's patients and parents will profit Trio whole genome sequencing has an excellent potential for future re-analysis and data-sharing increasing the chance to provide a genetic diagnosis and predict clinical prognosis. In this review, we explore the pitfalls and challenges in the analysis and interpretation of genetic information, present what is currently known and what still needs further study, and propose strategies to reap the benefits of genetic screening.
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Affiliation(s)
- Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Nina C J Peters
- Division of Obstetrics and Fetal Medicine, Department of Obstetrics and Gynecology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Kim S van Weelden
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Division of Obstetrics and Fetal Medicine, Department of Obstetrics and Gynecology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Charlotte Bendixen
- Unit of Pediatric Surgery, Department of General, Visceral, Vascular and Thoracic Surgery, University Hospital Bonn, Bonn, Germany
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Frank Sleutels
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Hennie T Bruggenwirth
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Wilfred F J van Ijcken
- Center for Biomics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Danielle C M Veenma
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Pediatrics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Suzan C M Cochius-Den Otter
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Rene M H Wijnen
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Alex J Eggink
- Division of Obstetrics and Fetal Medicine, Department of Obstetrics and Gynecology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Heiko Martin Reutter
- Institute of Human Genetics, University Hospital of Bonn, Bonn, Germany.,Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Robbert J Rottier
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - J Marco Schnater
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
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23
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Bogenschutz EL, Sefton EM, Kardon G. Cell culture system to assay candidate genes and molecular pathways implicated in congenital diaphragmatic hernias. Dev Biol 2020; 467:30-38. [PMID: 32827499 DOI: 10.1016/j.ydbio.2020.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 10/23/2022]
Abstract
The mammalian muscularized diaphragm is essential for respiration and defects in the developing diaphragm cause a common and frequently lethal birth defect, congenital diaphragmatic hernia (CDH). Human genetic studies have implicated more than 150 genes and multiple molecular pathways in CDH, but few of these have been validated because of the expense and time to generate mouse mutants. The pleuroperitoneal folds (PPFs) are transient embryonic structures in diaphragm development and defects in PPFs lead to CDH. We have developed a system to culture PPF fibroblasts from E12.5 mouse embryos and show that these fibroblasts, in contrast to the commonly used NIH 3T3 fibroblasts, maintain expression of key genes in normal diaphragm development. Using pharmacological and genetic manipulations that result in CDH in vivo, we also demonstrate that differences in proliferation provide a rapid means of distinguishing healthy and impaired PPF fibroblasts. Thus, the PPF fibroblast cell culture system is an efficient tool for assaying the functional significance of CDH candidate genes and molecular pathways and will be an important resource for elucidating the complex etiology of CDH.
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Affiliation(s)
- Eric L Bogenschutz
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, United States
| | - Elizabeth M Sefton
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, United States
| | - Gabrielle Kardon
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, United States.
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24
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Bogenschutz EL, Fox ZD, Farrell A, Wynn J, Moore B, Yu L, Aspelund G, Marth G, Yandell M, Shen Y, Chung WK, Kardon G. Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias. HGG ADVANCES 2020; 1:100008. [PMID: 33263113 PMCID: PMC7703690 DOI: 10.1016/j.xhgg.2020.100008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
The diaphragm is critical for respiration and separation of the thoracic and abdominal cavities, and defects in diaphragm development are the cause of congenital diaphragmatic hernias (CDH), a common and often lethal birth defect. The genetic etiology of CDH is complex. Single-nucleotide variants (SNVs), insertions/deletions (indels), and structural variants (SVs) in more than 150 genes have been associated with CDH, although few genes are recurrently mutated in multiple individuals and mutated genes are incompletely penetrant. This suggests that multiple genetic variants in combination, other not-yet-investigated classes of variants, and/or nongenetic factors contribute to CDH etiology. However, no studies have comprehensively investigated in affected individuals the contribution of all possible classes of variants throughout the genome to CDH etiology. In our study, we used a unique cohort of four individuals with isolated CDH with samples from blood, skin, and diaphragm connective tissue and parental blood and deep whole-genome sequencing to assess germline and somatic de novo and inherited SNVs, indels, and SVs. In each individual we found a different mutational landscape that included germline de novo and inherited SNVs and indels in multiple genes. We also found in two individuals a 343 bp deletion interrupting an annotated enhancer of the CDH-associated gene GATA4, and we hypothesize that this common SV (found in 1%-2% of the population) acts as a sensitizing allele for CDH. Overall, our comprehensive reconstruction of the genetic architecture of four CDH individuals demonstrates that the etiology of CDH is heterogeneous and multifactorial.
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Affiliation(s)
- Eric L. Bogenschutz
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Zac D. Fox
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Andrew Farrell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Barry Moore
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Lan Yu
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gudrun Aspelund
- Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gabor Marth
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
- JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gabrielle Kardon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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25
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Wild KT, Gordon T, Bhoj EJ, Du H, Jhangiani SN, Posey JE, Lupski JR, Scott DA, Zackai EH. Congenital diaphragmatic hernia as a prominent feature of a SPECC1L-related syndrome. Am J Med Genet A 2020; 182:2919-2925. [PMID: 32954677 DOI: 10.1002/ajmg.a.61878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/18/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022]
Abstract
Congenital diaphragmatic hernias (CDH) confer substantial morbidity and mortality. Genetic defects, including chromosomal anomalies, copy number variants, and sequence variants are identified in ~30% of patients with CDH. A genetic etiology is not yet found in 70% of patients, however there is a growing number of genetic syndromes and single gene disorders associated with CDH. While there have been two reported individuals with X-linked Opitz G/BBB syndrome with MID1 mutations who have CDH as an associated feature, CDH appears to be a much more prominent feature of a SPECC1L-related autosomal dominant Opitz G/BBB syndrome. Features unique to autosomal dominant Opitz G/BBB syndrome include branchial fistulae, omphalocele, and a bicornuate uterus. Here we present one new individual and five previously reported individuals with CDH found to have SPECC1L mutations. These cases provide strong evidence that SPECC1L is a bona fide CDH gene. We conclude that a SPECC1L-related Opitz G/BBB syndrome should be considered in any patient with CDH who has additional features of hypertelorism, a prominent forehead, a broad nasal bridge, anteverted nares, cleft lip/palate, branchial fistulae, omphalocele, and/or bicornuate uterus.
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Affiliation(s)
- K Taylor Wild
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Neonatology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tia Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Kennesaw State University, Kennesaw, Georgia, USA
| | - Elizabeth J Bhoj
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Elaine H Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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26
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Kunisaki SM, Jiang G, Biancotti JC, Ho KKY, Dye BR, Liu AP, Spence JR. Human induced pluripotent stem cell-derived lung organoids in an ex vivo model of the congenital diaphragmatic hernia fetal lung. Stem Cells Transl Med 2020; 10:98-114. [PMID: 32949227 PMCID: PMC7780804 DOI: 10.1002/sctm.20-0199] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/03/2020] [Accepted: 08/09/2020] [Indexed: 01/06/2023] Open
Abstract
Three‐dimensional lung organoids (LOs) derived from pluripotent stem cells have the potential to enhance our understanding of disease mechanisms and to enable novel therapeutic approaches in neonates with pulmonary disorders. We established a reproducible ex vivo model of lung development using transgene‐free human induced pluripotent stem cells generated from fetuses and infants with Bochdalek congenital diaphragmatic hernia (CDH), a polygenic disorder associated with fetal lung compression and pulmonary hypoplasia at birth. Molecular and cellular comparisons of CDH LOs revealed impaired generation of NKX2.1+ progenitors, type II alveolar epithelial cells, and PDGFRα+ myofibroblasts. We then subjected these LOs to disease relevant mechanical cues through ex vivo compression and observed significant changes in genes associated with pulmonary progenitors, alveolar epithelial cells, and mesenchymal fibroblasts. Collectively, these data suggest both primary cell‐intrinsic and secondary mechanical causes of CDH lung hypoplasia and support the use of this stem cell‐based approach for disease modeling in CDH.
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Affiliation(s)
- Shaun M Kunisaki
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Guihua Jiang
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Juan C Biancotti
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kenneth K Y Ho
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Briana R Dye
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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27
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Kirby E, Keijzer R. Congenital diaphragmatic hernia: current management strategies from antenatal diagnosis to long-term follow-up. Pediatr Surg Int 2020; 36:415-429. [PMID: 32072236 DOI: 10.1007/s00383-020-04625-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/21/2020] [Indexed: 12/16/2022]
Abstract
Congenital diaphragmatic hernia (CDH) is a developmental birth defect consisting of a diaphragmatic defect and abnormal lung development. CDH complicates 2.3-2.8 per 10,000 live births. Despite efforts to standardize clinical practice, management of CDH remains challenging. Frequent re-evaluation of clinical practices in CDH reveals that management of CDH is evolving from one of postnatal stabilization to prenatal optimization. Translational research reveals promising avenues for in utero therapeutic intervention, including fetoscopic endoluminal tracheal occlusion. These remain highly experimental and demand improved antenatal diagnostics. Timely diagnosis of CDH and identification of severely affected fetuses allow time for delivery planning or in utero therapeutics. Optimal perinatal care and surgical treatment strategies are highly debated. Improved CDH mortality rates have placed increased emphasis on identifying and monitoring the long-term sequelae of disease throughout childhood and into adulthood. We review the current management strategies for CDH, highlighting where progress has been made, and where future developments have the potential to revolutionize care in this vulnerable patient population.
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Affiliation(s)
- Eimear Kirby
- Trinity College Dublin School of Medicine, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Richard Keijzer
- Thorlakson Chair in Surgical Research, Division of Pediatric Surgery, Department of Surgery and Children's Hospital Research Institute of Manitoba, University of Manitoba, AE402-820 Sherbrook Street, Winnipeg, MB, R3A 1S1, Canada. .,Department of Pediatrics and Child Health and Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada. .,Department of Physiology and Pathophysiology and Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada.
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28
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Abstract
Congenital diaphragmatic hernia (CDH) is a common birth defect that is associated with significant morbidity and mortality, especially when associated with additional congenital anomalies. Both environmental and genetic factors are thought to contribute to CDH. The genetic contributions to CDH are highly heterogeneous and incompletely defined. No one genetic cause accounts for more than 1-2% of CDH cases. In this review, we summarize the known genetic causes of CDH from chromosomal anomalies to individual genes. Both de novo and inherited variants contribute to CDH. Genes causing CDH are increasingly identified from animal models and from genomic strategies including exome and genome sequencing in humans. CDH genes are often transcription factors, genes involved in cell migration or the components of extracellular matrix. We provide clinical genetic testing strategies in the clinical evaluation that can identify a genetic cause in up to ∼30% of patients with non-isolated CDH and can be useful to refine prognosis, identify associated medical and neurodevelopmental issues to address, and inform family planning options.
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Affiliation(s)
- Lan Yu
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Rebecca R. Hernan
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA.
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29
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Wagner R, Montalva L, Zani A, Keijzer R. Basic and translational science advances in congenital diaphragmatic hernia. Semin Perinatol 2020; 44:151170. [PMID: 31427115 DOI: 10.1053/j.semperi.2019.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Congenital Diaphragmatic Hernia (CDH) is a birth defect that is characterized by lung hypoplasia, pulmonary hypertension and a diaphragmatic defect that allows herniation of abdominal organs into the thoracic cavity. Although widely unknown to the public, it occurs as frequently as cystic fibrosis (1:2500). There is no monogenetic cause, but different animal models revealed various biological processes and epigenetic factors involved in the pathogenesis. However, the pathobiology of CDH is not sufficiently understood and its mortality still ranges between 30 and 50%. Future collaborative initiatives are required to improve our basic knowledge and advance novel strategies to (prenatally) treat the abnormal lung development. This review focusses on the genetic, epigenetic and protein background and the latest advances in basic and translational aspects of CDH research.
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Affiliation(s)
- Richard Wagner
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology & Pathophysiology (Adjunct), University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada; Department of Pediatric Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Louise Montalva
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto, Canada and Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada; Department of Pediatric Surgery, Hospital Robert Debré, Paris, France
| | - Augusto Zani
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto, Canada and Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Richard Keijzer
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology & Pathophysiology (Adjunct), University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada.
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30
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Zolotareva O, Kleine M. A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2018-0069/jib-2018-0069.xml. [PMID: 31494632 PMCID: PMC7074139 DOI: 10.1515/jib-2018-0069] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/12/2019] [Indexed: 12/16/2022] Open
Abstract
Modern high-throughput experiments provide us with numerous potential associations between genes and diseases. Experimental validation of all the discovered associations, let alone all the possible interactions between them, is time-consuming and expensive. To facilitate the discovery of causative genes, various approaches for prioritization of genes according to their relevance for a given disease have been developed. In this article, we explain the gene prioritization problem and provide an overview of computational tools for gene prioritization. Among about a hundred of published gene prioritization tools, we select and briefly describe 14 most up-to-date and user-friendly. Also, we discuss the advantages and disadvantages of existing tools, challenges of their validation, and the directions for future research.
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Affiliation(s)
- Olga Zolotareva
- Bielefeld University, Faculty of Technology and Center for Biotechnology, International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Genome Informatics, Universitätsstraße 25, Bielefeld, Germany
| | - Maren Kleine
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Universitätsstraße 25, Bielefeld, Germany
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31
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Jordan VK, Beck TF, Hernandez-Garcia A, Kundert PN, Kim BJ, Jhangiani SN, Gambin T, Starkovich M, Punetha J, Paine IS, Posey JE, Li AH, Muzny D, Hsu CW, Lashua AJ, Sun X, Fernandes CJ, Dickinson ME, Lally KP, Gibbs RA, Boerwinkle E, Lupski JR, Scott DA. The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia. Hum Mol Genet 2019; 27:2064-2075. [PMID: 29618029 DOI: 10.1093/hmg/ddy110] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/26/2018] [Indexed: 11/13/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) has been reported twice in individuals with a clinical diagnosis of Fraser syndrome, a genetic disorder that can be caused by recessive mutations affecting FREM2 and FRAS1. In the extracellular matrix, FREM2 and FRAS1 form a self-stabilizing complex with FREM1, a protein whose deficiency causes sac CDH in humans and mice. By sequencing FREM2 and FRAS1 in a CDH cohort, and searching online databases, we identified five individuals who carried recessive or double heterozygous, putatively deleterious variants in these genes which may represent susceptibility alleles. Three of these alleles were significantly enriched in our CDH cohort compared with ethnically matched controls. We subsequently demonstrated that 8% of Frem2ne/ne and 1% of Fras1Q1263*/Q1263* mice develop the same type of anterior sac CDH seen in FREM1-deficient mice. We went on to show that development of sac hernias in FREM1-deficient mice is preceded by failure of anterior mesothelial fold progression resulting in the persistence of an amuscular, poorly vascularized anterior diaphragm that is abnormally adherent to the underlying liver. Herniation occurs in the perinatal period when the expanding liver protrudes through this amuscular region of the anterior diaphragm that is juxtaposed to areas of muscular diaphragm. Based on these data, we conclude that deficiency of FREM2, and possibly FRAS1, are associated with an increased risk of developing CDH and that loss of the FREM1/FREM2/FRAS1 complex, or its function, leads to anterior sac CDH development through its effects on mesothelial fold progression.
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Affiliation(s)
- Valerie K Jordan
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tyler F Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter N Kundert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bum-Jun Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Molly Starkovich
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ingrid S Paine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander H Li
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amber J Lashua
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xin Sun
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin P Lally
- Department of Pediatric Surgery, McGovern Medical School at UT Health, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daryl A Scott
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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32
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Qi H, Yu L, Zhou X, Wynn J, Zhao H, Guo Y, Zhu N, Kitaygorodsky A, Hernan R, Aspelund G, Lim FY, Crombleholme T, Cusick R, Azarow K, Danko ME, Chung D, Warner BW, Mychaliska GB, Potoka D, Wagner AJ, ElFiky M, Wilson JM, Nickerson D, Bamshad M, High FA, Longoni M, Donahoe PK, Chung WK, Shen Y. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. PLoS Genet 2018; 14:e1007822. [PMID: 30532227 PMCID: PMC6301721 DOI: 10.1371/journal.pgen.1007822] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 12/20/2018] [Accepted: 11/08/2018] [Indexed: 12/24/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe birth defect that is often accompanied by other congenital anomalies. Previous exome sequencing studies for CDH have supported a role of de novo damaging variants but did not identify any recurrently mutated genes. To investigate further the genetics of CDH, we analyzed de novo coding variants in 362 proband-parent trios including 271 new trios reported in this study. We identified four unrelated individuals with damaging de novo variants in MYRF (P = 5.3x10(-8)), including one likely gene-disrupting (LGD) and three deleterious missense (D-mis) variants. Eight additional individuals with de novo LGD or missense variants were identified from our other genetic studies or from the literature. Common phenotypes of MYRF de novo variant carriers include CDH, congenital heart disease and genitourinary abnormalities, suggesting that it represents a novel syndrome. MYRF is a membrane associated transcriptional factor highly expressed in developing diaphragm and is depleted of LGD variants in the general population. All de novo missense variants aggregated in two functional protein domains. Analyzing the transcriptome of patient-derived diaphragm fibroblast cells suggest that disease associated variants abolish the transcription factor activity. Furthermore, we showed that the remaining genes with damaging variants in CDH significantly overlap with genes implicated in other developmental disorders. Gene expression patterns and patient phenotypes support pleiotropic effects of damaging variants in these genes on CDH and other developmental disorders. Finally, functional enrichment analysis implicates the disruption of regulation of gene expression, kinase activities, intra-cellular signaling, and cytoskeleton organization as pathogenic mechanisms in CDH.
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Affiliation(s)
- Hongjian Qi
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Applied Mathematics and Applied Physics, Columbia University, New York, New York, United States of America
| | - Lan Yu
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Xueya Zhou
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Julia Wynn
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Haoquan Zhao
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
| | - Yicheng Guo
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
| | - Na Zhu
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Alexander Kitaygorodsky
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
| | - Rebecca Hernan
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Gudrun Aspelund
- Department of Surgery, Columbia University Medical Center, New York, New York, United States of America
| | - Foong-Yen Lim
- Cincinnati Children's Hospital, Cincinnati, Ohio, United States of America
| | | | - Robert Cusick
- Children's Hospital & Medical Center of Omaha, University of Nebraska College of Medicine, Omaha, Nebraska, United States of America
| | - Kenneth Azarow
- Department of Surgery, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Brad W Warner
- Washington University, St. Louis Children's Hospital, St. Louis, Missouri, United States of America
| | - George B Mychaliska
- University of Michigan, CS Mott Children's Hospital, Ann Arbor, Michigan, United States of America
| | - Douglas Potoka
- Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amy J Wagner
- Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Mahmoud ElFiky
- Department of Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Jay M Wilson
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Debbie Nickerson
- University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- University of Washington, Seattle, Washington, United States of America
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mauro Longoni
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Patricia K Donahoe
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Wendy K Chung
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
- Department of Medicine, Columbia University, New York, New York, United States of America
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
- JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, New York, United States of America
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33
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Shimizu D, Iwashima S, Sato K, Hayano S, Fukami M, Saitsu H, Ogata T. GATA4 variant identified by whole-exome sequencing in a Japanese family with atrial septal defect: Implications for male sex development. Clin Case Rep 2018; 6:2229-2233. [PMID: 30455927 PMCID: PMC6230668 DOI: 10.1002/ccr3.1851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/20/2018] [Accepted: 09/19/2018] [Indexed: 01/21/2023] Open
Abstract
We identified a heterozygous p.(R284H) variant of GATA4 in a Japanese family with atrial septal defect, including boys with apparently normal male sex development. The findings, together with the previous data, imply that GATA4 variants primarily cause congenital heart disease and rarely result in 46,XY disorder of sex development.
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Affiliation(s)
- Daisuke Shimizu
- Department of PediatricsHamamatsu University School of MedicineHamamatsuJapan
| | - Satoru Iwashima
- Department of PediatricsChutoen General Medical CenterKakegawaJapan
| | - Keisuke Sato
- Cardiac Intensive Care UnitShizuoka Children’s HospitalShizuokaJapan
| | - Satoshi Hayano
- Department of PediatricsChutoen General Medical CenterKakegawaJapan
| | - Maki Fukami
- Department of Molecular EndocrinologyNational Research Institute for Child health and DevelopmentTokyoJapan
| | - Hirotomo Saitsu
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
| | - Tsutomu Ogata
- Department of PediatricsHamamatsu University School of MedicineHamamatsuJapan
- Department of Molecular EndocrinologyNational Research Institute for Child health and DevelopmentTokyoJapan
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34
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Dixit R, Narasimhan C, Balekundri VI, Agrawal D, Kumar A, Mohapatra B. Functionally significant, novel GATA4
variants are frequently associated with Tetralogy of Fallot. Hum Mutat 2018; 39:1957-1972. [DOI: 10.1002/humu.23620] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 08/13/2018] [Accepted: 08/20/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Ritu Dixit
- Cytogenetics Laboratory; Department of Zoology; Banaras Hindu University; Varanasi Uttar Pradesh India
| | - Chitra Narasimhan
- Department of Pediatric Cardiology; Sri Jayadeva Institute of Cardiovascular Sciences and Research; Bengaluru Karnataka India
| | - Vijyalakshmi I. Balekundri
- Super Speciality Hospital; Prime Minister Swasth Suraksha Yojana (PMSSY); Bengaluru Medical College and Research Institute; Bengaluru Karnataka India
| | - Damyanti Agrawal
- Department of Cardio-vascular and Thoracic Surgery; Institute of Medical Science; Banaras Hindu University; Varanasi Uttar Pradesh India
| | - Ashok Kumar
- Department of Pediatrics; Institute of Medical Sciences; Banaras Hindu University; Varanasi Uttar Pradesh India
| | - Bhagyalaxmi Mohapatra
- Cytogenetics Laboratory; Department of Zoology; Banaras Hindu University; Varanasi Uttar Pradesh India
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35
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Sac-Type Congenital Diaphragmatic Hernia: A Case Report of Two Siblings. Case Rep Obstet Gynecol 2018; 2018:3270526. [PMID: 30159188 PMCID: PMC6109563 DOI: 10.1155/2018/3270526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 07/12/2018] [Indexed: 11/25/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH), a herniation of the abdominal contents through a defect or hypoplasia of the diaphragm, is a relatively common, severe congenital anomaly. Here we present the first case of two siblings with possibly isolated sac-type CDH and with a suspected genetic etiology. Although sibling recurrence of isolated CDH is rare, the incidence is higher than in the general population. Additionally, the second child had a more severe respiratory disorder than the first child. It is to be noted that siblings of children having isolated CDH are at risk for CDH, and prenatal evaluation should be considered individually.
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36
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Kammoun M, Souche E, Brady P, Ding J, Cosemans N, Gratacos E, Devriendt K, Eixarch E, Deprest J, Vermeesch JR. Genetic profile of isolated congenital diaphragmatic hernia revealed by targeted next-generation sequencing. Prenat Diagn 2018; 38:654-663. [PMID: 29966037 DOI: 10.1002/pd.5327] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/24/2018] [Accepted: 06/25/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Congenital diaphragmatic hernia (CDH) is characterized by a defective closure of the diaphragm occurring as an isolated defect in 60% of cases. Lung size, liver herniation, and pulmonary circulation are major prognostic indices. Isolated CDH genetics is heterogeneous and poorly understood. Whether genetic lesions are also outcome determinants has never been explored. OBJECTIVES To identify isolated CDH genetic causes, to fine map the mutational burden, and to search for a correlation between the genotype and the disease severity and outcome. METHODS Targeted massively parallel sequencing of 143 human and mouse CDH causative and candidate genes in a cohort of 120 fetuses with isolated CDH and detailed outcome measures. RESULTS Pathogenic and likely pathogenic variants were identified in 10% of the cohort. These variants affect both known CDH causative genes, namely, ZFPM2, GATA4, and NR2F2, and new genes, namely, TBX1, TBX5, GATA5, and PBX1. In addition, mutation burden analysis identified LBR, CTBP2, NSD1, MMP14, MYOD1, and EYA1 as candidate genes with enrichment in rare but predicted deleterious variants. No obvious correlation between the genotype and the phenotype or short-term outcome has been found. CONCLUSION Targeted resequencing identifies a genetic cause in 10% of isolated CDH and identifies new candidate genes.
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Affiliation(s)
- Molka Kammoun
- Department for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Erika Souche
- Department for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Paul Brady
- Department for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jia Ding
- Department for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Nele Cosemans
- Department for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Eduard Gratacos
- Fetal i+D Fetal Medicine Research Center, BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain.,Centre for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Koen Devriendt
- Department for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Elisenda Eixarch
- Fetal i+D Fetal Medicine Research Center, BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain.,Centre for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Jan Deprest
- Department of Development and Regeneration, Katholieke Universiteit Leuven, Leuven, Belgium.,Clinical Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
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37
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Systematic analysis of copy number variation associated with congenital diaphragmatic hernia. Proc Natl Acad Sci U S A 2018; 115:5247-5252. [PMID: 29712845 PMCID: PMC5960281 DOI: 10.1073/pnas.1714885115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH), characterized by malformation of the diaphragm and hypoplasia of the lungs, is one of the most common and severe birth defects, and is associated with high morbidity and mortality rates. There is growing evidence demonstrating that genetic factors contribute to CDH, although the pathogenesis remains largely elusive. Single-nucleotide polymorphisms have been studied in recent whole-exome sequencing efforts, but larger copy number variants (CNVs) have not yet been studied on a large scale in a case control study. To capture CNVs within CDH candidate regions, we developed and tested a targeted array comparative genomic hybridization platform to identify CNVs within 140 regions in 196 patients and 987 healthy controls, and identified six significant CNVs that were either unique to patients or enriched in patients compared with controls. These CDH-associated CNVs reveal high-priority candidate genes including HLX, LHX1, and HNF1B We also discuss CNVs that are present in only one patient in the cohort but have additional evidence of pathogenicity, including extremely rare large and/or de novo CNVs. The candidate genes within these predicted disease-causing CNVs form functional networks with other known CDH genes and play putative roles in DNA binding/transcription regulation and embryonic development. These data substantiate the importance of CNVs in the etiology of CDH, identify CDH candidate genes and pathways, and highlight the importance of ongoing analysis of CNVs in the study of CDH and other structural birth defects.
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38
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McCulley DJ, Wienhold MD, Hines EA, Hacker TA, Rogers A, Pewowaruk RJ, Zewdu R, Chesler NC, Selleri L, Sun X. PBX transcription factors drive pulmonary vascular adaptation to birth. J Clin Invest 2018; 128:655-667. [PMID: 29251627 PMCID: PMC5785269 DOI: 10.1172/jci93395] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 11/07/2017] [Indexed: 01/14/2023] Open
Abstract
A critical event in the adaptation to extrauterine life is relaxation of the pulmonary vasculature at birth, allowing for a rapid increase in pulmonary blood flow that is essential for efficient gas exchange. Failure of this transition leads to pulmonary hypertension (PH), a major cause of newborn mortality associated with preterm birth, infection, hypoxia, and malformations including congenital diaphragmatic hernia (CDH). While individual vasoconstrictor and dilator genes have been identified, the coordination of their expression is not well understood. Here, we found that lung mesenchyme-specific deletion of CDH-implicated genes encoding pre-B cell leukemia transcription factors (Pbx) led to lethal PH in mice shortly after birth. Loss of Pbx genes resulted in the misexpression of both vasoconstrictors and vasodilators in multiple pathways that converge to increase phosphorylation of myosin in vascular smooth muscle (VSM) cells, causing persistent constriction. While targeting endothelin and angiotensin, which are upstream regulators that promote VSM contraction, was not effective, treatment with the Rho-kinase inhibitor Y-27632 reduced vessel constriction and PH in Pbx-mutant mice. These results demonstrate a lung-intrinsic, herniation-independent cause of PH in CDH. More broadly, our findings indicate that neonatal PH can result from perturbation of multiple pathways and suggest that targeting the downstream common effectors may be a more effective treatment for neonatal PH.
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Affiliation(s)
| | | | | | | | | | - Ryan J. Pewowaruk
- Department of Biomedical Engineering, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Rediet Zewdu
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, USA
| | - Naomi C. Chesler
- Department of Pediatrics
- Department of Biomedical Engineering, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Licia Selleri
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, USA
- Program in Craniofacial Biology, Institute of Human Genetics, Departments of Orofacial Sciences and Anatomy, UCSF, San Francisco, California, USA
| | - Xin Sun
- Laboratory of Genetics
- Department of Pediatrics, UCSD, San Diego, California, USA
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39
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Kardon G, Ackerman KG, McCulley DJ, Shen Y, Wynn J, Shang L, Bogenschutz E, Sun X, Chung WK. Congenital diaphragmatic hernias: from genes to mechanisms to therapies. Dis Model Mech 2017; 10:955-970. [PMID: 28768736 PMCID: PMC5560060 DOI: 10.1242/dmm.028365] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Congenital diaphragmatic hernias (CDHs) and structural anomalies of the diaphragm are a common class of congenital birth defects that are associated with significant morbidity and mortality due to associated pulmonary hypoplasia, pulmonary hypertension and heart failure. In ∼30% of CDH patients, genomic analyses have identified a range of genetic defects, including chromosomal anomalies, copy number variants and sequence variants. The affected genes identified in CDH patients include transcription factors, such as GATA4, ZFPM2, NR2F2 and WT1, and signaling pathway components, including members of the retinoic acid pathway. Mutations in these genes affect diaphragm development and can have pleiotropic effects on pulmonary and cardiac development. New therapies, including fetal endoscopic tracheal occlusion and prenatal transplacental fetal treatments, aim to normalize lung development and pulmonary vascular tone to prevent and treat lung hypoplasia and pulmonary hypertension, respectively. Studies of the association between particular genetic mutations and clinical outcomes should allow us to better understand the origin of this birth defect and to improve our ability to predict and identify patients most likely to benefit from specialized treatment strategies.
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Affiliation(s)
- Gabrielle Kardon
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Kate G Ackerman
- Departments of Pediatrics (Critical Care) and Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - David J McCulley
- Department of Pediatrics, University of Wisconsin, Madison, WI 53792, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Departments of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Linshan Shang
- Departments of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Eric Bogenschutz
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Xin Sun
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wendy K Chung
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
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40
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Abstract
The outcomes of patients diagnosed with congenital diaphragmatic hernia (CDH) have recently improved. However, mortality and morbidity remain high, and this is primarily caused by the abnormal lung development resulting in pulmonary hypoplasia and persistent pulmonary hypertension. The pathogenesis of CDH is poorly understood, despite the identification of certain candidate genes disrupting normal diaphragm and lung morphogenesis in animal models of CDH. Defects within the lung mesenchyme and interstitium contribute to disturbed distal lung development. Frequently, a disturbance in the development of the pleuroperitoneal folds (PPFs) leads to the incomplete formation of the diaphragm and subsequent herniation. Most candidate genes identified in animal models have so far revealed relatively few strong associations in human CDH cases. CDH is likely a highly polygenic disease, and future studies will need to reconcile how disturbances in the expression of multiple genes cause the disease. Herein, we summarize the available literature on abnormal lung development associated with CDH.
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Affiliation(s)
- Dustin Ameis
- Department of Surgery, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada; Biology of Breathing Theme, The Children׳s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Naghmeh Khoshgoo
- Department of Surgery, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada; Biology of Breathing Theme, The Children׳s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard Keijzer
- Department of Surgery, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada; Biology of Breathing Theme, The Children׳s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
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41
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Longoni M, High FA, Qi H, Joy MP, Hila R, Coletti CM, Wynn J, Loscertales M, Shan L, Bult CJ, Wilson JM, Shen Y, Chung WK, Donahoe PK. Genome-wide enrichment of damaging de novo variants in patients with isolated and complex congenital diaphragmatic hernia. Hum Genet 2017; 136:679-691. [PMID: 28303347 DOI: 10.1007/s00439-017-1774-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/01/2017] [Indexed: 12/31/2022]
Abstract
Congenital Diaphragmatic Hernia (CDH) is a common and often lethal birth defect characterized by diaphragmatic structural defects and pulmonary hypoplasia. CDH is isolated in 60% of newborns, but may also be part of a complex phenotype with additional anomalies. We performed whole exome sequencing (WES) on 87 individuals with isolated or complex CDH and on their unaffected parents, to assess the contribution of de novo mutations in the etiology of diaphragmatic and pulmonary defects and to identify new candidate genes. A combined analysis with 39 additional trios with complex CDH, previously published, revealed a significant genome-wide burden of de novo variants compared to background mutation rate and 900 control trios. We identified an increased burden of likely gene-disrupting (LGD, i.e. nonsense, frameshift, and canonical splice site) and predicted deleterious missense (D-mis) variants in complex and isolated CDH patients. Overall, an excess of predicted damaging de novo LGD and D-mis variants relative to the expected frequency contributed to 21% of complex cases and 12% of isolated CDH cases. The burden of de novo variants was higher in genes expressed in the developing mouse diaphragm and heart. Some overlap with genes responsible for congenital heart defects and neurodevelopmental disorders was observed in CDH patients within our cohorts. We propose that de novo variants contribute significantly to the development of CDH.
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Affiliation(s)
- Mauro Longoni
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA. .,Department of Surgery, Harvard Medical School, Boston, MA, USA.
| | - Frances A High
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA.,Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA.,Department of Surgery, Boston Children's Hospital, Boston, MA, USA
| | - Hongjian Qi
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Maliackal P Joy
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Regis Hila
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | - Caroline M Coletti
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | - Julia Wynn
- Departments of Pediatrics, Columbia University, New York, NY, USA
| | - Maria Loscertales
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Linshan Shan
- Departments of Pediatrics, Columbia University, New York, NY, USA
| | | | - Jay M Wilson
- Department of Surgery, Boston Children's Hospital, Boston, MA, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Departments of Pediatrics, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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42
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Takahashi T, Zimmer J, Friedmacher F, Puri P. Expression of Prx1 and Tcf4 is decreased in the diaphragmatic muscle connective tissue of nitrofen-induced congenital diaphragmatic hernia. J Pediatr Surg 2016; 51:1931-1935. [PMID: 27665494 DOI: 10.1016/j.jpedsurg.2016.09.007] [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: 08/06/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND/PURPOSE Pleuroperitoneal folds (PPFs) are the source of the primordial diaphragm's muscle connective tissue (MCT), and developmental mutations have been shown to result in congenital diaphragmatic hernia (CDH). The protein paired-related homeobox 1 (Prx1) labels migrating PPF cells and stimulates expression of transcription factor 4 (Tcf4), a novel MCT marker that controls morphogenesis of the fetal diaphragm. We hypothesized that diaphragmatic Prx1 and Tcf4 expression is decreased in the nitrofen-induced CDH model. METHODS Time-mated rats were exposed to either nitrofen or vehicle on gestational day 9 (D9). Fetal diaphragms were microdissected on D13, D15, and D18, and divided into control and nitrofen-exposed specimens. Gene expression levels of Prx1 and Tcf4 were analyzed by qRT-PCR. Immunofluorescence double staining for Prx1 and Tcf4 was performed to evaluate protein expression and localization. RESULTS Relative mRNA expression of Prx1 and Tcf4 was significantly downregulated in PPFs (D13), developing diaphragms (D15) and fully muscularized diaphragms (D18) of nitrofen-exposed fetuses compared to controls. Confocal laser scanning microscopy revealed markedly diminished Prx1 and Tcf4 expression in diaphragmatic MCT of nitrofen-exposed fetuses on D13, D15, and D18 compared to controls. CONCLUSIONS Decreased expression of Prx1 and Tcf4 in the fetal diaphragm may cause defects in the PPF-derived MCT, leading to development of CDH in the nitrofen model. LEVEL OF EVIDENCE Level 2c (Centre for Evidence-Based Medicine, Oxford).
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Affiliation(s)
- Toshiaki Takahashi
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Julia Zimmer
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Florian Friedmacher
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland; Conway Institute of Biomolecular and Biomedical Research, School of Medicine & Medical Science, University College Dublin, Dublin, Ireland.
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43
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Decreased expression of hepatocyte growth factor in the nitrofen model of congenital diaphragmatic hernia. Pediatr Surg Int 2016; 32:967-73. [PMID: 27480986 DOI: 10.1007/s00383-016-3944-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/23/2016] [Indexed: 10/21/2022]
Abstract
PURPOSE Pleuroperitoneal folds (PPFs) are essential for normal diaphragmatic development, representing the only source of the diaphragm's muscle connective tissue. Hepatocyte growth factor (Hgf), which is secreted in PPFs, plays a crucial role in the formation of the muscular diaphragmatic components by regulating the migration of myogenic progenitor cells into the primordial diaphragm. Hgf is also a known downstream target of Gata4 and it has been demonstrated that the expression of Hgf was significantly downregulated in PPF cells of Gata4 knockouts with congenital diaphragmatic hernia (CDH). Furthermore, mutations in PPF-derived cells have been shown to result in CDH. We hypothesized that Hgf expression is decreased in developing diaphragms of fetal rats with nitrofen-induced CDH. METHODS Timed-pregnant rats were exposed to either nitrofen or vehicle on gestational day 9 (D9). Fetuses were harvested on selected time-points D13, D15 and D18. Dissected diaphragms (n = 72) were divided into control and nitrofen-exposed specimens (n = 12 per time-point and experimental group, respectively). Diaphragmatic gene expression of Hgf was analyzed by qRT-PCR. Immunofluorescence double staining for Hgf and the mesenchymal marker Gata4 or muscular progenitor marker Myogenin was performed to evaluate protein expression and localization in fetal diaphragms. RESULTS Relative mRNA expression of Hgf was significantly downregulated in PPFs of nitrofen-exposed fetuses on D13 (3.08 ± 1.46 vs. 5.24 ± 1.93; p < 0.05), developing diaphragms of nitrofen-exposed fetuses on D15 (2.01 ± 0.79 vs. 4.10 ± 1.50; p < 0.05) and fully muscularized diaphragms of nitrofen-exposed fetuses on D18 (1.60 ± 0.78 vs. 3.21 ± 1.89; p < 0.05) compared to controls. Confocal laser scanning microscopy revealed markedly diminished diaphragmatic immunofluorescence of Hgf in nitrofen-exposed fetuses on D13, D15 and D18 compared to controls, which was associated with disruptions in muscle connective tissue formation and reduced myogenic progenitor cell invasion. CONCLUSION Decreased diaphragmatic expression of Hgf may disturb the formation of muscle connective tissue in PPFs and thus prevent essential migration of muscle progenitor cells into the developing diaphragm, leading to diaphragmatic defects in the nitrofen CDH model.
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44
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Donahoe PK, Longoni M, High FA. Polygenic Causes of Congenital Diaphragmatic Hernia Produce Common Lung Pathologies. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:2532-43. [PMID: 27565037 DOI: 10.1016/j.ajpath.2016.07.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 12/12/2022]
Abstract
Congenital diaphragmatic hernia (CDH) is one of the most common and lethal congenital anomalies, and significant evidence is available in support of a genetic contribution to its etiology, including single-gene knockout mice associated with diaphragmatic defects, rare monogenetic disorders in humans, familial aggregation, and association of CDH with chromosomal abnormalities. Structural lung defects in the form of lung hypoplasia are almost invariably seen in patients with CDH and frequently in animal models of this condition. Better understanding of the mechanisms of pulmonary defects in CDH has the potential for creating targeted therapies, particularly in postnatal stages, when therapeutics can have maximum clinical impact on the surviving cohorts. Successful treatment of CDH is dependent on the integration of human genomic and genetic data with developmental expression profiling, mouse knockouts, and gene network and pathway modeling, which have generated a large number of candidate genes and pathways for follow-up studies. In particular, defective alveolarization appears to be a common and potentially actionable phenotype in both patients and animal models.
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Affiliation(s)
- Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts; Department of Surgery, Harvard Medical School, Boston, Massachusetts; Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.
| | - Mauro Longoni
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts; Department of Surgery, Harvard Medical School, Boston, Massachusetts
| | - Frances A High
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts; Department of Surgery, Harvard Medical School, Boston, Massachusetts; Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts; Department of Surgery, Boston Children's Hospital, Boston, Massachusetts
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45
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Tranchevent LC, Ardeshirdavani A, ElShal S, Alcaide D, Aerts J, Auboeuf D, Moreau Y. Candidate gene prioritization with Endeavour. Nucleic Acids Res 2016; 44:W117-21. [PMID: 27131783 PMCID: PMC4987917 DOI: 10.1093/nar/gkw365] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/23/2016] [Indexed: 01/25/2023] Open
Abstract
Genomic studies and high-throughput experiments often produce large lists of candidate genes among which only a small fraction are truly relevant to the disease, phenotype or biological process of interest. Gene prioritization tackles this problem by ranking candidate genes by profiling candidates across multiple genomic data sources and integrating this heterogeneous information into a global ranking. We describe an extended version of our gene prioritization method, Endeavour, now available for six species and integrating 75 data sources. The performance (Area Under the Curve) of Endeavour on cross-validation benchmarks using ‘gold standard’ gene sets varies from 88% (for human phenotypes) to 95% (for worm gene function). In addition, we have also validated our approach using a time-stamped benchmark derived from the Human Phenotype Ontology, which provides a setting close to prospective validation. With this benchmark, using 3854 novel gene–phenotype associations, we observe a performance of 82%. Altogether, our results indicate that this extended version of Endeavour efficiently prioritizes candidate genes. The Endeavour web server is freely available at https://endeavour.esat.kuleuven.be/.
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Affiliation(s)
- Léon-Charles Tranchevent
- INSERM U1210, CNRS UMR5239, Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, Université de Lyon, 69364 Lyon, France
| | - Amin Ardeshirdavani
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
| | - Sarah ElShal
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
| | - Daniel Alcaide
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
| | - Jan Aerts
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
| | - Didier Auboeuf
- INSERM U1210, CNRS UMR5239, Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, Université de Lyon, 69364 Lyon, France
| | - Yves Moreau
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
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46
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Familial tetrasomy 4q35.2 associated with congenital diaphragmatic hernia and unilateral renal agenesis: a case report. J Med Case Rep 2016; 10:76. [PMID: 27036947 PMCID: PMC4818464 DOI: 10.1186/s13256-016-0855-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 02/26/2016] [Indexed: 12/05/2022] Open
Abstract
Background Previous reports of chromosomal aberrations in different forms of congenital diaphragmatic hernia have been described as comprising aneuploidies (for example, trisomy 21), microdeletions, and duplications (for example, monosomy 15q24, 22q11.2). Case presentation We describe the first association of a de novo partial tetrasomy 4q35.2 in a father with left-sided, isolated renal agenesis and left-sided, isolated congenital diaphragmatic hernia in his son, who inherited the chromosomal aberration from his father. Conclusions Given that the aberration occurred de novo in the father and was transmitted to his son, with both presenting with unilateral left-sided developmental field defects, we suggest a gene dosage effect of the tetrasomic region to be involved in the phenotype of our two patients. Furthermore, we suggest performing a genetic workup in multiplex families with congenital malformations.
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47
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Pihlajoki M, Färkkilä A, Soini T, Heikinheimo M, Wilson DB. GATA factors in endocrine neoplasia. Mol Cell Endocrinol 2016; 421:2-17. [PMID: 26027919 PMCID: PMC4662929 DOI: 10.1016/j.mce.2015.05.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/26/2015] [Accepted: 05/09/2015] [Indexed: 02/07/2023]
Abstract
GATA transcription factors are structurally-related zinc finger proteins that recognize the consensus DNA sequence WGATAA (the GATA motif), an essential cis-acting element in the promoters and enhancers of many genes. These transcription factors regulate cell fate specification and differentiation in a wide array of tissues. As demonstrated by genetic analyses of mice and humans, GATA factors play pivotal roles in the development, homeostasis, and function of several endocrine organs including the adrenal cortex, ovary, pancreas, parathyroid, pituitary, and testis. Additionally, GATA factors have been shown to be mutated, overexpressed, or underexpressed in a variety of endocrine tumors (e.g., adrenocortical neoplasms, parathyroid tumors, pituitary adenomas, and sex cord stromal tumors). Emerging evidence suggests that GATA factors play a direct role in the initiation, proliferation, or propagation of certain endocrine tumors via modulation of key developmental signaling pathways implicated in oncogenesis, such as the WNT/β-catenin and TGFβ pathways. Altered expression or function of GATA factors can also affect the metabolism, ploidy, and invasiveness of tumor cells. This article provides an overview of the role of GATA factors in endocrine neoplasms. Relevant animal models are highlighted.
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Affiliation(s)
- Marjut Pihlajoki
- Children's Hospital, Helsinki University Central Hospital, University of Helsinki, 00290 Helsinki, Finland
| | - Anniina Färkkilä
- Children's Hospital, Helsinki University Central Hospital, University of Helsinki, 00290 Helsinki, Finland; Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, 00290 Helsinki, Finland
| | - Tea Soini
- Children's Hospital, Helsinki University Central Hospital, University of Helsinki, 00290 Helsinki, Finland
| | - Markku Heikinheimo
- Children's Hospital, Helsinki University Central Hospital, University of Helsinki, 00290 Helsinki, Finland; Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David B Wilson
- Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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48
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A novel mutation of GATA4 (K300T) associated with familial atrial septal defect. Gene 2016; 575:473-477. [DOI: 10.1016/j.gene.2015.09.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 12/12/2022]
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49
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Delineation of New Disorders and Phenotypic Expansion of Known Disorders Through Whole Exome Sequencing. CURRENT GENETIC MEDICINE REPORTS 2015. [DOI: 10.1007/s40142-015-0079-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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50
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Yu L, Sawle AD, Wynn J, Aspelund G, Stolar CJ, Arkovitz MS, Potoka D, Azarow KS, Mychaliska GB, Shen Y, Chung WK. Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia. Hum Mol Genet 2015; 24:4764-73. [PMID: 26034137 DOI: 10.1093/hmg/ddv196] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/22/2015] [Indexed: 01/10/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a serious birth defect that accounts for 8% of all major birth anomalies. Approximately 40% of cases occur in association with other anomalies. As sporadic complex CDH likely has a significant impact on reproductive fitness, we hypothesized that de novo variants would account for the etiology in a significant fraction of cases. We performed exome sequencing in 39 CDH trios and compared the frequency of de novo variants with 787 unaffected controls from the Simons Simplex Collection. We found no significant difference in overall frequency of de novo variants between cases and controls. However, among genes that are highly expressed during diaphragm development, there was a significant burden of likely gene disrupting (LGD) and predicted deleterious missense variants in cases (fold enrichment = 3.2, P-value = 0.003), and these genes are more likely to be haploinsufficient (P-value = 0.01) than the ones with benign missense or synonymous de novo variants in cases. After accounting for the frequency of de novo variants in the control population, we estimate that 15% of sporadic complex CDH patients are attributable to de novo LGD or deleterious missense variants. We identified several genes with predicted deleterious de novo variants that fall into common categories of genes related to transcription factors and cell migration that we believe are related to the pathogenesis of CDH. These data provide supportive evidence for novel genes in the pathogenesis of CDH associated with other anomalies and suggest that de novo variants play a significant role in complex CDH cases.
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Affiliation(s)
- Lan Yu
- Division of Molecular Genetics, Department of Pediatrics
| | | | - Julia Wynn
- Division of Molecular Genetics, Department of Pediatrics
| | | | - Charles J Stolar
- California Pediatric Surgery Group, Santa Barbara, CA 93105, USA
| | - Marc S Arkovitz
- Division of Pediatric Surgery, Tel Hashomer Medical Center, Tel Hashomer, Israel
| | - Douglas Potoka
- Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Kenneth S Azarow
- Pediatric Surgery Division, Department of Surgery, Oregon Health Science University, Portland, OR 97239, USA and
| | - George B Mychaliska
- Section of Pediatric Surgery, Department of Surgery, University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Yufeng Shen
- Departments of System Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA,
| | - Wendy K Chung
- Division of Molecular Genetics, Department of Pediatrics,
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