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Haghshenas S, Karimi K, Stevenson RE, Levy MA, Relator R, Kerkhof J, Rzasa J, McConkey H, Lauzon-Young C, Balci TB, White-Brown AM, Carter MT, Richer J, Armour CM, Sawyer SL, Bhola PT, Tedder ML, Skinner CD, van Rooij IALM, van de Putte R, de Blaauw I, Koeck RM, Hoischen A, Brunner H, Esteki MZ, Pelet A, Lyonnet S, Amiel J, Boycott KM, Sadikovic B. Identification of a DNA methylation episignature for recurrent constellations of embryonic malformations. Am J Hum Genet 2024:S0002-9297(24)00247-7. [PMID: 39089258 DOI: 10.1016/j.ajhg.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 08/03/2024] Open
Abstract
The term "recurrent constellations of embryonic malformations" (RCEM) is used to describe a number of multiple malformation associations that affect three or more body structures. The causes of these disorders are currently unknown, and no diagnostic marker has been identified. Consequently, providing a definitive diagnosis in suspected individuals is challenging. In this study, genome-wide DNA methylation analysis was conducted on DNA samples obtained from the peripheral blood of 53 individuals with RCEM characterized by clinical features recognized as VACTERL and/or oculoauriculovertebral spectrum association. We identified a common DNA methylation episignature in 40 out of the 53 individuals. Subsequently, a sensitive and specific binary classifier was developed based on the DNA methylation episignature. This classifier can facilitate the use of RCEM episignature as a diagnostic biomarker in a clinical setting. The study also investigated the functional correlation of RCEM DNA methylation relative to other genetic disorders with known episignatures, highlighting the common genomic regulatory pathways involved in the pathophysiology of RCEM.
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Affiliation(s)
- Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Karim Karimi
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | | | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Carolyn Lauzon-Young
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada; Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, Canada
| | - Alexandre M White-Brown
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Melissa T Carter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Julie Richer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Christine M Armour
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Sarah L Sawyer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Priya T Bhola
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | | | - Iris A L M van Rooij
- Department IQ Health, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Romy van de Putte
- Department IQ Health, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ivo de Blaauw
- Department of Surgery-Pediatric Surgery, Radboudumc Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rebekka M Koeck
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, the Netherlands; Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics and Donders Center for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands; Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Han Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, the Netherlands; Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands; Department of Human Genetics and Donders Center for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, the Netherlands; Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands
| | - Anna Pelet
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France; Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France; Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada; Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
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Metry D, Copp HL, Rialon KL, Iacobas I, Baselga E, Dobyns WB, Drolet B, Frieden IJ, Garzon M, Haggstrom A, Hanson D, Hollenbach L, Keppler-Noreuil KM, Maheshwari M, Siegel DH, Waseem S, Dias M. Delphi Consensus on Diagnostic Criteria for LUMBAR Syndrome. J Pediatr 2024:114101. [PMID: 38759778 DOI: 10.1016/j.jpeds.2024.114101] [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: 04/07/2024] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
OBJECTIVE To develop consensus on diagnostic criteria for LUMBAR syndrome, the association of segmental infantile hemangiomas that affect the Lower body with Urogenital anomalies, Ulceration, spinal cord Malformations, Bony defects, Anorectal malformations, Arterial anomalies and/or Renal anomalies. STUDY DESIGN These diagnostic criteria were developed by an expert multidisciplinary and multi-institutional team based on analysis of peer-reviewed data, followed by electronic-Delphi consensus of a panel of 61 international pediatric specialists. RESULTS After two Delphi rounds, a 92% or higher level of agreement was reached for each Delphi statement. 98% of panelists agreed with the diagnostic criteria, and 100% agreed the criteria would be useful in clinical practice. The diagnosis of LUMBAR requires the presence of a segmental, or patterned, infantile hemangioma of the lumbosacral, sacrococcygeal, or pelvic cutaneous regions plus one additional criterion of the urogenital, spinal, bony, anorectal, arterial, or renal organ systems. CONCLUSIONS These diagnostic criteria will enhance clinical care by improving screening, detection, and overall awareness of this poorly understood neurocutaneous disorder. The criteria can be utilized by a wide variety of pediatric subspecialists. In addition, formal criteria will improve phenotypic uniformity among LUMBAR syndrome cohorts and a patient registry, allowing investigators to assess clinical features, long-term outcomes, and results of genetic sequencing in a standardized manner. Finally, these criteria will serve as a starting point for prospective studies to establish formal screening and management guidelines.
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Affiliation(s)
- Denise Metry
- Dept of Dermatology, Texas Children's Hospital, Baylor College of Medicine.
| | | | - Kristy L Rialon
- Dept of Surgery, Division of Pediatric Surgery, Texas Children's Hospital, Baylor College of Medicine
| | - Ionela Iacobas
- Dept of Pediatrics, Cancer and Hematology Centers, Texas Children's Hospital, Baylor College of Medicine
| | - Eulalia Baselga
- Dept of Dermatology, Hospital San Joan de Deu, Barcelona, Spain
| | | | - Beth Drolet
- Dept of Dermatology, University of Wisconsin
| | - Ilona J Frieden
- Depts of Dermatology and Pediatrics, University of California, San Francisco
| | - Maria Garzon
- Depts of Dermatology and Pediatrics, Columbia University
| | | | - Darrell Hanson
- Dept of Orthopedics and Sports Medicine, Houston Methodist Hospital
| | | | | | | | | | - Shamaila Waseem
- Dept of Gastroenterology, Indiana University School of Medicine
| | - Mark Dias
- Dept of Neurosurgery, Pennsylvania State College of Medicine
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3
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Ramadesikan S, Colwell CM, Supinger R, Hunter J, Thomas J, Varga E, Mardis ER, Wood RJ, Koboldt DC. Novel inherited CDX2 variant segregating in a family with diverse congenital malformations of the genitourinary system. Cold Spring Harb Mol Case Stud 2023; 9:a006294. [PMID: 37816608 PMCID: PMC10815271 DOI: 10.1101/mcs.a006294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
Anorectal malformations (ARMs) constitute a group of congenital defects of the gastrointestinal and urogenital systems. They affect males and females, with an estimated worldwide prevalence of 1 in 5000 live births. These malformations are clinically heterogeneous and can be part of a syndromic presentation (syndromic ARM) or as a nonsyndromic entity (nonsyndromic ARM). Despite the well-recognized heritability of nonsyndromic ARM, the genetic etiology in most patients is unknown. In this study, we describe three siblings with diverse congenital anomalies of the genitourinary system, anemia, delayed milestones, and skeletal anomalies. Genome sequencing identified a novel, paternally inherited heterozygous Caudal type Homeobox 2 (CDX2) variant (c.722A > G (p.Glu241Gly)), that was present in all three affected siblings. The variant identified in this family is absent from population databases and predicted to be damaging by most in silico pathogenicity tools. So far, only two other reports implicate variants in CDX2 with ARMs. Remarkably, the individuals described in these studies had similar clinical phenotypes and genetic alterations in CDX2 CDX2 encodes a transcription factor and is considered the master regulator of gastrointestinal development. This variant maps to the homeobox domain of the encoded protein, which is critical for interaction with DNA targets. Our finding provides a potential molecular diagnosis for this family's condition and supports the role of CDX2 in anorectal anomalies. It also highlights the clinical heterogeneity and variable penetrance of ARM predisposition variants, another well-documented phenomenon. Finally, it underscores the diagnostic utility of genomic profiling of ARMs to identify the genetic etiology of these defects.
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Affiliation(s)
- Swetha Ramadesikan
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Caitlyn M Colwell
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Rachel Supinger
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Jesse Hunter
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Jessica Thomas
- Department of Pediatric Colorectal & Pelvic Reconstructive Surgery, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Elizabeth Varga
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Elaine R Mardis
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
| | - Richard J Wood
- Department of Pediatric Colorectal & Pelvic Reconstructive Surgery, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
- Department of Surgery, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
| | - Daniel C Koboldt
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA;
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
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