Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Previous research in autism and other neurodevelopmental disorders(NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specificgenes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but hasyet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs inenhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer namedhs737.
We adapted the fitDNM statistical model to work in noncoding regions andtested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominalsignificance in the discovery (p = 0.0172), replication (p = 2.5 × 10-3), and combined dataset (p = 1.1 ×10-4). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitivefunction, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activityin a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcriptionfactor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 ×10-35, loss-of-function p = 2.26 × 10-13) and is widely expressed in the body. Throughcharacterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 ×10-6, OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypicseverity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncodingDNVs that have autism and hypotonia.
In this study, we identify DNVs in the hs737 enhancer in individualswith autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant inNDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact ongene regulatory networks in NDDs.
Autism; De novo; EBF3; Enhancer; Gene regulatory network; Genome; Neurodevelopmental disorder; Variant; hs737. Hum Genomics. 2021 Jul 13;15(1):44. doi: 10.1186/s40246-021-00342-3.


Other Contributors

Evin M Padhi 1Tristan J Hayeck 2 3Zhang Cheng 4Sumantra Chatterjee 5Brandon J Mannion 6Marta Byrska-Bishop 7Marjolaine Willems 8Lucile Pinson 8Sylvia Redon 9Caroline Benech 9Kevin Uguen 9Séverine Audebert-Bellanger 10Cédric Le Marechal 9Claude Férec 9Stephanie Efthymiou 11Fatima Rahman 12Shazia Maqbool 11 12Reza Maroofian 11Henry Houlden 11Rajeeva Musunuri 7Giuseppe Narzisi 7Avinash Abhyankar 7Riana D Hunter 6Jennifer Akiyama 6Lauren E Fries 5Jeffrey K Ng 1Elvisa Mehinovic 1Nick Stong 13Andrew S Allen 14 15 16Diane E Dickel 6Raphael A Bernier 17David U Gorkin 4 18Len A Pennacchio 6 19Michael C Zody 7Tychele N Turner 20


  • 1Department of Genetics, Washington
    University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA.
  • 2Department of Pathology and Laboratory
    Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
  • 3Department of Pathology and Laboratory
    Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
  • 4Center for Epigenomics, University of
    California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
  • 5Center for Human Genetics and Genomics,
    NYU School of Medicine, New York, NY, 10016, USA.
  • 6Environmental Genomics and Systems
    Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • 7New York Genome Center, New York, NY,
    10013, USA.
  • 8University of Montpellier, département de
    Génétique, maladies rares médecine personnalisée, U 1298, CHU Montpellier, University of Montpellier,
    Montpellier, France.
  • 9CHU Brest, Inserm, Univ Brest, EFS,UMR
    1078, GGB, F-29200, Brest, France.
  • 10Service de Génétique Médicale, CHRU de
    Brest, Brest, France.
  • 11Department of Neuromuscular Disorders,
    UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
  • 12Development and Behavioral Pediatrics
    Department, Institute of Child Health and Children Hospital, Lahore, Pakistan.
  • 13Institute for Genomic Medicine,
    Columbia University, New York, NY, 10027, USA.
  • 14Center for Statistical Genetics and
    Genomics, Duke University, Durham, NC, 27708, USA.
  • 15Division of Integrative Genomics, Duke
    University, Durham, NC, 27708, USA.
  • 16Department of Biostatistics and
    Bioinformatics, Duke University, Durham, NC, 27708, USA.
  • 17Department of Psychiatry and Behavioral
    Sciences, University of Washington, Seattle, WA, 98195, USA.
  • 18Department of Biology, Emory
    University, Atlanta, GA, 30322, USA.
  • 19U.S. Department of Energy Joint Genome
    Institute, Walnut Creek, CA, 94598, USA.
  • 20Department of Genetics, Washington
    University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA.