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

• Type of Material: Article
• Authors: Evin M Padhi, Washington University School of Medicine in St. Louis; Tristan J Hayeck, University of Pennsylvania Perelman School of Medicine; Zhang Cheng, UC San Diego School of Medicine; Sumantra Chatterjee, NYU Grossman School of Medicine; Brandon J Mannion, Lawrence Berkeley National Laboratory; Marta Byrska-Bishop, New York Genome Center; Marjolaine Willems, Université de Montpellier; Lucile Pinson, Université de Montpellier; Sylvia Redon, Université de Brest (UBO); Caroline Benech, Université de Brest (UBO); Kevin Uguen, Université de Brest (UBO); Séverine Audebert-Bellanger, Centre Hospitalier Universitaire de Brest; Cédric Le Marechal, Université de Brest (UBO); Claude Férec, Université de Brest (UBO); Stephanie Efthymiou, UCL Queen Square Institute of Neurology; Fatima Rahman, Children's Hospital Lahore; Shazia Maqbool, UCL Queen Square Institute of Neurology; Reza Maroofian, UCL Queen Square Institute of Neurology; Henry Houlden, UCL Queen Square Institute of Neurology; Rajeeva Musunuri, New York Genome Center; Giuseppe Narzisi, New York Genome Center; Avinash Abhyankar, New York Genome Center; Riana D Hunter, Lawrence Berkeley National Laboratory; Jennifer Akiyama, Lawrence Berkeley National Laboratory; Lauren E Fries, NYU Grossman School of Medicine; Jeffrey K Ng, Washington University School of Medicine in St. Louis; Elvisa Mehinovic, Washington University School of Medicine in St. Louis; Nick Stong, Columbia University; Andrew S Allen, Duke University; Diane E Dickel, Lawrence Berkeley National Laboratory; Raphael A Bernier, University of Washington; David Gorkin, Emory University; Len A Pennacchio, Lawrence Berkeley National Laboratory; Michael C Zody, New York Genome Center; Tychele N Turner, Washington University School of Medicine in St. Louis
• Language: English
• Date: 2021-12-01
• Publisher: BioMed Central Ltd
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2021
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1186/s40246-021-00342-3
• Title of Journal or Parent Work: Human Genomics
• Volume: 15
• Issue: 1
• Start Page: 44
• End Page: 44
• Grant/Funding Information: The Centers for Common Disease Genomics are funded by the National Human Genome Research Institute and the National Heart, Lung, and Blood Institute and the GSP Coordinating Center (U24HG008956) contributed to cross-program scientific initiatives and provided logistical and general study coordination.; This work was supported by grants from the National Institutes of Health (R00MH117165 to T.N.T., UM1HG008901 to M.C.Z.).; Research conducted at the E.O. Lawrence Berkeley National Laboratory was additionally supported by NIH grants (R01HG003988) (to L.A.P. and D.E.D.) and performed under a Department of Energy Contract (DE-AC02-05CH11231), University of California.
• Keywords: EBF3; Male; De novo; Neurons; Mutation; Autism; Neurodevelopmental disorder; Enhancer; Gene regulatory network; Variant; Exome; Neurodevelopmental Disorders; Humans; hs737; Enhancer Elements, Genetic; Gene Regulatory Networks; Female; Transcription Factors; Muscle Hypotonia; Genome; Autistic Disorder; Genetic Predisposition to Disease
• Research Categories: Health Sciences, Mental Health; Health Sciences, Pathology; Biology, Biostatistics

Abstract

Background: Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. Results: We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance 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 cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor 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. Through characterization 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 phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. Conclusions: In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.