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.