Rare variation in noncoding regions with evolutionary signatures contributes to autism spectrum disorder risk

Abstract

Little is known about the role of noncoding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of noncoding regions: Human Accelerated Regions (HARs), which show signatures of positive selection in humans; experimentally validated neural Vista Enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole genome analysis of >16,600 samples and >4900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in a VE near SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved noncoding regions in ASD risk and suggest potential mechanisms of how changes in regulatory regions can modulate social behavior.

A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders

“…Although we show that single cell chromatin accessibility is a strong predictor of cMN enhancer activity, even highly conserved and presumably functional enhancers can be surprisingly robust to mutagenesis 8,[112][113][114] . Therefore, to evaluate the functional consequences of our nominated CCDD variants, we selected 33 elements harboring cell type-aware candidate SNVs for in vivo humanized enhancer assays.…”

“…We in part leveraged sequence conservation and constraint to prioritize pathogenic variants. However, while the known genes and cREs underlying cMN development are highly conserved, a conservation-based strategy may not identify pathogenic variants in human-specific and/or rapidly evolving sequences 114,120,121 . Strikingly, we also found that even relatively subtle differences in cellular composition and ATAC/RNA collection strategies can distort cognate gene estimates.…”

A human-specific enhancer fine-tunes radial glia potency and corticogenesis

“…This suggests that brain size is relevant to HARE5 specific substitutions, but that HARE5 also impacts other features, related to the evolution of brain function. Further, the HARE5 locus also contains rare de novo mutations implicated in ASD 21,47,67 . We demonstrate that one ASD mutation, located adjacent to a human-specific variant, tempers enhancer activity in human NPCs.…”

“…De novo copy-number variations (CNVs) and biallelic point mutations within HARs are associated with Autism Spectrum Disorder (ASD) 21,47 . Thus, we examined if there are any ASD-associated mutations in Hs-HARE5 nearby these variants using databases 21 .…”

Rapid and Quantitative Functional Interrogation of Human Enhancer Variant Activity in Live Mice

“…For example, a typical gain-of-function enhancer variant can result in ectopic gene expression and cause pathogenic effects in cells where the enhancer is normally inactive (Claussnitzer et al, 2015; Doan et al, 2016; Eufrásio et al, 2020; Kvon et al, 2020; Lewis et al, 2014; Putlyaeva et al, 2017; Turner et al, 2017; Yanchus et al, 2022). Likewise, loss-of-function enhancer variants often result in loss of enhancer activity in one cell type, while in other cell types, its activity is unaffected (Bengani et al, 2021; Bhatia et al, 2015, 2021; Shin et al, 2023; Spieler et al, 2014). These cell-type-specific effects of enhancer variants are difficult to capture with high-throughput methods such as massively-parallel reporter assays (MPRAs) and CRISPR inhibitor/activator screens, both of which are primarily performed in vitro (Findlay, 2021; Inoue & Ahituv, 2015; Maricque et al, 2018) or in one tissue (Brown et al, 2022; Capauto et al, 2023; Deng et al, 2023; Lagunas et al, 2023; Patwardhan et al, 2012; White et al, 2013).…”