A foundational atlas of autism protein interactions reveals molecular convergence [CUT&Tag]

Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification. A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions. Dissociated forebrain organoids at D111 were used as input for CUT&Tag profiling binding of FOXP1, FOXP4, and H3K27me3 in WT and R513H organoids, with two technical replicates each.

将高可信度（high-confidence, hc）自闭症谱系障碍（autism spectrum disorder, ASD）相关基因转化为切实可行的治疗靶点，至今仍是一项尚未攻克的难题。我们在HEK293T细胞中构建了涵盖100个hcASD风险基因的基础蛋白质相互作用（protein-protein interaction, PPI）网络，共鉴定出超过1800组蛋白质相互作用，其中87%为全新发现。这些相互作用蛋白在人类大脑中表达，且显著富集于ASD的遗传风险因子中，而非精神分裂症的遗传风险因子，其功能聚集于神经发生、微管生物学、转录调控及染色质修饰相关的蛋白质复合物。我们针对54例患者来源的错义变异体构建了PPI图谱，鉴定到差异化的物理相互作用，并借助AlphaFold-Multimer的预测结果，优先筛选出可在热带爪蟾（Xenopus tropicalis）及人类前脑类器官中开展功能验证的直接PPI与特定变异体。转录因子FOXP1的一处突变可导致其DNA结合位点发生重排，并改变前脑类器官中大脑皮层深层神经元的发育进程。本研究为自闭症谱系障碍的潜在分子机制提供了全新的科学见解，并构建了一套高效的研究平台，用于开发与验证针对多种遗传明确病症的治疗策略。本研究采用D111天的解离前脑类器官作为实验样本，对野生型（WT）与R513H突变型类器官中FOXP1、FOXP4及H3K27me3的结合情况开展CUT&Tag分析，每组设置2次技术重复。