Table_1_Integrated analysis of endoplasmic reticulum stress regulators’ expression identifies distinct subtypes of autism spectrum disorder.XLSX

Endoplasmic reticulum (ER) stress has been demonstrated to play important roles in a variety of human diseases. However, their relevance to autism spectrum disorder (ASD) remains largely unknown. Herein, we aimed to investigate the expression patterns and potential roles of the ER stress regulators in ASD. The ASD expression profiles GSE111176 and GSE77103 were compiled from the Gene Expression Omnibus (GEO) database. ER stress score determined by the single sample gene set enrichment analysis (ssGSEA) was significantly higher in ASD patients. Differential analysis revealed that there were 37 ER stress regulators dysregulated in ASD. Based on their expression profile, the random forest and artificial neuron network techniques were applied to build a classifier that can effectively distinguish ASD from control samples among independent datasets. Weighted gene co-expression network analysis (WGCNA) screened out the turquoise module with 774 genes was closely related to the ER stress score. Through the overlapping results of the turquoise module and differential expression ER stress genes, hub regulators were gathered. The TF/miRNA-hub gene interaction networks were created. Furthermore, the consensus clustering algorithm was performed to cluster the ASD patients, and there were two ASD subclusters. Each subcluster has unique expression profiles, biological functions, and immunological characteristics. In ASD subcluster 1, the FAS pathway was more enriched, while subcluster 2 had a higher level of plasma cell infiltration as well as the BCR signaling pathway and interleukin receptor reaction reactivity. Finally, the Connectivity map (CMap) database was used to find prospective compounds that target various ASD subclusters. A total of 136 compounds were significantly enriched. In addition to some specific drugs which can effectively reverse the differential gene expression of each subcluster, we found that the PKC inhibitor BRD-K09991945 that targets Glycogen synthase kinase 3β (GSK3B) might have a therapeutic effect on both ASD subtypes that worth of the experimental validation. Our finding proved that ER stress plays a crucial role in the diversity and complexity of ASD, which may inform both mechanistic and therapeutic assessments of the disorder.

内质网应激已被证实在各种人类疾病中扮演着至关重要的角色。然而，其与自闭症谱系障碍（ASD）的相关性仍鲜为人知。本研究旨在探讨内质网应激调节因子在ASD中的表达模式及其潜在作用。本研究从基因表达综合数据库（GEO）中汇编了ASD表达谱GSE111176和GSE77103。通过单样本基因集富集分析（ssGSEA）确定的内质网应激评分在ASD患者中显著升高。差异分析揭示了37个在内质网应激中失调的调节因子。基于其表达谱，应用随机森林和人工神经元网络技术构建了一个分类器，能够在独立数据集中有效地区分ASD与对照组样本。加权基因共表达网络分析（WGCNA）筛选出了包含774个基因的青色模块，该模块与内质网应激评分密切相关。通过青色模块与差异表达的内质网应激基因的重叠结果，聚集了核心调节因子。构建了TF/miRNA-核心基因相互作用网络。此外，通过一致性聚类算法对ASD患者进行聚类，共分为两个亚群。每个亚群具有独特的表达谱、生物学功能和免疫学特征。在ASD亚群1中，FAS通路富集程度更高，而亚群2则具有更高水平的浆细胞浸润以及BCR信号通路和白细胞介素受体反应活性。最终，利用连通性图（CMap）数据库寻找针对各种ASD亚群的潜在化合物。共富集了136个化合物。除了某些能够有效逆转每个亚群差异基因表达的特定药物外，我们发现针对糖原合成酶激酶3β（GSK3B）的PKC抑制剂BRD-K09991945可能对两种ASD亚型都具有治疗作用，值得进行实验验证。我们的研究结果表明，内质网应激在ASD的多样性和复杂性中起着至关重要的作用，这或许能为该疾病的机制和治疗评估提供启示。