Single-cell multiomics of neuronal activation reveals context-dependent genetic control of brain disorders

Despite hundreds of genetic risk loci identified for neuropsychiatric disorders (NPD), most causal variants/genes remain unknown. A major hurdle is that disease risk variants may act in specific biological contexts, e.g., during neuronal activation, which is difficult to study in vivo at the population level. Here, we modeled neuronal activation in human iPSC-induced excitatory and inhibitory neurons from 100 donors. Single-cell multiomics analyses of over a million neurons uncovered complex activity-dependent transcriptomic and epigenomic regulation and significantly expanded the repertoire of stimulation-specific causal variants/genes for NPD. We identified thousands of genetic variants associated with activity-dependent gene expression (i.e., eQTL) and chromatin accessibility (i.e., caQTL). These caQTL explained considerably larger proportions of NPD heritability than the eQTL. Integrating the multiomic data with GWAS revealed NPD risk variants/genes whose effects were only detected ..., Human iPSC lines and cell culture
 
We initially started with 107 iPSC lines (European ancestry) of which 100 lines were successfully differentiated into both excitatory and inhibitory neurons (Table S1). Of the 100 iPSC lines used for data production, 58 with their IDs starting with “CD” were reprogrammed at Rutgers University Cell and DNA Repository (RUCDR)-NIMH Stem Cell Center using the cryopreserved lymphocytes (CPLs) of donors of Molecular Genetics of Schizophrenia (MGS) cohort, and have been used in previous studies(62, 63, 79-81). The rest were purchased from the California Institute of Regenerative Medicine (CIRM). 28 iPSC lines are from SCZ cases and 72 are from healthy controls. The donors’ average age is 52 (+/-17) years old, and 56 of them are males. All iPSC lines were verified for their identify based on the matching of snRNA/ATAC-seq-inferred genotypes with their known genotypes. Cells were maintained in feeder-free mTeSR Plus (Stemcell# 100-0276) and passaged using..., , # Single-cell multiomics of neuronal activation reveals context-dependent genetic control of brain disorders

[https://doi.org/10.5061/dryad.0zpc8677w](https://doi.org/10.5061/dryad.0zpc8677w)

## Description of the data and file structure

*Single-cell multiomics of neuronal activation reveals context-dependent genetic control of brain disorders*. 

Lifan Liang1,†, Siwei Zhang2,5,†, Zicheng Wang1,†, Hanwen Zhang2,†, Chuxuan Li2,3,†, Alexandra C. Duhe2, Xiaotong Sun1, Xiaoyuan Zhong1, Alena Kozlova2, Brendan Jamison1,2, Whitney Wood2, Zhiping P. Pang4, Alan R. Sanders2,5, Xin He1,‡, Jubao Duan2,5,‡

Affiliations:

1Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.

2Center for Psychiatric Genetics, Endeavor Health Research Institute, Evanston, IL 60201, USA.

3Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA

4Department of Neuroscience and Cell Biology, Child Health ...

尽管目前已发现数百个与神经精神疾病（neuropsychiatric disorders, NPD）相关的遗传风险位点，但绝大多数致病变异与致病基因仍未明确。核心瓶颈在于，疾病风险变异可能仅在特定生物学情境下发挥功能，例如神经元激活过程中，而这类情境在群体层面的体内研究中极难开展。本研究通过体外建模，对100名供者来源的人类诱导多能干细胞（induced pluripotent stem cell, iPSC）分化得到的兴奋性与抑制性神经元进行神经元激活模拟。针对超过100万个神经元开展的单细胞多组学分析，揭示了复杂的活性依赖型转录组与表观基因组调控机制，并大幅拓展了神经精神疾病特异性刺激相关的致病变异与致病基因库。本研究鉴定了数千个与活性依赖型基因表达（即表达数量性状位点，expression quantitative trait locus, eQTL）及染色质开放度（即染色质开放数量性状位点，chromatin accessibility quantitative trait locus, caQTL）相关的遗传变异。相较于eQTL，caQTL对神经精神疾病遗传力的解释度显著更高。将多组学数据与全基因组关联研究（genome-wide association study, GWAS）整合分析后，我们发现了仅在该情境下才能检测到效应的神经精神疾病风险变异与致病基因…… 人类诱导多能干细胞系与细胞培养

本研究最初纳入107株欧洲血统的iPSC细胞系，其中100株成功分化为兴奋性与抑制性神经元（补充表S1）。在用于数据生成的100株iPSC细胞系中，58株ID以"CD"开头的细胞系由罗格斯大学细胞与DNA库-美国国立精神卫生研究所干细胞中心（Rutgers University Cell and DNA Repository-NIMH Stem Cell Center, RUCDR-NIMH）利用精神分裂症分子遗传学队列（Molecular Genetics of Schizophrenia, MGS）供者的冻存淋巴细胞（cryopreserved lymphocytes, CPLs）重编程得到，并已在既往研究中被使用(62, 63, 79-81)。剩余细胞系购自加州再生医学研究所（California Institute of Regenerative Medicine, CIRM）。其中28株来自精神分裂症（schizophrenia, SCZ）患者，72株来自健康对照。供者平均年龄为52岁（±17岁），其中56名为男性。所有iPSC细胞系均通过比对单细胞核RNA测序/转座酶可及性测序（snRNA/ATAC-seq）推断的基因型与已知基因型，完成了身份验证。细胞在无饲养层mTeSR Plus培养基（Stemcell# 100-0276）中培养，并使用……进行传代。

# 神经元激活的单细胞多组学研究揭示脑疾病的情境依赖性遗传调控

[https://doi.org/10.5061/dryad.0zpc8677w](https://doi.org/10.5061/dryad.0zpc8677w)

## 数据与文件结构说明

*神经元激活的单细胞多组学研究揭示脑疾病的情境依赖性遗传调控*

Lifan Liang1,†, Siwei Zhang2,5,†, Zicheng Wang1,†, Hanwen Zhang2,†, Chuxuan Li2,3,†, Alexandra C. Duhe2, Xiaotong Sun1, Xiaoyuan Zhong1, Alena Kozlova2, Brendan Jamison1,2, Whitney Wood2, Zhiping P. Pang4, Alan R. Sanders2,5, Xin He1,‡, Jubao Duan2,5,‡

作者单位：
1. 美国伊利诺伊州芝加哥市芝加哥大学人类遗传学系，芝加哥 60637。
2. 美国伊利诺伊州埃文斯顿市奋进健康研究所精神病遗传学中心，埃文斯顿 60201。
3. 美国宾夕法尼亚州费城宾夕法尼亚大学佩雷尔曼医学院基因组与计算生物学研究生项目，费城 19104。
4. 儿童健康神经科学与细胞生物学系……