Tissue and cell-type specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models.

Chromosome 16p11.2 reciprocal genomic disorder due to recurrent copy number variants (CNVs) involves intellectual disability, autism spectrum disorder (ASD), and schizophrenia but the responsible mechanisms are not known. To systemically dissect molecular effects, we performed transcriptome profiling of 350 libraries from six tissues (cortex, cerebellum, striatum, liver, brown fat, white fat) in mouse models harboring CNVs of the syntenic 7qF3 region, as well as cellular, transcriptional, and single-cell analyses in 54 isogenic neural stem cell, induced neuron, and cerebral organoid models of CRISPR-engineered 16p11.2 CNVs. Transcriptome-wide differentially expressed genes were largely tissue, cell-type, and dosage specific, though more effects were shared between deletion and duplication and across tissue than expected by chance. The broadest effects were observed in the cerebellum (2163 differentially expressed genes) and the greatest enrichments were associated with synaptic pathways in mouse cerebellum and human induced neurons. Pathway and co-expression analyses identified energy and RNA metabolism as shared processes and enrichment for ASD-associated/loss-of-function constraint/FMRP gene sets. Intriguingly, reciprocal 16p11.2 dosage changes resulted in consistent decrements in neurite and electrophysiological features, while single-cell profiling of organoids showed reciprocal alterations to the proportions of excitatory and inhibitory GABAergic neurons. Both neuronal ratios and gene expression changes in our organoid analyses point most directly to calretinin GABAergic inhibitory neurons and the excitatory/inhibitory balance as targets of disruption in 16p11.2 carriers that may contribute to changes in neurodevelopmental and cognitive function. Collectively, our data indicate the genomic disorder involves disruption of multiple contributing biological processes, with relative impacts that are context-specific. bulk RNAseq based transcriptomic analyses of six tissues from 16p11.2 deletion and duplication as well as control mouse models; single cell RNAseq based transcriptomic analyses of human iPSC-derived 16p11.2 deletion and duplication as well as control organoids.由复发性拷贝数变异（copy number variants, CNVs）引发的16p11.2染色体区域双向基因组紊乱，可伴随智力障碍、孤独症谱系障碍（autism spectrum disorder, ASD）及精神分裂症，但目前其致病机制尚未阐明。为系统性解析该疾病的分子效应，本研究对携带同线7qF3区域CNVs的小鼠模型的6种组织（大脑皮层、小脑、纹状体、肝脏、棕色脂肪、白色脂肪）的350个转录组文库开展了测序分析；同时针对CRISPR编辑构建的16p11.2 CNVs的54株同基因系神经干细胞、诱导神经元及大脑类器官模型，进行了细胞水平、转录组及单细胞水平分析。 全转录组范围的差异表达基因大多具有组织、细胞类型及剂量特异性，尽管缺失型与重复型模型间以及跨组织的共享效应数量显著高于随机预期水平。本研究中效应范围最广的组织为小脑（共鉴定出2163个差异表达基因），小鼠小脑及人类诱导神经元中富集最显著的通路均为突触相关通路。通路与共表达分析显示，能量代谢与RNA代谢为共享的核心生物学过程，同时富集孤独症谱系障碍相关基因、功能缺失约束基因及脆性X智力低下蛋白（FMRP）靶基因集。 值得注意的是，16p11.2区域剂量的双向改变（缺失与重复）均会导致神经元突起及电生理特征出现一致性的减退；而类器官的单细胞测序分析则显示，兴奋性神经元与抑制性γ-氨基丁酸能神经元的比例呈现双向变化。本研究类器官分析中的神经元比例及基因表达变化，均直接指向钙视网膜蛋白阳性γ-氨基丁酸能抑制性神经元及兴奋/抑制平衡是16p11.2携带者的紊乱靶点，这可能参与神经发育及认知功能的异常改变。 综上，本研究数据表明该基因组紊乱涉及多个致病生物学过程的失调，且其相对影响具有情境特异性。本数据集包含两部分核心内容：一是针对16p11.2缺失型、重复型及对照小鼠模型的6种组织的批量RNA测序（bulk RNAseq）转录组分析；二是人类诱导多能干细胞（induced pluripotent stem cell, iPSC）衍生的16p11.2缺失型、重复型及对照类器官的单细胞RNA测序转录组分析。