Fang Liu, Chen Liang, Zhengchang Li, Sen Zhao, Haiming Yuan, Ruen Yao, Zailong Qin, Shaofang Shangguan, Shujie Zhang, Li-Ping Zou, Qian Chen, Zhijie Gao, Suiwen Wen, Jing Peng, Fei Yin, Fei Chen, Xiaoxia Qiu, Jingsi Luo, Yingjun Xie, Dian Lu, Yu Zhang, Hua Xie, Guozhuang Li, Terry Jianguo Zhang, Pengfei Luan, Hongying Wang, Xiaodai Cui, Hailiang Huang, Ruize Liu, Xiaofang Sun, Chao Chen, Nan Wu, Jian Wang, Chunyu Liu, Yiping Shen, James F Gusella, and Xiaoli Chen
Recurrent proximal 16p11.2 deletion (16p11.2del) is a risk factor for diverse neurodevelopmental disorders with incomplete penetrance and variable expressivity. Although investigation with human induced pluripotent stem cell models has confirmed disruption of neuronal development in 16p11.2del neuronal cells, which genes are responsible for abnormal cellular phenotypes and what determines the penetrance of neurodevelopmental abnormalities are unknown. We performed haplotype phasing of the 16p11.2 region in a 16p11.2del neurodevelopmental disorders cohort and generated human induced pluripotent stem cells for two 16p11.2del families with distinct residual haplotypes and variable neurodevelopmental disorder phenotypes. Using transcriptomic profiles and cellular phenotypes of the human induced pluripotent stem cell-differentiated cortex neuronal cells, we revealed MAPK3 to be a contributor to dysfunction in multiple pathways related to early neuronal development, with altered soma and electrophysiological properties in mature neuronal cells. Notably, MAPK3 expression in 16p11.2del neuronal cells varied on the basis of a 132 kb 58 single nucleotide polymorphism (SNP) residual haplotype, with the version composed entirely of minor alleles associated with reduced MAPK3 expression. Ten SNPs on the residual haplotype were mapped to enhancers of MAPK3. We functionally validated six of these SNPs by luciferase assay, implicating them in the residual haplotype-specific differences in MAPK3 expression via cis-regulation. Finally, the analysis of three different cohorts of 16p11.2del subjects showed that this minor residual haplotype is associated with neurodevelopmental disorder phenotypes in 16p11.2del carriers. TOC summary Liu et al. provide a molecular explanation for the variable penetrance of the neurodevelopmental disorder phenotype in 16p11.2 deletion syndrome, by characterizing residual haplotype-specific transcriptomic profiles and neuronal phenotypes.