Recurrent proximal 16p11.2 deletion (16p11.2del) is a risk factor for diverse neurodevelopmental disorders (NDDs) with incomplete penetrance and variable expressivity. Although investigation with human induced pluripotent stem cell (hiPSC) 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 NDD cohort and generated hiPSCs for two 16p11.2del families with distinct residual haplotypes and variable NDD phenotypes. Using transcriptomic profiles and cellular phenotypes of the hiPSC-differentiated cortex neuronal cells, we revealed MAPK3 as 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 based on a 132 kb 58 SNP residual haplotype, with the version composed entirely of minor alleles associated with reduced MAPK3 expression. Ten SNPs on the residual haplotype map 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 NDD phenotypes in 16p11.2del carriers.

Background: Multiple epiphyseal dysplasia (MED) is a skeletal disorder characterized by delayed and irregular ossification of the epiphyses and early-onset osteoarthritis. At least 66% of the reported autosomal dominant MED (AD-MED) cases are caused by COMP mutations. Methods: We recruited a four-generation Chinese family with early-onset hip osteoarthritis, flatfoot, brachydactyly, and mild short stature. The assessment of family history, detailed physical examinations, and radiographic evaluations were performed on the proband and other family members, followed by the performance of whole-exome sequencing (WES). The pathogenicity of the candidate mutation was also analyzed. Results: We recruited an AD-MED family with 10 affected members and 17 unaffected members. The main radiographic findings were symmetrical changes in the dysplastic acetabulum and femoral heads, irregular contours of the epiphyses, a shortened femoral neck, and flatfoot. Lower bone density was also observed in the ankle joints, wrist joints, and knees, as well as irregular vertebral end plates. In the proband, we identified the missense mutation c.1153G>T (p. Asp385Tyr), located in exon 11 of the COMP gene. This mutation was assessed as “pathogenic” because of its low allele frequency and its high likelihood of co-segregation with disease in the reported family. Sanger sequencing identified the novel heterozygous mutation c.1153G>T (p. Asp385Tyr) in exon 11 of COMP in all affected individuals in the family. Conclusions: Our result underlined a key role of the Asp385 amino acid in the protein function of COMP, and confirmed the pathogenicity of the COMP (c.1153G>T; p. Asp385Tyr) mutation in AD-MED disease. We have therefore expanded the known mutational spectrum of COMP and revealed new phenotypic information for AD-MED.

No abstract