Isogenic hiPSC models of Turner syndrome reveal shared roles of inactive X and Y in the human cranial neural crest network

Modeling the developmental etiology of viable human aneuploidies can be challenging in rodent models, where synteny with human chromosomes is affected, or primate-specific biology is implicated. In humans, monosomy-X (45,X) causes Turner syndrome (TS), altering craniofacial, skeletal, endocrine, and cardiovascular development, which remain largely unaffected in 39,X-mice. We derived human 45,X and isogenic euploid induced pluripotent stem cells (hiPSCs) from male and female mosaics to model how human monosomy-X may impact early embryonic development. Because several neural crest (NC) derived cell types are hypothesized to underpin craniofacial and cardiovascular changes in TS, we derived anterior neural crest from our hiPSCs and performed a highly-powered and extensive differential expression study. Across all three isogenic panels, 45,X neural crest cells (NCCs) show impaired acquisition of the PAX7/SOX10 double-positive NC state relative to euploid 46,XY controls. Monosomy-X NCCs also share similarly disrupted expression of NC-specific genes relative to their isogenic euploid control regardless of whether the latter carry an inactive X or Y. Gene-set enrichment analyses indicate monosomy-X NCCs increase cholesterol biosynthesis genes while dampening ribosomal protein and nuclear-encoded mitochondrial genes. These metabolic pathways are also over-represented in gene modules that are preserved in monogenic conditions involving neurocristopathy. Importantly, these gene modules are also significantly enriched in 28% of all TS-associated terms of the human phenotype ontology, and point to specific sex-linked genes that are expressed from two copies in euploid males and females alike, which may qualify as candidate haploinsufficient drivers of TS phenotypes in NC-derived lineages. Our study demonstrates that isogenic hiPSC-derived NCC panels representing monosomy-X can serve as a powerful model of early NC development in TS, and provides euploid and X-monosomic transcriptomic datasets relevant to exploration of TS and NC biology.