Mammalian sex chromosomes encode homologous X/Y gene pairs that were retained on the Y chromosome in males and escape X chromosome inactivation (XCI) in females. Inferred to reflect X/Y pair dosage sensitivity, monosomy X is a leading cause of miscarriage in humans with near full penetrance. This phenotype is shared with many other mammals but not the mouse, which offers sophisticated genetic tools to generate sex chromosomal aneuploidy but also tolerates its developmental impact. To address this critical gap, we generated X-monosomic human induced pluripotent stem cells (hiPSCs) alongside otherwise isogenic euploid controls from male and female mosaic samples. Phased genomic variants in these hiPSC panels enable systematic investigation of X/Y dosage-sensitive features using in vitro models of human development. Here, we demonstrate the utility of these validated hiPSC lines to test how X/Y-linked gene dosage impacts a widely used model for human syncytiotrophoblast development. While these isogenic panels trigger a GATA2/3- and TFAP2A/C -driven trophoblast gene circuit irrespective of karyotype, differential expression implicates monosomy X in altered levels of placental genes and in secretion of placental growth factor (PlGF) and human chorionic gonadotropin (hCG). Remarkably, weighted gene coexpression network modules that significantly reflect these changes are also preserved in first-trimester chorionic villi and term placenta. Our results suggest monosomy X may skew trophoblast cell type composition and function, and that the combined haploinsufficiency of the pseudoautosomal region likely plays a key role in these changes.

Mammalian sex chromosomes encode homologous X/Y gene pairs that were retained on the male Y and escape X chromosome inactivation (XCI) in females. Inferred to reflect X/Y-pair dosage sensitivity, monosomy X is a leading cause of miscarriage in humans with near full penetrance. This phenotype is shared with many other mammals but not the mouse, which offers sophisticated genetic tools to generate sex chromosomal aneuploidy but also tolerates its developmental impact. To address this critical gap, we generated X-monosomic human induced pluripotent stem cells (hiPSCs) alongside otherwise isogenic euploid controls from male and female mosaic samples. Phased genomic variants of these hiPSC panels enable systematic investigation of X/Y dosage-sensitive features using in vitro models of human development. Here, we demonstrate the utility of these validated hiPSC lines to test how X/Y-linked gene dosage impacts a widely-used model for the human syncytiotrophoblast. While these isogenic panels trigger a GATA2/3 and TFAP2A/C -driven trophoblast gene circuit irrespective of karyotype, differential expression implicates monosomy X in altered levels of placental genes, and in secretion of placental growth factor (PlGF) and human chorionic gonadotropin (hCG). Remarkably, weighted gene co-expression network modules that significantly reflect these changes are also preserved in first-trimester chorionic villi and term placenta. Our results suggest monosomy X may skew trophoblast cell type composition, and that the pseudoautosomal region likely plays a key role in these changes, which may facilitate prioritization of haploinsufficient drivers of 45,X extra-embryonic phenotypes.

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SUMMARYModeling 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.