Sex-specific differential gene expression changes in human iPS Cell-derived myoblasts

Various complex phenotypes in humans, such as disease prevalence, progression, age of onset, and anthropometric traits exhibit sex-differentiated characteristics. These sex-specific differences are often attributed to hormones, sex chromosomes, differences in environmental exposures and behavior, but their underlying molecular mechanism largely remains unknown. The aim of our study was to uncover the cell autonomous gene expression changes between men and women using human induced pluripotent stem cell (iPSC) derived from 8 male donors and 8 female donors that were differentiated into myoblasts (iMyos). Principal component analysis of the overall transcriptomics data revealed distinct gene expression changes in cells taken from male donors as compared to the female donors.
Indeed, we identified over 1500 differences in gene expression that were dependent on the sex of the cell donor and were equally divided into male dominant and female dominant genes. Only 7% of the differentially expressed sex-specific genes were encoded by the X- or Y-chromosomes, while 93% were spread across the autosomes. These autosomal sex-specific differences were independent of XIST levels or the X chromosome dosage but were associated with increased DNA methylation in cells from females as compared to males. Treatment of the iMyos with 5-azacytidine (5-AZ) reversed some of the post-pubertal sexual dimorphism in gene expression, as well as a previously observed sex-specific difference in RhoA activation. Thus, human iMyos in vitro exhibit significant differences in gene expression related to the sex of the donor, which occurred without the addition of sex hormones, thus showing cell autonomous sex-specific gene expression changes. A significant fraction of the sex-dependent differences appears to be epigenetic and related to DNA methylation changes. Thus, our study highlights an important contribution of sex in exerting gene expression changes, which might further impact physiology and disease.