Identification and functional study of the 18q deletion in hPSCs

Human pluripotent stem cells (hPSCs) hold a great promise in regenerative medicine and drug discovery, due to their unlimited capacity for self-renewal and pluripotency. However, hPSCs can exhibit genetic instability and acquire frequently chromosomal abnormalities, that can affect in vitro properties as well as clinical applicability. Deletions of chromosome 18q (18q21.2q.23 and 18q21.32q23) are relatively rare structural chromosomal abnormalities in hESCs, that has been linked to congenital malformations, intellectual disability, and some types of cancers. Moreover, the impact of 18q deletion on the differentiation capacity of hESCs is largely unknown. This study aims to examine the functional effects of the 18q deletions during the differentiation of hPSCs into the three embryonic germ layers. Our results from two different isogenic lines of hPSCs showed that cells with 18q deletion (hESCsdel18q) failed to differentiate properly into the endoderm and ectoderm germ layers, while their differentiation into the mesoderm germ layer was similar to that of normal cells. RNA-sequencing analysis of hESCsdel18q differentiated into retinal pigmented epithelium (RPE), revealed a potential misspecification of hESCsdel18q into trophoblast or extra-embryonic mesoderm. Furthermore, the losses of 18q mostly spans a very large chromosomic region, including SALL3 gene that has been reported prevouisly to regulate the differentiation propensity of hiPSCs. We hypothesized that SALL3 could be a driving gene that modulates the differentiation capacity of hESCsdel18q. To further investigate our hypothesis, we will perform SALL3 loss and gain of function studies in several lines of hPSCs and verify if SALL3 is the potential link between the 18q deletions and the impaired differentiation of hESCs. These findings will expand our knowledge on the functional consequences of genetic aberrations in hESCs-derived cells and the safety of their usage in clinical translation medicine.