RNA-seq on cells with or without pathogenic PAX1 variants at different stages of in vitro differentiation into thymic epithelial progenitor cells

Bi-allelic, loss-of-function PAX1 variants underlie a syndromic form of severe combined immunodeficiency (SCID) by disrupting thymus development. To assess if bi-allelic PAX1 variants affect differentiation of thymic epithelial cells in vitro, we reprogrammed fibroblasts from a healthy control and two patients with bi-allelic pathogenic PAX1 variants to induced pluripotent stem cells (iPSCs), and subsequently differentiated these to thymic epithelial progenitor cells (TEP). The cells were differentiated in 24-well-plates, in triplicate according to a treatment protocol summarized below. The samples labeled Control_1 and Control_2 correspond to two separate differentiations of cells derived from the same iPSC clone. Individual iPSC clones were used for Patient_1 or Patient_4 samples. Each differentiation was carried out in technical triplicates, starting from the iPSC stage. The samples corresponding to each triplicate are labeled _Rep1 through _Rep3. Samples were collected at the iPSC stage (day 0), definitive endoderm stage (day 5, only for Control_1), or TEP stage (day 14) of differentiation. Control_1 and Patient_1 iPSC clones were simultaneously differentiated toward TEPs. Control_2 and Patient_4 iPSC clones were simultaneously differentiated toward TEPs.