Upon observing aberrant expression of the NPC marker PAX6 in the BD patient nEBs, we next tested an expanded set of 48 genes consisting of differentially expressed genes identified from our PsychGene NanoString assays of the FACS-purified CXCR4+ NPCs along with WNT, NOTCH, and SHH pathway genes using the Fluidigm BioMark HD system (Sup. Fig. 18 & 19; Sup. Table 13). As expected, pluripotency genes, SOX2, OCT4 and NANOG were repressed upon nEB formation to similar extents comparing the BD and unaffected parental iPSCs. Significant differential expression of NKX6-1, LEF1, NEUROG1, NRG3, and SPARCL1 in the BD nEBs relative to the unaffected parental controls was observed (Sup Fig. 18 & 19). Taken together with the results from the analysis of the CXCR4+ NPCs using NanoString and RNA-seq, these finding provide further evidence for differential gene expression upon induction of neurodevelopment in the BD patient-derived cells compared to their parental controls from Family-811.
