Having established the capacity of all 12 of the Family-811 quartet iPSCs to differentiate into multiple cell lineages, we next sought to further establish the nature of the neurodevelopmental deficits that were observed. For this, we again isolated total RNA from replicate cultures of fibroblasts, iPSCs, CXCR4+ NPCs, and six week differentiated neurons from the Family-811 quartet and used NanoString digital mRNA profiling to generate molecular signatures of each cell line using a custom “PsychGene” probe set rather than the Bock scorecard. This PsychGene probe set was specifically designed to measure the expression of 352 genes and consisted of pluripotency genes, neural patterning genes, WNT pathway genes and genes implicated in the genetics of neuropsychiatric disorders (Sup. Table 7)12,45. Using principle component analysis (PCA) to analyze the global PsychGene mRNA signature, we found that the respective cell types clustered together (Fig. 4A). Consistent with the results of this global analysis and our previous characterization of the iPSC properties, analysis of the expression of pluripotency and neural stem cell markers in all 12 iPSC lines confirmed the expected changes in expression of these genes when comparing the various cell differentiation states (Fig. 4B).
