One major objective of this study was to conduct global gene expression analysis on iPSC-derived neurons of control and BPDs in order to generate hypotheses related to BPD biology. To ensure that the differentiation paradigm employed in this study was robust, we used the Affymetrix microarray platform to analyze RNA from iPSCs, NPs and E and L neurons. Consistent with signature gene markers analyzed by qPCR, the data subjected to Principal Component Analysis clearly demonstrated three isolated clusters of gene expression corresponding to iPSCs, NPs and neurons, validating the differentiation method we employed. Moreover, the Gene Ontology and Ingenuity Pathway analyses on DEGs associated with progressive differentiation of iPSCs confirmed the expected enrichment of genes and pathways associated with cell cycle regulation, neurogenesis and axon guidance as cells progressed from iPSCs to NPs to E or L neurons. These data are largely consistent with the recent report by Chen et al. [21] who also implemented withdrawal of growth factors to induce commitment of iPSCs to neuronal differentiation and observed enrichment of neuron specific markers in the transcriptome of neurons versus undifferentiated iPSCs.
