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Multiple research groups have observed neuropathological phenotypes and molecular symptoms  in vitro  using induced pluripotent stem cell (iPSC)-derived neural cell cultures (i.e. patient-specific neurons and glia). However, the global differences/similarities that may exist between  in vitro  neural cells and their tissue-derived counterparts remain largely unknown. In this study, we compared temporal series of iPSC-derived  in vitro  neural cell cultures to endogenous brain tissue from the same autopsy donor. Specifically, we utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of  in vitro -differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed  in vitro  progression towards the reference brain tissue, and the following three results support this conclusion: (i) there was a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) ( P  &lt; 0.05), consistent with the transcriptional complexity of the brain; (ii) there was an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue; and (iii) there was a significant decreasing monotonic correlation between the days of our timecourse and the percent of  in vitro  to brain-tissue differences ( P  &lt; 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. Taken together, these results are consistent with  in vitro  neural development and physiological progression occurring predominantly by transcriptional activation of downregulated genes rather than deactivation of upregulated genes.

In vitro -differentiated neural cell cultures progress towards donor-identical brain tissue