Second, analysis of DNA methylation reveals substantial differences between iPSC and embryo-derived ESC (ntESC and fESC). iPSC derived from non-hematopoietic cells (neural progenitors and fibroblasts) retain residual methylation at loci required for hematopoietic fate, which manifests as reduced blood-forming potential in vitro. Residual methylation signatures link iPSC to their tissue of origin, and even discriminate between the myeloid and lymphoid origins of blood-derived iPSC. Prior studies reporting residual hypermethylation in iPSC3722 did not establish a link between DMRs at specific loci, tissue of origin, and altered differentiation potential. While residual methylation is mostly repressive, we have shown for Wnt3 that residual gene body methylation in blood-derived iPSC is associated with enhanced blood potential. Interestingly, the poor blood potential of neural progenitor-derived iPSC, which lack this epigenetic mark and express lower levels of endogenous Wnt3, can be enhanced by supplementing differentiating cultures with exogenous Wnt3a cytokine, indicating that manipulating culture conditions can overcome epigenetic barriers.
