Epigenetic Memory: Lessons From iPS Cells Derived From Human β Cells

Incomplete reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) may be responsible for the heterogeneity in differentiation capacity observed among iPSC lines. It remains unclear whether it results from stochastic reprogramming events, or reflects consistent genetic or cell-of-origin differences. Some evidence suggests that epigenetic memory predisposes iPSCs to enhanced differentiation into the parental cell type. We investigated iPSCs reprogrammed from human pancreatic islet beta cells (BiPSCs), as a step in development of a robust differentiation protocol for generation of beta-like cells. BiPSCs derived from multiple human donors manifested enhanced and reproducible spontaneous and induced differentiation towards insulin-producing cells, compared with iPSCs derived from isogenic non-beta-cell types and fibroblast-derived iPSCs (FiPSCs). Genome-wide analyses of open chromatin in BiPSCs and FiPSCs identified thousands of differential open chromatin sites (DOCs) between the two iPSC types. DOCs more open in BiPSCs (Bi-DOCs) were significantly enriched for known regulators of endodermal development, including bivalent and weak enhancers, and FOXA2 binding sites. Bi-DOCs were associated with genes related to pancreas development and beta-cell function. These studies provide evidence for reproducible epigenetic memory in BiPSCs. Bi-DOCs may provide clues to genes and pathways involved in the differentiation process, which could be manipulated to increase the efficiency and reproducibility of differentiation of pluripotent stem cells from non-beta-cell sources.

Automated summary

Incomplete reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) may cause differentiation capacity heterogeneity. Epigenetic memory in BiPSCs predisposes them to enhanced differentiation into insulin-producing cells. Genome-wide analyses of open chromatin revealed differential sites and regulators of endodermal development enriched in BiPSCs, providing clues for improving differentiation efficiency of pluripotent stem cells.