iPSCs derived from different cell types exhibit distinguishable epigenetic signatures. (a) Hierarchical unsupervised clustering analysis of HELP genome-wide methylation data from indicated iPSC lines. (b) Correspondence analysis of SMP-iPSCs and Gra-iPSCs (left panel) from chimera no. 1, TTF-iPSCs and B-iPSCs (right panel) from chimera no. 2. (c) Graphic representation of DNA methylation quantification of specific CpGs (circles) in the promoter regions of the indicated candidate genes using EpiTYPER DNA methylation analyses. Yellow indicates 0% methylation and blue 100% methylation. (d) Chromatin immunoprecipitation (ChIP) for H3 pan-acetylated (H3Ac, in blue), H3K4 trimethylated (H3K4me3, in green), H3K27 trimethylated (H3K27me3, in red) and isotype control (IgG, in light blue) of granulocytes (Gra), SMPs, Gra-iPSCs and SMP-iPSCs. Chi no. 1, chimera no. 1; chi no. 2, chimera no. 2. The error bars depict the s.e.m. (n = 3).

Continuous passaging of iPSCs abrogates transcriptional, epigenetic and functional differences. (a) Hierarchical unsupervised clustering of expression profiles from B-iPSCs, T-iPSCs, TTF-iPSCs and Gra-iPSCs from chimera no. 2. Left panel shows clustering analysis of all iPSC samples at passage p4, the middle panel at p10 and the right panel at p16. (b) Number of differentially expressed probes between pairs of iPSC samples used in a; iPSCs at p4 are shown in blue bars, iPSCs at p10 are shown in orange bars and iPSCs at p16 are shown in red bars. The number of differently expressed probes between iPSCs was calculated using a pairwise analysis (twofold), with t-test P = 0.05, with Bejamini and Hochberg correction (n = 3). (c) Venn diagram and GO analysis showing overlap of genes that change from p4 to p16 in Gra-IPSCs, TTF-iPSCs and B-iPSCs. Red line marks functional GO cluster of genes shared between all three iPSC groups. Black line marks functional GO cluster of genes shared by at least two of the iPSC groups. Functional ontology cluster analysis was performed using the DAVIS algorithm. (d) Hierarchical unsupervised clustering using HELP genome-wide methylation profiles of B-iPSCs and TTF-iPSCs at p16. (e–g) Quantification of in vitro differentiation potentials of B-iPSCs and TTF-iPSCs at p16 into EryPs (e), macrophage colonies (f) and mixed hematopoietic colonies (g). The error bars depict the s.e.m. (n = 9).

iPSCs derived from different cell types are transcriptionally distinguishable. (a) Flow chart explaining the derivation and analysis of genetically matched iPSCs from different cell types. Secondary iPSCs were first injected into blastocysts to generate chimeric mice, from which the indicated somatic cell types were isolated. Exposure of these cells to doxycycline (dox) then gave rise to iPSCs. ChIP, chromatin immunoprecipitation. (b) Quantification of the expression levels of Cxcr4, Itgb1, Gr-1 and Lysozyme by quantitative PCR in SMP-iPSCs, in red, and Gra-iPSCs, in gray. The values were normalized to GAPDH expression; the error bars depict the s.e.m. (n = 3). (c) Heat map showing top 104 probes with highest variance in their expression levels. Left panel, SMP-iPSCs and Gra-iPSCs derived from chimera no. 1. Right panel, TTF-iPSCs and B-iPSCs derived from chimera no. 2. (d) Hierarchical, unsupervised clustering of iPSC expression profiles using the correlation distance and the Ward method. SMP-iPSCs and Gra-iPSCs were derived from chimera no. 1 (left panel), TTF-iPSCs and B-iPSCs originate from chimera no. 2 (right panel). Chi no. 1, chimera no. 1; chi no. 2, chimera no. 2.

iPSCs derived from different cell types have distinctive in vitro differentiation potentials. (a) experimental outline. iPSCs were first differentiated into embryoid bodies. At day 6, embryoid bodies were dissociated and plated in conditions to favor differentiation into erythrocyte progenitors (eryP) and macrophage and mixed hematopoietic colonies. (b) Phase contrast images showing embryoid bodies derived from B-iPSCs, TTF-iPSCs, Gra-iPSCs and SMP-iPSCs at same magnification. (c) Quantification of embryoid body sizes derived from B-iPSCs, TTF-iPSCs, Gra-iPSCs and SMP-iPSCs; the diameter of the embryoid bodies was measured using arbitrary units (AU). The error bars depict the s.e.m. (n = 30) (d) Representative images of erythrocyte progenitors (eryPs), macrophage colonies and mixed hematopoietic colonies. (e–g) Quantification of in vitro differentiation potentials of the different iPSCs into EryPs (e), macrophage colonies (f) and mixed hematopoietic colonies (g). Chi no. 1, chimera no. 1; chi no. 2, chimera no. 2. The error bars depict the s.e.m. (n = 12).

Model summarizing the presented data. iPSCs derived from different somatic cell types retain a transient epigenetic and transcriptional memory of their cell type of origin at early passage, despite acquiring pluripotent gene expression, transgene-independent growth and the ability to contribute to tissues in chimeras. Continuous passaging resolves these differences, giving rise to iPSCs that are molecularly and functionally indistinguishable. Note the difference between early passage iPSCs and partially reprogrammed cells, which require continuous viral transgene expression and fail to activate endogenous pluripotency genes or support the development of viable mice.