Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells

Abstract

We compared bona fide human induced pluripotent stem cells (iPSCs) derived from umbilical cord blood (CB) cells and neonatal keratinocytes (K). As a consequence of both incomplete erasure of tissue-specific methylation and aberrant de novo methylation, CB-iPSCs and K-iPSCs were distinct in genome-wide DNA methylation profiles and differentiation potential. Extended passage of some iPSC clones in culture did not improve their epigenetic resemblance to embryonic stem cells, implying that some human iPSCs retain a residual 'epigenetic memory' of their tissue of origin.

Figure 1. Derivation and differentiation of iPSC from neonatal umbilical cord blood and foreskin fibroblasts

(a) Experimental schema. (b) Q-PCR of the keratinocyte marker K14 in D6 EBs from CB-iPSC (n=6) and K-iPSC (n=7). Gene expression was normalized to Actin, and shown as fold difference relative to CB-iPSC. (c) Numbers of keratinocytes differentiated from CB-iPSC (n=6) and K-iPSC (n=7). (d) Numbers of hematopoietic colony forming cells in D14 EBs differentiated from CB-iPSC (n=6) and K-iPSC (n=7). Error bar = s.d.

Figure 2. Analysis of methylation in CB-iPSC, K-iPSC, ESC, and somatic cells

(a) Numbers of differentially methylated regions (DMRs) between CB-iPSC, K-iPSC, ESC, umbilical cord blood, and cultured keratinocytes. DMRs were defined by an area cutoff of 2.0. (b) Cluster dendrogram analysis using the top 1,000 most variable probes across all samples. (c, d) Gene enrichment analysis of DMRs. Blue histograms represent a probability distribution of the number of genes predicted to overlap DMRs by chance. Red vertical lines indicate the observed number of genes that overlap DMRs. (c) Genes differentially methylated between CB-iPSC and K-iPSC are enriched in DMR-associated genes (genes both differentially expressed and methylated between cord blood and keratinocytes). (d) Genes highly expressed in keratinocytes are enriched in DMRs that are both hypermethylated in K-iPSC relative to CB-iPSC and are located in gene bodies rather than promoters.

Figure 2. Analysis of methylation in CB-iPSC, K-iPSC, ESC, and somatic cells

(a) Numbers of differentially methylated regions (DMRs) between CB-iPSC, K-iPSC, ESC, umbilical cord blood, and cultured keratinocytes. DMRs were defined by an area cutoff of 2.0. (b) Cluster dendrogram analysis using the top 1,000 most variable probes across all samples. (c, d) Gene enrichment analysis of DMRs. Blue histograms represent a probability distribution of the number of genes predicted to overlap DMRs by chance. Red vertical lines indicate the observed number of genes that overlap DMRs. (c) Genes differentially methylated between CB-iPSC and K-iPSC are enriched in DMR-associated genes (genes both differentially expressed and methylated between cord blood and keratinocytes). (d) Genes highly expressed in keratinocytes are enriched in DMRs that are both hypermethylated in K-iPSC relative to CB-iPSC and are located in gene bodies rather than promoters.