Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells

Abstract

Generation of human induced pluripotent stem cells (hiPSCs) by the expression of specific transcription factors depends on successful epigenetic reprogramming to a pluripotent state. Although hiPSCs and human embryonic stem cells (hESCs) display a similar epigenome, recent reports demonstrated the persistence of specific epigenetic marks from the somatic cell type of origin and aberrant methylation patterns in hiPSCs. However, it remains unknown whether the use of different somatic cell sources, encompassing variable levels of selection pressure during reprogramming, influences the level of epigenetic aberrations in hiPSCs. In this work, we characterized the epigenomic integrity of 17 hiPSC lines derived from six different cell types with varied reprogramming efficiencies. We demonstrate that epigenetic aberrations are a general feature of the hiPSC state and are independent of the somatic cell source. Interestingly, we observe that the reprogramming efficiency of somatic cell lines inversely correlates with the amount of methylation change needed to acquire pluripotency. Additionally, we determine that both shared and linespecific epigenetic aberrations in hiPSCs can directly translate into changes in gene expression in both the pluripotent and differentiated states. Significantly, our analysis of different hiPSC lines from multiple cell types of origin allow us to identify a reprogrammingspecific epigenetic signature comprised of nine aberrantly methylated genes that is able to segregate hESC and hiPSC lines regardless of the somatic cell source or differentiation state.I nduction of pluripotency in human somatic cells is an inefficient process that can be achieved by the expression of defined transcription factors (1-5). This reprogramming process involves global epigenetic remodeling and overcoming similar roadblocks present during cell transformation, which might affect genomic and epigenomic integrity (6). In fact, several recent reports have shown that human induced pluripotent stem cells (hiPSCs) contain genetic and epigenetic aberrations throughout their genome compared with their parental somatic cell populations or to human embryonic stem cells (hESCs) (7-12). For example, the analysis of whole-genome DNA methylation profiles at single-nucleotide resolution in hiPSCs, their somatic cells of origin, and hESCs revealed the presence of more than 1,000 differentially methylated regions (DMRs) between hiPSCs and hESCs (11). Moreover, this analysis, and many others, demonstrated both the persistence of specific epigenetic marks from the somatic cell of origin (residual methylation) and the acquisition of unique methylation patterns in mouse iPSCs (miPSCs) and hiPSCs (11,(13)(14)(15)(16)(17)(18)(19)(20)(21). Interestingly, hiPSC lines also show incomplete reprogramming of non-CG methylation in regions proximal to telomeres and centromeres (11). Altogether, these epigenetic aberrations might explain some of the observed transcriptional variation between hESC and hiPSC lines (22)(23)(24). In one of the most co...

Embryonic stem cell and induced pluripotent stem cell: an epigenetic perspective

“…Apart from the remnant somatic cell DNA methylation patterns, multiple reports have shown that certain genomic loci in iPSCs bear aberrant DNA methylation [12,55,152]. Such an aberrant methylation pattern is neither a feature of ESCs nor that of the originating somatic cells.…”

“…A second study showed that the aberrant methylation hotspots in human iPSCs, although mostly occurring at CpG sites, can be at nonCpG sites around centromeres and telomeres, which may potentially affect chromatin structure [12]. Both studies suggest that the aberrant methylation patterns can be transmitted through differentiation, therefore they may potentially interfere with developmental programs [12,152]. However, since these analyses are carried out with ESCs and iPSCs with different genetic backgrounds, it is unknown whether and how differences in genetic background contribute to the observed differential DNA methylation patterns between iPSCs and ESCs.…”

“…Genome-wide single-base mapping of DNA methylation uncovers certain iPSC-specific DNA methylation patterns in human iPSCs [12,152]. One study identified nine aberrantly methylated genes that distinguish human iPSCs from human ESCs [152]. A second study showed that the aberrant methylation hotspots in human iPSCs, although mostly occurring at CpG sites, can be at nonCpG sites around centromeres and telomeres, which may potentially affect chromatin structure [12].…”

“…Second, the established iPSCs may harbor aberrant traits resulted from the reprogramming process. These traits are frequently reflected in aberrant DNA methylation, which can be translated into altered transcription output and/or abnormal functional phenotypes [12,55,152]. These aberrant traits may be caused by technical issues, such as stoichiometry of the reprogramming factors used [189] and culturing conditions [190].…”

“…Instead, it is gained through the reprogramming process. Genome-wide single-base mapping of DNA methylation uncovers certain iPSC-specific DNA methylation patterns in human iPSCs [12,152]. One study identified nine aberrantly methylated genes that distinguish human iPSCs from human ESCs [152].…”