Human Induced Pluripotent Stem Cells: From Cell Origin, Genomic Stability, and Epigenetic Memory to Translational Medicine

Abstract

The potential of human induced pluripotent stem cells (iPSCs) to self-renew indefinitely and to differentiate virtually into any cell type in unlimited quantities makes them attractive for in vitro disease modeling, drug screening, personalized medicine, and regenerative therapies. As the genome of iPSCs thoroughly reproduces that of the somatic cells from which they are derived, they may possess genetic abnormalities, which would seriously compromise their utility and safety. Genetic aberrations could be present in donor somatic cells and then transferred during iPSC generation, or they could occur as de novo mutations during reprogramming or prolonged cell culture. Therefore, to warrant the safety of human iPSCs for clinical applications, analysis of genetic integrity, particularly during iPSC generation and differentiation, should be carried out on a regular basis. On the other hand, reprogramming of somatic cells to iPSCs requires profound modifications in the epigenetic landscape. Changes in chromatin structure by DNA methylations and histone tail modifications aim to reset the gene expression pattern of somatic cells to facilitate and establish self-renewal and pluripotency. However, residual epigenetic memory influences the iPSC phenotype, which may affect their application in disease therapeutics. The present review discusses the somatic cell origin, genetic stability, and epigenetic memory of iPSCs and their impact on basic and translational research.

Keywords: epigenetic memory; genetic aberrations; genetic stability; human induced pluripotent stem cells; point mutations; somatic origin.

Graphical Abstract

Figure 1.

Process toward reprogramming of somatic cells to generate patient-specific iPSCs and application fields of iPSC-derived specialized cells. (A) Generation of iPSCs from a variety of somatic cell types by using integrative or non-integrative reprogramming approaches. Reprogramming of somatic cells by integrative strategies yields iPSCs with the integrations of transgenes into the genome, which may possess an increased mutagenic potential and are therefore considered unsafe. Alternatively, non-integrative strategies for reprogramming yield iPSCs, which are free of transgenes and are considered safe. Overall, the generated iPSCs can be differentiated into specialized cells and used as a tool for disease modeling, personalized medicine, regenerative therapy, and tissue engineering, in addition to their use for drug screening or drug testing. (B) Pre-existing genetic abnormalities of somatic cells can, when remaining undiscovered in the generated iPSCs, seriously limit their utility and safety for clinical or regenerative therapy. Genetic aberrations could be acquired during the process of reprogramming or due to extended passaging of iPSCs, which likewise limit their utility and safety. Therefore, to warrant safety of iPSCs for clinical applications, analysis of genetic integrity should be carried out on a regular basis. Furthermore, epigenetic memory of the somatic cells in iPSCs may influence lineage-specific differentiation and with-it utility and safety for clinical use.

Figure 2.

Sources and consequences of genomic instability in iPSCs. (A) Genetic alterations in iPSCs mainly arise via 3 routes: (i) Mutations are already present in the parental somatic cells from which iPSCs are derived and are subsequent cultured and expanded (upper panel), (ii) mutations can be induced during the process of reprogramming (middle panel), and (iii) mutations can be induced during extended passaging and prolonged culturing (lower panel). (B) Chromosomal rearrangements commonly observed in iPSCs, including gain of whole chromosomes, translocation of a chromosomal part from one to another chromosome, deletion of a chromosomal part, and duplications of a chromosomal part. (C) Changes in the DNA sequence commonly observed in iPSCs, including single nucleotide variation, ie, substitution of a single nucleotide at a specific position in the genome by another single nucleotide, and loss (deletion) or gain (insertion) of a single nucleotide. (D) Cell autonomous and cell interaction consequences of iPSC mutant variants, including growth advantage of the mutant variant as a result of faster cell cycle (left panel), block of differentiation by the mutant variant (middle panel), and alteration of differentiation patterns by the mutant variant (right panel).

Figure 3.

Changes of the epigenetic landscape occurring during generation of iPSCs. (A) Profound and intense modification of the histone tail, ie, histone H3 acetylation at lysine residues (upper panel) and histone H3 methylation at lysine residues (middle panel), in addition to DNA modification, ie, DNA methylation (black boxes) or DNA hypomethylation (white boxes) (lower panel). (B) Changes in the epigenetic landscape occurring during reprogramming of parental somatic cells with respect to tissue-specific (upper panel) and pluripotency-specific genes (lower panel). In somatic cells, tissue-specific gene promoters are demethylated and enriched for the active histone tail modification H3K4me3, by which they remain in an active state. Opposite, pluripotency-specific genes remain silenced by both DNA methylation and repressive H3K9me3 and H3K27me3. During reprogramming, silencing of somatic genes is directed by repressive H3K9me3, while activation of pluripotency-specific genes is instructed by H3K4me3 and H3K36me3, in addition to histone acetylation and promoter hypomethylation. (C) Epigenetic dynamics toward activation of pluripotency-specific genes occurring during successful reprogramming of somatic cells to iPSCs as indicated by a color gradient. Black colors of the bars indicate high abundance, white colors low abundance of prominent histone tail modifications or DNA demethylation patterns of pluripotency-specific genes.