DNA methylation dynamics in human induced pluripotent stem cells

Abstract

Indeed human induced pluripotent stem cells (hiPSCs) are considered to be powerful tools in regenerative medicine. To enable the use of hiPSCs in the field of regenerative medicine, it is necessary to understand the mechanisms of reprogramming during the transformation of somatic cells into hiPSCs. Genome-wide epigenetic modification constitutes a critical event in the generation of iPSCs. In other words, to analyze epigenetic changes in iPSCs means to elucidate reprogramming processes. We have established a large number of hiPSCs derived from various human tissues and have obtained their DNA methylation profiles. Comparison analyses indicated that the epigenetic patterns of various hiPSCs, irrespective of their source tissue, were very similar to one another and were similar to those of human embryonic stem cells (hESCs). However, the profiles of hiPSCs and hESCs exhibited epigenetic differences, which were caused by random aberrant hypermethylation at early passages. Interestingly, continuous passaging of the hiPSCs diminished the differences between DNA methylation profiles of hiPSCs and hESCs. The number of aberrant DNA methylation regions may thus represent a useful epigenetic index for evaluating hiPSCs in the context of therapeutic applications.

Epigenetic aberrations in human pluripotent stem cells

“…Nevertheless, reprogramming mouse and human somatic cells by nuclear transfer facilitated a less aberrant methylation pattern which is similar to that of ESCs (Kim et al , ; Ma et al , ). Additional methylation alterations, which are not found in either the normal somatic source cells or hESCs, are acquired during reprogramming and vary between different hiPSC lines (Doi et al , ; Bock et al , ; Lister et al , ; Nishino et al , ; Koyanagi‐Aoi et al , ; Planello et al , ; Nishino & Umezawa, ; Tesarova et al , ). It was shown that employing different combinations of reprogramming factors result in distinct patterns of 5‐mC aberrations.…”

“…Importantly, some of these methylation aberrations are also implicated in different tumors (Ohm et al , ) and are transmitted throughout differentiation (Lister et al , ; Ruiz et al , ). Nevertheless, while somatic memory and aberrations in DNA methylation exist in early‐passage iPSCs, some studies found that many of them were diminished over time, at which point iPSCs become highly similar to ESCs in their methylation pattern (Nishino et al , ; Nishino & Umezawa, ; Tesarova et al , ), whereas others demonstrated a preservation of epigenetic memory over time (Kim et al , ). Even though reprogramming is often considered the cause for acquiring methylation aberrations, it was shown that it can also enable the reversal of 5‐mC alterations in some tumor suppressors and cancer‐related genes, which were abnormally methylated and silenced in somatic cells (Ron‐Bigger et al , ).…”

Bioengineering Considerations for a Nurturing Way to Enhance Scalable Expansion of Human Pluripotent Stem Cells

“…The development of targeted DNA methylation manipulation tools can address epigenetic changes that support the memory formation and maintenance, leading to new insights into how DNA methylation governs gene expression . Recent studies revealed that genotypic expression can be turned on or off through DNA methylation as a key mediator of memory formation and maintenance . More recently, with the growing understanding that various molecules function as readers, writers, or erasers of epigenetic codes, strategies for epigenetic modification have focused on control of pluripotency and differentiation .…”

“…Recently, there has been considerable interest in the impact of culture‐induced genetic and epigenetic alterations . hPSCs may carry a genetic “memory” of the starting cell type, influencing their ability to be reprogrammed and affecting their differentiation capacity . Genotypic or epigenetic variations in hPSCs can contribute to the inherent differences resulting from donor‐dependent variability, changes induced during the process of cellular reprogramming, or their accumulation during culture expansion .…”

The silver lining of induced pluripotent stem cell variation

“…Many studies have provided evidence that epigenetic memory affects the differentiation capacity (8)(9)(10), however these studies recognize the fact that the results may have been influenced by cell passage number, transfection techniques, and variability due to manual handling procedures across different labs. A recent large study of 200 iPSC lines suggests that, independently of the cell source, iPSCs exhibit altered epigenetic patterns caused by early aberrant hypermethylation, that decrease over time in culture (11). In line with these findings, the Yoshida group found that the origin of the cells to be reprogrammed and the reprogramming method were not key factors in further differentiation efficiency of those lines.…”