Characterization of DNA Methylomic Signatures in Induced Pluripotent Stem Cells During Neuronal Differentiation

Abstract

In development, differentiation from a pluripotent state results in global epigenetic changes, although the extent to which this occurs in induced pluripotent stem cell-based neuronal models has not been extensively characterized. In the present study, induced pluripotent stem cell colonies (33Qn1 line) were differentiated and collected at four time-points, with DNA methylation assessed using the Illumina Infinium Human Methylation EPIC BeadChip array. Dynamic changes in DNA methylation occurring during differentiation were investigated using a data-driven trajectory inference method. We identified a large number of Bonferroni-significant loci that showed progressive alterations in DNA methylation during neuronal differentiation. A gene–gene interaction network analysis identified 60 densely connected genes that were influential in the differentiation of neurons, with STAT3 being the gene with the highest connectivity.

Increased Cholesterol Synthesis Drives Neurotoxicity in Patient Stem Cell-Derived Model of Multiple Sclerosis

“…As iPSC reprogramming has been demonstrated to rejuvenate the epigenome 28 , we next utilized direct reprogramming technology to generate cell lines that retain aging-related markers (Park, Nicaise, Tsitsipatis, et al, manuscript in preparation ). We reprogrammed skin fibroblasts from 3 non-diseased individuals (Ctrl) and 4 people with PMS between 25 to 63 years of age into iNSCs ( Table 1 ).…”

“…Full reprogramming has been found to completely wipe the epigenetic clock back to fetal age. 28 Conversely, direct induction of patient fibroblasts to neurons was found to preserve epigenetic and aging hallmarks [56][57][58] , which has also led to the development of disease modeling in a dish methodologies for neurodegenerative diseases. Here we took advantage of direct reprogramming technology for a novel patient stem cell-derived model of MS, and generated directly reprogrammed iNSCs from people with PMS, maintaining epigenetic hallmarks from the somatic cells (Park, Nicaise, Tsitsipatis, et al, manuscript in preparation).…”

High content screening miniaturization and single cell imaging of mature human feeder layer-free iPSC-derived neurons

“…When adult somatic cells are reprogrammed into iPSCs by enforced expression of transcription factors, they are reverted to an embryonic state [ 42 , 43 ]. Previous work indicates that the epigenetic signatures of the iPSCs reflect a “fetal” or “prenatal” age [ 44 ] versus the actual chronological age of the “donor” somatic cells, which are typically adult or “aged”, and that fetal state endures during the subsequent conversion to NPCs and differentiation into neurons. This is understandably problematic when one is using iPSC-derived neurons in studies of neurodegenerative disorders typically associated with aged human populations.…”

The Neuroepigenetic Landscape of Vertebrate and Invertebrate Models of Neurodegenerative Diseases

“…These attractive technologies come with their own limitations, however; for example, as a consequence of their cellular reprograming, involving epigenetic remodeling, iPSC-derived brain cells are transcriptionally and epigenetically similar to immature brain cells. 160 This makes them great for studying neuronal development but poses challenges when studying aging-associated diseases. Studies using iPSCs have already contributed greatly to our understanding of certain aspects of neurodegenerative diseases, and, in parallel to studies using animal models, can be very powerful in understanding and validating findings in mice.…”