Induced pluripotent stem cells (iPSCs) can be derived from adult somatic tissues by the enforced expression of defined transcription factors. This process is referred to as reprogramming. As iPSCs can differentiate into any adult cell type and are fully matched to the individual they were derived from, reprogramming technology has radically altered the ability to model disease and led to new concepts for personalized cellular therapies. However, iPSCs can acquire detrimental epigenetic abnormalities during the reprogramming process. This occurs in manners that remain poorly understood. In an important proof-of-principle we have previously shown that DNA hypermethylation of the imprinted Dlk1-Dio3 cluster is a frequent iPSC normality that can be efficiently prevented by reprogramming in media containing ascorbic acid, one of several chemical compounds frequently used to increase reprogramming efficiencies. The goal of this research project is to develop a mechanistic understanding of recurrent gene-specific and genome-wide epigenetic iPSC abnormalities and for how reprogramming enhancing chemicals can prevent or trigger their occurrence. Using unique transgenic mouse models, we will pursue the following three aims. 1) We will identify the genes responsible for aberrant hypermethylation of Dlk1-Dio3 as well as those involved in mediating the protective effect of ascorbic acid on this gene cluster. 2) We will conduct genome-wide studies to determine how several frequently used reprogramming enhancing chemicals facilitate chromatin remodeling during iPSCs formation and how this relates to the maintenance of epigenetic integrity during this process. 3) We will systematically identify molecular and functional properties of iPSCs that are affected in a lasting manner by exposure to specific frequently used chemical compounds during the reprogramming process. Together, these experiments will provide a better understanding of why epigenetic abnormalities are introduced into iPSCs and how their occurrence relates to epigenetic remodeling crucial for successful reprogramming. In addition, our work will reveal possible benefits and risks of chemical reprogramming and thereby aid the derivation of high-quality human iPSCs, possibly by the use of chemical compounds alone.

Public Health Relevance

Induced pluripotent stem cells (iPSCs) hold great potential for the study and treatment of human disease. The aim of this proposal is to understand the reasons for the occurrence of detrimental epigenetic abnormalities in iPSCs and to identify efficient ways to prevent them. This will aid the rational design of improved protocols for the derivation of patient-specific stem cell lines.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Cellular, Molecular and Integrative Reproduction Study Section (CMIR)
Program Officer
Haynes, Susan R
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New York University
Anatomy/Cell Biology
Schools of Medicine
New York
United States
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Apostolou, Effie; Stadtfeld, Matthias (2018) Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr Opin Genet Dev 52:77-85
Donato, Valerio; Bonora, Massimo; Simoneschi, Daniele et al. (2017) The TDH-GCN5L1-Fbxo15-KBP axis limits mitochondrial biogenesis in mouse embryonic stem cells. Nat Cell Biol 19:341-351
Swanzey, Emily; Stadtfeld, Matthias (2016) A reporter model to visualize imprinting stability at the Dlk1 locus during mouse development and in pluripotent cells. Development 143:4161-4166
Tu, Shengjiang; Narendra, Varun; Yamaji, Masashi et al. (2016) Co-repressor CBFA2T2 regulates pluripotency and germline development. Nature 534:387-90
Vidal, Simon E; Amlani, Bhishma; Chen, Taotao et al. (2014) Combinatorial modulation of signaling pathways reveals cell-type-specific requirements for highly efficient and synchronous iPSC reprogramming. Stem Cell Reports 3:574-84