# Dissecting genetic determinants of epigenetic instability in pluripotent stem cells

> **NIH NIH R01** · WEILL MEDICAL COLL OF CORNELL UNIV · 2024 · $423,731

## Abstract

Project Summary
The remarkable ability of pluripotent stem cells (PSCs) to give rise to a plethora of fully functional somatic cell
types becomes progressively impaired upon ex vivo culture by aberrant gain or loss of DNA methylation marks
at essential developmental gene loci. This pervasive epigenetic instability represents a significant hurdle for
biomedical applications using PSCs, but the underlying molecular reasons remain almost entirely unknown. An
important example for epigenetic instability in PSCs is loss of genomic imprinting, an essential gene regulatory
mechanism in mammals. By combining transgenic reporter alleles for imprint stability with mouse genetics, we
found that imprint dysregulation in PSCs is caused by identifiable genetic variants that affect trans acting
chromatin regulators. The goal of this proposal is to develop a comprehensive molecular understanding on
how specific genetic variants affect the stability of vital epigenetic marks in PSCs. To work towards this goal,
we will first functionally dissect the causal variants within a genomic susceptibility region that we discovered
and which drives locus-specific DNA hypermethylation and loss of developmental potential. This will allow us to
pinpoint gene regulatory features that predispose imprinted and other genes to aberrant gain of DNA
methylation (Aim 1). We will then use genetic mapping in hybrid PSCs to discover quantitative trait loci that
can protect against detrimental DNA hypomethylation and validate the function of associated gene products in
both mouse and human pluripotent cells (Aim 2). Finally, we will model the genetics of imprint stability in a
panel of PSCs with highly diverse yet well-characterized genomes. This will enable us to dissect the molecular
regulation of epigenetic stability in complex genetic backgrounds resembling the human population and help us
to establish new biomarkers for the identification of culture conditions that preserve developmental potential in
PSCs of unknown genetic background (Aim 3). Our work will establish novel conceptual and mechanistic
frameworks for the detrimental epigenetic vulnerability of pluripotent cells, which will aid the safe and reliable
use of these cells to study developmental and disease processes. In addition, our findings will have relevance
for a wide range of human diseases and developmental syndromes characterized by epigenetic instability.

## Key facts

- **NIH application ID:** 10781989
- **Project number:** 5R01GM145864-03
- **Recipient organization:** WEILL MEDICAL COLL OF CORNELL UNIV
- **Principal Investigator:** Matthias Stadtfeld
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $423,731
- **Award type:** 5
- **Project period:** 2022-04-15 → 2026-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10781989

## Citation

> US National Institutes of Health, RePORTER application 10781989, Dissecting genetic determinants of epigenetic instability in pluripotent stem cells (5R01GM145864-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10781989. Licensed CC0.

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