# DNA methylation in orofacial clefting

> **NIH NIH R01** · UNIVERSITY OF WISCONSIN-MADISON · 2024 · $465,023

## Abstract

Understanding the role of malleable epigenetic mechanisms in birth defects is a direct path to prevention
strategies. Orofacial clefts (OFCs) of the lip and palate are among the most common human structural birth
defects, affecting 1 in 800 newborns, and pose serious individual, familial, and societal burdens. Prevention
strategies for OFCs are elusive because our current understanding of causative factors is inadequate.
Epidemiologic and traditional genetic studies have shown that OFCs are etiologically complex outcomes that
result from multifactorial genetic and environmental influences. Epigenetic mechanisms are an exciting new
focus in understanding the genesis of OFCs because they mediate the effect of environmental influences on the
genome during sensitive embryonic periods. Our proposal specifically focuses on DNA methylation because
this epigenetic mechanism is environmentally sensitive and a practical target of prevention and therapeutic
strategies. While implicated by multiple lines of evidence, the biological role of DNA methylation in orofacial
development is unclear. We have established novel models and generated key proofs of concepts that poise us
to uncover how DNA methylation regulates orofacial morphogenesis and to define the role that DNA
methylation plays in modulating OFC susceptibility. In this project, integrated genome-wide methylation and
bulk and single-cell transcriptome approaches will be applied to define molecular and cellular mechanisms of
OFC pathogenesis resulting from disrupted DNA methylation in the cranial neural crest. The role of DNA
methylation in multifactorial OFC susceptibility will then be defined by integrating multiple environmental and
dietary modulators of DNA methylation to genetic (Wnt9b KO) and chemical (Shh antagonist) mouse models
of incompletely penetrant OFCs. Finally, epigenome editing will be applied to evaluate the functional impact of
OFC-associated methylation changes on gene expression and cranial neural crest biology. Completion of the
proposed studies will bring fundamental insight into how DNA methylation regulates cranial neural crest
biology and orofacial morphogenesis. By defining environmental- and dietary-mediated methylome-
transcriptome responses that alter OFC susceptibility, these studies will also provide a necessary foundation for
identification of environmental influences that modulate DNA methylation and contribute to OFC risk.
Pursuing this line of investigation will advance our long-term goal of developing prevention strategies for
etiologically complex birth defects by identifying culpable environmental influences and defining their
mechanisms of action.

## Key facts

- **NIH application ID:** 10814313
- **Project number:** 5R01DE032710-02
- **Recipient organization:** UNIVERSITY OF WISCONSIN-MADISON
- **Principal Investigator:** Robert Lipinski
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $465,023
- **Award type:** 5
- **Project period:** 2023-05-01 → 2027-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10814313

## Citation

> US National Institutes of Health, RePORTER application 10814313, DNA methylation in orofacial clefting (5R01DE032710-02). Retrieved via AI Analytics 2026-06-01 from https://api.ai-analytics.org/grant/nih/10814313. Licensed CC0.

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