# Genomic and Functional Analysis of IRF6 Target Genes in Orofacial Cleft Pathogenesis

> **NIH NIH R01** · MASSACHUSETTS GENERAL HOSPITAL · 2022 · $408,794

## Abstract

Project Summary
Orofacial clefts (OFC) such as cleft lip and/or palate (CL/P) are among the most
common congenital structural anomalies. Most OFC cases are non-syndromic with
complex genetic mechanisms that are yet to be elucidated. The majority of heritable
OFC risk is expected to reside in rare or de novo variations. With expanding clinical use
of prenatal DNA tests, there is a pressing need to improve the genetic interpretation of
whole exome/genome sequence data. A major challenge is assignment of pathogenicity
to both coding and non-coding variants. The gene encoding transcription factor IRF6 is
strongly associated with non-syndromic CL/P, plus mutations in IRF6 cause the most
common form of syndromic CL/P. We and others have shown that genes in the IRF6
pathway are good candidates to harbor rare variants that influence risk for CL/P, such as
GRHL3, ARHGAP29 and KLF4. In this proposal, we extend this successful strategy to
elucidate CL/P pathogenesis with a comprehensive and deep analysis of the IRF6
downstream gene pathway. We employed a rigorous gene prioritization strategy where
critical IRF6 transcriptional target genes were identified via ChIP-seq from wild type
embryos, enriched by subtraction against irf6 mutant dataset. The target genes were
then selected for differential expression between wild type and irf6 mutants via RNA-seq.
This IRF6 candidate target gene list was then cross-referenced for spatiotemporal
expression patterns relevant for craniofacial development with zebrafish WISH and
mouse gene expression data from the FaceBase project. Finally we selected genes
associated with human CL/P pathology from a recent 800 CL/P case-parent trios WGS
dataset from the Gabriella Miller Kids First sequencing project. Our central hypothesis
is that IRF6 target genes are critical for palate development, and that rare and de novo
mutations in such genes, whether coding or non-coding, are present in patients with
non-syndromic OFC. To test this hypothesis, we propose three complementary aims to
1) gain new biological insight from known (Tfap2a) and newly identified (Dact1) genes in
craniofacial development, 2) gain new functional and clinical insight of de novo coding
gene variants important for OFC, 3) develop methodology and analyze non-coding gene
variants implicated for OFC. The expected impact of this work will be to bridge the gap
between WGS data and biological insight, an essential step to meaningfully translate
genetic research data to inform clinical decisions.

## Key facts

- **NIH application ID:** 10371069
- **Project number:** 5R01DE027983-04
- **Recipient organization:** MASSACHUSETTS GENERAL HOSPITAL
- **Principal Investigator:** Eric Chien-Wei Liao
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $408,794
- **Award type:** 5
- **Project period:** 2019-04-01 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10371069

## Citation

> US National Institutes of Health, RePORTER application 10371069, Genomic and Functional Analysis of IRF6 Target Genes in Orofacial Cleft Pathogenesis (5R01DE027983-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10371069. Licensed CC0.

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