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Identification of functional non-coding variants associated with orofacial cleft.

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Researchers identified specific genetic variations, or single nucleotide polymorphisms (SNPs), linked to oral facial clefts (OFC). These functional SNPs directly impact gene expression and transcription factor binding in embryonic oral epithelium, revealing new insights into OFC pathogenesis.

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Area of Science:

  • Genetics
  • Developmental Biology
  • Genomic Medicine

Background:

  • Oral facial cleft (OFC) is a common birth defect with complex genetic underpinnings.
  • Genome-wide association studies (GWAS) have identified numerous genomic loci associated with OFC, but the functional variants remain largely unknown.
  • Effector genes implicated in OFC are often expressed in embryonic oral epithelium.

Purpose of the Study:

  • To identify functional single nucleotide polymorphisms (SNPs) associated with oral facial clefts (OFC) at known risk loci.
  • To investigate the impact of these SNPs on enhancer activity and gene expression in relevant cellular models.
  • To connect genetic variations in OFC to specific molecular mechanisms of pathogenesis.

Main Methods:

  • Massively parallel reporter assays (MPRA) were used to screen for SNPs with allele-specific enhancer activity in a fetal oral epithelial cell line.
  • Chromatin-mark data was utilized to filter candidate SNPs, prioritizing those located in active enhancers.
  • Engineered induced pluripotent stem cells (iPSCs) were differentiated into embryonic oral epithelium to assess the functional impact of top candidate SNPs on gene expression and transcription factor binding.

Main Results:

  • Several SNPs demonstrated allele-specific effects on enhancer activity in oral epithelial cells.
  • SNPs near FOXE1, IRF6, MAFB, TFAP2A, and TP63 were validated as potential functional variants.
  • In iPSC-derived oral epithelium, specific SNPs near IRF6 and FOXE1 altered effector gene expression and transcription factor binding.
  • Conditional GWAS analyses indicated that two functional SNPs near IRF6 significantly contribute to cleft lip with or without cleft palate (CL/P) risk.

Conclusions:

  • This study successfully identified functional SNPs associated with OFC, demonstrating allele-specific effects on gene regulation in oral epithelium.
  • The findings provide a mechanistic link between genetic variations and the pathogenesis of OFC, particularly CL/P.
  • The identified functional variants near IRF6 are major contributors to CL/P risk, offering targets for future research and potential therapeutic strategies.