Speaker
Description
Background: Dysregulation of the intricate molecular and cellular processes governing the formation of orofacial complex may culminate in congenital orofacial clefts (OFCs). OFCs may present as cleft lip (CL), cleft palate (CP), cleft lip and palate (CLP) and facial clefts or Tessier. The aetiology of the condition is complex, with both genetic and environmental contributions. Twins provide a great avenue to study these risk factors as they share a common intra-uterine environment during gestation. The current study utilised opposite-sex twins that were discordant for OFC phenotypes to decipher genetic risk factors.
Methods: Twelve opposite-sex twins discordant for OFCs and their parents were recruited. Whole-exome sequencing (WES) was conducted on DNA from these individuals at 100X utilising the Illumina HiSeq based on GRCh38. Sentieon workflow-based bioinformatics analyses of WES datasets encompassed quality control checks, trimming of poor reads, read alignment and variant calling. Normalised variant calls were annotated using Ensembl VEP. Variant classification and prioritisation were based on the American College of Medical Genetics and Genomics guidelines. Gene expression, interactome, and pathway enrichment analyses were conducted using Mouse Genome Informatics, STRING and g:Profiler, respectively.
Results: Pathogenic variants were observed in genes implicated in craniofacial development. These included PAX7, SBDS, POMGNT2, HKDC1, FOXD4L4, SSC5D, LIMCH1, GDF11, DISP2, NOTCH3, RUNX1, LEF1, NOTCH4, FN1, AGBL3, ANK3, DVL2, FAT4, DMD, MMP8, LRP1, TSC2, HOXB7, RUNX1, EFTUD2, RFX3, FOXD4L6, FOXC2, EGFR, RBMX, CRISPLD1, ANKS6, SCN8A, MMP2, KIF15, and TBX22. These genes are enriched in various processes, including molecular (DNA-binding transcription factor activity), biological function (anatomical structure morphogenesis, cell differentiation, developmental process, epithelium, cell and skeletal development, face morphogenesis, cell adhesion), and signalling pathways (Notch signalling, Wnt B-catenin signalling, neural crest differentiation).
Conclusion: Genes involved in notch signalling, Wnt B-catenin signalling, and neural crest differentiation are risk factors for OFCs. These observations inform molecular pathology of OFCs.