Back to 2025 Abstracts
Comprehensive Genome Wide Identification And Functional Study Of Epithelial Mesenchymal Transition Genes That Regulate Cleft Pathogenesis And Regeneration
Eric C. Liao, M.D., Ph.D., Sogand Schafer, MD, Fegn Wang, PhD, Yongjun Li, PhD, Shannon Carroll, PhD, Yi Xing, PhD.
Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Purpose: RNA makeup of epithelium is regulated by binding proteins Esrp1/2 that govern epithelial mesenchymal transition (EMT), a central cell process that underpins embryogenesis and regeneration. Loss of Esrp1/2 results in global mRNA isoform dysregulation, resulting in orofacial clefts in all vertebrates. Given the central role of Esrp1/2 to regulate EMT, there is an urgent unmet need to understand its function.
Methods: We applied advanced long read sequencing and RNA computation to comprehensively identify RNA isoforms genome wide, between wild-type and Esrp1/2 mutant mouse and zebrafish. Differentially expressed isoforms were prioritized based on biological pathway, relative abundance and isoform differences.
Results: We found that >60% of isoform switches identified involved complex or combinatorial AS patterns, which are missed by standard short-read RNA-seq. We discovered novel isoforms that were absent from existing annotations, including in genes with important EMT functions. We discovered that a key transcription factor tp63 is regulated by esrp. Over-expression of tp63 isoforms was sufficient to rescue esrp1/2 mutant clefts.
Conclusion: We discovered that tp63 isoforms require esrp1/2 function, and that expression of specific tp63 isoforms is sufficient to rescue cleft palate of the esrp1/2 mutant. These results provide the scientific basis of a gene therapy strategy to exploit modulation of exon usage. We have also generated a EMT long-read RNAseq atlas that will inform broad research questions in cancer, embryology and regeneration.
Back to 2025 Abstracts