Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes

Tara N. Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A. Rosenfeld, Jennifer VanOudenhove, Daryl A. Scott, Elizabeth J. Leslie and Justin Cotney ()
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Tara N. Yankee: UConn Health
Sungryong Oh: University of Connecticut School of Medicine, Department of Genetics and Genome Sciences
Emma Wentworth Winchester: UConn Health
Andrea Wilderman: UConn Health
Kelsey Robinson: Emory University School of Medicine
Tia Gordon: Baylor College of Medicine
Jill A. Rosenfeld: Baylor College of Medicine
Jennifer VanOudenhove: University of Connecticut School of Medicine, Department of Genetics and Genome Sciences
Daryl A. Scott: Baylor College of Medicine
Elizabeth J. Leslie: Emory University School of Medicine
Justin Cotney: University of Connecticut School of Medicine, Department of Genetics and Genome Sciences

Nature Communications, 2023, vol. 14, issue 1, 1-23

Abstract: Abstract Craniofacial disorders arise in early pregnancy and are one of the most common congenital defects. To fully understand how craniofacial disorders arise, it is essential to characterize gene expression during the patterning of the craniofacial region. To address this, we performed bulk and single-cell RNA-seq on human craniofacial tissue from 4-8 weeks post conception. Comparisons to dozens of other human tissues revealed 239 genes most strongly expressed during craniofacial development. Craniofacial-biased developmental enhancers were enriched +/− 400 kb surrounding these craniofacial-biased genes. Gene co-expression analysis revealed that regulatory hubs are enriched for known disease causing genes and are resistant to mutation in the normal healthy population. Combining transcriptomic and epigenomic data we identified 539 genes likely to contribute to craniofacial disorders. While most have not been previously implicated in craniofacial disorders, we demonstrate this set of genes has increased levels of de novo mutations in orofacial clefting patients warranting further study.

Date: 2023
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DOI: 10.1038/s41467-023-40363-1

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