Investigating Gene Functions and Single-Cell Expression Profiles of De Novo Variants in Orofacial Clefts

Authors

Toshiyuki Itai
Fangfang Yan
Andi Liu
Yulin Dai
Chihiro Iwaya
Sarah W Curtis
Elizabeth J Leslie
Lukas M Simon
Peilin Jia
Xiangning Chen
Junichi Iwata
Zhongming Zhao

Publication Date

7-18-2024

Journal

HGG Advances

Abstract

Orofacial clefts (OFCs) are common congenital birth defects with various etiologies, including genetic variants. Online Mendelian Inheritance in Man (OMIM) annotated several hundred genes involving OFCs. Furthermore, several hundreds of de novo variants (DNVs) have been identified from individuals with OFCs. Some DNVs are related to known OFC genes or pathways, but there are still many DNVs whose relevance to OFC development is unknown. To explore novel gene functions and their cellular expression profiles, we focused on DNVs in genes that were not listed in OMIM. We collected 960 DNVs in 853 genes from published studies and curated these genes, based on the DNVs' deleteriousness, into 230 and 23 genes related to cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO), respectively. For comparison, we curated 178 CL/P and 277 CPO genes from OMIM. In CL/P, the pathways enriched in DNV and OMIM genes were significantly overlapped (p = 0.002). Single-cell RNA sequencing (scRNA-seq) analysis of mouse lip development revealed that both gene sets had abundant expression in the ectoderm (DNV genes: adjusted p = 0.032, OMIM genes: adjusted p < 0.0002), while only DNV genes were enriched in the endothelium (adjusted p = 0.032). Although we did not achieve significant findings using CPO gene sets, which was mainly due to the limited number of DNV genes, scRNA-seq analysis implicated various expression patterns among DNV and OMIM genes. Our results suggest that combinatory pathway and scRNA-seq data analyses are helpful for contextualizing genes in OFC development.

Keywords

Cleft Lip, Cleft Palate, Single-Cell Analysis, Humans, Mice, Animals, Transcriptome, Genetic Variation, Gene Expression Profiling, nonsyndromic orofacial clefts, cleft lip with or without palate, de novo variant, single-cell RNA sequencing, endothelium

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Associated Data

PMID: 38807368