Investigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts
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
Affiliations
Toshiyuki Itai
Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
Fangfang Yan
Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
Andi Liu
Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, Houston, TX 77030, USA
Yulin Dai
Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
Chihiro Iwaya
Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; Center for Craniofacial Research, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
Sarah W. Curtis
Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
Elizabeth J. Leslie
Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
Lukas M. Simon
Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
Peilin Jia
Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
Xiangning Chen
Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
Junichi Iwata
Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; Center for Craniofacial Research, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; Pediatric Research Center, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
Zhongming Zhao
Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Corresponding author
Summary: 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.
