An Integrative Omics Approach Identifies Genetic Effect of CircRNA on Nonsyndromic Cleft Lip With or Without Cleft Palate Susceptibility

Objective Circular RNAs (circRNAs) affect fundamental biological processes, but their genetic effects on nonsyndromic cleft lip with or without cleft palate (NSCL/P) remain unclear. Methods RNA sequencing of human embryonic palate mesenchyme cells identified circRNAs and their microRNA response elements (MREs) involved in NSCL/P. Genetic effects of single-nucleotide polymorphisms (SNPs) in MREs were evaluated in 858 NSCL/P cases and 1248 controls. Weighted genetic risk score (wGRS) and the predictive performance were evaluated through areas under the receiver operating characteristic curve (AUC). Results We identified 6272 MREs of 574 known and 53 novel circRNAs harboring 130 SNPs. Rs629772 in circPRKCE and rs365132 in circUIMC1 showed significant associations with NSCL/P [rs629772: OR = 0.82, P = 6.45E-03; rs365132: OR = 0.78, P = 7.85E-04]. Adding these SNPs to wGRS improved AUC to 0.707 for NSCL/P prediction. Additionally, rs629772 T>C increased the binding affinity of hsa-miR-628-5p and circPRKCE, and rs365132 G>T increased the binding of hsa-miR-374c-3p and hsa-miR-3916 to circUIMC1, followed by the alteration of 9, 6, and 65 target genes for hsa-miR-628-5p, hsa-miR-374c-3p, and hsa-miR-3916, respectively, which participated in key biological pathways. Conclusion This study indicated genetic effects in circRNA MREs associated with NSCL/P, offering insights into the genetic regulation and functional mechanisms of the disease.