Functional Effects of SNPs in MYH9 and Risks of Nonsyndromic Orofacial Clefts

Abstract

Nonsyndromic orofacial clefts (NSOCs) are congenital newborn malformations. Myosin heavy chain 9 (MYH9) is a candidate gene of NSOCs. To investigate the associations between single-nucleotide polymorphisms (SNPs) of MYH9 and NSOC susceptibility, a 2-stage case-control study was designed and 4 potentially functional SNPs of MYH9 (rs12107, rs2269529, rs9619601, rs5756130) were selected and genotyped by iPLEX Sequenom MassARRAY and TaqMan assay in the first stage (599 NSOC cases and 590 controls). The significant SNPs in the first stage were replicated in the second stage (676 NSOC cases and 705 controls) by TaqMan assay. Reverse transcription polymerase chain reaction, cell transfection, and luciferase assay were performed accordingly to explore their functionality. In stage I, rs12107 was nominally associated with NSOCs, whereas rs2269529 showed a significant association (rs12107: Phet = 0.028; rs2269529: Phet = 0.001). In stage II, rs12107 was nominally associated with NSOCs, and rs2269529 showed a significant association (rs12107: Phom = 0.014; rs2269529: Phet = 0.006). In combined stages, these 2 SNPs gained significant associations (rs12107: Pdom = 0.004; rs2269529: Pdom = 4.4 × 10–5). In subphenotype analysis, these 2 SNPs were associated with cleft lip only (CLO) and cleft lip with palate (CLP), and rs2269529 was also associated with cleft palate only (CPO). Haplotype analysis revealed associations between rs12107-G/rs2269529-T and NSOC susceptibility (P = 0.011). Combined analysis of rs12107 and rs2269529 indicated the risk of NSOCs increased with the number of risk alleles (rs12107-G and rs2269529-T, P for trend = 0.008). MYH9 SNP rs12107 AG + GG and rs2269529 CT + TT were associated with higher MYH9 expression in lip tissues compared with their corresponding wild-type homozygote. For rs12107, higher luciferase activities of G allele than A allele were observed in the luciferase assay. MYH9 was downregulated when transfecting its putative binding target miR-196b-3p into human embryo plate mesenchyme (HEPM) and C2C12 cell lines. For rs2269529, C > T contributed to increased MYH9 messenger RNA. In conclusion, rs12107 and rs2269529 were associated with the expression of MYH9 and contributed to the susceptibility of NSOCs.