Abstract
Although genetic variants in autophagy pathway genes were associated with the risk of oral cancers and early development in embryos, their associations with non-syndromic cleft lip with or without cleft palate (NSCL/P) risk remained unclear. A two-stage case-control study (2,027 NSCL/P cases and 1,843 controls) was performed to investigate the associations between single nucleotide polymorphisms (SNPs) in 23 autophagy pathway genes and NSCL/P susceptibility. The logistic regression model was used to calculate effects of SNPs on NSCL/P susceptibility. Gene-based analysis was performed via the sequence kernel association test (SKAT) and multi-marker analysis of genomic annotation (MAGMA) methods. Expression quantitative trait loci (eQTL) analysis was conducted using NSCL/P lip tissue samples. Gene expression during embryonic development was evaluated using RNA-Seq. Functional roles were explored by luciferase activity assay, cell apoptosis, proliferation, and cycle in vitro. Rs2301104 in HIF1A was significantly associated with NSCL/P susceptibility in the combined analysis (OR: 1.29, 95% CI: 1.09–1.29, P = 3.39 × 10–03), and showed strong evidence of association heterogeneity (P = 9.06 × 10–03) with obvious association in the female (OR: 1.80; 95% CI: 1.32–2.45; P = 1.79 × 10–04). The G allele of rs2301104 was associated with enhanced transcription activity and high expression of HIF1A compared with that of C allele. Moreover, rs2301104 exhibited an eQTL effect for HIF1A with its GC/CC genotypes associated with decreased HIF1A expression compared with those with GG genotypes (P = 3.1 × 10–2). Knockdown of HIF1A induced cell apoptosis and inhibited cell proliferation in human embryonic palate mesenchyme (HEPM) and human oral epithelium cells (HOEC). This study demonstrated that rs2301104 in autophagy pathway gene HIF1A was associated with susceptibility of NSCL/P.
Highlights
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common human birth defects contributing huge health and financial burdens to the affected individuals, families, and societies (Mangold et al, 2010; Heike and Evans, 2016)
146 putative functional single nucleotide polymorphisms (SNPs) were picked out, and their associations with risk of NSCL/P were examined in the stage I that was comprised of 504 NSCL/P cases and 455 newborn controls
HIF1A achieved consistent associations in both methods (Supplementary Table 4); rs2301104 in HIF1A remained for further analysis
Summary
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common human birth defects contributing huge health and financial burdens to the affected individuals, families, and societies (Mangold et al, 2010; Heike and Evans, 2016). It occurs in in 700 live births worldwide, with prevalence varying by population (Birnbaum et al, 2009). Proliferation, and apoptosis in both epithelial cells and cranial neural crest (CNC)derived mesenchymal cells are involved in mechanisms leading to cleft lip and palate (Tian et al, 2017)
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