Association Study of Genetic Variants in Autophagy Pathway and Risk of Non-syndromic Cleft Lip With or Without Cleft Palate
Association Study of Genetic Variants in Autophagy Pathway and Risk of Non-syndromic Cleft Lip With or Without Cleft Palate
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DOI：
10.3389/fcell.2020.00576
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发表时间：
2020-07-14
影响因子：
5.5
通讯作者：
Pan, Yongchu
中科院分区：
文献类型：
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作者：
Lou, Shu;Ma, Lan;Pan, Yongchu
虽然自噬途径基因的遗传变异与口腔癌的风险和胚胎的早期发育相关，但它们与非综合征性唇裂伴或不伴腭裂(NSCL/P)风险的相关性尚不清楚。采用两阶段病例对照研究(2 027例NSCL/P病例和1,843例对照)，研究23个自噬途径基因的单核苷酸多态(SNPs)与NSCL/P易感性的关系。用Logistic回归模型计算SNPs对NSCL/P易感性的影响。通过序列核关联检验(SKAT)和多标记基因组注释分析(MAGMA)方法进行基于基因的分析。对NSCL/P唇部组织标本进行表达数量性状基因座(EQTL)分析。用RNA-Seq分析胚胎发育过程中的基因表达。通过荧光素酶活性测定、细胞凋亡、细胞增殖、细胞周期等体外实验，探讨其功能作用。在联合分析中，HIF1A中的Rs2301104与NSCL/P的易感性显著相关(OR：1.29，95%CI：1.09~1.29，P=3.39×10(-03))，并显示出强烈的关联异质性(P=9.06×10(-03))，女性有明显的关联(OR：1.80；95%CI：1.32~2.45；P=1.79×10(-04))。与C等位基因相比，rs2301104的G等位基因与转录活性增强和HIF1的高表达有关。此外，rs2301104对HIF1A存在eQTL效应，其GC/CC基因型与GG基因型相比，HIF1A表达降低(P=3.1×10(-2))。HIF1α基因敲除可诱导人胚胎腭间充质细胞(HEPM)和口腔上皮细胞(HOEC)凋亡，抑制细胞增殖。本研究证实自噬途径基因HIF1A中的rs2301104与NSCL/P的易感性有关。
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 cyclein vitro. Rs2301104 inHIF1Awas significantly associated with NSCL/P susceptibility in the combined analysis (OR: 1.29, 95% CI: 1.09-1.29,P= 3.39 x 10(-03)), and showed strong evidence of association heterogeneity (P= 9.06 x 10(-03)) with obvious association in the female (OR: 1.80; 95% CI: 1.32-2.45;P= 1.79 x 10(-04)). The G allele of rs2301104 was associated with enhanced transcription activity and high expression ofHIF1Acompared with that of C allele. Moreover, rs2301104 exhibited an eQTL effect forHIF1Awith its GC/CC genotypes associated with decreasedHIF1Aexpression compared with those with GG genotypes (P= 3.1 x 10(-2)). Knockdown ofHIF1Ainduced 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 geneHIF1Awas associated with susceptibility of NSCL/P.