AUTHOR=Lou Shu , Ma Lan , Kan Shiyi , Yu Xin , Wang Yuting , Yang Fan , Zhu Guirong , Fan Liwen , Li Dandan , Wang Hua , Wang Wei , Zhang Weibing , Wang Lin , Pan Yongchu 

TITLE=Association Study of Genetic Variants in Autophagy Pathway and Risk of Non-syndromic Cleft Lip With or Without Cleft Palate

JOURNAL=Frontiers in Cell and Developmental Biology

VOLUME=8

YEAR=2020

URL=https://www.frontiersin.org/journals/cell-and-developmental-biology/articles/10.3389/fcell.2020.00576

DOI=10.3389/fcell.2020.00576

ISSN=2296-634X

ABSTRACT=<p>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 <italic>in vitro</italic>. Rs2301104 in <italic>HIF1A</italic> was significantly associated with NSCL/P susceptibility in the combined analysis (OR: 1.29, 95% CI: 1.09–1.29, <italic>P</italic> = 3.39 × 10<sup>–03</sup>), and showed strong evidence of association heterogeneity (<italic>P</italic> = 9.06 × 10<sup>–03</sup>) with obvious association in the female (OR: 1.80; 95% CI: 1.32–2.45; <italic>P</italic> = 1.79 × 10<sup>–04</sup>). The G allele of rs2301104 was associated with enhanced transcription activity and high expression of <italic>HIF1A</italic> compared with that of C allele. Moreover, rs2301104 exhibited an eQTL effect for <italic>HIF1A</italic> with its GC/CC genotypes associated with decreased <italic>HIF1A</italic> expression compared with those with GG genotypes (<italic>P</italic> = 3.1 × 10<sup>–2</sup>). Knockdown of <italic>HIF1A</italic> 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 <italic>HIF1A</italic> was associated with susceptibility of NSCL/P.</p>