A meta-analysis of genome-wide association studies using Japanese and Taiwanese has revealed novel loci associated with gout susceptibility.
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ABSTRACT:
SUBMITTER: Chang SJ
PROVIDER: S-EPMC8866370 | biostudies-literature | 2022 Mar
REPOSITORIES: biostudies-literature
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A meta-analysis of genome-wide association studies using Japanese and Taiwanese has revealed novel loci associated with gout susceptibility.
Chang Shun-Jen SJ Toyoda Yu Y Kawamura Yusuke Y Nakamura Takahiro T Nakatochi Masahiro M Nakayama Akiyoshi A Liao Wei-Ting WT Shimizu Seiko S Takada Tappei T Takeuchi Kenji K Wakai Kenji K Shi Yongyong Y Shinomiya Nariyoshi N Chen Chung-Jen CJ Li Changgui C Okada Yukinori Y Ichida Kimiyoshi K Matsuo Hirotaka H
Human cell 20220115 2
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Project description:ObjectiveThe first ever genome-wide association study (GWAS) of clinically defined gout cases and asymptomatic hyperuricaemia (AHUA) controls was performed to identify novel gout loci that aggravate AHUA into gout.MethodsWe carried out a GWAS of 945 clinically defined gout cases and 1003 AHUA controls followed by 2 replication studies. In total, 2860 gout cases and 3149 AHUA controls (all Japanese men) were analysed. We also compared the ORs for each locus in the present GWAS (gout vs AHUA) with those in the previous GWAS (gout vs normouricaemia).ResultsThis new approach enabled us to identify two novel gout loci (rs7927466 of CNTN5 and rs9952962 of MIR302F) and one suggestive locus (rs12980365 of ZNF724) at the genome-wide significance level (p<5.0×10- 8). The present study also identified the loci of ABCG2, ALDH2 and SLC2A9. One of them, rs671 of ALDH2, was identified as a gout locus by GWAS for the first time. Comparing ORs for each locus in the present versus the previous GWAS revealed three 'gout vs AHUA GWAS'-specific loci (CNTN5, MIR302F and ZNF724) to be clearly associated with mechanisms of gout development which distinctly differ from the known gout risk loci that basically elevate serum uric acid level.ConclusionsThis meta-analysis is the first to reveal the loci associated with crystal-induced inflammation, the last step in gout development that aggravates AHUA into gout. Our findings should help to elucidate the molecular mechanisms of gout development and assist the prevention of gout attacks in high-risk AHUA individuals.
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Project description:Genome-wide association studies (GWAS) have identified approximately 50 loci associated with colorectal cancer (CRC) risk. However, the target genes and underlying mechanisms are largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using data from the Genotype-Tissue Expression (GTEx), The Cancer Genome Atlas (TCGA), and the Colonomics projects. We identified 24 putative target genes for 17 index SNPs at Benjamini-Hochberg adjusted P < 0.05 in at least one of the datasets. By analyzing functional genomic data, our result further indicated that 18 genes (75%) showed evidence of cis-regulation by putative functional SNPs via promoter or enhancer-promoter interactions. We next performed in vitro functional assays for three genes, TMBIM1, AAMP, and CABLES2, and confirmed that they play a vital role in colorectal carcinogenesis via disruption of cell behavior. Furthermore, our results indicate that silencing CABLES2 can promote the PI3K/AKT pathway. Our study reveals new candidate susceptibility genes and provides novel insight into the biological mechanisms for CRC development.
2018-10-23 | GSE121553 | GEO
Project description:BACKGROUND: Several novel susceptibility loci for type 2 diabetes have been identified through genome-wide association studies (GWAS) for type 2 diabetes or quantitative traits related to glucose metabolism in European populations. To investigate the association of the 13 new European GWAS-derived susceptibility loci with type 2 diabetes in the Japanese population, we conducted a replication study using 3 independent Japanese case-control studies. METHODOLOGY/PRINCIPAL FINDINGS: We examined the association of single nucleotide polymorphisms (SNPs) within 13 loci (MTNR1B, GCK, IRS1, PROX1, BCL11A, ZBED3, KLF14, TP53INP1, KCNQ1, CENTD2, HMGA2, ZFAND6 and PRC1) with type 2 diabetes using 4,964 participants (2,839 cases and 2,125 controls) from 3 independent Japanese samples. The association of each SNP with type 2 diabetes was analyzed by logistic regression analysis. Further, we performed combined meta-analyses for the 3 studies and previously performed Japanese GWAS data (4,470 cases vs. 3,071 controls). The meta-analysis revealed that rs2943641 in the IRS1 locus was significantly associated with type 2 diabetes, (P = 0.0034, OR = 1.15 95% confidence interval; 1.05-1.26) and 3 SNPs, rs10930963 in the MTNR1B locus, rs972283 in the KLF14 locus, and rs231362 in the KCNQ1 locus, had nominal association with type 2 diabetes in the present Japanese samples (P<0.05). CONCLUSIONS: These results indicate that IRS1 locus may be common locus for type 2 diabetes across different ethnicities.
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Project description:Background & aimsA genome-wide association study (GWAS) of 280 cases identified the hepatic cholesterol transporter ABCG8 as a locus associated with risk for gallstone disease, but findings have not been reported from any other GWAS of this phenotype. We performed a large-scale, meta-analysis of GWASs of individuals of European ancestry with available prior genotype data, to identify additional genetic risk factors for gallstone disease.MethodsWe obtained per-allele odds ratio (OR) and standard error estimates using age- and sex-adjusted logistic regression models within each of the 10 discovery studies (8720 cases and 55,152 controls). We performed an inverse variance weighted, fixed-effects meta-analysis of study-specific estimates to identify single-nucleotide polymorphisms that were associated independently with gallstone disease. Associations were replicated in 6489 cases and 62,797 controls.ResultsWe observed independent associations for 2 single-nucleotide polymorphisms at the ABCG8 locus: rs11887534 (OR, 1.69; 95% confidence interval [CI], 1.54-1.86; P = 2.44 × 10(-60)) and rs4245791 (OR, 1.27; P = 1.90 × 10(-34)). We also identified and/or replicated associations for rs9843304 in TM4SF4 (OR, 1.12; 95% CI, 1.08-1.16; P = 6.09 × 10(-11)), rs2547231 in SULT2A1 (encodes a sulfoconjugation enzyme that acts on hydroxysteroids and cholesterol-derived sterol bile acids) (OR, 1.17; 95% CI, 1.12-1.21; P = 2.24 × 10(-10)), rs1260326 in glucokinase regulatory protein (OR, 1.12; 95% CI, 1.07-1.17; P = 2.55 × 10(-10)), and rs6471717 near CYP7A1 (encodes an enzyme that catalyzes conversion of cholesterol to primary bile acids) (OR, 1.11; 95% CI, 1.08-1.15; P = 8.84 × 10(-9)). Among individuals of African American and Hispanic American ancestry, rs11887534 and rs4245791 were associated positively with gallstone disease risk, whereas the association for the rs1260326 variant was inverse.ConclusionsIn this large-scale GWAS of gallstone disease, we identified 4 loci in genes that have putative functions in cholesterol metabolism and transport, and sulfonylation of bile acids or hydroxysteroids.
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Project description:There is a paucity of genome-wide association study on Han Chinese gout patients. We performed a genome-wide association meta-analysis on two Taiwanese cohorts consisting of 758 gout cases and 14166 controls of Han Chinese ancestry. All the participants were recruited from the Taiwan Biobank. For pathway analysis, we applied ICSNPathway (Identify candidate Causal SNPs and Pathways) analysis, and to investigate whether expression-associated genetic variants contribute to gout susceptibility, we systematically integrated lymphoblastoid expression quantitative trait loci (eQTL) and genome-wide association data of gout using Sherlock, a Bayesian statistical frame-work. In the meta-analysis, we found 4 SNPs that reached genome-wide statistical significance (P < 5.0 × 10-8). These SNPs are in or close to ABCG2, PKD2 and NUDT9 gene on chromosome 4. ICSNPathway analysis identified rs2231142 as the candidate causal SNP, and ABCG2 as the candidate gene. Sherlcok analysis identified three genes, which were significantly associated with the risk of gout (PKD2, NUTD9, and NAP1L5). To conclude, we reported novel susceptible loci for gout that has not been previously addressed in the literature.
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Project description:Genome-wide association studies (GWASs) have identified more than 150 common genetic loci for breast cancer risk. However, the target genes and underlying mechanisms remain largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using normal or tumor breast transcriptome data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), The Cancer Genome Atlas (TCGA), and the Genotype-Tissue Expression (GTEx) project. We identified a total of 101 genes for 51 lead variants after combing the results of a meta-analysis of METABRIC and TCGA, and the results from GTEx at a Benjamini-Hochberg (BH)-adjusted p < 0.05. Using luciferase reporter assays in both estrogen-receptor positive (ER+) and negative (ER-) cell lines, we showed that alternative alleles of potential functional single-nucleotide polymorphisms (SNPs), rs11552449 (DCLRE1B), rs7257932 (SSBP4), rs3747479 (MRPS30), rs2236007 (PAX9), and rs73134739 (ATG10), could significantly change promoter activities of their target genes compared to reference alleles. Furthermore, we performed in vitro assays in breast cancer cell lines, and our results indicated that DCLRE1B, MRPS30, and ATG10 played a vital role in breast tumorigenesis via certain disruption of cell behaviors. Our findings revealed potential target genes for associations of genetic susceptibility risk loci and provided underlying mechanisms for a better understanding of the pathogenesis of breast cancer.
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