A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival
Abstract The genetic architecture of non-small cell lung cancer (NSCLC) is relevant to smoking status. However, the genetic contribution of long-term smoking cessation to the prognosis of NSCLC patients remains largely unknown. We conducted a genome-wide association study primarily on the prognosis...
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Nature Portfolio
2021
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oai:doaj.org-article:1ca3d9325fa341efb51b71a031edf4712021-12-02T14:58:42ZA multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival10.1038/s41698-021-00182-32397-768Xhttps://doaj.org/article/1ca3d9325fa341efb51b71a031edf4712021-05-01T00:00:00Zhttps://doi.org/10.1038/s41698-021-00182-3https://doaj.org/toc/2397-768XAbstract The genetic architecture of non-small cell lung cancer (NSCLC) is relevant to smoking status. However, the genetic contribution of long-term smoking cessation to the prognosis of NSCLC patients remains largely unknown. We conducted a genome-wide association study primarily on the prognosis of 1299 NSCLC patients of long-term former smokers from independent discovery (n = 566) and validation (n = 733) sets, and used in-silico function prediction and multi-omics analysis to identify single nucleotide polymorphisms (SNPs) on prognostics with NSCLC. We further detected SNPs with at least moderate association strength on survival within each group of never, short-term former, long-term former, and current smokers, and compared their genetic similarity at the SNP, gene, expression quantitative trait loci (eQTL), enhancer, and pathway levels. We identified two SNPs, rs34211819 TNS3 at 7p12.3 (P = 3.90 × 10−9) and rs1143149 SEPT7 at 7p14.2 (P = 9.75 × 10−9), were significantly associated with survival of NSCLC patients who were long-term former smokers. Both SNPs had significant interaction effects with years of smoking cessation (rs34211819 TNS3 : P interaction = 8.0 × 10−4; rs1143149 SEPT7 : P interaction = 0.003). In addition, in silico function prediction and multi-omics analysis provided evidence that these QTLs were associated with survival. Moreover, comparison analysis found higher genetic similarity between long-term former smokers and never-smokers, compared to short-term former smokers or current smokers. Pathway enrichment analysis indicated a unique pattern among long-term former smokers that was related to immune pathways. This study provides important insights into the genetic architecture associated with long-term former smoking NSCLC.Sipeng ShenYongyue WeiYi LiWeiwei DuanXuesi DongLijuan LinDongfang YouAdonina TardonChu ChenJohn K. FieldRayjean J. HungGeoffrey LiuDakai ZhuChristopher I. AmosLi SuYang ZhaoZhibin HuHongbing ShenRuyang ZhangFeng ChenDavid C. ChristianiNature PortfolioarticleNeoplasms. Tumors. Oncology. Including cancer and carcinogensRC254-282ENnpj Precision Oncology, Vol 5, Iss 1, Pp 1-9 (2021) |
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DOAJ |
| collection |
DOAJ |
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EN |
| topic |
Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282 |
| spellingShingle |
Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282 Sipeng Shen Yongyue Wei Yi Li Weiwei Duan Xuesi Dong Lijuan Lin Dongfang You Adonina Tardon Chu Chen John K. Field Rayjean J. Hung Geoffrey Liu Dakai Zhu Christopher I. Amos Li Su Yang Zhao Zhibin Hu Hongbing Shen Ruyang Zhang Feng Chen David C. Christiani A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival |
| description |
Abstract The genetic architecture of non-small cell lung cancer (NSCLC) is relevant to smoking status. However, the genetic contribution of long-term smoking cessation to the prognosis of NSCLC patients remains largely unknown. We conducted a genome-wide association study primarily on the prognosis of 1299 NSCLC patients of long-term former smokers from independent discovery (n = 566) and validation (n = 733) sets, and used in-silico function prediction and multi-omics analysis to identify single nucleotide polymorphisms (SNPs) on prognostics with NSCLC. We further detected SNPs with at least moderate association strength on survival within each group of never, short-term former, long-term former, and current smokers, and compared their genetic similarity at the SNP, gene, expression quantitative trait loci (eQTL), enhancer, and pathway levels. We identified two SNPs, rs34211819 TNS3 at 7p12.3 (P = 3.90 × 10−9) and rs1143149 SEPT7 at 7p14.2 (P = 9.75 × 10−9), were significantly associated with survival of NSCLC patients who were long-term former smokers. Both SNPs had significant interaction effects with years of smoking cessation (rs34211819 TNS3 : P interaction = 8.0 × 10−4; rs1143149 SEPT7 : P interaction = 0.003). In addition, in silico function prediction and multi-omics analysis provided evidence that these QTLs were associated with survival. Moreover, comparison analysis found higher genetic similarity between long-term former smokers and never-smokers, compared to short-term former smokers or current smokers. Pathway enrichment analysis indicated a unique pattern among long-term former smokers that was related to immune pathways. This study provides important insights into the genetic architecture associated with long-term former smoking NSCLC. |
| format |
article |
| author |
Sipeng Shen Yongyue Wei Yi Li Weiwei Duan Xuesi Dong Lijuan Lin Dongfang You Adonina Tardon Chu Chen John K. Field Rayjean J. Hung Geoffrey Liu Dakai Zhu Christopher I. Amos Li Su Yang Zhao Zhibin Hu Hongbing Shen Ruyang Zhang Feng Chen David C. Christiani |
| author_facet |
Sipeng Shen Yongyue Wei Yi Li Weiwei Duan Xuesi Dong Lijuan Lin Dongfang You Adonina Tardon Chu Chen John K. Field Rayjean J. Hung Geoffrey Liu Dakai Zhu Christopher I. Amos Li Su Yang Zhao Zhibin Hu Hongbing Shen Ruyang Zhang Feng Chen David C. Christiani |
| author_sort |
Sipeng Shen |
| title |
A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival |
| title_short |
A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival |
| title_full |
A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival |
| title_fullStr |
A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival |
| title_full_unstemmed |
A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival |
| title_sort |
multi-omics study links tns3 and sept7 to long-term former smoking nsclc survival |
| publisher |
Nature Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/1ca3d9325fa341efb51b71a031edf471 |
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