Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS
The use of metabolome genome-wide association studies (mGWAS) has been shown to be effective in identifying functional genes in complex diseases. While mGWAS has been applied to biomedical and pharmaceutical studies, its potential in predicting gastric cancer prognosis has yet to be explored. This s...
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MDPI AG
2023-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/20/15259 |
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| author | Yuling Zhang Yanping Lyu Liangping Chen Kang Cao Jingwen Chen Chenzhou He Xuejie Lyu Yu Jiang Jianjun Xiang Baoying Liu Chuancheng Wu |
| author_facet | Yuling Zhang Yanping Lyu Liangping Chen Kang Cao Jingwen Chen Chenzhou He Xuejie Lyu Yu Jiang Jianjun Xiang Baoying Liu Chuancheng Wu |
| author_sort | Yuling Zhang |
| collection | DOAJ |
| description | The use of metabolome genome-wide association studies (mGWAS) has been shown to be effective in identifying functional genes in complex diseases. While mGWAS has been applied to biomedical and pharmaceutical studies, its potential in predicting gastric cancer prognosis has yet to be explored. This study aims to address this gap and provide insights into the genetic basis of GC survival, as well as identify vital regulatory pathways in GC cell progression. Genome-wide association analysis of plasma metabolites related to gastric cancer prognosis was performed based on the Generalized Linear Model (GLM). We used a log-rank test, LASSO regression, multivariate Cox regression, GO enrichment analysis, and the Cytoscape software to visualize the complex regulatory network of genes and metabolites and explored in-depth genetic variation in gastric cancer prognosis based on mGWAS. We found 32 genetic variation loci significantly associated with GC survival-related metabolites, corresponding to seven genes, <i>VENTX</i>, <i>PCDH 7</i>, <i>JAKMIP1</i>, <i>MIR202HG</i>, <i>MIR378D1</i>, <i>LINC02472</i>, and <i>LINC02310</i>. Furthermore, this study identified 722 Single nucleotide polymorphism (SNP) sites, suggesting an association with GC prognosis-related metabolites, corresponding to 206 genes. These 206 possible functional genes for gastric cancer prognosis were mainly involved in cellular signaling molecules related to cellular components, which are mainly involved in the growth and development of the body and neurological regulatory functions related to the body. The expression of 23 of these genes was shown to be associated with survival outcome in gastric cancer patients in The Cancer Genome Atlas (TCGA) database. Based on the genome-wide association analysis of prognosis-related metabolites in gastric cancer, we suggest that gastric cancer survival-related genes may influence the proliferation and infiltration of gastric cancer cells, which provides a new idea to resolve the complex regulatory network of gastric cancer prognosis. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T21:11:47Z |
| publishDate | 2023-10-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-69bca718046a498e9b548fa681c193e82023-11-19T16:44:04ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-10-0124201525910.3390/ijms242015259Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWASYuling Zhang0Yanping Lyu1Liangping Chen2Kang Cao3Jingwen Chen4Chenzhou He5Xuejie Lyu6Yu Jiang7Jianjun Xiang8Baoying Liu9Chuancheng Wu10Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaDepartment of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, ChinaThe use of metabolome genome-wide association studies (mGWAS) has been shown to be effective in identifying functional genes in complex diseases. While mGWAS has been applied to biomedical and pharmaceutical studies, its potential in predicting gastric cancer prognosis has yet to be explored. This study aims to address this gap and provide insights into the genetic basis of GC survival, as well as identify vital regulatory pathways in GC cell progression. Genome-wide association analysis of plasma metabolites related to gastric cancer prognosis was performed based on the Generalized Linear Model (GLM). We used a log-rank test, LASSO regression, multivariate Cox regression, GO enrichment analysis, and the Cytoscape software to visualize the complex regulatory network of genes and metabolites and explored in-depth genetic variation in gastric cancer prognosis based on mGWAS. We found 32 genetic variation loci significantly associated with GC survival-related metabolites, corresponding to seven genes, <i>VENTX</i>, <i>PCDH 7</i>, <i>JAKMIP1</i>, <i>MIR202HG</i>, <i>MIR378D1</i>, <i>LINC02472</i>, and <i>LINC02310</i>. Furthermore, this study identified 722 Single nucleotide polymorphism (SNP) sites, suggesting an association with GC prognosis-related metabolites, corresponding to 206 genes. These 206 possible functional genes for gastric cancer prognosis were mainly involved in cellular signaling molecules related to cellular components, which are mainly involved in the growth and development of the body and neurological regulatory functions related to the body. The expression of 23 of these genes was shown to be associated with survival outcome in gastric cancer patients in The Cancer Genome Atlas (TCGA) database. Based on the genome-wide association analysis of prognosis-related metabolites in gastric cancer, we suggest that gastric cancer survival-related genes may influence the proliferation and infiltration of gastric cancer cells, which provides a new idea to resolve the complex regulatory network of gastric cancer prognosis.https://www.mdpi.com/1422-0067/24/20/15259gastric cancerplasma metabolitesmetabolome genome-wide association studiesprognosis |
| spellingShingle | Yuling Zhang Yanping Lyu Liangping Chen Kang Cao Jingwen Chen Chenzhou He Xuejie Lyu Yu Jiang Jianjun Xiang Baoying Liu Chuancheng Wu Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS International Journal of Molecular Sciences gastric cancer plasma metabolites metabolome genome-wide association studies prognosis |
| title | Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS |
| title_full | Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS |
| title_fullStr | Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS |
| title_full_unstemmed | Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS |
| title_short | Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS |
| title_sort | exploring the prognosis related genetic variation in gastric cancer based on mgwas |
| topic | gastric cancer plasma metabolites metabolome genome-wide association studies prognosis |
| url | https://www.mdpi.com/1422-0067/24/20/15259 |
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