Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer
Abstract In recent years, molecular and genetic research hotspots of gastric cancer have been investigated, including microRNAs, long noncoding RNAs (lncRNAs) and messenger RNA (mRNAs). The study on the role of lncRNAs may help to develop personalized treatment and identify potential prognostic biom...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-09-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-41444-3 |
| _version_ | 1797559638636363776 |
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| author | Jun Xu Shengnan Hu Qiuli Chen Lilu Shu Peter Wang Jianjiang Wang |
| author_facet | Jun Xu Shengnan Hu Qiuli Chen Lilu Shu Peter Wang Jianjiang Wang |
| author_sort | Jun Xu |
| collection | DOAJ |
| description | Abstract In recent years, molecular and genetic research hotspots of gastric cancer have been investigated, including microRNAs, long noncoding RNAs (lncRNAs) and messenger RNA (mRNAs). The study on the role of lncRNAs may help to develop personalized treatment and identify potential prognostic biomarkers in gastric cancer. The RNA-seq and miRNA-seq data of gastric cancer were downloaded from the TCGA database. Differential analysis of RNA expression between gastric cancer samples and normal samples was performed using the edgeR package. The ceRNA regulatory network was visualized using Cytoscape. KEGG pathway analysis of mRNAs in the ceRNA network was performed using the clusterProfiler package. CIBERSORT was used to distinguish 22 immune cell types and the prognosis-related genes and immune cells were determined using Kaplan-Meier and Cox proportional hazard analyses. To estimate these nomograms, we used receiver operating characteristic and calibration curve studies. The ceRNA regulation network of gastric cancer was built in this study, and the genes in the network were analyzed for prognosis. A total of 980 lncRNAs were differentially expressed, of which 774 were upregulated and 206 were downregulated. A survival study identified 15 genes associated with gastric cancer prognosis, including VCAN-AS1, SERPINE1, AL139002.1, LINC00326, AC018781.1, C15orf54, hsa-miR-145. Monocytes and Neutrophils were associated with the survival rate of gastric cancer. Our research uncovers new ceRNA network for the detection, treatment, and monitoring of gastric cancer. |
| first_indexed | 2024-03-10T17:49:06Z |
| format | Article |
| id | doaj.art-af2ef5b924e0496dbdd0856a49abfed8 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T17:49:06Z |
| publishDate | 2023-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-af2ef5b924e0496dbdd0856a49abfed82023-11-20T09:26:36ZengNature PortfolioScientific Reports2045-23222023-09-0113111610.1038/s41598-023-41444-3Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancerJun Xu0Shengnan Hu1Qiuli Chen2Lilu Shu3Peter Wang4Jianjiang Wang5First People’s Hospital of Hangzhou Lin’an District, Affiliated Lin’an People’s Hospital, Hangzhou Medical CollegeFirst People’s Hospital of Hangzhou Lin’an District, Affiliated Lin’an People’s Hospital, Hangzhou Medical CollegeDepartment of Research and Development, Zhejiang Zhongwei Medical Research CenterDepartment of Research and Development, Zhejiang Zhongwei Medical Research CenterDepartment of Research and Development, Zhejiang Zhongwei Medical Research CenterFirst People’s Hospital of Hangzhou Lin’an District, Affiliated Lin’an People’s Hospital, Hangzhou Medical CollegeAbstract In recent years, molecular and genetic research hotspots of gastric cancer have been investigated, including microRNAs, long noncoding RNAs (lncRNAs) and messenger RNA (mRNAs). The study on the role of lncRNAs may help to develop personalized treatment and identify potential prognostic biomarkers in gastric cancer. The RNA-seq and miRNA-seq data of gastric cancer were downloaded from the TCGA database. Differential analysis of RNA expression between gastric cancer samples and normal samples was performed using the edgeR package. The ceRNA regulatory network was visualized using Cytoscape. KEGG pathway analysis of mRNAs in the ceRNA network was performed using the clusterProfiler package. CIBERSORT was used to distinguish 22 immune cell types and the prognosis-related genes and immune cells were determined using Kaplan-Meier and Cox proportional hazard analyses. To estimate these nomograms, we used receiver operating characteristic and calibration curve studies. The ceRNA regulation network of gastric cancer was built in this study, and the genes in the network were analyzed for prognosis. A total of 980 lncRNAs were differentially expressed, of which 774 were upregulated and 206 were downregulated. A survival study identified 15 genes associated with gastric cancer prognosis, including VCAN-AS1, SERPINE1, AL139002.1, LINC00326, AC018781.1, C15orf54, hsa-miR-145. Monocytes and Neutrophils were associated with the survival rate of gastric cancer. Our research uncovers new ceRNA network for the detection, treatment, and monitoring of gastric cancer.https://doi.org/10.1038/s41598-023-41444-3 |
| spellingShingle | Jun Xu Shengnan Hu Qiuli Chen Lilu Shu Peter Wang Jianjiang Wang Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer Scientific Reports |
| title | Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer |
| title_full | Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer |
| title_fullStr | Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer |
| title_full_unstemmed | Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer |
| title_short | Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer |
| title_sort | integrated bioinformatics analysis of noncoding rnas with tumor immune microenvironment in gastric cancer |
| url | https://doi.org/10.1038/s41598-023-41444-3 |
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