A novel RNA modification prognostic signature for predicting the characteristics of the tumor microenvironment in gastric cancer
Gastric cancer (GC) is one of the most common neoplastic malignancies, which permutes a fourth of cancer-related mortality globally. RNA modification plays a significant role in tumorigenesis, the underlying molecular mechanism of how different RNA modifications directly affect the tumor microenviro...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-02-01
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| Series: | Frontiers in Oncology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2023.905139/full |
| _version_ | 1828014353458135040 |
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| author | Qiangan Jing Qiangan Jing Hongfeng Yao Huanjuan Li Chen Yuan Jiayu Hu Ping Zhang Yunyi Wu Yi Zhou Xueying Ren Chen Yang Guojie Lei Jing Du Xia Ke Jun Xia Xiangmin Tong Xiangmin Tong |
| author_facet | Qiangan Jing Qiangan Jing Hongfeng Yao Huanjuan Li Chen Yuan Jiayu Hu Ping Zhang Yunyi Wu Yi Zhou Xueying Ren Chen Yang Guojie Lei Jing Du Xia Ke Jun Xia Xiangmin Tong Xiangmin Tong |
| author_sort | Qiangan Jing |
| collection | DOAJ |
| description | Gastric cancer (GC) is one of the most common neoplastic malignancies, which permutes a fourth of cancer-related mortality globally. RNA modification plays a significant role in tumorigenesis, the underlying molecular mechanism of how different RNA modifications directly affect the tumor microenvironment (TME) in GC is unclear. Here, we profiled the genetic and transcriptional alterations of RNA modification genes (RMGs) in GC samples from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) cohorts. Through the unsupervised clustering algorithm, we identified three distinct RNA modification clusters and found that they participate in different biological pathways and starkly correlate with the clinicopathological characteristics, immune cell infiltration, and prognosis of GC patients. Subsequently, univariate Cox regression analysis unveiled 298 of 684 subtype-related differentially expressed genes (DEGs) are tightly interwoven to prognosis. In addition, we conducted the principal component analysis to develop the RM_Score system, which was used to quantify and predict the prognostic value of RNA modification in GC. Our analysis indicated that patients with high RM_Score were characterized by higher tumor mutational burden, mutation frequency, and microsatellite instability which were more susceptible to immunotherapy and had a favorable prognosis. Altogether, our study uncovered RNA modification signatures that may have a potential role in the TME and prediction of clinicopathological characteristics. Identification of these RNA modifications may provide a new understanding of immunotherapy strategies for gastric cancer. |
| first_indexed | 2024-04-10T10:00:52Z |
| format | Article |
| id | doaj.art-235c6ee3c0554694b6f99ca8c5cc23ee |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-04-10T10:00:52Z |
| publishDate | 2023-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj.art-235c6ee3c0554694b6f99ca8c5cc23ee2023-02-16T08:14:09ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2023-02-011310.3389/fonc.2023.905139905139A novel RNA modification prognostic signature for predicting the characteristics of the tumor microenvironment in gastric cancerQiangan Jing0Qiangan Jing1Hongfeng Yao2Huanjuan Li3Chen Yuan4Jiayu Hu5Ping Zhang6Yunyi Wu7Yi Zhou8Xueying Ren9Chen Yang10Guojie Lei11Jing Du12Xia Ke13Jun Xia14Xiangmin Tong15Xiangmin Tong16College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaDepartment of Clinical Laboratory, Zhuji People’s Hospital of Zhejiang Province, Zhuji, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaCollege of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaCollege of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, ChinaLaboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, ChinaGastric cancer (GC) is one of the most common neoplastic malignancies, which permutes a fourth of cancer-related mortality globally. RNA modification plays a significant role in tumorigenesis, the underlying molecular mechanism of how different RNA modifications directly affect the tumor microenvironment (TME) in GC is unclear. Here, we profiled the genetic and transcriptional alterations of RNA modification genes (RMGs) in GC samples from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) cohorts. Through the unsupervised clustering algorithm, we identified three distinct RNA modification clusters and found that they participate in different biological pathways and starkly correlate with the clinicopathological characteristics, immune cell infiltration, and prognosis of GC patients. Subsequently, univariate Cox regression analysis unveiled 298 of 684 subtype-related differentially expressed genes (DEGs) are tightly interwoven to prognosis. In addition, we conducted the principal component analysis to develop the RM_Score system, which was used to quantify and predict the prognostic value of RNA modification in GC. Our analysis indicated that patients with high RM_Score were characterized by higher tumor mutational burden, mutation frequency, and microsatellite instability which were more susceptible to immunotherapy and had a favorable prognosis. Altogether, our study uncovered RNA modification signatures that may have a potential role in the TME and prediction of clinicopathological characteristics. Identification of these RNA modifications may provide a new understanding of immunotherapy strategies for gastric cancer.https://www.frontiersin.org/articles/10.3389/fonc.2023.905139/fullgastric cancerRNA modificationtumor microenvironmenttumor mutational burdenimmunotherapy |
| spellingShingle | Qiangan Jing Qiangan Jing Hongfeng Yao Huanjuan Li Chen Yuan Jiayu Hu Ping Zhang Yunyi Wu Yi Zhou Xueying Ren Chen Yang Guojie Lei Jing Du Xia Ke Jun Xia Xiangmin Tong Xiangmin Tong A novel RNA modification prognostic signature for predicting the characteristics of the tumor microenvironment in gastric cancer Frontiers in Oncology gastric cancer RNA modification tumor microenvironment tumor mutational burden immunotherapy |
| title | A novel RNA modification prognostic signature for predicting the characteristics of the tumor microenvironment in gastric cancer |
| title_full | A novel RNA modification prognostic signature for predicting the characteristics of the tumor microenvironment in gastric cancer |
| title_fullStr | A novel RNA modification prognostic signature for predicting the characteristics of the tumor microenvironment in gastric cancer |
| title_full_unstemmed | A novel RNA modification prognostic signature for predicting the characteristics of the tumor microenvironment in gastric cancer |
| title_short | A novel RNA modification prognostic signature for predicting the characteristics of the tumor microenvironment in gastric cancer |
| title_sort | novel rna modification prognostic signature for predicting the characteristics of the tumor microenvironment in gastric cancer |
| topic | gastric cancer RNA modification tumor microenvironment tumor mutational burden immunotherapy |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2023.905139/full |
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