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He X, Chen X, Yang C, Wang W, Sun H, Wang J, Fu J, Dong H. Prognostic value of RNA methylation-related genes in gastric adenocarcinoma based on bioinformatics. PeerJ 2024; 12:e16951. [PMID: 38436027 PMCID: PMC10909369 DOI: 10.7717/peerj.16951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024] Open
Abstract
Background Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa and has a poor prognosis. Stomach adenocarcinoma (STAD) covers 95% of total gastric cancer. This study aimed to identify the prognostic value of RNA methylation-related genes in gastric cancer. Methods In this study, The Cancer Genome Atlas (TCGA)-STAD and GSE84426 cohorts were downloaded from public databases. Patients were classified by consistent cluster analysis based on prognosis-related differentially expressed RNA methylation genes Prognostic genes were obtained by differential expression, univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. The prognostic model was established and validated in the training set, test set and validation set respectively. Independent prognostic analysis was implemented. Finally, the expression of prognostic genes was affirmed by reverse transcription quantitative PCR (RT-qPCR). Results In total, four prognostic genes (ACTA2, SAPCD2, PDK4 and APOD) related to RNA methylation were identified and enrolled into the risk signature. The STAD patients were divided into high- and low-risk groups based on the medium value of the risk score, and patients in the high-risk group had a poor prognosis. In addition, the RNA methylation-relevant risk signature was validated in the test and validation sets, and was authenticated as a reliable independent prognostic predictor. The nomogram was constructed based on the independent predictors to predict the 1/3/5-year survival probability of STAD patients. The gene set enrichment analysis (GSEA) result suggested that the poor prognosis in the high-risk subgroup may be related to immune-related pathways. Finally, the experimental results indicated that the expression trends of RNA methylation-relevant prognostic genes in gastric cancer cells were in agreement with the result of bioinformatics. Conclusion Our study established a novel RNA methylation-related risk signature for STAD, which was of considerable significance for improving prognosis of STAD patients and offering theoretical support for clinical therapy.
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Affiliation(s)
- Xionghui He
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Xiang Chen
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Changcheng Yang
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Wei Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Hening Sun
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Junjie Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Jincheng Fu
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Huaying Dong
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
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Liu T, Tang W, Chen Y, Liu Y, Xu D, Jiang Y, Zhou S, Qin X, Ren L, Chang W, Xu J. The m6A RNA Modification Quantity and the Prognostic Effect of Reader YTHDC2 in Colorectal Cancer. Clin Med Insights Oncol 2022; 16:11795549221104441. [PMID: 35898390 PMCID: PMC9310211 DOI: 10.1177/11795549221104441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/15/2022] [Indexed: 11/17/2022] Open
Abstract
Background: N6-methyladenosine (m6A) modification plays crucial roles in cancers. However, its alteration in colorectal cancer (CRC) is still poorly described. The purpose of this study is to explore the change of m6A modification and the function of m6A binding protein YTHDC2 in CRC. Methods: The global level of m6A modification was detected by mass spectrometry and dot blotting assay. The expression of YTHDC2 was investigated using The Cancer Genome Atlas and using real-time polymerase chain reaction (RT-qPCR), western blotting, and immunohistochemistry based on CRC tissues. Kaplan–Meier analysis and Cox proportional hazards regression were performed to analyze the prognostic value of YTHDC2. RNA immunoprecipitation (RIP)-seq and m6A immunoprecipitation (MeRIP)-seq were used to explore the direct targets of YTHDC2. Gene oncology (GO) and Gene Set Enrichment Analysis (GSEA) were used to explore the pathways that could be influenced by YTHDC2. Results: No significant difference was observed in the global level of m6A modification on total RNA or mRNA between CRC and adjacent nontumor tissues. We further found a significant decreasing of YTHDC2 in CRC tissues. Kaplan–Meier analysis indicated that lower expression of YTHDC2 was related to the worse disease-free survival and overall survival. In addition, lower expression of YTHDC2 was an independent worse prognostic factor in univariate and multivariate Cox regression analysis. Using YTHDC2-RIP-seq and MeRIP-seq, we identified that YTHDC2 could participate in several important biological signal pathways. Conclusions: In summary, this study suggested that the global level of m6A did not change in CRC and identified that lower YTHDC2 as a prognostic marker for worse survival of CRC.
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Affiliation(s)
- Tianyu Liu
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wentao Tang
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
| | - Yijiao Chen
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu Liu
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Donghao Xu
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yudong Jiang
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shizhao Zhou
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaorui Qin
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Ren
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
| | - Wenju Chang
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China.,General Surgery Department, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianmin Xu
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
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Chai XK, Qi W, Zou CY, He CX, Su M, Zhao DQ. Potential Prognostic Value of a Seven m6A-Related LncRNAs Signature and the Correlative Immune Infiltration in Colon Adenocarcinoma. Front Genet 2022; 12:774010. [PMID: 35003214 PMCID: PMC8727540 DOI: 10.3389/fgene.2021.774010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) and their N6-methyladenosine (m6A) modifications play an essential role in tumorigenesis and cancer progression. This study was designed to explore the value of m6A-related lncRNAs in prognosis and therapeutic applications of immune infiltration of colon adenocarcinoma (COAD). We downloaded the COAD gene expression and clinical data from The Cancer Genome Atlas project. By co-expression analysis, Lasso Cox regression analysis, and univariate and multivariate Cox regression, we constructed an independent prognostic signature of seven m6A-related lncRNAs. The prognostic lncRNAs were divided into two clusters by consistent clustering analysis, as well as into two groups of low–high risk based on the signature. Then we identified the relationship between the different groups with clinical features and immune cell infiltration. Cluster 2 had a higher risk score with a lower survival rate. The risk score was higher in groups with advanced clinical features, such as stage III–IV, N1-3, and M1. The expression of AC156455.1 was increased in tumor tissues and cluster 2, and the lncRNA ZEB1−AS1 was notably higher in the high-risk group. Five types of immune cells showed differences in two clusters, and most were upregulated in type 2. The expression of memory B cells was positively correlated with the risk score. The prognostic model was verified by the Gene Expression Omnibus (GEO) dataset. Besides, we found that the expression of these seven lncRNAs in tumor tissues was significantly higher than that in normal tissues, which verified the feasibility of the model. Thus, the signature of seven m6A-related lncRNAs can independently predict the prognosis of COAD. This signature is also closely associated with immune cell infiltration, and new therapeutic targets can be explored from this field.
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Affiliation(s)
- Xiu-Kun Chai
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wei Qi
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chun-Yan Zou
- Department of Gastroenterology, Qinhuagdao First Hospital, Qinhuangdao, China
| | - Chen-Xi He
- Department of Gastroenterology, Xingtai City People's Hospital, Xingtai, China
| | - Miao Su
- Department of Gastroenterology, Harrison International Peace Hospital, Hengshui, China
| | - Dong-Qiang Zhao
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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Zhang Y, Chen L, Wu X, Sun Z, Wang F, Wang B, Dong P. The RNA N6-Methyladenosine Demethylase FTO Promotes Head and Neck Squamous Cell Carcinoma Proliferation and Migration by Increasing CTNNB1. Int J Gen Med 2021; 14:8785-8795. [PMID: 34853532 PMCID: PMC8627861 DOI: 10.2147/ijgm.s339095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022] Open
Abstract
Objective In this study, we aimed to investigate the role of RNA N6-methyladenosine demethylase fat mass and obesity-associated protein (FTO) in head and neck squamous cell carcinoma (HNSCC). Methods Clinical data downloaded from The Cancer Genome Atlas (TCGA) database were used to analyze the relationship between mRNA levels of FTO, METTL3, METTL14, and ALKBH5, and the overall survival in cancer and para-cancer datasets. FTO expression in tumor and normal tissues was compared using immunohistochemistry, and its relationship with overall survival was analyzed based on the Kaplan–Meier method. The FaDu cell line with high FTO levels was chosen from five HNSCC cell lines for further experiments. FTO was verified as an oncogene in HNSCC by in vitro loss-of-function and overexpression studies, cell proliferation assay, wound healing assay, and identification of expression changes of epithelial–mesenchymal transition (EMT)-related markers. Catenin beta 1 (CTNNB1) was confirmed as a downstream target gene of FTO with additional methods like the GEPIA online tool, qRT-PCR, Western blotting, and dot blot assay. Results We found that FTO expression was significantly upregulated in HNSCC datasets and tissues. Increased FTO expression indicated a trend towards poor prognosis and was found to promote disease proliferation and migration. Mechanistically, cell proliferation assay, wound healing assay, and identification of expression changes of EMT-related markers demonstrated that FTO could act as an oncogene in HNSCC. FTO expression was significantly correlated with CTNNB1 expression. Moreover, it exerted a tumorigenic effect by increasing CTNNB1 expression in an m6A-dependent manner. Conclusion FTO promotes head and neck squamous cell carcinoma proliferation and migration by increasing CTNNB1 in an m6A-dependent manner.
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Affiliation(s)
- Yu Zhang
- Department of Otolaryngology, Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Lixiao Chen
- Department of Otolaryngology, Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Xiaoliang Wu
- Tailai Bioscience, Shenzhen, People's Republic of China
| | - Zhenfeng Sun
- Department of Otolaryngology, Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Fei Wang
- Department of Otolaryngology, Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Baoxin Wang
- Department of Otolaryngology, Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Pin Dong
- Department of Otolaryngology, Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
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Szyfter K. Genetics and Molecular Biology of Head and Neck Cancer. Biomolecules 2021; 11:biom11091293. [PMID: 34572506 PMCID: PMC8469154 DOI: 10.3390/biom11091293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
Head and neck cancer (HNC) is a multistep process proceeding from single gene mutations generated by carcinogens to the substantial dysregulation of metabolic processes [...].
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Affiliation(s)
- Krzysztof Szyfter
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
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