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Lai F, He L, Lia T, Yang Z, Huang C. Identification and validation of basement membrane-related genes predicting prognosis and immune infiltration associated with bladder cancer. Medicine (Baltimore) 2024; 103:e38858. [PMID: 39029072 PMCID: PMC11398827 DOI: 10.1097/md.0000000000038858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/21/2024] Open
Abstract
Bladder cancer (BC) is fatal during muscle invasion and treatment progress is limited. In this study, we aimed to construct and validate basement membrane (BM)-associated gene prognosis to predict BC progression and tumor immune infiltration correlation. We choreographed BM-related genes in the Cancer Genome Atlas (TCGA) database using COX regression and least absolute shrinkage and selection operator (LASSO) analysis, and the predictive value of BM-related genes was further validated by the GSE32548, GSE129845, and immunohistochemistry staining. All analyses were performed with R-version 4.2.2, and its appropriate packages. Three genes were identified to construct a gene signature to predictive of BC prognosis. We divided the TCGA database into 2 groups, and patients in the high-risk group had worse overall survival (OS) than those in the low-risk group. In GSE32548, we confirmed that patients in the high-risk group had a poorer prognosis compared to those in the low-risk group in terms of OS. Immunohistochemical staining of EPEMP1, GPC2, and ITGA3 showed significantly higher expression at the protein level in BC tissues than in normal tissues. The Spearman analysis showed risk score was positively correlated with B cell naïve, Macrophages M2, and Mast cells resting. stromal score, immune score, and ESTIMATE scores were significantly higher in the high-risk group. drugs sensitivity analysis showed IC50 of Cisplatin, Gemcitabine, and Methotrexate in the high-risk group was significantly higher than that in the low-risk group. We identified 3 prognostic genes from a novel perspective of BM genes as effective risk stratification tools for BC patients.
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Affiliation(s)
- Fie Lai
- Department of Urology Surgery, Chengdu Second People's Hospital, Chengdu, Sichuan, China
| | - Lin He
- Department of Pathology, Chengdu Second People's Hospital, Chengdu, Sichuan, China
| | - Thongher Lia
- Department of Urology Surgery, Chengdu Second People's Hospital, Chengdu, Sichuan, China
| | - Zhen Yang
- Department of Urology Surgery, Chengdu Second People's Hospital, Chengdu, Sichuan, China
| | - Chaoyou Huang
- Department of Urology Surgery, Chengdu Second People's Hospital, Chengdu, Sichuan, China
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2
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Yang L, Tang L, Min Q, Tian H, Li L, Zhao Y, Wu X, Li M, Du F, Chen Y, Li W, Li X, Chen M, Gu L, Sun Y, Xiao Z, Shen J. Emerging role of RNA modification and long noncoding RNA interaction in cancer. Cancer Gene Ther 2024; 31:816-830. [PMID: 38351139 PMCID: PMC11192634 DOI: 10.1038/s41417-024-00734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
RNA modification, especially N6-methyladenosine, 5-methylcytosine, and N7-methylguanosine methylation, participates in the occurrence and progression of cancer through multiple pathways. The function and expression of these epigenetic regulators have gradually become a hot topic in cancer research. Mutation and regulation of noncoding RNA, especially lncRNA, play a major role in cancer. Generally, lncRNAs exert tumor-suppressive or oncogenic functions and its dysregulation can promote tumor occurrence and metastasis. In this review, we summarize N6-methyladenosine, 5-methylcytosine, and N7-methylguanosine modifications in lncRNAs. Furthermore, we discuss the relationship between epigenetic RNA modification and lncRNA interaction and cancer progression in various cancers. Therefore, this review gives a comprehensive understanding of the mechanisms by which RNA modification affects the progression of various cancers by regulating lncRNAs, which may shed new light on cancer research and provide new insights into cancer therapy.
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Affiliation(s)
- Liqiong Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Lu Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Qi Min
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Hua Tian
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Linwei Li
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Wanping Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Xiaobing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Meijuan Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Li Gu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Yuhong Sun
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
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HajiEsmailpoor Z, Fayazi A, Teymouri M, Tabnak P. Role of long non-coding RNA ELFN1-AS1 in carcinogenesis. Discov Oncol 2024; 15:74. [PMID: 38478184 PMCID: PMC10937879 DOI: 10.1007/s12672-024-00929-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
Abstract
As one of the leading causes of death worldwide, cancer significantly burdens patients and the healthcare system. The role of long non-protein coding RNAs (lncRNAs) in carcinogenesis has been extensively studied. The lncRNA ELFN1-AS1 was discovered recently, and subsequent studies have revealed its aberrantly high expression in various cancer tissues. In vitro and in vivo experiments have consistently demonstrated the close association between increased ELFN1-AS1 expression and malignant tumor characteristics, particularly in gastrointestinal malignancies. Functional assays have further revealed the mechanistic role of ELFN1-AS1 as a competitive endogenous RNA for microRNAs, inducing tumor growth, invasive features, and drug resistance. Additionally, the investigation into the clinical implication of ELFN1-AS1 has demonstrated its potential as a diagnostic, therapeutic, and, notably, prognostic marker. This review provides a comprehensive summary of evidence regarding the involvement of ELFN1-AS1 in cancer initiation and development, highlighting its clinical significance.
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Affiliation(s)
| | - Alireza Fayazi
- Department of Metal Engineering, Cellular and Molecular Biology, Islamic Azad University Najafabad Branch, Isfahan, Iran
| | | | - Peyman Tabnak
- Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Gao Y, Ren J, Chen K, Guan G. Construction and validation of a prognostic signature for mucinous colonic adenocarcinoma based on N7-methylguanosine-related long non-coding RNAs. J Gastrointest Oncol 2024; 15:203-219. [PMID: 38482248 PMCID: PMC10932661 DOI: 10.21037/jgo-23-980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/21/2024] [Indexed: 10/05/2024] Open
Abstract
BACKGROUND Mucinous colonic adenocarcinoma remains a challenging disease due to its high propensity for metastasis and recurrence. N7-methylguanosine (m7G) and long non-coding RNA (lncRNA) are closely associated with the occurrence and progression of tumors. However, research on m7G-related lncRNA in mucinous colonic adenocarcinoma is lacking. Therefore, we sought to explore the prognostic impact of m7G-related lncRNAs in mucinous adenocarcinoma (MC) patients. METHODS In this study, Pearson analysis was used to identify m7G-related lncRNAs from transcriptome data in The Cancer Genome Atlas (TCGA). Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression were used to further screen m7G-related lncRNAs and incorporate them into a prognostic signature. Based on the risk model, patients were divided into low- and high-risk groups and randomly assigned to the training set and test sets in a 6:4 ratio. Kaplan-Meier, receiver operating characteristic (ROC) curve, multivariate regression, and nomogram analyses were used to confirm the accuracy of the signature. The CIBERSORT algorithm was used to calculate the degree of immune cell infiltration (ICI). Finally, the correlation of the prognostic signature with tumor mutational burden (TMB) and immunophenotype score (IPS) was evaluated. RESULTS A total of 432 m7G-related lncRNAs were identified by Pearson analysis. Univariate Cox regression, LASSO regression and survival analysis were performed to further select six m7G-related lncRNAs (P<0.05): AC254629.1, LINC01133, LINC01134, MHENCR, SMIM2-AS1, and XACT. Based on the risk model, heat maps, Kaplan-Meier curves, and ROC curves were constructed, and the results showed that there were significant differences in expression levels and survival status between the two risk groups. The area under the ROC curve (AUC) values for 3-, 5-, and 10-year survival in the training set were 0.944, 0.957, and 1.000, respectively. And in the test set were 0.964, 1.000, and 1.000, respectively. Subsequently, univariate and multivariate regression analyses of clinical characteristics and risk score were performed. The results of risk score were [hazard ratio (HR): 6.458, 95% confidence interval (CI): 2.708-15.403, P<0.001; HR: 7.280, 95% CI: 2.500-21.203, P<0.001], respectively. Using the risk score as an independent prognostic factor, the AUC of it over 3, 5, and 10 years was 0.911, 0.955, and 0.961, respectively. Calibration plots for the nomogram show that the model calibration line is very close to the ideal calibration line, indicating good calibration. The level of ICI was significantly different in the different risk groups. Survival analysis showed that, regardless of TMB risk, patients with MC and a high-risk score consistently had a poor overall survival (OS). CONCLUSIONS The m7G-related lncRNA prognostic signature has potential value for the prognosis of mucinous colonic adenocarcinoma.
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Affiliation(s)
- Yuan Gao
- Department of Colorectal Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Colorectal Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jinjin Ren
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Kunqi Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Guoxian Guan
- Department of Colorectal Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Colorectal Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Abdominal Surgery Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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Han M, Huang Q, Li X, Chen X, Zhu H, Pan Y, Zhang B. M7G-related tumor immunity: novel insights of RNA modification and potential therapeutic targets. Int J Biol Sci 2024; 20:1238-1255. [PMID: 38385078 PMCID: PMC10878144 DOI: 10.7150/ijbs.90382] [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: 09/21/2023] [Accepted: 01/09/2024] [Indexed: 02/23/2024] Open
Abstract
RNA modifications play a pivotal role in regulating cellular biology by exerting influence over distribution features and molecular functions at the post-transcriptional level. Among these modifications, N7-methylguanosine (m7G) stands out as one of the most prevalent. Over recent years, significant attention has been directed towards understanding the implications of m7G modification. This modification is present in diverse RNA molecules, including transfer RNAs, messenger RNAs, ribosomal RNAs, and other noncoding RNAs. Its regulation occurs through a series of specific methyltransferases and m7G-binding proteins. Notably, m7G modification has been implicated in various diseases, prominently across multiple cancer types. Earlier studies have elucidated the significance of m7G modification in the context of immune biology regulation within the tumor microenvironment. This comprehensive review culminates in a synthesis of findings related to the modulation of immune cells infiltration, encompassing T cells, B cells, and various innate immune cells, all orchestrated by m7G modification. Furthermore, the interplay between m7G modification and its regulatory proteins can profoundly affect the efficacy of diverse adjuvant therapeutics, thereby potentially serving as a pivotal biomarker and therapeutic target for combinatory interventions in diverse cancer types.
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Affiliation(s)
- Mengzhen Han
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Qibo Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Xinxin Li
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - He Zhu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Yonglong Pan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
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Nylund P, Garrido-Zabala B, Kalushkova A, Wiklund HJ. The complex nature of lncRNA-mediated chromatin dynamics in multiple myeloma. Front Oncol 2023; 13:1303677. [PMID: 38148842 PMCID: PMC10750364 DOI: 10.3389/fonc.2023.1303677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Extensive genome-wide sequencing efforts have unveiled the intricate regulatory potential of long non-protein coding RNAs (lncRNAs) within the domain of haematological malignancies. Notably, lncRNAs have been found to directly modulate chromatin architecture, thereby impacting gene expression and disease progression by interacting with DNA, RNA, and proteins in a tissue- or condition-specific manner. Furthermore, recent studies have highlighted the intricate epigenetic control of lncRNAs in cancer. Consequently, this provides a rationale to explore the possibility of therapeutically targeting lncRNAs themselves or the epigenetic mechanisms that govern their activity. Within the scope of this review, we will assess the current state of knowledge regarding the epigenetic regulation of lncRNAs and how, in turn, lncRNAs contribute to chromatin remodelling in the context of multiple myeloma.
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Affiliation(s)
| | | | | | - Helena Jernberg Wiklund
- Science for Life Laboratory, Department of Immunology, Genetic and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Yang L, Yuan L. Identification of novel N7-methylguanine-related gene signatures associated with ulcerative colitis and the association with biological therapy. Inflamm Res 2023; 72:2169-2180. [PMID: 37889323 DOI: 10.1007/s00011-023-01806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 07/23/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
OBJECTIVE Ulcerative colitis (UC) is an inflammatory disease characterized by recurrent episodes of chronic intestinal inflammation. It is closely associated with immune dysregulation in the intestines. However, the mechanisms underlying the role of immune-related N7-methylguanosine (m7G) internal modification in UC remain unclear. METHODS We conducted a screening of differentially expressed genes (DEGs) associated with m7G and performed immune infiltration analysis. We then investigated the correlation between m7G-related DEGs and immune cells or pathways. To further explore the functional implications, we conducted functional enrichment analysis to identify gene modules that strongly correlated with hub gene expression. In addition, we constructed a miRNA regulatory network for the hub genes in UC. Furthermore, we examined the association between hub genes and disease remission in UC patients undergoing biologic therapy. RESULTS We obtained 13 m7G-related DEGs and conducted an in-depth analysis of immune infiltration. Among them, we identified five hub genes (NUDT7, NUDT12, POLR2H, QKI, and PRKCB) that showed diagnostic potential for UC. Through WGCNA and KEGG analysis, we found that gene modules strongly correlated with m7G hub gene expression were enriched in inflammation-related pathways. Furthermore, Kaplan-Meier survival analysis revealed a significant association between changes in hub gene expression levels and disease remission in UC patients undergoing biologic therapy. CONCLUSION The findings of this study demonstrate that five m7G-related DEGs, including the m7G-modified recognition protein QKI, play a key role in the occurrence and progression of UC intestinal inflammation, which is closely related to intestinal immunity. These results provide valuable insights into the mechanisms of m7G modification in UC development and offer new perspectives for exploring novel therapeutic targets for UC.
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Affiliation(s)
- Lichao Yang
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Lianwen Yuan
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
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Sun D, Song N, Li M, Chen X, Zhang X, Yu Y, Ying J, Xu M, Zheng W, Han C, Ji H, Jiang Y. Comprehensive analysis of circRNAs for N7-methylguanosine methylation modification in human oral squamous cell carcinoma. FASEB Bioadv 2023; 5:305-320. [PMID: 37554544 PMCID: PMC10405248 DOI: 10.1096/fba.2023-00036] [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: 03/29/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 08/10/2023] Open
Abstract
N7-methylguanosine (m7G) modification is closely related to the occurrence of tumors. However, the m7G modification of circRNAs in oral squamous cell carcinoma (OSCC) remains to be investigated. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to measure the methylation levels of m7G and identify m7G sites in circRNAs in human OSCC and normal tissues. The host genes of differentially methylated and differentially expressed circRNAs were analyzed by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and circRNA-miRNA-mRNA networks were predicted using the miRanda and miRDB databases. The analysis identified 2348 m7G peaks in 624 circRNAs in OSCC tissues. In addition, the source of m7G-methylated circRNAs in OSCC was mainly the sense overlap region compared with normal tissues. The most conserved m7G motif in OSCC tissues was CCUGU, whereas the most conserved motif in normal tissues was RCCUG (R = G/A). Importantly, GO enrichment and KEGG pathway analysis showed that the host genes of differentially methylated and differentially expressed circRNAs were involved in many cellular biological functions. Furthermore, the significantly differentially expressed circRNAs were analyzed to predict the circRNA-miRNA-mRNA networks. This study revealed the whole profile of circRNAs of differential m7G methylation in OSCC and suggests that m7G-modified circRNAs may impact the development of OSCC.
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Affiliation(s)
- Dongyuan Sun
- School of StomatologyWeifang Medical UniversityWeifangChina
- Department of StomatologyAffiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Ning Song
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Minmin Li
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Xi Chen
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Xinyue Zhang
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Yang Yu
- School of StomatologyWeifang Medical UniversityWeifangChina
- Department of StomatologyAffiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Jicheng Ying
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Mengqi Xu
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Wentian Zheng
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Chengbing Han
- Department of StomatologyFirst Affiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Honghai Ji
- School of StomatologyWeifang Medical UniversityWeifangChina
- Department of StomatologyAffiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Yingying Jiang
- School of StomatologyWeifang Medical UniversityWeifangChina
- Department of StomatologyAffiliated Hospital of Weifang Medical UniversityWeifangChina
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Lu J, Yang P, Yu L, Xie N, Wu Y, Li B. Identification of m7G-Related LncRNA Signature for Predicting Prognosis and Evaluating Tumor Immune Infiltration in Pancreatic Adenocarcinoma. Diagnostics (Basel) 2023; 13:diagnostics13101697. [PMID: 37238181 DOI: 10.3390/diagnostics13101697] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
N7-Methylguanosine (m7G) modification holds significant importance in regulating posttranscriptional gene expression in epigenetics. Long non-coding RNAs (lncRNAs) have been demonstrated to play a crucial role in cancer progression. m7G-related lncRNA may be involved in the progression of pancreatic cancer (PC), although the underlying mechanism of regulation remains obscure. We obtained RNA sequence transcriptome data and relevant clinical information from the TCGA and GTEx databases. Univariate and multivariate Cox proportional risk analyses were performed to build a twelve-m7G-associated lncRNA risk model with prognostic value. The model was verified using receiver operating characteristic curve analysis and Kaplan-Meier analysis. The expression level of m7G-related lncRNAs in vitro was validated. Knockdown of SNHG8 increased the proliferation and migration of PC cells. Differentially expressed genes between high- and low-risk groups were identified for gene set enrichment analysis, immune infiltration, and potential drug exploration. We conducted an m7G-related lncRNA predictive risk model for PC patients. The model had independent prognostic significance and offered an exact survival prediction. The research provided us with better knowledge of the regulation of tumor-infiltrating lymphocytes in PC. The m7G-related lncRNA risk model may serve as a precise prognostic tool and indicate prospective therapeutic targets for PC patients.
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Affiliation(s)
- Jiawei Lu
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Pusheng Yang
- Department of Obstetrics and Gynecology, Shanghai Key Laboratory of Gynecology Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lanting Yu
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Ni Xie
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Ying Wu
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Baiwen Li
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
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A Prognostic Cuproptosis-Related LncRNA Signature for Colon Adenocarcinoma. JOURNAL OF ONCOLOGY 2023; 2023:5925935. [PMID: 36844874 PMCID: PMC9957631 DOI: 10.1155/2023/5925935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/13/2022] [Accepted: 11/24/2022] [Indexed: 02/19/2023]
Abstract
Background Cuproptosis, a recently discovered form of cell death, is caused by copper levels exceeding homeostasis thresholds. Although Cu has a potential role in colon adenocarcinoma (COAD), its role in the development of COAD remains unclear. Methods In this study, 426 patients with COAD were extracted from the Cancer Genome Atlas (TCGA) database. The Pearson correlation algorithm was used to identify cuproptosis-related lncRNAs. Using the univariate Cox regression analysis, the least absolute shrinkage and selection operator (LASSO) was used to select cuproptosis-related lncRNAs associated with COAD overall survival (OS). A risk model was established based on the multivariate Cox regression analysis. A nomogram model was used to evaluate the prognostic signature based on the risk model. Finally, mutational burden and sensitivity analyses of chemotherapy drugs were performed for COAD patients in the low- and high-risk groups. Result Ten cuproptosis-related lncRNAs were identified and a novel risk model was constructed. A signature based on ten cuproptosis-related lncRNAs was an independent prognostic predictor for COAD. Mutational burden analysis suggested that patients with high-risk scores had higher mutation frequency and shorter survival. Conclusion Constructing a risk model based on the ten cuproptosis-related lncRNAs could accurately predict the prognosis of COAD patients, providing a fresh perspective for future research on COAD.
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Guo P, Wang P, Liu L, Wang P, Qu Z, Yu Z, Liu N. A novel
N7
‐methylguanosine‐related long noncoding
RNAs
signature for predicting prognosis and immune microenvironment in gastric cancer patients. PRECISION MEDICAL SCIENCES 2022. [DOI: 10.1002/prm2.12087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Peisen Guo
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Panpan Wang
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
| | - Limin Liu
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Peixi Wang
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Zhi Qu
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Zengli Yu
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
| | - Nan Liu
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
- Institute of Environment and Health, South China Hospital, Health Science Center Shenzhen University Shenzhen People's Republic of China
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Lai G, Zhong X, Liu H, Deng J, Li K, Xie B. A Novel m7G-Related Genes-Based Signature with Prognostic Value and Predictive Ability to Select Patients Responsive to Personalized Treatment Strategies in Bladder Cancer. Cancers (Basel) 2022; 14:5346. [PMID: 36358764 PMCID: PMC9656096 DOI: 10.3390/cancers14215346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 09/08/2023] Open
Abstract
Although N7-methylguanosine (m7G) modification serves as a tumor promoter in bladder cancer (BLCA), the comprehensive role of m7G-related characterization in BLCA remains unclear. In this study, we systematically evaluated the m7G-related clusters of 760 BLCA patients through consensus unsupervised clustering analysis. Next, we investigated the underlying m7G-related genes among these m7G-related clusters. Univariate Cox and LASSO regressions were used for screening out prognostic genes and for reducing the dimension, respectively. Finally, we developed a novel m7G-related scoring system via the GSVA algorithm. The correlation between tumor microenvironment, prediction of personalized therapies and this m7G-related signature was gradually revealed. We first identified three m7G-related clusters and 1108 differentially expressed genes relevant to the three clusters. Based on the profile of 1108 genes, we divided BLCA patients into two clusters, which were quantified by our established m7G-related scoring system. Patients with higher m7G-related scores tended to have a better OS and more chances to benefit from immunotherapy. A significantly negative connection between sensitivity to classic chemotherapeutic drugs and m7G-related signature was uncovered. In summary, our data show that m7G-related characterization of BLCA patients can be of value for prognostic stratification and for patient-oriented therapeutic options, designing personalized treatment strategies in the preclinical setting.
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Affiliation(s)
| | - Xiaoni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing 400016, China
| | | | | | | | - Biao Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing 400016, China
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