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Ozato Y, Hara T, Meng S, Sato H, Tatekawa S, Uemura M, Yabumoto T, Uchida S, Ogawa K, Doki Y, Eguchi H, Ishii H. RNA methylation in inflammatory bowel disease. Cancer Sci 2024; 115:723-733. [PMID: 38263895 PMCID: PMC10920996 DOI: 10.1111/cas.16048] [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: 10/17/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 01/25/2024] Open
Abstract
RNA modifications, including the renowned m6A, have recently garnered significant attention. This chemical alteration, present in mRNA, exerts a profound influence on protein expression levels by affecting splicing, nuclear export, stability, translation, and other critical processes. Although the role of RNA methylation in the pathogenesis and progression of IBD and colorectal cancer has been reported, many aspects remain unresolved. In this comprehensive review, we present recent studies on RNA methylation in IBD and colorectal cancer, with a particular focus on m6A and its regulators. We highlight the pivotal role of m6A in the pathogenesis of IBD and colorectal cancer and explore the potential applications of m6A modifications in the diagnosis and treatment of these diseases.
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Grants
- 18KK0251 19K22658 20H00541 21K19526 Ministry of Education, Culture, Sports, Science and Technology
- 22H03146 22K19559 23K19505 16H06279 (PAGS) Ministry of Education, Culture, Sports, Science and Technology
- grant nos. 17cm0106414h0002 JP21lm0203007 Ministry of Education, Culture, Sports, Science and Technology
- 2021-48 Mitsubishi Foundation
- Ministry of Education, Culture, Sports, Science and Technology
- Mitsubishi Foundation
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Affiliation(s)
- Yuki Ozato
- Department of Medical Data ScienceCenter of Medical Innovation and Translational Research, Osaka University Graduate School of MedicineSuitaJapan
- Department of Gastrointestinal SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Tomoaki Hara
- Department of Medical Data ScienceCenter of Medical Innovation and Translational Research, Osaka University Graduate School of MedicineSuitaJapan
| | - Sikun Meng
- Department of Medical Data ScienceCenter of Medical Innovation and Translational Research, Osaka University Graduate School of MedicineSuitaJapan
| | - Hiromichi Sato
- Department of Medical Data ScienceCenter of Medical Innovation and Translational Research, Osaka University Graduate School of MedicineSuitaJapan
- Department of Gastrointestinal SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Shotaro Tatekawa
- Department of Radiation OncologyOsaka University Graduate School of MedicineSuitaJapan
| | - Mamoru Uemura
- Department of Gastrointestinal SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | | | - Shizuka Uchida
- Department of Clinical Medicine, Center for RNA MedicineAalborg UniversityCopenhagen SVDenmark
| | - Kazuhiko Ogawa
- Department of Radiation OncologyOsaka University Graduate School of MedicineSuitaJapan
| | - Yuichiro Doki
- Department of Gastrointestinal SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Hidetoshi Eguchi
- Department of Gastrointestinal SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Hideshi Ishii
- Department of Medical Data ScienceCenter of Medical Innovation and Translational Research, Osaka University Graduate School of MedicineSuitaJapan
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2
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Moreta-Moraleda C, Queralt C, Vendrell-Ayats C, Forcales S, Martínez-Balibrea E. Chromatin factors: Ready to roll as biomarkers in metastatic colorectal cancer? Pharmacol Res 2023; 196:106924. [PMID: 37709185 DOI: 10.1016/j.phrs.2023.106924] [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: 04/14/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
Colorectal cancer (CRC) ranks as the third most prevalent cancer globally and stands as the fourth leading cause of cancer-related fatalities in 2020. Survival rates for metastatic disease have slightly improved in recent decades, with clinical trials showing median overall survival of approximately 24-30 months. This progress can be attributed to the integration of chemotherapeutic treatments alongside targeted therapies and immunotherapy. Despite these modest improvements, the primary obstacle to successful treatment for advanced CRC lies in the development of chemoresistance, whether inherent or acquired, which remains the major cause of treatment failure. Epigenetics has emerged as a hallmark of cancer, contributing to master transcription regulation and genome stability maintenance. As a result, epigenetic factors are starting to appear as potential clinical biomarkers for diagnosis, prognosis, and prediction of treatment response in CRC.In recent years, numerous studies have investigated the influence of DNA methylation, histone modifications, and chromatin remodelers on responses to chemotherapeutic treatments. While there is accumulating evidence indicating their significant involvement in various types of cancers, the exact relationship between chromatin landscapes and treatment modulation in CRC remains elusive. This review aims to provide a comprehensive summary of the most pertinent and extensively researched epigenetic-associated mechanisms described between 2015 and 2022 and their potential usefulness as predictive biomarkers in the metastatic disease.
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Affiliation(s)
- Cristina Moreta-Moraleda
- Immunology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, University of Barcelona, c/Feixa Llarga s/n, 08917 L'Hospitalet de Llobregat, Barcelona, Spain; Group of Inflammation, Immunity and Cancer, Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), The Bellvitge Biomedical Research Institute ( IDIBELL), Hospital Duran i Reynals 3a Planta, Av. Gran Via de l'Hospitalet 199, 08908 L'Hospitalet de Llobregat, Spain
| | - Cristina Queralt
- ProCURE Program, Catalan Instiute of Oncology, Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain
| | - Carla Vendrell-Ayats
- ProCURE Program, Catalan Instiute of Oncology, Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain; CARE Program, Germans Trias I Pujol Research Institute (IGTP), Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain
| | - Sonia Forcales
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, University of Barcelona, c/Feixa Llarga s/n, 08917 L'Hospitalet de Llobregat, Barcelona, Spain; Group of Inflammation, Immunity and Cancer, Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), The Bellvitge Biomedical Research Institute ( IDIBELL), Hospital Duran i Reynals 3a Planta, Av. Gran Via de l'Hospitalet 199, 08908 L'Hospitalet de Llobregat, Spain.
| | - Eva Martínez-Balibrea
- ProCURE Program, Catalan Instiute of Oncology, Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain; CARE Program, Germans Trias I Pujol Research Institute (IGTP), Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain.
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3
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Yu L, Wang L, Sun J, Zhou X, Hu Y, Hu L, He Y, Lin C, Chen J, Xu X, Dunlop MG, Theodoratou E, Ding K, Li X. N6-methyladenosine related gene expression signatures for predicting the overall survival and immune responses of patients with colorectal cancer. Front Genet 2023; 14:885930. [PMID: 36936424 PMCID: PMC10020527 DOI: 10.3389/fgene.2023.885930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
N6-methyladenosine (m6A) modification has been demonstrated to exhibit a crucial prognostic effect on colorectal cancer (CRC). Nonetheless, potential mechanism of m6A in survival rate and immunotherapeutic response remains unknown. Here we investigated the genes associated with m6A regulators and developed a risk score for predicting the overall survival (OS) of CRC patients. RNA-seq transcriptomic profiling data of COAD/READ samples were obtained from The Cancer Genome Atlas (TCGA) database. Absolute Shrinkage and Selection Operator (LASSO)- Cox regression analysis was conducted to identify the m6A-related gene expression signatures and the selected genes were inputted into stepwise regression to develop a prognostic risk score in TCGA, and its predictive performance of CRC survival was further validated in Gene Expression Omnibus (GEO) datasets. According to our results, the risk score comprising 18 m6A-related mRNAs was significantly associated with CRC survival in both TCGA and GEO datasets. And the stratified analysis also confirmed that high-risk score acted as a poor factor in different age, sex, T stage, and tumour, node, metastasis (TNM) stages. The m6A-related prognostic score in combination with clinical characteristics yielded time-dependent area under the receiver operating characteristic curve (AUCs) of 0.85 (95%CI: 0.79-0.91), 0.84 (95%CI: 0.79-0.90) and 0.80 (95%CI: 0.71-0.88) for the prediction of the 1-, 3-, 5-year OS of CRC in TCGA cohort. Furthermore, mutation of oncogenes occurred more frequently in the high-risk group and the composition of immune cells in tumour microenvironment (TME) was significantly distinct between the low- and high-risk groups. The low-risk group had a lower microsatellite instability (MSI) score, T-cell exclusion score and dysfunction score, implying that low-risk patients may have a better immunotherapy response than high-risk patients. In summary, a prognostic risk score derived from m6A-related gene expression signatures could serve as a potential prognostic predictor for CRC survival and indicator for predicting immunotherapy response in CRC patients.
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Affiliation(s)
- Lili Yu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijuan Wang
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Sun
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuan Zhou
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Yeting Hu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lidan Hu
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yazhou He
- Department of Oncology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chunqing Lin
- National Cancer Center, National Clinical Research Center for Cancer, and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Chen
- Center for Global Health, Zhejiang University, Hangzhou, China
| | - Xiaolin Xu
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Malcolm G. Dunlop
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Evropi Theodoratou
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Kefeng Ding
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Xue Li
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
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4
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Cui W, Zhao D, Jiang J, Tang F, Zhang C, Duan C. tRNA Modifications and Modifying Enzymes in Disease, the Potential Therapeutic Targets. Int J Biol Sci 2023; 19:1146-1162. [PMID: 36923941 PMCID: PMC10008702 DOI: 10.7150/ijbs.80233] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/26/2023] [Indexed: 03/14/2023] Open
Abstract
tRNA is one of the most conserved and abundant RNA species, which plays a key role during protein translation. tRNA molecules are post-transcriptionally modified by tRNA modifying enzymes. Since high-throughput sequencing technology has developed rapidly, tRNA modification types have been discovered in many research fields. In tRNA, numerous types of tRNA modifications and modifying enzymes have been implicated in biological functions and human diseases. In our review, we talk about the relevant biological functions of tRNA modifications, including tRNA stability, protein translation, cell cycle, oxidative stress, and immunity. We also explore how tRNA modifications contribute to the progression of human diseases. Based on previous studies, we discuss some emerging techniques for assessing tRNA modifications to aid in discovering different types of tRNA modifications.
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Affiliation(s)
- Weifang Cui
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Deze Zhao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Junjie Jiang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Faqing Tang
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, PR China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China.,National Clinical Research Center for Geriatric Disorders, Changsha, 410008, Hunan, PR China.,Institute of Medical Sciences, Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, PR China
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5
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Zhang Z, Mei Y, Hou M. Knockdown RBM15 Inhibits Colorectal Cancer Cell Proliferation and Metastasis Via N6-Methyladenosine (m6A) Modification of MyD88 mRNA. Cancer Biother Radiopharm 2022; 37:976-986. [PMID: 34842457 DOI: 10.1089/cbr.2021.0226] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. In this study, we explored the role of RNA binding motif protein 15 (RBM15)-mediated MyD88 mRNA N6-methyladenosine (m6A) in CRC development. Cell proliferation, apoptosis, and invasion were detected by EdU, Annexin V-FITC/PI staining, and Transwell assays, respectively. RBM15 and MyD88 expression was detected by RT-qPCR and Western blot. RNA-seq, RIP-seq, and MeRIP-seq were used for RBM15 downstream target gene prediction and expression detection. In this research, we confirmed that RBM15 was highly expressed in CRC tissues and was negatively correlated with overall and disease-free survival rate. Silencing RBM15 significantly inhibited the proliferative and invasive abilities and promoted cell apoptosis in the CRC cell lines (SW480 and HCT116). Moreover, tumor growth and CRC liver metastasis were inhibited by silencing RBM15 in vivo. m6A methylation level was decreased in RBM15-silenced SW480 and HCT116 cells. MyD88 was the target mRNA of RBM15-mediated m6A methylation in CRC. MyD88 was lowly expressed in CRC and negatively correlated with RBM15 expression. Taken together, RBM15 silencing inhibited the CRC growth and metastasis in vitro and in vivo. RBM15 mediated m6A methylation modification of MyD88 mRNA in CRC cells.
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Affiliation(s)
- Zhen Zhang
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Yan Mei
- Health Management (Physical Examination) Center, Inner Mongolia Autonomous Region People's Hospital, Hohhot, China
| | - Mingxing Hou
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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6
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The functions of N6-methyladenosine (m6A) RNA modifications in colorectal cancer. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:235. [PMID: 36175777 DOI: 10.1007/s12032-022-01827-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/17/2022] [Indexed: 10/14/2022]
Abstract
Colorectal cancers (CRC), which includes colon cancer (CC) and rectal cancer (RC), are some of the most common malignant tumors that are prone to distant metastasis. Its high incidence rate and high mortality rate have attracted much attention. In recent years, epigenetics has attracted increasing attention and has been the focus of many research studies. N6-methyladenosine(m6A) RNA modifications can modify eukaryotic mRNA to impact metabolism. The changes in the m6A regulatory genes are related to the occurrence and development of CRC and play an important role in the pathogenesis of CRC. The effect of m6A RNA modification is regulated by its related regulatory factors ("writer", "eraser", "reader"). In this review, we comprehensively analyzed the effect of m6A methylation on CRC and the relationship between the expression of related regulatory factors and the development and occurrence of CRC. Then, we summarized the roles of m6A and its regulatory factors in CRC and its potential clinical value, which provides a basis for further research on the mechanism of m6A methylation in CRC.
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Effects of N6-Methyladenosine Regulators on LAG3 and Immune Infiltrates in Lung Adenocarcinoma. DISEASE MARKERS 2022; 2022:1829528. [PMID: 36051357 PMCID: PMC9427291 DOI: 10.1155/2022/1829528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 06/30/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]
Abstract
Background. Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer, which is one of the most commonly diagnosed tumors and the leading causes of death from cancer around the world. Since RNA methylation is a posttranscriptional modification and affects so much biological progress, it is urged to explore the role of N6-methyladenosine (m6A) methylation in LUAD. Methods. We explored the expression of 24 m6A methylation genes, as well as their correlations with LAG3 in 561 LUAD samples from TCGA. Consensus clustering was applied to m6A methylation genes, and two LUAD subgroups were identified. The expression of m6A genes was analyzed by the Wilcoxon test. KEGG and GO enrichment analyses were performed to indicate the pathway affected by differentially expressed genes in the two groups. A prognostic model based on LASSO regression using an eleven-m6A gene signature was constructed according to the expression of these genes. Receiver operating characteristic (ROC) curve was used to confirm the accuracy of the model in the TCGA cohort, as well as in the test cohort from the Gene Expression Omnibus (GEO) database. Results. Compared to cluster 1, cluster 2 showed poorer overall survival (OS) and higher LAG3 expression. In addition, KEGG and GO enrichment analyses indicated that differentially expressed genes are enriched in the immune response. We also observed that the expression of LAG3 is positively correlated with IGF2BP2, CBLL1, and HNRNPA2B1 and negatively correlated with YTHDF2, YTHDF3, and FTO. For patients in the TCGA cohort, the AUC score is 0.7, and the AUC score for the GSE50081 cohort is 0.675. Patients with lower risk scores exhibited better overall survival and lower expression of LAG3 than patients with higher risk scores. Conclusions. In brief, our results indicated the important role of m6 methylation in affecting the tumor immune microenvironment and the survival of patients with LUAD. The m6A methylation gene signatures might serve as promising therapeutic targets and help the immunotherapy of LUAD in the future.
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Shi B, Liu WW, Yang K, Jiang GM, Wang H. The role, mechanism, and application of RNA methyltransferase METTL14 in gastrointestinal cancer. Mol Cancer 2022; 21:163. [PMID: 35974338 PMCID: PMC9380308 DOI: 10.1186/s12943-022-01634-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Gastrointestinal cancer is the most common human malignancy characterized by high lethality and poor prognosis. Emerging evidences indicate that N6-methyladenosine (m6A), the most abundant post-transcriptional modification in eukaryotes, exerts important roles in regulating mRNA metabolism including stability, decay, splicing, transport, and translation. As the key component of the m6A methyltransferase complex, methyltransferase-like 14 (METTL14) catalyzes m6A methylation on mRNA or non-coding RNA to regulate gene expression and cell phenotypes. Dysregulation of METTL14 was deemed to be involved in various aspects of gastrointestinal cancer, such as tumorigenesis, progression, chemoresistance, and metastasis. Plenty of findings have opened up new avenues for exploring the therapeutic potential of gastrointestinal cancer targeting METTL14. In this review, we systematically summarize the recent advances regarding the biological functions of METTL14 in gastrointestinal cancer, discuss its potential clinical applications and propose the research forecast.
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Affiliation(s)
- Bin Shi
- Department of Anorectal Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Heifei, China
| | - Wei-Wei Liu
- School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Ke Yang
- School of Clinical Medicine, Clinical College of Anhui Medical University, Hefei, China
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, China.
| | - Hao Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. .,Core Unit of National Clinical Research Center for Laboratory Medicine, Heifei, China.
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9
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Xiong Z, Li X, Yin S, Xie M, Mao C, Zhang F, Chen H, Jin L, Lian L. Prognostic Value of N6-Methyladenosine-Related lncRNAs in Early-Stage Colorectal Cancer: Association With Immune Cell Infiltration and Chemotherapeutic Drug Sensitivity. Front Mol Biosci 2021; 8:724889. [PMID: 34712696 PMCID: PMC8546174 DOI: 10.3389/fmolb.2021.724889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/28/2021] [Indexed: 01/01/2023] Open
Abstract
Purpose: Accumulating evidence indicates that N6-methyladenosine-related long non-coding RNAs (m6A-related lncRNAs) play a crucial role in the occurrence and development of several cancers. We aimed to explore the potential role of m6A-related lncRNA signatures in predicting prognosis for early-stage (stages I and II) colorectal cancer (CRC). Methods: m6A-related lncRNA data were obtained from The Cancer Genome Atlas. Univariate Cox regression analysis was used to screen for prognostic m6A-related lncRNAs. Immune characteristics were analyzed in different subgroups created via unsupervised clustering analysis. Next, patients were randomly divided into training and test cohorts. In the training cohort, least absolute shrinkage and selection operator (LASSO) regression was performed to establish a prognostic model. The predictive value of the signature was evaluated in the training and test cohorts. Drug sensitivity was also examined. Results: A total of 1,478 m6A-related lncRNAs were identified. Two subgroups were created based on the expression of seven prognostic m6A-related lncRNAs. Prognosis was worse for cluster 1 than for cluster 2, and cluster 1 was characterized by increased numbers of M2 macrophages, decreased numbers of memory B cells, and higher expression of checkpoint genes when compared with cluster 2. Five m6A-related lncRNAs were selected to establish a risk prediction signature via LASSO regression. The 3 years overall survival (OS) was higher in the low-risk group than in the high-risk group. The area under the curve at 1, 2, and 3 years was 0.929, 0.954, and 0.841 in the training cohort and 0.664, 0.760, and 0.754 in the test cohort, respectively. Multivariate Cox regression analysis suggests that the risk score was an independent predictor of OS in both the training and test cohorts. A prognostic nomogram based on the five m6A-related lncRNAs and their clinical features was built and verified. The high-risk group was more sensitive to chemotherapeutic drugs (camptothecin and cisplatin) than the low-risk group. Conclusion: We identified two molecular subgroups of early-stage CRC with unique immune features based on seven prognostic m6A-related lncRNAs. Subsequent analyses demonstrated the usefulness of a five m6A-related lncRNA signature as a potential indicator of prognosis in patients with early-stage CRC.
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Affiliation(s)
- Zhizhong Xiong
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xianzhe Li
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Shi Yin
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Minghao Xie
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Chaobin Mao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Fengxiang Zhang
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Huaxian Chen
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Longyang Jin
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Lei Lian
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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10
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Xu H, Li X, Wang S, Li F, Gao J, Yan L, Zhu L. Multiomics analysis identifies key genes and pathways related to N6-methyladenosine RNA modification in ovarian cancer. Epigenomics 2021; 13:1359-1383. [PMID: 34550011 DOI: 10.2217/epi-2021-0204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aims: To explore the pathways and target genes related to N6-methyladenosine (m6A) methylation in ovarian cancer and their effect on patient prognosis. Methods & materials: The Cancer Genome Atlas was used to screen genes related to m6A regulators in terms of gene expression, mutation and copy number variation. These genes were subjected to pathway enrichment analysis. Prognosis-related genes were screened and involved in risk signature construction. Immunohistochemistry was used for verification. Results: We obtained 1408 genes dysregulated in parallel to m6A regulators, which were mainly involved in the platelet activation pathway. The m6A-related signature was constructed based on the expression of four prognosis-related genes (RPS6KA2, JUNB, HNF4A and P2RX1). Conclusion: This work provides new insights into the mechanism of m6A methylation in ovarian cancer.
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Affiliation(s)
- Haoya Xu
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province & Key Laboratory of Obstetrics & Gynecology of Higher Education of Liaoning Province, Shenyang, 110004, Liaoning, China
| | - Xianli Li
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province & Key Laboratory of Obstetrics & Gynecology of Higher Education of Liaoning Province, Shenyang, 110004, Liaoning, China
| | - Shengtan Wang
- Department of Gynecology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, 570011, Hainan, China
| | - Feifei Li
- Department of Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Jian Gao
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province & Key Laboratory of Obstetrics & Gynecology of Higher Education of Liaoning Province, Shenyang, 110004, Liaoning, China
| | - Limei Yan
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province & Key Laboratory of Obstetrics & Gynecology of Higher Education of Liaoning Province, Shenyang, 110004, Liaoning, China
| | - Liancheng Zhu
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province & Key Laboratory of Obstetrics & Gynecology of Higher Education of Liaoning Province, Shenyang, 110004, Liaoning, China
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11
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Liu C, Yang S, Zhang Y, Wang C, Du D, Wang X, Liu T, Liang G. Emerging Roles of N6-Methyladenosine Demethylases and Its Interaction with Environmental Toxicants in Digestive System Cancers. Cancer Manag Res 2021; 13:7101-7114. [PMID: 34526822 PMCID: PMC8437382 DOI: 10.2147/cmar.s328188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/19/2021] [Indexed: 01/02/2023] Open
Abstract
Digestive system cancers are common cancers with high cancer deaths worldwide. They have become a major threat to public health and economic burden. As one of the most universal RNA modifications in eukaryotes, the N6-methyladenosine (m6A) modification is involved in the occurrence, development, prognosis, and treatment response of various cancers, including digestive system cancers. M6A demethylases shape the m6A landscape dynamically, playing important roles in cancers. In addition, accumulating evidence reveal that many environmental toxicants are the established risk factors for digestive system cancers and associated with m6A modification. In this review, we summarize the multiple functions of M6A demethylases (fat mass and obesity-associated protein (FTO), AlkB homolog 5 (ALKBH5) and AlkB homolog 3 (ALKBH3)) in digestive system cancers, which are aberrantly expressed and affect cancer progression. We also discuss the potential roles of m6A demethylases in the assessment of environmental exposure, the signature for prevention and diagnosis of digestive system cancers.
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Affiliation(s)
- Caiping Liu
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Sheng Yang
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Yanqiu Zhang
- Department of Environmental Occupational Health, Taizhou Center for Disease Control and Prevention, Taizhou, 225300, Jiangsu, People's Republic of China
| | - Chuntao Wang
- Jiangsu Vocational College of Medicine, Yancheng, 224000, Jiangsu, People's Republic of China
| | - Dandan Du
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Xian Wang
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Tong Liu
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Geyu Liang
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
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12
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Zhang Z, Zhang X. Identification of m6A-Related Biomarkers Associated with Prognosis of Colorectal Cancer. Med Sci Monit 2021; 27:e932370. [PMID: 34373442 PMCID: PMC8364289 DOI: 10.12659/msm.932370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Colorectal cancer (CRC) is the second most deadly cancer in the world according to GLOBOCAN 2020 data. Accumulating evidence suggests that RNA methylation modification is also misregulated in human cancers and may be a potential ideal target for cancer treatment. Material/Methods m6A-related differentially expressed genes (DEGs) were identified from colon adenocarcinoma and rectum adenocarcinoma esophageal carcinoma patients with different pathological stages. The protein-protein interaction (PPI) network construction, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs were conducted. Cox regression analysis was applied to the screening of m6A-related DEGs significantly associated with the overall survival (OS), and those selected genes were used for LASSO regression analysis to construct prognostic signature and calculate patients’ risk scores. Results We identified 673 m6A-related DEGs from CRC patients in different pathologic stages, and 146 of them were associated with OS. CTNNB1, TRIM37, RAB7A, CASC5/KNL1, CENPE, CCNB1, UBE2H, HSPA8, KIF1A, and FBXW4 were hub genes of the PPI network. Nine m6A-related genes were screened out to build the prognostic risk model. TNM stage, vascular invasion, and the risk score were independently related to the OS of CRC patients. Conclusions Nine candidate m6A-related mRNA biomarkers (LRRC17, NFKB1, NOS2, PCDHB2, RAB7A, RPS6KA1, RRNAD1, TLE6, and UBE2H) were found to be closely related to the clinicopathology and prognosis of colorectal cancer, indicating that they could be potential prognostic biomarkers for patients with colorectal cancer.
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Affiliation(s)
- Zhiyong Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Xin Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
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13
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Huang L, Zhu J, Kong W, Li P, Zhu S. Expression and Prognostic Characteristics of m6A RNA Methylation Regulators in Colon Cancer. Int J Mol Sci 2021; 22:ijms22042134. [PMID: 33670062 PMCID: PMC7926939 DOI: 10.3390/ijms22042134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/14/2022] Open
Abstract
Colon cancer is a common and leading cause of death and malignancy worldwide. N6-methylation of adenosine (m6A) is the most common reversible mRNA modification in eukaryotes, and it plays a crucial role in various biological functions in vivo. Dysregulated expression and genetic changes of m6A regulators have been correlated with tumorigenesis, cancer cell proliferation, tumor microenvironment, and prognosis in cancers. This study used RNA-seq and colon cancer clinical data to explore the relationship between N6-methylation and colon cancer. Based on the seven m6A regulators related to prognosis, three molecular subgroups of colon cancer were identified. Surprisingly, we found that each subgroup had unique survival characteristics. We then identified three subtypes of tumors based on 299 m6A phenotype-related genes, and one subtype was characterized as an immunosuppressive tumor and patients in this subtype may be more suitable for immunotherapy than other subtypes. Finally, using m6A-related genes and clinical information from The Cancer Genome Atlas cohort, we constructed a prognosis model, and this model could be used to predict the prognosis of patients in clinics.
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Affiliation(s)
- Liting Huang
- Institute of Translational Medicine, College of Medicine, Qingdao University, Qingdao 266021, China;
| | - Jie Zhu
- Peking University Health Science Center, Department of Pharmacology, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China; (J.Z.); (W.K.)
| | - Weikaixin Kong
- Peking University Health Science Center, Department of Pharmacology, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China; (J.Z.); (W.K.)
| | - Peifeng Li
- Institute of Translational Medicine, College of Medicine, Qingdao University, Qingdao 266021, China;
- Correspondence: (P.L.); (S.Z.); Tel.: +86-0532-82991791 (S.Z.)
| | - Sujie Zhu
- Institute of Translational Medicine, College of Medicine, Qingdao University, Qingdao 266021, China;
- Correspondence: (P.L.); (S.Z.); Tel.: +86-0532-82991791 (S.Z.)
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