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Wu W, Li M, Wu Y, Wei Q, Yu N. METTL14-mediated m6A mRNA modification of G6PD promotes lung adenocarcinoma. Cell Death Discov 2024; 10:361. [PMID: 39138186 PMCID: PMC11322390 DOI: 10.1038/s41420-024-02133-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/24/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024] Open
Abstract
METTL14 functions as an RNA methyltransferase involved in m6A modification, influencing mRNA biogenesis, decay, and translation processes. However, the specific mechanism by which METTL14 regulates glucose-6-phosphate dehydrogenase (G6PD) to promote the progression of lung adenocarcinoma (LUAD) is not well understood. Quantitative measurement and immunohistochemistry (IHC) analysis have demonstrated higher levels of m6A in LUAD tissues compared to adjacent normal tissues. Additionally, the expression of METTL14 was significantly increased in LUAD tissues. In LUAD cell lines, both METTL14 and m6A levels were elevated compared to normal human lung epithelial cells. Knockdown of METTL14 markedly reduced LUAD cell proliferation, migration, and invasion. Conversely, overexpression of METTL14, but not the mutant form, significantly enhanced these cellular processes in LUAD. In vivo studies using nude mice with subcutaneously transplanted LUAD cells demonstrated that stable METTL14 knockdown led to notably reduced tumor volume and weight, along with fewer Ki67-positive cells and lung metastatic sites. Importantly, METTL14 knockdown reduced glycolytic activity in LUAD cells. Through a combination of RNA sequencing and MeRIP-sequencing, we identified numerous altered genes and confirmed that IGF2BP2 enhances G6PD mRNA stability after METTL14-mediated m6A modification, thereby promoting tumor growth and metastasis. Moreover, LUAD patients with higher levels of G6PD had poorer overall survival (OS). In conclusion, our study indicates that METTL14 upregulates G6PD expression post-transcriptionally through an m6A-IGF2BP2-dependent mechanism, thereby stabilizing G6PD mRNA. These findings propose potential diagnostic biomarkers and effective targets for anti-metabolism therapy in LUAD.
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Affiliation(s)
- Weidong Wu
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
- Fujian Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou, 350122, Fujian, China
- National Key Clinical Specialty of Thoracic Surgery, Fuzhou, 350001, Fujian, China
- Clinical Research Center for Thoracic Tumors of Fujian Province, Fuzhou, 350001, Fujian, China
| | - Mengling Li
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
- Department of Geriatric Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
| | - Yingxiao Wu
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
- Department of Geriatric Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
| | - Qiongying Wei
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
- Department of Geriatric Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
| | - Nanding Yu
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.
- Department of Geriatric Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.
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Yu N, Wu Y, Wei Q, Li X, Li M, Wu W. m 6A modification of CDC5L promotes lung adenocarcinoma progression through transcriptionally regulating WNT7B expression. Am J Cancer Res 2024; 14:3565-3583. [PMID: 39113868 PMCID: PMC11301290 DOI: 10.62347/qhfa9669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/25/2024] [Indexed: 08/10/2024] Open
Abstract
Cell division cycle 5-like (CDC5L) protein is implicated in the development of various cancers. However, its role in the progression of lung adenocarcinoma (LUAD) remains uncertain. Our findings revealed frequent upregulation of CDC5L in LUAD, which correlated with poorer overall survival rates and advanced clinical stages. In vitro experiments demonstrated that CDC5L overexpression stimulated the proliferation, migration, and invasion of LUAD cells, whereas CDC5L knockdown exerted suppressive effects on these cellular processes. Furthermore, silencing CDC5L significantly inhibited tumor growth and metastasis in a xenograft mouse model. Mechanistically, CDC5L activates the Wnt/β-catenin signaling pathway by transcriptionally regulating WNT7B, thereby promoting LUAD progression. Besides, METTL14-mediated m6A modification contributed to CDC5L upregulation in an IGF2BP2-dependent manner. Collectively, our study uncovers a novel molecular mechanism by which the m6A-induced CDC5L functions as an oncogene in LUAD by activating the Wnt/β-catenin pathway through transcriptional regulation of WNT7B, suggesting that CDC5L may serve as a promising prognostic marker and therapeutic target for LUAD.
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Affiliation(s)
- Nanding Yu
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
- Department of Geriatric Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
| | - Yingxiao Wu
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
- Department of Geriatric Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
| | - Qiongying Wei
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
- Department of Geriatric Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
| | - Xiaoping Li
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
- Department of Geriatric Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
| | - Mengling Li
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
- Department of Geriatric Medicine, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
| | - Weidong Wu
- Department of Thoracic Surgery, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
- Fujian Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical UniversityFuzhou 350122, Fujian, China
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3
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Wu H, Jiao Y, Guo X, Wu Z, Lv Q. METTL14/miR-29c-3p axis drives aerobic glycolysis to promote triple-negative breast cancer progression though TRIM9-mediated PKM2 ubiquitination. J Cell Mol Med 2024; 28:e18112. [PMID: 38263865 PMCID: PMC10844685 DOI: 10.1111/jcmm.18112] [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: 09/21/2023] [Revised: 11/05/2023] [Accepted: 11/22/2023] [Indexed: 01/25/2024] Open
Abstract
The energy metabolic rearrangement of triple-negative breast cancer (TNBC) from oxidative phosphorylation to aerobic glycolysis is a significant biological feature and can promote the malignant progression. However, there is little knowledge about the functional mechanisms of methyltransferase-like protein 14 (METTL14) mediated contributes to TNBC malignant progression. Our study found that METTL14 expression was significantly upregulated in TNBC tissues and cell lines. Silencing METTL14 significantly inhibited TNBC cell growth and invasion in vitro, as well as suppressed tumour growth. Mechanically, METTL14 was first found to activate miR-29c-3p through m6A and regulate tripartite motif containing 9 (TRIM9) to promote ubiquitination of pyruvate kinase isoform M2 (PKM2) and lead to its transition from tetramer to dimer, resulting in glucose metabolic reprogramming from oxidative phosphorylation to aerobic glycolysis to promote the progress of TNBC. Taken together, these findings reveal important roles of METTL14 in TNBC tumorigenesis and energy metabolism, which might represent a novel potential therapeutic target for TNBC.
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Affiliation(s)
- Hao Wu
- Division of Breast Surgery, Department of General SurgeryWest China Hospital, Sichuan UniversityChengduChina
- Breast Center, West China HospitalSichuan UniversityChengduChina
| | - Yile Jiao
- Division of Breast Surgery, Department of General SurgeryWest China Hospital, Sichuan UniversityChengduChina
- Breast Center, West China HospitalSichuan UniversityChengduChina
| | - Xinyi Guo
- Division of Breast Surgery, Department of General SurgeryWest China Hospital, Sichuan UniversityChengduChina
- Breast Center, West China HospitalSichuan UniversityChengduChina
| | - Zhenru Wu
- Laboratory of Pathology, West China HospitalSichuan UniversityChengduChina
| | - Qing Lv
- Division of Breast Surgery, Department of General SurgeryWest China Hospital, Sichuan UniversityChengduChina
- Breast Center, West China HospitalSichuan UniversityChengduChina
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Ramakrishnan M, Rajan KS, Mullasseri S, Ahmad Z, Zhou M, Sharma A, Ramasamy S, Wei Q. Exploring N6-methyladenosine (m 6A) modification in tree species: opportunities and challenges. HORTICULTURE RESEARCH 2024; 11:uhad284. [PMID: 38371641 PMCID: PMC10871907 DOI: 10.1093/hr/uhad284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/17/2023] [Indexed: 02/20/2024]
Abstract
N 6-methyladenosine (m6A) in eukaryotes is the most common and widespread internal modification in mRNA. The modification regulates mRNA stability, translation efficiency, and splicing, thereby fine-tuning gene regulation. In plants, m6A is dynamic and critical for various growth stages, embryonic development, morphogenesis, flowering, stress response, crop yield, and biomass. Although recent high-throughput sequencing approaches have enabled the rapid identification of m6A modification sites, the site-specific mechanism of this modification remains unclear in trees. In this review, we discuss the functional significance of m6A in trees under different stress conditions and discuss recent advancements in the quantification of m6A. Quantitative and functional insights into the dynamic aspect of m6A modification could assist researchers in engineering tree crops for better productivity and resistance to various stress conditions.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - K Shanmugha Rajan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi 682018, Kerala, India
| | - Zishan Ahmad
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin’an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin’an, Hangzhou 311300, Zhejiang, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin’an, Hangzhou 311300, Zhejiang, China
| | - Subbiah Ramasamy
- Cardiac Metabolic Disease Laboratory, Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, Tamilnadu, India
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
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Jayasree PJ, Dutta S, Karemore P, Khandelia P. Crosstalk Between m6A RNA Methylation and miRNA Biogenesis in Cancer: An Unholy Nexus. Mol Biotechnol 2023:10.1007/s12033-023-00921-w. [PMID: 37831403 DOI: 10.1007/s12033-023-00921-w] [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: 07/01/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
N6-methyladenosine (m6A) is one of the most prevalent internal reversible chemical modification of RNAs in eukaryotes, which has attracted widespread attention recently owing to its regulatory roles in a plethora of normal developmental processes and human diseases like cancer. Deposition of the m6A mark on RNAs is mediated by the dynamic interplay between m6A regulatory proteins such as m6A RNA methyltransferases (m6A writers), m6A RNA demethylases (m6A erasers) and m6A RNA binding proteins (m6A readers). m6A regulators are ectopically expressed in various cancer types, often leading to aberrant expression of tumor-suppressor and oncogenic mRNAs either directly or indirectly via regulating the biogenesis of non-coding RNAs like miRNAs. miRNAs are tiny regulators of gene expression, which often impact various hallmarks of cancer and thus influence tumorigenesis. It is becoming increasingly clear that m6A RNA modification impacts biogenesis and function of miRNAs, and recent studies have interestingly, uncovered many miRNAs whose biogenesis and function are regulated by m6A writers, erasers and readers. In this review, we discuss various mechanisms by which m6A RNA methylation regulates miRNA biogenesis, the functional crosstalk between m6A RNA methylation and miRNAs and how it modulates various aspects of tumorigenesis. The potential of m6A RNA methylation regulated miRNAs as biomarkers and novel therapeutic targets to treat various cancers is also addressed.
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Affiliation(s)
- P J Jayasree
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Hyderabad, Telangana, 500078, India
| | - Shalmoli Dutta
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Hyderabad, Telangana, 500078, India
| | - Pragati Karemore
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Hyderabad, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Hyderabad, Telangana, 500078, India.
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Yang Y, Long J, Yang J, Zheng H, Lai Y, Chen C, Tang F, Gao Y, Chen L, He Z. METTL3-dependent m6A modification mediates bladder remodeling after partial bladder outlet obstruction through CCN2 activation. Neurourol Urodyn 2023; 42:1506-1521. [PMID: 37455557 DOI: 10.1002/nau.25233] [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: 03/14/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
AIMS N6-methyladenosine (m6A) modification is a critical posttranscriptional event in gene regulation. Thus, identifying methyltransferase, demethylase, or m6A binding protein-mediated m6A modifications in cancer or noncancer transcriptomes has become a promising novel strategy for disease therapy development. However, novel insights into m6A modification in partial bladder outlet obstruction (pBOO) and detailed information about the drivers of bladder remodeling remain to be elucidated. Here, we first characterized the m6A modification landscape in pBOO and investigated potential actionable pharmaceutical targets for future therapies. METHODS We generated an improved animal model of pBOO in SD rats with urethral meatus stricture induced by suturing. Urodynamic investigations and cystometry were carried out to evaluate the physiologic changes elicited by pBOO. Whole-transcriptome sequencing (RNA-seq) and m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq) were subsequently performed to analyze the expression pattern associated with bladder remodeling in pBOO. RESULTS The cystometric evaluation of bladder function demonstrated obvious increases in pressure-related parameters in the pBOO group. Hematoxylin and eosin staining and Masson's trichrome staining validated the occurrence of bladder remodeling. A global elevation in m6A RNA methylation levels was observed in parallel to a increased expression of METTL3 in the pBOO group. High-throughput sequencing revealed the differences in expression patterns between the pBOO and sham-operated groups. Furthermore, potential m6A-modified genes, including CCN2, may serve as new pharmaceutical targets to reverse bladder remodeling. CONCLUSIONS Exploring the roles of m6A-modified genes identified as associated with bladder remodeling by integrating RNA-seq and MeRIP-seq data can offer new insights for developing promising treatments for pBOO patients.
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Affiliation(s)
- Yafei Yang
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jun Long
- Department of Urology, Affiliated Hospital of Chengdu University, Chengdu, Sichuan, China
- Graduate School, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jin Yang
- Department of Urology, Affiliated Hospital of Chengdu University, Chengdu, Sichuan, China
| | - Hanxiong Zheng
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yongchang Lai
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Chiheng Chen
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Fucai Tang
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yibo Gao
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Lin Chen
- Department of Urology, Affiliated Hospital of Chengdu University, Chengdu, Sichuan, China
| | - Zhaohui He
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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Bou Antoun N, Chioni AM. Dysregulated Signalling Pathways Driving Anticancer Drug Resistance. Int J Mol Sci 2023; 24:12222. [PMID: 37569598 PMCID: PMC10418675 DOI: 10.3390/ijms241512222] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
One of the leading causes of death worldwide, in both men and women, is cancer. Despite the significant development in therapeutic strategies, the inevitable emergence of drug resistance limits the success and impedes the curative outcome. Intrinsic and acquired resistance are common mechanisms responsible for cancer relapse. Several factors crucially regulate tumourigenesis and resistance, including physical barriers, tumour microenvironment (TME), heterogeneity, genetic and epigenetic alterations, the immune system, tumour burden, growth kinetics and undruggable targets. Moreover, transforming growth factor-beta (TGF-β), Notch, epidermal growth factor receptor (EGFR), integrin-extracellular matrix (ECM), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), phosphoinositol-3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/Akt/mTOR), wingless-related integration site (Wnt/β-catenin), Janus kinase/signal transducers and activators of transcription (JAK/STAT) and RAS/RAF/mitogen-activated protein kinase (MAPK) signalling pathways are some of the key players that have a pivotal role in drug resistance mechanisms. To guide future cancer treatments and improve results, a deeper comprehension of drug resistance pathways is necessary. This review covers both intrinsic and acquired resistance and gives a comprehensive overview of recent research on mechanisms that enable cancer cells to bypass barriers put up by treatments, and, like "satellite navigation", find alternative routes by which to carry on their "journey" to cancer progression.
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Affiliation(s)
| | - Athina-Myrto Chioni
- School of Life Sciences Pharmacy and Chemistry, Biomolecular Sciences Department, Kingston University London, Kingston-upon-Thames KT1 2EE, UK;
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Sharma R, Rakshit B. Global burden of cancers attributable to tobacco smoking, 1990-2019: an ecological study. EPMA J 2023; 14:167-182. [PMID: 36866162 PMCID: PMC9971393 DOI: 10.1007/s13167-022-00308-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022]
Abstract
Aim and background Identifying risk factors for cancer initiation and progression is the cornerstone of the preventive approach to cancer management and control (EPMA J. 4(1):6, 2013). Tobacco smoking is a well-recognized risk factor for initiation and spread of several cancers. The predictive, preventive, and personalized medicine (PPPM) approach to cancer management and control focuses on smoking cessation as an essential cancer prevention strategy. Towards this end, this study examines the temporal patterns of cancer burden due to tobacco smoking in the last three decades at global, regional, and national levels. Data and methods The data pertaining to the burden of 16 cancers attributable to tobacco smoking at global, regional, and national levels were procured from the Global Burden of Disease 2019 Study. Two main indicators, deaths and disability-adjusted life years (DALYs), were used to describe the burden of cancers attributable to tobacco smoking. The socio-economic development of countries was measured using the socio-demographic index (SDI). Results Globally, deaths due to neoplasms caused by tobacco smoking increased from 1.5 million in 1990 to 2.5 million in 2019, whereas the age-standardized mortality rate (ASMR) decreased from 39.8/100,000 to 30.6/100,000 and the age-standardized DALY rate (ASDALR) decreased from 948.9/100,000 to 677.3/100,000 between 1990 and 2019. Males accounted for approximately 80% of global deaths and DALYs in 2019. Populous regions of Asia and a few regions of Europe account for the largest absolute burden, whereas countries in Europe and America have the highest age-standardized rates of cancers due to tobacco smoking. In 8 out of 21 regions, there were more than 100,000 deaths due to cancers attributable to tobacco smoking led by East Asia, followed by Western Europe in 2019. The regions of Sub-Saharan Africa (except southern region) had one of the lowest absolute counts of deaths, DALYs, and age-standardized rates. In 2019, tracheal, bronchus, and lung (TBL), esophageal, stomach, colorectal, and pancreatic cancer were the top 5 neoplasms attributable to tobacco smoking, with different burdens in regions as per their development status. The ASMR and ASDALR of neoplasms due to tobacco smoking were positively correlated with SDI, with pairwise correlation coefficient of 0.55 and 0.52, respectively. Conclusion As a preventive tool, tobacco smoking cessation has the biggest potential among all risk factors for preventing millions of cancer deaths every year. Cancer burden due to tobacco smoking is found to be higher in males and is positively associated with socio-economic development of countries. As tobacco smoking begins mostly at younger ages and the epidemic is unfolding in several parts of the world, more accelerated efforts are required towards tobacco cessation and preventing youth from entering this addiction. The PPPM approach to medicine suggests that not only personalized and precision medicine must be provided to cancer patients afflicted by tobacco smoking but personalized and targeted preventive solutions must be provided to prevent initiation and progression of smoking. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-022-00308-y.
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Affiliation(s)
- Rajesh Sharma
- Humanities and Social Sciences, National Institute of Technology Kurukshetra, Kurukshetra, India
| | - Bijoy Rakshit
- Economics and Business Environment, Indian Institute of Management Jammu, Jammu and Kashmir, India
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Zhang G, Hou J, Mei C, Wang X, Wang Y, Wang K. Effect of circular RNAs and N6-methyladenosine (m6A) modification on cancer biology. Biomed Pharmacother 2023; 159:114260. [PMID: 36657303 DOI: 10.1016/j.biopha.2023.114260] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/09/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023] Open
Abstract
N6-methyladenosine (m6A), as the most abundant and well-known RNA modification, has been found to play an important role in cancer. Circular RNAs (circRNAs) are a class of single-stranded covalently closed RNA molecules generated by the reverse splicing process. Recent studies have revealed the vital roles of circRNAs in many diseases, including tumorigenesis. Accumulating evidence also shows an association between m6A modification and circRNAs. This study aimed to review the interactions between m6A modification and circRNAs and illustrate their roles in tumorigenesis. m6A modification can modulate the biogenesis, translation, cytoplasmic export, degradation, and other functions of circRNAs in different tumors. circRNAs can also modulate m6A modification by affecting writers, erasers, and readers. We focused on the potential regulatory mechanisms and the biological consequences of m6A modification of circRNAs, as well as the interactions in tumors of different systems. Finally, we listed the possible development directions of m6A modification and circRNAs, which might facilitate the clinical application of tumor therapy. AVAILABILITY OF DATA AND MATERIALS: Not applicable. Keywords.
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Affiliation(s)
- Gong Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Junhui Hou
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Chenxue Mei
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yuan Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, China.
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KIAA1429 promotes tumorigenesis and gefitinib resistance in lung adenocarcinoma by activating the JNK/ MAPK pathway in an m 6A-dependent manner. Drug Resist Updat 2023; 66:100908. [PMID: 36493511 DOI: 10.1016/j.drup.2022.100908] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/09/2022]
Abstract
Non-small cell lung cancer is the leading cause of cancer related mortality worldwide, and lung adenocarcinoma (LUAD) is one of the most common subtypes. The role of N6-methyladenosine (m6A) modification in tumorigenesis and drug resistance in LUAD remains unclear. In this study, we evaluated the effects of vir-like m6A methyltransferase-associated protein (KIAA1429) depletion on proliferation, migration, invasion, and drug resistance of LUAD cells, and identified m6A-dependent downstream genes influenced by KIAA1429. We found that KIAA1429 activated Jun N-terminal kinase (JNK) mitogen-activated protein kinase (MAPK) pathway as a novel signaling event, which is responsible for tumorigenesis and resistance to gefitinib in LUAD cells. KIAA1429 and MAP3K2 showed high expression in LUAD patients' tissues. Knockdown of KIAA1429 inhibited MAP3K2 expression in an m6A methylation-dependent manner, restraining the progression of LUAD cells and inhibiting growth of gefitinib-resistant HCC827 cells. KIAA1429 positively regulated MAP3K2 expression, activated JNK/ MAPK pathway, and promoted drug resistance in gefitinib-resistant HCC827 cells. We reproduced the in vitro results in nude mouse xenografted with KIAA1429 knockdown cells. Our study showed that the mechanism of m6A KIAA1429-mediated gefitinib resistance in LUAD cells occurs by activating JNK/ MAPK signaling pathway. These findings provide potential targets for molecular therapy and clinical treatment in LUAD patients with gefitinib resistance.
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Tabnak P, Ghasemi Y, Natami M, Khorram R, Ebrahimnezhad M. Role of m 6A modification in dysregulation of Wnt/β-catenin pathway in cancer. Biomed Pharmacother 2023; 157:114023. [PMID: 36403567 DOI: 10.1016/j.biopha.2022.114023] [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: 10/04/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
N6-methyladenosine (m6A) modification is the most abundant post-transcriptional regulation of RNAs in eukaryotes. Dysregulation of m6A readers, writers, and erasers can significantly promote tumorigenesis by altering the expression of various genes. Wnt/β-catenin is an evolutionarily conserved signaling pathway that has recently been linked to the pathogenesis of many cancers. Given the significance of this pathway in regulating normal tissue homeostasis and stem cell differentiation, a subtle understanding of the molecular mechanism underlying its dysregulation is required for effective targeting. There is mounting evidence that m6A regulators are highly implicated in the dysregulation of the Wnt/β-catenin signaling pathway. Since m6A regulators can affect Wnt pathway components and dysregulation of either leads to carcinogenesis, this study aims to clarify the relationship between m6A regulators and the Wnt/β-catenin signaling pathway to investigate their combined impact on tumorigenesis.
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Affiliation(s)
- Peyman Tabnak
- Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5165665931, Iran.
| | - Yaser Ghasemi
- Faculty of Pharmacy, Ramsar Campus, Mazandaran University of Medical Sciences, Ramsar, Iran.
| | - Mohammad Natami
- Department of Urology, Shahid Mohammadi Hospital, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Roya Khorram
- Bone and Joint Diseases Research Center, Department of Orthopedic Surgery, Shiraz University of Medical Sciences, Shiraz, Iran.
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12
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Wang J, Wang L, Tian X, Luo L. N 6-methyladenosine reader YTHDF1 regulates the proliferation and migration of airway smooth muscle cells through m 6A/cyclin D1 in asthma. PeerJ 2023; 11:e14951. [PMID: 36992945 PMCID: PMC10042154 DOI: 10.7717/peerj.14951] [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: 09/19/2022] [Accepted: 02/03/2023] [Indexed: 03/31/2023] Open
Abstract
Asthma is a chronic inflammatory respiratory disease, which is involved in multiple pathologic molecular mechanisms and presents a huge challenge to clinic nursing. Emerging evidence suggests that N6-methyladenosine (m6A) plays critical roles in respiratory system disease. Thus, present work tried to investigate the functions of m6A reader YTHDF 1 in asthma. The results indicated that YTHDF1 significantly upregulated in platelet-derived growth factor (PDGF) induced airway smooth muscle cells (ASMCs). Functionally, overexpression of YTHDF1 promoted the proliferation and migration of ASMCs, while YTHDF1 knockdown repressed the proliferation and migration. Mechanistically, there was a m6A modification site on cyclin D1 RNA (CCND1 genome) and YTHDF1 combined with cyclin D1 mRNA, thereby enhancing its mRNA stability via m6A-dependent manner. Collectively, these findings reveal a novel axis of YTHDF1/m6A/cyclin D1 in asthma's airway remodeling, which may provide novel therapeutic strategy for asthma.
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Affiliation(s)
- Juan Wang
- Department of Nursing, Fenyang Colleage of Shanxi Medical University, Fenyang, China
| | - Lei Wang
- College of Nursing, Shanxi Medical University, Taiyuan, China
| | - Xingfeng Tian
- Department of Student Affairs, Fenyang Colleage of Shanxi Medical University, Fenyang, China
| | - Lingping Luo
- Department of Nursing, Fenyang Colleage of Shanxi Medical University, Fenyang, China
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13
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Quan L, Jia C, Guo Y, Chen Y, Wang X, Xu Q, Zhang Y. HNRNPA2B1-mediated m6A modification of TLR4 mRNA promotes progression of multiple myeloma. J Transl Med 2022; 20:537. [PMID: 36401285 PMCID: PMC9673362 DOI: 10.1186/s12967-022-03750-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Multiple myeloma (MM) is a malignancy of plasma cells that remains incurable. Toll-like receptor 4 (TLR4) acts as a stress-responsive signal, protecting mitochondria during proteasome inhibitor (PI) exposure, maintaining mitochondrial metabolism and increasing drug resistance in MM. However, the mechanism of TLR4 regulation remains elusive. AIMS The purpose of this study was to investigate the methylation pattern of multiple myeloma and its effect on the expression of HNRNPA2B1 and downstream targets. METHODS The methylation level in MM and normal bone marrow specimens was detected using a colorimetric assay. HNRNPA2B1 gene knockdown was achieved in RPMI 8226 MM cells via adenovirus transfection. CCK8 and flow cytometric assays were used to detect proliferation and apoptosis, respectively. Transcriptome sequencing and m6A methylation MeRIP sequencing were applied, and differentially expressed genes (DEGs) were detected. Three independent NCBI GEO datasets were applied to examine the effects of HNRNPA2B1 and TLR4 expression on MM patient survival. RESULTS HNRNPA2B1 promoted MM progression. Clinical data from database revealed that HNRNPA2B1 was adverse prognostic factor for survival among MM patients. Furthermore, transcriptome sequencing and methylation sequencing showed that HNRNPA2B1 recognized and was enriched at the m6A sites of TLR4 and TLR4 was down-regulated of both the m6A level and transcription level in HNRNPA2B1-knockdown MM cells. Moreover, TLR4 was an adverse survival prognostic factor based on database analysis. CONCLUSION Overall, our study implies that the RNA-binding protein HNRNPA2B1 increases cell proliferation and deregulates cell apoptosis in MM through TLR4 signaling. Our study suggests HNRNPA2B1 as a potential therapeutic target for MM.
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Affiliation(s)
- Lina Quan
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Chuiming Jia
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Yiwei Guo
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Yao Chen
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Xinya Wang
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Qiuting Xu
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Yu Zhang
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
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14
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Chang Y, Yu S, Zhang M, Zhu X, Jiang T, Liu Y. N6-Methyladenosine-related alternative splicing events play a role in bladder cancer. Open Life Sci 2022. [DOI: 10.1515/biol-2022-0479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
This study investigated the role of N6-methyladenosine (m6A) and alternative splicing (AS) in bladder cancer (BLCA). The BLCA-related RNA expression profiles and AS events were downloaded from the UCSC Xena and SpliceSeq databases, respectively. Differentially expressed AS (DEAS) was screened, and prognostic-related DEAS events were used to construct prognostic risk models based on Cox proportional hazards regression analysis. Receiver operating characteristic curves and multivariate Cox analysis were used to evaluate the predictive efficiency and independence of these models. We also constructed a protein-to-protein interaction (PPI) network and a regulation network of splicing factors (SFs) and DEAS events. In total, 225 m6A-related prognostic-related DEAS events were identified. The predictive ability of each prognostic model was good, and the alternate terminator model showed the best performance when the area under the curve was 0.793. The risk score of the model was an independent prognostic factor for BLCA. The PPI network revealed that AKT serine/threonine kinase 1, serine- and arginine-rich SF6, and serine- and arginine-rich SF2 had higher-node degrees. A complex regulator correlation was shown in the SF and DEAS networks. This study provides insights for the subsequent understanding of the role of AS events in BLCA.
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Affiliation(s)
- Yuan Chang
- Department of Nursing, Affiliated Hospital of Beihua University , No. 12 Jiefangzhong Road, Chuanying District , Jilin , Jilin Province, 132011 , China
| | - Shukun Yu
- Department of Nursing, Affiliated Hospital of Beihua University , No. 12 Jiefangzhong Road, Chuanying District , Jilin , Jilin Province, 132011 , China
| | - Miao Zhang
- Department of Nursing, College of Nursing, Beihua University , Jilin , 132013 , China
| | - Xiuyun Zhu
- Department of Nursing, College of Nursing, Beihua University , Jilin , 132013 , China
| | - Tianshu Jiang
- Department of Nursing, College of Nursing, Beihua University , Jilin , 132013 , China
| | - Yuan Liu
- Department of Nursing, College of Nursing, Beihua University , Jilin , 132013 , China
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15
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Xu L, Zhou L, Yan C, Li L. Emerging role of N6-methyladenosine RNA methylation in lung diseases. Exp Biol Med (Maywood) 2022; 247:1862-1872. [PMID: 36278325 PMCID: PMC9679358 DOI: 10.1177/15353702221128564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In recent years, with the increase of air pollution, smoking, aging, and respiratory infection, the incidence rate and mortality of lung diseases are increasing annually, which has become a major hazard to human health. N6-methyladenosine (m6A) RNA methylation is the most abundant modifications in eukaryotes, and such modified RNA can be specifically recognized and combined by m6A recognition proteins and then mediate RNA splicing, maturation, enucleation, degradation, and translation. More and more studies have revealed that the m6A modification is involved in the pathogenesis and development of some diseases; however, the mechanisms of m6A in lung diseases are poorly understood. In this review, we summarize the latest progress in the biological function of m6A modifications in lung diseases and discuss the potential therapeutic and prognostic strategies. The dysregulation of global m6A levels and m6A regulators may affect the occurrence and development of asthma, chronic obstructive pulmonary disease, lung cancer, and other lung diseases through inflammation and immune function. In lung cancer, this modification has an important impact on malignant cell proliferation, migration, invasion, and drug resistance. In addition, abnormally changed m6A-modified proteins in lung cancer tissue samples and circulating tumor cells (CTCs) may be used as diagnostic and prognostic markers of lung cancer. Models composed of multiple m6A regulators can be used to evaluate the risk prediction or prognosis of asthma and pulmonary fibrosis. In general, the in-depth study of m6A modifications is a frontier direction in disease research. It provides novel insights for understanding of the molecular mechanisms underlying disease occurrence, development, and drug resistance, as well as for the development of effective novel therapeutics.
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Affiliation(s)
- Limin Xu
- Huzhou Central Hospital, Affiliated Hospital of Huzhou Normal University, Huzhou 313000, China,Huzhou Hospital, Zhejiang University, Huzhou 313000, China
| | - Lingyan Zhou
- Huzhou Central Hospital, Affiliated Hospital of Huzhou Normal University, Huzhou 313000, China,Huzhou Hospital, Zhejiang University, Huzhou 313000, China
| | - Chenxin Yan
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Liqin Li
- Huzhou Central Hospital, Affiliated Hospital of Huzhou Normal University, Huzhou 313000, China,Huzhou Hospital, Zhejiang University, Huzhou 313000, China,Liqin Li.
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16
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Deng H, Tang F, Zhou M, Shan D, Chen X, Cao K. Identification and Validation of N6-Methyladenosine-Related Biomarkers for Bladder Cancer: Implications for Immunotherapy. Front Oncol 2022; 12:820242. [PMID: 35311150 PMCID: PMC8924666 DOI: 10.3389/fonc.2022.820242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022] Open
Abstract
N6-methyladenosine (m6A) has emerged as one of the most important modifications of RNA. Based on the expression of 23 different modes of m6A regulatory factors, we identified three different m6A modification patterns in bladder cancer. The effects of the three different modes of m6A modification on clinicopathological characteristics, immune cell infiltration levels and expression levels of immune checkpoint genes were comprehensively analyzed. In addition, the effects of different modes of m6A modification on the therapeutic efficacy of anti-PD-L1 immunotherapy (atezolizumab) are also discussed. Our results confirm that m6A methylation plays an important role in immune cell recruitment in the tumor microenvironment of bladder cancer, which influences the efficacy of anti-PD-L1 therapy for bladder cancer. We further confirmed the important role of FTO protein in the biological function of bladder cancer cells by performing in vitro experiments. FTO functions as an oncogene in bladder cancer cells, and upon FTO knockdown, the level of m6A enzyme activity in bladder cancer cells was significantly increased, apoptosis was increased, and cell proliferation and cell invasion were reduced. In addition, our study also confirmed that K216H and K216E are probably important targets for regulating FTO. We provide new insights into the regulatory pathways of the immune microenvironment and the methylation function of m6A in bladder cancer, which will help in designing novel diagnostic methods, prognostic tools, and therapeutic targets.
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Affiliation(s)
- Hongyu Deng
- Department of Clinical Laboratory, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Faqing Tang
- Department of Clinical Laboratory, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Ming Zhou
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Dongyong Shan
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Xingyu Chen
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Ke Cao
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
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17
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Quan Y, Zhang X, Ping H. Construction of a risk prediction model using m6A RNA methylation regulators in prostate cancer: comprehensive bioinformatic analysis and histological validation. Cancer Cell Int 2022; 22:33. [PMID: 35045837 PMCID: PMC8772220 DOI: 10.1186/s12935-021-02438-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/30/2021] [Indexed: 02/06/2023] Open
Abstract
Background Epigenetic reprogramming reportedly has a crucial role in prostate cancer (PCa) progression. RNA modification is a hot topic in epigenetics, and N6-methyladenosine (m6A) accounts for approximately 60% of RNA chemical modifications. The aim of this study was to evaluate the m6A modification patterns in PCa patients and construct a risk prediction model using m6A RNA regulators. Materials and methods Analyses were based on the levels of 25 m6A regulators in The Cancer Genome Atlas (TCGA). Differentially expressed gene (DEG) and survival analyses were performed according to TCGA-PRAD clinicopathologic and follow-up information. To detect the influences of m6A regulators and their DEGs, consensus clustering analysis was performed, and tumor mutational burden (TMB) estimation and tumor microenvironment (TME) cell infiltration were assessed. mRNA levels of representative genes were verified using clinical PCa data. Results Diverse expression patterns of m6A regulators between tumor and normal (TN) tissues were detected regarding Gleason score (GS), pathological T stage (pT), TP53 mutation, and survival comparisons, with HNRNPA2B1 and IGFBP3 being intersecting genes. HNRNPA2B1 was upregulated in advanced stages (GS > 7, pT3, HR > 1, and TP53 mutation), as verified using clinical PCa tissue. Three distinct m6A modification patterns were identified through consensus clustering analysis, but no significant difference was found among these groups in recurrence-free survival (RFS) analysis. Six DEGs of m6A clusters (m6Aclusters) were screened through univariate Cox regression analysis. MMAB and PAIAP2 were intersecting genes for the five clinical factors. MMAB, which was upregulated in PCa compared with TN, was verified using clinical PCa samples. Three distinct subgroups were established according to the 6 DEGs. Cluster A involved the most advanced stages and had the poorest RFS. The m6A score (m6Ascore) was calculated based on the 6 genes, and the low m6Ascore group showed poor RFS with a negative association with infiltration for 16 of 23 immune-related cells. Conclusion We screened DEGs of m6Aclusters and identified 6 genes (BAIAP2, TEX264, MMAB, JAGN1, TIMM8AP1, and IMP3), with which we constructed a highly predictive model with prognostic value by dividing TCGA-PRAD into three distinct subgroups and performing m6Ascore analysis. This study helps to elucidate the integral effects of m6A modification patterns on PCa progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02438-1.
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18
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Zhang Q, Xu K. The role of regulators of RNA m6A methylation in lung cancer. Genes Dis 2022; 10:495-504. [DOI: 10.1016/j.gendis.2021.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022] Open
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19
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Tan S, Li Z, Li K, Li Y, Liang G, Tang Z, Kang J, Chen W, Li M, Zou Z, Pi G, Zhu X. The Regulators Associated With N6-Methyladenosine in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma Reveal New Clinical and Prognostic Markers. Front Cell Dev Biol 2021; 9:741521. [PMID: 34957092 PMCID: PMC8695426 DOI: 10.3389/fcell.2021.741521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/07/2021] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine (m6A) methylation is of significant importance in the initiation and progression of tumors, but how specific genes take effect in different lung cancers still needs to be explored. The aim of this study is to analyze the correlation between the m6A RNA methylation regulators and the occurrence and development of lung cancer. The data of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) were obtained through the TCGA database. We systematically analyzed the related pathological characteristics and prognostic factors by applying univariate and multivariate Cox regression, as well as LASSO Cox regression. Some of 23 m6A regulators are identified as having high expression in lung cancer. In addition, risk score has been shown to be an independent prognostic factor in lung cancer. Our research not only fully reveals that m6A regulators and clinical pathological characteristics are potentially useful with respect to survival and prognosis in different lung tumors but also can lay a theoretical root for the treatment for lung cancer—notably, to point out a new direction for the development of treatment.
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Affiliation(s)
- Shuzhen Tan
- Anhui Clinical and Preclinical Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China
| | - Zesong Li
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, China
| | - Kai Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China
| | - Yingqi Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China
| | - Guosheng Liang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China
| | - Zhenye Tang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China
| | - Jianhao Kang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China
| | - Wenqing Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China
| | - Minhua Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China
| | - Zhilin Zou
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China
| | - Guoliang Pi
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao Zhu
- Anhui Clinical and Preclinical Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, China
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20
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Zhang N, Zuo Y, Peng Y, Zuo L. Function of N6-Methyladenosine Modification in Tumors. JOURNAL OF ONCOLOGY 2021; 2021:6461552. [PMID: 34858499 PMCID: PMC8632389 DOI: 10.1155/2021/6461552] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 02/08/2023]
Abstract
N6-Methyladenosine (m6A) modification is a dynamic and reversible methylation modification at the N6-position of adenosine. As one of the most prevalent posttranscriptional methylation modifications of RNA, m6A modification participates in several mRNA processes, including nuclear export, splicing, translation, and degradation. Some proteins, such as METTL3, METTL14, WTAP, ALKBH5, FTO, and YTHDF1/2/3, are involved in methylation. These proteins are subdivided into writers (METTL3, METTL14, WTAP), erasers (ALKBH5, FTO), and readers (YTHDF1/2/3) according to their functions in m6A modification. Several studies have shown that abnormal m6A modification occurs in tumors, including colorectal cancer, liver cancer, breast cancer, nasopharyngeal carcinoma, and gastric cancer. The proteins for m6A modification are involved in tumor proliferation, angiogenesis, metastasis, immunity, and other processes. Herein, the roles of m6A modification in cancer are discussed, which will improve the understanding of tumorigenesis, as well as the diagnosis, treatment, and prognosis of tumors.
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Affiliation(s)
- Nan Zhang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical School, University of South China, 28 West Changsheng Road, Hengyang 421001, Hunan, China
| | - Yuxin Zuo
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical School, University of South China, 28 West Changsheng Road, Hengyang 421001, Hunan, China
| | - Yu Peng
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical School, University of South China, 28 West Changsheng Road, Hengyang 421001, Hunan, China
| | - Lielian Zuo
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical School, University of South China, 28 West Changsheng Road, Hengyang 421001, Hunan, China
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21
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Chen T, Li Y, Ma DZ, Zhang Z, Xi JF, Luo GZ. Establishment of transposase-assisted low-input m 6A sequencing technique. J Genet Genomics 2021; 48:1036-1039. [PMID: 34474182 DOI: 10.1016/j.jgg.2021.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/21/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Tao Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yan Li
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Dong-Zhao Ma
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhang Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian-Fei Xi
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Guan-Zheng Luo
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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22
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Si C, Chen C, Guo Y, Kang Q, Sun Z. Effect, Mechanism, and Applications of Coding/Non-coding RNA m6A Modification in Tumor Microenvironment. Front Cell Dev Biol 2021; 9:711815. [PMID: 34660577 PMCID: PMC8514707 DOI: 10.3389/fcell.2021.711815] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
The tumor microenvironment (TME), which includes immune cells, fibroblasts, and other components, is the site of tumor cell growth and metastasis and significantly impacts tumor development. Among them, N6-methyladenosine RNA modifications (m6A RNA modifications) are the most abundant internal modifications in coding and non-coding RNAs, which can significantly influence the cancer process and have potential as biomarkers and potential therapeutic targets for tumor therapy. This manuscript reviews the role of m6A RNA modifications in TME and their application in tumor therapy. To some extent, an in-depth understanding of the relationship between TME and m6A RNA modifications will provide new approaches and ideas for future cancer therapy.
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Affiliation(s)
- Chaohua Si
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Chen Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yaxin Guo
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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23
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Xie S, Wang Y, Huang J, Li G. A novel m6A-related prognostic signature for predicting the overall survival of hepatocellular carcinoma patients. IET Syst Biol 2021; 16:1-17. [PMID: 34647424 PMCID: PMC8849219 DOI: 10.1049/syb2.12036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/25/2021] [Accepted: 10/03/2021] [Indexed: 12/13/2022] Open
Abstract
Liver hepatocellular carcinoma (LIHC) comprises most cases of liver cancer with a poor prognosis. N6‐methyladenosine (m6A) plays important biological functions in cancers. Thus, the present research was aimed to determine biomarkers of m6A regulators that could effectively predict the prognosis of LIHC patients. Based on the data collected from the Cancer Genome Atlas (TCGA) database, the correlation between the mRNA expression levels and copy number variation (CNV) patterns were determined. Higher mRNA expression resulted from the increasing number of 9 genes. Using the univariate Cox regression analysis, 11 m6A regulators that had close correlations with the LIHC prognosis were identified. In addition, under the support of the multivariate Cox regression models and the least absolute shrinkage and selection operator, a 4‐gene (YTHDF2, IGF2BP3, KIAA1429, and ALKBH5) signature of m6A regulators was constructed. This signature was expected to present a prognostic value in LIHC (log‐rank test p value < 0.0001). The GSE76427 (n = 94) and ICGC‐LIRI‐JP (n = 212) datasets were used to validate the prognostic signature, suggesting strong power to predict patients' prognosis for LIHC. To sum up, genetic alterations in m6A regulatory genes were identified as reliable and effective biomarkers for predicting the prognosis of LIHC patients.
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Affiliation(s)
- Shiyang Xie
- Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang, China
| | - Yaxuan Wang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Jin Huang
- Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang, China
| | - Guang Li
- Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang, China
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Su X, Shen Y, Jin Y, Kim IM, Weintraub NL, Tang Y. Aging-Associated Differences in Epitranscriptomic m6A Regulation in Response to Acute Cardiac Ischemia/Reperfusion Injury in Female Mice. Front Pharmacol 2021; 12:654316. [PMID: 34413770 PMCID: PMC8369344 DOI: 10.3389/fphar.2021.654316] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/20/2021] [Indexed: 01/14/2023] Open
Abstract
Elderly patients are more susceptible to ischemic injury. N6-methyladenosine (m6A) modification is the most abundant reversible epitranscriptomic modification in mammalian RNA and plays a vital role in many biological processes. However, it is unclear whether age difference impacts m6A RNA methylation in hearts and their response to acute myocardial ischemia/reperfusion (I/R) injury. In this study, we measured the global level of m6A RNA methylation as well as the expression of m6A RNA "writers" (methylation enzymes) and "erasers" (demethylation enzymes) in the hearts of young and elderly female mice undergone sham surgery or acute MI/R injury. We found that m6A RNA level and associate modifier gene expression was similar in intact young and old female hearts. However, young hearts show a significant reduction in m6A RNA while elderly hearts showed only a slight reduction in m6A RNA in response to acute I/R injury. To explore the mechanism of differential level of m6A RNA modification, we use qRT-PCR and Western blotting to compare the mRNA and protein expression of major m6A-related "writers" (Mettl3, Mettl14, and WTAP) and 'erasers" (ALKBH5 and FTO). Mettl3 mRNA and protein expression were significantly reduced in both young and elderly hearts. However, the levels of FTO's mRNA and protein were only significantly reduced in ischemic elderly hearts, and age-related downregulation of FTO may offset the effect of reduced Mettl3 on reduced m6A RNA level in the hearts of aging mice hearts with acute I/R injury, indicating aging-related differences in epitranscriptomic m6A regulation in hearts in response to acute I/R injury. To further investigate specific I/R related targets of Mettl3, we overexpressed Mettl3 in cardiomyocyte line (HL1) using lentiviral vector, and the m6A enrichment of Bcl2, Bax and PTEN were quantified with m6A RIP-qPCR, we found that m6A modification of PTEN mRNA decreased after in vitro hypoxia/reperfusion injury (iH/R) while Mettl3 augments m6A levels of both Bax and PTEN after iH/R, indicating that Bax and PTEN are target genes of Mettl3 under iH/R stress.
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Affiliation(s)
- Xuan Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Yan Shen
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Yue Jin
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Il-man Kim
- Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Neal L. Weintraub
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Yaoliang Tang
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
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25
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Xiang Y, Zhou C, Zeng Y, Guo Q, Huang J, Wu T, Liu J, Liang Q, Zeng H, Liang X. NAT10-Mediated N4-Acetylcytidine of RNA Contributes to Post-transcriptional Regulation of Mouse Oocyte Maturation in vitro. Front Cell Dev Biol 2021; 9:704341. [PMID: 34395433 PMCID: PMC8363255 DOI: 10.3389/fcell.2021.704341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
N4-acetylcytidine (ac4C), a newly identified epigenetic modification within mRNA, has been characterized as a crucial regulator of mRNA stability and translation efficiency. However, the role of ac4C during oocyte maturation, the process mainly controlled via post-transcriptional mechanisms, has not been explored. N-acetyltransferase 10 (NAT10) is the only known enzyme responsible for ac4C production in mammals and ac4C-binding proteins have not been reported yet. In this study, we have documented decreasing trends of both ac4C and NAT10 expression from immature to mature mouse oocytes. With NAT10 knockdown mediated by small interfering RNA (siRNA) in germinal vesicle (GV)-stage oocytes, ac4C modification was reduced and meiotic maturation in vitro was significantly retarded. Specifically, the rate of first polar body extrusion was significantly decreased with NAT10 knockdown (34.6%) compared to control oocytes without transfection (74.6%) and oocytes transfected with negative control siRNA (72.6%) (p < 0.001), while rates of germinal vesicle breakdown (GVBD) were not significantly different (p = 0.6531). RNA immunoprecipitation and high-throughput sequencing using HEK293T cells revealed that the modulated genes were enriched in biological processes associated with nucleosome assembly, chromatin silencing, chromatin modification and cytoskeletal anchoring. In addition, we identified TBL3 as a potential ac4C-binding protein by a bioinformatics algorithm and RNA pulldown with HEK293T cells, which may mediate downstream cellular activities. Taken together, our results suggest that NAT10-mediated ac4C modification is an important regulatory factor during oocyte maturation in vitro and TBL3 is a potential ac4C-binding protein.
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Affiliation(s)
- Yuting Xiang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chuanchuan Zhou
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanyan Zeng
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qi Guo
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiana Huang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Taibao Wu
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiawen Liu
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qiqi Liang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haitao Zeng
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Liang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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26
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Dang Q, Shao B, Zhou Q, Chen C, Guo Y, Wang G, Liu J, Kan Q, Yuan W, Sun Z. RNA N 6-Methyladenosine in Cancer Metastasis: Roles, Mechanisms, and Applications. Front Oncol 2021; 11:681781. [PMID: 34211849 PMCID: PMC8239292 DOI: 10.3389/fonc.2021.681781] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/24/2021] [Indexed: 12/29/2022] Open
Abstract
Cancer metastasis is a symptom of adverse prognosis, a prime origin of therapy failure, and a lethal challenge for cancer patients. N6-methyladenosine (m6A), the most prevailing modification in messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) of higher eukaryotes, has attracted increasing attention. Growing studies have verified the pivotal roles of m6A methylation in controlling mRNAs and ncRNAs in diverse physiological processes. Remarkably, recent findings have showed that aberrant methylation of m6A-related RNAs could influence cancer metastasis. In this review, we illuminate how m6A modifiers act on mRNAs and ncRNAs and modulate metastasis in several cancers, and put forward the clinical application prospects of m6A methylation.
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Affiliation(s)
- Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bo Shao
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Quanbo Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chen Chen
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yaxin Guo
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.,Department of Basic Medical, Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China.,Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Guixian Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Quancheng Kan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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27
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Liu C, Yang Z, Li R, Wu Y, Chi M, Gao S, Sun X, Meng X, Wang B. Potential roles of N6-methyladenosine (m6A) in immune cells. J Transl Med 2021; 19:251. [PMID: 34103054 PMCID: PMC8186046 DOI: 10.1186/s12967-021-02918-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/29/2021] [Indexed: 12/20/2022] Open
Abstract
N6-methyl-adenosine (m6A) is one of the most common internal modifications on RNA molecules present in mammalian cells. Deregulation of m6A modification has been recently implicated in many types of human diseases. Therefore, m6A modification has become a research hotspot for its potential therapeutic applications in the treatment of various diseases. The immune system mostly involves different types of immune cells to provide the first line of defense against infections. The immunoregulatory network that orchestrate the immune responses to new pathogens plays a pivotal role in the development of the disease. And m6A modification has been demonstrated to be a major post-transcriptional regulator of immune responses in cells. In this review, we summarize the participants involved in m6A regulation and try to reveal how m6A modification affects the immune responses via changing the immunoregulatory networks.
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Affiliation(s)
- Chang Liu
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, No. 155 NanJing North Road, Shenyang, China
| | - Zhe Yang
- College of Life Science, Liaoning University, 66 Chongshan Road, Shenyang, 110036, People's Republic of China
| | - Rong Li
- College of Life Science, Liaoning University, 66 Chongshan Road, Shenyang, 110036, People's Republic of China
| | - Yanju Wu
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Ming Chi
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Shuting Gao
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Xun Sun
- Department of Immunology, College of Basic Medical Sciences of China Medical University, , No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Xin Meng
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Biao Wang
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China.
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28
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Zhang Q, Luan J, Song L, Wei X, Xia J, Song N. Malignant Evaluation and Clinical Prognostic Values of M6A RNA Methylation Regulators in Prostate Cancer. J Cancer 2021; 12:3575-3586. [PMID: 33995635 PMCID: PMC8120168 DOI: 10.7150/jca.55140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/09/2021] [Indexed: 01/09/2023] Open
Abstract
Objective: M6A RNA modification is closely associated with tumor genesis and progression of several malignancies; however, its role in prostate cancer (PCa) remains poorly understood. Materials and methods: Expression data and corresponding clinicopathologic information were available freely from the Cancer Genome Atlas (TCGA) dataset. We compared the expression level of m6A RNA methylation regulators in PCa with different clinicopathologic characteristics and identified subgroups based on their expressions with consensus clustering. To build the signature and assess its prognostic value, several methods were used for the analysis, including univariate Cox regression analysis, Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis, time-dependent receiver operating curve (ROC), and Kaplan-Meier (KM) survival analysis. Results: Most of the m6A RNA methylation regulators were differentially expressed not only between normal and tumor tissue but also among PCa stratified by different clinicopathologic characteristics. There were obvious differences between two clusters, cluster 1 and 2, regarding clinicopathologic features, and the recurrence-free survival (RFS) in cluster 2 was significantly worse than cluster 1. We developed an eleven-gene signature which exhibited a high prognostic value and was able to independently predict RFS. Moreover, a nomogram which integrated clinical information and the gene signature was capable of distinguishing high-risk recurrent patients. Conclusion: These methylation regulators are correlated to clinicopathologic characteristics in PCa and a prognostic model using m6A methylation-related genes is constructed and of high predictive value for recurrence after RP.
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Affiliation(s)
- Qijie Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiaochen Luan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lebin Song
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiyi Wei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiadong Xia
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ninghong Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The Affiliated Kezhou People's Hospital of Nanjing Medical University, Kezhou, Xinjiang, China
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29
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Xu F, Guan Y, Ma Y, Xue L, Zhang P, Yang X, Chong T. Bioinformatic analyses and experimental validation of the role of m6A RNA methylation regulators in progression and prognosis of adrenocortical carcinoma. Aging (Albany NY) 2021; 13:11919-11941. [PMID: 33952721 PMCID: PMC8109058 DOI: 10.18632/aging.202896] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/14/2021] [Indexed: 04/11/2023]
Abstract
M6A-related genes have been proven to play an important role in many cancers. However, the role of that in adrenocortical carcinoma (ACC) has not been fully elucidated. In the present study, 77 ACC samples from TCGA database were divided into localized (n = 46) and metastatic (n = 31) groups. Three differential expression genes (DEGs) and five prognostic m6A genes were screened out. M6A-related risk signature (RBM15 and HNRNPC) was constructed by the Lasso regression analysis. In TCGA cohort (training cohort), the risk signature was identified as an ACC-independent prognostic factor and can distinguish the prognostic difference of ACC patients with clinical stage I-II, T3-4 and N0 stages. A nomogram combining T stage and m6A risk score was constructed to predict the overall survival rate (OSR) of individual at 1,2,3 year. Meanwhile, its prognostic value was also confirmed in the validation cohort (GSE33371 dataset). The potential associations between m6A risk level and immune checkpoint inhibitors (ICIs) therapy were also investigated via the TISIDB online tool. High m6A risk not only can suppress immunotherapy-related biological processes, but also repress the expressions of immune-checkpoint markers. Moreover, five pairs of clinical specimens were collected to confirm the overexpression of HNRNPC and non-ectopic expression of RBM15 in tumor tissues. HNRNPC was proven to promote the proliferation, migration and invasion of H295R and SW13 cells through MTT and Transwell assays. In conclusion, the m6A-related risk signature was beneficial for prognostic analysis and can affect immune microenvironment in ACC. HNRNPC played a pro-cancer role in ACC progression.
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Affiliation(s)
- Fangshi Xu
- Department of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi 710061, China
| | - Yibing Guan
- Department of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi 710061, China
| | - Yubo Ma
- Department of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi 710061, China
| | - Li Xue
- Department of Urology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710000, China
| | - Peng Zhang
- Department of Urology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710000, China
| | - Xiaojie Yang
- Department of Urology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710000, China
| | - Tie Chong
- Department of Urology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710000, China
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30
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Jing JJ, Zhao X, Li H, Sun LP, Yuan Y. Expression profiles and prognostic roles of m6A writers, erasers and readers in gastric cancer. FUTURE ONCOLOGY (LONDON, ENGLAND) 2021; 17:2605-2620. [PMID: 33878934 DOI: 10.2217/fon-2020-0630] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aim: To explore the expression profiles of N6-methyladenosine (m6A) enzymes (writers, erasers and readers) and their associations with gastric cancer (GC) prognosis. Methods: Gene expression was analyzed using the UALCAN and Oncomine web resources. The prognostic roles of these genes in GC were analyzed using data from The Cancer Genome Atlas. Results: Thirteen m6A enzymes were found to be upregulated in GC tissues. The expression of m6A writers METTL3, RBM15 and WTAP was associated with pathological stage. The m6A eraser FTO was related to tumor stage and ALKBH5 expression was related to GC prognosis. The m6A reader YTHDF3 expression was associated with tumor stage. YTHDC2 was associated with survival of GC patients. Conclusion: Abnormal changes of key genes involved in m6A RNA methylation may have an important impact on GC development and prognosis.
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Affiliation(s)
- Jing-Jing Jing
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Xu Zhao
- Mathematical Computer Teaching & Research Office, Liaoning Vocational College of Medicine, Shenyang, 110101, China
| | - Hao Li
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Li-Ping Sun
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Yuan Yuan
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
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31
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Fu Y, Sun S, Bi J, Kong C, Yin L. Expression patterns and prognostic value of m6A RNA methylation regulators in adrenocortical carcinoma. Medicine (Baltimore) 2021; 100:e25031. [PMID: 33725886 PMCID: PMC7969304 DOI: 10.1097/md.0000000000025031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 02/05/2021] [Indexed: 01/05/2023] Open
Abstract
Adrenocortical carcinoma (ACC) is considered a rare cancer with poor prognosis. We used public datasets from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases to assess the relationships between N6-methyladenosine (m6A)-related genes and ACC.We used the Wilcoxon signed-rank test to compare m6A-related gene expression in ACC tissues with that in normal tissues. Then, ACC patients were grouped based on a cluster analysis of m6A-related gene expression. m6A-related genes that were significantly associated with survival were incorporated into a risk signature, and 2 groups were divided according to median risk score. Fisher exact tests were utilized to analyze differences in clinical variables between groups. We compared the overall survival (OS) rates of the groups by means of Kaplan-Meier curves and Cox regression analyses.We found that RBM15, ZC3H3, YTDHF1, YTDHF2, and ALBH5 were overexpressed in ACC and that KIAA1429, YTHDC1, HNRNPC, WTAP, METTL3, and FTO were down regulated in ACC. In addition, membership in cluster 2 or the high-risk group was associated with advanced clinical factors and poor prognosis. The univariable and multivariable Cox regression analyses showed that risk score can be considered an independent prognostic factor for ACC.We found that the expression of m6A-related genes could be used as an independent prognostic factor in ACC. However, the current study has some limitations, and further studies of m6A-related genes in ACC are needed.
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Affiliation(s)
| | - Shanshan Sun
- Department of Pharmacy, The First Hospital of China Medical University, Shenyang, PR China
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32
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FTO overexpression inhibits apoptosis of hypoxia/reoxygenation-treated myocardial cells by regulating m6A modification of Mhrt. Mol Cell Biochem 2021; 476:2171-2179. [PMID: 33548009 DOI: 10.1007/s11010-021-04069-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/12/2021] [Indexed: 12/19/2022]
Abstract
Heart failure (HF) is the end stage of many cardiovascular diseases and seriously threatens people's health. This article aimed to explore the biological role of fat-mass and obesity-associated gene (FTO) in HF. We constructed HF mouse model by transverse aortic constriction or intraperitoneal injection of doxorubicin. Mouse myocardial cells were exposed to hypoxia/reoxygenation (H/R). FTO and Mhrt were downregulated in heart tissues of HF mice. HF mice exhibited an increase in the total levels of N6 methyladenosine (m6A) and the m6A levels of Mhrt. Moreover, FTO overexpression caused an upregulation of Mhrt and reduced m6A modification of Mhrt in the H/R-treated myocardial cells. FTO upregulation repressed apoptosis of H/R-treated myocardial cells. FTO knockdown had the opposite results. Mhrt overexpression reduced apoptosis of H/R-treated myocardial cells. Moreover, the influence conferred by FTO upregulation was abolished by Mhrt knockdown. In conclusion, our data demonstrate that FTO overexpression inhibits apoptosis of hypoxia/reoxygenation-treated myocardial cells by regulating m6A modification of Mhrt. Thus, FTO may be a target gene for HF treatment.
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33
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Identification of a Two-m6A RNA Methylation Regulator Risk Signature as an Independent Prognostic Biomarker in Papillary Renal Cell Carcinoma by Bioinformatic Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4582082. [PMID: 33628782 PMCID: PMC7884118 DOI: 10.1155/2021/4582082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/20/2020] [Accepted: 01/28/2021] [Indexed: 01/22/2023]
Abstract
N6-Methyladenosine (m6A), the most common form of mRNA modification, is dynamically regulated by the m6A RNA methylation regulators, which play an important role in regulating the gene expression and phenotype in both health and disease. However, the role of m6A in papillary renal cell carcinoma (pRCC) is unknown. The purpose of this work is to investigate the prognostic value of m6A RNA methylation regulators in pRCC; thus, we can build a risk score model based on m6A RNA methylation regulators as a risk signature for predicting the prognosis of pRCC. Here, we investigated the expression and corresponding clinical data by bioinformatic analysis based on 289 pRCC tissues and 32 normal kidney tissues obtained from TCGA database. As a result, we identified the landscape of m6A RNA methylation regulators in pRCC. We grouped all pRCC patients into two clusters by consensus clustering to m6A RNA methylation regulators, but we found that the clusters were not correlated to the prognosis and clinicopathological features of pRCC. Therefore, we additionally built a two-m6A RNA methylation regulator risk score model as a risk signature by the univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) Cox regression. The risk signature was constructed as follows: 0.031HNRNPC + 0.199KIAA1429. It revealed that the risk score was associated with the clinicopathological features such as pT status and pN status of pRCC. More importantly, the risk score was an independent prognostic marker for pRCC patients. Thus, m6A RNA methylation regulators contributed to the malignant progression of pRCC influencing its prognosis.
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34
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Pan Y, Yan TM, Wang JR, Jiang ZH. The nature of the modification at position 37 of tRNAPhe correlates with acquired taxol resistance. Nucleic Acids Res 2021; 49:38-52. [PMID: 33290562 PMCID: PMC7797046 DOI: 10.1093/nar/gkaa1164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/30/2020] [Accepted: 11/15/2020] [Indexed: 11/12/2022] Open
Abstract
Acquired drug resistance is a major obstacle in cancer therapy. Recent studies revealed that reprogramming of tRNA modifications modulates cancer survival in response to chemotherapy. However, dynamic changes in tRNA modification were not elucidated. In this study, comparative analysis of the human cancer cell lines and their taxol resistant strains based on tRNA mapping was performed by using UHPLC-MS/MS. It was observed for the first time in all three cell lines that 4-demethylwyosine (imG-14) substitutes for hydroxywybutosine (OHyW) due to tRNA-wybutosine synthesizing enzyme-2 (TYW2) downregulation and becomes the predominant modification at the 37th position of tRNAphe in the taxol-resistant strains. Further analysis indicated that the increase in imG-14 levels is caused by downregulation of TYW2. The time courses of the increase in imG-14 and downregulation of TYW2 are consistent with each other as well as consistent with the time course of the development of taxol-resistance. Knockdown of TYW2 in HeLa cells caused both an accumulation of imG-14 and reduction in taxol potency. Taken together, low expression of TYW2 enzyme promotes the cancer survival and resistance to taxol therapy, implying a novel mechanism for taxol resistance. Reduction of imG-14 deposition offers an underlying rationale to overcome taxol resistance in cancer chemotherapy.
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MESH Headings
- A549 Cells
- Base Sequence
- Cell Line, Tumor
- Chromatography, High Pressure Liquid
- Down-Regulation
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/physiology
- Female
- Gene Expression Regulation, Enzymologic
- Gene Knockdown Techniques
- Guanosine/analogs & derivatives
- Guanosine/chemistry
- Guanosine/metabolism
- HeLa Cells
- Humans
- Molecular Structure
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Nucleic Acid Conformation
- Ovarian Neoplasms/pathology
- Paclitaxel/pharmacology
- RNA Processing, Post-Transcriptional/genetics
- RNA, Neoplasm/chemistry
- RNA, Neoplasm/physiology
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/physiology
- Tandem Mass Spectrometry
- Tumor Stem Cell Assay
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Affiliation(s)
- Yu Pan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Tong-Meng Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jing-Rong Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
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35
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Guo W, Zhang C, Feng P, Li M, Wang X, Xia Y, Chen D, Li J. M6A methylation of DEGS2, a key ceramide-synthesizing enzyme, is involved in colorectal cancer progression through ceramide synthesis. Oncogene 2021; 40:5913-5924. [PMID: 34363020 PMCID: PMC8497269 DOI: 10.1038/s41388-021-01987-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent RNA epigenetic regulator in cancer. However, the understanding of m6A modification on lipid metabolism regulation in colorectal cancer (CRC) is very limited. Here, we observed that human CRCs exhibited increased m6A mRNA methylation mediated by dysregulation of m6A erasers and readers. By performing methylated RNA-immunoprecipitation sequencing (MeRIP-seq) and transcriptomic sequencing (RNA-seq), we identified DEGS2 as a downstream target of m6A dysregulation. Overexpression or knockdown of DEGS2 confirmed the role of DEGS2 in proliferation, invasion and metastasis of CRC both in vitro and in vivo. Mechanistic studies identified the specific m6A modification site within DEGS2 mRNA, and mutation of this target site was found to drastically enhance the proliferative and invasive ability of CRC cells in vitro and promote tumorigenicity in vivo. Lipidome analysis showed that lipid metabolism was dysregulated in CRC. Moreover, ceramide synthesis was suppressed due to DEGS2 upregulation mediated by m6A modification in CRC tissues. Our findings highlight that the function of DEGS2 m6A methylation in CRC and extend the understanding of the importance of RNA epigenetics in cancer biology.
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Affiliation(s)
- Wei Guo
- grid.27255.370000 0004 1761 1174Department of Colorectal Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Cuiyu Zhang
- grid.27255.370000 0004 1761 1174Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Panpan Feng
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Mingying Li
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Xia Wang
- grid.27255.370000 0004 1761 1174Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Yuan Xia
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Dawei Chen
- grid.411374.40000 0000 8607 6858Laboratory of Medical Chemistry, Interdisciplinary Cluster for Applied Genoproteomics (GIGA) Stem Cells, Faculty of Medicine, University of Liège, CHU, Sart-Tilman, Liège, Belgium
| | - Jingxin Li
- grid.27255.370000 0004 1761 1174Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
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36
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Povedano E, Gamella M, Torrente-Rodríguez RM, Montero-Calle A, Pedrero M, Solís-Fernández G, Navarro-Villoslada F, Barderas R, Campuzano S, Pingarrón JM. Magnetic microbeads-based amperometric immunoplatform for the rapid and sensitive detection of N6-methyladenosine to assist in metastatic cancer cells discrimination. Biosens Bioelectron 2021; 171:112708. [PMID: 33049562 DOI: 10.1016/j.bios.2020.112708] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022]
Abstract
This work describes the preparation of an immunoplatform for the sensitive and selective determination of N6-methyladenosine (m6A). The simple and fast protocol involves for the first time the use of micromagnetic immunoconjugates to establish a direct competitive assay between the m6A target and a biotinylated RNA oligomer bearing a single m6A enzymatically labelled with a commercial conjugate of streptavidin-peroxidase (Strep-HRP) as tracer. The cathodic current change measured in the presence of H2O2/hydroquinone (HQ) at screen-printed carbon electrodes (SPCEs) upon surface capturing the magnetic bioconjugates is inversely proportional to the m6A target concentration. After evaluating the effect of key variables, the analytical characteristics were established for the determination of three different targets: the N6-methyladenosine-5'-triphosphate (m6ATP) ribonucleotide, a short synthetic RNA oligomer bearing a single m6A and the positive control provided in a commercial colorimetric kit for m6A-RNA quantification. The obtained results show that this immunoplatform is competitive with other methods reported to date, achieving an improved sensitivity (limit of detection of 0.9 pM for the short synthetic oligomer) using a much simpler and faster protocol (~1 h) and disposable electrodes for the transduction. Furthermore, the applicability for discriminating the metastatic potential of cancer cells by directly analyzing a small amount of raw total RNA without enriching or fragmenting was also preliminary assessed.
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Affiliation(s)
- Eloy Povedano
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - María Gamella
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Rebeca M Torrente-Rodríguez
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Ana Montero-Calle
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - María Pedrero
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | | | - Fernando Navarro-Villoslada
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Rodrigo Barderas
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
| | - Susana Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain.
| | - José M Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
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37
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Liu T, Yang S, Cheng YP, Kong XL, Du DD, Wang X, Bai YF, Yin LH, Pu YP, Liang GY. The N6-Methyladenosine (m6A) Methylation Gene YTHDF1 Reveals a Potential Diagnostic Role for Gastric Cancer. Cancer Manag Res 2020; 12:11953-11964. [PMID: 33244271 PMCID: PMC7685380 DOI: 10.2147/cmar.s279370] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose Gastric cancer (GC) is aggressive cancer with a high mortality rate worldwide. N6-methyladenosine (m6A) RNA methylation is related to tumorigenesis, which is dynamically regulated by m6A modulators ("writer," "eraser," and "reader"). We conducted a comprehensive analysis of the m6A genes of GC patients in TCGA datasets to identify the potential diagnostic biomarkers. Materials and Methods We analyzed the expression profile of m6A genes in the TCGA cohort and constructed a diagnostic-m6A-score (DMS) by the LASSO-logistic model. In addition, by consensus cluster analysis, we identified two different subgroups of GC risk individuals by the expression profile of m6A modulators, revealing that YTHDF1's expression variation profile in GC diagnosis. We also performed RT-qPCR and WB verification in 17 pairs of GC specimens and paired adjacent non-tumor tissues and GC cell lines, and verified the expression trend of YTHDF1 in five GEO GC datasets. YTHDF1 expression and clinical features of GC patients were assessed by the UALCAN. Results The DMS with high specificity and sensitivity (AUC = 0.986) is proven to distinguish cancer from normal controls better. Moreover, we found that the expression profile variation of YTHDF1 was significantly associated with the high-risk subtype of GC patients. RT-qPCR and Western blot results are consistent with silicon analysis, revealing that YTHDF1's potential oncogene role in GC tumor. Conclusion In conclusion, we developed the m6A gene-based diagnostic signature for GC and found that YTHDF1 was significantly correlated with the high-risk subtype of GC patients, suggesting that YTHDF1 might be a potential target in GC early diagnosis.
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Affiliation(s)
- Tong Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210096, People's Republic of China
| | - Sheng Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210096, People's Republic of China
| | - Yan-Ping Cheng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210096, People's Republic of China
| | - Xiao-Ling Kong
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210096, People's Republic of China
| | - Dan-Dan Du
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210096, People's Republic of China
| | - Xian Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210096, People's Republic of China
| | - Yun-Fei Bai
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Li-Hong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210096, People's Republic of China
| | - Yue-Pu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210096, People's Republic of China
| | - Ge-Yu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210096, People's Republic of China
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38
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Xu F, Zhang Z, Yuan M, Zhao Y, Zhou Y, Pei H, Bai L. M6A Regulatory Genes Play an Important Role in the Prognosis, Progression and Immune Microenvironment of Pancreatic Adenocarcinoma. Cancer Invest 2020; 39:39-54. [PMID: 33176521 DOI: 10.1080/07357907.2020.1834576] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The specific roles of N6-methyladenosine (m6A) regulatory genes in pancreatic adenocarcinoma (PAAD) have not been fully elucidated. In present study, a novel risk signature was constructed by five m6A-related genes (including METTL3, METTL14, KIAA1429, ALKBH5 and YTHDF1) and was identified as an independent prognostic factor (HR = 13.192) via TCGA (185 samples) databases. The immune abundances of 22 leukocyte subtypes in each PAAD sample were exhibited via the CIBERSORT algorithm. High risk group promoted infiltration levels of Macrophages M0 and M2 cells and decreased that of B cells naive, T cells CD8 and T regulatory cells.
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Affiliation(s)
- Fangshi Xu
- Department of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Zhengliang Zhang
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Miao Yuan
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Yidi Zhao
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Yang Zhou
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Honghong Pei
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Ling Bai
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
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39
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Huo FC, Zhu ZM, Pei DS. N 6 -methyladenosine (m 6 A) RNA modification in human cancer. Cell Prolif 2020; 53:e12921. [PMID: 33029866 PMCID: PMC7653258 DOI: 10.1111/cpr.12921] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/04/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
N6 -methyladenosine (m6 A) RNA modification, first discovered in 1974, is the most prevalent, abundant and penetrating messenger RNA (mRNA) modification in eukaryotes. This governs the fate of modified transcripts, regulates RNA metabolism and biological processes, and participates in pathogenesis of numerous human diseases, especially in cancer through the reciprocal regulation of m6 A methyltransferases ("writers") and demethylases ("erasers") and the binding proteins decoding m6 A methylation ("readers"). Accumulating evidence indicates a complicated regulation network of m6 A modification involving multiple m6 A-associated regulatory proteins whose biological functions have been further analysed. This review aimed to summarize the current knowledge on the potential significance and molecular mechanisms of m6 A RNA modification in the initiation and progression of cancer.
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Affiliation(s)
- Fu-Chun Huo
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
| | - Zhi-Man Zhu
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
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40
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Tang R, Zhang Y, Liang C, Xu J, Meng Q, Hua J, Liu J, Zhang B, Yu X, Shi S. The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma. PeerJ 2020; 8:e9602. [PMID: 33062408 PMCID: PMC7528816 DOI: 10.7717/peerj.9602] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background Pancreatic adenocarcinoma (PAAD) is among the most lethal diseases and has a dismal prognosis; however, efficient treatment is currently limited. Several studies have observed epigenetic variation during tumorigenesis, suggesting the potential role of RNA methylation, especially N6-methyladenosine (m6A) modification, as a novel epigenetic modification mediating PAAD prognosis. Methods The expression levels of m6A-related genes were downloaded from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA) and Genotype-Tissue Expression (GTEx) projects, and the findings were validated in four Expression Omnibus (GEO) datasets. A predictive model was constructed using a lasso regression and evaluated by a survival analysis and receiver operating characteristic curve. Consensus clustering identified two distinct subgroups with different immune activity signatures based on the expression pattern of m6A-related genes. The relationship between the mutation state of m6A-related genes and infiltration of immune cells was established and visualized using Tumor Immune Estimation Resource (https://cistrome.shinyapps.io/timer/). Results Fourteen of twenty-one m6A-related genes were differentially expressed between PAAD and normal tissues in TCGA-GTEx cohort. Among these genes, HNRNPC, IGF2BP2 and YTHDF1 were further validated in four GEO datasets. Moreover, an m6A-based model exhibited moderate accuracy in predicting overall survival in PAAD samples. Additionally, potential m6A modification targets were screened by selecting genes from a set of 23,391 genes that not only harbored the most m6A-modified sites but also showed a robust correlation with PAAD survival. Moreover, we correlated the expression level of m6A-related genes with the immune microenvironment of pancreatic cancer for the first time. Specifically, both arm-level gain and deletion of ALKBH5 decreased the infiltration of CD8+T cells (P < 0.05 and P < 0.01, respectively). Conclusion Collectively, our findings suggest a novel anticancer strategy for restoring balanced RNA methylation in tumor cells and guide clinical physicians in developing a new practical approach for considering the impact of related genes on prognosis.
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Affiliation(s)
- Rong Tang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Yiyin Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Chen Liang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Qingcai Meng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jie Hua
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jiang Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
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41
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m6A RNA methylation regulators can contribute to malignant progression and impact the prognosis of bladder cancer. Biosci Rep 2020; 39:221434. [PMID: 31808521 PMCID: PMC6923333 DOI: 10.1042/bsr20192892] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/24/2019] [Accepted: 12/05/2019] [Indexed: 01/01/2023] Open
Abstract
N6-methyladenosine (m6A) is the most common form of messenger RNA (mRNA) modification. An increasing number of studies have proven that m6A RNA methylation regulators are overexpressed in many cancers and participate in the development of cancer through the dynamic regulation of m6A RNA methylation regulators. However, the prognostic role of m6A RNA methylation regulators in bladder cancer (BC) is poorly understood. In the present study, we downloaded the mRNA expression data from The Cancer Genome Atlas (TCGA) database and the corresponding clinical and prognostic information. The relationship between m6A RNA methylation regulators and clinicopathological variables of BC patients was assessed by the Kolmogorov–Smirnov test. The expression of the m6A RNA methylation regulators was differentially associated with different clinicopathological variables of BC patients. The least absolute shrinkage and selection operator (LASSO) Cox regression model was then applied to identify three m6A RNA methylation regulators. The risk signature was constructed as follows: 0.164FTO − (0.081YTHDC1+0.032WTAP). Based on the risk signature, the risk score of each patient was calculated, and the patients were divided into a high-risk group and a low-risk group. The overall survival (OS) rate of the high-risk group was significantly lower than that of the low-risk group. The risk signature was not only an independent prognostic marker for BC patients but also a predictor of clinicopathological variables. In conclusion, m6A RNA methylation regulators can participate in the malignant progression of BC, and a risk signature with three selected m6A RNA methylation regulators may be a promising prognostic biomarker to guide personalized treatment for BC patients.
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42
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Zhang L, Qiao Y, Huang J, Wan D, Zhou L, Lin S, Zheng S. Expression Pattern and Prognostic Value of Key Regulators for m6A RNA Modification in Hepatocellular Carcinoma. Front Med (Lausanne) 2020; 7:556. [PMID: 33072775 PMCID: PMC7534531 DOI: 10.3389/fmed.2020.00556] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/04/2020] [Indexed: 01/12/2023] Open
Abstract
As the most prevalent type of mRNA modification in mammals, N6-methyladenosine (m6A) is involved in various biological processes. Accumulating studies have indicated that the deregulation of m6A RNA modification is linked to cancer and other diseases. However, its implications in hepatocellular carcinoma (HCC) remain poorly characterized. Herein, we sought to investigate the expression pattern of 13 key regulators for m6A RNA modification and to evaluate their prognostic value in HCC. First, we systematically analyzed data from The Cancer Genome Atlas (TCGA) database pertaining to patient clinical information and mRNA gene expression data. We found that 11 out of 13 key regulators for m6A RNA modification showed significantly higher expression levels in HCC. Subsequently, we identified two subgroups (clusters 1 and 2) via consensus clustering based on the expression of 13 m6A RNA methylation regulators. Cluster 2 had a worse prognosis and was also significantly correlated with higher histological grade and pathological stage when compared with cluster 1. Moreover, cluster 2 was remarkedly enriched for cancer-related pathways. We further constructed a robust risk signature of five regulators for m6A RNA modification. Further analysis indicated that this risk signature could be an independent prognostic factor for HCC, and the prognostic relevance of this five-gene risk signature was successfully validated using the Gene Expression Omnibus (GEO) dataset. Finally, we established a novel prognostic nomogram on the basis of age, gender, histological grade, pathological stage, and risk score to precisely predict the prognosis of patients with HCC. In summary, we herein uncovered the vital role of regulators for m6A RNA modification in HCC and developed a risk signature as a promising prognostic marker in HCC patients.
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Affiliation(s)
- Lele Zhang
- The First Affiliated Hospital, Zhejiang University School of Medicine, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, China
| | - Yiting Qiao
- The First Affiliated Hospital, Zhejiang University School of Medicine, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, China
| | - Jiacheng Huang
- The First Affiliated Hospital, Zhejiang University School of Medicine, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, China
| | - Dalong Wan
- The First Affiliated Hospital, Zhejiang University School of Medicine, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Hangzhou, China
| | - Lin Zhou
- The First Affiliated Hospital, Zhejiang University School of Medicine, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, China
| | - Shengzhang Lin
- School of Medicine, Zhejiang University, Hangzhou, China.,Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
| | - Shusen Zheng
- The First Affiliated Hospital, Zhejiang University School of Medicine, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, China.,Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
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Li N, Zhan X. Identification of pathology-specific regulators of m 6A RNA modification to optimize lung cancer management in the context of predictive, preventive, and personalized medicine. EPMA J 2020; 11:485-504. [PMID: 32849929 DOI: 10.1007/s13167-020-00220-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
Abstract
Relevance Lung cancer is the most common malignant tumor with high morbidity (11.6% of the total diagnosed cancer cases) and mortality (18.4% of the total cancer deaths), and its 5-year survival rate is very low (20%). Clarification of any molecular events and the discovery of effective biomarkers will offer increasing promise for lung canner management. N6-methyladenosine (m6A) modification is one of the important RNA modifications that are closely associated with lung cancer, and are tightly regulated by m6A regulators. Elucidation of pathology-specific m6A regulators will directly contribute to lung cancer medical services in the context of predictive, preventive, and personalized medicine (PPPM). Purpose To investigate pathology-specific regulators of m6A RNA modifications in lung cancer and further inspect the m6A regulator gene signature as useful tools for PPPM in lung cancers. Methods The gene expression data of 19 m6A regulators (m6A-methyltransferases-ZC3H13, KIAA1429, RBM15/15B, WTAP, and METTL3/14; demethylases-FTO and ALKBH5; and m6A-binding proteins-HNRNPC, YTHDF1/2/3, YTHDC1/2, IGF2BP1/2/3, and HNRNPA2B1) and clinical data of 1013 lung cancer patients [511 lung adenocarcinoma (LUAD) and 502 lung squamous carcinoma (LUSC)] and 109 controls (Con) were obtained from the TCGA database. Quantitative real-time PCR (qRT-PCR) was used to verify m6A regulators in lung cancer cell lines. Protein-protein interaction (PPI), gene co-expression, survival analysis, and heatmap were used to analyze these m6A regulators in this set of lung cancer clinical data. Lasso regression was used to optimize the pathology-specific m6A regulator gene signature. Gene set enrichment analysis (GSEA) was used to reveal the functional characteristics of m6A regulators. Results Those 19 m6A regulator profiling was significantly differentially expressed in lung cancer tissues relative to control tissues, which was also verified in lung cancer cell lines. Those m6A regulators interacted mutually, and those regulator-based sample clusters were correlated with clinical traits, including survival status, gender, tobacco smoking history, primary disease, and pathologic stage. Further, lasso regression based on the 19 m6A regulators optimized and identified a three-m6A-regulator signature (KIAA1429, METTL3, and IGF2BP1) as independent prognostic factor, which classified 1013 lung cancer patients into high-risk and low-risk groups according to median value (0.84) of the lasso regression risk scores. This three-m6A-regulator signature profiling was significantly related to lung cancer overall survival, cancer status, and the above-described clinical traits. Further, GSEA revealed that KIAA1429, METTL3, and IGF2BP1 were significantly related to multiple biological behaviors, including proliferation, apoptosis, metastasis, energy metabolism, drug resistance, and recurrence, and that KIAA1429 and IGF2BP1 had potential target genes, including E2F3, WTAP, CCND1, CDK4, EGR2, YBX1, and TLX, which were associated with cancers. Conclusion This study provided the first view of the pathology-specific regulators of m6A RNA modification in lung cancers and identified the three-m6A-regulator signature (KIAA1429, METTL3, and IGF2BP1) as an independent prognostic model to classify lung cancers into high- and low-risk groups for patient stratification, prognostic assessment, and personalized treatment toward PPPM in lung cancers.
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Affiliation(s)
- Na Li
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, 250117 Shandong People's Republic of China.,Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China.,State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, 250117 Shandong People's Republic of China.,Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China.,State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China.,Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China
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Wang Q, Chen C, Ding Q, Zhao Y, Wang Z, Chen J, Jiang Z, Zhang Y, Xu G, Zhang J, Zhou J, Sun B, Zou X, Wang S. METTL3-mediated m 6A modification of HDGF mRNA promotes gastric cancer progression and has prognostic significance. Gut 2020; 69:1193-1205. [PMID: 31582403 DOI: 10.1136/gutjnl-2019-319639] [Citation(s) in RCA: 501] [Impact Index Per Article: 125.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE N6-methyladenosine (m6A) RNA methylation and its associated methyltransferase METTL3 are involved in tumour initiation and progression via the regulation of RNA function. This study explored the biological function and clinical significance of METTL3 in gastric cancer (GC). DESIGN The prognostic value of METTL3 expression was evaluated using tissue microarray and immunohistochemical staining analyses in a human GC cohort. The biological role and mechanism of METTL3 in GC tumour growth and liver metastasis were determined in vitro and in vivo. RESULTS The level of m6A RNA was significantly increased in GC, and METTL3 was the main regulator involved in the abundant m6A RNA modification. METTL3 expression was significantly elevated in GC tissues and associated with poor prognosis. Multivariate Cox regression analysis revealed that METTL3 expression was an independent prognostic factor and effective predictor in human patients with GC. Moreover, METTL3 overexpression promoted GC proliferation and liver metastasis in vitro and in vivo. Mechanistically, P300-mediated H3K27 acetylation activation in the promoter of METTL3 induced METTL3 transcription, which stimulated m6A modification of HDGF mRNA, and the m6A reader IGF2BP3 then directly recognised and bound to the m6A site on HDGF mRNA and enhanced HDGF mRNA stability. Secreted HDGF promoted tumour angiogenesis, while nuclear HDGF activated GLUT4 and ENO2 expression, followed by an increase in glycolysis in GC cells, which was correlated with subsequent tumour growth and liver metastasis. CONCLUSIONS Elevated METTL3 expression promotes tumour angiogenesis and glycolysis in GC, indicating that METTL3 expression is a potential prognostic biomarker and therapeutic target for human GC.
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Affiliation(s)
- Qiang Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Chen Chen
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Qingqing Ding
- Department of Geriatric Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yan Zhao
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Zhangding Wang
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Junjie Chen
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Zerun Jiang
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yan Zhang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Guifang Xu
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Jingjing Zhang
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Beicheng Sun
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaoping Zou
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Shouyu Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China .,Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China.,Center for Public Health Research, Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China
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Decreased Peripheral Blood ALKBH5 Correlates with Markers of Autoimmune Response in Systemic Lupus Erythematosus. DISEASE MARKERS 2020; 2020:8193895. [PMID: 32685056 PMCID: PMC7334764 DOI: 10.1155/2020/8193895] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 06/02/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022]
Abstract
Although it has been proved that the epigenetic modification of DNA and histones is involved in the pathogenesis of systemic lupus erythematosus (SLE), there is no study to explore whether the modification of N6-methyladenosine (m6A) in RNA is involved. In this study, the mRNA levels of m6A "writers" (METTL3, MTEEL14, and WTAP), "erasers" (FTO and ALKBH5), and "readers" (YTHDF2) in peripheral blood were determined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The results demonstrated that the mRNA levels of METTL3, WTAP, FTO, ALKBH5, and YTHDF2 in peripheral blood from SLE patients were significantly decreased. The levels of ALKBH5 mRNA in SLE patients were associated with anti-dsDNA, antinucleosome, rash, and ulceration. Multivariate logistic regression analysis showed that the level of ALKBH5 mRNA in peripheral blood is a risk factor of SLE (P < 0.001). Moreover, our results suggested that there was a positive correlation between m6A"writers" (METTL3 and WTAP), "erasers" (FTO and ALKBH5), and "readers" (YTHDF2) in SLE patients. This study suggests that the mRNA level of ALKBH5 in peripheral blood may be involved in the pathogenesis of SLE.
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Wu KJ. The role of miRNA biogenesis and DDX17 in tumorigenesis and cancer stemness. Biomed J 2020; 43:107-114. [PMID: 32513392 PMCID: PMC7283569 DOI: 10.1016/j.bj.2020.03.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 03/03/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
Cancer stemness represents one of the major mechanisms that predispose patients to tumor aggressiveness, metastasis, and treatment resistance. MicroRNA biogenesis is an important process controlling miRNA processing and maturation. Deregulation of miRNA biogenesis can lead to tumorigenesis and cancer stemness. DDX17 is a co-factor of the miRNA microprocessor. Misregulation of DDX17 can be associated with cancer stemness. K63-linked polyubiquitination of DDX17 presents a concerted mechanism of decreased synthesis of stemness-inhibiting miRNAs and increased transcriptional activation of stemness-related gene expression. K63-linked polyubiquitination of HAUSP serves as a scaffold to anchor HIF-1α, CBP, the mediator complex, and the super-elongation complex to enhance HIF-1α-induced gene transcription. Recent progress in RNA modifications shows that RNA N6-methyladenosine (m6A) modification is a crucial mechanism to regulate RNA levels. M6A modification of miRNAs can also be linked to tumorigenesis and cancer stemness. Overall, miRNA biogenesis and K63-linked polyubiquitination of DDX17 play an important role in the induction of cancer stemness. Delineation of the mechanisms and identification of suitable targets may provide new therapeutic options for treatment-resistant cancers.
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Affiliation(s)
- Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan; Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan.
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Garcia CM, Toms SA. The Role of Circulating MicroRNA in Glioblastoma Liquid Biopsy. World Neurosurg 2020; 138:425-435. [PMID: 32251831 DOI: 10.1016/j.wneu.2020.03.128] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/20/2020] [Accepted: 03/22/2020] [Indexed: 12/29/2022]
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive primary malignancy of the central nervous system. The standard used to monitor disease progression and therapeutic response has been magnetic resonance imaging, which is usually obtained preoperatively and postoperatively. Patients with GBM are monitored every 2-3 months and scans are repeated until progression is detected. Sometimes there is an inability to detect tumor progression or difficulty in differentiating tumor progression from pseudoprogression. With the difficulty of distinguishing disease progression, as well as the cost of imaging, there may be a need for the existence of a noninvasive liquid biopsy. There is no reliable biomarker for GBM that can be used for liquid biopsy, but if one could be detected in serum or cerebrospinal fluid and vary with tumor burden, then, it could be developed into one. MicroRNAs (miRNAs) are short, single-stranded, noncoding RNAs that posttranscriptionally control gene expression. They play vital roles in tumor progression, migration, invasion, and stemness. Because miRNAs are secreted in stable forms in bodily fluid, either via extracellular vesicles or in cell-free form, they have great potential as biomarkers that can be used for liquid biopsy. Various miRNAs that are dysregulated in GBM have been identified in tissue, cerebrospinal fluid, and serum samples. There needs to be standardization of sample collection and quantification for both cell-free and exosomal-derived samples. Further studies need to be performed on larger cohorts to evaluate the sensitivity and specificity of not just miRNAs but most potential biomarkers.
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Affiliation(s)
- Catherine M Garcia
- Department of Neurosurgery, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Steven A Toms
- Department of Neurosurgery, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA.
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Du J, Hou K, Mi S, Ji H, Ma S, Ba Y, Hu S, Xie R, Chen L. Malignant Evaluation and Clinical Prognostic Values of m6A RNA Methylation Regulators in Glioblastoma. Front Oncol 2020; 10:208. [PMID: 32211315 PMCID: PMC7075451 DOI: 10.3389/fonc.2020.00208] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/06/2020] [Indexed: 12/18/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation, the most common form of mRNA modification and regulated by the m6A RNA methylation regulators ("writers," "erasers," and "readers"), has been reported to be associated with the progression of the malignant tumor. However, its role in glioblastoma (GBM) has been poorly known. This study aimed to identify the expression, potential functions, and prognostic values of m6A RNA methylation regulators in GBM. Here, we revealed that the 13 central m6A RNA methylation regulators were firmly related to the clinical and molecular phenotype of GBM. Taking advantage of consensus cluster analysis, we obtained two categories of GBM samples and found malignancy-related processes of m6A methylation regulators and compounds that specifically targeted the malignant processes. Besides, we also obtained a list of genes with poor prognosis in GBM. Finally, we derived a risk-gene signature with three selected m6A RNA methylation regulators, which allowed us to extend the in-depth study and dichotomized the OS of patients with GBM into high- and low-risk subgroups. Notably, this risk-gene signature could be used as independent prognostic markers and accurate clinicopathological parameter predictors. In conclusion, m6A RNA methylation regulators are a type of vital participant in the malignant progression of GBM, with a critical potential in the prognostic stratification and treatment strategies of GBM.
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Affiliation(s)
- Jianyang Du
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Kuiyuan Hou
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Shan Mi
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Hang Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Shuai Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yixu Ba
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Shaoshan Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Rui Xie
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
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Liu L, Wang Y, Wu J, Liu J, Qin Z, Fan H. N 6-Methyladenosine: A Potential Breakthrough for Human Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:804-813. [PMID: 31958696 PMCID: PMC7005339 DOI: 10.1016/j.omtn.2019.12.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023]
Abstract
Among more than 100 types of identified RNA modification, N6-methyladenosine (m6A) modification is the predominant mRNA modification, which regulates RNA splicing, translocation, stability, and translation. m6A modification plays critical roles in the growth, differentiation, and metabolism of cells. As a dynamic and reversible modification, m6A is catalyzed by "writers" (RNA methyltransferases), removed by "erasers" (demethylases), and interacts with "readers" (m6A-binding proteins). With more advanced technology applied to research, the molecular mechanisms of RNA methyltransferase, demethylase, and m6A-binding protein have been revealed. An increasing number of studies have implicated the correlation between m6A modification and human cancers. In this review, we summarize that the occurrence and development of various human cancers are associated with aberrant m6A modification. We also discuss the progress in research related to m6A modification, providing novel therapeutic insight and potential breakthrough in anticancer therapy.
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Affiliation(s)
- Lina Liu
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China
| | - Yuwei Wang
- School of Stomatology, Qingdao University, Qingdao 266071, P.R. China
| | - Jie Wu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Jingwen Liu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, P.R. China.
| | - Zongchang Qin
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China.
| | - Hong Fan
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China.
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Zhang S, Liu F, Wu Z, Xie J, Yang Y, Qiu H. Contribution of m6A subtype classification on heterogeneity of sepsis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:306. [PMID: 32355750 PMCID: PMC7186660 DOI: 10.21037/atm.2020.03.07] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Sepsis is a highly heterogeneous syndrome with diverse immune status and varied bioprocesses among individuals. The heterogeneity of sepsis could be associated with N6-methyladenosine (m6A) RNA methylation, due to m6A as a common and reversible posttranscriptional RNA modification involved in the regulation of whole bioprocesses. Therefore, we aim to identify m6A induced molecular subtypes of sepsis and furthermore explore the probable mechanism. Methods Gene expression datasets with 479 consecutive patients admitted for sepsis to the intensive care unit (ICU) in the Amsterdam Academic Medical Center were included in present study at first. Secondly, twelve m6A methylation regulatory genes were determined via systematic review in published researches. Furthermore, we utilized unsupervised clustering (consensus k means clustering) to identify m6A induced molecular subtypes in sepsis based on m6A prognostic molecular, and assess the association of these subtypes with clinical traits and survival outcomes. Moreover, the probable mechanism and regulatory relationship of m6A in sepsis was also explored through Gene Set Enrichment Analysis (GSEA), Weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) analysis and Co-expression analysis. Results Three m6A subtypes with different outcome were identified in sepsis cohort through unsupervised clustering on m6A prognostic molecular, designated Cluster 1/2/3 (log-rank P=0.004). The best outcome was found for patients classified as having cluster 3, and at 28 days, 21 of 144 people with cluster 3 had died [hazard ratio (HR) vs. all other clusters 5.42 (95% CI: 0.359–0.819); P=0.011], compared with 57 of 224 people with cluster 1 (HR 0.579, 95% CI: 0.364–0.920; P=0.037), and 36 of 112 people with cluster 2 (HR 0.477, 95% CI: 0.272–0.833; P=0.003). For exploration of the relationship between m6A subtypes and immunity, the GSEA found that patients in cluster 1 suffered from hyper-activated immunocompetent status; patients in cluster 2 indicated immunosuppressive status; and patients in cluster 3 showed the moderate immune activity (P<0.05). Co-expression analysis furthermore identified 82 immune molecules and 40 autophagy-related molecules could be regulated by prognostic m6A RNA methylation regulators (P<0.05) and correlation coefficient >0.6. In addition, WGCNA and GO analysis indicated that autophagy was significantly and widely activated in patients with cluster 3 (P<0.05). Conclusions According to the heterogeneity in m6A methylation regulatory genes, three distinct subtypes in sepsis were identified with different RNA epigenetics, immune status, biological processes and outcomes, which initially uncovered that heterogeneity of sepsis may be largely caused by m6A RNA methylation.
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Affiliation(s)
- Shi Zhang
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Feng Liu
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Zongsheng Wu
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Jianfeng Xie
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Yi Yang
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Haibo Qiu
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
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