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Song P, Li X, Chen S, Gong Y, Zhao J, Jiao Y, Dai Y, Yang H, Qian J, Li Y, He J, Tang L. YTHDF1 mediates N-methyl-N-nitrosourea-induced gastric carcinogenesis by controlling HSPH1 translation. Cell Prolif 2024:e13619. [PMID: 38444279 DOI: 10.1111/cpr.13619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
YT521-B homology (YTH) domain family (YTHDF) proteins serve as readers that directly recognise m6A modifications. In this study, we aim to probe the role of YTHDF1 in environmental carcinogen-induced malignant transformation of gastric cells and gastric cancer (GC) carcinogenesis. We established a long-term low-dose MNU-induced malignant transformation model in gastric epithelial cells. In vivo and in vitro experiments were conducted to validate the malignant phenotype and characterise the roles of YTHDF1 and its downstream genes in malignant transformation cells. Additionally, we explored downstream m6A modification targets of YTHDF1 using RNA-sequencing, RNA immunoprecipitation, and proteomics analyses, and conducted validation experiments in cell experiments and clinical samples. Long-term low-dose exposure of MNU converted normal Gges-1 cells into malignant cells. YTHDF1 mRNA and protein expression are increased in MNU-induced malignant cells (p<0.001). Meanwhile, YTHDF1 knockdown inhibits the malignant potential of MNU-treated cells (p<0.01). YTHDF1 knockdown specifically suppresses HSPH1 protein, but not RNA levels. RIP-qPCR validates HSPH1 is the target of YTHDF1 (p<0.01). HSPH1 knockdown impairs the malignant potential of MNU-induced transformed cells. The increased expression of the key regulatory factor YTHDF1 in MNU-induced gastric carcinogenesis affects malignant transformation and tumorigenesis by regulating the translation of downstream HSPH1. These findings provide new potential targets for preventing and treating environmental chemical-induced gastric carcinogenesis.
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Affiliation(s)
- Peng Song
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Xiang Li
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Shuai Chen
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Yu Gong
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Jie Zhao
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Yuwen Jiao
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Yi Dai
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Haojun Yang
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Jun Qian
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Yuan Li
- The Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jian He
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Liming Tang
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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Huang J, Li H, Yang Z, Liu R, Li Y, Hu Y, Zhao S, Gao X, Yang X, Wei J. SALL4 promotes cancer stem-like cell phenotype and radioresistance in oral squamous cell carcinomas via methyltransferase-like 3-mediated m6A modification. Cell Death Dis 2024; 15:139. [PMID: 38355684 PMCID: PMC10866932 DOI: 10.1038/s41419-024-06533-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 01/27/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Radioresistance imposes a great challenge in reducing tumor recurrence and improving the clinical prognosis of individuals having oral squamous cell carcinoma (OSCC). OSCC harbors a subpopulation of CD44(+) cells that exhibit cancer stem-like cell (CSC) characteristics are involved in malignant tumor phenotype and radioresistance. Nevertheless, the underlying molecular mechanisms in CD44( + )-OSCC remain unclear. The current investigation demonstrated that methyltransferase-like 3 (METTL3) is highly expressed in CD44(+) cells and promotes CSCs phenotype. Using RNA-sequencing analysis, we further showed that Spalt-like transcription factor 4 (SALL4) is involved in the maintenance of CSCs properties. Furthermore, the overexpression of SALL4 in CD44( + )-OSCC cells caused radioresistance in vitro and in vivo. In contrast, silencing SALL4 sensitized OSCC cells to radiation therapy (RT). Mechanistically, we illustrated that SALL4 is a direct downstream transcriptional regulation target of METTL3, the transcription activation of SALL4 promotes the nuclear transport of β-catenin and the expression of downstream target genes after radiation therapy, there by activates the Wnt/β-catenin pathway, effectively enhancing the CSCs phenotype and causing radioresistance. Herein, this study indicates that the METTL3/SALL4 axis promotes the CSCs phenotype and resistance to radiation in OSCC via the Wnt/β-catenin signaling pathway, and provides a potential therapeutic target to eliminate radioresistant OSCC.
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Affiliation(s)
- Junhong Huang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China
| | - Huan Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China
| | - Zihui Yang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China
| | - Rong Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yahui Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yating Hu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China
| | - Shengnan Zhao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China
| | - Xiang Gao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China
| | - Xinjie Yang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China.
| | - Jianhua Wei
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral & Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, 710032, China.
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3
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Sheikhshabani SH, Modarres P, Ghafouri‐Fard S, Amini‐Farsani Z, Khodaee L, Shaygan N, Amini‐Farsani Z, Omrani MD. Meta-analysis of microarray data to determine gene indicators involved in cisplatin resistance in non-small cell lung cancer. Cancer Rep (Hoboken) 2024; 7:e1970. [PMID: 38351531 PMCID: PMC10864718 DOI: 10.1002/cnr2.1970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/02/2023] [Accepted: 12/28/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Lung cancer is a major cause of cancer-related mortality worldwide, with a 5-year survival rate of approximately 22%. Cisplatin is one of the standard first-line chemotherapeutic agents for non-small cell lung cancer (NSCLC), but its efficacy is often limited by the development of resistance. Despite extensive research on the molecular mechanisms of chemoresistance, the underlying causes remain elusive and complex. AIMS We analyzed three microarray datasets to find the gene signature and key pathways related to cisplatin resistance in NSCLC. METHODS AND RESULTS We compared the gene expression of sensitive and resistant NSCLC cell lines treated with cisplatin. We found 274 DEGs, including 111 upregulated and 163 downregulated genes, in the resistant group. Gene set enrichment analysis showed the potential roles of several DEGs, such as TUBB2B, MAPK7, TUBAL3, MAP2K5, SMUG1, NTHL1, PARP3, NTRK1, G6PD, PDK1, HEY1, YTHDF2, CD274, and MAGEA1, in cisplatin resistance. Functional analysis revealed the involvement of pathways, such as gap junction, base excision repair, central carbon metabolism, and Notch signaling in the resistant cell lines. CONCLUSION We identified several molecular factors that contribute to cisplatin resistance in NSCLC cell lines, involving genes and pathways that regulate gap junction communication, DNA damage repair, ROS balance, EMT induction, and stemness maintenance. These genes and pathways could be targets for future studies to overcome cisplatin resistance in NSCLC.
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Affiliation(s)
| | - Paratoo Modarres
- Department of Cell and Molecular Biology and Microbiology, Faculty of Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Soudeh Ghafouri‐Fard
- Department of Medical GeneticsShahid Beheshti University of Medical SciencesTehranIran
| | - Zeinab Amini‐Farsani
- Department of Medical GeneticsShahid Beheshti University of Medical SciencesTehranIran
| | - Lavin Khodaee
- Department of Biotechnology and Plant BreedingIslamic Azad University Science and Research BranchTehranIran
| | - Nasibeh Shaygan
- Department of Medical GeneticsShahid Beheshti University of Medical SciencesTehranIran
| | - Zahra Amini‐Farsani
- Bayesian Imaging and Spatial Statistics Group, Institute of StatisticsLudwig‐Maximilian‐Universität MünchenMunichGermany
- Department of StatisticsLorestan UniversityKhorramabadIran
| | - Mir Davood Omrani
- Urogenital Stem Cell Research CenterShahid Beheshti University of Medical SciencesTehranIran
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4
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Chen X, Qin Y, Wang X, Lei H, Zhang X, Luo H, Guo C, Sun W, Fang S, Qin W, Jin Z. METTL3-Mediated m6A Modification Regulates the Osteogenic Differentiation through LncRNA CUTALP in Periodontal Mesenchymal Stem Cells of Periodontitis Patients. Stem Cells Int 2024; 2024:3361794. [PMID: 38283119 PMCID: PMC10817817 DOI: 10.1155/2024/3361794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/29/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
Objective Periodontitis is a chronic inflammatory disease that causes loss of periodontal support tissue. Our objective was to investigate the mechanism by which METTL3-mediated N6-methyladenosine modification regulates the osteogenic differentiation through lncRNA in periodontal mesenchymal stem cells in patients with periodontitis (pPDLSCs). Material and Methods. We carried out a series of experiments, including methylated RNA immunoprecipitation-PCR, quantitative real-time polymerase chain reaction, and western blotting. The expressions of alkaline phosphatase (ALP), Runx2, Col1, Runx2 protein level, ALP staining, and Alizarin red staining were used to demonstrate the degree of osteogenic differentiation. Results We found that METTL3 was the most significantly differentially expressed methylation-related enzyme in pPDLSCs and promoted osteogenic differentiation of pPDLSCs. METTL3 regulated the stability and expression of lncRNA CUTALP, while lncRNA CUTALP promoted osteogenic differentiation of pPDLSCs by inhibiting miR-30b-3p. At different time points of osteogenic differentiation, lncRNA CUTALP expression was positively correlated with Runx2, while miR-30b-3p showed the opposite pattern. The attenuated osteogenic differentiation induced by METTL3 knockdown was recovered by lncRNA CUTALP overexpression. The attenuated osteogenic differentiation induced by lncRNA CUTALP knockdown could be reversed by the miR-30b-3p inhibitor. Conclusions In summary, METTL3/lncRNA CUTALP/miR-30b-3p/Runx2 is a regulatory network in the osteogenic differentiation of pPDLSCs.
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Affiliation(s)
- Xin Chen
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
| | - Yuan Qin
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
| | - Xian Wang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
| | - Hao Lei
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 730070, China
| | - Xiaochen Zhang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
| | - Houzhuo Luo
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
| | - Changgang Guo
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
| | - Weifu Sun
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
| | - Shishu Fang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
| | - Wen Qin
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
| | - Zuolin Jin
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi'an 710032, China
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5
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Xu D, Li P, Zhang C, Shen Y, Cai J, Wei Q, Cao M, Xu Z, Wu D, Wang H, Bi X, Wang B, Li K. Development of an m6A-Related lncRNAs Signature Predicts Tumor Stemness and Prognosis for Low-Grade Glioma Patients. Stem Cells Int 2024; 2024:2062283. [PMID: 38229597 PMCID: PMC10791469 DOI: 10.1155/2024/2062283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
Background Growing evidence has revealed that m6A modification of long noncoding RNAs (lncRNAs) dynamically controls tumor stemness and tumorigenesis-related processes. However, the prognostic significance of m6A-related lncRNAs and their associations with stemness in low-grade glioma (LGG) remain to be clarified. Methods A multicenter transcriptome analysis of lncRNA expression in 1,247 LGG samples was performed in this study. The stemness landscape of LGG tumors was presented and associations with clinical features were revealed. The m6A-related lncRNAs were identified between stemness groups and were further prioritized via least absolute shrinkage and selection operator Cox regression analysis. A risk score model based on m6A-related lncRNAs was constructed and validated in external LGG datasets. Results Based on the expression of LINC02984, PFKP-DT, and CRNDE, a risk model and nomogram were constructed; they successfully predicted the survival of patients and were extended to external datasets. Significant correlations were observed between the risk score and tumor stemness. Moreover, patients in different risk groups exhibited distinct tumor immune microenvironments and immune signatures. We finally provided several potential compounds suitable for specific risk groups, which may aid in LGG treatment. Conclusions This novel signature presents noteworthy value in the prediction of prognosis and stemness status for LGG patients and will foster future research on the development of clinical regimens.
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Affiliation(s)
- Dahua Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Peihu Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Chunrui Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100020, China
| | - Yutong Shen
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Jiale Cai
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Qingchen Wei
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Meng Cao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Zhizhou Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Deng Wu
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Hong Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Xiaoman Bi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Bo Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Kongning Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
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Zhigalova NA, Oleynikova KY, Ruzov AS, Ermakov AS. The Functions of N 6-Methyladenosine in Nuclear RNAs. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:159-172. [PMID: 38467552 DOI: 10.1134/s0006297924010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 03/13/2024]
Abstract
N6-methyladenosine (m6A) is one of the most common modifications in both eukaryotic and prokaryotic mRNAs. It has been experimentally confirmed that m6A methylation is involved in the regulation of stability and translation of various mRNAs. Until recently, the majority of m6A-related studies have been focused on the cytoplasmic functions of this modification. Here, we review new data on the role of m6A in several key biological processes taking place in the cell nucleus, such as transcription, chromatin organization, splicing, nuclear-cytoplasmic transport, and R-loop metabolism. Based on analysis of these data, we suggest that m6A methylation of nuclear RNAs is another level of gene expression regulation which, together with DNA methylation and histone modifications, controls chromatin structure and functioning in various biological contexts.
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Affiliation(s)
- Nadezhda A Zhigalova
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Katerina Yu Oleynikova
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Alexey S Ruzov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Alexander S Ermakov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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7
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Nie Q, Wu X, Huang Y, Guo T, Kuang J, Du C. RNA N6-methyladenosine-modified-binding protein YTHDF1 promotes prostate cancer progression by regulating androgen function-related gene TRIM68. Eur J Med Res 2023; 28:552. [PMID: 38042806 PMCID: PMC10693040 DOI: 10.1186/s40001-023-01533-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/16/2023] [Indexed: 12/04/2023] Open
Abstract
PURPOSE There is no report about the direct relationship between m6A modification and androgen receptor (AR)-related genes in prostate cancer (PC). We aimed to study the mechanisms of m6A methylation in regulating the pathogenesis of PC from the perspective of AR-related genes. METHODS qRT-PCR was applied to detect the expression of m6A-related genes in PC cell with or without AR inhibitor. The effects of YTHDF1 knockdown on PC cell viability, apoptosis, migration and invasion were investigated using flow cytometry, wound healing and transwell assays, respectively. The mechanism of YTHDF1 action was investigated using m6A RNA immunoprecipitation (MeRIP) sequencing. The biological functions of YTHDF1 were also explored through in vivo experiments. RESULTS YTHDF1 was significantly down-regulated in AR inhibitor group. YTHDF1 knockdown significantly decreased AR level, viability and m6A methylation level of PC cells. TRIM68 was identified as a direct target of YTHDF1. Both YTHDF1 and TRIM68 knockdown increased apoptosis, and decreased cell viability, migration, and invasion of PC cells, while TRIM68 overexpression reversed the effects of YTHDF1 knockdown on PC cells. In addition, knockdown of YTHDF1 or TRIM68 significantly decreased the m6A methylation level, and mRNA and protein levels of YTHDF1, TRIM68 and AR in PC cells, while TRIM68 overexpression increased the expression levels above. Furthermore, subcutaneous xenografts of nude mice also revealed that TRIM68 could reverse the effects of YTHDF1 knockdown in PC in vivo. CONCLUSION This study suggested the key role of YTHDF1-mediated m6A modification in PC progression by regulating androgen function-related gene TRIM68 in PC.
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Affiliation(s)
- Qihong Nie
- Department of Oncology, Ganzhou People's Hospital, Ganzhou, 341000, Jiangxi, Jiangxi, China
| | - Xiaoyuan Wu
- Department of Urology, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, 341000, Jiangxi, China
| | - Yongming Huang
- Department of Urology, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, 341000, Jiangxi, China
| | - Tao Guo
- Department of Urology, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, 341000, Jiangxi, China
| | - Jin Kuang
- Department of Urology, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, 341000, Jiangxi, China
| | - Chuance Du
- Department of Urology, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, 341000, Jiangxi, China.
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8
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Yang S, Li K, Zhang J, Liu J, Liu L, Tan Y, Xu C. Link between m6A modification and infiltration characterization of tumor microenvironment in lung adenocarcinoma. Exp Biol Med (Maywood) 2023; 248:2273-2288. [PMID: 38166412 PMCID: PMC10903232 DOI: 10.1177/15353702231214266] [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: 05/11/2023] [Accepted: 08/30/2023] [Indexed: 01/04/2024] Open
Abstract
N6-methyladenosine (m6A) RNA methylation plays a pivotal role in immune responses and the onset and advancement of cancer. Nonetheless, the precise impact of m6A modification in lung adenocarcinoma (LUAD) and its associated tumor microenvironment (TME) remains to be fully elucidated. Here, we distinguished distinct m6A modification patterns within two separate LUAD cohorts using a set of 21 m6A regulators. The TME characteristics associated with these two patterns align with the immune-inflamed and immune-excluded phenotypes, respectively. We identified 2064 m6A-related genes, which were used as a basis to divide all LUAD samples into three distinct m6A gene clusters. We applied a scoring system to evaluate the m6A gene signature of the m6A modification pattern in individual patients. To authenticate the categorization significance of m6A modification patterns, we established a correlation between m6A score and TME infiltration profiling, tumor somatic mutations, and responses to immunotherapy. A high level of m6A modification may be associated with the aggressiveness and poor prognosis of LUAD. Further studies should investigate the mechanism of action of m6A regulators and m6A-related genes to improve the diagnosis and treatment of patients with LUAD.
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Affiliation(s)
- Sha Yang
- Guizhou University Medical College, Guiyang 550025, China
| | - Ke Li
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Jiqin Zhang
- Department of Anesthesiology, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Jian Liu
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Lin Liu
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Ying Tan
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Chuan Xu
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
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Liang Y, Chen S, Xie J, Yan G, Guo T, Li T, Liu S, Zeng W, Zhang S, Ma K, Chen H, Ou Y, Wang B, Gu W, Duan Y. Establishment of a prognostic model based on m 6A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data. J Cancer Res Clin Oncol 2023; 149:12881-12896. [PMID: 37466793 PMCID: PMC10587019 DOI: 10.1007/s00432-023-05045-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/28/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) with high incidence and mortality is one of the most common malignant cancers worldwide. Increasing evidence has reported that N6-methyladenosine (m6A) modification has been considered as a major contribution to the occurrence and development of tumors. METHOD In our study, we comprehensively analyzed the connection between m6A regulatory factors and cancer stem cells (CSCs) of HCC to establish a clinical tool for predicting its outcome. First, we concluded that the expression level of m6A regulatory factors was related with the stemness of hepatocellular carcinoma. Subsequently, we gained a ten hub regulatory factors that were associated with prognosis of hepatocellular carcinoma by overall survival (OS) analysis using ICGC and TCGA datasets, and these regulatory factors included YTHDF1, IGF2BP1, METTL3, IGF2BP3, HNRNPA2B1, IGF2BP2, RBM15B, HNRNPC, RBMX, and LRPPR. Next, we found that these ten hub m6A regulatory factors were highly expressed in CSCs, and CSCs related pathways were also enriched by the gene set variation analysis (GSVA). Then, correlation, consensus clustering and PCA analysis were performed to reveal potential therapeutic benefits of HCC. Moreover, univariate Cox regression (UNICOX), LASSON and multivariate Cox regression (MULTICOX) analyses were adopted to establish HCC prognosis prediction signature. RESULTS Four regulatory factors RBM15B, LRPPRC, IGF2BP1, and IGF2BP3 were picked as valuable prognostic indicators. CONCLUSION In summary, these ten hub regulatory factors would be useful therapeutic targets for HCC treatment, and RBM15B/LRPPRC/IGF2BP1/IGF2BP3 prognostic indicators can be used to guide therapy for HCC patients.
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Affiliation(s)
- Yan Liang
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Sen Chen
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Laboratory of Stem Cells and Translational Medicine, Institute for Medical Research, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China
| | - Jinghe Xie
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Guanrong Yan
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Tingting Guo
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Laboratory of Stem Cells and Translational Medicine, Institute for Medical Research, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China
| | - Tianyang Li
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, No.1 Panfu Road, Guangzhou, 510180, People's Republic of China
| | - Shoupei Liu
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Laboratory of Stem Cells and Translational Medicine, Institute for Medical Research, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China
| | - Weiping Zeng
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510180, China
| | - Shuai Zhang
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, No.1 Panfu Road, Guangzhou, 510180, People's Republic of China
| | - Keqiang Ma
- Department of Hepatobiliary Pancreatic Surgery, Huadu District People's Hospital of Guangzhou, Guangzhou, 510800, People's Republic of China
| | - Honglin Chen
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Yimeng Ou
- Department of General Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, 19 Nonglin Xia Road, Guangzhou, 510699, People's Republic of China.
| | - Bailin Wang
- Department of General Surgery, Guangzhou Red Cross Hospital, Jinan University, 601 Huangpu Dadao West Road, Guangzhou, 510220, People's Republic of China.
| | - Weili Gu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, No.1 Panfu Road, Guangzhou, 510180, People's Republic of China.
| | - Yuyou Duan
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- Laboratory of Stem Cells and Translational Medicine, Institute for Medical Research, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China.
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510180, China.
- Laboratory of Stem Cells and Translational Medicine, Institute for Clinical Medicine, The Second Affiliated Hospital, School of Medicine, South China University of Technology, No.1 Panfu Road, Guangzhou, 510180, People's Republic of China.
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10
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Chen X, Xu H, Shu X, Song CX. Mapping epigenetic modifications by sequencing technologies. Cell Death Differ 2023:10.1038/s41418-023-01213-1. [PMID: 37658169 DOI: 10.1038/s41418-023-01213-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/03/2023] Open
Abstract
The "epigenetics" concept was first described in 1942. Thus far, chemical modifications on histones, DNA, and RNA have emerged as three important building blocks of epigenetic modifications. Many epigenetic modifications have been intensively studied and found to be involved in most essential biological processes as well as human diseases, including cancer. Precisely and quantitatively mapping over 100 [1], 17 [2], and 160 [3] different known types of epigenetic modifications in histone, DNA, and RNA is the key to understanding the role of epigenetic modifications in gene regulation in diverse biological processes. With the rapid development of sequencing technologies, scientists are able to detect specific epigenetic modifications with various quantitative, high-resolution, whole-genome/transcriptome approaches. Here, we summarize recent advances in epigenetic modification sequencing technologies, focusing on major histone, DNA, and RNA modifications in mammalian cells.
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Affiliation(s)
- Xiufei Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Haiqi Xu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Xiao Shu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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11
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Petri BJ, Cave MC, Klinge CM. Changes in m6A in Steatotic Liver Disease. Genes (Basel) 2023; 14:1653. [PMID: 37628704 PMCID: PMC10454815 DOI: 10.3390/genes14081653] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Fatty liver disease is one of the major causes of morbidity and mortality worldwide. Fatty liver includes non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), now replaced by a consensus group as metabolic dysfunction-associated steatotic liver disease (MASLD). While excess nutrition and obesity are major contributors to fatty liver, the underlying mechanisms remain largely unknown and therapeutic interventions are limited. Reversible chemical modifications in RNA are newly recognized critical regulators controlling post-transcriptional gene expression. Among these modifications, N6-methyladenosine (m6A) is the most abundant and regulates transcript abundance in fatty liver disease. Modulation of m6A by readers, writers, and erasers (RWE) impacts mRNA processing, translation, nuclear export, localization, and degradation. While many studies focus on m6A RWE expression in human liver pathologies, limitations of technology and bioinformatic methods to detect m6A present challenges in understanding the epitranscriptomic mechanisms driving fatty liver disease progression. In this review, we summarize the RWE of m6A and current methods of detecting m6A in specific genes associated with fatty liver disease.
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Affiliation(s)
- Belinda J. Petri
- Department of Biochemistry, University of Louisville School of Medicine, Louisville, KY 40292, USA;
| | - Matthew C. Cave
- Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA;
- Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Carolyn M. Klinge
- Department of Biochemistry, University of Louisville School of Medicine, Louisville, KY 40292, USA;
- Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA;
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12
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Tsuji Y, Hara T, Meng S, Sato H, Arao Y, Ofusa K, Ishii H. Role of RNA methylation in the regulation of pancreatic cancer stem cells (Review). Oncol Lett 2023; 26:336. [PMID: 37427348 PMCID: PMC10326658 DOI: 10.3892/ol.2023.13922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/21/2023] [Indexed: 07/11/2023] Open
Abstract
Pancreatic cancer stem cells (CSCs) play a key role in the initiation and progression of pancreatic adenocarcinoma (PDAC). CSCs are responsible for resistance to chemotherapy and radiation, and for cancer metastasis. Recent studies have indicated that RNA methylation, a type of RNA modification, predominantly occurring as m6A methylation, plays an important role in controlling the stemness of cancer cells, therapeutic resistance against chemotherapy and radiation therapy, and their overall relevance to a patient's prognosis. CSCs regulate various behaviors of cancer through cell-cell communication by secreting factors, through their receptors, and through signal transduction. Recent studies have shown that RNA methylation is involved in the biology of the heterogeneity of PDAC. The present review provides an update on the current understanding of RNA modification-based therapeutic targets against deleterious PDAC. Several key pathways and agents that can specifically target CSCs have been identified, thus providing novel insights into the early diagnosis and efficient treatment of PDAC.
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Affiliation(s)
- Yoshiko Tsuji
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Tomoaki Hara
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Sikun Meng
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Hiromichi Sato
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Department of Gastrointestinal Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yasuko Arao
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Ken Ofusa
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Prophoenix Division, Food and Life-Science Laboratory, IDEA Consultants, Inc., Osaka, Osaka 559-8519, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
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13
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Li Y, Sun Y, Yang W, Yang L, Su M, Fang L, Zheng J, Yuan R, Liang W. A novel photoelectrochemical strategy for sequence-spot bispecific analysis of N 6-methyladenosine modification based on proximity ligation-triggered cascade amplification. Anal Chim Acta 2023; 1265:341287. [PMID: 37230570 DOI: 10.1016/j.aca.2023.341287] [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: 02/16/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
N6-methyladenosine (m6A) modification as the most prevalent mammalian RNA internal modification has been considered as the invasive biomarkers in clinical diagnosis and biological mechanism researches. It is still challenged to explore m6A functions due to technical limitations on base- and location-resolved m6A modification. Herein, we firstly proposed a sequence-spot bispecific photoelectrochemical (PEC) strategy based on in situ hybridization mediated proximity ligation assay for m6A RNA characterization with high sensitivity and accuracy. Firstly, the target m6A methylated RNA could be transferred to the exposed cohesive terminus of H1 based on the special self-designed auxiliary proximity ligation assay (PLA) with sequence-spot bispecific recognition. The exposed cohesive terminus of H1 could furtherly trigger the next catalytic hairpin assembly (CHA) amplification and in situ exponential nonlinear hyperbranched hybridization chain reaction for highly sensitive monitoring of m6A methylated RNA. Compared with conventional technologies, the proposed sequence-spot bispecific PEC strategy for m6A methylation of special RNA based on proximity ligation-triggered in situ nHCR performed improved sensitivity and selectivity with a detection limit of 53 fM, providing new insights into highly sensitive monitoring m6A methylation of RNA in bioassay, disease diagnosis and RNA mechanism.
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Affiliation(s)
- Yan Li
- Analytical & Testing Center, Southwest University, Chongqing, 400715, PR China; Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, PR China
| | - Yumeng Sun
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, PR China
| | - Weiguo Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Lan Yang
- Analytical & Testing Center, Southwest University, Chongqing, 400715, PR China
| | - Mingli Su
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, PR China
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, PR China
| | - Ruo Yuan
- Analytical & Testing Center, Southwest University, Chongqing, 400715, PR China; Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Wenbin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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14
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Wang L, Tang Y. N6-methyladenosine (m6A) in cancer stem cell: From molecular mechanisms to therapeutic implications. Biomed Pharmacother 2023; 163:114846. [PMID: 37167725 DOI: 10.1016/j.biopha.2023.114846] [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: 03/18/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023] Open
Abstract
The emergence of drug resistance and metastasis has long been a difficult problem for cancer treatment. Recent studies have shown that cancer stem cell populations are key factors in the regulation of cancer aggressiveness, relapse and drug resistance. Cancer stem cell (CSC) populations are highly plastic and self-renewing, giving them unique metabolic, metastatic, and chemotherapy resistance properties. N6-methyladenosine (m6A) is the most abundant internal modification of mRNA and is involved in a variety of cell growth and development processes, including RNA transcription, alternative splicing, degradation, and translation. It has also been linked to the development of various cancers. At present, the important role of m6A in tumour progression is gradually attracting attention, especially in the tumour stemness regulation process. Abnormal m6A modifications regulate tumour metastasis, recurrence and drug resistance. This paper aims to explore the regulatory mechanism of m6A in CSCs and clinical therapy, clarify its regulatory network, and provide theoretical guidance for the development of clinical targets and improvement of therapeutic effects.
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Affiliation(s)
- Liming Wang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China
| | - Yuanxin Tang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China.
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15
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Zou T, Shi D, Wang W, Chen G, Zhang X, Tian Y, Gong P. Identification of a New m6A Regulator-Related Methylation Signature for Predicting the Prognosis and Immune Microenvironment of Patients with Pancreatic Cancer. Mediators Inflamm 2023; 2023:5565054. [PMID: 37181810 PMCID: PMC10169250 DOI: 10.1155/2023/5565054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/21/2023] [Accepted: 03/31/2023] [Indexed: 05/16/2023] Open
Abstract
Pancreatic cancer (PC) is a malignant tumor of the digestive system that has a bad prognosis. N6-methyladenosine (m6A) is involved in a wide variety of biological activities due to the fact that it is the most common form of mRNA modification in mammals. Numerous research has accumulated evidence suggesting that a malfunction in the regulation of m6A RNA modification is associated with various illnesses, including cancers. However, its implications in PC remain poorly characterized. The methylation data, level 3 RNA sequencing data, and clinical information of PC patients were all retrieved from the TCGA datasets. Genes associated with m6A RNA methylation were compiled from the existing body of research and made available for download from the m6Avar database. The LASSO Cox regression method was used to construct a 4-gene methylation signature, which was then used to classify all PC patients included in the TCGA dataset into either a low- or high-risk group. In this study, based on the set criteria of |cor| > 0.4 and p value < 0.05. A total of 3507 gene methylation were identified to be regulated by m6A regulators. Based on the univariate Cox regression analysis and identified 3507 gene methylation, 858 gene methylation was significantly associated with the patient's prognosis. The multivariate Cox regression analysis identified four gene methylation (PCSK6, HSP90AA1, TPM3, and TTLL6) to construct a prognosis model. Survival assays indicated that the patients in the high-risk group tend to have a worse prognosis. ROC curves showed that our prognosis signature had a good prediction ability on patient survival. Immune assays suggested a different immune infiltration pattern in patients with high- and low-risk scores. Moreover, we found that two immune-related genes, CTLA4 and TIGIT, were downregulated in high-risk patients. We generated a unique methylation signature that is related to m6A regulators and is capable of accurately predicting the prognosis for patients with PC. The findings might prove useful for therapeutic customization and the process of making medical decisions.
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Affiliation(s)
- Tianle Zou
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
- College of Nursing, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Dan Shi
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Weiwei Wang
- Hepatobiliary Surgery, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Guoyong Chen
- Hepatobiliary Surgery, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xianbin Zhang
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yu Tian
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
- School of Public Health, Benedictine University, Lisle, USA
| | - Peng Gong
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
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16
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Ding Y, Gong Y, Zeng H, Zhou X, Yu Z, Pan J, Zhou M, Liu S, Lai W. Biological function analysis of ARHGAP39 as an independent prognostic biomarker in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:2631-2666. [PMID: 37059586 PMCID: PMC10120899 DOI: 10.18632/aging.204635] [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: 01/01/2023] [Accepted: 03/11/2023] [Indexed: 04/16/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common subtype of liver cancer, with a high morbidity and low survival rate. Rho GTPase activating protein 39 (ARHGAP39) is a crucial activating protein of Rho GTPases, a novel target in cancer therapy, and it was identified as a hub gene for gastric cancer. However, the expression and role of ARHGAP39 in hepatocellular carcinoma remain unclear. Accordingly, the cancer genome atlas (TCGA) data were used to analyze the expression and clinical value of ARHGAP39 in hepatocellular carcinoma. Further, the LinkedOmics tool suggested functional enrichment pathways for ARHGAP39. To investigate in depth the possible role of ARHGAP39 on immune infiltration, we analyzed the relationship between ARHGAP39 and chemokines in HCCLM3 cells. Finally, the GSCA website was used to explore drug resistance in patients with high ARHGAP39 expression. Studies have shown that ARHGAP39 is highly expressed in hepatocellular carcinoma and relevant to clinicopathological features. In addition, the overexpression of ARHGAP39 leads to a poor prognosis. Besides, co-expressed genes and enrichment analysis showed a correlation with the cell cycle. Notably, ARHGAP39 may worsen the survival of hepatocellular carcinoma patients by increasing the level of immune infiltration through chemokines. Moreover, N6-methyladenosine (m6A) modification-related factors and drug sensitivity were also found to be associated with ARHGAP39. In brief, ARHGAP39 is a promising prognostic factor for hepatocellular carcinoma patients that is closely related to cell cycle, immune infiltration, m6A modification, and drug resistance.
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Affiliation(s)
- Yongqi Ding
- Department of Health Management Medical, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Shiwen Liu
- Emergency Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Lai
- Department of Health Management Medical, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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17
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Kumari S, Kumar S, Muthuswamy S. RNA N6-methyladenosine modification in regulating cancer stem cells and tumor immune microenvironment and its implication for cancer therapy. J Cancer Res Clin Oncol 2023; 149:1621-1633. [PMID: 35796777 DOI: 10.1007/s00432-022-04158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
Therapy resistance is a well-known phenomenon in cancer treatment. It can be intrinsic or acquired, accountable for frequent tumor relapse and death worldwide. The interplay between cancer cells and their neighboring environment can activate complex signaling mechanisms influencing epigenetic changes and maintain cancer cell survival leading to the malignant phenotype. Cancer stem cells (CSCs) are tumor-initiating cells (TICs) and constitute the primary source of drug resistance and tumor recurrence. Studies have shown that cancer cells exhibit dysregulated RNA N6-methyladenosine (m6A) "writers," "erasers," and "readers" levels after acquiring drug resistance. The present review provides novel insight into the role of m6A modifiers involved in CSC generation, cancer cell proliferation, and therapy resistance. m6A RNA modifications in the cross-talk between CSC and the tumor immune microenvironment (TIME) have also been highlighted. Further, we have discussed the therapeutic potential of targeting m6A machinery for cancer diagnosis and the development of new therapies for cancer treatment.
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Affiliation(s)
- Subhadra Kumari
- Department of Life Science, National Institute of Technology, Rourkela, India
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology, Rourkela, India
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18
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Zhao J, Ding C, Li HB. N 6 - Methyladenosine defines a new checkpoint in γδ T cell development. Bioessays 2023; 45:e2300002. [PMID: 36942692 DOI: 10.1002/bies.202300002] [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: 01/05/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
T cells, which are derived from hematopoietic stem cells (HSCs), are the most important components of adaptive immune system. Based on the expression of αβ and γδ receptors, T cells are mainly divided into αβ and γδ T cells. In the thymus, they share common progenitor cells, while undergoing a series of well-characterized and different developmental processes. N6 -Methyladenosine (m6 A), one of the most abundant modifications in mRNAs, plays critical roles in cell development and maintenance of function. Recently, we have demonstrated that the depletion of m6 A demethylase ALKBH5 in lymphocytes specifically induces an expansion of γδ T cells through the regulation of Jag1/Notch2 signaling, but not αβ T cells, indicating a checkpoint role of ALKBH5 and m6 A modification in the early development of γδ T cells. Based on previous studies, many key pathway molecules, which exert dominant roles in γδ T cell fate determination, have been identified as the targets regulated by m6 A modification. In this review, we mainly summarize the potential regulation between m6 A modification and these key signaling molecules in the γδ T cell lineage commitment, to provide new perspectives in the checkpoint of γδ T cell development.
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Affiliation(s)
- Jiachen Zhao
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenbo Ding
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Wang ZY, Li P, Hu J, Xu Q, Zhang CY. Construction of a Single-Molecule Biosensor for Antibody-Free Detection of Locus-Specific N6-Methyladenosine in Cancer Cells and Tissues. Anal Chem 2023; 95:5454-5462. [PMID: 36930460 DOI: 10.1021/acs.analchem.3c00730] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
N6-Methyladenosine (m6A) has emerged as a key post-transcriptional regulator in mRNA metabolism, and its dysregulation is associated with multiple human diseases. Herein, we construct a single-molecule fluorescent biosensor for antibody-free detection of locus-specific m6A in cancer cells and tissues. A 5'-biotinylated capture probe and a 3'-hydroxylated assistant probe are designed for the recognition of specific m6A-mRNA. The m6A-sensitive endoribonuclease MazF can identify and cleave the unmethylated mRNA, and the retained intact m6A-mRNA can hybridize with assistant probes and capture probes to achieve sandwich hybrids. The sandwich hybrids are immobilized on magnetic beads (MBs) to initiate the terminal deoxynucleotidyl transferase (TdT)-assisted polymerization, facilitating the continuous incorporation of Cy5-dATP to form long Cy5-polyA tails for the production of an on-bead amplified fluorescence signal. After magnetic separation and exonuclease digestion, numerous Cy5 fluorophores are released and subsequently measured by single-molecule detection. Especially, this biosensor is implemented simply and isothermally without the involvement of either radiolabeling or m6A-specific antibody. Moreover, this biosensor shows ultrahigh sensitivity with a detection limit of 2.24 × 10-17 M, and it can discriminate a 0.01% m6A level from a large pool of coexisting counterparts. Furthermore, this biosensor can be used for monitoring cellular m6A-mRNA expression and differentiating the m6A level in the breast cancer patient tissues from that in the healthy person tissues, providing a new avenue for clinical diagnosis and epitranscriptomic research.
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Affiliation(s)
- Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Peng Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Jinping Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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20
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Ren W, Yuan Y, Li Y, Mutti L, Peng J, Jiang X. The function and clinical implication of YTHDF1 in the human system development and cancer. Biomark Res 2023; 11:5. [PMID: 36650570 PMCID: PMC9847098 DOI: 10.1186/s40364-023-00452-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/26/2022] [Indexed: 01/19/2023] Open
Abstract
YTHDF1 is a well-characterized m6A reader protein that is essential for protein translation, stem cell self-renewal, and embryonic development. YTHDF1 regulates target gene expression by diverse molecular mechanisms, such as promoting protein translation or modulating the stability of mRNA. The cellular levels of YTHDF1 are precisely regulated by a complicated transcriptional, post-transcriptional, and post-translational network. Very solid evidence supports the pivotal role of YTHDF1 in embryonic development and human cancer progression. In this review, we discuss how YTHDF1 influences both the physiological and pathological biology of the central nervous, reproductive and immune systems. Therefore we focus on some relevant aspects of the regulatory role played by YTHDF1 as gene expression, complex cell networking: stem cell self-renewal, embryonic development, and human cancers progression. We propose that YTHDF1 is a promising future cancer biomarker for detection, progression, and prognosis. Targeting YTHDF1 holds therapeutic potential, as the overexpression of YTHDF1 is associated with tumor resistance to chemotherapy and immunotherapy.
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Affiliation(s)
- Wenjun Ren
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Yixiao Yuan
- grid.452206.70000 0004 1758 417XKey Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongwu Li
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Luciano Mutti
- grid.264727.20000 0001 2248 3398Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122 USA ,grid.158820.60000 0004 1757 2611Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2 67100 L’Aquila, Italy
| | - Jun Peng
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Xiulin Jiang
- grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
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21
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Shao W, Zhao H, Zhang S, Ding Q, Guo Y, Hou K, Kan Y, Deng F, Xu Q. A pan-cancer landscape of IGF2BPs and their association with prognosis, stemness and tumor immune microenvironment. Front Oncol 2023; 12:1049183. [PMID: 36686749 PMCID: PMC9846525 DOI: 10.3389/fonc.2022.1049183] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Background The human insulin-like growth factor 2 mRNA binding proteins 1-3 (IGF2BP1-3, also called IMP1-3) play essential roles in mRNA regulation, including its splicing, translocation, stability, and translation. However, knowledge regarding the involvement of IGF2BPs in tumor immunity and stemness across cancer types is still lacking. Methods In this study, we comprehensively analyzed pan-cancer multi-omic data to determine the correlation of IGF2BPs mRNA and protein expression with various cancer parameters such as mutation frequency, prognostic value, the tumor microenvironment (TME), checkpoint blockade, tumor immune infiltration, stemness and drug sensitivity. Validation of the expression of IGF2BPs in cancer samples and glioma cells were performed by quantitative real-time (qRT)-PCR, and immunofluorescence staining. Investigation of the functional role of IGF2BP3 in glioma stem cells(GSCs) were performed by sphere formation, cytotoxicity, transwell, and wound healing assays. Results We found that IGF2BP1 and 3 are either absent or expressed at very low levels in most normal tissues. However, IGF2BP1-3 can be re-expressed in a broad range of cancer types and diverse cancer cell lines, where their expression often correlates with poor prognosis. Immunofluorescence staining and qRT-PCR analyses also showed that the expression of IGF2BP2 and IGF2BP3 were higher in cancer tissues than that in adjacent normal tissues. Moreover, IGF2BPs are associated with TME and stemness in human pan-cancer. Remarkably, IGF2BP3 participated in the maintenance and self-renewal of glioma stem cell (GSCs). Knockdown of IGF2BP3 attenuated GSC and glioma cell proliferation, invasion, and migration. Conclusions Our systematic pan-cancer study confirmed the identification of IGF2BPs as therapeutic targets and highlighted the need to study their association with stemness, and the TME, which contribute to the cancer drug-discovery research. Especially, preliminary studies demonstrate the IGF2BP3 as a potential negative regulator of glioma tumorigenesis by modulating stemness.
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Affiliation(s)
- Wei Shao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Hui Zhao
- The Department of Science and Technology, Zhengzhou Revogene Ltd, Zhengzhou, Henan, China
| | - Shoudu Zhang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Qian Ding
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Yugang Guo
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Kaiqi Hou
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Fan Deng
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China,*Correspondence: Qian Xu, ; Fan Deng,
| | - Qian Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China,*Correspondence: Qian Xu, ; Fan Deng,
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22
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Ye F, Wu J, Zhang F. METTL16 epigenetically enhances GPX4 expression via m6A modification to promote breast cancer progression by inhibiting ferroptosis. Biochem Biophys Res Commun 2023; 638:1-6. [PMID: 36434904 DOI: 10.1016/j.bbrc.2022.10.065] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 02/02/2023]
Abstract
Breast cancer is malignant cancer that severely threatens the life quality of female patients. N6-methyladenosine (m6A) is a prevalent modification of RNA. METTL16 is an important methyltransferase. This work aims to study the role of METTL16 in breast cancer cell death. The expression of METTL16 in clinical breast cancer specimens was analyzed by qPCR assay. The in vitro and in vivo breast cancer cell proliferation was measured by CCK8, colony formation, and xenograft mouse model. Cell ferroptosis was assessed by measuring the accumulation of iron, Fe2+, and lipid ROS. The mechanistic study was performed by RNA degradation, qPCR, and Western blotting assay. METTL16 was overexpressed in tumor tissues from breast cancer patients compared with the para-tumor tissues. Knockdown of METTL16 suppressed in vitro cell proliferation and in vivo tumor growth of breast cancer cells. Meanwhile, METTL16 silencing led to elevated intracellular levels of iron, Fe2+, and lipid ROS, indicating the incidence of ferroptosis. Furthermore, siMETTL16 decreased m6A methylation and enhanced the degradation of GPX4 RNA. METTL16-regulated m6A methylation of GPX4 stimulates proliferation and suppresses ferroptosis of breast cancer cells. Therefore, we concluded that METTL16 epigenetically enhanced GPX4 expression via m6A modification to promote breast cancer progression by inhibiting ferroptosis.
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Affiliation(s)
- Feng Ye
- Jianghan University Hospital, Wuhan Sixth Hospital, Wuhan, 430000, China
| | - Jin Wu
- Jianghan University Hospital, Wuhan Sixth Hospital, Wuhan, 430000, China
| | - Fan Zhang
- Jianghan University Hospital, Wuhan Sixth Hospital, Wuhan, 430000, China.
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23
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Cerneckis J, Cui Q, Liu W, Shi Y. RNA Modifications in Cancer Stem Cell Biology. Cancer Treat Res 2023; 190:25-47. [PMID: 38112998 DOI: 10.1007/978-3-031-45654-1_2] [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] [Indexed: 12/21/2023]
Abstract
Post-transcriptional regulation of gene expression shapes the cell state both in health and disease. RNA modifications-especially N6-methyladenosine (m6A)-have recently emerged as key players in RNA processing that depends on a sophisticated interplay between proteins of the RNA modification machinery. Importantly, the RNA epitranscriptome becomes dysregulated in cancer and promotes cancer-associated gene expression programs as well as cancer cell adaptation to the tumor microenvironment. At the top of the tumor hierarchy, cancer stem cells (CSCs) are master regulators of tumorigenesis and resistance to therapeutic intervention. Therefore, defining how RNA modifications influence the CSC state is of great importance for cancer drug development. In this chapter, we summarize the current knowledge of the roles of RNA modifications in shaping the CSC state and driving gene expression programs that confer stem-like properties to CSCs, promote CSC adaptation to the local microenvironment, and endow CSCs with metastatic potential and drug resistance.
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Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Qi Cui
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Wei Liu
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Department of Immunology, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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24
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Zhang Q, Zhang Y, Chen H, Sun LN, Zhang B, Yue DS, Wang CL, Zhang ZF. METTL3-induced DLGAP1-AS2 promotes non-small cell lung cancer tumorigenesis through m 6A/c-Myc-dependent aerobic glycolysis. Cell Cycle 2022; 21:2602-2614. [PMID: 35972892 PMCID: PMC9704390 DOI: 10.1080/15384101.2022.2105885] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 01/09/2023] Open
Abstract
The critical roles of N6-methyladenosine (m6A) modification have been demonstrated by more and more evidence. However, the cross talk of m6A and long noncoding RNAs (lncRNAs) in non-small cell lung cancer (NSCLC) tumorigenesis is still unclear. Here, this work focused on the functions and molecular mechanism of m6A-modified lncRNA DLGAP1 antisense RNA 2 (DLGAP1-AS2) in NSCLC. Microarray analysis found that lncRNA DLGAP1-AS2 is upregulated in NSCLC cells. Clinical data showed that DLGAP1-AS2 high-expression was correlated with advanced pathological stage and poor prognosis. Functionally, DLGAP1-AS2 overexpression promoted the aerobic glycolysis and DLGAP1-AS2 knockdown suppressed the tumor growth of NSCLC cells. Mechanistically, m6A methyltransferase METTL3 enhanced the stability of DLGAP1-AS2 via m6A site binding. Moreover, DLGAP1-AS2 interacted with YTHDF1 to enhance the stability of c-Myc mRNA through DLGAP1-AS2/YTHDF1/m6A/c-Myc mRNA. In conclusion, our work indicates the functions of m6A-modified DLGAP1-AS2 in the NSCLC aerobic glycolysis, disclosing a potential m6A-dependent manner for NSCLC treatment.
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Affiliation(s)
- Qiang Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin Lung Cancer Center, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yu Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin Lung Cancer Center, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Hui Chen
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin Lung Cancer Center, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Lei-Na Sun
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin Lung Cancer Center, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Pathology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Bin Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin Lung Cancer Center, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Dong-Sheng Yue
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin Lung Cancer Center, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Chang-Li Wang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin Lung Cancer Center, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Zhen-Fa Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin Lung Cancer Center, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
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25
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Zeng QC, Sun Q, Su WJ, Li JC, Liu YS, Zhang K, Yang LQ. Analysis of m 6A modulator-mediated methylation modification patterns and the tumor microenvironment in lung adenocarcinoma. Sci Rep 2022; 12:20684. [PMID: 36450735 PMCID: PMC9712433 DOI: 10.1038/s41598-022-20730-6] [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: 07/14/2021] [Accepted: 02/21/2022] [Indexed: 12/02/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer. In the development and progression of LUAD, epigenetic aberration plays a crucial role. However, the function of RNA N6-methyladenosine (m6A) modifications in the LUAD progression is unknown. The m6A regulator modification patterns in 955 LUAD samples were analyzed comprehensively. Patterns were systematically correlated with the tumor microenvironment (TME) cell-infiltration characteristics. Using principal component analysis algorithms, the m6Ascore was generated to quantify m6A modification patterns in individual tumors. Then, their values for predicting prognoses and therapeutic response in LUAD patients were assessed. Three distinct m6A modification patterns in LUAD were identified. Among them, the prognosis of m6Acluster C was the best, while the prognosis of m6Acluster A was the worst. Interestingly, the characterization of TME cell infiltration and biological behavior differed among the three patterns. To evaluate m6A modification patterns within individual tumors, an m6Ascore signature was constructed. The results showed that the high m6Ascore group was associated with a better prognosis; tumor somatic mutations and tumor microenvironment differed significantly between the high- and low- m6Ascore groups. Furthermore, in the cohort with anti-CTLA-4 treatment alone, patients with a high m6Ascore had higher ICI scores, which indicated significant therapeutic advantage and clinical benefits.
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Affiliation(s)
- Qing-Cui Zeng
- grid.410646.10000 0004 1808 0950Department of Geriatric Intensive Care Unit, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China ,grid.9227.e0000000119573309Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Qin Sun
- grid.410646.10000 0004 1808 0950Department of Geriatric Intensive Care Unit, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China ,grid.9227.e0000000119573309Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Wen-Jie Su
- grid.410646.10000 0004 1808 0950Department of Anesthesiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China ,grid.9227.e0000000119573309Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Jia-Cen Li
- grid.410646.10000 0004 1808 0950Department of Anesthesiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China ,grid.9227.e0000000119573309Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Yi-Sha Liu
- grid.410646.10000 0004 1808 0950Department of Pathology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China ,grid.9227.e0000000119573309Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Kun Zhang
- grid.410646.10000 0004 1808 0950Department of Chest Surgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China ,grid.9227.e0000000119573309Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Li-Qing Yang
- grid.410646.10000 0004 1808 0950Department of Respiratory Medicine, Eastern Hospital, Sichuan Academy of Medical Sciences, Sichuan Provincial People’s Hospital, Sichuan Province, No. 585, Honghe North Road, LongQuanYi District, Chengdu, 610000 China ,grid.9227.e0000000119573309Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
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YTHDC1 Promotes Stemness Maintenance and Malignant Progression in Head and Neck Squamous Cell Carcinoma. Stem Cells Int 2022; 2022:7494354. [DOI: 10.1155/2022/7494354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/27/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background. YTH domain containing 1 (YTHDC1), an N6-methyladenosine (m6A) modification reading protein, plays a key role in regulating RNA translation and degradation. However, the role of YTHDC1 in head and neck squamous cell carcinoma (HNSCC) cancer stem cells remains largely unknown. This study is aimed at investigating the role of YTHDC1 in HNSCC and exploring its role in regulating cancer stem cells. Methods. RNA sequencing was used to detect differentially expressed genes (DEGs) between SCC9 spheres and SCC9 cells and to uncover molecular pathways and target molecules associated with CSCs. We detected YTHDC1 expression in The Cancer Genome Atlas (TCGA) database data and clinical samples. Subsequently, YTHDC1 gene suppression assays were performed in HNSCC cell lines to investigate the effect of YTHDC1 on tumor cell stemness maintenance, proliferation, and migration capacity. To further confirm the role of YTHDC1 in regulating cancer stem cells in HNSCC, we analyzed online HNSCC single-cell transcriptomic data to investigate YTHDC1 expression patterns at the single-cell level and the correlation of these levels with the expression of stem cell markers. Results. YTHDC1 expression levels were significantly upregulated in SCC9 spheres, and YTHDC1 was aberrantly expressed in HNSCC tumor tissues. The increased YTHDC1 expression was closely correlated with the clinical characteristics of HNSCC patients. YTHDC1 regulates the malignant phenotype of HNSCC in both in vivo and in vitro studies. Further single-cell transcriptomic data analysis revealed that YTHDC1 positively correlated with malignant epithelial cell stemness capacity at the single-cell level, and that YTHDC1 was involved in regulating stemness maintenance in HNSCC. Conclusions. These findings suggest that YTHDC1 may serve as a biomarker for stem maintenance and malignant progression in HNSCC, providing new insights into the treatment of cancer.
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27
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Zhang X, Li MJ, Xia L, Zhang H. The biological function of m6A methyltransferase KIAA1429 and its role in human disease. PeerJ 2022; 10:e14334. [PMID: 36389416 PMCID: PMC9657180 DOI: 10.7717/peerj.14334] [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: 07/25/2022] [Accepted: 10/12/2022] [Indexed: 11/11/2022] Open
Abstract
KIAA1429 is a major m6A methyltransferase, which plays important biological and pharmacological roles in both human cancer or non-cancer diseases. KIAA1429 produce a tumorigenic role in various cancers through regulating DAPK3, ID2, GATA3, SMC1A, CDK1, SIRT1 and other targets, promoting cell proliferation, migration, invasion, metastasis and tumor growth . At the same time, KIAA1429 is also effective in non-tumor diseases, such as reproductive system and cardiovascular system diseases. The potential regulatory mechanism of KIAA1429 dependent on m6A modification is related to mRNA, lncRNA, circRNA and miRNAs. In this review, we summarized the current evidence on KIAA1429 in various human cancers or non-cancer diseases and its potential as a prognostic target.
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Affiliation(s)
- Xiaoyu Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Meng jiao Li
- Liaocheng Vocational and Technical College, Liaocheng, China
| | - Lei Xia
- Shandong University of Traditional Chinese Medicine, Department of Pathology, Jinan, China
| | - Hairong Zhang
- Shandong Provincial Third Hospital, Department of Obstetrics and Gynecology, Jinan, China
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28
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Shi H, Xiong J, Gan L, Zhang Y, Zhang C, Kong Y, Miao Q, Tian C, Li R, Liu J, Zhang E, Bu W, Wang Y, Cheng X, Sun J, Chen H. N6-methyladenosine reader YTHDF3 regulates melanoma metastasis via its 'executor'LOXL3. Clin Transl Med 2022; 12:e1075. [PMID: 36324258 PMCID: PMC9630608 DOI: 10.1002/ctm2.1075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND A number of studies have demonstrated that N6-methyladenosine (m6A) plays a vital role in the pathological process of various tumours. Recently, it was found that m6A writers or erasers affect the tumourigenesis of melanoma. However, the relationship between m6A readers such as YTH domain family (YTHDF) proteins and melanoma was still elusive. METHODS RT-qPCR, Western blot and immunohistochemistry were conducted to measure the expression level of YTH N6-methyladenosine RNA binding protein 3 (YTHDF3) and lysyl oxidase-like 3 (LOXL3) in melanoma tissues and cells. The effects of YTHDF3 and LOXL3 on melanoma were verified in vitro and in vivo. Multi-omics analysis including RNA-seq, MeRIP-seq, RIP-seq and mass spectrometry analyses was performed to identify the target. The interaction between YTHDF3 and LOXL3 was verified by RT-PCR, Western blot, MeRIP-qPCR, RIP-qPCR and CRISPR-Cas13b-based epitranscriptome engineering. RESULTS In this study, we found that m6A reader YTHDF3 could affect the metastasis of melanoma both in vitro and in vivo. The downstream targets of YTHDF3, such as LOXL3, phosphodiesterase 3A (PDE3A) and chromodomain helicase DNA-binding protein 7 (CHD7) were identified by means of RNA-seq, MeRIP-seq, RIP-seq and mass spectrometry analyses. Besides, RT-qPCR, Western blot, RIP-qPCR and MeRIP-qPCR were performed for subsequent validation. Among various targets of YTHDF3, LOXL3 was found to be the optimal target of YTHDF3. With the application of CRISPR-Cas13b-based epitranscriptome engineering, we further confirmed that the transcript of LOXL3 was captured and regulated by YTHDF3 via m6A binding sites. YTHDF3 augmented the protein expression of LOXL3 without affecting its mRNA level via the enrichment of eukaryotic translation initiation factor 3 subunit A (eIF3A) on the transcript of LOXL3. LOXL3 downregulation inhibited the metastatic ability of melanoma cells, and overexpression of LOXL3 ameliorated the inhibition of melanoma metastasis caused by YTHDF3 downregulation. CONCLUSIONS The YTHDF3-LOXL3 axis could serve as a promising target to be interfered with to inhibit the metastasis of melanoma.
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Affiliation(s)
- Hao‐ze Shi
- Department of Pathology, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Jing‐shu Xiong
- Laboratory of Mycobacteriology, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Lu Gan
- Department of Sexually Transmitted Disease, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Ying Zhang
- Department of Pathology, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Cong‐cong Zhang
- Department of Pathology, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Ying‐qi Kong
- Department of Pathology, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Qiu‐ju Miao
- Department of Pathology, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Cui‐cui Tian
- Department of Pathology, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Rong Li
- Department of Physiotherapy, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Jin‐quan Liu
- National Center for STD ControlChina CDCNanjingChina
| | - Er‐jia Zhang
- Department of DermatologyChina Aerospace Science & Industry Corporation 731 HospitalBeijingChina
| | - Wen‐bo Bu
- Department of Surgery, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Yan Wang
- Department of Surgery, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Xian‐feng Cheng
- Department of Clinical Laboratory, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Jian‐fang Sun
- Department of Pathology, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Hao Chen
- Department of Pathology, Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
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29
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Ge F, Li Z, Hu J, Pu Y, Zhao F, Kong L. METTL3/m 6A/IFIT2 regulates proliferation, invasion and immunity in esophageal squamous cell carcinoma. Front Pharmacol 2022; 13:1002565. [PMID: 36386128 PMCID: PMC9644211 DOI: 10.3389/fphar.2022.1002565] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/22/2022] [Indexed: 08/04/2023] Open
Abstract
Epigenetic regulation plays a critical role in the development, progression, and treatment of tumors. The most common chemical modification of mRNA, called m6A, is essential for controlling mRNA stability, splicing, and translation. Methyltransferase-like 3 (METTL3) is an important m6A methyltransferase. The mechanism of action of METTL3 in esophageal squamous cell carcinoma (ESCC) remains unclear. In this investigation, we sought to clarify the function and clinical importance of METTL3 in ESCC and investigate its underlying mechanisms. We discovered that METTL3 has a significant proliferative effect in ESCC cells by using lentiviral construction of stable cell lines overexpressing METTL3 (METTL3-OE) and knocking down METTL3 (sh-METTL3). To create a xenograft tumor model, we inoculated KYSE510 cells subcutaneously into BALB/c nude mice and discovered that sh-METTL3 inhibited the tumorigenicity of esophageal cancer KYSE510 cells in the nude mouse tumor model. MeRIP-seq and RNA-seq analysis revealed IFIT2 to be a METTL3 target gene. The findings revealed that METTL3 regulates IFIT2 and thus influences malignant biological behaviors such as proliferation, migration, and invasion of ESCC, as well as the immune microenvironment of tumors.
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Affiliation(s)
- Fangfang Ge
- Department of Anesthesiology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Provincial Clinical College, Wannan Medical College, Wuhu, China
| | - Zhenyu Li
- Department of Anesthesiology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Provincial Clinical College, Wannan Medical College, Wuhu, China
| | - Jiaru Hu
- Division of Life Sciences and Medicine, Department of the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Youguang Pu
- Division of Life Sciences and Medicine, Department of Cancer Epigenetics Program, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Fangfang Zhao
- Division of Life Sciences and Medicine, Department of Cancer Epigenetics Program, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Lingsuo Kong
- Department of Anesthesiology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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30
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Wu Z, Yu X, Zhang S, He Y, Guo W. Mechanism underlying circRNA dysregulation in the TME of digestive system cancer. Front Immunol 2022; 13:951561. [PMID: 36238299 PMCID: PMC9550895 DOI: 10.3389/fimmu.2022.951561] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Circular RNAs (circRNAs) are a new series of noncoding RNAs (ncRNAs) that have been reported to be expressed in eukaryotic cells and have a variety of biological functions in the regulation of cancer pathogenesis and progression. The TME, as a microscopic ecological environment, consists of a variety of cells, including tumor cells, immune cells and other normal cells, ECM and a large number of signaling molecules. The crosstalk between circRNAs and the TME plays a complicated role in affecting the malignant behaviors of digestive system cancers. Herein, we summarize the mechanisms underlying aberrant circRNA expression in the TME of the digestive system cancers, including immune surveillance, angiogenesis, EMT, and ECM remodelling. The regulation of the TME by circRNA is expected to be a new therapeutic method.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhi Guo, ; Yuting He,
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhi Guo, ; Yuting He,
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31
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Cao Q, Chen Y. Integrated Analyses of m6A Regulator-Mediated Methylation Modification Patterns and Tumor Microenvironment Infiltration Characterization in Pan-Cancer. Int J Mol Sci 2022; 23:ijms231911182. [PMID: 36232485 PMCID: PMC9570346 DOI: 10.3390/ijms231911182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
The invasion of immune cells in the tumor microenvironment (TME) is closely related to cancer development. Studies have demonstrated that N6-methyladenosine (m6A) can affect the invasion of immune cells in TME as well as cancer development. We comprehensively analyzed the RNA-seq data of 16 different cancer types based on 20 m6A regulators and identified two distinct m6A modification patterns, which were closely associated with TME cell infiltration and overall patient survival. Then, we used principal component analysis (PCA) to construct m6Ascore based on the expression of m6A-related prognostic genes, which can successfully predict patient survival. The low-m6Ascore subtype is characterized by more immune cell infiltration, good prognosis and lower TNM stages, while the high-m6Ascore subtype is characterized by low immune infiltration, stromal activation, and poor prognosis. m6Ascore was also closely associated with immunotherapy response and was significantly higher in complete response/partial response (CR/PR) patients than in stable disease/progressive disease (SD/PD) patients in both immunotherapy cohorts. Therefore, our study indicates that m6A modification plays an important role in the prognosis of pan-cancer and the formation of complex TME in pan-cancer. Our research helps to improve the cognition of m6A modifications at pan-cancer levels and identify more effective strategies for immunotherapy.
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32
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Akinlalu AO, Njoku PC, Nzekwe CV, Oni RO, Fojude T, Faniyi AJ, Olagunju AS. Recent developments in the significant effect of mRNA modification (M6A) in glioblastoma and esophageal cancer. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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33
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Wang X, Zhao C, Huang D, Liu Z, Liu M, Lin F, Lu Y, Jia J, Lin L, Lin X, Li H, Chen Z. A Novel M6A-Related Genes Signature Can Impact the Immune Status and Predict the Prognosis and Drug Sensitivity of Lung Adenocarcinoma. Front Immunol 2022; 13:923533. [PMID: 35860262 PMCID: PMC9289247 DOI: 10.3389/fimmu.2022.923533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/01/2022] [Indexed: 01/22/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is a primary cause of cancer-related death around the world and has a poor outcome and high incidence. Treatment options are, however, restricted. One of the most critical factors in cancer and metastasis is the N6-methyladenine (m6A) alteration on RNA. This modification could alter gene expression and even function at numerous levels, such as the stability, translocation and translation of RNA splicing. This study aimed to construct an m6A-related genes signature to accurately predict the prognosis of LUAD patients. From TCGA datasets, the LUAD patient data and m6A-related genes were retrieved. LUAD patients’ mutational features and differentially expressed genes (DEGs) were investigated. An univariate and LASSO model with m6A-related genes were constructed for the prediction of outcomes in LUAD. It was possible to develop a prognostic nomogram that could quantitatively predict LUAD patients’ overall survival chances at 1, 3, and 5 years. Research into biological processes and cell pathways was carried out using GSEA. This study found six m6A-related DEGs in LUAD patients, and three of these DEGs(HNRNPC, IGFBP3 and IGF2BP1) were linked to the clinical outcomes of LUAD patients. We found that the overall survival rate for all LUAD patients with high-risk subgroup was considerably lower. According to ROC curves, the prognostic signature demonstrated a high degree of accuracy in predicting future outcomes. In addition, we created a novel nomogram achieved great accuracy with this one as well. The researchers also found that the novel signature might favorably modulate the immune response, and high-risk scores samples were more susceptible to numerous chemotherapeutic medicines. Overall, we developed a m6A-related gene prognostic signature that effectively predicted outcomes of LUAD patients and gave an immunological perspective for creating customized therapeutics.
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Affiliation(s)
- Xuewen Wang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Chengfei Zhao
- Department of Pharmacy, School of Pharmacy and Medical Technology, Putian University, Putian, China
| | - Dandan Huang
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Zhoujie Liu
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Mengmeng Liu
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Fei Lin
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Yingyu Lu
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Jing Jia
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Liqing Lin
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Xinhua Lin
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, China
- Key Laboratory of Nanomedical Technology (Education Department of Fujian Province), School of Pharmacy, Nano Medical Technology Research Institute, Fujian Medical University, Fuzhou, China
- *Correspondence: Zhiwei Chen, ; Huangyuan Li, ; Xinhua Lin,
| | - Huangyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
- *Correspondence: Zhiwei Chen, ; Huangyuan Li, ; Xinhua Lin,
| | - Zhiwei Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, China
- Fuzhou Center for Disease Control and Prevention, Fuzhou, China
- *Correspondence: Zhiwei Chen, ; Huangyuan Li, ; Xinhua Lin,
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34
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Qing X, Chen Q, Wang K. m6A Regulator-Mediated Methylation Modification Patterns and Characteristics in COVID-19 Patients. Front Public Health 2022; 10:914193. [PMID: 35655464 PMCID: PMC9152098 DOI: 10.3389/fpubh.2022.914193] [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: 04/06/2022] [Accepted: 04/25/2022] [Indexed: 01/14/2023] Open
Abstract
Background RNA N6-methyladenosine (m6A) regulators may be necessary for diverse viral infectious diseases, and serve pivotal roles in various physiological functions. However, the potential roles of m6A regulators in coronavirus disease 2019 (COVID-19) remain unclear. Methods The gene expression profile of patients with or without COVID-19 was acquired from Gene Expression Omnibus (GEO) database, and bioinformatics analysis of differentially expressed genes was conducted. Random forest modal and nomogram were established to predict the occurrence of COVID-19. Afterward, the consensus clustering method was utilized to establish two different m6A subtypes, and associations between subtypes and immunity were explored. Results Based on the transcriptional data from GSE157103, we observed that the m6A modification level was markedly enriched in the COVID-19 patients than those in the non-COVID-19 patients. And 18 essential m6A regulators were identified with differential analysis between patients with or without COVID-19. The random forest model was utilized to determine 8 optimal m6A regulators for predicting the emergence of COVID-19. We then established a nomogram based on these regulators, and its predictive reliability was validated by decision curve analysis. The consensus clustering algorithm was conducted to categorize COVID-19 patients into two m6A subtypes from the identified m6A regulators. The patients in cluster A were correlated with activated T-cell functions and may have a superior prognosis. Conclusions Collectively, m6A regulators may be involved in the prevalence of COVID-19 patients. Our exploration of m6A subtypes may benefit the development of subsequent treatment modalities for COVID-19.
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Affiliation(s)
- Xin Qing
- School of Medicine, Southeast University, Nanjing, China.,Clinical Laboratory, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Qian Chen
- Department of Pediatrics, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ke Wang
- Clinical Laboratory, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
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35
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Zhang L, Wang X, Che W, Yi Y, Zhou S, Feng Y. Methyltransferase-like 3 silenced inhibited the ferroptosis development via regulating the glutathione peroxidase 4 levels in the intracerebral hemorrhage progression. Bioengineered 2022; 13:14215-14226. [PMID: 35758287 PMCID: PMC9342256 DOI: 10.1080/21655979.2022.2084494] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This study examined the effects of methyltransferase-like 3 (METTL3) on ferroptosis during intracerebral hemorrhage (ICH) progression. The brain microvascular endothelial cells (BMVECs) were stimulated with oxygen and glucose deprivation (OGD) and hemin to establish an ICH model. Cell viability was tested using a CCK8 assay. The levels of Fe2+, glutathione, reactive oxygen species, LPO, and MDA were determined using the corresponding commercial kits. Cell death was analyzed using TUNEL and propidium iodide staining. The correlation between METTL3 and glutathione peroxidase 4 (GPX4) was analyzed using Spearman’s correlation test and further confirmed using the CHIP assay. Western blotting and RT-qPCR were performed to measure the relative expression levels. Mice were injected with 0.2 units collagenase IV to establish an ICH model in vivo. We found that the Fe2+, reactive oxygen species, LPO, and MDA levels were enhanced, and glutathione was depleted in OGD/H-treated BMVECs as well as in ICH mice. Additionally, cell viability and SLC7A11 protein levels decreased, and cell death and TFR1 protein levels increased in OGD/H-treated BMVECs. METTL3 silencing relieves OGD/H-induced injury in BMVECs. In addition, METTL3 was significantly negatively related to GPX4, which was further confirmed by the CHIP assay. Silencing of METTL3 decreased the N6-methyladenosine levels of GPX4 and increased its mRNA levels of GPX4. GPX4 knockdown neutralized the role of METTL3 in OGD/H-treated BMVECs. These results implied that ferroptosis occurred in the ODG/H-treated BMVECs and ICH mouse models. METTL3 silencing effectively suppressed ferroptosis by regulating N6-methyladenosine and mRNA levels of GPX4.
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Affiliation(s)
- Liu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xiangyu Wang
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Wenqiang Che
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yongjun Yi
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Shuoming Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yongjian Feng
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
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36
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Chen F, Xie X, Chao M, Cao H, Wang L. The Potential Value of m6A RNA Methylation in the Development of Cancers Focus on Malignant Glioma. Front Immunol 2022; 13:917153. [PMID: 35711459 PMCID: PMC9196637 DOI: 10.3389/fimmu.2022.917153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/09/2022] [Indexed: 11/18/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is an epigenetic modification that has emerged in the last few years and has received increasing attention as the most abundant internal RNA modification in eukaryotic cells. m6A modifications affect multiple aspects of RNA metabolism, and m6A methylation has been shown to play a critical role in the progression of multiple cancers through a variety of mechanisms. This review summarizes the mechanisms by which m6A RNA methylation induced peripheral cancer cell progression and its potential role in the infiltration of immune cell of the glioblastoma microenvironment and novel immunotherapy. Assessing the pattern of m6A modification in glioblastoma will contribute to improving our understanding of microenvironmental infiltration and novel immunotherapies, and help in developing immunotherapeutic strategies.
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Affiliation(s)
- Fan Chen
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi’an, China
| | - Xuan Xie
- Reproductive Medicine Center, Department of Gynecology & Obstetrics, Xijing Hospital of Fourth Military Medical University, Xi’an, China
| | - Min Chao
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi’an, China
| | - Haiyan Cao
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi’an, China
| | - Liang Wang
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi’an, China
- *Correspondence: Liang Wang,
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37
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Huang J, Xu Z, Teh BM, Zhou C, Yuan Z, Shi Y, Shen Y. Construction of a necroptosis-related lncRNA signature to predict the prognosis and immune microenvironment of head and neck squamous cell carcinoma. J Clin Lab Anal 2022; 36:e24480. [PMID: 35522142 PMCID: PMC9169178 DOI: 10.1002/jcla.24480] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 01/05/2023] Open
Abstract
Background Previous studies have determined that necroptosis‐related genes are potential biomarkers in head and neck squamous cell carcinoma (HNSCC). Herein, we established a novel risk model based on necroptosis‐related lncRNAs (nrlncRNAs) to predict the prognosis of HNSCC patients. Methods Transcriptome and related information were obtained from TCGA database, and an nrlncRNA signature was established based on univariate Cox analysis and least absolute shrinkage and selection operator Cox regression. Kaplan–Meier analysis and time‐dependent receiver operating characteristic (ROC) analysis were used to evaluate the model, and a nomogram for survival prediction was established. Gene set enrichment analysis, immune analysis, drug sensitivity analysis, correlation with N6‐methylandenosin (m6A), and tumor stemness analysis were performed. Furthermore, the entire set was divided into two clusters for further discussion. Results A novel signature was established with six nrlncRNAs. The areas under the ROC curves (AUCs) for 1‐, 3‐, and 5‐year overall survival (OS) were 0.699, 0.686, and 0.645, respectively. Patients in low‐risk group and cluster 2 had a better prognosis, more immune cell infiltration, higher immune function activity, and higher immune scores; however, patients in high‐risk group and cluster 1 were more sensitive to chemotherapy. Moreover, the risk score had negative correlation with m6A‐related gene expression and tumor stemness. Conclusion According to this study, we constructed a novel signature with nrlncRNA pairs to predict the survival of HNSCC patients and guide immunotherapy and chemotherapy. This may possibly promote the development of individualized and precise treatment for HNSCC patients.
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Affiliation(s)
- Juntao Huang
- Department of Otolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.,School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Ziqian Xu
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Mei Teh
- Department of Ear Nose and Throat, Head and Neck Surgery, Eastern Health, Box Hill, Victoria, Australia.,Department of Otolaryngology, Head and Neck Surgery, Monash Health, Clayton, Victoria, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Chongchang Zhou
- Department of Otolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.,School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Zhechen Yuan
- Department of Otolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.,School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yunbin Shi
- Department of Otolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yi Shen
- Department of Otolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.,School of Medicine, Ningbo University, Ningbo, Zhejiang, China
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38
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Comprehensive analysis of m 6A regulator-based methylation modification patterns characterized by distinct immune profiles in colon adenocarcinomas. Gene 2022; 821:146250. [PMID: 35151825 DOI: 10.1016/j.gene.2022.146250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/05/2022] [Accepted: 01/21/2022] [Indexed: 01/02/2023]
Abstract
Mounting evidences have indicated that RNA N6-methyladenosine (m6A) modification played important roles in tumor formation and growth. However, it is rarely reported that m6A modifications are involved in the immune regulation and tumor microenvironment (TME) formation. In this study, we aimed to investigate the correlation between m6A modifications and TME regulation of colon adenocarcinoma (COAD) by bioinformatic analysis. NMF algorithm was applied to carry out consensus molecular subtype analysis on 36 selected m6A regulators regarding methylation modification, to identify m6A modification patterns and characteristics of m6A related genes in colon adenocarcinoma (COAD). Further, the relative infiltration levels of different immune cell subsets were quantified by ssGSEA and CIBERSORT algorithms, and a m6Sig scoring scheme was constructed to predict the prognosis and evaluate the response to immunotherapy in the patients with COAD. Among 579 COAD samples, we identified three different m6A modification patterns which were related to different biological pathways and clinical outcomes. Then, a scoring scheme termed "m6Sig score" was developed based on m6A-related characteristic genes, and was utilized to score patients with COAD into groups. We found that COAD patients with lower m6Sig scores exhibited prolonged survival and potentiated immune infiltration, which were associated with higher tumor mutation load, lower PD-L1 expression, and higher mutation rates of SMG (such as TTN and KRAS). Moreover, analysis regarding evaluation of immune response revealed that the patients with lower m6Sig scores had higher Immunophenoscore. Collectively, our study provided in depth insight into the interactions between m6A modification and regulation of TME. In addition, the quantitative evaluation of m6A modification patterns in our results may have implications in further immunotherapy for individual COAD patients.
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39
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Kong H, Wang XQ, Zhang XA. Exercise for Osteoarthritis: A Literature Review of Pathology and Mechanism. Front Aging Neurosci 2022; 14:854026. [PMID: 35592699 PMCID: PMC9110817 DOI: 10.3389/fnagi.2022.854026] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
Osteoarthritis (OA) has a very high incidence worldwide and has become a very common joint disease in the elderly. Currently, the treatment methods for OA include surgery, drug therapy, and exercise therapy. In recent years, the treatment of certain diseases by exercise has received increasing research and attention. Proper exercise can improve the physiological function of various organs of the body. At present, the treatment of OA is usually symptomatic. Limited methods are available for the treatment of OA according to its pathogenesis, and effective intervention has not been developed to slow down the progress of OA from the molecular level. Only by clarifying the mechanism of exercise treatment of OA and the influence of different exercise intensities on OA patients can we choose the appropriate exercise prescription to prevent and treat OA. This review mainly expounds the mechanism that exercise alleviates the pathological changes of OA by affecting the degradation of the ECM, apoptosis, inflammatory response, autophagy, and changes of ncRNA, and summarizes the effects of different exercise types on OA patients. Finally, it is found that different exercise types, exercise intensity, exercise time and exercise frequency have different effects on OA patients. At the same time, suitable exercise prescriptions are recommended for OA patients.
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Affiliation(s)
- Hui Kong
- College of Kinesiology, Shenyang Sport University, Shenyang, China
| | - Xue-Qiang Wang
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
- Department of Rehabilitation Medicine, Shanghai Shangti Orthopedic Hospital, Shanghai, China
- *Correspondence: Xin-An Zhang,
| | - Xin-An Zhang
- College of Kinesiology, Shenyang Sport University, Shenyang, China
- Xue-Qiang Wang,
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40
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Ren Z, Hu Y, Sun J, Kang Y, Li G, Zhao H. N 6-methyladenosine methyltransferase WTAP-stabilized FOXD2-AS1 promotes the osteosarcoma progression through m 6A/FOXM1 axis. Bioengineered 2022; 13:7963-7973. [PMID: 35356854 PMCID: PMC9161975 DOI: 10.1080/21655979.2021.2008218] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play critical roles in tumor progression regulation, including osteosarcoma. Evidence indicates that N6-methyladenosine (m6A) modification modulates mRNA stability to regulate osteosarcoma tumorigenesis. Here, present research aims to detect the roles of m6A-modified lncRNA FOXD2-AS1 in the osteosarcoma pathophysiological process. Clinical data unveiled that osteosarcoma patients with higher FOXD2-AS1 expression had a poorer overall survival rate compared to those with lower FOXD2-AS1 expression. Functional research illuminated that FOXD2-AS1 accelerated the migration, proliferation and tumor growth in vitro and in vivo. Mechanistically, a remarkable m6A-modified site was found on the 3ʹ-UTR of FOXD2-AS1, and m6A methyltransferase WTAP (Wilms’ tumor 1 associated protein) promoted the methylation modification, thus enhancing the stability of FOXD2-AS1 transcripts. Furthermore, FOXD2-AS1 interacted with downstream target FOXM1 mRNA through m6A sites, forming a FOXD2-AS1/m6A/FOXM1 complex to heighten FOXM1 mRNA stability. In conclusion, these findings propose a novel regulatory mechanism in which m6A-modified FOXD2-AS1 accelerates the osteosarcoma progression through m6A manner, which may provide new concepts for osteosarcoma tumorigenesis.
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Affiliation(s)
- Zhipeng Ren
- Department of Orthopaedics, Tianjin Hospital, Tianjin, China
| | - Yongcheng Hu
- Department of Orthopaedics, Tianjin Hospital, Tianjin, China
| | - Jie Sun
- Department of Orthopaedics, Tianjin Hospital, Tianjin, China
| | - Yuxiang Kang
- Department of Orthopaedics, Tianjin Hospital, Tianjin, China
| | - Guishi Li
- Department of Joint Orthopaedics, Yantai Yuhuangding Hospital, Yantai, China
| | - Hejun Zhao
- Department of Endocrinology, Tianjin First Central Hospital, Tianjin, China
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41
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Ma Q, Zhang SW, Zhang SY. m6Acancer-Net: Identification of m6A-mediated cancer driver genes from gene-site heterogeneous network. Methods 2022; 203:125-138. [DOI: 10.1016/j.ymeth.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/21/2022] [Accepted: 04/11/2022] [Indexed: 02/08/2023] Open
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Zhao Y, Yan X, Wang Y, Zhou J, Yu Y. N6-Methyladenosine Regulators Promote Malignant Progression of Gastric Adenocarcinoma. Front Oncol 2022; 11:726018. [PMID: 35299934 PMCID: PMC8921461 DOI: 10.3389/fonc.2021.726018] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/23/2021] [Indexed: 12/24/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is dynamically and reversibly regulated by methyltransferases, binding proteins, and demethylases. The restoration of m6A to adenosine could result in demethylation modifications. Abnormalities in m6A epigenetic modifications in cancer are of increasing interest in recent years. According to the progression and prognostic performance of m6A epigenetic modifications in gastric adenocarcinoma (STAD), this study comprehensively analyzed the m6A modification patterns of gastric adenocarcinoma specimens in The Cancer Genome Atlas (TCGA) database based on 20 m6A regulators. Here, we found that 20 m6A RNA methylation regulators were high-expressed in gastric adenocarcinoma. m6A RNA methylation regulators were closely associated with pT staging of gastric cancer. Based on such findings, we developed a prognostic model using four m6A RNA methylation regulators (IGF2BP1, RBM15, FTO, ALKBH5), and the FTO was confirmed as an independent prognostic marker.
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Affiliation(s)
- Yibin Zhao
- Department of Anus & Intestine Surgery, Ningbo Medical Center LiHuiLi Hospital, Ningbo, China
| | - Xiao Yan
- Department of Hematology, Ningbo First Hospital, Ningbo, China
| | - Yu Wang
- Department of Anus & Intestine Surgery, Ningbo Medical Center LiHuiLi Hospital, Ningbo, China
| | - Juan Zhou
- Department of Medical Oncology, Xuzhou Central Hospital, Xuzhou, China
| | - Yang Yu
- Department of Medical Oncology, Xuzhou Central Hospital, Xuzhou, China
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43
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Wang L, Cao H, Zhong Y, Ji P, Chen F. The Role of m6A Regulator-Mediated Methylation Modification and Tumor Microenvironment Infiltration in Glioblastoma Multiforme. Front Cell Dev Biol 2022; 10:842835. [PMID: 35265626 PMCID: PMC8898963 DOI: 10.3389/fcell.2022.842835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/01/2022] [Indexed: 01/12/2023] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is an emerging epigenetic modification in recent years and epigenetic regulation of the immune response has been demonstrated, but the potential role of m6A modification in GBM tumor microenvironment (TME) cell infiltration and stemness remain unknown. The m6A modification patterns of 310 GBM samples were comprehensively evaluated based on 21 m6A regulators, and we systematically correlated these modification patterns with TME cell infiltration characteristics and stemness characteristics. Construction of m6Ascore to quantify the m6A modification patterns of individual GBM samples using a principal component analysis algorithm. We identified two distinct patterns of m6A modification. The infiltration characteristics of TME cells in these two patterns were highly consistent with the immunophenotype of the GBM, including the immune activation differentiation pattern and the immune desert dedifferentiation pattern. We also identified two modes of regulation of immunity and stemness by m6A methylation. Stromal activation and lack of effective immune infiltration were observed in the high m6Ascore subtype. Pan-cancer analysis results illustrate a significant correlation between m6AScore and tumor clinical outcome, immune infiltration, and stemness. Our work reveals that m6A modifications play an important role in the development of TME and stemness diversity and complexity. Patients with a low m6AScore showed significant therapeutic advantages and clinical benefits. Assessing the m6A modification pattern of individual tumors will help enhance our knowledge of TME infiltration and stemness characteristics, contribute to the development of immunotherapeutic strategies.
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Affiliation(s)
- Liang Wang
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Haiyan Cao
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Ying Zhong
- Department of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Peigang Ji
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Fan Chen
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
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44
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Liu J, Cui G, Shen S, Gao F, Zhu H, Xu Y. Establishing a Prognostic Signature Based on Epithelial-Mesenchymal Transition-Related Genes for Endometrial Cancer Patients. Front Immunol 2022; 12:805883. [PMID: 35095892 PMCID: PMC8795518 DOI: 10.3389/fimmu.2021.805883] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/21/2021] [Indexed: 12/24/2022] Open
Abstract
Backgrounds Epithelial-mesenchymal transition (EMT) is a sequential process where tumor cells develop from the epithelial state to the mesenchymal state. EMT contributes to various tumor functions including initiation, propagating potential, and resistance to therapy, thus affecting the survival time of patients. The aim of this research is to set up an EMT-related prognostic signature for endometrial cancer (EC). Methods EMT-related gene (ERG) expression and clinical data were acquired from The Cancer Genome Atlas (TCGA). The entire set was randomly divided into two sets, one for contributing the risk model (risk score) and the other for validating. Univariate and multivariate Cox proportional hazards regression analyses were applied to the training set to select the prognostic ERGs. The expression of 10 ERGs was confirmed by qRT-PCR in clinical samples. Then, we developed a nomogram predicting 1-/3-/5-year survival possibility combining the risk score and clinical factors. The entire set was stratified into the high- and low-risk groups, which was used to analyze the immune infiltrating, tumorigenesis pathways, and response to drugs. Results A total of 220 genes were screened out from 1,316 ERGs for their differential expression in tumor versus normal. Next, 10 genes were found to be associated with overall survival (OS) in EC, and the expression was validated by qRT-PCR using clinical samples, so we constructed a 10-ERG-based risk score to distinguish high-/low-risk patients and a nomogram to predict survival rate. The calibration plots proved the predictive value of our model. Gene Set Enrichment Analysis (GSEA) discovered that in the low-risk group, immune-related pathways were enriched; in the high-risk group, tumorigenesis pathways were enriched. The low-risk group showed more immune activities, higher tumor mutational burden (TMB), and higher CTAL4/PD1 expression, which was in line with a better response to immune checkpoint inhibitors. Nevertheless, response to chemotherapeutic drugs turned out better in the high-risk group. The high-risk group had higher N 6-methyladenosine (m6A) RNA expression, microsatellite instability level, and stemness indices. Conclusion We constructed the ERG-related signature model to predict the prognosis of EC patients. What is more, it might offer a reference for predicting individualized response to immune checkpoint inhibitors and chemotherapeutic drugs.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Shuning Shen
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Gao
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hongjun Zhu
- Department of Oncology, Nantong Third People's Hospital Affiliated to Nantong University, Nantong, China
| | - Yinghua Xu
- Department of Radiation Oncology, Nantong Third People's Hospital Affiliated to Nantong University, Nantong, China
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45
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Chen H, Yu Y, Yang M, Huang H, Ma S, Hu J, Xi Z, Guo H, Yao G, Yang L, Huang X, Zhang F, Tan G, Wu H, Zheng W, Li L. YTHDF1 promotes breast cancer progression by facilitating FOXM1 translation in an m6A-dependent manner. Cell Biosci 2022; 12:19. [PMID: 35197112 PMCID: PMC8867832 DOI: 10.1186/s13578-022-00759-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/10/2022] [Indexed: 12/20/2022] Open
Abstract
Background N6-methyladenosine (m6A) is the most common post-transcriptional modification at the RNA level. However, the exact molecular mechanisms of m6A epigenetic regulation in breast cancer remain largely unknown and need to be fully elucidated. Methods The integrating bioinformatics analyses were used to screen clinical relevance and dysregulated m6A “reader” protein YTHDF1 in breast cancer from TCGA databases, which was further validated in a cohort of clinical specimens. Furthermore, functional experiments such as the CCK-8 assay, EdU assay, wound healing assay, transwell invasion assay and cell cycle assay were used to determine the biological role of YTHDF1 in breast cancer. RIP, m6A-IP, and CLIP assays were used to find the target of YTHDF1 and further verification by RT-qPCR, western blot, polysome profiling assay. The protein–protein interaction between YTHDF1 and FOXM1 was detected via co-immunoprecipitation. Results Our study showed that YTHDF1 was overexpressed in breast cancer cells and clinical tissues specimens. At the same time, the high expression level of YTHDF1 was positively correlated with tumor size, lymph node invasion, and distant metastasis in breast cancer patients. YTHDF1 depletion repressed the proliferation, invasion and epithelial-mesenchymal transformation (EMT) and induced G0/G1 phase cell cycle arrest of breast cancer cells in vitro and in vivo. We also demonstrated that FOXM1 is a target of YTHDF1. Through recognizing and binding to the m6A-modified mRNA of FOXM1, YTHDF1 accelerated the translation process of FOXM1 and promoted breast cancer metastasis. Whereas overexpression of FOXM1 in breast cancer cells partially counteracted the tumor suppressed effects caused by YTHDF1 silence, which further verified the regulatory relationship between YTHDF1 and FOXM1. Conclusion Our study reveals a novel YTHDF1/FOXM1 regulatory pathway that contributes to metastasis and progression of breast cancer, suggesting that YTHDF1 might be applied as a potential biomarker and therapeutic target. That also advances our understanding of the tumorigenesis for breast cancer from m6A epigenetic regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00759-w.
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Affiliation(s)
- Hengyu Chen
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University, Key Laboratory of Tropical Translational Medicine of Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine, Haikou, 570311, China.,Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yuanhang Yu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ming Yang
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Haohao Huang
- Department of Neurosurgery, General Hospital of Central Theater Command of Chinese People's Liberation Army, Wuhan, 430070, China
| | - Shenghui Ma
- Medical College Wuhan University of Science and Technology, Wuhan, 430070, China
| | - Jin Hu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zihan Xi
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hui Guo
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Guojie Yao
- Department of Neurosurgery, General Hospital of Central Theater Command of Chinese People's Liberation Army, Wuhan, 430070, China
| | - Liu Yang
- Department of Neurosurgery, General Hospital of Central Theater Command of Chinese People's Liberation Army, Wuhan, 430070, China
| | - Xiaoqing Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Feng Zhang
- Department of Emergency Medicine, Affiliated Hospital of Sergeant School Affiliated to Army Medical University, Shijiazhuang, 050047, China
| | - Guanghong Tan
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University, Key Laboratory of Tropical Translational Medicine of Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine, Haikou, 570311, China.
| | - Huangfu Wu
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University, Key Laboratory of Tropical Translational Medicine of Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine, Haikou, 570311, China.
| | - Wuping Zheng
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University, Key Laboratory of Tropical Translational Medicine of Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine, Haikou, 570311, China.
| | - Lei Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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46
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Zhang Y, Li J, Feng D, Peng X, Wang B, Han T, Zhang Y. Systematic Analysis of Molecular Characterization and Clinical Relevance of Liquid–Liquid Phase Separation Regulators in Digestive System Neoplasms. Front Cell Dev Biol 2022; 9:820174. [PMID: 35252219 PMCID: PMC8891544 DOI: 10.3389/fcell.2021.820174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/21/2021] [Indexed: 01/02/2023] Open
Abstract
Background: The role of liquid–liquid phase separation (LLPS) in cancer has also attracted more and more attention, which is found to affect transcriptional regulation, maintaining genomic stability and signal transduction, and contribute to the occurrence and progression of tumors. However, the role of LLPS in digestive system tumors is still largely unknown. Results: Here, we characterized the expression profiles of LLPS regulators in 3 digestive tract tumor types such as COAD, STAD, and ESCA with The Cancer Genome Atlas (TCGA) data. Our results for the first time showed that LLPS regulatory factors, such as Brd4, FBN1, and TP53, were frequently mutated in all types of digestive system tumors. Variant allele frequency (VAF) and APOBEC analysis demonstrated that genetic alterations of LLPS regulators were related to the progression of digestive system neoplasms (DSNs), such as TP53, NPHS1, TNRC6B, ITSN1, TNPO1, PML, AR, BRD4, DLG4, and PTPN1. KM plotter analysis showed that the mutation status of LLPS regulators was significantly related to the overall survival (OS) time of DSNs, indicating that they may contribute to the progression of DSN. The expression analysis of LLPS regulatory factors showed that a variety of LLPS regulatory factors were significantly dysregulated in digestive system tumors, such as SYN2 and MAPT. It is worth noting that we first found that LLPS regulatory factors were significantly correlated with tumor immune infiltration of B cells, CD4+ T cells, and CD8+ T cells in digestive system tumors. Bioinformatics analysis showed that the LLPS regulators’ expression was closely related to multiple signaling, including the ErbB signaling pathway and T-cell receptor signaling pathway. Finally, several LLPS signatures were constructed and had a strong prognostic stratification ability in different digestive gland tumors. Finally, the results demonstrated the LLPS regulators’ signature score was significantly positively related to the infiltration levels of CD4+ T cells, neutrophil cells, macrophage cells, and CD8+ T cells. Conclusion: Our study for the first time showed the potential roles of LLPS regulators in carcinogenesis and provide novel insights to identify novel biomarkers for the prediction of immune therapy and prognosis of DSNs.
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Affiliation(s)
- Yaxin Zhang
- Department of Oncology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jie Li
- Department of Oncology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Dan Feng
- Department of Oncology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xiaobo Peng
- Department of Oncology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Bin Wang
- Department of Oncology, Changhai Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Bin Wang, ; Ting Han, ; Yingyi Zhang,
| | - Ting Han
- Departments of General Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Bin Wang, ; Ting Han, ; Yingyi Zhang,
| | - Yingyi Zhang
- Department of Oncology, Changhai Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Bin Wang, ; Ting Han, ; Yingyi Zhang,
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Liu Q. Current Advances in N6-Methyladenosine Methylation Modification During Bladder Cancer. Front Genet 2022; 12:825109. [PMID: 35087575 PMCID: PMC8787278 DOI: 10.3389/fgene.2021.825109] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022] Open
Abstract
N6-methyladenosine (m6A) is a dynamic, reversible post-transcriptional modification, and the most common internal modification of eukaryotic messenger RNA (mRNA). Considerable evidence now shows that m6A alters gene expression, thereby regulating cell self-renewal, differentiation, invasion, and apoptotic processes. M6A methylation disorders are directly related to abnormal RNA metabolism, which may lead to tumor formation. M6A methyltransferase is the dominant catalyst during m6A modification; it removes m6A demethylase, promotes recognition by m6A binding proteins, and regulates mRNA metabolic processes. Bladder cancer (BC) is a urinary system malignant tumor, with complex etiology and high incidence rates. A well-differentiated or moderately differentiated pathological type at initial diagnosis accounts for most patients with BC. For differentiated superficial bladder urothelial carcinoma, the prognosis is normally good after surgery. However, due to poor epithelial cell differentiation, BC urothelial cell proliferation and infiltration may lead to invasive or metastatic BC, which lowers the 5-years survival rate and significantly affects clinical treatments in elderly patients. Here, we review the latest progress in m6A RNA methylation research and investigate its regulation on BC occurrence and development.
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Affiliation(s)
- Qiang Liu
- Department of Urology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
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48
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Hu Z, Zhu L, Zhang Y, Chen B. N6-methyladenosine-induced SVIL antisense RNA 1 restrains lung adenocarcinoma cell proliferation by destabilizing E2F1. Bioengineered 2022; 13:3093-3107. [PMID: 35068325 PMCID: PMC8973833 DOI: 10.1080/21655979.2022.2025697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidence indicates that N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play crucial roles in cancer development. However, the biological roles of m6A and lncRNAs in lung cancer tumorigenesis are largely unknown. In this study, SVIL antisense RNA 1 (SVIL-AS1) was downregulated in lung adenocarcinoma (LUAD) tissues and was associated with a favorable prognosis in patients with LUAD. SVIL-AS1 overexpression suppressed LUAD cell proliferation and blocked cell cycle arrest. Mechanistically, METTL3 increased the m6A modification and transcript stability of SVIL-AS1. The enhanced SVIL-AS1 expression mediated by METTL3 suppressed E2F1 and E2F1-target genes. Moreover, SVIL-AS1 accelerated E2F1 degradation. The reduction in cell proliferation induced by SVIL-AS1 overexpression could be rescued by E2F1 overexpression or METTL3 knockdown. In conclusion, our work demonstrated the role and mechanism of METTL3-induced SVIL-AS1 in LUAD, which connects m6A and lncRNA in lung cancer carcinogenesis.
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Affiliation(s)
- Zedong Hu
- Second Department of Thoracic Surgery, Anhui Chest Hospital, Hefei, China
| | - Liang Zhu
- Second Department of Thoracic Surgery, Anhui Chest Hospital, Hefei, China
| | - Yilin Zhang
- Second Department of Thoracic Surgery, Anhui Chest Hospital, Hefei, China
| | - Bing Chen
- Second Department of Thoracic Surgery, Anhui Chest Hospital, Hefei, China
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49
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Zhang N, Ding C, Zuo Y, Peng Y, Zuo L. N6-methyladenosine and Neurological Diseases. Mol Neurobiol 2022; 59:1925-1937. [PMID: 35032318 DOI: 10.1007/s12035-022-02739-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/08/2022] [Indexed: 12/14/2022]
Abstract
N6-methyladenosine (m6A) is a dynamic reversible methylation modification of the adenosine N6 position and is the most common chemical epigenetic modification among mRNA post-transcriptional modifications, including methylation, demethylation, and recognition. Post-transcriptional modification involves multiple protein molecules, including METTL3, METTL14, WTAP, KIAA1429, ALKBH5, YTHDF1/2/3, and YTHDC1/2. m6A-related proteins are expressed in almost all cells. However, the abnormal expression of m6A-related proteins may occur in the nervous system, thereby affecting neuritogenesis, brain volume, learning and memory, memory formation and consolidation, etc., and is implicated in the development of diseases, such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, depression, epilepsy, and brain tumors. This review focuses on the functions of m6A in the development of central nervous system diseases, thus contributing to a deeper understanding of disease pathogenesis and providing potential clinical therapeutic targets for neurological diseases.
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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 College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Chunhong Ding
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, 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 College, 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 College, 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 College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China.
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50
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Huang ZD, Lin LL, Liu ZZ, Hu C, Gu HY, Wei RX. m6A Modification Patterns With Distinct Immunity, Metabolism, and Stemness Characteristics in Soft Tissue Sarcoma. Front Immunol 2022; 12:765723. [PMID: 35003079 PMCID: PMC8739240 DOI: 10.3389/fimmu.2021.765723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation has been shown to have prognostic value in cancer. Nonetheless, its potential role regarding immunity, metabolism, and stemness in soft tissue sarcoma (STS) remains unknown. We comprehensively estimated the m6A modification patterns and corresponding immunity, metabolism, and stemness characteristics based on 568 STS samples and 21 m6A regulators. The m6Ascore was constructed to quantify m6A modification patterns in individuals using machine learning algorithms. Two distinct m6A modification patterns among the STS patients were identified, which exhibited differences in prognosis, immune cell infiltration, metabolic pathways, stemness, somatic mutation, and copy number variation. Thereafter, immunity-, metabolism-, and stemness phenotype-related genes associated with m6A modification were identified. Furthermore, patients with lower m6Ascores had increased antitumor immune responses, survival benefit under immunotherapy, tumor mutation burden, immunogenicity, and response to anti-PD-1/L1 immunotherapy. Immunotherapy sensitivity was validated using the IMvigor210 dataset. STS patients with lower m6Ascore might be more sensitive to docetaxel and gemcitabine. Finally, pan-cancer analysis illustrated the significant correlations of m6Ascore with clinical outcomes, immune cell infiltration, metabolism, and stemness. This study revealed that m6A modification plays an important role in immunity, metabolism, and stemness in STS. Evaluating the m6A modification pattern and development of m6Ascore may help to guide more effective immunotherapy and chemotherapy strategies.
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Affiliation(s)
- Zhen-Dong Huang
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Stomatology, Southern Medical University, Guangzhou, China
| | - Lu-Lu Lin
- Department of Pathology and Pathophysiology, School of Basic Medicine, Wuhan University, Wuhan, China
| | - Zi-Zhen Liu
- The Third Clinical School, Hubei University of Medicine, Shiyan, China
| | - Chao Hu
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui-Yun Gu
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ren-Xiong Wei
- Department of Spine and Orthopedic Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
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