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Fang Z, Ding H, Han J, Fu L, Jin J, Feng W. Functions of N6-methyladenosine (m6A) RNA modifications in acute myeloid leukemia. J Leukoc Biol 2024; 116:662-671. [PMID: 38721720 DOI: 10.1093/jleuko/qiae106] [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: 11/15/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 10/03/2024] Open
Abstract
N6-methyladenosine is the most common modification of eukaryotic RNA. N6-methyladenosine participates in RNA splicing, nuclear export, translation, and degradation through regulation by methyltransferases, methylation readers, and demethylases, affecting messenger RNA stability and translation efficiency. Through the dynamic and reversible regulatory network composed of "writers, erasers, and readers," N6-methyladenosine modification plays a unique role in the process of hematopoiesis. Acute myeloid leukemia is a heterogeneous disease characterized by malignant proliferation of hematopoietic stem cells/progenitor cells. Many studies have shown that N6-methyladenosine-related proteins are abnormally expressed in acute myeloid leukemia and play an important role in the occurrence and development of acute myeloid leukemia, acting as carcinogenic or anticancer factors. Here, we describe the mechanisms of action of reversing N6-methyladenosine modification in hematopoiesis and acute myeloid leukemia occurrence and progression to provide a basis for further research on the role of N6-methyladenosine methylation and its regulatory factors in normal hematopoiesis and acute myeloid leukemia, to ultimately estimate its potential clinical value.
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Affiliation(s)
- Zehao Fang
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Hanyi Ding
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Jiongping Han
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Leihua Fu
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Jing Jin
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Weiying Feng
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
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Sun X, Wang H, Pu X, Wu Y, Yuan X, Wang X, Lu H. Manipulating the tumour immune microenvironment by N6-methyladenosine RNA modification. Cancer Gene Ther 2024; 31:1315-1322. [PMID: 38834772 DOI: 10.1038/s41417-024-00791-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
N6-methyladenosine (m6A), a posttranscriptional regulatory mechanism, is the most common epigenetic modification in mammalian mRNA. M6A modifications play a crucial role in the developmental network of immune cells. The expression of m6A-related regulators often affects carcinogenesis and tumour suppression networks. In the tumour microenvironment, m6A-modified enzymes can affect the occurrence and progression of tumours by regulating the activation and invasion of tumour-associated immune cells. Immunotherapy, which utilises immune cells, has been demonstrated to be a powerful weapon in tumour treatment and is increasingly being used in the clinic. Here, we provide an updated and comprehensive overview of how m6A modifications affect invasive immune cells and their potential role in immune regulation. In addition, we summarise the regulation of epigenetic regulators associated with m6A modifications in tumour cells on the antitumour response of immune cells in the tumour immune microenvironment. These findings provide new insights into the role of m6A modifications in the immune response and tumour development, leading to the development of novel immunotherapies for cancer treatment.
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Affiliation(s)
- Xinyu Sun
- Department of Otorhinolaryngology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Radiation Oncology, Cancer Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Huirong Wang
- Department of Otorhinolaryngology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xi Pu
- Department of Radiation Oncology, Cancer Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuting Wu
- Department of Radiation Oncology, Cancer Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Yuan
- Department of Radiation Oncology, Cancer Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xu Wang
- Department of Radiation Oncology, Cancer Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hanqiang Lu
- Department of Otorhinolaryngology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.
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3
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Yang L, Ying J, Tao Q, Zhang Q. RNA N 6-methyladenosine modifications in urological cancers: from mechanism to application. Nat Rev Urol 2024; 21:460-476. [PMID: 38347160 DOI: 10.1038/s41585-023-00851-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2023] [Indexed: 08/04/2024]
Abstract
The N6-methyladenosine (m6A) modification is the most common modification of messenger RNAs in eukaryotes and has crucial roles in multiple cancers, including in urological malignancies such as renal cell carcinoma, bladder cancer and prostate cancer. The m6A RNA modification is controlled by three types of regulators, including methyltransferases (writers), demethylases (erasers) and RNA-binding proteins (readers), which are responsible for gene regulation at the post-transcriptional level. This Review summarizes the current evidence indicating that aberrant or dysregulated m6A modification is associated with urological cancer development, progression and prognosis. The complex and context-dependent effects of dysregulated m6A modifications in urological cancers are described, along with the potential for aberrantly expressed m6A regulators to provide valuable diagnostic and prognostic biomarkers as well as new therapeutic targets.
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Affiliation(s)
- Lei Yang
- Department of Urology, Peking University First Hospital, Institute of Urology, National Research Center for Genitourinary Oncology, Peking University, Beijing, China
| | - Jianming Ying
- Department of Pathology, Cancer Institute and Cancer Hospital, Peking Union Medical College (PUMC), Chinese Academy of Medical Sciences, Beijing, China
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Qian Zhang
- Department of Urology, Peking University First Hospital, Institute of Urology, National Research Center for Genitourinary Oncology, Peking University, Beijing, China.
- Department of Urology, Peking University Binhai Hospital, Tianjin, China.
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Jia HR, Li WC, Wu L. The prognostic value of immune escape-related genes in lung adenocarcinoma. Transl Cancer Res 2024; 13:2647-2661. [PMID: 38988926 PMCID: PMC11231773 DOI: 10.21037/tcr-23-2295] [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: 12/16/2023] [Accepted: 04/24/2024] [Indexed: 07/12/2024]
Abstract
Background Lung cancer is one of the most common cancers in humans, and lung adenocarcinoma (LUAD) has become the most common histological type of lung cancer. Immune escape promotes progression of LUAD from the early to metastatic late stages and is one of the main obstacles to improving clinical outcomes for immunotherapy targeting immune detection points. Our study aims to explore the immune escape related genes that are abnormally expressed in lung adenocarcinoma, providing assistance in predicting the prognosis of lung adenocarcinoma and targeted. Methods RNA data and related clinical details of patients with LUAD were obtained from The Cancer Genome Atlas (TCGA) database. Through weighted gene coexpression network analysis (WGCNA), 3112 key genes were screened and intersected with 182 immune escape genes obtained from a previous study to identify the immune escape-related genes (IERGs). The role of IERGs in LUAD was systematically explored through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, which were used to enrich the relevant pathways of IERGs. The least absolute shrinkage and selection operator (LASSO) algorithm and multivariate Cox regression analysis were used to identify the key prognostic genes, and a prognostic risk model was constructed. Estimation of Stromal and Immune Cells in Malignant Tumor Tissues Using Expression Data (ESTIMATE) and microenvironment cell populations (MCP) counter methods (which can accurately assess the amount of eight immune cell populations and two stromal cell groups) were used to analyze the tumor immune status of the high and low risk subgroups. The protein expression level of the differentially expressed genes in lung cancer samples was determined by using the Human Protein Atlas (HPA) database. A nomogram was constructed, and the prognostic risk model was verified via the Gene Expression Omnibus (GEO) datasets GSE72094 and GSE30219. Results Twenty differentially expressed IERGs were obtained. GO analysis of these 20 IERGs revealed that they were mainly associated with the regulation of immune system processes, immune responses, and interferon-γ enrichment in mediating signaling pathways and apoptotic signaling pathways; meanwhile, KEGG analysis revealed that IERGs were associated with necroptosis, antigen processing and presentation, programmed cell death ligand 1 (PD-L1) expression and programmed cell death 1 (PD-1) pathway in tumors, cytokine-cytokine receptor interactions, T helper cell 1 (Th1) and Th2 differentiation, and tumor necrosis factor signaling pathways. Using LASSO and Cox regression analysis, we constructed a four-gene model that could predict the prognosis of patients with LUAD, and the model was validated with a validation cohort. The immunohistochemical results of the HPA database showed that AHSA1 and CEP55 had low expression in normal lung tissue but high expression in lung cancer tissue. Conclusions We constructed an IERG-based model for predicting the prognosis of LUAD. Among the genes identified, CEP55 and AHSA1 may be potential prognostic and therapeutic targets, and reducing their expression may represent a novel approach in the treatment of LUAD.
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Affiliation(s)
- Hao Ran Jia
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Wen Chao Li
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lin Wu
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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Li Y, Jin H, Li Q, Shi L, Mao Y, Zhao L. The role of RNA methylation in tumor immunity and its potential in immunotherapy. Mol Cancer 2024; 23:130. [PMID: 38902779 PMCID: PMC11188252 DOI: 10.1186/s12943-024-02041-8] [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: 12/24/2023] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
RNA methylation, a prevalent post-transcriptional modification, has garnered considerable attention in research circles. It exerts regulatory control over diverse biological functions by modulating RNA splicing, translation, transport, and stability. Notably, studies have illuminated the substantial impact of RNA methylation on tumor immunity. The primary types of RNA methylation encompass N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N7-methylguanosine (m7G), and 3-methylcytidine (m3C). Compelling evidence underscores the involvement of RNA methylation in regulating the tumor microenvironment (TME). By affecting RNA translation and stability through the "writers", "erasers" and "readers", RNA methylation exerts influence over the dysregulation of immune cells and immune factors. Consequently, RNA methylation plays a pivotal role in modulating tumor immunity and mediating various biological behaviors, encompassing proliferation, invasion, metastasis, etc. In this review, we discussed the mechanisms and functions of several RNA methylations, providing a comprehensive overview of their biological roles and underlying mechanisms within the tumor microenvironment and among immunocytes. By exploring how these RNA modifications mediate tumor immune evasion, we also examine their potential applications in immunotherapy. This review aims to provide novel insights and strategies for identifying novel targets in RNA methylation and advancing cancer immunotherapy efficacy.
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Affiliation(s)
- Yan Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haoer Jin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Qingling Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Liangrong Shi
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Yang W, Zhao Y, Yang Y. Dynamic RNA methylation modifications and their regulatory role in mammalian development and diseases. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2526-2. [PMID: 38833084 DOI: 10.1007/s11427-023-2526-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/15/2023] [Indexed: 06/06/2024]
Abstract
Among over 170 different types of chemical modifications on RNA nucleobases identified so far, RNA methylation is the major type of epitranscriptomic modifications existing on almost all types of RNAs, and has been demonstrated to participate in the entire process of RNA metabolism, including transcription, pre-mRNA alternative splicing and maturation, mRNA nucleus export, mRNA degradation and stabilization, mRNA translation. Attributing to the development of high-throughput detection technologies and the identification of both dynamic regulators and recognition proteins, mechanisms of RNA methylation modification in regulating the normal development of the organism as well as various disease occurrence and developmental abnormalities upon RNA methylation dysregulation have become increasingly clear. Here, we particularly focus on three types of RNA methylations: N6-methylcytosine (m6A), 5-methylcytosine (m5C), and N7-methyladenosine (m7G). We summarize the elements related to their dynamic installment and removal, specific binding proteins, and the development of high-throughput detection technologies. Then, for a comprehensive understanding of their biological significance, we also overview the latest knowledge on the underlying mechanisms and key roles of these three mRNA methylation modifications in gametogenesis, embryonic development, immune system development, as well as disease and tumor progression.
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Affiliation(s)
- Wenlan Yang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Yongliang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Yungui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- China National Center for Bioinformation, Beijing, 100101, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China.
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Hashemi M, Daneii P, Zandieh MA, Raesi R, Zahmatkesh N, Bayat M, Abuelrub A, Khazaei Koohpar Z, Aref AR, Zarrabi A, Rashidi M, Salimimoghadam S, Entezari M, Taheriazam A, Khorrami R. Non-coding RNA-Mediated N6-Methyladenosine (m 6A) deposition: A pivotal regulator of cancer, impacting key signaling pathways in carcinogenesis and therapy response. Noncoding RNA Res 2024; 9:84-104. [PMID: 38075202 PMCID: PMC10700483 DOI: 10.1016/j.ncrna.2023.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/23/2023] [Accepted: 11/08/2023] [Indexed: 06/20/2024] Open
Abstract
The emergence of RNA modifications has recently been considered as critical post-transcriptional regulations which governed gene expression. N6-methyladenosine (m6A) modification is the most abundant type of RNA modification which is mediated by three distinct classes of proteins called m6A writers, readers, and erasers. Accumulating evidence has been made in understanding the role of m6A modification of non-coding RNAs (ncRNAs) in cancer. Importantly, aberrant expression of ncRNAs and m6A regulators has been elucidated in various cancers. As the key role of ncRNAs in regulation of cancer hallmarks is well accepted now, it could be accepted that m6A modification of ncRNAs could affect cancer progression. The present review intended to discuss the latest knowledge and importance of m6A epigenetic regulation of ncRNAs including mircoRNAs, long non-coding RNAs, and circular RNAs, and their interaction in the context of cancer. Moreover, the current insight into the underlying mechanisms of therapy resistance and also immune response and escape mediated by m6A regulators and ncRNAs are discussed.
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Affiliation(s)
- Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Pouria Daneii
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammad Arad Zandieh
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Rasoul Raesi
- Department of Health Services Management, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical-Surgical Nursing, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Zahmatkesh
- Department of Genetics, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Mehrsa Bayat
- Department of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Anwar Abuelrub
- Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
| | - Zeinab Khazaei Koohpar
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran
| | - Amir Reza Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul, 34396, Turkey
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Xie J, Gan L, Xue B, Wang X, Pei X. Emerging roles of interactions between ncRNAs and other epigenetic modifications in breast cancer. Front Oncol 2023; 13:1264090. [PMID: 37901333 PMCID: PMC10602744 DOI: 10.3389/fonc.2023.1264090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023] Open
Abstract
Up till the present moment, breast cancer is still the leading cause of cancer-related death in women worldwide. Although the treatment methods and protocols for breast cancer are constantly improving, the long-term prognosis of patients is still not optimistic due to the complex heterogeneity of the disease, multi-organ metastasis, chemotherapy and radiotherapy resistance. As a newly discovered class of non-coding RNAs, ncRNAs play an important role in various cancers. Especially in breast cancer, lncRNAs have received extensive attention and have been confirmed to regulate cancer progression through a variety of pathways. Meanwhile, the study of epigenetic modification, including DNA methylation, RNA methylation and histone modification, has developed rapidly in recent years, which has greatly promoted the attention to the important role of non-coding RNAs in breast cancer. In this review, we carefully and comprehensively describe the interactions between several major classes of epigenetic modifications and ncRNAs, as well as their different subsequent biological effects, and discuss their potential for practical clinical applications.
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Affiliation(s)
| | | | | | | | - Xinhong Pei
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Ren Q, Li Q, Shao C, Zhang P, Hu Z, Li J, Wang W, Yu Y. Establishing a prognostic model based on immune-related genes and identification of BIRC5 as a potential biomarker for lung adenocarcinoma patients. BMC Cancer 2023; 23:897. [PMID: 37741993 PMCID: PMC10517491 DOI: 10.1186/s12885-023-11249-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/03/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is an extraordinarily malignant tumor, with rapidly increasing morbidity and poor prognosis. Immunotherapy has emerged as a hopeful therapeutic modality for lung adenocarcinoma. Furthermore, a prognostic model (based on immune genes) can fulfill the purpose of early diagnosis and accurate prognostic prediction. METHODS Immune-related mRNAs (IRmRNAs) were utilized to construct a prognostic model that sorted patients into high- and low-risk groups. Then, the prediction efficacy of our model was evaluated using a nomogram. The differences in overall survival (OS), the tumor mutation landscape, and the tumor microenvironment were further explored between different risk groups. In addition, the immune genes comprising the prognostic model were subjected to single-cell RNA sequencing to investigate the expression of these immune genes in different cells. Finally, the functions of BIRC5 were validated through in vitro experiments. RESULTS Patients in different risk groups exhibited sharply significant variations in OS, pathway activity, immune cell infiltration, mutation patterns, and immune response. Single-cell RNA sequencing revealed that the expression level of BIRC5 was significantly high in T cells. Cell experiments further revealed that BIRC5 knockdown markedly reduced LUAD cell proliferation. CONCLUSION This model can function as an instrumental variable in the prognostic, molecular, and therapeutic prediction of LUAD, shedding new light on the optimal clinical practice guidelines for LUAD patients.
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Affiliation(s)
- Qianhe Ren
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qifan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chenye Shao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhuangzhuang Hu
- Department of Urology, Shuyang First People's Hospital, Suqian, China
| | - Jun Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Yue Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Luo Y, He M, Yang J, Zhang F, Chen J, Wen X, Fan J, Fan X, Chai P, Jia R. A novel MYCN-YTHDF1 cascade contributes to retinoblastoma tumor growth by eliciting m 6A -dependent activation of multiple oncogenes. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2138-2151. [PMID: 36949231 DOI: 10.1007/s11427-022-2288-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/20/2022] [Indexed: 03/24/2023]
Abstract
Retinoblastoma, the most prevalent primary intraocular tumor in children, leads to vision impairment, disability and even death. In addition to RB1 inactivation, MYCN activation has been documented as another common oncogenic alteration in retinoblastoma and represents one of the high-risk molecular subtypes of retinoblastoma. However, how MYCN contributes to the progression of retinoblastoma is still incompletely understood. Here, we report that MYCN upregulates YTHDF1, which encodes one of the reader proteins for N6-methyladenosine (m6A) RNA modification, in retinoblastoma. We further found that this MYCN-upregulated m6A reader functions to promote retinoblastoma cell proliferation and tumor growth in an m6A binding-dependent manner. Mechanistically, YTHDF1 promotes the expression of multiple oncogenes by binding to their mRNAs and enhancing mRNA stability and translation in retinoblastoma cells. Taken together, our findings reveal a novel MYCN-YTHDF1 regulatory cascade in controlling retinoblastoma cell proliferation and tumor growth, pinpointing an unprecedented mechanism for MYCN amplification and/or activation to promote retinoblastoma progression.
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Affiliation(s)
- Yingxiu Luo
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China
| | - Mengjia He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China
| | - Jie Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China
| | - Feifei Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China
| | - Jie Chen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China
| | - Xuyang Wen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China
| | - Jiayan Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China.
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200023, China.
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Lian B, Yan S, Li J, Bai Z, Li J. HNRNPC promotes collagen fiber alignment and immune evasion in breast cancer via activation of the VIRMA-mediated TFAP2A/DDR1 axis. Mol Med 2023; 29:103. [PMID: 37528369 PMCID: PMC10394847 DOI: 10.1186/s10020-023-00696-5] [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: 03/29/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Cancers aggressively reorganize collagen in their microenvironment, leading to the evasion of tumor cells from immune surveillance. However, the biological significance and molecular mechanism of collagen alignment in breast cancer (BC) have not been well established. METHODS In this study, BC-related RNA-Seq data were obtained from the TCGA database to analyze the correlation between DDR1 and immune cells. Mouse BC cells EO771 were selected for in vitro validation, and dual-luciferase experiments were conducted to examine the effect of TFAP2A on DDR1 promoter transcription activity. ChIP experiments were performed to assess TFAP2A enrichment on the DDR1 promoter, while Me-RIP experiments were conducted to detect TFAP2A mRNA m6A modification levels, and PAR-CLIP experiments were conducted to determine VIRMA's binding to TFAP2A mRNA and RIP experiments to investigate HNRNPC's recognition of m6A modification on TFAP2A mRNA. Additionally, an in vivo mouse BC transplant model and the micro-physiological system was constructed for validation, and Masson staining was used to assess collagen fiber arrangement. Immunohistochemistry was conducted to identify the number of CD8-positive cells in mouse BC tumors and Collagen IV content in ECM, while CD8 + T cell migration experiments were performed to measure CD8 + T cell migration. RESULTS Bioinformatics analysis showed that DDR1 was highly expressed in BC and negatively correlated with the proportion of anti-tumor immune cell infiltration. In vitro cell experiments indicated that VIRMA, HNRNPC, TFAP2A, and DDR1 were highly expressed in BC cells. In addition, HNRNPC promoted TFAP2A expression and, therefore, DDR1 transcription by recognizing the m6A modification of TFAP2A mRNA by VIRMA. In vivo animal experiments further confirmed that VIRMA and HNRNPC enhanced the TFAP2A/DDR1 axis, promoting collagen fiber alignment, reducing anti-tumor immune cell infiltration, and promoting immune escape in BC. CONCLUSION This study demonstrated that HNRNPC promoted DDR1 transcription by recognizing VIRMA-unveiled m6A modification of TFAP2A mRNA, which enhanced collagen fiber alignment and ultimately resulted in the reduction of anti-tumor immune cell infiltration and promotion of immune escape in BC.
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Affiliation(s)
- Bin Lian
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, No. 804, Shengli Street, Xingqing District, Yinchuan, 750004, Ningxia Hui Autonomous Region, China
| | - Shuxun Yan
- Ningxia Medical University, Yinchuan, 750004, China
| | - Jiayi Li
- Northwest University for Nationalities, Lanzhou, 730030, China
| | | | - Jinping Li
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, No. 804, Shengli Street, Xingqing District, Yinchuan, 750004, Ningxia Hui Autonomous Region, China.
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12
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Zhou SM, Li JZ, Chen HQ, Zeng Y, Yuan WB, Shi Y, Wang N, Fan J, Zhang Z, Xu Y, Cao J, Liu WB. FTO-Nrf2 axis regulates bisphenol F-induced leydig cell toxicity in an m6A-YTHDF2-dependent manner. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 325:121393. [PMID: 36878272 DOI: 10.1016/j.envpol.2023.121393] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/19/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Studies have shown that Bisphenol F (BPF) as an emerging bisphenol pollutant also has caused many hazards to the reproductive systems of humans and animals. However, its specific mechanism is still unclear. The mouse TM3 Leydig cell was used to explore the mechanism of BPF-induced reproductive toxicity in this study. The results showed BPF (0, 20, 40 and 80 μM) exposure for 72 h significantly increased cell apoptosis and decreased cell viability. Correspondingly, BPF increased the expression of P53 and BAX, and decreased the expression of BCL2. Moreover, BPF significantly increased the intracellular ROS level in TM3 cells, and significantly decreased oxidative stress-related molecule Nrf2. BPF decreased the expression of FTO and YTHDF2, and increased the total cellular m6A level. ChIP results showed that AhR transcriptionally regulated FTO. Differential expression of FTO revealed that FTO reduced the apoptosis rate of BPF-exposed TM3 cells and increased the expression of Nrf2, MeRIP confirmed that overexpression of FTO reduced the m6A of Nrf2 mRNA. After differential expression of YTHDF2, it was found that YTHDF2 enhanced the stability of Nrf2, and RIP assay showed that YTHDF2 was bound to Nrf2 mRNA. Nrf2 agonist enhanced the protective effect of FTO on TM3 cells exposure to BPF. Our study is the first to demonstrate that AhR transcriptionally regulated FTO, and then FTO regulated Nrf2 in a m6A-modified manner through YTHDF2, thereby affecting apoptosis in BPF-exposed TM3 cells to induce reproductive damage. It provides new insights into the importance of FTO-YTHDF2-Nrf2 signaling axis in BPF-induced reproductive toxicity and provided a new idea for the prevention of male reproductive injury.
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Affiliation(s)
- Shi-Meng Zhou
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China; School of Public Health, China Medical University, Shenyang, Liaoning, 110122, China
| | - Jing-Zhi Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Hong-Qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Yong Zeng
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Wen-Bo Yuan
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Yu Shi
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China; College of Pharmacy & Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Na Wang
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China; School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, China
| | - Jun Fan
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Zhe Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Yuanyuan Xu
- School of Public Health, China Medical University, Shenyang, Liaoning, 110122, China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Wen-Bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China.
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13
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Hu Y, Lei L, Jiang L, Zeng H, Zhang Y, Fu C, Guo H, Dong Y, Ouyang Y, Zhang X, Huang J, Zeng Q, Chen J. LncRNA UCA1 promotes keratinocyte-driven inflammation via suppressing METTL14 and activating the HIF-1α/NF-κB axis in psoriasis. Cell Death Dis 2023; 14:279. [PMID: 37076497 PMCID: PMC10115875 DOI: 10.1038/s41419-023-05790-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/21/2023]
Abstract
Keratinocytes are closely associated with innate immunity and inflammatory responses, and are dysregulated during the development of psoriasis, but the underlying mechanisms are not yet fully understood. This work aims to reveal the effects of long non-coding RNA (lncRNA) UCA1 in psoriatic keratinocytes. UCA1 was identified as a psoriasis-related lncRNA that highly expressed in psoriatic lesions. The transcriptome and proteome data of keratinocyte cell line HaCaT showed that UCA1 could positively regulate inflammatory functions, such as response to cytokine. Furthermore, UCA1 silencing decreased inflammatory cytokine secretion and innate immunity gene expression in HaCaT, its culture supernatant also decreased the migration and tube formation ability of vascular endothelial cells (HUVECs). Mechanistically, UCA1 activated the NF-κB signaling pathway, which is regulated by HIF-1α and STAT3. We also observed a direct interaction between UCA1 and N6-methyladenosine (m6A) methyltransferase METTL14. Knocking down METTL14 counteracted the effects of UCA1 silencing, indicating that it can suppress inflammation. In addition, the levels of m6A-modified HIF-1α were decreased in psoriatic lesions, indicating that HIF-1α is a potential target of METTL14. Taken together, this work indicates that UCA1 positively regulates keratinocyte-driven inflammation and psoriasis development by binding to METTL14, and activating HIF-1α and NF-κB signaling pathway. Our findings provide new insights into the molecular mechanisms of keratinocyte-driven inflammation in psoriasis.
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Affiliation(s)
- Yibo Hu
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Li Lei
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Ling Jiang
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Hongliang Zeng
- Center of Medical Laboratory Animal, Hunan Academy of Chinese Medicine, No.128 Yuehua Road, Changsha, Hunan, 410013, PR China
| | - Yushan Zhang
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Chuhan Fu
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Haoran Guo
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Yumeng Dong
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Yujie Ouyang
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Xiaolin Zhang
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Jinhua Huang
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Qinghai Zeng
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China.
| | - Jing Chen
- Department of Dermatology, the Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Changsha, Hunan, 410013, PR China.
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14
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Zhu X, Zhou C, Zhao S, Zheng Z. Role of m6A methylation in retinal diseases. Exp Eye Res 2023; 231:109489. [PMID: 37084873 DOI: 10.1016/j.exer.2023.109489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/06/2023] [Accepted: 04/19/2023] [Indexed: 04/23/2023]
Abstract
Retinal diseases remain among the leading causes of visual impairment in developed countries, despite great efforts in prevention and early intervention. Due to the limited efficacy of current retinal therapies, novel therapeutic methods are urgently required. Over the past two decades, advances in next-generation sequencing technology have facilitated research on RNA modifications, which can elucidate the relevance of epigenetic mechanisms to disease. N6-methyladenosine (m6A), formed by methylation of adenosine at the N6-position, is the most widely studied RNA modification and plays an important role in RNA metabolism. It is dynamically regulated by writers (methyltransferases) and erasers (demethylases), and recognized by readers (m6A binding proteins). Although the discovery of m6A methylation can be traced back to the 1970s, its regulatory roles in retinal diseases are rarely appreciated. Here, we provide an overview of m6A methylation, and discuss its effects and possible mechanisms on retinal diseases, including diabetic retinopathy, age-related macular degeneration, retinoblastoma, retinitis pigmentosa, and proliferative vitreoretinopathy. Furthermore, we highlight potential agents targeting m6A methylation for retinal disease treatment and discuss the limitations and challenges of research in the field of m6A methylation.
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Affiliation(s)
- Xinyu Zhu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, 200080, China
| | - Chuandi Zhou
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, 200080, China
| | - Shuzhi Zhao
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, 200080, China.
| | - Zhi Zheng
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, 200080, China.
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15
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Cao X, Geng Q, Fan D, Wang Q, Wang X, Zhang M, Zhao L, Jiao Y, Deng T, Liu H, Zhou J, Jia L, Xiao C. m 6A methylation: a process reshaping the tumour immune microenvironment and regulating immune evasion. Mol Cancer 2023; 22:42. [PMID: 36859310 PMCID: PMC9976403 DOI: 10.1186/s12943-022-01704-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/19/2022] [Indexed: 03/03/2023] Open
Abstract
N6-methyladenosine (m6A) methylation is the most universal internal modification in eukaryotic mRNA. With elaborate functions executed by m6A writers, erasers, and readers, m6A modulation is involved in myriad physiological and pathological processes. Extensive studies have demonstrated m6A modulation in diverse tumours, with effects on tumorigenesis, metastasis, and resistance. Recent evidence has revealed an emerging role of m6A modulation in tumour immunoregulation, and divergent m6A methylation patterns have been revealed in the tumour microenvironment. To depict the regulatory role of m6A methylation in the tumour immune microenvironment (TIME) and its effect on immune evasion, this review focuses on the TIME, which is characterized by hypoxia, metabolic reprogramming, acidity, and immunosuppression, and outlines the m6A-regulated TIME and immune evasion under divergent stimuli. Furthermore, m6A modulation patterns in anti-tumour immune cells are summarized.
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Affiliation(s)
- Xiaoxue Cao
- grid.415954.80000 0004 1771 3349Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China ,grid.506261.60000 0001 0706 7839Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Qishun Geng
- grid.415954.80000 0004 1771 3349Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China ,grid.506261.60000 0001 0706 7839Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Danping Fan
- grid.410318.f0000 0004 0632 3409Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qiong Wang
- grid.24695.3c0000 0001 1431 9176China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Xing Wang
- grid.24695.3c0000 0001 1431 9176China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Mengxiao Zhang
- grid.415954.80000 0004 1771 3349Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Lu Zhao
- grid.24696.3f0000 0004 0369 153XChina-Japan Friendship Hospital, Capital Medical University, Beijing, China
| | - Yi Jiao
- grid.24695.3c0000 0001 1431 9176China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Tingting Deng
- grid.415954.80000 0004 1771 3349Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Honglin Liu
- grid.415954.80000 0004 1771 3349Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Jing Zhou
- grid.256607.00000 0004 1798 2653Department of Physiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi China
| | - Liqun Jia
- Oncology Department of Integrated Traditional Chinese and Western Medicine, China-Japan Friendship Hospital, Beijing, China.
| | - Cheng Xiao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China. .,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China. .,Department of Emergency, China-Japan Friendship Hospital, Beijing, China.
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16
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m6A Modification-Association with Oxidative Stress and Implications on Eye Diseases. Antioxidants (Basel) 2023; 12:antiox12020510. [PMID: 36830067 PMCID: PMC9952187 DOI: 10.3390/antiox12020510] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
Oxidative stress (OS) refers to a state of imbalance between oxidation and antioxidation. OS is considered to be an important factor leading to aging and a range of diseases. The eyes are highly oxygen-consuming organs. Due to its continuous exposure to ultraviolet light, the eye is particularly vulnerable to the impact of OS, leading to eye diseases such as corneal disease, cataracts, glaucoma, etc. The N6-methyladenosine (m6A) modification is the most investigated RNA post-transcriptional modification and participates in a variety of cellular biological processes. In this study, we review the role of m6A modification in oxidative stress-induced eye diseases and some therapeutic methods to provide a relatively overall understanding of m6A modification in oxidative stress-related eye diseases.
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17
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Integrated investigation of the clinical implications and targeted landscape for RNA methylation modifications in hepatocellular carcinoma. Eur J Med Res 2023; 28:46. [PMID: 36707911 PMCID: PMC9881284 DOI: 10.1186/s40001-023-01016-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/14/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND RNA methylation (RM) is a crucial post-translational modification (PTM) that directs epigenetic regulation. It mostly consists of N1-methyladenosine (m1A), 5-methylcytosine (m5C), N3-methylcytidine (m3C), N6-methyladenosine (m6A), and 2'-O-methylation (Nm). The "writers" mainly act as intermediaries between these modifications and associated biological processes. However, little is known about the interactions and potential functions of these RM writers in hepatocellular carcinoma (HCC). METHODS The expression properties and genetic alterations of 38 RM writers were assessed in HCC samples from five bioinformatic datasets. Two patterns associated with RM writers were identified using consensus clustering. Then, utilizing differentially expressed genes (DEGs) from different RM subtypes, we built a risk model called RM_Score. Additionally, we investigated the correlation of RM_Score with clinical characteristics, tumor microenvironment (TME) infiltration, molecular subtypes, therapeutic response, immunotherapy effectiveness, and competing endogenous RNA (ceRNA) network. RESULTS RM writers were correlated with TME cell infiltration and prognosis. Cluster_1/2 and gene.cluster_A/B were shown to be capable of distinguishing the HCC patients with poor prognosis after consensus and unsupervised clustering of RNA methylation writers. Additionally, we constructed RNA modification pattern-specific risk model and subdivided the cases into RM_Score high and RM_Score low subgroups. In individual cohorts or merged datasets, the high RM_Score was related to a worse overall survival of HCC patients. RM_Score also exhibited correlations with immune and proliferation related pathways. In response to anti-cancer treatments, the RM_Score had a negative correlation (drug sensitive) with drugs that focused on the MAPK/ERK and metabolism signaling, and a positive correlation (drug resistant) with compounds targeting RKT and PI3K/mTOR signaling pathway. Notably, the RM_Score was connected to the therapeutic effectiveness of PD-L1 blockage, implying that RM writers may be the target of immunotherapy to optimize clinical outcomes. Additionally, a ceRNA network was generated including 2 lncRNAs, 4 miRNAs, and 7 mRNAs that was connected to RM writers. CONCLUSIONS We thoroughly investigated the potential functions of RNA methylation writers and established an RM_patterns-based risk model for HCC patients. This study emphasized the critical functions of RM modification in TME infiltration, targeted therapy, and immunotherapy, providing potential targets for HCC.
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Zhang J, Zhang Y, Wang Z, Zhao J, Li Z, Wang K, Tian L, Yao B, Wu Q, Wang T, Wang J. Genes related to N6-methyladenosine in the diagnosis and prognosis of idiopathic pulmonary fibrosis. Front Genet 2023; 13:1102422. [PMID: 36685949 PMCID: PMC9846232 DOI: 10.3389/fgene.2022.1102422] [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: 11/18/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Introduction: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive pulmonary fibrotic disease with unknown etiology and poor outcomes. It severely affects the quality of life. In this study, we comprehensively analyzed the expression of N6-methyladenosine (m6A) RNA methylation regulators using gene expression data from various tissue sources in IPF patients and healthy volunteers. Methods: The gene expression matrix and clinical characteristics of IPF patients were retrieved from the Gene Expression Omnibus database. A random forest model was used to construct diagnosis signature m6A regulators. Regression analysis and correlation analysis were used to identify prognosis m6A regulators. Consensus cluster analysis was used to construct different m6A prognosis risk groups, then functional enrichment, immune infiltration and drug sensitivity analysis were performed. Result: Five candidate m6A genes from lung tissue were used to predict the incidence, and the incidence was validated using datasets from bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells. Subsequently, the BALF dataset containing outcomes data was used for the prognosis analysis of m6A regulators. METTL14, G3BP2, and ZC3H13 were independent protective factors. Using correlation analysis with lung function in the lung tissue-derived dataset, METTL14 was a protective factor in IPF. Based on METTL14 and G3BP2, a consensus cluster analysis was applied to distinguish the prognostic m6A regulation patterns. The low-risk group's prognosis was significantly better than the high-risk group. Biological processes regulated by various risk groups included fibrogenesis and cell adhesion. Analysis of immune cell infiltration showed upregulation of neutrophils in the m6A high-risk group. Subsequently, five m6A high-risk group sensitive drugs and one m6A low-risk group sensitive drug were identified. Discussion: These findings suggest that m6A regulators are involved in the diagnosis and prognosis of IPF, and m6A patterns are a method to identify IPF outcomes.
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Affiliation(s)
- Jingcheng Zhang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Ying Zhang
- Department of Respiratory, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Ziyuan Wang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jiachao Zhao
- College of Integrated Traditional Chinese and Western Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Zhenyu Li
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Keju Wang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Lin Tian
- Department of Respiratory, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Baojin Yao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Qibiao Wu
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, China,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong University of Technology, Guangzhou, China,Zhuhai MUST Science and Technology Research Institute, Zhuhai, China,*Correspondence: Qibiao Wu, ; Tan Wang, ; Jing Wang,
| | - Tan Wang
- Department of Respiratory, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Qibiao Wu, ; Tan Wang, ; Jing Wang,
| | - Jing Wang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China,Department of Respiratory, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Qibiao Wu, ; Tan Wang, ; Jing Wang,
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19
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Wang S, Ding B, Wang S, Yan W, Xia Q, Meng D, Xie S, Shen S, Yu B, Liu H, Hu J, Zhang X. Gene signature of m 6A RNA regulators in diagnosis, prognosis, treatment, and immune microenvironment for cervical cancer. Sci Rep 2022; 12:17667. [PMID: 36271283 PMCID: PMC9587246 DOI: 10.1038/s41598-022-22211-2] [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: 07/30/2022] [Accepted: 10/11/2022] [Indexed: 01/18/2023] Open
Abstract
Continuing studies imply that m6A RNA modification is involved in the development of cervical cancer (CC), but lack strong support on recurrence and diagnosis prediction. In this research, a comprehensive analysis of 33 m6A regulators was performed to fulfill them. Here, we performed diagnostic and prognosis models and identified key regulators, respectively. Then the CC patients were separated into two clusters in accordance with 33 regulators, and participants in the cluster 1 had a worse prognosis. Subsequently, the m6AScore was calculated to quantify the m6A modification pattern based on regulators and we found that patients in cluster 1 had higher m6AScore. Afterwards, immune microenvironment, cell infiltration, escape analyses and tumor burden mutation analyses were executed, and results showed that m6AScore was correlated with them, but to a limited extent. Interestingly, HLAs and immune checkpoint expression, and immunophenoscore in patients with high-m6AScores were significantly lower than those in the low-m6AScore group. These suggested the m6AScores might be used to predict the feasibility of immunotherapy in patients. Results provided a distinctive perspective on m6A modification and theoretical basis for CC diagnosis, prognosis, clinical treatment strategies, and potential mechanism exploration.
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Affiliation(s)
- Shizhi Wang
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Bo Ding
- grid.263826.b0000 0004 1761 0489Department of Gynecology and Obstetrics, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Shiyuan Wang
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Wenjing Yan
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Qianqian Xia
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Dan Meng
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Shuqian Xie
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Siyuan Shen
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Bingjia Yu
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Haohan Liu
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Jing Hu
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
| | - Xing Zhang
- grid.263826.b0000 0004 1761 0489Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Gulou District, Nanjing, 210009 China
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