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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 2024:10.1038/s41417-024-00791-7. [PMID: 38834772 DOI: 10.1038/s41417-024-00791-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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2
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Ramini D, Giuliani A, Kwiatkowska KM, Guescini M, Storci G, Mensà E, Recchioni R, Xumerle L, Zago E, Sabbatinelli J, Santi S, Garagnani P, Bonafè M, Olivieri F. Replicative senescence and high glucose induce the accrual of self-derived cytosolic nucleic acids in human endothelial cells. Cell Death Discov 2024; 10:184. [PMID: 38643201 PMCID: PMC11032409 DOI: 10.1038/s41420-024-01954-z] [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: 01/20/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/22/2024] Open
Abstract
Recent literature shows that loss of replicative ability and acquisition of a proinflammatory secretory phenotype in senescent cells is coupled with the build-in of nucleic acids in the cytoplasm. Its implication in human age-related diseases is under scrutiny. In human endothelial cells (ECs), we assessed the accumulation of intracellular nucleic acids during in vitro replicative senescence and after exposure to high glucose concentrations, which mimic an in vivo condition of hyperglycemia. We showed that exposure to high glucose induces senescent-like features in ECs, including telomere shortening and proinflammatory cytokine release, coupled with the accrual in the cytoplasm of telomeres, double-stranded DNA and RNA (dsDNA, dsRNA), as well as RNA:DNA hybrid molecules. Senescent ECs showed an activation of the dsRNA sensors RIG-I and MDA5 and of the DNA sensor TLR9, which was not paralleled by the involvement of the canonical (cGAS) and non-canonical (IFI16) activation of the STING pathway. Under high glucose conditions, only a sustained activation of TLR9 was observed. Notably, senescent cells exhibit increased proinflammatory cytokine (IL-1β, IL-6, IL-8) production without a detectable secretion of type I interferon (IFN), a phenomenon that can be explained, at least in part, by the accumulation of methyl-adenosine containing RNAs. At variance, exposure to exogenous nucleic acids enhances both IL-6 and IFN-β1 expression in senescent cells. This study highlights the accrual of cytoplasmic nucleic acids as a marker of senescence-related endothelial dysfunction, that may play a role in dysmetabolic age-related diseases.
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Affiliation(s)
- Deborah Ramini
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
| | - Angelica Giuliani
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | | | - Michele Guescini
- Department of Biomolecular Science, University of Urbino Carlo Bo, Urbino, Italy
| | - Gianluca Storci
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy
| | - Emanuela Mensà
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Rina Recchioni
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
| | | | | | - Jacopo Sabbatinelli
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy.
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy.
| | - Spartaco Santi
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" - Unit of Bologna, Bologna, Italy.
- IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
| | - Paolo Garagnani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy
| | - Massimiliano Bonafè
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy
| | - Fabiola Olivieri
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
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3
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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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4
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Mishra T, Phillips S, Wu L. Method for the Enrichment of N 6-Methyladenosine-Modified Cellular and HIV-1 RNA. Methods Mol Biol 2024; 2807:195-208. [PMID: 38743230 PMCID: PMC11160405 DOI: 10.1007/978-1-0716-3862-0_14] [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] [Indexed: 05/16/2024]
Abstract
N6-methyladenosine (m6A) modification of RNA is an important area in studying viral replication, cellular responses, and host immunity. HIV-1 RNA contains multiple m6A modifications that regulate viral replication and gene expression. HIV-1 infection of CD4+ T-cells or HIV-1 envelope protein treatment upregulates m6A levels of cellular RNA. Changes in the m6A modification of cellular transcripts in response to HIV-1 infection provide new insights into the mechanisms of posttranscriptional gene regulation in the host cell. To better investigate the functions of m6A modification in HIV-1 infection and innate immune responses, it is helpful to standardize basic protocols. Here, we describe a method for the selective enrichment of m6A-modified RNA from HIV-1-infected primary CD4+ T-cells based on immunoprecipitation. The enriched RNA with m6A modifications can be used in a variety of downstream applications to determine the methylation status of viral or cellular RNA at resolution from transcript level down to single nucleotide.
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Affiliation(s)
- Tarun Mishra
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Stacia Phillips
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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5
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Denolly S, Stukalov A, Barayeu U, Rosinski AN, Kritsiligkou P, Joecks S, Dick TP, Pichlmair A, Bartenschlager R. Zika virus remodelled ER membranes contain proviral factors involved in redox and methylation pathways. Nat Commun 2023; 14:8045. [PMID: 38052817 DOI: 10.1038/s41467-023-43665-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023] Open
Abstract
Zika virus (ZIKV) has emerged as a global health issue, yet neither antiviral therapy nor a vaccine are available. ZIKV is an enveloped RNA virus, replicating in the cytoplasm in close association with ER membranes. Here, we isolate ER membranes from ZIKV-infected cells and determine their proteome. Forty-six host cell factors are enriched in ZIKV remodeled membranes, several of these having a role in redox and methylation pathways. Four proteins are characterized in detail: thioredoxin reductase 1 (TXNRD1) contributing to folding of disulfide bond containing proteins and modulating ZIKV secretion; aldo-keto reductase family 1 member C3 (AKR1C3), regulating capsid protein abundance and thus, ZIKV assembly; biliverdin reductase B (BLVRB) involved in ZIKV induced lipid peroxidation and increasing stability of viral transmembrane proteins; adenosylhomocysteinase (AHCY) indirectly promoting m6A methylation of ZIKV RNA by decreasing the level of S- adenosyl homocysteine and thus, immune evasion. These results highlight the involvement of redox and methylation enzymes in the ZIKV life cycle and their accumulation at virally remodeled ER membranes.
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Affiliation(s)
- Solène Denolly
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120, Heidelberg, Germany
| | - Alexey Stukalov
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Uladzimir Barayeu
- Division of Redox Regulation, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alina N Rosinski
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120, Heidelberg, Germany
| | - Paraskevi Kritsiligkou
- Division of Redox Regulation, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Sebastian Joecks
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120, Heidelberg, Germany
| | - Tobias P Dick
- Division of Redox Regulation, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Andreas Pichlmair
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Ralf Bartenschlager
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120, Heidelberg, Germany.
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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6
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Luo P, Li S, Jing W, Tu J, Long X. N 6-methyladenosine RNA modification in nonalcoholic fatty liver disease. Trends Endocrinol Metab 2023; 34:838-848. [PMID: 37758602 DOI: 10.1016/j.tem.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide, influencing numerous regulatory axes and extrahepatic vital organs. The molecular mechanisms that lead to the progression of NAFLD remain unclear and knowledge on the pathways causing hepatocellular damage followed by lipid accumulation is limited. Recently, a number of studies have shown that mRNA N6-methyladenosine (m6A) modification contributes to the progression of NAFLD. In this review, we summarize current knowledge on m6A modification in the metabolic processes associated with NAFLD and discuss the challenges of and prospects for therapeutic avenues based on m6A regulation for the treatment of liver disease.
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Affiliation(s)
- Ping Luo
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shiqi Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wei Jing
- Department of Clinical Laboratory, First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan, Zhengzhou, China
| | - Jiancheng Tu
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinghua Long
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
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7
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Shen S, Zhang LS. The regulation of antiviral innate immunity through non-m 6A RNA modifications. Front Immunol 2023; 14:1286820. [PMID: 37915585 PMCID: PMC10616867 DOI: 10.3389/fimmu.2023.1286820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
The post-transcriptional RNA modifications impact the dynamic regulation of gene expression in diverse biological and physiological processes. Host RNA modifications play an indispensable role in regulating innate immune responses against virus infection in mammals. Meanwhile, the viral RNAs can be deposited with RNA modifications to interfere with the host immune responses. The N6-methyladenosine (m6A) has boosted the recent emergence of RNA epigenetics, due to its high abundance and a transcriptome-wide widespread distribution in mammalian cells, proven to impact antiviral innate immunity. However, the other types of RNA modifications are also involved in regulating antiviral responses, and the functional roles of these non-m6A RNA modifications have not been comprehensively summarized. In this Review, we conclude the regulatory roles of 2'-O-methylation (Nm), 5-methylcytidine (m5C), adenosine-inosine editing (A-to-I editing), pseudouridine (Ψ), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), and N4-acetylcytidine (ac4C) in antiviral innate immunity. We provide a systematic introduction to the biogenesis and functions of these non-m6A RNA modifications in viral RNA, host RNA, and during virus-host interactions, emphasizing the biological functions of RNA modification regulators in antiviral responses. Furthermore, we discussed the recent research progress in the development of antiviral drugs through non-m6A RNA modifications. Collectively, this Review conveys knowledge and inspiration to researchers in multiple disciplines, highlighting the challenges and future directions in RNA epitranscriptome, immunology, and virology.
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Affiliation(s)
- Shenghai Shen
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
- Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
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Ning J, Hou X, Hao J, Zhang W, Shi Y, Huang Y, Ruan X, Zheng X, Gao M. METTL3 inhibition induced by M2 macrophage-derived extracellular vesicles drives anti-PD-1 therapy resistance via M6A-CD70-mediated immune suppression in thyroid cancer. Cell Death Differ 2023; 30:2265-2279. [PMID: 37648786 PMCID: PMC10589295 DOI: 10.1038/s41418-023-01217-x] [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: 01/31/2023] [Revised: 07/04/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023] Open
Abstract
The treatment options for advanced papillary thyroid cancer (PTC) and anaplastic thyroid cancer (ATC) refractory to standard therapies are limited. Although anti-PD-1 therapy has a manageable safety profile and has been effective in a small percentage of patients with advanced PTC and refractory ATC, the majority of the patients either do not respond or develop resistance to anti-PD-1 therapy. N6-methyladenosine (m6A) modification is a critical determinant of the complexity of the tumor microenvironment (TME). However, it is unclear whether and how m6A modification in tumor cells shapes the immune landscape of PTC and ATC. In this study, we performed bulk and single cell RNA sequencing analysis of PTC and ATC tissues, and found that low METTL3 expression not only correlated to poor response to immune checkpoint blockade (ICB) but was also associated with increased TNF family-related ligand-receptor interactions in the immunosuppressive Tregs and exhausted T cells. Furthermore, overexpression of METTL3 in PTC and ATC cells enhanced the efficacy of anti-PD-1 therapy in a peripheral blood mononuclear cell humanized NCG (huPBMC-NCG) mouse model. Mechanistically, M2 macrophage-derived extracellular vesicles (M2 EVs) inhibited METTL3 expression in PTC and ATC cells via miR-21-5p. Downregulation of METTL3 promoted demethylation of CD70 mRNA, which prevented YTHDF2-mediated degradation of the transcripts. The stabilization of CD70 mRNA, and the subsequent upregulation in CD70 protein levels increased the abundance of the immunosuppressive Tregs and terminally exhausted T cells, thereby inducing resistance to anti-PD-1 therapy. Furthermore, blocking CD70 using cusatuzumab, a high-affinity monoclonal antibody, reversed the anti-PD-1 therapy resistance induced by M2 EVs in vivo. Finally, we demonstrated that METTL3 expression negatively correlated with CD70 expression and M2 macrophages and Tregs infiltration in PTC and ATC tissues. Our findings provide new insights into developing novel therapies for advanced PTC and ATC.
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Affiliation(s)
- Junya Ning
- Department of Thyroid and Breast Surgery, Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center, Tianjin, 300121, China
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xiukun Hou
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Jie Hao
- Department of Thyroid and Breast Surgery, Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center, Tianjin, 300121, China
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Wei Zhang
- Department of Thyroid and Breast Surgery, Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center, Tianjin, 300121, China
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- The School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yi Shi
- The School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yue Huang
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xianhui Ruan
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| | - Xiangqian Zheng
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| | - Ming Gao
- Department of Thyroid and Breast Surgery, Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center, Tianjin, 300121, China.
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
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9
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Ribeiro DR, Nunes A, Ribeiro D, Soares AR. The hidden RNA code: implications of the RNA epitranscriptome in the context of viral infections. Front Genet 2023; 14:1245683. [PMID: 37614818 PMCID: PMC10443596 DOI: 10.3389/fgene.2023.1245683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023] Open
Abstract
Emerging evidence highlights the multifaceted roles of the RNA epitranscriptome during viral infections. By modulating the modification landscape of viral and host RNAs, viruses enhance their propagation and elude host surveillance mechanisms. Here, we discuss how specific RNA modifications, in either host or viral RNA molecules, impact the virus-life cycle and host antiviral responses, highlighting the potential of targeting the RNA epitranscriptome for novel antiviral therapies.
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10
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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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11
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Yang D, Zhao G, Zhang HM. m 6A reader proteins: the executive factors in modulating viral replication and host immune response. Front Cell Infect Microbiol 2023; 13:1151069. [PMID: 37325513 PMCID: PMC10266107 DOI: 10.3389/fcimb.2023.1151069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
N6-Methyladenosine (m6A) modification is the most abundant covalent modification of RNA. It is a reversible and dynamic process induced by various cellular stresses including viral infection. Many m6A methylations have been discovered, including on the genome of RNA viruses and on RNA transcripts of DNA viruses, and these methylations play a positive or negative role on the viral life cycle depending on the viral species. The m6A machinery, including the writer, eraser, and reader proteins, achieves its gene regulatory role by functioning in an orchestrated manner. Notably, data suggest that the biological effects of m6A on target mRNAs predominantly depend on the recognition and binding of different m6A readers. These readers include, but are not limited to, the YT521-B homology (YTH) domain family, heterogeneous nuclear ribonucleoproteins (HNRNPs), insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs), and many others discovered recently. Indeed, m6A readers have been recognized not only as regulators of RNA metabolism but also as participants in a variety of biological processes, although some of these reported roles are still controversial. Here, we will summarize the recent advances in the discovery, classification, and functional characterization of m6A reader proteins, particularly focusing on their roles and mechanisms of action in RNA metabolism, gene expression, and viral replication. In addition, we also briefly discuss the m6A-associated host immune responses in viral infection.
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Affiliation(s)
- Decheng Yang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Guangze Zhao
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Huifang Mary Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
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12
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Yamagami R, Hori H. Functional analysis of tRNA modification enzymes using mutational profiling. Methods Enzymol 2023; 692:69-101. [PMID: 37925188 DOI: 10.1016/bs.mie.2023.02.021] [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: 11/06/2023]
Abstract
Transfer RNA (tRNA) delivers amino acids to the ribosome and functions as an essential adapter molecule for decoding codons on the messenger RNA (mRNA) during protein synthesis. Before attaining their proper activity, tRNAs undergo multiple post-transcriptional modifications with highly diversified roles such as stabilization of the tRNA structure, recognition of aminoacyl tRNA synthetases, precise codon-anticodon recognition, support of viral replication and onset of immune responses. The synthesis of the majority of modified nucleosides is catalyzed by a site-specific tRNA modification enzyme. This chapter provides a detailed protocol for using mutational profiling to analyze the enzymatic function of a tRNA methyltransferase in a high-throughput manner. In a previous study, we took tRNA m1A22 methyltransferase TrmK from Geobacillus stearothermophilus as a model tRNA methyltransferase and applied this protocol to gain mechanistic insights into how TrmK recognizes the substrate tRNAs. In theory, this protocol can be used unaltered for studying enzymes that catalyze modifications at the Watson-Crick face such as 1-methyladenosine (m1A), 3-methylcytosine (m3C), 3-methyluridine (m3U), 1-methylguanosine (m1G), and N2,N2-dimethylguanosine (m22G).
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Affiliation(s)
- Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
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13
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Shi G, Li Y, Gao H, Wei Y, Wang Y. Development a m 6A regulators characterized by the immune cell infiltration in stomach adenocarcinoma for predicting the prognosis and immunotherapy response. Aging (Albany NY) 2023; 15:1944-1963. [PMID: 37019148 PMCID: PMC10085598 DOI: 10.18632/aging.204574] [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: 11/08/2022] [Accepted: 02/20/2023] [Indexed: 03/19/2023]
Abstract
N6-Methyladenosine (m6A) has attracted growing interest among scholars as an important regulator of mRNA expression. Although the significant role of m6A in multiple biological processes (like proliferation and growth of cancers) has been comprehensively described, an analysis of its possible role in stomach adenocarcinoma (STAD) of tumor immune microenvironment (TIME) remains lacking. The data for RNA expression, single nucleotide polymorphism (SNP), and copy number variation (CNV) were downloaded from The Cancer Genome Atlas (TCGA). Subsequently, 23 m6A regulators were curated, with patients being clustered into three m6A subtypes and m6A-related gene subtypes. Furthermore, they were compared based on overall survival (OS). This study also evaluates the association between m6A regulators and immune as well as response to the treatment. According to the TCGA-STAD cohort, three m6A clusters conformed to three phenotypes, immune-inflamed, immune-dessert, and immune-excluded, respectively. Patients who displayed lower m6A scores presented better overall survival outcomes. The GEO cohort demonstrated that those with a low m6A score had obvious general survival benefits and clinical advantages. Low m6A scores can carry the enhanced neoantigen loads, triggering an immune response. Meanwhile, three anti-PD-1 cohorts have confirmed the value of predicting survival outcomes. The results of this study indicate that m6A regulators are associated with TIME, and the m6A score is an efficient prognostic biomarker and predictive indicator for immunotherapy and chemotherapeutics. Moreover, comprehensive evaluations of m6A regulators in tumors will broaden our comprehension of TIME, efficiently guiding enhancing explorations on immunotherapy and chemotherapy strategies for STAD.
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Affiliation(s)
- Guodong Shi
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yang Li
- Department of Obstetrics, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Huijiang Gao
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yucheng Wei
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yuanyong Wang
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
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14
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Luo P, Li S, Long X. N6-methyladenosine RNA modification in PD-1/PD-L1: Novel implications for immunotherapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188873. [PMID: 36842764 DOI: 10.1016/j.bbcan.2023.188873] [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: 01/12/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Cancer immunotherapy has been shown to achieve significant antitumor effects in a variety of malignancies. Out of all the immune checkpoint molecules, PD-1/PD-L1 inhibitor therapy has achieved great success. However, only some cancer patients benefit from this treatment strategy owing to drug resistance. Therefore, identifying the underlying modulators of the PD-1/PD-L1 pathway to completely comprehend the mechanisms of anti-PD-1/PD-L1 treatment is crucially important. Recent research has validated that m6A modification plays a critical role in the PD-1/PD-L1 axis, thus regulating the immune response and immunotherapy strategies. In this review, we summarized the latest research on the regulation of m6A modification in PD-1/PD-L1 pathways in cancer proliferation, invasion, and prognosis based on different kinds of cancers and discussed the possible mechanisms. We also reviewed m6A-associated lncRNAs in the regulation of the PD-1/PD-L1 pathway. More importantly, we outlined the influence of m6A modulation on anti-PD-1 therapy and m6A-related molecules that could predict the curative effect of anti-PD-1/PD-L1 therapy. Further studies exploring the definitive regulation of m6A on the PD1/PD-1 pathway and immunotherapy are needed, which may address some of the current limitations in immunotherapy.
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Affiliation(s)
- Ping Luo
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shiqi Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinghua Long
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
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15
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Promotion of the resistance of human oral epithelial cells to herpes simplex virus type I infection via N6-methyladenosine modification. BMC Oral Health 2023; 23:121. [PMID: 36814204 PMCID: PMC9948413 DOI: 10.1186/s12903-023-02744-2] [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: 06/08/2022] [Accepted: 01/13/2023] [Indexed: 02/24/2023] Open
Abstract
OBJECTIVE This study aimed to explore the mechanism behind N6-methyladenosine (m6A) modification of the total ribonucleic acid (RNA) involved in the resistance to herpes simplex virus type I (HSV-1) infection in oral epithelial cells. METHOD The variation in m6A modification level on messenger RNA following HSV-1 infection was determined using the RNA dot blot method. The expression levels of alpha-ketoglutarate-dependent dioxygenase lab homolog 5 (ALKBH5) protein and fatty mass and obesity-associated genes (FTO) were determined using real-time fluorescence quantification polymerase chain reaction and the western blot technique, respectively. Next, after suppressing the expression of ALKBH5 or FTO via small interfering RNA, human immortalised oral epithelial cells (HIOECs) were infected with HSV-1, followed by measurement of the viral load or expression level of type I interferon (I-IFN) and interferon-stimulated genes (ISGs). RESULTS The m6A modification level was significantly increased following HSV-1 infection of the HIOECs (P < 0.05), while the expression of ALKBH5 and FTO genes was reduced (P < 0.01). Moreover, the suppression of ALKBH5 or FTO increased the production of I-IFN and ISGs during the HSV-1 infection of the HIOECs (P < 0.01), and the viral load was significantly reduced (P < 0.01). CONCLUSION During oral HSV-1 infection, the m6A level was increased through the down-regulation of ALBHK5 and FTO expression, increasing I-IFN production and the promotion of HSV-1 clearing in HIOECs.
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Zhang Y, Shi J, Luo J, Liu C, Zhu L. Metabolic heterogeneity in early-stage lung adenocarcinoma revealed by RNA-seq and scRNA-seq. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023; 25:1844-1855. [PMID: 36692643 DOI: 10.1007/s12094-023-03082-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023]
Abstract
PURPOSE Cancer cells maintain cell growth, division, and survival through altered energy metabolism. However, research on metabolic reprogramming in lung adenocarcinoma (LUAD) is limited METHODS: We downloaded TCGA and GEO sequencing data. Consistent clustering with the ConsensusClusterPlus package was employed to detect the scores for four metabolism-related pathways. The LUAD samples in the TCGA dataset were clustered with ConsensusClusterPlus, and the optimal number of clusters was determined according to the cumulative distribution function (CDF). The cell score for each sample in the TCGA dataset was calculated using the MCPcounter estimate function of the MCPcounter package. RESULTS We identified two subtypes by scoring the samples based on the 4 metabolism-related pathways and cluster dimensionality reduction. The prognosis of cluster B was obviously poorer than that of cluster A in patients with LUAD. The analysis of single-nucleotide variation (SNV) data showed that the top 15 genes in the four metabolic pathways with the most mutations were TKTL2, PGK2, HK3, EHHADH, GLUD2, PKLR, TKTL1, HADHB, CPT1C, HK1, HK2, PFKL, SLC2A3, PFKFB1, and CPT1A. The IFNγ score of cluster B was significantly higher than that of cluster A. The immune T-cell lytic activity score of cluster B was significantly higher than that of cluster A. We further identified 5 immune cell subsets from single-cell sequencing data. The top 5 marker genes of B cells were IGHM, JCHAIN, IGLC3, IGHA1, and IGKC. The C0 subgroup of monocytes had a higher pentose phosphate pathway (PPP) score than the C6 subgroup. CONCLUSIONS Metabolism-related subtypes could be potential biomarkers in the prognosis prediction and treatment of LUAD.
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Affiliation(s)
- Yang Zhang
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Jiang Shi
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Junfang Luo
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Cong Liu
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Lixu Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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17
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Huang Y, Zou Y, Tian Y, Yang Z, Hou Z, Li P, Liu F, Ling J, Wen Y. N6-methylandenosine-related immune genes correlate with prognosis and immune landscapes in gastric cancer. Front Oncol 2022; 12:1009881. [PMID: 36523987 PMCID: PMC9745091 DOI: 10.3389/fonc.2022.1009881] [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: 08/02/2022] [Accepted: 11/16/2022] [Indexed: 11/10/2023] Open
Abstract
OBJECTIVES This study aimed to probe into the significance of N6-methyladenosine (m6A)-related immune genes (m6AIGs) in predicting prognoses and immune landscapes of patients with gastric cancer (GC). METHODS The clinical data and transcriptomic matrix of GC patients were acquired from The Cancer Genome Atlas database. The clinically meaningful m6AIGs were acquired by univariate Cox regression analysis. GC patients were stratified into different clusters via consensus clustering analysis and different risk subgroups via m6AIGs prognostic signature. The clinicopathological features and tumor microenvironment (TME) in the different clusters and different risk subgroups were explored. The predictive performance was evaluated using the KM method, ROC curves, and univariate and multivariate regression analyses. Moreover, we fabricated a nomogram based on risk scores and clinical risk characteristics. Biological functional analysis was performed based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. The connectivity map was used to screen out potential small molecule drugs for GC patients. RESULTS A total of 14 prognostic m6AIGs and two clusters based on 14 prognostic m6AIGs were identified. A prognostic signature based on 4 m6AIGs and a nomogram based on independent prognostic factors was constructed and validated. Different clusters and different risk subgroups were significantly correlated with TME scores, the distribution of immune cells, and the expression of immune checkpoint genes. Some malignant and immune biological processes and pathways were correlated with the patients with poor prognosis. Ten small molecular drugs with potential therapeutic effect were screened out. CONCLUSIONS This study revealed the prognostic role and significant values of m6AIGs in GC, which enhanced the understanding of m6AIGs and paved the way for developing predictive biomarkers and therapeutic targets for GC.
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Affiliation(s)
- Yuancheng Huang
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yushan Zou
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yanhua Tian
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zehong Yang
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhengkun Hou
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Peiwu Li
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Fengbin Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Department of Gastroenterology, Baiyun Branch of the First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Jiasheng Ling
- Department of Gastroenterology, Huizhou Hospital of Traditional Chinese Medicine, Huizhou, Guangdong, China
| | - Yi Wen
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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18
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Senescent neutrophils-derived exosomal piRNA-17560 promotes chemoresistance and EMT of breast cancer via FTO-mediated m6A demethylation. Cell Death Dis 2022; 13:905. [PMID: 36302751 PMCID: PMC9613690 DOI: 10.1038/s41419-022-05317-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/19/2022]
Abstract
Cellular senescence is characterized by a tumor-suppressive program as well as a pro-inflammatory secretome. Neutrophils constitute significant compositions of malignancies and play key roles in tumor development. However, the role of senescent neutrophils in cancer progression is presently unexplored. Here, we demonstrate that neutrophils display enhanced senescence in breast cancer patients receiving chemotherapy. The senescent neutrophils produce increased number of exosomes, which confer drug resistance to tumor cells in vitro and in vivo. Mechanistically, senescent neutrophils-derived exosomal piRNA-17560 enhances the expression of fat mass and obesity-associated protein (FTO) in breast cancer cells. The upregulation of FTO further strengthens ZEB1 transcripts stability and expression by decreasing N6-methyladenosine (m6A) RNA methylation, leading to chemoresistance and epithelial-mesenchymal transition (EMT) of tumor cells. Clinically, the level of exosomal piR-17560 correlates with poor chemotherapy response in patients with breast cancer. In addition, YTHDF2 is essential for the posttranscriptional regulation of ZEB1 by piRNA-17560/FTO signaling. Senescent neutrophils secret exosomal piR-17560 in a STAT3-dependent manner. Altogether, this study suggests that senescent neutrophils-derived exosomal piR-17560 confers chemoresistance to tumor cells and senescent neutrophils may serve as a potential therapeutic target in breast cancer.
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Wan L, Liu J, Huang C, Zhu Z, Wang K, Sun G, Zhu L, Hu Z. Comprehensive Analysis and Functional Characteristics of Differential Expression of N6-Methyladenosine Methylation Modification in the Whole Transcriptome of Rheumatoid Arthritis. Mediators Inflamm 2022; 2022:4766992. [PMID: 36330380 PMCID: PMC9626244 DOI: 10.1155/2022/4766992] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/22/2022] [Indexed: 08/04/2023] Open
Abstract
N6-methyladenosine (m6A) modification is the most prevalent chemical modification in eukaryotic mRNA and is associated with the development of various immune diseases. However, the role of m6A methylation in rheumatoid arthritis (RA) development is unclear. We preliminarily explored the role of m6A methylation-related mRNAs in RA for its clinical application. The discovery of m6A methylation-modifying genes in this study may provide a fresh perspective on the development of drugs for RA treatment. High-throughput sequencing combined with methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing were used to assess whole-transcriptome m6A modifications in the synovium of patients with RA. The relationship between m6A-modified target genes and RA inflammation and macrophages was determined. The expression of the m6A-modified significant transcript-enriched inflammatory signaling pathway was assessed through animal experiments. Differentially expressed m6A genes were correlated with macrophage activation involved in immune response, vascular endothelium, MAPK signaling pathway, PI3K - Akt signaling pathway, and other inflammatory processes. Furthermore, combined analysis with m6A-seq and RNA-seq revealed 120 genes with significant changes in both m6A modification and mRNA expression. We selected the top 3 candidate mRNAs that were upregulated and downregulated simultaneously. The expression of phosphatase and tensin homolog deleted on chromosome ten (PTEN) mRNA and protein in RA patients was lower than that in healthy control (HC). SHC-binding protein 1 (SHCBP1) and neurexophilin-3 (NXPH3) mRNA expressions were increased in RA patients. The expression of M1 macrophages was increased in RA patients. RA markers are such as rheumatoid factor (RF) and peptide containing citrulline (CCP). Further animal experiments showed that the expression of synovial MAPK, PI3K, and Akt1 proteins in the RA model was increased, and the PTEN, p-PTEN protein expression was decreased. PI3K, Akt1, PTEN, and p-PTEN were correlated to RA joint inflammation. This study revealed a unique pattern of differential m6A methylation modifications in RA and concluded that m6A modification is related to the occurrence of RA synovial inflammation.
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Affiliation(s)
- Lei Wan
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
- Key Laboratory of Xin'an Medical Education Ministry, Hefei 230038, China
| | - Jian Liu
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
- Key Laboratory of Xin'an Medical Education Ministry, Hefei 230038, China
| | - Chuanbing Huang
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
| | - Ziheng Zhu
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
| | - Kun Wang
- Key Laboratory of Xin'an Medical Education Ministry, Hefei 230038, China
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Guanghan Sun
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Lei Zhu
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
| | - Zhongxiang Hu
- The First Affiliated Hospital of University of Science and Technology of China, Hefei 230000, China
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Elsabbagh RA, Rady M, Watzl C, Abou-Aisha K, Gad MZ. Impact of N6-methyladenosine (m6A) modification on immunity. Cell Commun Signal 2022; 20:140. [PMID: 36085064 PMCID: PMC9461097 DOI: 10.1186/s12964-022-00939-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022] Open
Abstract
N6-methyl-adenosine (m6A) is the most prevalent modification on mRNAs and long noncoding RNAs (lnRNAs) in higher eukaryotes. Modulation of m6A relies on m6A writers, erasers and readers. m6A modification contributes to diverse fundamental biological functions at the molecular, cellular, and physiological levels. The dysregulation of m6A modification has been implicated in various human diseases. Thus, m6A modification has now become a research hotspot for its potential therapeutic applications in the treatment of various cancers and diseases. The immune system is essential to provide defense against infections and cancers. This review summarizes the current knowledge about the roles of m6A in regulating immune cell functions and immune responses. Video abstract
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Shi B, Liu WW, Yang K, Jiang GM, Wang H. The role, mechanism, and application of RNA methyltransferase METTL14 in gastrointestinal cancer. Mol Cancer 2022; 21:163. [PMID: 35974338 PMCID: PMC9380308 DOI: 10.1186/s12943-022-01634-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Gastrointestinal cancer is the most common human malignancy characterized by high lethality and poor prognosis. Emerging evidences indicate that N6-methyladenosine (m6A), the most abundant post-transcriptional modification in eukaryotes, exerts important roles in regulating mRNA metabolism including stability, decay, splicing, transport, and translation. As the key component of the m6A methyltransferase complex, methyltransferase-like 14 (METTL14) catalyzes m6A methylation on mRNA or non-coding RNA to regulate gene expression and cell phenotypes. Dysregulation of METTL14 was deemed to be involved in various aspects of gastrointestinal cancer, such as tumorigenesis, progression, chemoresistance, and metastasis. Plenty of findings have opened up new avenues for exploring the therapeutic potential of gastrointestinal cancer targeting METTL14. In this review, we systematically summarize the recent advances regarding the biological functions of METTL14 in gastrointestinal cancer, discuss its potential clinical applications and propose the research forecast.
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Affiliation(s)
- Bin Shi
- Department of Anorectal Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Heifei, China
| | - Wei-Wei Liu
- School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Ke Yang
- School of Clinical Medicine, Clinical College of Anhui Medical University, Hefei, China
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, China.
| | - Hao Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. .,Core Unit of National Clinical Research Center for Laboratory Medicine, Heifei, China.
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22
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m6A-Related lncRNA Signature Is Involved in Immunosuppression and Predicts the Patient Prognosis of the Age-Associated Ovarian Cancer. J Immunol Res 2022; 2022:3258400. [PMID: 35991123 PMCID: PMC9385364 DOI: 10.1155/2022/3258400] [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] [Received: 04/07/2022] [Revised: 06/12/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background Epithelial ovarian cancers are age-associated diseases, usually diagnosed at an advanced stage. lncRNA has been discovered to interplay with N6-methyladenosine (m6A), working in tandem to promote cancer progression and worsening patient outcomes. This study is aimed at investigating the roles and mechanism of m6A-related lncRNA signature on ovarian cancers. Methods We retrieved TCGA and CGGA sequencing data to identify m6A-related lncRNA signature and constructed an m6A score (MS) using the LASSO algorithm. A clinical nomogram was then established to predict the overall survival of patients. Subsequently, GSEA analyses were conducted to obtain pathways involved. Expression of HLA genes, 28 tumor-infiltrating lymphocyte infiltration, and anticancer cycle were analyzed the immunological differences between high-MS and low-MS groups. Finally, immune checkpoint gene expressions and IC50 of chemotherapeutic drugs were calculated, and CMap was run to identify the potential compounds and their corresponding mechanisms. Results We identified 16 m6A-related lncRNAs and constructed an MS model. The high-MS group showed a poor prognosis. A clinical nomogram consists of MS, and age was constructed and predicted the 1-, 3-, and 5-year survival with high accuracy. GSEA analyses presented downregulated antigen processing and presentation pathways. Immunocyte infiltrating analyses demonstrated that high-MS was associated with high infiltration of Treg cells, macrophages, and low Th1/Th2 rate. Also, high expression of immune checkpoint genes NRP1, TNFSF9, and VSIR was observed in the high-MS group. Finally, the high-MS group also predicted low IC50 of vinorelbine and vorinostat. Conclusion This study constructed a robust prediction model for prognostic management and revealed the cross-talk between m6A and immunosuppression. Besides, the m6A lncRNA signature can predict the chemotherapeutic drug response. These will shed light on the development of novel therapeutic strategies and render survival benefits for ovarian patients.
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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24
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Zhang T, Zhang SW, Feng J, Zhang B. m 6 Aexpress-BHM: predicting m6A regulation of gene expression in multiple-groups context by a Bayesian hierarchical mixture model. Brief Bioinform 2022; 23:6644383. [PMID: 35848879 DOI: 10.1093/bib/bbac295] [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: 05/06/2022] [Revised: 06/16/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022] Open
Abstract
As the most abundant RNA modification, N6-methyladenosine (m6A) plays an important role in various RNA activities including gene expression and translation. With the rapid application of MeRIP-seq technology, samples of multiple groups, such as the involved multiple viral/ bacterial infection or distinct cell differentiation stages, are extracted from same experimental unit. However, our current knowledge about how the dynamic m6A regulating gene expression and the role in certain biological processes (e.g. immune response in this complex context) is largely elusive due to lack of effective tools. To address this issue, we proposed a Bayesian hierarchical mixture model (called m6Aexpress-BHM) to predict m6A regulation of gene expression (m6A-reg-exp) in multiple groups of MeRIP-seq experiment with limited samples. Comprehensive evaluations of m6Aexpress-BHM on the simulated data demonstrate its high predicting precision and robustness. Applying m6Aexpress-BHM on three real-world datasets (i.e. Flaviviridae infection, infected time-points of bacteria and differentiation stages of dendritic cells), we predicted more m6A-reg-exp genes with positive regulatory mode that significantly participate in innate immune or adaptive immune pathways, revealing the underlying mechanism of the regulatory function of m6A during immune response. In addition, we also found that m6A may influence the expression of PD-1/PD-L1 via regulating its interacted genes. These results demonstrate the power of m6Aexpress-BHM, helping us understand the m6A regulatory function in immune system.
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Affiliation(s)
- Teng Zhang
- School of Automation from the Northwestern Polytechnical University, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, China
| | - Jian Feng
- department of microbiology and molecular genetics, University of Pittsburgh
| | - Bei Zhang
- Henan University of Science and Technology Affiliated First Hospital
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25
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Liu A, Wang X. The Pivotal Role of Chemical Modifications in mRNA Therapeutics. Front Cell Dev Biol 2022; 10:901510. [PMID: 35912117 PMCID: PMC9326091 DOI: 10.3389/fcell.2022.901510] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
After over a decade of development, mRNA has recently matured into a potent modality for therapeutics. The advantages of mRNA therapeutics, including their rapid development and scalability, have been highlighted due to the SARS-CoV-2 pandemic, in which the first two clinically approved mRNA vaccines have been spotlighted. These vaccines, as well as multiple other mRNA therapeutic candidates, are modified to modulate their immunogenicity, stability, and translational efficiency. Despite the importance of mRNA modifications for harnessing the full efficacy of mRNA drugs, the full breadth of potential modifications has yet to be explored clinically. In this review, we survey the field of mRNA modifications, highlighting their ability to tune the properties of mRNAs. These include cap and tail modifications, nucleoside substitutions, and chimeric mRNAs, each of which represents a component of mRNA that can be exploited for modification. Additionally, we cover clinical and preclinical trials of the modified mRNA platform not only to illustrate the promise of modified mRNAs but also to call attention to the room for diversifying future therapeutics.
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Affiliation(s)
- Albert Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- *Correspondence: Xiao Wang,
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26
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Zhu Y, Peng X, Zhou Q, Tan L, Zhang C, Lin S, Long M. METTL3-mediated m6A modification of STEAP2 mRNA inhibits papillary thyroid cancer progress by blocking the Hedgehog signaling pathway and epithelial-to-mesenchymal transition. Cell Death Dis 2022; 13:358. [PMID: 35436987 PMCID: PMC9016063 DOI: 10.1038/s41419-022-04817-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/22/2022] [Accepted: 03/31/2022] [Indexed: 12/23/2022]
Abstract
Papillary thyroid cancer (PTC) is a common endocrine system malignancy all over the world. Aberrant expression of six transmembrane epithelial antigen of the prostate 2 (STEAP2) has been functionally associated with cancer progression in many cancers. Nevertheless, its biological function in PTC is still unclear. Here, we found that PTC tissues had preferentially downregulated STEAP2 as compared with noncancerous tissues. Low STEAP2 expression correlated with aggressive clinicopathological characteristics and dismal prognosis in patients with PTC. We performed gain- and loss-of-function experiments, including cell proliferation assay (Cell Counting Kit-8 assay), EdU (5-ethynyl-2'-deoxyuridine) and colony formation assays, transwell migration, and invasion assays, and constructed a nude mouse xenograft tumor model. The results demonstrated that STEAP2 overexpression inhibited PTC cell proliferation, migration, and invasion in vitro and inhibited lung metastasis and tumorigenicity in vivo. Conversely, silencing STEAP2 yielded the opposite results in vitro. Mechanistically, bioinformatics analysis combined with validation experiments identified STEAP2 as the downstream target of methyltransferase-like 3 (METTL3)-mediated N6-methyladenosine (m6A) modification. METTL3 stabilized STEAP2 mRNA and regulated STEAP2 expression positively in an m6A-dependent manner. We also showed that m6A-mediated STEAP2 mRNA translation initiation relied on a pathway dependent on the m6A reader protein YTHDF1. Rescue experiments revealed that silencing STEAP2 partially rescued the tumor-suppressive phenotype induced by METTL3 overexpression. Lastly, we verified that the METTL3-STEAP2 axis functions as an inhibitor in PTC by suppressing epithelial-mesenchymal transition and the Hedgehog signaling pathway. Taken together, these findings strongly suggest that METTL3-mediated STEAP2 m6A modification plays a critical tumor-suppressive role in PTC progression. The METTL3-STEAP2 axis may be a potential therapeutic molecular target against PTC.
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Affiliation(s)
- Yue Zhu
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Guangzhou, 510120, China
| | - Xinzhi Peng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Guangzhou, 510120, China
| | - Qianlei Zhou
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Guangzhou, 510120, China
| | - Langping Tan
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Guangzhou, 510120, China
| | - Cheng Zhang
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Guangzhou, 510120, China
| | - Shaojian Lin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Guangzhou, 510120, China
| | - Miaoyun Long
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China. .,Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Guangzhou, 510120, China.
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27
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Huang Y, Huang C, Jiang X, Yan Y, Zhuang K, Liu F, Li P, Wen Y. Exploration of Potential Roles of m5C-Related Regulators in Colon Adenocarcinoma Prognosis. Front Genet 2022; 13:816173. [PMID: 35281843 PMCID: PMC8908034 DOI: 10.3389/fgene.2022.816173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/26/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives: The purpose of this study was to investigate the role of 13 m5C-related regulators in colon adenocarcinoma (COAD) and determine their prognostic value. Methods: Gene expression and clinicopathological data were obtained from The Cancer Genome Atlas (TCGA) datasets. The expression of m5C-related regulators was analyzed with clinicopathological characteristics and alterations within m5C-related regulators. Subsequently, different subtypes of patients with COAD were identified. Then, the prognostic value of m5C-related regulators in COAD was confirmed via univariate Cox regression and least absolute shrinkage and selection operator (LASSO) Cox regression analyses. The prognostic value of risk scores was evaluated using the Kaplan-Meier method, receiver operating characteristic (ROC) curve. The correlation between the two m5C-related regulators, risk score, and clinicopathological characteristics were explored. Additionally, Gene Set Enrichment Analysis (GSEA), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and Gene Ontology (GO) analysis were performed for biological functional analysis. Finally, the expression level of two m5C-related regulators in clinical samples and cell lines was detected by quantitative reverse transcription-polymerase chain reaction and through the Human Protein Atlas database. Results: m5C-related regulators were found to be differentially expressed in COAD with different clinicopathological features. We observed a high alteration frequency in these genes, which were significantly correlated with their mRNA expression levels. Two clusters with different prognostic features were identified. Based on two independent prognostic m5C-related regulators (NSUN6 and ALYREF), a risk signature with good predictive significance was constructed. Univariate and multivariate Cox regression analyses suggested that the risk score was an independent prognostic factor. Furthermore, this risk signature could serve as a prognostic indicator for overall survival in subgroups of patients with different clinical characteristics. Biological processes and pathways associated with cancer, immune response, and RNA processing were identified. Conclusion: We revealed the genetic signatures and prognostic values of m5C-related regulators in COAD. Together, this has improved our understanding of m5C RNA modification and provided novel insights to identify predictive biomarkers and develop molecular targeted therapy for COAD.
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Affiliation(s)
- Yuancheng Huang
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chaoyuan Huang
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaotao Jiang
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yanhua Yan
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kunhai Zhuang
- Department of Gastroenterology, Baiyun Branch of the First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fengbin Liu
- Department of Gastroenterology, Baiyun Branch of the First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Fengbin Liu, ; Peiwu Li, ; Yi Wen,
| | - Peiwu Li
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Fengbin Liu, ; Peiwu Li, ; Yi Wen,
| | - Yi Wen
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Fengbin Liu, ; Peiwu Li, ; Yi Wen,
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28
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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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29
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Choubey P, Kaur H, Bansal K. Modulation of DNA/RNA Methylation Signaling Mediating Metabolic Homeostasis in Cancer. Subcell Biochem 2022; 100:201-237. [PMID: 36301496 DOI: 10.1007/978-3-031-07634-3_7] [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: 06/16/2023]
Abstract
Nucleic acid methylation is a fundamental epigenetic mechanism that impinges upon several cellular attributes, including metabolism and energy production. The dysregulation of deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) methylation can lead to metabolic rewiring in the cell, which in turn facilitates tumor development. Here, we review the current knowledge on the interplay between DNA/RNA methylation and metabolic programs in cancer cells. We also discuss the mechanistic role of these pathways in tumor development and progression.
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Affiliation(s)
- Pallawi Choubey
- Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, India
| | - Harshdeep Kaur
- Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, India
| | - Kushagra Bansal
- Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, India.
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30
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Guo L, Yang H, Zhou C, Shi Y, Huang L, Zhang J. N6-Methyladenosine RNA Modification in the Tumor Immune Microenvironment: Novel Implications for Immunotherapy. Front Immunol 2021; 12:773570. [PMID: 34956201 PMCID: PMC8696183 DOI: 10.3389/fimmu.2021.773570] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/25/2021] [Indexed: 01/24/2023] Open
Abstract
N6-methyladenosine (m6A) methylation is one of the most common modifications of RNA in eukaryotic cells, and is mainly regulated by m6A methyltransferases (writers), m6A demethylases (erasers), and m6A binding proteins (readers). Recently, accumulating evidence has shown that m6A methylation plays crucial roles in the regulation of the tumor immune microenvironment, greatly impacting the initiation, progression, and metastasis processes of various cancers. In this review we first briefly summarizes the m6A-related concepts and detection methods, and then describes in detail the associations of m6A methylation modification with various tumor immune components especially immune cells (e.g., regulatory T cells, dendritic cells, macrophages, and myeloid-derived suppressor cells) in a variety of cancers. We discuss the relationship between m6A methylation and cancer occurrence and development with the involvement of tumor immunity highlighted, suggesting novel markers and potential targets for molecular pathological diagnosis and immunotherapy of various cancers.
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Affiliation(s)
- Liting Guo
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Yang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenfei Zhou
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Shi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Huang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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31
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Zhou C, Wang S, Shen Z, Shen Y, Li Q, Shen Y, Huang J, Deng H, Ye D, Zhan G, Li J. Construction of an m6A-related lncRNA pair prognostic signature and prediction of the immune landscape in head and neck squamous cell carcinoma. J Clin Lab Anal 2021; 36:e24113. [PMID: 34783061 PMCID: PMC8761472 DOI: 10.1002/jcla.24113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/19/2021] [Accepted: 10/29/2021] [Indexed: 01/01/2023] Open
Abstract
Background Mounting evidence indicates that aberrantly expressed N6‐methylandenosine (m6A) modification regulators and long noncoding RNA (lncRNA) influence the development of head and neck squamous cell carcinoma (HNSCC). However, the prognosis of m6A‐related lncRNA (mrlncRNA) in HNSCC has not yet been evaluated. Methods We retrieved transcriptome, somatic mutation, and clinical information from The Cancer Genome Atlas database and established a differently expressed mrlncRNA (DEmrlncRNA) pair signature based on least absolute shrinkage and selection operator Cox regression and multivariate Cox analyses. Each sample's risk score was computed premised on the signature, which accurately classified patients into low‐ and high‐risk group by the cut‐off point. The signature was evaluated from the perspective of survival, clinicopathological characteristics, tumor mutation burden (TMB), immune cell infiltration, efficacy of chemotherapeutics, tumor immune microenvironment, and immune checkpoint inhibitor (ICI)‐related genes. Results 11 DEmrlncRNA pairs were identified and were used to construct the prediction signature. Kaplan–Meier plotter revealed a worse prognosis in high‐risk patients over low‐risk patients (log rank p < 0.001). According to multivariate Cox regression analysis, the hazard ratio of the risk score and 95% confidence interval of 1.722 and (1.488–1.992) (p < 0.001) were obtained. Furthermore, an increased risk score was associated with aggressive clinicopathological features, specific tumor immune infiltration status, increased expression of ICI‐related genes, higher TMB, and higher chemotherapeutics sensitivity (all p < 0.05). Conclusion This research demonstrated that the signature premised on DEmrlncRNA pairs was an efficient independent prognostic indicator and may provide a rationale for research on immunotherapeutic and chemotherapeutics strategies for HNSCC patients.
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Affiliation(s)
- Chongchang Zhou
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina
- Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Shumin Wang
- Department of StomatologyHuashan HospitalFudan UniversityShanghaiChina
| | - Zhisen Shen
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina
- Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Yiming Shen
- Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Qun Li
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina
- Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Yi Shen
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina
- Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Juntao Huang
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina
- Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Hongxia Deng
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina
- Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Dong Ye
- Department of Otorhinolaryngology Head and Neck SurgeryNingbo Medical Center Lihuili HospitalNingboChina
- Department of Otorhinolaryngology Head and Neck SurgeryLihuili Hospital affiliated to Ningbo UniversityNingboChina
| | - Guowen Zhan
- Department of Otolaryngology Head and Neck SurgeryNingbo Yinzhou Second HospitalNingboChina
| | - Jinyun Li
- Department of Oncology and HematologyThe Affiliated Hospital of Medical School of Ningbo UniversityNingboChina
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Si C, Chen C, Guo Y, Kang Q, Sun Z. Effect, Mechanism, and Applications of Coding/Non-coding RNA m6A Modification in Tumor Microenvironment. Front Cell Dev Biol 2021; 9:711815. [PMID: 34660577 PMCID: PMC8514707 DOI: 10.3389/fcell.2021.711815] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
The tumor microenvironment (TME), which includes immune cells, fibroblasts, and other components, is the site of tumor cell growth and metastasis and significantly impacts tumor development. Among them, N6-methyladenosine RNA modifications (m6A RNA modifications) are the most abundant internal modifications in coding and non-coding RNAs, which can significantly influence the cancer process and have potential as biomarkers and potential therapeutic targets for tumor therapy. This manuscript reviews the role of m6A RNA modifications in TME and their application in tumor therapy. To some extent, an in-depth understanding of the relationship between TME and m6A RNA modifications will provide new approaches and ideas for future cancer therapy.
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Affiliation(s)
- Chaohua Si
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Chen Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yaxin Guo
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Huang Y, Yang Z, Huang C, Jiang X, Yan Y, Zhuang K, Wen Y, Liu F, Li P. Identification of N6-Methylandenosine-Related lncRNAs for Subtype Identification and Risk Stratification in Gastric Adenocarcinoma. Front Oncol 2021; 11:725181. [PMID: 34646770 PMCID: PMC8504261 DOI: 10.3389/fonc.2021.725181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/02/2021] [Indexed: 01/11/2023] Open
Abstract
Objectives The purpose of this study was to investigate the role of m6A-related lncRNAs in gastric adenocarcinoma (STAD) and to determine their prognostic value. Methods Gene expression and clinicopathological data were obtained from The Cancer Genome Atlas (TCGA) database. Correlation analysis and univariate Cox regression analysis were conducted to identify m6A-related prognostic lncRNAs. Subsequently, different clusters of patients with STAD were identified via consensus clustering analysis, and a prognostic signature was established by least absolute shrinkage and selection operator (LASSO) Cox regression analyses. The clinicopathological characteristics, tumor microenvironment (TME), immune checkpoint genes (ICGs) expression, and the response to immune checkpoint inhibitors (ICIs) in different clusters and subgroups were explored. The prognostic value of the prognostic signature was evaluated using the Kaplan-Meier method, receiver operating characteristic curves, and univariate and multivariate regression analyses. Additionally, Gene Set Enrichment Analysis (GSEA), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Gene Ontology (GO) analysis were performed for biological functional analysis. Results Two clusters based on 19 m6A-related lncRNAs were identified, and a prognostic signature comprising 14 m6A-related lncRNAs was constructed, which had significant value in predicting the OS of patients with STAD, clinicopathological characteristics, TME, ICGs expression, and the response to ICIs. Biological processes and pathways associated with cancer and immune response were identified. Conclusions We revealed the role and prognostic value of m6A-related lncRNAs in STAD. Together, our finding refreshed the understanding of m6A-related lncRNAs and provided novel insights to identify predictive biomarkers and immunotherapy targets for STAD.
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Affiliation(s)
- Yuancheng Huang
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zehong Yang
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chaoyuan Huang
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaotao Jiang
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yanhua Yan
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kunhai Zhuang
- Department of Gastroenterology, Baiyun Branch of the First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yi Wen
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fengbin Liu
- Department of Gastroenterology, Baiyun Branch of the First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peiwu Li
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Cai Z, Zhang J, Liu Z, Su J, Xu J, Li Z, Meng H, Zhang H, Huang M, Zhao D, Duan C, He X. Identification of an N6-methyladenosine (m6A)-related signature associated with clinical prognosis, immune response, and chemotherapy in primary glioblastomas. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1241. [PMID: 34532378 PMCID: PMC8421967 DOI: 10.21037/atm-21-3139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022]
Abstract
Background N6-methyladenosine (m6A) RNA methylation regulators play crucial role in tumorigenicity and progression. However, their biological significance in primary glioblastomas (GBM) has not been fully elucidated. Methods In the present study, we evaluated the 22 m6A RNA regulators using the integrated data of primary GBM samples from The Cancer Genome Atlas and Chinese Glioma Genome Atlas databases. The different m6A modification patterns and m6A-related gene signature in primary GBM were distinguished by using principal component analysis. Single-sample gene set enrichment analysis was introduced to assess the relative level of immune infiltration. Gene set variation analysis was performed to calculate the enrichment score of the signaling pathways for different clusters. An m6A scoring scheme was established to evaluate the m6A modification pattern in individual tumors in order to predict prognosis and evaluate tumor microenvironment (TME) cell infiltration, immune response, and chemotherapy effect in primary GBM. Results Two distinct m6A modification subgroups associated with different clinical features and biological pathways were identified among the 371 primary GBM. Based on 132 prognostic m6A phenotype-related differentially expressed genes (DEGs) between 2 m6A cluster subgroups, an m6A scoring model was constructed to assess the m6A modification pattern in individual tumors. The high-m6A score group was associated with better prognosis and immune response and worse chemotherapy effect. Conclusions The findings of the present study indicate the potential role of m6A modification in primary GBM, which will help enhance our understanding of TME characteristics, predict clinical prognosis, and provide important insight into effective immunotherapy and chemotherapy.
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Affiliation(s)
- Zhiqiang Cai
- Department of Cerebrovascular Surgery, Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Neurosurgery, Langzhong City People's Hospital, Langzhong, China
| | - Jianbo Zhang
- Department of Neurosurgery, Zhongshan City People's Hospital, Zhongshan, China
| | - Ziying Liu
- Department of Neurosurgery, Zhongshan City People's Hospital, Zhongshan, China
| | - Jiahao Su
- Department of Neurosurgery, Zhongshan City People's Hospital, Zhongshan, China
| | - Jing Xu
- Department of Neurosurgery, Zhongshan City People's Hospital, Zhongshan, China
| | - Zhenjun Li
- Department of Cerebrovascular Surgery, Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hongliang Meng
- Department of Cerebrovascular Surgery, Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Heng Zhang
- Department of Neurosurgery, Langzhong City People's Hospital, Langzhong, China
| | - Minjie Huang
- Department of Neurosurgery, Zhongshan City People's Hospital, Zhongshan, China
| | - Donghai Zhao
- Department of Neurosurgery, Zhongshan City People's Hospital, Zhongshan, China
| | - Chuanzhi Duan
- Department of Cerebrovascular Surgery, Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xuying He
- Department of Cerebrovascular Surgery, Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Cong Y, Liu J, Chen G, Qiao G. The Emerging Role of T-Cell Immunoglobulin Mucin-3 in Breast Cancer: A Promising Target For Immunotherapy. Front Oncol 2021; 11:723238. [PMID: 34504800 PMCID: PMC8421567 DOI: 10.3389/fonc.2021.723238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/06/2021] [Indexed: 01/08/2023] Open
Abstract
Cancer treatment through immune checkpoint receptor blockade has made significant advances in the recent years. However, resistance to the current immune checkpoint inhibitors (ICIs) has been observed in many patients, who consequently do not respond to these treatments. T-cell immunoglobulin mucin-3 (Tim-3) is a novel immune checkpoint molecule emerging as a potential therapeutic target for cancer immunotherapy. Epidemiologic findings reveal that genetic polymorphisms in the Tim-3 gene are associated with increased susceptibility to breast cancer. In patients with breast cancer, Tim-3 is expressed both on immune and tumor cells. Accumulating evidence demonstrates that Tim-3 can notably affect breast cancer treatment outcome and prognosis. Therefore, Tim-3 is being regarded as a high-potential target for improving breast cancer therapy. In this review, we summarize the role of Tim-3 in breast cancer and the regulation mechanisms of Tim-3 to furnish evidences for future research and therapy.
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Affiliation(s)
- Yizi Cong
- Department of Breast Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Jing Liu
- Department of Pathology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Gang Chen
- Department of Breast Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Guangdong Qiao
- Department of Breast Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
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Long non-coding RNA ILF3-AS1 facilitates hepatocellular carcinoma progression by stabilizing ILF3 mRNA in an m 6A-dependent manner. Hum Cell 2021; 34:1843-1854. [PMID: 34491544 DOI: 10.1007/s13577-021-00608-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Increasing evidences have demonstrated that ILF3 antisense RNA 1 (ILF3-AS1) acts as an oncogenic long noncoding RNA (lncRNA) in several types of human cancers. However, the expression pattern, functional role and underlying mechanism of ILF3-AS1 in HCC remains largely unclear. Here, we found that ILF3-AS1 expression was significantly elevated in HCC tissues and also associated with prognosis of patients with HCC. Functional assays demonstrated that knockdown of ILF3-AS1 expression resulted in the suppression of proliferation, migration and invasion in HCC cells, whereas overexpression of ILF3-AS1 exerted opposite effects. Additionally, knockdown of IFL3-AS1 attenuated HCC tumorigenesis and metastasis in vivo. Mechanistically, ILF3-AS1 associated with ILF3 mRNA and inhibited its degradation. ILF3-AS1 increased ILF3 m6A level via recruiting N6-methyladenosine (m6A) RNA methyltransferase METTL3. Moreover, IFL3-AS1 enhanced the interaction between ILF3 mRNA and m6A reader IGF2BP1. Overall, our study revealed the function and mechanism of ILF3-AS1 in the malignant phenotypes of HCC cells, which provides a novel therapeutic target for HCC.
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Rengaraj P, Obrdlík A, Vukić D, Varadarajan NM, Keegan LP, Vaňáčová Š, O'Connell MA. Interplays of different types of epitranscriptomic mRNA modifications. RNA Biol 2021; 18:19-30. [PMID: 34424827 PMCID: PMC8677042 DOI: 10.1080/15476286.2021.1969113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Eukaryotic mRNAs are modified by several chemical marks which have significant impacts on mRNA biology, gene expression, and cellular metabolism as well as on the survival and development of the whole organism. The most abundant and well-studied mRNA base modifications are m6A and ADAR RNA editing. Recent studies have also identified additional mRNA marks such as m6Am, m5C, m1A and Ψ and studied their roles. Each type of modification is deposited by a specific writer, many types of modification are recognized and interpreted by several different readers and some types of modifications can be removed by eraser enzymes. Several works have addressed the functional relationships between some of the modifications. In this review we provide an overview on the current status of research on the different types of mRNA modifications and about the crosstalk between different marks and its functional consequences.
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Affiliation(s)
- Praveenkumar Rengaraj
- Central European Institute of Technology (CEITEC), CEITEC, Masaryk University Brno, Brno, Czech Republic
| | - Aleš Obrdlík
- Central European Institute of Technology (CEITEC), CEITEC, Masaryk University Brno, Brno, Czech Republic
| | - Dragana Vukić
- Central European Institute of Technology (CEITEC), CEITEC, Masaryk University Brno, Brno, Czech Republic
| | - Nandan Mysore Varadarajan
- Central European Institute of Technology (CEITEC), CEITEC, Masaryk University Brno, Brno, Czech Republic
| | - Liam P Keegan
- Central European Institute of Technology (CEITEC), CEITEC, Masaryk University Brno, Brno, Czech Republic
| | - Štěpánka Vaňáčová
- Central European Institute of Technology (CEITEC), CEITEC, Masaryk University Brno, Brno, Czech Republic
| | - Mary A O'Connell
- Central European Institute of Technology (CEITEC), CEITEC, Masaryk University Brno, Brno, Czech Republic
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Diaz-Muñoz MD, Osma-Garcia IC. The RNA regulatory programs that govern lymphocyte development and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1683. [PMID: 34327847 DOI: 10.1002/wrna.1683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/25/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022]
Abstract
Lymphocytes require of constant and dynamic changes in their transcriptome for timely activation and production of effector molecules to combat external pathogens. Synthesis and translation of messenger (m)RNAs into these effector proteins is controlled both quantitatively and qualitatively by RNA binding proteins (RBPs). RBP-dependent regulation of RNA editing, subcellular location, stability, and translation shapes immune cell development and immunity. Extensive evidences have now been gathered from few model RBPs, HuR, PTBP1, ZFP36, and Roquin. However, recently developed methodologies for global characterization of protein:RNA interactions suggest the existence of complex RNA regulatory networks in which RBPs co-ordinately regulate the fate of sets of RNAs controlling cellular pathways and functions. In turn, RNA can also act as scaffolding of functionally related proteins modulating their activation and function. Here we review current knowledge about how RBP-dependent regulation of RNA shapes our immune system and discuss about the existence of a hidden immune cell epitranscriptome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Manuel D Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
| | - Ines C Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
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Feng P, Chen W. iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae. Methods 2021; 203:28-31. [PMID: 33882361 DOI: 10.1016/j.ymeth.2021.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/11/2021] [Accepted: 04/15/2021] [Indexed: 01/28/2023] Open
Abstract
The 5-methyluridine (m5U)modification plays important roles in a series of biological processes. Accurate identification of m5U sites will be helpful to decode its biological functions. Although experimental techniques have been proposed to detect m5U, they are still expensive and time consuming. In the present work, a support vector machine based method, called iRNA-m5U, was developed to identify the m5U sites in the Saccharomyces cerevisiae transcriptome. The performance of iRNA-m5U was validated based on different datasets. The accuracies obtained by iRNA-m5U is promising, indicating that it holds the potential to become an useful tool for the identification of m5U sites.
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Affiliation(s)
- Pengmian Feng
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
| | - Wei Chen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China; Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China; School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China.
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