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Li Y, Jin H, Li Q, Shi L, Mao Y, Zhao L. The role of RNA methylation in tumor immunity and its potential in immunotherapy. Mol Cancer 2024; 23:130. [PMID: 38902779 PMCID: PMC11188252 DOI: 10.1186/s12943-024-02041-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
RNA methylation, a prevalent post-transcriptional modification, has garnered considerable attention in research circles. It exerts regulatory control over diverse biological functions by modulating RNA splicing, translation, transport, and stability. Notably, studies have illuminated the substantial impact of RNA methylation on tumor immunity. The primary types of RNA methylation encompass N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N7-methylguanosine (m7G), and 3-methylcytidine (m3C). Compelling evidence underscores the involvement of RNA methylation in regulating the tumor microenvironment (TME). By affecting RNA translation and stability through the "writers", "erasers" and "readers", RNA methylation exerts influence over the dysregulation of immune cells and immune factors. Consequently, RNA methylation plays a pivotal role in modulating tumor immunity and mediating various biological behaviors, encompassing proliferation, invasion, metastasis, etc. In this review, we discussed the mechanisms and functions of several RNA methylations, providing a comprehensive overview of their biological roles and underlying mechanisms within the tumor microenvironment and among immunocytes. By exploring how these RNA modifications mediate tumor immune evasion, we also examine their potential applications in immunotherapy. This review aims to provide novel insights and strategies for identifying novel targets in RNA methylation and advancing cancer immunotherapy efficacy.
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Affiliation(s)
- Yan Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haoer Jin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Qingling Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Liangrong Shi
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Zhao Z, Zhou Y, Lv P, Zhou T, Liu H, Xie Y, Wu Z, Wang X, Zhao H, Zheng J, Jiang X. NSUN4 mediated RNA 5-methylcytosine promotes the malignant progression of glioma through improving the CDC42 mRNA stabilization. Cancer Lett 2024; 597:217059. [PMID: 38876383 DOI: 10.1016/j.canlet.2024.217059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 06/16/2024]
Abstract
5-Methylcytosine (m5C) methylation is a significant post-transcriptional modification that play a crucial role in the development and progression of numerous cancers. Whereas the functions and molecular mechanisms underlying m5C methylation in gliomas remain unclear. This study dedicated to explore changes of m5C levels and the clinical significance of the m5C writer NSUN4 in gliomas. We found that high m5C levels were negatively related to prognosis of patients with glioma. Moreover, gain- and loss-of-function experiments revealed the role of NSUN4 in enhancing m5C modification of mRNA to promote the malignant progression of glioma. Mechanistically speaking, NSUN4-mediated m5C alterations regulated ALYREF binding to CDC42 mRNA, thereby impacting the mRNA stability of CDC42. We also demonstrated that CDC42 promoted glioma proliferation, migration, and invasion by activating the PI3K-AKT pathway. Additionally, rescue experiments proved that CDC42 overexpression weaken the inhibitory effect of NSUN4 knockdown on the malignant progression of gliomas in vitro and in vivo. Our findings elucidated that NSUN4-mediated high m5C levels promote ALYREF binding to CDC42 mRNA and regulate its stability, thereby driving the malignant progression of glioma. This provides theoretical support for targeted the treatment of gliomas.
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Affiliation(s)
- Zhen Zhao
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yujie Zhou
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Peng Lv
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ting Zhou
- Department of Gynaecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hanyuan Liu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Youxi Xie
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhipeng Wu
- Department of Neurosurgery, Weifang People's Hospital, Weifang, China
| | - Xuan Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongyang Zhao
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Jianglin Zheng
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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Chen M, Chen Y, Wang K, Deng X, Chen J. Non‐m 6A RNA modifications in haematological malignancies. Clin Transl Med 2024; 14:e1666. [PMID: 38880983 PMCID: PMC11180698 DOI: 10.1002/ctm2.1666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 06/18/2024] Open
Abstract
Dysregulated RNA modifications, stemming from the aberrant expression and/or malfunction of RNA modification regulators operating through various pathways, play pivotal roles in driving the progression of haematological malignancies. Among RNA modifications, N6-methyladenosine (m6A) RNA modification, the most abundant internal mRNA modification, stands out as the most extensively studied modification. This prominence underscores the crucial role of the layer of epitranscriptomic regulation in controlling haematopoietic cell fate and therefore the development of haematological malignancies. Additionally, other RNA modifications (non-m6A RNA modifications) have gained increasing attention for their essential roles in haematological malignancies. Although the roles of the m6A modification machinery in haematopoietic malignancies have been well reviewed thus far, such reviews are lacking for non-m6A RNA modifications. In this review, we mainly focus on the roles and implications of non-m6A RNA modifications, including N4-acetylcytidine, pseudouridylation, 5-methylcytosine, adenosine to inosine editing, 2'-O-methylation, N1-methyladenosine and N7-methylguanosine in haematopoietic malignancies. We summarise the regulatory enzymes and cellular functions of non-m6A RNA modifications, followed by the discussions of the recent studies on the biological roles and underlying mechanisms of non-m6A RNA modifications in haematological malignancies. We also highlight the potential of therapeutically targeting dysregulated non-m6A modifiers in blood cancer.
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Affiliation(s)
- Meiling Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Yuanzhong Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
| | - Kitty Wang
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Xiaolan Deng
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Jianjun Chen
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
- Gehr Family Center for Leukemia ResearchCity of Hope Medical Center and Comprehensive Cancer CenterDuarteCaliforniaUSA
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Wang X, Gan M, Wang Y, Wang S, Lei Y, Wang K, Zhang X, Chen L, Zhao Y, Niu L, Zhang S, Zhu L, Shen L. Comprehensive review on lipid metabolism and RNA methylation: Biological mechanisms, perspectives and challenges. Int J Biol Macromol 2024; 270:132057. [PMID: 38710243 DOI: 10.1016/j.ijbiomac.2024.132057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/08/2024]
Abstract
Adipose tissue plays a crucial role in maintaining energy balance, regulating hormones, and promoting metabolic health. To address disorders related to obesity and develop effective therapies, it is essential to have a deep understanding of adipose tissue biology. In recent years, RNA methylation has emerged as a significant epigenetic modification involved in various cellular functions and metabolic pathways. Particularly in the realm of adipogenesis and lipid metabolism, extensive research is ongoing to uncover the mechanisms and functional importance of RNA methylation. Increasing evidence suggests that RNA methylation plays a regulatory role in adipocyte development, metabolism, and lipid utilization across different organs. This comprehensive review aims to provide an overview of common RNA methylation modifications, their occurrences, and regulatory mechanisms, focusing specifically on their intricate connections to fat metabolism. Additionally, we discuss the research methodologies used in studying RNA methylation and highlight relevant databases that can aid researchers in this rapidly advancing field.
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Affiliation(s)
- Xingyu Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Mailin Gan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Saihao Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhang Lei
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
| | - Linyuan Shen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
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Huang G, Huang X, Jiang J. Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues. Methods 2024; 226:1-8. [PMID: 38485031 DOI: 10.1016/j.ymeth.2024.03.004] [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: 11/06/2023] [Revised: 02/20/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent, abundant, and conserved internal modification in the eukaryotic messenger RNA (mRNAs) and plays a crucial role in the cellular process. Although more than ten methods were developed for m6A detection over the past decades, there were rooms left to improve the predictive accuracy and the efficiency. In this paper, we proposed an improved method for predicting m6A modification sites, which was based on bi-directional gated recurrent unit (Bi-GRU) and convolutional neural networks (CNN), called Deepm6A-MT. The Deepm6A-MT has two input channels. One is to use an embedding layer followed by the Bi-GRU and then by the CNN, and another is to use one-hot encoding, dinucleotide one-hot encoding, and nucleotide chemical property codes. We trained and evaluated the Deepm6A-MT both by the 5-fold cross-validation and the independent test. The empirical tests showed that the Deepm6A-MT achieved the state of the art performance. In addition, we also conducted the cross-species and the cross-tissues tests to further verify the Deepm6A-MT for effectiveness and efficiency. Finally, for the convenience of academic research, we deployed the Deepm6A-MT to the web server, which is accessed at the URL http://www.biolscience.cn/Deepm6A-MT/.
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Affiliation(s)
- Guohua Huang
- School of Information Technology and Administration, Hunan University of Finance and Economics, Changsha, Hunan 410205, China.
| | - Xiaohong Huang
- College of Information Science and Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Jinyun Jiang
- College of Information Science and Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
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Cui Y, Lv P, Zhang C. NSUN6 mediates 5-methylcytosine modification of METTL3 and promotes colon adenocarcinoma progression. J Biochem Mol Toxicol 2024; 38:e23749. [PMID: 38800929 DOI: 10.1002/jbt.23749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/12/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024]
Abstract
Colon adenocarcinoma (COAD) is a common and fatal malignant tumor of digestive system with complex etiology. 5-Methylcytosine (m5C) modification of RNA by the NSUN gene family (NSUN1-NSUN7) and DNMT2 reshape cell biology and regulate tumor development. However, the expression profile, prognostic significance and function of these m5C modifiers in COAD remain largely unclear. By mining multiple integrated tumor databases, we found that NSUN1, NSUN2, NSUN5, and NSUN6 were overexpressed in COAD tumor samples relative to normal samples. Clinically, high expression of NSUN6 was significantly associated with shorter survival (including both disease-free survival and overall survival) in COAD patients. NSUN6 was further confirmed to be upregulated at both tissue and cellular levels of COAD, suggesting that NSUN6 plays a critical role in disease progression. Through comprehensive gene enrichment analysis and cell-based functional validation, it was revealed that NSUN6 promoted the cell cycle progression and cell proliferation of COAD. Mechanistically, NSUN6 upregulates the expression of oncogenic METTL3 and catalyzes its m5C modification in COAD cells. Overexpression of METTL3 significantly relieved the cell cycle inhibition of COAD caused by NSUN6 deficiency. Furthermore, NSUN6 was negatively associated with the abundance of infiltrating immune cells in COAD tumors, such as activated B cells, natural killer cells, effector memory CD8 T cells, and regulatory T cells. Importantly, pan-cancer analysis further uncovered that NSUN6 was dysregulated and heterogeneous in various tumors. Thus our findings extend the role of m5C transferase in COAD and suggest that NSUN6 is a potential biomarker and target for this malignancy.
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Affiliation(s)
- Yuanbo Cui
- Department of Translational Medicine Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Pengju Lv
- Department of Clinical Laboratory, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Chunyan Zhang
- Department of Clinical Laboratory, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
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Meng S, Jiangtao B, Haisong W, Mei L, Long Z, Shanfeng L. RNA m 5C methylation: a potential modulator of innate immune pathways in hepatocellular carcinoma. Front Immunol 2024; 15:1362159. [PMID: 38807595 PMCID: PMC11131105 DOI: 10.3389/fimmu.2024.1362159] [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: 12/27/2023] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
RNA 5-methylcytosine (m5C) methylation plays a crucial role in hepatocellular carcinoma (HCC). As reported, aberrant m5C methylation is closely associated with the progression, therapeutic efficacy, and prognosis of HCC. The innate immune system functions as the primary defense mechanism in the body against pathogenic infections and tumors since it can activate innate immune pathways through pattern recognition receptors to exert anti-infection and anti-tumor effects. Recently, m5C methylation has been demonstrated to affect the activation of innate immune pathways including TLR, cGAS-STING, and RIG-I pathways by modulating RNA function, unveiling new mechanisms underlying the regulation of innate immune responses by tumor cells. However, research on m5C methylation and its interplay with innate immune pathways is still in its infancy. Therefore, this review details the biological significance of RNA m5C methylation in HCC and discusses its potential regulatory relationship with TLR, cGAS-STING, and RIG-I pathways, thereby providing fresh insights into the role of RNA methylation in the innate immune mechanisms and treatment of HCC.
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Affiliation(s)
| | | | | | | | | | - Li Shanfeng
- Department of Interventional Vascular Surgery, Affiliated Hospital of Hebei University, Baoding, China
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Uddin IA, Stec E, Papadantonakis GA. Ionization Patterns and Chemical Reactivity of Cytosine-Guanine Watson-Crick Pairs. Chemphyschem 2024; 25:e202300946. [PMID: 38381922 DOI: 10.1002/cphc.202300946] [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: 12/11/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 02/23/2024]
Abstract
Gas-phase and aqueous vertical ionization potentials, vIPgas and vIPaq respectively and measurements of the molecular electrostatic and local ionization maps calculated at the DFT/B3LYP-D3/ 6-311+G** level of theory and the C-PCM reaction field model for single- and double-stranded CpG and 5MeCpG pairs show that the vIPaq for single- and double-stranded pairs of C-G and 5MeC-G are practically the same, in the range of 5.79 to 5.81 eV. The aqueous adiabatic ionization potentials for single-stranded CpG and 5MeCpG are 5.52 eV and 5.51 eV respectively and they reflect the nuclear reorganization that takes place after the abstraction of the electron. The aqueous adiabatic ionization energy values that correspond to the CpG+. radical cation and the hydrated electron, e-,, being at infinite distance, adIPaq+Vo, are 3.92 eV and 3.91 eV respectively with (Vo=-1.6 eV) Analysis of data suggest that the HOMO-LUMO energy gap in the hard/soft-acid/base (HSAB) concept cannot be used a priori to determine the effect of cytosine methylation on the guanine enhanced oxidative damage in DNA.
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Affiliation(s)
- Ismihan A Uddin
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
| | - Ewa Stec
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
| | - George A Papadantonakis
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
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Huang Y, Li X, Wei L, Ma S, Ma L, Zan Y, He X, Tang Y, Ding Y. NSUN2 relies on ALYREF to regulate Nrf2-mediated oxidative stress and alleviate Dox-induced liver injury. Biol Direct 2024; 19:32. [PMID: 38685056 PMCID: PMC11057147 DOI: 10.1186/s13062-024-00477-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Doxorubicin (Dox) is associated with various liver injuries, limiting its clinical utility. This study investigates whether NSUN2 participates in Dox-induced liver injury and the associated molecular mechanism. METHODS In vivo and in vitro liver cell injury models were constructed based on Dox therapy. The protein levels of NSUN2 and oxidative stress indicators Nrf2, HO-1, and NQO1 were evaluated by Western blot. The RNA binding potential was detected by RNA methylation immunoprecipitation (RIP). Additionally, the effect of NSUN2 on Nrf2 mRNA synthesis and localization was evaluated using an RNA fluorescence probe. RESULTS NSUN2 was downregulated, and liver tissue suffered significant pathological damage in the Dox group. The levels of ALT and AST significantly increased. NSUN2 interference exacerbated Dox-induced liver cell damage, which was reversed by NSUN2 overexpression. RIP demonstrated that NSUN2 recognized and bound to Nrf2 mRNA. Western blot analysis showed the protein level of Nrf2 in the NSUN2-WT group was significantly higher than that of the control group, whereas there was no significant change in Nrf2 level in the mutant NSUN2 group. Luciferase analysis demonstrated that NSUN2 could recognize and activate the Nrf2 5'UTR region of LO2 cells. In addition, RIP analysis revealed that ALYREF could recognize and bind to Nrf2 mRNA and that ALYREF controls the regulatory effect of NSUN2 on Nrf2. CONCLUSION NSUN2 regulates Dox-induced liver cell damage by increasing Nrf2 mRNA m5C methylation to inhibit inhibiting antioxidant stress. The regulatory effect of NSUN2 on Nrf2 depends on ALYREF.
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Affiliation(s)
- Yingying Huang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xiao Li
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Lin Wei
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Shinan Ma
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
- Department of Pulmonary and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Liming Ma
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Yuxin Zan
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xiju He
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Yijun Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
- Department of Pulmonary and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China.
| | - Yan Ding
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
- Department of Pulmonary and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China.
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10
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Chen B, Qiu M, Gong R, Liu Y, Zhou Z, Wen Q, Wei X, Liang X, Jiang Y, Chen P, Wei Y, Huang Q, Mo Q, Lin Q, Yu H. Genetic variants in m5C modification genes are associated with survival of patients with HBV-related hepatocellular carcinoma. Arch Toxicol 2024; 98:1125-1134. [PMID: 38438738 DOI: 10.1007/s00204-024-03687-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with a high mortality rate. The 5-methylcytosine (m5C), a type of RNA modification, plays crucial regulatory roles in HCC carcinogenesis, metastasis, and prognosis. However, a few studies have investigated the effect of genetic variants in m5C modification genes on survival of patients with hepatitis B virus (HBV)-related HCC. In the present study, we evaluated associations between 144 SNPs in 15 m5C modification genes and overall survival (OS) in 866 patients with the HBV-related HCC. Expression quantitative trait loci (eQTL) analysis and differential expression analysis were conducted to investigate biological mechanisms. As a result, we identified that two SNPs (NSUN7 rs2437325 A > G and TRDMT1 rs34434809 G > C) were significantly associated with HBV-related HCC OS with adjusted allelic hazards ratios of 1.25 (95% confidence interval = 1.05-1.48 and P = 0.011) and 1.19 (1.02-1.38 and P = 0.027), respectively, with a trend of combined risk genotypes (Ptrend < 0.001). Moreover, the results of eQTL analyses showed that both NSUN7 rs2437325 G and TRDMT1 rs34434809 C alleles were associated with a reduced mRNA expression level in 208 normal liver tissues (P = 0.007 and P < 0.001, respectively). Taken together, genetic variants in the m5C modification genes may be potential prognostic biomarkers of HBV-related HCC after hepatectomy, likely through mediating the mRNA expression of corresponding genes.
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Affiliation(s)
- Bowen Chen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
| | - Moqin Qiu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Department of Respiratory Oncology, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Rongbin Gong
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, China
| | - Yingchun Liu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health Commission, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Zihan Zhou
- Department of Cancer Prevention and Control, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Qiuping Wen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health Commission, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Xiaoxia Wei
- Department of Clinical Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Xiumei Liang
- Department of Disease Process Management, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Yanji Jiang
- Department of Scientific Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Peiqin Chen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Editorial Department of Chinese Journal of Oncology Prevention and Treatment, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Yuying Wei
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
| | - Qiongguang Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, China
| | - Qiuyan Mo
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
| | - Qiuling Lin
- Department of Clinical Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, China.
| | - Hongping Yu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China.
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health Commission, Guangxi Medical University Cancer Hospital, Nanning, 530021, China.
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, 530021, China.
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11
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Chen H, Liu H, Zhang C, Xiao N, Li Y, Zhao X, Zhang R, Gu H, Kang Q, Wan J. RNA methylation-related inhibitors: Biological basis and therapeutic potential for cancer therapy. Clin Transl Med 2024; 14:e1644. [PMID: 38572667 PMCID: PMC10993167 DOI: 10.1002/ctm2.1644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/05/2024] Open
Abstract
RNA methylation is widespread in nature. Abnormal expression of proteins associated with RNA methylation is strongly associated with a number of human diseases including cancer. Increasing evidence suggests that targeting RNA methylation holds promise for cancer treatment. This review specifically describes several common RNA modifications, such as the relatively well-studied N6-methyladenosine, as well as 5-methylcytosine and pseudouridine (Ψ). The regulatory factors involved in these modifications and their roles in RNA are also comprehensively discussed. We summarise the diverse regulatory functions of these modifications across different types of RNAs. Furthermore, we elucidate the structural characteristics of these modifications along with the development of specific inhibitors targeting them. Additionally, recent advancements in small molecule inhibitors targeting RNA modifications are presented to underscore their immense potential and clinical significance in enhancing therapeutic efficacy against cancer. KEY POINTS: In this paper, several important types of RNA modifications and their related regulatory factors are systematically summarised. Several regulatory factors related to RNA modification types were associated with cancer progression, and their relationships with cancer cell migration, invasion, drug resistance and immune environment were summarised. In this paper, the inhibitors targeting different regulators that have been proposed in recent studies are summarised in detail, which is of great significance for the development of RNA modification regulators and cancer treatment in the future.
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Affiliation(s)
- Huanxiang Chen
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
- School of Life ScienceZhengzhou UniversityZhengzhouChina
| | - Hongyang Liu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Chenxing Zhang
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Nan Xiao
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yang Li
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | | | - Ruike Zhang
- Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Huihui Gu
- Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Qiaozhen Kang
- School of Life ScienceZhengzhou UniversityZhengzhouChina
| | - Junhu Wan
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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12
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Zhang Y, Jia Q, Li F, Luo X, Wang Z, Wang X, Wang Y, Zhang Y, Li M, Bian L. Identification of molecular subtypes and a prognostic signature based on m6A/m5C/m1A-related genes in lung adenocarcinoma. Sci Rep 2024; 14:7543. [PMID: 38555384 PMCID: PMC10981664 DOI: 10.1038/s41598-024-57910-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/22/2024] [Indexed: 04/02/2024] Open
Abstract
Lung cancer, specifically the histological subtype lung adenocarcinoma (LUAD), has the highest global occurrence and fatality rate. Extensive research has indicated that RNA alterations encompassing m6A, m5C, and m1A contribute actively to tumorigenesis, drug resistance, and immunotherapy responses in LUAD. Nevertheless, the absence of a dependable predictive model based on m6A/m5C/m1A-associated genes hinders accurately predicting the prognosis of patients diagnosed with LUAD. In this study, we collected patient data from The Cancer Genome Atlas (TCGA) and identified genes related to m6A/m5C/m1A modifications using the GeneCards database. The "ConsensusClusterPlus" R package was used to produce molecular subtypes by utilizing genes relevant to m6A/m5C/m1A identified through differential expression and univariate Cox analyses. An independent prognostic factor was identified by constructing a prognostic signature comprising six genes (SNHG12, PABPC1, IGF2BP1, FOXM1, CBFA2T3, and CASC8). Poor overall survival and elevated expression of human leukocyte antigens and immune checkpoints were correlated with higher risk scores. We examined the associations between the sets of genes regulated by m6A/m5C/m1A and the risk model, as well as the immune cell infiltration, using algorithms such as ESTIMATE, CIBERSORT, TIMER, ssGSEA, and exclusion (TIDE). Moreover, we compared tumor stemness indices (TSIs) by considering the molecular subtypes related to m6A/m5C/m1A and risk signatures. Analyses were performed based on the risk signature, including stratification, somatic mutation analysis, nomogram construction, chemotherapeutic response prediction, and small-molecule drug prediction. In summary, we developed a prognostic signature consisting of six genes that have the potential for prognostication in patients with LUAD and the design of personalized treatments that could provide new versions of personalized management for these patients.
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Affiliation(s)
- Yu Zhang
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Qiuye Jia
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Fangfang Li
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Xuan Luo
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Zhiyuan Wang
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Xiaofang Wang
- Department of Pathology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yanghao Wang
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Yinglin Zhang
- Wenshan People's Hospital, Yunnan, Yunnan Province, China
| | - Muye Li
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Li Bian
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China.
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13
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Qin W, Fei G, Zhou Q, Li Z, Li W, Wei P. Nuclear protein NOP2 serves as a poor-prognosis predictor of LUAD and aggravates the malignancy of lung adenocarcinoma cells. Funct Integr Genomics 2024; 24:58. [PMID: 38489049 DOI: 10.1007/s10142-024-01337-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/29/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
Recent studies have shown that NOP2, a nucleolar protein, is up-regulated in various cancers, suggesting a potential link to tumor aggressiveness and unfavorable outcomes. This study examines NOP2's role in lung adenocarcinoma (LUAD), a context where its implications remain unclear. Utilizing bioinformatics, we assessed 513 LUAD and 59 normal tissue samples from The Cancer Genome Atlas (TCGA) to explore NOP2's diagnostic and prognostic significance in LUAD. Additionally, in vitro experiments compared NOP2 expression between Beas-2b and A549 cells. Advanced databases and analytical tools, including LINKEDOMICS, STRING, and TISIDB, were employed to further elucidate NOP2's association with LUAD. Our findings indicate a significantly higher expression of NOP2 mRNA and protein in A549 cells compared to Beas-2b cells (P < 0.001). In LUAD, elevated NOP2 levels were linked to decreased Overall Survival (OS) and advanced clinical stages. Univariate Cox analysis revealed that high NOP2 expression correlated with poorer OS in LUAD (P < 0.01), a finding independently supported by multivariate Cox analysis (P < 0.05). The relationship between NOP2 expression and LUAD risk was presented via a Nomogram. Additionally, Gene Set Enrichment Analysis (GSEA) identified seven NOP2-related signaling pathways. A focal point of our research was the interplay between NOP2 and tumor-immune interactions. Notably, a negative correlation was observed between NOP2 expression and the immune infiltration levels of macrophages, neutrophils, mast cells, Natural Killer (NK) cells, and CD8 + T cells in LUAD. Moreover, the expression of NOP2 was related to the sensitivity of various chemotherapeutic drugs. In vitro, we found that downregulating NOP2 can decrease the proliferation, migration and invasion of A549 cells. Furthermore, NOP2 can regulate Caspase3-mediated apoptosis. Collectively, particularly regarding prognosis, immune infiltration and vitro experiments, these findings suggest NOP2's potential of serving as a poor-prognostic biomarker for LUAD and aggravating the malignancy of lung adenocarcinoma cells.
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Affiliation(s)
- Weizhuo Qin
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing City, 210009, Jiangsu Province, China
| | - Gaoqiang Fei
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing City, 210009, Jiangsu Province, China
| | - Qian Zhou
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing City, 210009, Jiangsu Province, China
| | - Zhijie Li
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing City, 210009, Jiangsu Province, China
| | - Wei Li
- Department of Quality Management, Children's Hospital of Nanjing Medical University, No. 8 Jiangdong South Road, Jianye District, Nanjing City, 210008, Jiangsu Province, China.
| | - Pingmin Wei
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing City, 210009, Jiangsu Province, China.
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14
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Zeng Z, Zou Y, Cai W, Lin FC, Wang H. Roles of CcDFR and CcOMT9 in the cyanidin biosynthesis and development of Cordyceps cicadae. Front Microbiol 2024; 15:1353710. [PMID: 38511011 PMCID: PMC10953825 DOI: 10.3389/fmicb.2024.1353710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Cordyceps cicadae is a traditional Chinese medicinal fungus known for its rich production of bioactive substances, particularly cyanidin, an anthocyanin commonly found in plants with notable anti-inflammatory, anti-tumor, antiviral, and antibacterial properties. This study revealed two key genes, CcDFR and CcOMT9, affecting cyanidin biosynthesis in C. cicadae. Methods The roles of these genes in cyanidin production, growth, and development were elucidated through the gene knockout method, phenotypic analysis, transcriptomics, and metabolomics. Results CcDFR deletion led to reduced cyanidin-3-O-glucoside (C3G), suppressed expression of cyanidin biosynthesis genes, impaired synnemata formation, decreased polysaccharide and adenosine content, and diminished chitinase activity. Meanwhile, the ΔCcOMT9 mutant exhibited an increase in C3G production, promoted expression of cyanidin biosynthesis genes and rising bioactive compounds, suppressed RNA methylation, and led to phenylalanine accumulation with no effect on fruiting body formation. Discussion We revealed a distinct anthocyanin biosynthesis pathway in C. cicadae and identified two genes with opposite functions, laying the foundation for future genetic modification of cyanidin-producing strains using modern biological techniques. This will shorten the production period of this valuable compound, facilitating the industrial-scale production of cyanidin.
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Affiliation(s)
- Zixuan Zeng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yu Zou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Weiming Cai
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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15
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Wu J, Li X, Kong D, Zheng X, Du W, Zhang Y, Jiao Y, Li X. Exploring the importance of m5c in the diagnosis and subtype classification of COPD using the GEO database. Gene 2024; 895:147987. [PMID: 37972696 DOI: 10.1016/j.gene.2023.147987] [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: 09/25/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND 5-Methylcytosine (m5C) is an mRNA modifier that is associated with the occurrence and development of viral infection, pulmonary fibrosis, lung cancer, and other diseases. However, the role of m5C regulators in chronic obstructive pulmonary disease (COPD) remains unknown. METHODS In this study, by analysing the GSE42057 dataset, the differential expression of m5c regulators in the COPD group and control group was obtained, and a correlation analysis was conducted. The random forest model and support vector machine model were used to predict the occurrence of COPD. A nomogram model was also constructed to predict the prevalence of COPD. The COPD patients were divided into subtypes by consistent cluster analysis based on m5c methylation regulators. Immune cell infiltration was performed on the m5c methylation subtypes. Differentially expressed genes (DEGs) between m5c methylation subtypes were screened, and the DEGs were analysed by Gene Ontology (GO) Kyoto Encyclopedia of Genes and Genomes (KEGG). Finally, we verified the expression of several m5C regulators and related pathways using a COPD cell model. RESULTS Seven m5c methylation regulators were differentially expressed. The random forest model based on the above genes was the most accurate for predicting the occurrence of COPD. A nomogram model based on the above genes could also accurately predict the prevalence of COPD, and the implementation of these models could benefit COPD patients. The consistent cluster analysis divided the COPD patients into two subtypes (Cluster A and Cluster B). The main component analysis algorithm determined the m5c methylation subtypes and found that patients in Cluster A had a higher m5c score than those in Cluster B. GO analysis of the DEGs between the m5c methylation COPD patient subtypes revealed that DEGS were mainly enriched in leukocyte-mediated immunity and regulation of T-cell activation. KEGG analysis revealed that DEGS were mainly enriched in Th1 and Th2 cell differentiation, neutrophil extracellular trap formation, and the NF-κB signalling pathway. Immunocyte correlation analysis revealed that Cluster B was associated with neutrophil- and macrophage-mediated immunity, while Cluster A was associated with CD4 + T-cell- and CD8 + T-cell-mediated immunity. Cell experiments have also verified some of the above research results. CONCLUSION The diagnosis and subtype classification of COPD patients based on m5c regulators may provide a new strategy for the diagnosis and treatment of COPD.
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Affiliation(s)
- Jianjun Wu
- Respiratory Department, The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China.
| | - Xiaoning Li
- Respiratory Department, The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Deyu Kong
- Respiratory Department, The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xudong Zheng
- Respiratory Department, The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Weisha Du
- Respiratory Department, The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yi Zhang
- Respiratory Department, The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yang Jiao
- Respiratory Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing 100078, China.
| | - Xin Li
- Glaucoma, Eye Hospital China academy of Chinese Medical Sciences, Beijing 100040, China.
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16
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YE XING, TUO ZHOUTING, CHEN KAI, WU RUICHENG, WANG JIE, YU QINGXIN, YE LUXIA, MIYAMOTO AKIRA, YOO KOOHAN, ZHANG CHI, WEI WURAN, LI DENGXIONG, FENG DECHAO. Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF). Oncol Res 2024; 32:503-515. [PMID: 38361753 PMCID: PMC10865740 DOI: 10.32604/or.2024.045050] [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: 08/16/2023] [Accepted: 12/01/2023] [Indexed: 02/17/2024] Open
Abstract
The increasing interest in RNA modifications has significantly advanced epigenomic and epitranscriptomic technologies. This study focuses on the immuno-oncological impact of ALYREF in human cancer through a pan-cancer analysis, enhancing understanding of this gene's role in cancer. We observed differential ALYREF expression between tumor and normal samples, correlating strongly with prognosis in various cancers, particularly kidney renal papillary cell carcinoma (KIRP) and liver hepatocellular carcinoma (LIHC). ALYREF showed a negative correlation with most tumor-infiltrating cells in lung squamous cell carcinoma (LUSC) and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), while positive correlations were noted in LIHC, kidney chromophobe (KICH), mesothelioma (MESO), KIRP, pheochromocytoma and paraganglioma (PARD), and glioma (GBMLGG). Additionally, ALYREF expression was closely associated with tumor heterogeneity, stemness indices, and a high mutation rate in TP53 across these cancers. In conclusion, ALYREF may serve as an oncogenic biomarker in numerous cancers, meriting further research attention.
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Affiliation(s)
- XING YE
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - ZHOUTING TUO
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - KAI CHEN
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - RUICHENG WU
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - JIE WANG
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - QINGXIN YU
- Department of Pathology, Ningbo Diagnostic Pathology Center, Ningbo, 315021, China
| | - LUXIA YE
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - AKIRA MIYAMOTO
- Department of Rehabilitation, West Kyushu University, Kanzaki-shi, 842-8585, Japan
| | - KOO HAN YOO
- Department of Urology, Kyung Hee University, Seoul, 446 701, South Korea
| | - CHI ZHANG
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - WURAN WEI
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - DENGXIONG LI
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - DECHAO FENG
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
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17
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Amalric A, Attina A, Bastide A, Buffard M, Mateus S, Planque C, Rivals E, Hirtz C, David A. Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation. Anal Chem 2024; 96:1825-1833. [PMID: 38275837 PMCID: PMC10851184 DOI: 10.1021/acs.analchem.3c02635] [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: 06/16/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024]
Abstract
Cancer onset and progression are known to be regulated by genetic and epigenetic events, including RNA modifications (a.k.a. epitranscriptomics). So far, more than 150 chemical modifications have been described in all RNA subtypes, including messenger, ribosomal, and transfer RNAs. RNA modifications and their regulators are known to be implicated in all steps of post-transcriptional regulation. The dysregulation of this complex yet delicate balance can contribute to disease evolution, particularly in the context of carcinogenesis, where cells are subjected to various stresses. We sought to discover RNA modifications involved in cancer cell adaptation to inhospitable environments, a peculiar feature of cancer stem cells (CSCs). We were particularly interested in the RNA marks that help the adaptation of cancer cells to suspension culture, which is often used as a surrogate to evaluate the tumorigenic potential. For this purpose, we designed an experimental pipeline consisting of four steps: (1) cell culture in different growth conditions to favor CSC survival; (2) simultaneous RNA subtype (mRNA, rRNA, tRNA) enrichment and RNA hydrolysis; (3) the multiplex analysis of nucleosides by LC-MS/MS followed by statistical/bioinformatic analysis; and (4) the functional validation of identified RNA marks. This study demonstrates that the RNA modification landscape evolves along with the cancer cell phenotype under growth constraints. Remarkably, we discovered a short epitranscriptomic signature, conserved across colorectal cancer cell lines and associated with enrichment in CSCs. Functional tests confirmed the importance of selected marks in the process of adaptation to suspension culture, confirming the validity of our approach and opening up interesting prospects in the field.
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Affiliation(s)
- Amandine Amalric
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
| | - Aurore Attina
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
| | - Amandine Bastide
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Marion Buffard
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
- LIRMM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Stéphanie Mateus
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Chris Planque
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Eric Rivals
- LIRMM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Christophe Hirtz
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
| | - Alexandre David
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
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18
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Chen SJ, Zhang J, Zhou T, Rao SS, Li Q, Xiao LY, Wei ST, Zhang HF. Epigenetically upregulated NSUN2 confers ferroptosis resistance in endometrial cancer via m 5C modification of SLC7A11 mRNA. Redox Biol 2024; 69:102975. [PMID: 38042059 PMCID: PMC10711489 DOI: 10.1016/j.redox.2023.102975] [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: 10/22/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/04/2023] Open
Abstract
Endometrial cancer (EC) is a prevalent gynecological malignancy worldwide, and 5-methylcytosine (m5C) modification of mRNA is a crucial epigenetic modification associated with the development and occurrence of several cancers. However, the precise function of m5C modification in EC remains elusive. This study aimed to investigate the expression and clinical significance of the primary m5C modification writer, NSUN2, in EC. Our findings indicated that NSUN2 exhibited a substantial up-regulation in EC as a result of an epigenetic augmentation in H3K4me3 levels within the promoter region, which was triggered by the down-regulation of KDM5A. Moreover, gain- and loss-of-function experiments revealed the role of NSUN2 in enhancing m5C modification of mRNA, thereby promoting EC cell proliferation. RNA bisulfite sequencing and transcriptomic sequencing were employed to elucidate the involvement of NSUN2 in the regulation of ferroptosis. Subsequent in vitro experiments confirmed that the knockdown of NSUN2 significantly up-regulated the levels of lipid peroxides and lipid ROS in EC cells, thereby augmenting the susceptibility of EC to ferroptosis. Mechanistically, NSUN2 stimulated the m5C modification of SLC7A11 mRNA, and the m5C reader YBX1 exhibited direct recognition and binding to the m5C sites on SLC7A11 mRNA via its internal cold shock domain (CSD), leading to an increase in SLC7A11 mRNA stability and elevated levels of SLC7A11. Additionally, rescue experiments showed that NSUN2 functioned as a suppressor of ferroptosis, which was dependent on SLC7A11. Overall, targeting the NSUN2/SLC7A11 axis inhibited tumor growth by increasing lipid peroxidation and ferroptosis of EC cells both in vitro and in vivo. Therefore, our study provides new insight into the role of NSUN2, suggesting that NSUN2 may serve as a prognostic biomarker and therapeutic target in patients with EC.
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Affiliation(s)
- Shuai-Jun Chen
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China; Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ting Zhou
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shan-Shan Rao
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Qian Li
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ling-Yan Xiao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Si-Tian Wei
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Hong-Feng Zhang
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China.
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Wei H, Xu Y, Lin L, Li Y, Zhu X. A review on the role of RNA methylation in aging-related diseases. Int J Biol Macromol 2024; 254:127769. [PMID: 38287578 DOI: 10.1016/j.ijbiomac.2023.127769] [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: 09/18/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Senescence is the underlying mechanism of organism aging and is robustly regulated at the post-transcriptional level. This regulation involves the chemical modifications, of which the RNA methylation is the most common. Recently, a rapidly growing number of studies have demonstrated that methylation is relevant to aging and aging-associated diseases. Owing to the rapid development of detection methods, the understanding on RNA methylation has gone deeper. In this review, we summarize the current understanding on the influence of RNA modification on cellular senescence, with a focus on mRNA methylation in aging-related diseases, and discuss the emerging potential of RNA modification in diagnosis and therapy.
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Affiliation(s)
- Hong Wei
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Department of Neurology, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuhao Xu
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Li Lin
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuefeng Li
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China.
| | - Xiaolan Zhu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China.
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20
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Gionco JT, Bernstein AI. Emerging Role of Environmental Epitranscriptomics and RNA Modifications in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2024; 14:643-656. [PMID: 38578904 PMCID: PMC11191529 DOI: 10.3233/jpd-230457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/10/2024] [Indexed: 04/07/2024]
Abstract
Environmental risk factors and gene-environment interactions play a critical role in Parkinson's disease (PD). However, the relatively large contribution of environmental risk factors in the overwhelming majority of PD cases has been widely neglected in the field. A "PD prevention agenda" proposed in this journal laid out a set of research priorities focused on preventing PD through modification of environmental risk factors. This agenda includes a call for preclinical studies to employ new high-throughput methods for analyzing transcriptomics and epigenomics to provide a deeper understanding of the effects of exposures linked to PD. Here, we focus on epitranscriptomics as a novel area of research with the potential to add to our understanding of the interplay between genes and environmental exposures in PD. Both epigenetics and epitranscriptomics have been recognized as potential mediators of the complex relationship between genes, environment, and disease. Multiple studies have identified epigenetic alterations, such as DNA methylation, associated with PD and PD-related exposures in human studies and preclinical models. In addition, recent technological advancements have made it possible to study epitranscriptomic RNA modifications, such as RNA N6-methyladenosine (m6A), and a handful of recent studies have begun to explore epitranscriptomics in PD-relevant exposure models. Continued exploration of epitranscriptomic mechanisms in environmentally relevant PD models offers the opportunity to identify biomarkers, pre-degenerative changes that precede symptom onset, and potential mitigation strategies for disease prevention and treatment.
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Affiliation(s)
- John T. Gionco
- Graduate Program in Cell and Developmental Biology, Rutgers University, Piscataway, NJ, USA
| | - Alison I. Bernstein
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NJ, USA
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA
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21
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Yang S, Zhou D, Zhang C, Xiang J, Xi X. Function of m 5C RNA methyltransferase NOP2 in high-grade serous ovarian cancer. Cancer Biol Ther 2023; 24:2263921. [PMID: 37800580 PMCID: PMC10561575 DOI: 10.1080/15384047.2023.2263921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023] Open
Abstract
RNA methyltransferase nucleolar protein p120 (NOP2), commonly referred to as NOP2/Sun RNA methyltransferase family member 1 (NSUN1), is involved in cell proliferation and is highly expressed in various cancers. However, its role in high-grade serous ovarian cancer (HGSOC) remains unclear. Our study investigated the expression of NOP2 in HGSOC tissues and normal fimbria tissues, and found that NOP2 was significantly upregulated in HGSOC tissues. Our experiments showed that NOP2 overexpression promoted cell proliferation in vivo and in vitro and increased the migration and invasion ability of HGSOC cells in vitro. Furthermore, we identified Rap guanine nucleotide exchange factor 4 (RAPGEF4) as a potential downstream target of NOP2 in HGSOC. Finally, our findings suggest that the regulation of NOP2 and RAPGEF4 may depend on m5C methylation levels.
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Affiliation(s)
- Shimin Yang
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongmei Zhou
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunxiao Zhang
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiangdong Xiang
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaowei Xi
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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22
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Chen Y, Jiang Z, Yang Y, Zhang C, Liu H, Wan J. The functions and mechanisms of post-translational modification in protein regulators of RNA methylation: Current status and future perspectives. Int J Biol Macromol 2023; 253:126773. [PMID: 37690652 DOI: 10.1016/j.ijbiomac.2023.126773] [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: 06/10/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
RNA methylation, an epigenetic modification that does not alter gene sequence, may be important to diverse biological processes. Protein regulators of RNA methylation include "writers," "erasers," and "readers," which respectively deposit, remove, and recognize methylated RNA. RNA methylation, particularly N6-methyladenosine (m6A), 5-methylcytosine (m5C), N3-methylcytosine (m3C), N1-methyladenosine (m1A) and N7-methylguanosine (m7G), has been suggested as disease therapeutic targets. Despite advances in the structure and pharmacology of RNA methylation regulators that have improved drug discovery, regulating these proteins by various post-translational modifications (PTMs) has received little attention. PTM modifies protein structure and function, affecting all aspects of normal biology and pathogenesis, including immunology, cell differentiation, DNA damage repair, and tumors. It is becoming evident that RNA methylation regulators are also regulated by diverse PTMs. PTM of RNA methylation regulators induces their covalent linkage to new functional groups, hence modifying their activity and function. Mass spectrometry has identified many PTMs on protein regulators of RNA methylation. In this review, we describe the functions and PTM of protein regulators of RNA methylation and summarize the recent advances in the regulatory mode of human disease and its underlying mechanisms.
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Affiliation(s)
- Youming Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zuli Jiang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ying Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chenxing Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongyang Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Junhu Wan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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23
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Liu HT, Rau CS, Liu YW, Hsieh TM, Huang CY, Chien PC, Lin HP, Wu CJ, Chuang PC, Hsieh CH. Deciphering the Divergent Gene Expression Landscapes of m6A/m5C/m1A Methylation Regulators in Hepatocellular Carcinoma Through Single-Cell and Bulk RNA Transcriptomic Analysis. J Hepatocell Carcinoma 2023; 10:2383-2395. [PMID: 38164510 PMCID: PMC10758181 DOI: 10.2147/jhc.s448047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction RNA modifications mediated by the m6A, m1A, and m5C regulatory genes are crucial for the progression of malignancy. This study aimed to explore the expression of regulator genes for m6A/m5C/m1A methylation at the single-cell level and to validate their expression in cancerous and adjacent para-cancerous liver tissues of adult patients with HCC who underwent tumor resection. Methods The bulk sequencing from The Cancer Genome Atlas (TCGA) database and the single-cell RNA sequencing (scRNA-seq) data obtained from the Gene Expression Omnibus (GEO) database were used to identify the dysregulated m6A/m5C/m1A genes for hepatocellular carcinoma (HCC). A real-time polymerase chain reaction (real-time PCR) was used to measure the expression of dysregulated m6A/m5C/m1A genes in collected human HCC tissues and compared with adjacent para-cancerous liver tissues. Immune cell infiltration with these significantly expressed methylation-related genes was evaluated using Timer2.0. Results A discrepancy in m6A/m5C/m1A gene expression was observed between bulk sequencing and scRNA-seq. The clustered heatmap of the scRNA-seq-identified dysregulated m6A/m5C/m1A genes in TCGA cohort revealed heterogeneous expression of these methylation regulators within the cancer, whereas their expression in the adjacent liver tissues was more homogeneous. The real-time PCR validated the significant overexpression of DNMT1, NSUN5, TRMT6, IGF2BP1, and IGFBP3, which were identified using scRNA-seq, and IGFBP2, which was identified using bulk sequencing. These dysregulated methylation genes are mainly correlated with the infiltration of natural killer cells. Discussion This study suggests that cellular diversity inside tumors contributes to the discrepancy in the expression of methylation regulator genes between traditional bulk sequencing and scRNA-seq. This study identified five regulatory genes that will be the focus of further studies regarding the function of m6A/m5C/m1A in HCC.
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Affiliation(s)
- Hang-Tsung Liu
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Cheng-Shyuan Rau
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Yueh-Wei Liu
- Department of General Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Ting-Min Hsieh
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Chun-Ying Huang
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Peng-Chen Chien
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Hui-Ping Lin
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Chia-Jung Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Pei-Chin Chuang
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, 83301, Taiwan
| | - Ching-Hua Hsieh
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
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24
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Zhou X, Zhu H, Luo C, Yan Z, Zheng G, Zou X, Zou J, Zhang G. The role of RNA modification in urological cancers: mechanisms and clinical potential. Discov Oncol 2023; 14:235. [PMID: 38117350 PMCID: PMC10733275 DOI: 10.1007/s12672-023-00843-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
RNA modification is a post-transcriptional level of regulation that is widely distributed in all types of RNAs, including mRNA, tRNA, rRNA, miRNA, and lncRNA, where N6-methyladenine (m6A) is the most abundant mRNA methylation modification. Significant evidence has depicted that m6A modifications are closely related to human diseases, especially cancer, and play pivotal roles in RNA transcription, splicing, stabilization, and translation processes. The most common urological cancers include prostate, bladder, kidney, and testicular cancers, accounting for a certain proportion of human cancers, with an ever-increasing incidence and mortality. The recurrence, systemic metastasis, poor prognosis, and drug resistance of urologic tumors have prompted the identification of new therapeutic targets and mechanisms. Research on m6A modifications may provide new solutions to the current puzzles. In this review, we provide a comprehensive overview of the key roles played by RNA modifications, especially m6A modifications, in urologic cancers, as well as recent research advances in diagnostics and molecularly targeted therapies.
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Affiliation(s)
- Xuming Zhou
- First Clinical College, Gannan Medical University, Ganzhou, 341000, China
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Hezhen Zhu
- First Clinical College, Gannan Medical University, Ganzhou, 341000, China
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Cong Luo
- First Clinical College, Gannan Medical University, Ganzhou, 341000, China
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Zhaojie Yan
- First Clinical College, Gannan Medical University, Ganzhou, 341000, China
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Guansong Zheng
- First Clinical College, Gannan Medical University, Ganzhou, 341000, China
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Xiaofeng Zou
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
- Institute of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
- Jiangxi Engineering Technology Research Center of Calculi Prevention, Ganzhou, 341000, China
| | - Junrong Zou
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
- Institute of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
- Jiangxi Engineering Technology Research Center of Calculi Prevention, Ganzhou, 341000, China
| | - Guoxi Zhang
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China.
- Institute of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China.
- Jiangxi Engineering Technology Research Center of Calculi Prevention, Ganzhou, 341000, China.
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25
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Zheng L, Duan Y, Li M, Wei J, Xue C, Chen S, Wei Q, Tang F, Xiong W, Zhou M, Deng H. Deciphering the vital roles and mechanism of m5C modification on RNA in cancers. Am J Cancer Res 2023; 13:6125-6146. [PMID: 38187052 PMCID: PMC10767349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
5-methylcytosine (m5C modification) plays an essential role in tumors, which affects different types of RNA, the expression of downstream target genes, and downstream pathways, thus participating in the tumor process. However, the effect of m5C modification on RNA in tumors and the exact mechanism have not been systematically reviewed. Therefore, we reviewed the status and sites of m5C modification, as well as the expression pattern and biological functions of m5C regulators in tumors, and further summarized the effects and regulation mechanism of m5C modification on messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA) and other RNA in tumors. Finally, we summed up the interaction network, potential application, and value in clinical diagnosis and treatment of tumors. Taken together, this review benefits revealing the mechanism of m5C modification in tumor progression and provides new strategies for tumor diagnosis and treatment.
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Affiliation(s)
- Lemei Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Yumei Duan
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Shipeng Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Qingqing Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Faqing Tang
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Hongyu Deng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
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Xing C, Zhu S, Yan W, zhu H, Huang Z, Zhao Y, Guo W, Zhang H, Yin L, Ruan X, Deng Z, Wang P, Cheng Z, Wang Z, Peng H. Identification and validation of 5-methylcytosine-associated genes in diffuse large B-cell lymphoma. Heliyon 2023; 9:e22209. [PMID: 38045198 PMCID: PMC10689887 DOI: 10.1016/j.heliyon.2023.e22209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
5-methylcytosine modifications play a significant role in carcinogenesis; however, studies exploring 5-methylcytosine-related genes in diffuse large B-cell lymphoma patients are lacking. In this study, we aimed to understand the potential role and clinical prognostic impact of 5-methylcytosine regulators in diffuse large B-cell lymphoma and identify a prognostic biomarker based on 5-methylcytosine-associated genes. Gene expression profiles and corresponding clinical information of diffuse large B-cell lymphoma patients and normal controls were obtained from The Cancer Genome Atlas, Gene Expression Omnibus, and Genotype-Tissue Expression databases. Diffuse large B-cell lymphoma was divided into three clusters according to the 5-methylcytosine regulators, and differentially expressed genes were screened among the three clusters. Univariate Cox and Lasso-Cox regression analyses were used to screen prognostic genes and construct a prognostic risk model. Kaplan-Meier curve analysis, univariate and multivariate Cox regression analyses, and time-dependent receiver operator characteristic curve analysis were used to evaluate prognostic factors. GSVA was used to enrich potential pathways associated with 5-methylcytosine modification patterns. SsGSEA and CIBERSORT were used to assess immune cell infiltration. Six 5-methylcytosine-related genes (TUBB4A, CD3E, ZNF681, HAP1, IL22RA2, and POSTN) were used to construct a prognostic risk model, which was proved to have a good predictive effect. In addition, univariate and multivariate Cox regression risk scores were independent prognostic factors for diffuse large B-cell lymphoma. Further analysis showed that the 5-methylcytosine risk score was significantly correlated with immune cell infiltration and immune checkpoint of diffuse large B-cell lymphoma. Our study reveals for the first time a potential role for 5-methylcytosine modifications in diffuse large B-cell lymphoma, provides novel insights for future studies on diffuse large B-cell lymphoma, and offers potential prognostic biomarkers and therapeutic targets for patients with diffuse large B-cell lymphoma.
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Affiliation(s)
- Cheng Xing
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Shicong Zhu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenzhe Yan
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Hongkai zhu
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Zineng Huang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Yan Zhao
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Wancheng Guo
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Huifang Zhang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Le Yin
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Xueqin Ruan
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Zeyue Deng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Peilong Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Zhao Cheng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Zhihua Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, Changsha, Hunan, China
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Li P, Wang W, Zhou R, Ding Y, Li X. The m 5 C methyltransferase NSUN2 promotes codon-dependent oncogenic translation by stabilising tRNA in anaplastic thyroid cancer. Clin Transl Med 2023; 13:e1466. [PMID: 37983928 PMCID: PMC10659772 DOI: 10.1002/ctm2.1466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Translation dysregulation plays a crucial role in tumourigenesis and cancer progression. Oncogenic translation relies on the stability and availability of tRNAs for protein synthesis, making them potential targets for cancer therapy. METHODS This study performed immunohistochemistry analysis to assess NSUN2 levels in thyroid cancer. Furthermore, to elucidate the impact of NSUN2 on anaplastic thyroid cancer (ATC) malignancy, phenotypic assays were conducted. Drug inhibition and time-dependent plots were employed to analyse drug resistance. Liquid chromatography-mass spectrometry and bisulphite sequencing were used to investigate the m5 C methylation of tRNA at both global and single-base levels. Puromycin intake and high-frequency codon reporter assays verified the protein translation level. By combining mRNA and ribosome profiling, a series of downstream proteins and codon usage bias were identified. The acquired data were further validated by tRNA sequencing. RESULTS This study observed that the tRNA m5 C methyltransferase NSUN2 was up-regulated in ATC and is associated with dedifferentiation. Furthermore, NSUN2 knockdown repressed ATC formation, proliferation, invasion and migration both in vivo and in vitro. Moreover, NSUN2 repression enhanced the sensitivity of ATC to genotoxic drugs. Mechanically, NSUN2 catalyses tRNA structure-related m5 C modification, stabilising tRNA that maintains homeostasis and rapidly transports amino acids, particularly leucine. This stable tRNA has a substantially increased efficiency necessary to support a pro-cancer translation program including c-Myc, BCL2, RAB31, JUNB and TRAF2. Additionally, the NSUN2-mediated variations in m5C levels and different tRNA Leu iso-decoder families, partially contribute to a codon-dependent translation bias. Surprisingly, targeting NSUN2 disrupted the c-Myc to NSUN2 cycle in ATC. CONCLUSIONS This research revealed that a pro-tumour m5C methyltransferase, dynamic tRNA stability regulation and downstream oncogenes, c-Myc, elicits a codon-dependent oncogenic translation network that enhances ATC growth and formation. Furthermore, it provides new opportunities for targeting translation reprogramming in cancer cells.
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Affiliation(s)
- Peng Li
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunan ProvinceChina
- Department of Hepatobiliary SurgerySichuan Provincial People's HospitalSchool of MedicineUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Wenlong Wang
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunan ProvinceChina
| | - Ruixin Zhou
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Ying Ding
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xinying Li
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunan ProvinceChina
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28
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Lewinska A, Adamczyk-Grochala J, Wnuk M. TRDMT1-mediated RNA C-5 methylation as a novel target in anticancer therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188964. [PMID: 37625528 DOI: 10.1016/j.bbcan.2023.188964] [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: 06/23/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023]
Abstract
Affected landscape of RNA modifications is frequently observed in different cancer cells that can be associated with the development of cancer cell phenotypic traits such as sustained proliferation, migration and invasion, apoptosis resistance and metabolic reprograming. DNMT2/TRDMT1 5-methylcytosine methyltransferase, initially classified as DNA methyltransferase, can methylate both tRNA and mRNA promoting tRNA stability and proper protein synthesis, and orchestrating DNA damage response (DDR) and DNA stability, respectively. TRDMT1 is associated with cancer progression as its levels can be elevated and its mutations can be observed in a number of cancer types. TRDMT1 gene knockout (KO) can sensitize cancer cells of different origin to radiotherapy and chemotherapy. In the present review paper, based on literature data, the physiological and pathophysiological roles of TRDMT1 in different biological systems are described with the emphasis on human normal and cancer cells. Potential TRDMT1 substrates, inhibitors and regulatory mechanisms of catalytic activity and cellular localization are also presented and evaluated. TRDMT1 as a novel promising target in anticancer therapy is proposed and discussed.
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Affiliation(s)
- Anna Lewinska
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
| | - Jagoda Adamczyk-Grochala
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Maciej Wnuk
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
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29
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Papakonstantinou E, Pappa I, Androutsopoulos G, Adonakis G, Maroulis I, Tzelepi V. Comprehensive Analysis of DNA Methyltransferases Expression in Primary and Relapsed Ovarian Carcinoma. Cancers (Basel) 2023; 15:4950. [PMID: 37894317 PMCID: PMC10605797 DOI: 10.3390/cancers15204950] [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: 08/14/2023] [Revised: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Despite recent advances in epithelial ovarian carcinoma (EOC) treatment, its recurrence and mortality rates have not improved significantly. DNA hypermethylation has generally been associated with an ominous prognosis and chemotherapy resistance, but the role of DNA methyltransferases (DNMTs) in EOC remains to be investigated. METHODS In the current study, we systematically retrieved gene expression data from patients with EOC and studied the immunohistochemical expression of DNMTs in 108 primary and 26 relapsed tumors. RESULTS Our results showed that the DNMT1, DNMT3A, DNMT3B and DNMT3L RNA levels were higher and the DNMT2 level was lower in tumors compared to non-neoplastic tissue, and DNMT3A and DNMT2 expression decreased from Stage-II to Stage-IV carcinomas. The proteomic data also suggested that the DNMT1 and DNMT3A levels were increased in the tumors. Similarly, the DNMT1, DNMT3A and DNMT3L protein levels were overexpressed and DNMT2 expression was reduced in high-grade carcinomas compared to non-neoplastic tissue and low-grade tumors. Moreover, DNMT1 and DNMT3L were increased in relapsed tumors compared to their primaries. The DNMT3A, DNMT1 and DNMT3B mRNA levels were correlated with overall survival. CONCLUSIONS Our study demonstrates that DNMT1 and DNMT3L are upregulated in primary high-grade EOC and further increase in relapses, whereas DNMT3A is upregulated only in the earlier stages of cancer progression. DNMT2 downregulation highlights the presumed tumor-suppressor activity of this gene in ovarian carcinoma.
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Affiliation(s)
- Efthymia Papakonstantinou
- Department of Obstetrics and Gynecology, School of Medicine, University of Patras, 26504 Patras, Greece; (E.P.); (G.A.)
| | - Ioanna Pappa
- Multidimensional Data Analysis and Knowledge Management Laboratory, Computer Engineering and Informatics Department, School of Engineering, University of Patras, 26504 Patras, Greece;
| | - Georgios Androutsopoulos
- Gynecological Oncology Unit, Department of Obstetrics and Gynecology, Medical School, University of Patras, 26504 Patras, Greece;
| | - Georgios Adonakis
- Department of Obstetrics and Gynecology, School of Medicine, University of Patras, 26504 Patras, Greece; (E.P.); (G.A.)
| | - Ioannis Maroulis
- Department of General Surgery, School of Medicine, University of Patras, 26504 Patras, Greece;
| | - Vasiliki Tzelepi
- Department of Pathology, School of Medicine, University of Patras, 26504 Patras, Greece
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30
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Ma Y, Sun Y, Zhao X, Li J, Fu X, Gong T, Zhang X. Identification of m 5C-related lncRNAs signature to predict prognosis and therapeutic responses in esophageal squamous cell carcinoma patients. Sci Rep 2023; 13:14499. [PMID: 37666951 PMCID: PMC10477299 DOI: 10.1038/s41598-023-41495-6] [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: 09/28/2022] [Accepted: 08/28/2023] [Indexed: 09/06/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) has a dismal prognosis because of atypical early symptoms and heterogeneous therapeutic responses. 5-methylcytosine (m5C) modification plays an important role in the onset and development of many tumors and is widespread in long non-coding RNA (lncRNA) transcripts. However, the functions of m5C and lncRNAs in ESCC have not been completely elucidated. Herein, this study aimed to explore the role of m5C-related lncRNAs in ESCC. The RNA-seq transcriptome profiles and clinical information were downloaded from the TCGA-ESCC database. Pearson analysis was used to identify m5C-related lncRNAs. Then we established the m5C-related lncRNAs prognostic signature (m5C-LPS) using univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analysis. Then, the prognostic value of m5C-LPS was evaluated internally and externally using the TCGA-ESCC and GSE53622 databases through multiple methods. We also detected the expression of these lncRNAs in ESCC cell lines and patient tissues. Fluorescence in situ hybridization (FISH) was used to detect the prognostic value of specific lncRNA. In addition, clinical parameters, immune status, genomic variants, oncogenic pathways, enrichment pathways, and therapeutic response features associated with m5C-LPS were explored using bioinformatics methods. We constructed and validated a prognostic signature based on 9 m5C-related lncRNAs (AC002091.2, AC009275.1, CAHM, LINC02057.1, AC0006329.1, AC037459.3, AC064807.1, ATP2B1-AS1, and UBAC2-AS1). The quantitative real-time polymerase chain reaction (qRT-PCR) revealed that most lncRNAs were upregulated in ESCC cell lines and patient tissues. And AC002091.2 was validated to have significant prognostic value in ESCC patients. A composite nomogram was generated to facilitate clinical practice by integrating this signature with the N stage. Besides, patients in the low-risk group were characterized by good clinical outcomes, favorable immune status, and low oncogenic alteration. Function enrichment analysis indicated that the risk score was associated with mRNA splicing, ncRNA processing, and DNA damage repair response. At the same time, we found significant differences in the responses to chemoradiotherapy between the two groups, proving the value of m5C-LPS in treatment decision-making in ESCC. This study established a novel prognostic signature based on 9 m5C-related lncRNAs, which is a promising biomarker for predicting clinical outcomes and therapeutic response in ESCC.
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Affiliation(s)
- Yuan Ma
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Yuchen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xu Zhao
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Jing Li
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xing Fu
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Tuotuo Gong
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China.
| | - Xiaozhi Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China.
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Li C, Xu P, Huang Y, Wang Y, Wu Y, Li H, Peng Y, Wang X, Li G, He J, Miao C. RNA methylations in depression, from pathological mechanism to therapeutic potential. Biochem Pharmacol 2023; 215:115750. [PMID: 37595670 DOI: 10.1016/j.bcp.2023.115750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Depression is caused by a variety of factors such as genetic factors, biological factors, and psychosocial factors, and the pathogenesis is complex. RNA methylations and related downstream signaling pathways influence a variety of biological mechanisms, including cell differentiation, tumorigenesis, sex determination, and stress response. In this work, we searched the PubMed, Web of Science, National Library of Science and Technology (NSTL), and ScienceDirect Online (SDOL) databases to summarize the biological roles of RNA methylations and their impact on the pathological mechanisms of depression. RNA methylations play a key role in the development of many diseases, and current research shows that RNA methylations are also closely linked to depression. RNA methylations in depression mainly involve "writers" (mediating the methylation modification process of RNAs), "erasers" (mediating the demethylation modification process of RNA methylation). Fat Mass and Obesity Associated (FTO) influences the development of depression by increasing body mass index (BMI), decreases the dopamine level, inhibits the adrenoceptor beta 2 (ADRB2)-c-Myc-sirt1 pathway, results in the m6A/m6Am dysregulation in brain, and may be involved in the pathogenesis of depression. The study of RNA methylations in depression has further deepened our understanding of the pathogenesis and development process of depression, provides new perspectives for the study of the pathological mechanism of depression, and provides new targets for the prevention and treatment of this disease.
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Affiliation(s)
- Chen Li
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Pengfei Xu
- Department of Orthopedics, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Yurong Huang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yuting Wang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yajie Wu
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Hui Li
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yanhui Peng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xiao Wang
- Department of Clinical Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China.
| | - Guoying Li
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China.
| | - Juan He
- Department of Gynecology, Anhui Maternal and Child Health Hospital, Hefei, Anhui, China.
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China; Institute of Traditional Chinese Medicine for the Prevention and Treatment of Rheumatology, Anhui University of Chinese Medicine, Hefei, Anhui, China.
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32
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Patrasso EA, Raikundalia S, Arango D. Regulation of the epigenome through RNA modifications. Chromosoma 2023; 132:231-246. [PMID: 37138119 PMCID: PMC10524150 DOI: 10.1007/s00412-023-00794-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023]
Abstract
Chemical modifications of nucleotides expand the complexity and functional properties of genomes and transcriptomes. A handful of modifications in DNA bases are part of the epigenome, wherein DNA methylation regulates chromatin structure, transcription, and co-transcriptional RNA processing. In contrast, more than 150 chemical modifications of RNA constitute the epitranscriptome. Ribonucleoside modifications comprise a diverse repertoire of chemical groups, including methylation, acetylation, deamination, isomerization, and oxidation. Such RNA modifications regulate all steps of RNA metabolism, including folding, processing, stability, transport, translation, and RNA's intermolecular interactions. Initially thought to influence all aspects of the post-transcriptional regulation of gene expression exclusively, recent findings uncovered a crosstalk between the epitranscriptome and the epigenome. In other words, RNA modifications feedback to the epigenome to transcriptionally regulate gene expression. The epitranscriptome achieves this feat by directly or indirectly affecting chromatin structure and nuclear organization. This review highlights how chemical modifications in chromatin-associated RNAs (caRNAs) and messenger RNAs (mRNAs) encoding factors involved in transcription, chromatin structure, histone modifications, and nuclear organization affect gene expression transcriptionally.
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Affiliation(s)
- Emmely A Patrasso
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Medical and Pharmaceutical Biotechnology Program, IMC University of Applied Sciences, Krems, Austria
| | - Sweta Raikundalia
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel Arango
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:25. [PMID: 37612540 PMCID: PMC10447785 DOI: 10.1186/s43556-023-00139-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.
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Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Qian Jing
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yanbo Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
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Huang M, Ming L, Jiang H, Jiang P, Jiang X, Yin H, Hong H. Diagnostic value of aberrant decreased 5-Methylcytosine RNA modification in leukocytes for non-small cell lung cancer. J Cancer 2023; 14:2198-2208. [PMID: 37576401 PMCID: PMC10414042 DOI: 10.7150/jca.85681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Background: Non-small cell lung cancer (NSCLC) was a disease with poor outcomes, partly because there were no high-efficiency non-invasive diagnostic biomarkers. The RNA modification status of 5-Methylcytosine (m5C) has been shown to be a biomarker for various diseases, but its potentiality to be a diagnostic biomarker for NSCLC remained inconclusive. Methods: In this research, we collected peripheral leukocyte samples from 141 patients with NSCLC and 90 normal people as controls to evaluate the extent of m5C RNA modification. Results: We found that the m5C modification levels in leukocytes of NSCLC patients were decreased dramatically, which were compared to the normal controls, and levels of m5C modification decreased progressively with tumor stage. Importantly, m5C modification exhibited superior diagnostic value compared to carcinoembryonic antigen (CEA), squamous cell carcinoma antigen (SCC), cytokeratin 19 fragment (Cyfra21-1), and carbohydrate antigen 125 (CA125), which demonstrated area under the curves (AUCs) of 0.912, 0.773, 0.669, 0.754, and 0.732, respectively. The combination of m5C modification with these serum tumor biomarkers further improved the AUC to 0.960. A nomogram model incorporating m5C modification also provided an effectively diagnostic tool for NSCLC. Conclusion: Collectively, our findings suggested that m5C modification in leukocytes held promise as a prospective biomarker for NSCLC diagnosis.
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Affiliation(s)
- Mao Huang
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, Guangdong, China
| | - Liang Ming
- Department of Clinical Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Hongbo Jiang
- Department of Clinical Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Ping Jiang
- Department of Clinical Medical Laboratory, Guangzhou First' People Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Xi Jiang
- Department of Clinical Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Haofan Yin
- Department of Medical Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Department of Clinical Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Honghai Hong
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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35
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Huang J, Xu Z, Zhou C, Cheng L, Zeng H, Shen Y. 5-Methylcytosine-related lncRNAs: predicting prognosis and identifying hot and cold tumor subtypes in head and neck squamous cell carcinoma. World J Surg Oncol 2023; 21:180. [PMID: 37312123 DOI: 10.1186/s12957-023-03067-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/04/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND 5-Methylcytosine (m5C) methylation is recognized as an mRNA modification that participates in biological progression by regulating related lncRNAs. In this research, we explored the relationship between m5C-related lncRNAs (mrlncRNAs) and head and neck squamous cell carcinoma (HNSCC) to establish a predictive model. METHODS RNA sequencing and related information were obtained from the TCGA database, and patients were divided into two sets to establish and verify the risk model while identifying prognostic mrlncRNAs. Areas under the ROC curves were assessed to evaluate the predictive effectiveness, and a predictive nomogram was constructed for further prediction. Subsequently, the tumor mutation burden (TMB), stemness, functional enrichment analysis, tumor microenvironment, and immunotherapeutic and chemotherapeutic responses were also assessed based on this novel risk model. Moreover, patients were regrouped into subtypes according to the expression of model mrlncRNAs. RESULTS Assessed by the predictive risk model, patients were distinguished into the low-MLRS and high-MLRS groups, showing satisfactory predictive effects with AUCs of 0.673, 0.712, and 0.681 for the ROCs, respectively. Patients in the low-MLRS groups exhibited better survival status, lower mutated frequency, and lower stemness but were more sensitive to immunotherapeutic response, whereas the high-MLRS group appeared to have higher sensitivity to chemotherapy. Subsequently, patients were regrouped into two clusters: cluster 1 displayed immunosuppressive status, but cluster 2 behaved as a hot tumor with a better immunotherapeutic response. CONCLUSIONS Referring to the above results, we established a m5C-related lncRNA model to evaluate the prognosis, TME, TMB, and clinical treatments for HNSCC patients. This novel assessment system is able to precisely predict the patients' prognosis and identify hot and cold tumor subtypes clearly for HNSCC patients, providing ideas for clinical treatment.
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Affiliation(s)
- Juntao Huang
- Department of Otolaryngology, Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Ziqian Xu
- Department of Dermatology, Ningbo First Hospital, Zhejiang University, Zhejiang, China
| | - Chongchang Zhou
- Department of Otolaryngology, Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Lixin Cheng
- Department of Otolaryngology, Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Hong Zeng
- Department of Otolaryngology, Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yi Shen
- Department of Otolaryngology, Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.
- Department of Otolaryngology, Head and Neck Surgery, Ningbo No.2 Hospital, Ningbo, China.
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Muhammad N, Hussain SI, Rehman ZU, Khan SA, Jan S, Khan N, Muzammal M, Abbasi SW, Kakar N, Rehman ZU, Khan MA, Mirza MU, Muhammad N, Khan S, Wasif N. Autosomal recessive variants c.953A>C and c.97-1G>C in NSUN2 causing intellectual disability: a molecular dynamics simulation study of loss-of-function mechanisms. Front Neurol 2023; 14:1168307. [PMID: 37305761 PMCID: PMC10249782 DOI: 10.3389/fneur.2023.1168307] [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: 02/17/2023] [Accepted: 04/28/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Intellectual disability (ID) is a clinically and genetically heterogeneous disorder. It drastically affects the learning capabilities of patients and eventually reduces their IQ level below 70. Methods The current genetic study ascertained two consanguineous Pakistani families suffering from autosomal recessive intellectual developmental disorder-5 (MRT5). We have used exome sequencing followed by Sanger sequencing to identify the disease-causing variants. Results and discussion Genetic analysis using whole exome sequencing in these families identified two novel mutations in the NSUN2 (NM_017755.5). Family-A segregated a novel missense variant c.953A>C; p.Tyr318Ser in exon-9 of the NSUN2. The variant substituted an amino acid Tyr318, highly conserved among different animal species and located in the functional domain of NSUN2 known as "SAM-dependent methyltransferase RsmB/NOP2-type". Whereas in family B, we identified a novel splice site variant c.97-1G>C that affects the splice acceptor site of NSUN2. The identified splice variant (c.97-1G>C) was predicted to result in the skipping of exon-2, which would lead to a frameshift followed by a premature stop codon (p. His86Profs*16). Furthermore, it could result in the termination of translation and synthesis of dysfunctional protein, most likely leading to nonsense-mediated decay. The dynamic consequences of NSUN2 missense variant was further explored together with wildtype through molecular dynamic simulations, which uncovered the disruption of NSUN2 function due to a gain in structural flexibility. The present molecular genetic study further extends the mutational spectrum of NSUN2 to be involved in ID and its genetic heterogeneity in the Pakistani population.
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Affiliation(s)
- Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Syeda Iqra Hussain
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ur Rehman
- Department of General Medicine, Northwest General Hospital & Research Center, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Samin Jan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Niamatullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Muzammal
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Khyber Pakhtunkhwa, Pakistan
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi, Punjab, Pakistan
| | - Naseebullah Kakar
- Department of Biotechnology, Faculty of Life Sciences and Informatics, BUITEMS, Quetta, Pakistan
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Zia Ur Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, D.I.Khan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Naveed Wasif
- Institute of Human Genetics, Ulm University, and Ulm University Medical Center, Ulm, Germany
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
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Wang Y, Wei J, Feng L, Li O, Huang L, Zhou S, Xu Y, An K, Zhang Y, Chen R, He L, Wang Q, Wang H, Du Y, Liu R, Huang C, Zhang X, Yang YG, Kan Q, Tian X. Aberrant m5C hypermethylation mediates intrinsic resistance to gefitinib through NSUN2/YBX1/QSOX1 axis in EGFR-mutant non-small-cell lung cancer. Mol Cancer 2023; 22:81. [PMID: 37161388 PMCID: PMC10169458 DOI: 10.1186/s12943-023-01780-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/21/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND RNA 5-methylcytosine (m5C) modification plays critical roles in the pathogenesis of various tumors. However, the function and molecular mechanism of RNA m5C modification in tumor drug resistance remain unclear. METHODS The correlation between RNA m5C methylation, m5C writer NOP2/Sun RNA methyltransferase family member 2 (NSUN2) and EGFR-TKIs resistance was determined in non-small-cell lung cancer (NSCLC) cell lines and patient samples. The effects of NSUN2 on EGFR-TKIs resistance were investigated by gain- and loss-of-function assays in vitro and in vivo. RNA-sequencing (RNA-seq), RNA bisulfite sequencing (RNA-BisSeq) and m5C methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) were performed to identify the target gene of NSUN2 involved in EGFR-TKIs resistance. Furthermore, the regulatory mechanism of NSUN2 modulating the target gene expression was investigated by functional rescue and puromycin incorporation assays. RESULTS RNA m5C hypermethylation and NSUN2 were significantly correlated with intrinsic resistance to EGFR-TKIs. Overexpression of NSUN2 resulted in gefitinib resistance and tumor recurrence, while genetic inhibition of NSUN2 led to tumor regression and overcame intrinsic resistance to gefitinib in vitro and in vivo. Integrated RNA-seq and m5C-BisSeq analyses identified quiescin sulfhydryl oxidase 1 (QSOX1) as a potential target of aberrant m5C modification. NSUN2 methylated QSOX1 coding sequence region, leading to enhanced QSOX1 translation through m5C reader Y-box binding protein 1 (YBX1). CONCLUSIONS Our study reveals a critical function of aberrant RNA m5C modification via the NSUN2-YBX1-QSOX1 axis in mediating intrinsic resistance to gefitinib in EGFR-mutant NSCLC.
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Affiliation(s)
- Yueqin Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Jingyao Wei
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Luyao Feng
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Ouwen Li
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Lan Huang
- Biotherapy Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Shaoxuan Zhou
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Yingjie Xu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Ke An
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Yu Zhang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Ruiying Chen
- Department of Respiratory Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Lulu He
- Biobank of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Han Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Yue Du
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Ruijuan Liu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Chunmin Huang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
| | - Xiaojian Zhang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China.
| | - Quancheng Kan
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China.
| | - Xin Tian
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China.
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Petri BJ, Klinge CM. m6A readers, writers, erasers, and the m6A epitranscriptome in breast cancer. J Mol Endocrinol 2023; 70:JME-22-0110. [PMID: 36367225 PMCID: PMC9790079 DOI: 10.1530/jme-22-0110] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/11/2022] [Indexed: 11/13/2022]
Abstract
Epitranscriptomic modification of RNA regulates human development, health, and disease. The true diversity of the transcriptome in breast cancer including chemical modification of transcribed RNA (epitranscriptomics) is not well understood due to limitations of technology and bioinformatic analysis. N-6-methyladenosine (m6A) is the most abundant epitranscriptomic modification of mRNA and regulates splicing, stability, translation, and intracellular localization of transcripts depending on m6A association with reader RNA-binding proteins. m6A methylation is catalyzed by the METTL3 complex and removed by specific m6A demethylase ALKBH5, with the role of FTO as an 'eraser' uncertain. In this review, we provide an overview of epitranscriptomics related to mRNA and focus on m6A in mRNA and its detection. We summarize current knowledge on altered levels of writers, readers, and erasers of m6A and their roles in breast cancer and their association with prognosis. We summarize studies identifying m6A peaks and sites in genes in breast cancer cells.
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Affiliation(s)
- Belinda J. Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Carolyn M. Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS)
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Hui L, Ziyue Z, Chao L, Bin Y, Aoyu L, Haijing W. Epigenetic Regulations in Autoimmunity and Cancer: from Basic Science to Translational Medicine. Eur J Immunol 2023; 53:e2048980. [PMID: 36647268 DOI: 10.1002/eji.202048980] [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: 05/28/2021] [Revised: 08/25/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
Epigenetics, as a discipline that aims to explain the differential expression of phenotypes arising from the same gene sequence and the heritability of epigenetic expression, has received much attention in medicine. Epigenetic mechanisms are constantly being discovered, including DNA methylation, histone modifications, noncoding RNAs and m6A. The immune system mainly achieves an immune response through the differentiation and functional expression of immune cells, in which epigenetic modification will have an important impact. Because of immune infiltration in the tumor microenvironment, immunotherapy has become a research hotspot in tumor therapy. Epigenetics plays an important role in autoimmune diseases and cancers through immunology. An increasing number of drugs targeting epigenetic mechanisms, such as DNA methyltransferase inhibitors, histone deacetylase inhibitors, and drug combinations, are being evaluated in clinical trials for the treatment of various cancers (including leukemia and osteosarcoma) and autoimmune diseases (systemic lupus erythematosus, rheumatoid arthritis, systemic sclerosis). This review summarizes the progress of epigenetic regulation for cancers and autoimmune diseases to date, shedding light on potential therapeutic strategies.
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Affiliation(s)
- Li Hui
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Zhao Ziyue
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Liu Chao
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Yu Bin
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Li Aoyu
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Wu Haijing
- Hunan Key Laboratory of Medical Epigenetics, Department of Dermatology, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
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Wang X, Deng D, Yan Y, Cai M, Liu X, Luo A, Liu S, Zhang X, Jiang H, Liu X. Genetic variants in m5C modification core genes are associated with the risk of Chinese pediatric acute lymphoblastic leukemia: A five-center case-control study. Front Oncol 2023; 12:1082525. [PMID: 36698387 PMCID: PMC9868168 DOI: 10.3389/fonc.2022.1082525] [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: 10/28/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
Objective To explore the functions of the polymorphisms in 5-methylcytosine (m5C) modification-related coding genes on the susceptibility of pediatric acute lymphoblastic leukemia (ALL). Methods Case-control study and multinomial logistic regression analysis were performed to construct models to evaluate the susceptibility of pediatric ALL. The relationship between five functional SNPs in m5C modification-coding genes and pediatric ALL risk was analyzed. Genotyping of 808 cases and 1,340 healthy samples from South China was identified using a TaqMan assay; odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the relationship between the five selected SNPs and pediatric ALL susceptibility. Results Among the five analyzed SNPs, NOL1 rs3764909 and NSUN4 rs10252 variants significantly increased the susceptibility of pediatric ALL, while NSUN3 rs7653521, NSUN5 rs1880948, and NSUN6 rs3740102 variants were not associated with the risk of ALL. Stratification analyses demonstrated that NOL1 rs3764909 C>A exhibited a significant association with increased pediatric ALL risk in subgroups of common B ALL, pre-B ALL, T-cell ALL, low and middle risk, other gene fusion types, non-gene fusion, hypodiploid, normal diploid, primitive lymphocytes in marrow < 5% on week 12, and minimal residual disease (MRD) <0.01% on week 12 after induced therapy; NSUN4 rs10252 G>A was related to increased risk of ALL children in subgroups of age ≥ 120 months, normal white blood cell (WBC) number, middle risk, non-gene fusion, MRD ≥ 0.01 on days 15-19, and primitive lymphocytes in marrow < 5% on day 33 after induced therapy. Compared with the reference haplotype CAGTA, children who harbored haplotypes CCGTG and ACATA were remarkably related to increased ALL susceptibility. rs3764909 and rs10252 varieties of alleles were not associated with MRD levels after the selected chemotherapeutics. Conclusions In conclusion, NOL1 rs3764909 and NSUN4 rs10252 variants were enhanced by pediatric ALL risk and were suggested to be potential biomarkers for pediatric ALL.
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Affiliation(s)
- Xueliang Wang
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Decheng Deng
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Yaping Yan
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Mansi Cai
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Xiaodan Liu
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Ailing Luo
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Shanshan Liu
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Xiaohong Zhang
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Hua Jiang
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Xiaoping Liu
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
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Zhang P, Zhang T, Chen D, Gong L, Sun M. Prognosis and Novel Drug Targets for Key lncRNAs of Epigenetic Modification in Colorectal Cancer. Mediators Inflamm 2023; 2023:6632205. [PMID: 37091904 PMCID: PMC10116225 DOI: 10.1155/2023/6632205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/20/2022] [Accepted: 03/20/2023] [Indexed: 04/25/2023] Open
Abstract
Background Colorectal cancer (CRC) has been the 3rd most commonly malignant tumor of the gastrointestinal tract in the world. 5-Methylcytosine (m5C) and long noncoding RNAs (lncRNAs) have an essential role in predicting the prognosis and immune response for CRC patients. Therefore, we built a m5C-related lncRNA (m5CRlncRNA) model to investigate the prognosis and treatment methods for CRC patients. Methods Firstly, we secured the transcriptome and clinical data for CRC from The Cancer Genome Atlas (TCGA). Then, m5CRlncRNAs were recognized by coexpression analysis. Then, univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were utilized to build m5C-related prognostic characteristics. Besides, Kaplan-Meier analysis, ROC, PCA, C-index, enrichment analysis, and nomogram were performed to investigate the model. Additionally, immunotherapy responses and antitumor medicines were explored for CRC patients. Results A total of 8 m5C-related lncRNAs (AC093157.1, LINC00513, AC025171.4, AC090948.2, ZEB1-AS1, AC109449.1, AC009041.3, and LINC02516) were adopted to construct a risk model to investigate survival and prognosis for CRC patients. CRC samples were separated into low- and high-risk groups, with the latter having a worse prognosis. The m5C-related lncRNA model helps us to better distinguish immunotherapy responses and IC50 of antitumor medicines in different groups of CRC patients. Conclusion The research may give new perspectives on tailored therapy approaches as well as novel theories for forecasting the prognosis of CRC patients.
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Affiliation(s)
- Peng Zhang
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Tingting Zhang
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Denggang Chen
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Li Gong
- Department of Endocrinology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Min Sun
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
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Cui W, Zhao D, Jiang J, Tang F, Zhang C, Duan C. tRNA Modifications and Modifying Enzymes in Disease, the Potential Therapeutic Targets. Int J Biol Sci 2023; 19:1146-1162. [PMID: 36923941 PMCID: PMC10008702 DOI: 10.7150/ijbs.80233] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/26/2023] [Indexed: 03/14/2023] Open
Abstract
tRNA is one of the most conserved and abundant RNA species, which plays a key role during protein translation. tRNA molecules are post-transcriptionally modified by tRNA modifying enzymes. Since high-throughput sequencing technology has developed rapidly, tRNA modification types have been discovered in many research fields. In tRNA, numerous types of tRNA modifications and modifying enzymes have been implicated in biological functions and human diseases. In our review, we talk about the relevant biological functions of tRNA modifications, including tRNA stability, protein translation, cell cycle, oxidative stress, and immunity. We also explore how tRNA modifications contribute to the progression of human diseases. Based on previous studies, we discuss some emerging techniques for assessing tRNA modifications to aid in discovering different types of tRNA modifications.
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Affiliation(s)
- Weifang Cui
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Deze Zhao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Junjie Jiang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Faqing Tang
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, PR China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China.,National Clinical Research Center for Geriatric Disorders, Changsha, 410008, Hunan, PR China.,Institute of Medical Sciences, Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, PR China
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Wang X, Guo Z, Yan F. RNA Epigenetics in Chronic Lung Diseases. Genes (Basel) 2022; 13:genes13122381. [PMID: 36553648 PMCID: PMC9777603 DOI: 10.3390/genes13122381] [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: 10/07/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Chronic lung diseases are highly prevalent worldwide and cause significant mortality. Lung cancer is the end stage of many chronic lung diseases. RNA epigenetics can dynamically modulate gene expression and decide cell fate. Recently, studies have confirmed that RNA epigenetics plays a crucial role in the developing of chronic lung diseases. Further exploration of the underlying mechanisms of RNA epigenetics in chronic lung diseases, including lung cancer, may lead to a better understanding of the diseases and promote the development of new biomarkers and therapeutic strategies. This article reviews basic information on RNA modifications, including N6 methylation of adenosine (m6A), N1 methylation of adenosine (m1A), N7-methylguanosine (m7G), 5-methylcytosine (m5C), 2'O-methylation (2'-O-Me or Nm), pseudouridine (5-ribosyl uracil or Ψ), and adenosine to inosine RNA editing (A-to-I editing). We then show how they relate to different types of lung disease. This paper hopes to summarize the mechanisms of RNA modification in chronic lung disease and finds a new way to develop early diagnosis and treatment of chronic lung disease.
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Affiliation(s)
- Xiaorui Wang
- Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Zhihou Guo
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Furong Yan
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
- Correspondence:
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Lu Q, Liu L, Wang S, Zhang Q, Li L. Comprehensive analysis of m5C-Related lncRNAs in the prognosis and immune landscape of hepatocellular carcinoma. Front Genet 2022; 13:990594. [PMID: 36339006 PMCID: PMC9630339 DOI: 10.3389/fgene.2022.990594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/03/2022] [Indexed: 02/13/2024] Open
Abstract
5-Methyladenosine (m5C) is a type of epigenetic modification involved in the progression of various cancers. To investigate the role of m5C-related long non-coding RNAs (lncRNAs) in the prognosis and immune cell infiltration in hepatocellular carcinoma (HCC), we obtained patients' clinical information and transcriptome data of HCC from the Cancer Genome Atlas (TCGA) database. We applied Pearson correlation analysis to construct an m5C-related lncRNA-messenger RNA (mRNA) co-expression network. Univariate Cox analysis, least absolute shrinkage and selection operator (LASSO), and multivariate Cox analysis were employed to establish an m5C-related lncRNA prognostic risk model. We then verified the model using Kaplan-Meier analysis, principal component analysis, as well as univariate and multivariate Cox analyses. The expression of m5C-related lncRNAs was validated in HCC tissues and different cell lines. Combining the risk score and clinicopathological features, a nomogram was established for predicting the overall survival (OS) of HCC patients. Furthermore, gene set enrichment analysis (GSEA) revealed that some tumor-associated pathways were significantly enriched in the high-risk group. Immune cell infiltration analysis demonstrated that the levels of Treg cells, neutrophils, and M2 macrophages were higher in the high-risk group. In addition, patients with high tumor mutation burden (TMB) had worse OS than those with low TMB. We also assessed the immune checkpoint level and chemotherapeutic agent sensibility. Then in vitro experiments were performed to examine the biological function of MKLN1-AS in HCC cells and found that knockdown of MKLN1-AS suppressed the proliferation, migration, and invasion. In conclusion, m5C-related lncRNAs played a critical role in predicting the prognosis of patients with HCC and may serve as new therapeutic targets for HCC patients.
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Affiliation(s)
- Qian Lu
- Department of Gastroenterology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Lianyu Liu
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Shuai Wang
- The Graduate School, Xuzhou Medical University, Xuzhou, China
| | - Qi Zhang
- Department of Gastroenterology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Li Li
- Department of Gastroenterology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
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