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Zhang X, Ma Y, Yu J, Su R, Wang X. Internal m 6 A and m 7 G RNA modifications in hematopoietic system and acute myeloid leukemia. Chin Med J (Engl) 2024; 137:1033-1043. [PMID: 38545694 PMCID: PMC11062654 DOI: 10.1097/cm9.0000000000003073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Indexed: 05/03/2024] Open
Abstract
ABSTRACT Epitranscriptomics focuses on the RNA-modification-mediated post-transcriptional regulation of gene expression. The past decade has witnessed tremendous progress in our understanding of the landscapes and biological functions of RNA modifications, as prompted by the emergence of potent analytical approaches. The hematopoietic system provides a lifelong supply of blood cells, and gene expression is tightly controlled during the differentiation of hematopoietic stem cells (HSCs). The dysregulation of gene expression during hematopoiesis may lead to severe disorders, including acute myeloid leukemia (AML). Emerging evidence supports the involvement of the mRNA modification system in normal hematopoiesis and AML pathogenesis, which has led to the development of small-molecule inhibitors that target N6-methyladenosine (m 6 A) modification machinery as treatments. Here, we summarize the latest findings and our most up-to-date information on the roles of m 6 A and N7-methylguanine in both physiological and pathological conditions in the hematopoietic system. Furthermore, we will discuss the therapeutic potential and limitations of cancer treatments targeting m 6 A.
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Affiliation(s)
- Xiaoxu Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing 100005, China
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Yanni Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing 100005, China
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu,Sichuan 610052, China
- Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing 100005, China
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu,Sichuan 610052, China
- Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Xiaoshuang Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing 100005, China
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu,Sichuan 610052, China
- Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
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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 2024:132057. [PMID: 38710243 DOI: 10.1016/j.ijbiomac.2024.132057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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Qian W, Yang L, Li T, Li W, Zhou J, Xie S. RNA modifications in pulmonary diseases. MedComm (Beijing) 2024; 5:e546. [PMID: 38706740 PMCID: PMC11068158 DOI: 10.1002/mco2.546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 05/07/2024] Open
Abstract
Threatening public health, pulmonary disease (PD) encompasses diverse lung injuries like chronic obstructive PD, pulmonary fibrosis, asthma, pulmonary infections due to pathogen invasion, and fatal lung cancer. The crucial involvement of RNA epigenetic modifications in PD pathogenesis is underscored by robust evidence. These modifications not only shape cell fates but also finely modulate the expression of genes linked to disease progression, suggesting their utility as biomarkers and targets for therapeutic strategies. The critical RNA modifications implicated in PDs are summarized in this review, including N6-methylation of adenosine, N1-methylation of adenosine, 5-methylcytosine, pseudouridine (5-ribosyl uracil), 7-methylguanosine, and adenosine to inosine editing, along with relevant regulatory mechanisms. By shedding light on the pathology of PDs, these summaries could spur the identification of new biomarkers and therapeutic strategies, ultimately paving the way for early PD diagnosis and treatment innovation.
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Affiliation(s)
- Weiwei Qian
- Emergency Department of Emergency MedicineLaboratory of Emergency Medicine, West China Hospital, And Disaster Medical, Sichuan UniversityChengduSichuanChina
- Emergency DepartmentShangjinnanfu Hospital, West China Hospital, Sichuan UniversityChengduSichuanChina
| | - Lvying Yang
- The Department of Respiratory and Critical Care MedicineThe First Veterans Hospital of Sichuan ProvinceChengduSichuanChina
| | - Tianlong Li
- Department of Critical Care Medicine Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Wanlin Li
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's HospitalShenzhenGuangdongChina
| | - Jian Zhou
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National‐Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical SchoolShenzhenChina
- Department of ImmunologyInternational Cancer Center, Shenzhen University Health Science CenterShenzhenGuangdongChina
| | - Shenglong Xie
- Department of Thoracic SurgerySichuan Provincial People's Hospital, University of Electronic Science and Technology of ChinaChengduSichuanChina
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Oleynikov M, Jaffrey SR. RNA tertiary structure and conformational dynamics revealed by BASH MaP. bioRxiv 2024:2024.04.11.589009. [PMID: 38645201 PMCID: PMC11030352 DOI: 10.1101/2024.04.11.589009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging. To address this, we developed BASH MaP, a single-molecule dimethyl sulfate (DMS) footprinting method and DAGGER, a computational pipeline, to identify alternative tertiary structures adopted by different molecules of RNA. BASH MaP utilizes potassium borohydride to reveal the chemical accessibility of the N7 position of guanosine, a key mediator of tertiary structures. We used BASH MaP to identify diverse conformational states and dynamics of RNA G-quadruplexes, an important RNA tertiary motif, in vitro and in cells. BASH MaP and DAGGER analysis of the fluorogenic aptamer Spinach reveals that it adopts alternative tertiary conformations which determine its fluorescence states. BASH MaP thus provides an approach for structural analysis of RNA by revealing previously undetectable tertiary structures.
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5
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Lin S, Kuang M. RNA modification-mediated mRNA translation regulation in liver cancer: mechanisms and clinical perspectives. Nat Rev Gastroenterol Hepatol 2024; 21:267-281. [PMID: 38243019 DOI: 10.1038/s41575-023-00884-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/21/2024]
Abstract
Malignant liver cancer is characterized by rapid tumour progression and a high mortality rate, whereas the molecular mechanisms underlying liver cancer initiation and progression are still poorly understood. The dynamic and reversible RNA modifications have crucial functions in gene expression regulation by modulating RNA processing and mRNA translation. Emerging evidence has revealed that alterations in RNA modifications facilitate the selective translation of oncogenic transcripts and promote the diverse tumorigenic processes of liver cancer. In this Review, we first highlight the current progress on the functions and mechanisms underlying RNA modifications in the regulation of mRNA translation and then summarize the exciting discoveries on aberrant RNA modification-mediated mRNA translation in the regulation of tumour initiation, metastasis, metabolism, tumour microenvironment, and drug and radiotherapy resistance in liver cancer. Finally, we discuss the diagnostic and therapeutic potentials of targeting RNA modifications and mRNA translation for the clinical management of liver cancer.
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Affiliation(s)
- Shuibin Lin
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Ming Kuang
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Liu WW, Zheng SQ, Li T, Fei YF, Wang C, Zhang S, Wang F, Jiang GM, Wang H. RNA modifications in cellular metabolism: implications for metabolism-targeted therapy and immunotherapy. Signal Transduct Target Ther 2024; 9:70. [PMID: 38531882 DOI: 10.1038/s41392-024-01777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
Cellular metabolism is an intricate network satisfying bioenergetic and biosynthesis requirements of cells. Relevant studies have been constantly making inroads in our understanding of pathophysiology, and inspiring development of therapeutics. As a crucial component of epigenetics at post-transcription level, RNA modification significantly determines RNA fates, further affecting various biological processes and cellular phenotypes. To be noted, immunometabolism defines the metabolic alterations occur on immune cells in different stages and immunological contexts. In this review, we characterize the distribution features, modifying mechanisms and biological functions of 8 RNA modifications, including N6-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), N7-methylguanosine (m7G), Pseudouridine (Ψ), adenosine-to-inosine (A-to-I) editing, which are relatively the most studied types. Then regulatory roles of these RNA modification on metabolism in diverse health and disease contexts are comprehensively described, categorized as glucose, lipid, amino acid, and mitochondrial metabolism. And we highlight the regulation of RNA modifications on immunometabolism, further influencing immune responses. Above all, we provide a thorough discussion about clinical implications of RNA modification in metabolism-targeted therapy and immunotherapy, progression of RNA modification-targeted agents, and its potential in RNA-targeted therapeutics. Eventually, we give legitimate perspectives for future researches in this field from methodological requirements, mechanistic insights, to therapeutic applications.
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Affiliation(s)
- Wei-Wei Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- School of Clinical Medicine, Shandong University, Jinan, China
| | - Si-Qing Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Tian Li
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Yun-Fei Fei
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Chen Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Shuang Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Fei Wang
- Neurosurgical Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
| | - Hao Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China.
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Stixová L, Tichý V, Bártová E. RNA-related DNA damage and repair: The role of N7-methylguanosine in the cell nucleus exposed to UV light. Heliyon 2024; 10:e25599. [PMID: 38370261 PMCID: PMC10869776 DOI: 10.1016/j.heliyon.2024.e25599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024] Open
Abstract
Background Chemical modifications in mRNAs, tRNAs, rRNAs, and non-coding RNAs stabilize these nucleic acids and regulate their function. In addition to regulating the translation of genetic information from mRNA to proteins, it has been revealed that modifications in RNAs regulate repair processes in the genome. Methods Using local laser microirradiation, confocal microscopy, dot blots, and mass spectrometry we studied the role of N7-methylguanosine (m7G), which is co-transcriptionally installed in RNA. Results Here, we show that after UVC and UVA irradiation, the level of m7G RNA is increased initially in the cytoplasm, and after local laser microirradiation, m7G RNA is highly abundant in UVA-damaged chromatin. This process is poly(ADP-ribose) polymerase (PARP)-dependent, but not accompanied by changes in the level of m7G-writers, including methyltransferases RNMT, METTL1, and WBSCR22. We also observed that METTL1 deficiency does not affect the recruitment of m7G RNA to microirradiated chromatin. Analyzing the levels of mRNA, let-7e, and miR-203a in both the cytoplasm and the cell nucleus, we revealed that UVC irradiation changed the level of mRNA, and significantly increased the pool of both let-7e and miR-203a, which correlated with radiation-induced m7G RNA increase in the cytoplasm. Conclusions Irradiation by UV light increases the m7G RNA pool in the cytoplasm and in the microirradiated genome. Thus, epigenetically modified RNAslikely contribute to DNA damage responses or m7G signals the presence of RNA damage.
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Affiliation(s)
- Lenka Stixová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| | - Vlastimil Tichý
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| | - Eva Bártová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
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Chen Y, Xie Y, Bi L, Ci H, Li W, Liu D. A novel serum m 7G-harboring microRNA signature for cancer detection. Front Genet 2024; 15:1270302. [PMID: 38384713 PMCID: PMC10879580 DOI: 10.3389/fgene.2024.1270302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Background: Emerging evidence points to the exceptional importance and value of m7G alteration in the diagnosis and prognosis of cancers. Nonetheless, a biomarker for precise screening of various cancer types has not yet been developed based on serum m7G-harboring miRNAs. Methods: A total of 20,702 serum samples, covering 12 cancer types and consisting of 7,768 cancer samples and 12,934 cancer-free samples were used in this study. A m7G target miRNA diagnostic signature (m7G-miRDS) was established through the least absolute shrinkage and selection operator (LASSO) analyses in a training dataset (n = 10,351), and validated in a validation dataset (n = 10,351). Results: The m7G-miRDS model, a 12 m7G-target-miRNAs signature, demonstrated high accuracy and was qualified for cancer detection. In the training and validation cohort, the area under the curve (AUC) reached 0.974 (95% CI 0.971-0.977) and 0.972 (95% CI 0.969-0.975), respectively. The m7G-miRDS showed superior sensitivity in each cancer type and had a satisfactory AUC in identifying bladder cancer, lung cancer and esophageal cancer. Additionally, the diagnostic performance of m7G-miRDS was not interfered by the gender, age and benign disease. Conclusion: Our results greatly extended the value of serum circulating miRNAs and m7G in cancer detection, and provided a new direction and strategy for the development of novel biomarkers with high accuracy, low cost and less invasiveness for mass cancer screening, such as ncRNA modification.
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Affiliation(s)
- Yaxin Chen
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yufang Xie
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Jiujiang First People’s Hospital, Jiujiang, Jiangxi, China
| | - Liyun Bi
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hang Ci
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dan Liu
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Han M, Huang Q, Li X, Chen X, Zhu H, Pan Y, Zhang B. M7G-related tumor immunity: novel insights of RNA modification and potential therapeutic targets. Int J Biol Sci 2024; 20:1238-1255. [PMID: 38385078 PMCID: PMC10878144 DOI: 10.7150/ijbs.90382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/09/2024] [Indexed: 02/23/2024] Open
Abstract
RNA modifications play a pivotal role in regulating cellular biology by exerting influence over distribution features and molecular functions at the post-transcriptional level. Among these modifications, N7-methylguanosine (m7G) stands out as one of the most prevalent. Over recent years, significant attention has been directed towards understanding the implications of m7G modification. This modification is present in diverse RNA molecules, including transfer RNAs, messenger RNAs, ribosomal RNAs, and other noncoding RNAs. Its regulation occurs through a series of specific methyltransferases and m7G-binding proteins. Notably, m7G modification has been implicated in various diseases, prominently across multiple cancer types. Earlier studies have elucidated the significance of m7G modification in the context of immune biology regulation within the tumor microenvironment. This comprehensive review culminates in a synthesis of findings related to the modulation of immune cells infiltration, encompassing T cells, B cells, and various innate immune cells, all orchestrated by m7G modification. Furthermore, the interplay between m7G modification and its regulatory proteins can profoundly affect the efficacy of diverse adjuvant therapeutics, thereby potentially serving as a pivotal biomarker and therapeutic target for combinatory interventions in diverse cancer types.
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Affiliation(s)
- Mengzhen Han
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Qibo Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Xinxin Li
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - He Zhu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Yonglong Pan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
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12
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Zhang C, Wen R, Wu G, Li G, Wu X, Guo Y, Yang Z. Identification and validation of a prognostic risk-scoring model for AML based on m 7G-associated gene clustering. Front Oncol 2024; 13:1301236. [PMID: 38273850 PMCID: PMC10808397 DOI: 10.3389/fonc.2023.1301236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024] Open
Abstract
Background Acute myeloid leukemia (AML) patients still suffer from poor 5-year survival and relapse after remission. A better prognostic assessment tool is urgently needed. New evidence demonstrates that 7-methylguanosine (m7G) methylation modifications play an important role in AML, however, the exact role of m7G-related genes in the prognosis of AML remains unclear. Methods The study obtained AML expression profiles and clinical information from TCGA, GEO, and TARGET databases. Using the patient data from the TCGA cohort as the training set. Consensus clustering was performed based on 29 m7G-related genes. Survival analysis was performed by KM curves. The subgroup characteristic gene sets were screened using WGCNA. And tumor immune infiltration correlation analysis was performed by ssGSEA. Results The patients were classified into 3 groups based on m7G-related genebased cluster analysis, and the differential genes were screened by differential analysis and WGCNA. After LASSO regression analysis, 6 characteristic genes (including CBR1, CCDC102A, LGALS1, RD3L, SLC29A2, and TWIST1) were screened, and a prognostic risk-score model was constructed. The survival rate of low-risk patients was significantly higher than that of high-risk patients (p < 0.0001). The area under the curve values at 1, 3, and 5 years in the training set were 0.871, 0.874, and 0.951, respectively, indicating that this predictive model has an excellent predictive effect. In addition, after univariate and multivariate Cox regression screening, histograms were constructed with clinical characteristics and prognostic risk score models to better predict individual survival. Further analysis showed that the prognostic risk score model was associated with immune cell infiltration. Conclusion These findings suggest that the scoring model and essential risk genes could provide potential prognostic biomarkers for patients with acute myeloid leukemia.
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Affiliation(s)
- Chiyi Zhang
- Department of Hematology, Central People’s Hospital of Zhanjiang, Zhanjiang, China
- Zhanjiang Key Laboratory of Leukemia Pathogenesis and Targeted Therapy Research, Zhanjiang, China
| | - Ruiting Wen
- Department of Hematology, Central People’s Hospital of Zhanjiang, Zhanjiang, China
- Zhanjiang Key Laboratory of Leukemia Pathogenesis and Targeted Therapy Research, Zhanjiang, China
| | - Guocai Wu
- Department of Hematology, Central People’s Hospital of Zhanjiang, Zhanjiang, China
- Zhanjiang Key Laboratory of Leukemia Pathogenesis and Targeted Therapy Research, Zhanjiang, China
| | - Guangru Li
- Zhanjiang Institute of Clinical Medicine, Central People’s Hospital of Zhanjiang, Zhanjiang, China
| | - Xiaoqing Wu
- Department of Hematology, Central People’s Hospital of Zhanjiang, Zhanjiang, China
- Zhanjiang Key Laboratory of Leukemia Pathogenesis and Targeted Therapy Research, Zhanjiang, China
| | - Yunmiao Guo
- Zhanjiang Institute of Clinical Medicine, Central People’s Hospital of Zhanjiang, Zhanjiang, China
| | - Zhigang Yang
- Department of Hematology, Central People’s Hospital of Zhanjiang, Zhanjiang, China
- Zhanjiang Key Laboratory of Leukemia Pathogenesis and Targeted Therapy Research, Zhanjiang, China
- Zhanjiang Institute of Clinical Medicine, Central People’s Hospital of Zhanjiang, Zhanjiang, China
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Long S, Yan Y, Xu H, Wang L, Jiang J, Xu Z, Liu R, Zhou Q, Huang X, Chen J, Li Z, Wei W, Li X. Insights into the regulatory role of RNA methylation modifications in glioma. J Transl Med 2023; 21:810. [PMID: 37964279 PMCID: PMC10644640 DOI: 10.1186/s12967-023-04653-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023] Open
Abstract
Epitranscriptomic abnormalities, which are highly prevalent in primary central nervous system malignancies, have been identified as crucial contributors to the development and progression of gliomas. RNA epitranscriptomic modifications, particularly the reversible modification methylation, have been observed throughout the RNA cycle. Epitranscriptomic modifications, which regulate RNA transcription and translation, have profound biological implications. These modifications are associated with the development of several cancer types. Notably, three main protein types-writers, erasers, and readers, in conjunction with other related proteins, mediate these epitranscriptomic changes. This review primarily focuses on the role of recently identified RNA methylation modifications in gliomas, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), and N1-methyladenosine (m1A). We delved into their corresponding writers, erasers, readers, and related binding proteins to propose new approaches and prognostic indicators for patients with glioma.
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Affiliation(s)
- Shengrong Long
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yu Yan
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Hongyu Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Lesheng Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jiazhi Jiang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Ziyue Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Runming Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Qiangqiang Zhou
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaopeng Huang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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15
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Imbriano C, Moresi V, Belluti S, Renzini A, Cavioli G, Maretti E, Molinari S. Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives. Int J Mol Sci 2023; 24:15161. [PMID: 37894843 PMCID: PMC10606696 DOI: 10.3390/ijms242015161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Epitranscriptomics refers to post-transcriptional regulation of gene expression via RNA modifications and editing that affect RNA functions. Many kinds of modifications of mRNA have been described, among which are N6-methyladenosine (m6A), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), and 5-methylcytidine (m5C). They alter mRNA structure and consequently stability, localization and translation efficiency. Perturbation of the epitranscriptome is associated with human diseases, thus opening the opportunity for potential manipulations as a therapeutic approach. In this review, we aim to provide an overview of the functional roles of epitranscriptomic marks in the skeletal muscle system, in particular in embryonic myogenesis, muscle cell differentiation and muscle homeostasis processes. Further, we explored high-throughput epitranscriptome sequencing data to identify RNA chemical modifications in muscle-specific genes and we discuss the possible functional role and the potential therapeutic applications.
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Affiliation(s)
- Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Viviana Moresi
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy;
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Giorgia Cavioli
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Eleonora Maretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Susanna Molinari
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
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16
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Liberman N, Rothi MH, Gerashchenko MV, Zorbas C, Boulias K, MacWhinnie FG, Ying AK, Flood Taylor A, Al Haddad J, Shibuya H, Roach L, Dong A, Dellacona S, Lafontaine DLJ, Gladyshev VN, Greer EL. 18S rRNA methyltransferases DIMT1 and BUD23 drive intergenerational hormesis. Mol Cell 2023; 83:3268-3282.e7. [PMID: 37689068 DOI: 10.1016/j.molcel.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/25/2023] [Accepted: 08/10/2023] [Indexed: 09/11/2023]
Abstract
Heritable non-genetic information can regulate a variety of complex phenotypes. However, what specific non-genetic cues are transmitted from parents to their descendants are poorly understood. Here, we perform metabolic methyl-labeling experiments to track the heritable transmission of methylation from ancestors to their descendants in the nematode Caenorhabditis elegans (C. elegans). We find heritable methylation in DNA, RNA, proteins, and lipids. We find that parental starvation elicits reduced fertility, increased heat stress resistance, and extended longevity in fed, naïve progeny. This intergenerational hormesis is accompanied by a heritable increase in N6'-dimethyl adenosine (m6,2A) on the 18S ribosomal RNA at adenosines 1735 and 1736. We identified DIMT-1/DIMT1 as the m6,2A and BUD-23/BUD23 as the m7G methyltransferases in C. elegans that are both required for intergenerational hormesis, while other rRNA methyltransferases are dispensable. This study labels and tracks heritable non-genetic material across generations and demonstrates the importance of rRNA methylation for regulating epigenetic inheritance.
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Affiliation(s)
- Noa Liberman
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - M Hafiz Rothi
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Christiane Zorbas
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark Campus, 6041 Gosselies, Belgium
| | - Konstantinos Boulias
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Fiona G MacWhinnie
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Albert Kejun Ying
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Anya Flood Taylor
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Joseph Al Haddad
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Hiroki Shibuya
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Lara Roach
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Anna Dong
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Scarlett Dellacona
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark Campus, 6041 Gosselies, Belgium
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric Lieberman Greer
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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17
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Zhang X, Zhu WY, Shen SY, Shen JH, Chen XD. Biological roles of RNA m7G modification and its implications in cancer. Biol Direct 2023; 18:58. [PMID: 37710294 PMCID: PMC10500781 DOI: 10.1186/s13062-023-00414-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023] Open
Abstract
M7G modification, known as one of the common post-transcriptional modifications of RNA, is present in many different types of RNAs. With the accurate identification of m7G modifications within RNAs, their functional roles in the regulation of gene expression and different physiological functions have been revealed. In addition, there is growing evidence that m7G modifications are crucial in the emergence of cancer. Here, we review the most recent findings regarding the detection techniques, distribution, biological functions and Regulators of m7G. We also summarize the connections between m7G modifications and cancer development, drug resistance, and tumor microenvironment as well as we discuss the research's future directions and trends.
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Affiliation(s)
- Xin Zhang
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Wen-Yan Zhu
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Shu-Yi Shen
- Department of Dermatology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jia-Hao Shen
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xiao-Dong Chen
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
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Strong E, Mervis CB, Tam E, Morris CA, Klein-Tasman BP, Velleman SL, Osborne LR. DNA methylation profiles in individuals with rare, atypical 7q11.23 CNVs correlate with GTF2I and GTF2IRD1 copy number. NPJ Genom Med 2023; 8:25. [PMID: 37709781 PMCID: PMC10502022 DOI: 10.1038/s41525-023-00368-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
Williams-Beuren syndrome (WBS) and 7q11.23 duplication syndrome (Dup7) are rare neurodevelopmental disorders caused by deletion and duplication of a 1.5 Mb region that includes at least five genes with a known role in epigenetic regulation. We have shown that CNV of this chromosome segment causes dose-dependent, genome-wide changes in DNA methylation, but the specific genes driving these changes are unknown. We measured genome-wide whole blood DNA methylation in six participants with atypical CNV of 7q11.23 (three with deletions and three with duplications) using the Illumina HumanMethylation450k array and compared their profiles with those from groups of individuals with classic WBS or classic Dup7 and with typically developing (TD) controls. Across the top 1000 most variable positions we found that only the atypical rearrangements that changed the copy number of GTF2IRD1 and/or GTF2I (coding for the TFII-IRD1 and TFII-I proteins) clustered with their respective syndromic cohorts. This finding was supported by results from hierarchical clustering across a selection of differentially methylated CpGs, in addition to pyrosequencing validation. These findings suggest that CNV of the GTF2I genes at the telomeric end of the 7q11.23 interval is a key contributor to the large changes in DNA methylation that are seen in blood DNA from our WBS and Dup7 cohorts, compared to TD controls. Our findings suggest that members of the TFII-I protein family are involved in epigenetic processes that alter DNA methylation on a genome-wide level.
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Affiliation(s)
- Emma Strong
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospital, Vancouver, BC, Canada
| | - Carolyn B Mervis
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, USA
| | - Elaine Tam
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Colleen A Morris
- Department of Pediatrics, Kirk Kerkorian School of Medicine at University of Nevada Las Vegas, Las Vegas, NV, USA
| | | | - Shelley L Velleman
- Department of Communication Sciences and Disorders, University of Vermont, Burlington, VT, USA
| | - Lucy R Osborne
- Departments of Medicine and Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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Zhang Y, Wang X, Zhang C, Yi H. The dysregulation of lncRNAs by epigenetic factors in human pathologies. Drug Discov Today 2023; 28:103664. [PMID: 37348827 DOI: 10.1016/j.drudis.2023.103664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
Dysregulation of long noncoding RNAs (lncRNAs) contributes to numerous human diseases, including cancers and autoimmune diseases (ADs). Given the importance of lncRNAs in disease initiation and progression, a deeper understanding of their complex regulatory network is required to facilitate their use as therapeutic targets for ADs. In this review, we summarize how lncRNAs are dysregulated in pathological states by epigenetic factors, including RNA-binding proteins, chemical modifications (N6-methyladenosine, 5-methylcytosine, 7-methylguanosine, adenosine-to-inosine editing, microRNA, alternative splicing, DNA methylation, and histone modification). Moreover, the roles of lncRNA epigenetic regulators in immune response and ADs are discussed, providing new insights into the complicated epigenetic factor-lncRNA network, thus, laying a theoretical foundation for future research and clinical application of lncRNAs.
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Affiliation(s)
- Yanli Zhang
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China; Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, Jilin 130021, China; Department of Echocardiography, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiaocong Wang
- Department of Echocardiography, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Chen Zhang
- Colorectal and Anal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Huanfa Yi
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China; Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, Jilin 130021, China.
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20
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Ye L, Yao X, Xu B, Chen W, Lou H, Tong X, Fang S, Zou R, Hu Y, Wang Z, Xiang D, Lin Q, Feng S, Xue X, Guo G. RNA epigenetic modifications in ovarian cancer: The changes, chances, and challenges. Wiley Interdiscip Rev RNA 2023; 14:e1784. [PMID: 36811232 DOI: 10.1002/wrna.1784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/23/2023]
Abstract
Ovarian cancer (OC) is the most common female cancer worldwide. Patients with OC have high mortality because of its complex and poorly understood pathogenesis. RNA epigenetic modifications, such as m6 A, m1 A, and m5 C, are closely associated with the occurrence and development of OC. RNA modifications can affect the stability of mRNA transcripts, nuclear export of RNAs, translation efficiency, and decoding accuracy. However, there are few overviews that summarize the link between m6 A RNA modification and OC. Here, we discuss the molecular and cellular functions of different RNA modifications and how their regulation contributes to the pathogenesis of OC. By improving our understanding of the role of RNA modifications in the etiology of OC, we provide new perspectives for their use in OC diagnosis and treatment. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Lele Ye
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xuyang Yao
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Binbing Xu
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Wenwen Chen
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Han Lou
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ruanmin Zou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yingying Hu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhibin Wang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dan Xiang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoai Lin
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shiyu Feng
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
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21
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Sun D, Song N, Li M, Chen X, Zhang X, Yu Y, Ying J, Xu M, Zheng W, Han C, Ji H, Jiang Y. Comprehensive analysis of circRNAs for N7-methylguanosine methylation modification in human oral squamous cell carcinoma. FASEB Bioadv 2023; 5:305-320. [PMID: 37554544 PMCID: PMC10405248 DOI: 10.1096/fba.2023-00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 08/10/2023] Open
Abstract
N7-methylguanosine (m7G) modification is closely related to the occurrence of tumors. However, the m7G modification of circRNAs in oral squamous cell carcinoma (OSCC) remains to be investigated. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to measure the methylation levels of m7G and identify m7G sites in circRNAs in human OSCC and normal tissues. The host genes of differentially methylated and differentially expressed circRNAs were analyzed by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and circRNA-miRNA-mRNA networks were predicted using the miRanda and miRDB databases. The analysis identified 2348 m7G peaks in 624 circRNAs in OSCC tissues. In addition, the source of m7G-methylated circRNAs in OSCC was mainly the sense overlap region compared with normal tissues. The most conserved m7G motif in OSCC tissues was CCUGU, whereas the most conserved motif in normal tissues was RCCUG (R = G/A). Importantly, GO enrichment and KEGG pathway analysis showed that the host genes of differentially methylated and differentially expressed circRNAs were involved in many cellular biological functions. Furthermore, the significantly differentially expressed circRNAs were analyzed to predict the circRNA-miRNA-mRNA networks. This study revealed the whole profile of circRNAs of differential m7G methylation in OSCC and suggests that m7G-modified circRNAs may impact the development of OSCC.
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Affiliation(s)
- Dongyuan Sun
- School of StomatologyWeifang Medical UniversityWeifangChina
- Department of StomatologyAffiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Ning Song
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Minmin Li
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Xi Chen
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Xinyue Zhang
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Yang Yu
- School of StomatologyWeifang Medical UniversityWeifangChina
- Department of StomatologyAffiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Jicheng Ying
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Mengqi Xu
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Wentian Zheng
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Chengbing Han
- Department of StomatologyFirst Affiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Honghai Ji
- School of StomatologyWeifang Medical UniversityWeifangChina
- Department of StomatologyAffiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Yingying Jiang
- School of StomatologyWeifang Medical UniversityWeifangChina
- Department of StomatologyAffiliated Hospital of Weifang Medical UniversityWeifangChina
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22
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Tang Q, Li L, Wang Y, Wu P, Hou X, Ouyang J, Fan C, Li Z, Wang F, Guo C, Zhou M, Liao Q, Wang H, Xiang B, Jiang W, Li G, Zeng Z, Xiong W. RNA modifications in cancer. Br J Cancer 2023; 129:204-221. [PMID: 37095185 PMCID: PMC10338518 DOI: 10.1038/s41416-023-02275-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
Currently, more than 170 modifications have been identified on RNA. Among these RNA modifications, various methylations account for two-thirds of total cases and exist on almost all RNAs. Roles of RNA modifications in cancer are garnering increasing interest. The research on m6A RNA methylation in cancer is in full swing at present. However, there are still many other popular RNA modifications involved in the regulation of gene expression post-transcriptionally besides m6A RNA methylation. In this review, we focus on several important RNA modifications including m1A, m5C, m7G, 2'-O-Me, Ψ and A-to-I editing in cancer, which will provide a new perspective on tumourigenesis by peeking into the complex regulatory network of epigenetic RNA modifications, transcript processing, and protein translation.
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Affiliation(s)
- Qiling Tang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Lvyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Pan Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Xiangchan Hou
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Jiawei Ouyang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Chunmei Fan
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Zheng Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Hui Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Weihong Jiang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China.
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Kapinova A, Mazurakova A, Halasova E, Dankova Z, Büsselberg D, Costigliola V, Golubnitschaja O, Kubatka P. Underexplored reciprocity between genome-wide methylation status and long non-coding RNA expression reflected in breast cancer research: potential impacts for the disease management in the framework of 3P medicine. EPMA J 2023; 14:249-273. [PMID: 37275549 PMCID: PMC10236066 DOI: 10.1007/s13167-023-00323-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
Breast cancer (BC) is the most common female malignancy reaching a pandemic scale worldwide. A comprehensive interplay between genetic alterations and shifted epigenetic regions synergistically leads to disease development and progression into metastatic BC. DNA and histones methylations, as the most studied epigenetic modifications, represent frequent and early events in the process of carcinogenesis. To this end, long non-coding RNAs (lncRNAs) are recognized as potent epigenetic modulators in pathomechanisms of BC by contributing to the regulation of DNA, RNA, and histones' methylation. In turn, the methylation status of DNA, RNA, and histones can affect the level of lncRNAs expression demonstrating the reciprocity of mechanisms involved. Furthermore, lncRNAs might undergo methylation in response to actual medical conditions such as tumor development and treated malignancies. The reciprocity between genome-wide methylation status and long non-coding RNA expression levels in BC remains largely unexplored. Since the bio/medical research in the area is, per evidence, strongly fragmented, the relevance of this reciprocity for BC development and progression has not yet been systematically analyzed. Contextually, the article aims at:consolidating the accumulated knowledge on both-the genome-wide methylation status and corresponding lncRNA expression patterns in BC andhighlighting the potential benefits of this consolidated multi-professional approach for advanced BC management. Based on a big data analysis and machine learning for individualized data interpretation, the proposed approach demonstrates a great potential to promote predictive diagnostics and targeted prevention in the cost-effective primary healthcare (sub-optimal health conditions and protection against the health-to-disease transition) as well as advanced treatment algorithms tailored to the individualized patient profiles in secondary BC care (effective protection against metastatic disease). Clinically relevant examples are provided, including mitochondrial health control and epigenetic regulatory mechanisms involved.
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Affiliation(s)
- Andrea Kapinova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Alena Mazurakova
- Department of Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Erika Halasova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dietrich Büsselberg
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, 24144 Doha, Qatar
| | | | - Olga Golubnitschaja
- Predictive, Preventive, and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
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Jiang S, Xiao M, Shi Y, Wang Y, Xu Z, Wang K. Identification of m7G-Related miRNA Signatures Associated with Prognosis, Oxidative Stress, and Immune Landscape in Lung Adenocarcinoma. Biomedicines 2023; 11:1569. [PMID: 37371664 DOI: 10.3390/biomedicines11061569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/13/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The role of N7-methylguanosine(m7G)-related miRNAs in lung adenocarcinoma (LUAD) remains unclear. We used LUAD data from The Cancer Genome Atlas (TCGA) to establish a risk model based on the m7G-related miRNAs, and divided patients into high-risk or low-risk subgroups. A nomogram for predicting overall survival (OS) was then constructed based on the independent risk factors. In addition, we performed a functional enrichment analysis and defined the oxidative stress-related genes, immune landscape as well as a drug response profile in the high-risk and low-risk subgroups. This study incorporated 28 m7G-related miRNAs into the risk model. The data showed a significant difference in the OS between the high-risk and low-risk subgroups. The receiver operating characteristic curve (ROC) predicted that the area under the curve (AUC) of one-year, three-year and five-year OS was 0.781, 0.804 and 0.853, respectively. The C-index of the prognostic nomogram for predicting OS was 0.739. We then analyzed the oxidative stress-related genes and immune landscape in the high-risk and low-risk subgroups. The data demonstrated significant differences in the expression of albumin (ALB), estimated score, immune score, stromal score, immune cell infiltration and functions between the high-risk and low-risk subgroups. In addition, the drug response analysis showed that low-risk subgroups may be more sensitive to tyrosine kinase inhibitor (TKI) and histone deacetylase (HDAC) inhibitors. We successfully developed a novel risk model based on m7G-related miRNAs in this study. The model can predict clinical prognosis and guide therapeutic regimens in patients with LUAD. Our data also provided new insights into the molecular mechanisms of m7G in LUAD.
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Affiliation(s)
- Sujing Jiang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Mingshu Xiao
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Yueli Shi
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Yongfang Wang
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Zhiyong Xu
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
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25
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Zhang L, Xu X, Su X. Modifications of noncoding RNAs in cancer and their therapeutic implications. Cell Signal 2023:110726. [PMID: 37230201 DOI: 10.1016/j.cellsig.2023.110726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/06/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
In the last 50 years, over 150 various chemical modifications on RNA molecules, including mRNAs, rRNAs, tRNAs, and other noncoding RNAs (ncRNAs), have been identified and characterized. These RNA modifications regulate RNA biogenesis and biological functions and are widely involved in various physiological processes and diseases, including cancer. In recent decades, broad interest has arisen in the epigenetic modification of ncRNAs due to the increased knowledge of the critical roles of ncRNAs in cancer. In this review, we summarize the various modifications of ncRNAs and highlight their roles in cancer initiation and progression. In particular, we discuss the potential of RNA modifications as novel biomarkers and therapeutic targets in cancer.
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Affiliation(s)
- Le Zhang
- Center for Reproductive Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China
| | - Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612-9497, USA
| | - Xiulan Su
- Clinical Medical Research Center, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China.
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Du D, He J, Ju C, Wang C, Li H, He F, Zhou M. When N7-methyladenosine modification meets cancer: Emerging frontiers and promising therapeutic opportunities. Cancer Lett 2023; 562:216165. [PMID: 37028699 DOI: 10.1016/j.canlet.2023.216165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023]
Abstract
N7-methylguanosine (m7G) methylation, one of the most common RNA modifications in eukaryotes, has recently gained considerable attention. The biological functions of m7G modification in RNAs, including tRNA, rRNA, mRNA, and miRNA, remain largely unknown in human diseases. Owing to rapid advances in high-throughput technologies, increasing evidence suggests that m7G modification plays a critical role in cancer initiation and progression. As m7G modification and hallmarks of cancer are inextricably linked together, targeting m7G regulators may provide new possibilities for future cancer diagnoses and potential intervention targets. This review summarizes various detection methods for m7G modification, recent advances in m7G modification and tumor biology regarding their interplay and regulatory mechanisms. We conclude with an outlook on the future of diagnosing and treating m7G-related diseases.
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Huang H, Pan R, Wang S, Guan Y, Zhao Y, Liu X. Current and potential roles of RNA modification-mediated autophagy dysregulation in cancer. Arch Biochem Biophys 2023; 736:109542. [PMID: 36758911 DOI: 10.1016/j.abb.2023.109542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/09/2023]
Abstract
Autophagy, a cellular lysosomal degradation and survival pathway, supports nutrient recycling and adaptation to metabolic stress and participates in various stages of tumor development, including tumorigenesis, metastasis, and malignant state maintenance. Among the various factors contributing to the dysregulation of autophagy in cancer, RNA modification can regulate autophagy by directly affecting the expression of core autophagy proteins. We propose that autophagy disorder mediated by RNA modification is an important mechanism for cancer development. Therefore, this review mainly discusses the role of RNA modification-mediated autophagy regulation in tumorigenesis. We summarize the molecular basis of autophagy and the core proteins and complexes at different stages of autophagy, especially those involved in cancer development. Moreover, we describe the crosstalk of RNA modification and autophagy and review the recent advances and potential role of the RNA modification/autophagy axis in the development of multiple cancers. Furthermore, the dual role of the RNA modification/autophagy axis in cancer drug resistance is discussed. A comprehensive understanding and extensive exploration of the molecular crosstalk of RNA modifications with autophagy will provide important insights into tumor pathophysiology and provide more options for cancer therapeutic strategies.
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Affiliation(s)
- Hua Huang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Ruining Pan
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Sijia Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Yifei Guan
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Yue Zhao
- Intensive Care Unit, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China.
| | - Xinhui Liu
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China.
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Liu C, Guo H, Zhao X, Zou B, Sun T, Feng J, Zeng Z, Wen X, Chen J, Hu Z, Lou S, Li H. Overexpression of 18S rRNA methyltransferase CrBUD23 enhances biomass and lutein content in Chlamydomonas reinhardtii. Front Bioeng Biotechnol 2023; 11:1102098. [PMID: 36815903 PMCID: PMC9935685 DOI: 10.3389/fbioe.2023.1102098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Post-transcriptional modification of nucleic acids including transfer RNA (tRNA), ribosomal RNA (rRNA) and messenger RNA (mRNA) is vital for fine-tunning of mRNA translation. Methylation is one of the most widespread post-transcriptional modifications in both eukaryotes and prokaryotes. HsWBSCR22 and ScBUD23 encodes a 18S rRNA methyltransferase that positively regulates cell growth by mediating ribosome maturation in human and yeast, respectively. However, presence and function of 18S rRNA methyltransferase in green algae are still elusive. Here, through bioinformatic analysis, we identified CrBUD23 as the human WBSCR22 homolog in genome of the green algae model organism Chlamydonomas reinhardtii. CrBUD23 was a conserved putative 18S rRNA methyltransferase widely exited in algae, plants, insects and mammalians. Transcription of CrBUD23 was upregulated by high light and down-regulated by low light, indicating its role in photosynthesis and energy metabolism. To characterize its biological function, coding sequence of CrBUD23 fused with a green fluorescence protein (GFP) tag was derived by 35S promoter and stably integrated into Chlamydomonas genome by glass bead-mediated transformation. Compared to C. reinhardtii wild type CC-5325, transgenic strains overexpressing CrBUD23 resulted in accelerated cell growth, thereby leading to elevated biomass, dry weight and protein content. Moreover, overexpression of CrBUD23 increased content of photosynthetic pigments but not elicit the activation of antioxidative enzymes, suggesting CrBUD23 favors growth and proliferation in the trade-off with stress responses. Bioinformatic analysis revealed the G1177 was the putative methylation site in 18S rRNA of C. reinhardtii CC-849. G1177 was conserved in other Chlamydonomas isolates, indicating the conserved methyltransferase activity of BUD23 proteins. In addition, CrTrm122, the homolog of BUD23 interactor Trm112, was found involved in responses to high light as same as CrBUD23. Taken together, our study revealed that cell growth, protein content and lutein accumulation of Chlamydomonas were positively regulated by the 18S rRNA methyltransferase CrBUD23, which could serve as a promising candidate for microalgae genetic engineering.
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Affiliation(s)
- Chenglong Liu
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China,College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Haoze Guo
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xinmei Zhao
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Bingxi Zou
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ting Sun
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jinwei Feng
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhiyong Zeng
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xueer Wen
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jun Chen
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhangli Hu
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Sulin Lou
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China,*Correspondence: Hui Li, ; Sulin Lou,
| | - Hui Li
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China,*Correspondence: Hui Li, ; Sulin Lou,
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Zhao J, Xu H, Su Y, Pan J, Xie S, Xu J, Qin L. Emerging Regulatory Mechanisms of N 6-Methyladenosine Modification in Cancer Metastasis. Phenomics 2023; 3:83-100. [PMID: 36939763 PMCID: PMC9883376 DOI: 10.1007/s43657-021-00043-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 12/21/2021] [Accepted: 12/27/2021] [Indexed: 12/20/2022]
Abstract
Cancer metastasis is the major cause of cancer-related deaths and accounts for poor therapeutic outcomes. A metastatic cascade is a series of complicated biological processes. N6-methyladenosine (m6A) is the most abundant and conserved epitranscriptomic modification in eukaryotic cells, which has great impacts on RNA production and metabolism, including RNA splicing, processing, degradation and translation. Accumulating evidence demonstrates that m6A plays a critical role in regulating cancer metastasis. However, there is a lack of studies that review the recent advances of m6A in cancer metastasis. Here, we systematically retrieved the functions and mechanisms of how the m6A axis regulates metastasis, and especially summarized the organ-specific liver, lung and brain metastasis mediated by m6A in various cancers. Moreover, we discussed the potential application of m6A modification in cancer diagnosis and therapy, as well as the present limitations and future perspectives of m6A in cancer metastasis. This review provides a comprehensive knowledge on the m6A-mediated regulation of gene expression, which is helpful to extensively understand the complexity of cancer metastasis from a new epitranscriptomic point of view and shed light on the developing novel strategies to anti-metastasis based on m6A alteration.
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Affiliation(s)
- Jing Zhao
- Department of General Surgery, Huashan Hospital, Fudan University, 12 Urumqi Road (M), Shanghai, 200040 China
- Cancer Metastasis Institute, Fudan University, Shanghai, 200120 China
| | - Hao Xu
- Department of General Surgery, Huashan Hospital, Fudan University, 12 Urumqi Road (M), Shanghai, 200040 China
- Cancer Metastasis Institute, Fudan University, Shanghai, 200120 China
| | - Yinghan Su
- Department of General Surgery, Huashan Hospital, Fudan University, 12 Urumqi Road (M), Shanghai, 200040 China
- Cancer Metastasis Institute, Fudan University, Shanghai, 200120 China
| | - Junjie Pan
- Department of General Surgery, Huashan Hospital, Fudan University, 12 Urumqi Road (M), Shanghai, 200040 China
- Cancer Metastasis Institute, Fudan University, Shanghai, 200120 China
| | - Sunzhe Xie
- Department of General Surgery, Huashan Hospital, Fudan University, 12 Urumqi Road (M), Shanghai, 200040 China
- Cancer Metastasis Institute, Fudan University, Shanghai, 200120 China
| | - Jianfeng Xu
- Department of General Surgery, Huashan Hospital, Fudan University, 12 Urumqi Road (M), Shanghai, 200040 China
- Cancer Metastasis Institute, Fudan University, Shanghai, 200120 China
| | - Lunxiu Qin
- Department of General Surgery, Huashan Hospital, Fudan University, 12 Urumqi Road (M), Shanghai, 200040 China
- Cancer Metastasis Institute, Fudan University, Shanghai, 200120 China
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30
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Hori H. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Genes (Basel) 2023; 14:genes14020382. [PMID: 36833309 PMCID: PMC9957541 DOI: 10.3390/genes14020382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The existence of the thiouridine synthetase, methyltransferase and pseudouridine synthase (THUMP) domain was originally predicted by a bioinformatic study. Since the prediction of the THUMP domain more than two decades ago, many tRNA modification enzymes containing the THUMP domain have been identified. According to their enzymatic activity, THUMP-related tRNA modification enzymes can be classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase. In this review, I focus on the functions and structures of these tRNA modification enzymes and the modified nucleosides they produce. Biochemical, biophysical and structural studies of tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase have established the concept that the THUMP domain captures the 3'-end of RNA (in the case of tRNA, the CCA-terminus). However, in some cases, this concept is not simply applicable given the modification patterns observed in tRNA. Furthermore, THUMP-related proteins are involved in the maturation of other RNAs as well as tRNA. Moreover, the modified nucleosides, which are produced by the THUMP-related tRNA modification enzymes, are involved in numerous biological phenomena, and the defects of genes for human THUMP-related proteins are implicated in genetic diseases. In this review, these biological phenomena are also introduced.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
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31
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Adamopoulos PG, Athanasopoulou K, Daneva GN, Scorilas A. The Repertoire of RNA Modifications Orchestrates a Plethora of Cellular Responses. Int J Mol Sci 2023; 24. [PMID: 36768716 DOI: 10.3390/ijms24032387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Although a plethora of DNA modifications have been extensively investigated in the last decade, recent breakthroughs in molecular biology, including high throughput sequencing techniques, have enabled the identification of post-transcriptional marks that decorate RNAs; hence, epitranscriptomics has arisen. This recent scientific field aims to decode the regulatory layer of the transcriptome and set the ground for the detection of modifications in ribose nucleotides. Until now, more than 170 RNA modifications have been reported in diverse types of RNA that contribute to various biological processes, such as RNA biogenesis, stability, and transcriptional and translational accuracy. However, dysfunctions in the RNA-modifying enzymes that regulate their dynamic level can lead to human diseases and cancer. The present review aims to highlight the epitranscriptomic landscape in human RNAs and match the catalytic proteins with the deposition or deletion of a specific mark. In the current review, the most abundant RNA modifications, such as N6-methyladenosine (m6A), N5-methylcytosine (m5C), pseudouridine (Ψ) and inosine (I), are thoroughly described, their functional and regulatory roles are discussed and their contributions to cellular homeostasis are stated. Ultimately, the involvement of the RNA modifications and their writers, erasers, and readers in human diseases and cancer is also discussed.
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Murphy JC, Harrington EM, Schumann S, Vasconcelos EJR, Mottram TJ, Harper KL, Aspden JL, Whitehouse A. Kaposi's sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs. Nat Commun 2023; 14:300. [PMID: 36653366 DOI: 10.1038/s41467-023-35914-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Historically, ribosomes were viewed as unchanged homogeneous macromolecular machines with no regulatory capacity for mRNA translation. An emerging concept is that heterogeneity of ribosomal composition exists, exerting a regulatory function or specificity in translational control. This is supported by recent discoveries identifying compositionally distinct specialised ribosomes that actively regulate mRNA translation. Viruses lack their own translational machinery and impose high translational demands on the host during replication. We explore the possibility that KSHV manipulates ribosome biogenesis producing specialised ribosomes which preferentially translate viral transcripts. Quantitative proteomic analysis identified changes in the stoichiometry and composition of precursor ribosomal complexes during the switch from latent to lytic replication. We demonstrate the enhanced association of ribosomal biogenesis factors BUD23 and NOC4L, and the KSHV ORF11 protein, with small ribosomal subunit precursor complexes during lytic replication. BUD23 depletion resulted in significantly reduced viral gene expression, culminating in dramatic reduction of infectious virion production. Ribosome profiling demonstrated BUD23 is essential for reduced association of ribosomes with KSHV uORFs in late lytic genes, required for the efficient translation of the downstream coding sequence. Results provide mechanistic insights into KSHV-mediated manipulation of cellular ribosome composition inducing a population of specialised ribosomes facilitating efficient translation of viral mRNAs.
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Abstract
In recent years, N7-methylguanosine (m7G) methylation, originally considered as messenger RNA (mRNA) 5' caps modifications, has been identified at defined internal positions within multiple types of RNAs, including transfer RNAs, ribosomal RNAs, miRNA, and mRNAs. Scientists have put substantial efforts to discover m7G methyltransferases and methylated sites in RNAs to unveil the essential roles of m7G modifications in the regulation of gene expression and determine the association of m7G dysregulation in various diseases, including neurological disorders. Here, we review recent findings regarding the distribution, abundance, biogenesis, modifiers, and functions of m7G modifications. We also provide an up-to-date summary of m7G detection and profile mapping techniques, databases for validated and predicted m7G RNA sites, and web servers for m7G methylation prediction. Furthermore, we discuss the pathological roles of METTL1/WDR-driven m7G methylation in neurological disorders. Last, we outline a roadmap for future directions and trends of m7G modification research, particularly in the central nervous system.
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Affiliation(s)
- Xiaohuan Xia
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China,Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai 200331, China,Corresponding author: Xiaohuan Xia, Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200065, China.
| | - Yi Wang
- Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai 200331, China,Translational Research Center, Shanghai Yangzhi Rehabilitation Hospital affiliated to Tongji University School of Medicine, Shanghai 201613, China
| | - Jialin C. Zheng
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China,Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai 200331, China,Corresponding author: Jialin C. Zheng, Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200065, China.
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Naarmann-de Vries IS, Zorbas C, Lemsara A, Piechotta M, Ernst FGM, Wacheul L, Lafontaine DLJ, Dieterich C. Comprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2. RNA Biol 2023; 20:652-665. [PMID: 37635368 PMCID: PMC10464549 DOI: 10.1080/15476286.2023.2248752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
Ribosomal RNAs are decorated by numerous post-transcriptional modifications whose exact roles in ribosome biogenesis, function, and human pathophysiology remain largely unknown. Here, we report a targeted direct rRNA sequencing approach involving a substrate selection step and demonstrate its suitability to identify differential modification sites in combination with the JACUSA2 software. We compared JACUSA2 to other tools designed for RNA modification detection and show that JACUSA2 outperforms other software with regard to detection of base modifications such as methylation, acetylation and aminocarboxypropylation. To illustrate its widespread usability, we applied our method to a collection of CRISPR-Cas9 engineered colon carcinoma cells lacking specific enzymatic activities responsible for particular rRNA modifications and systematically compared them to isogenic wild-type RNAs. Besides the numerous 2'-O methylated riboses and pseudouridylated residues, our approach was suitable to reliably identify differential base methylation and acetylation events. Importantly, our method does not require any prior knowledge of modification sites or the need to train complex models. We further report for the first time detection of human rRNA modifications by direct RNA-sequencing on Flongle flow cells, the smallest-scale nanopore flow cell available to date. The use of these smaller flow cells reduces RNA input requirements, making our workflow suitable for the analysis of samples with limited availability and clinical work.
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Affiliation(s)
- Isabel S. Naarmann-de Vries
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christiane Zorbas
- RNA Molecular Biology, Université libre de Bruxelles (ULB), Fonds de la Recherche Scientifique (F.R.S./FNRS), Gosselies, Belgium
| | - Amina Lemsara
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Piechotta
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix G. M. Ernst
- RNA Molecular Biology, Université libre de Bruxelles (ULB), Fonds de la Recherche Scientifique (F.R.S./FNRS), Gosselies, Belgium
| | - Ludivine Wacheul
- RNA Molecular Biology, Université libre de Bruxelles (ULB), Fonds de la Recherche Scientifique (F.R.S./FNRS), Gosselies, Belgium
| | - Denis L. J. Lafontaine
- RNA Molecular Biology, Université libre de Bruxelles (ULB), Fonds de la Recherche Scientifique (F.R.S./FNRS), Gosselies, Belgium
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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36
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Hamar R, Varga M. The role of post-transcriptional modifications during development. Biol Futur 2022. [PMID: 36481986 DOI: 10.1007/s42977-022-00142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
AbstractWhile the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological advances, such as high-throughput next-generation sequencing (NGS) methods and nanopore-based mapping technologies, have made it possible to map the position of these modifications with single nucleotide accuracy, and genetic screens have uncovered the “writer”, “reader” and “eraser” proteins that help to install, interpret and remove such modifications, respectively. These discoveries led to intensive research programmes with the aim of uncovering the roles of these modifications during diverse biological processes. In this review, we assess novel discoveries related to the role of post-transcriptional modifications during animal development, highlighting how these discoveries can affect multiple aspects of development from fertilization to differentiation in many species.
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37
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Liu P, Dong C, Shi H, Yan Z, Zhang J, Liu J. Constructing and validating of m7G-related genes prognostic signature for hepatocellular carcinoma and immune infiltration: potential biomarkers for predicting the overall survival. J Gastrointest Oncol 2022; 13:3169-3182. [PMID: 36636051 PMCID: PMC9830319 DOI: 10.21037/jgo-22-1134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Background To investigate the prognostic significance of N7-methylguanosine (m7G) regulators and immune infiltration in liver hepatocellular carcinoma (LIHC). Methods The research measured predictive m7G genes in LIHC samples from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets. Data on the stemness index based on mRNA expression (mRNAsi), gene mutations, and corresponding clinical characteristics were obtained from TCGA and ICGC. Lasso regression was used to construct the prediction model to assess the m7G prognostic signals in LIHC. Based on these genes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to identify key biological functions and pathways. The correlation between m7G RNA methylation regulators and the prognosis and immune infiltration of LIHC was evaluated. Results There were 21 m7G-related differentially expressed genes (DEGs) in LIHC and healthy tissues, and LIHC patients could be divided into two categories by consensus clustering of these DEGs. A five-gene predictive approach was employed using least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Patients in the low-risk group showed a significantly higher survival rate compared with those in the high-risk group (P=0.001). Validations using the ICGC database. Also, univariate and multivariate Cox regression analyses suggested that the risk score produced by the predictive model is an independent predictor for LIHC [hazard ratio (HR): 1.848, 95% confidence interval (CI): 1.286-2.656; HR: 2.597, 95% CI: 1.358-4.965]. The ROC curves of the ICGC cohort revealed that the five-gene prediction model performed well [area under the curve (AUC) =0.642 at 1 year, AUC =0.686 at 2 years, and AUC =0.667 at 3 years]. Immuno-oncology scoring revealed that in the high-risk group, among 16 immune cells, the expressions of neutrophils and natural killer (NK) cells were low and that of regulatory T-cells (Tregs) was high. Conclusions LIHC occurrence and progression are linked to m7G-related genes. Corresponding prognostic models help forecast the prognosis of LIHC patients. m7G-related genes and associated immune cell infiltration in the TME may serve as potential therapeutic targets in LIHC, which requires further trials. In addition, the m7G-related gene signature offers a viable alternative to predict LIHC, and these m7G-related genes show a prospective research area for LIHC targeted treatment in the future.
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Affiliation(s)
- Pulin Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chengda Dong
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hongshuo Shi
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhaojun Yan
- Department of Psychosomatic Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Junlong Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China;,National International Joint Research Center of Molecular Traditional Chinese Medicine, Shanxi University of Traditional Chinese Medicine, Jinzhong, China;,Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Shanxi University of Traditional Chinese Medicine, Jinzhong, China
| | - Jianmin Liu
- Department of Psychosomatic Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:ijms232213851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
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Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
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Ma S, Zhu J, Wang M, Zhu J, Wang W, Xiong Y, Jiang R, Liu L, Jiang T. Comprehensive analysis of m7G modification patterns based on potential m7G regulators and tumor microenvironment infiltration characterization in lung adenocarcinoma. Front Genet 2022; 13:996950. [PMID: 36246663 PMCID: PMC9559715 DOI: 10.3389/fgene.2022.996950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The non-negligible role of epigenetic modifications in cancer development and tumor microenvironment (TME) has been demonstrated in recent studies. Nonetheless, the potential regulatory role of N7-methylguanosine (m7G) modification in shaping and impacting the TME remains unclear. Methods: A comprehensive analysis was performed to explore the m7G modification patterns based on 24 potential m7G regulators in 817 lung adenocarcinoma (LUAD) patients, and the TME landscape in distinct m7G modification patterns were evaluated. The m7G score was established based on principal component analysis (PCA) to quantify m7G modification patterns and evaluate the TME cell infiltrating characteristics of individual tumors. Further, correlation analyses of m7Gscore with response to chemotherapy and immunotherapy were performed. Results: We identified three distinct m7G modification patterns with the biological pathway enrichment and TME cell infiltrating characteristics corresponded to immune-desert, immune-inflamed and immune-excluded phenotype, respectively. We further demonstrated the m7Gscore could predict the TME infiltrating characteristics, tumor mutation burden (TMB), response to immunotherapy and chemotherapy, as well as prognosis of individual tumors. High m7Gscore was associated with increased component of immune cell infiltration, low TMB and survival advantage, while low m7Gscore was linked to decreased immune cell infiltration and increased TMB. Additionally, patients with lower m7Gscore demonstrated significant therapeutic advantages. Conclusion: This study demonstrated the regulatory mechanisms of m7G modification on TME formation and regulation of lung adenocarcinoma. Identification of individual tumor m7G modification patterns will contribute to the understanding of TME characterization and guiding more effective immunotherapy strategies.
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Affiliation(s)
- Shouzheng Ma
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Jun Zhu
- Department of General Surgery, The Southern Theater Air Force Hospital, Guangzhou, China
| | - Mengmeng Wang
- Department of Drug and Equipment, Lintong Rehabilitation and Convalescent Centre, Xi’an, China
| | - Jianfei Zhu
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Wenchen Wang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Yanlu Xiong
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Runmin Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Lei Liu
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
- *Correspondence: Lei Liu, ; Tao Jiang,
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
- *Correspondence: Lei Liu, ; Tao Jiang,
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Xu J, Cen X, Yao Y, Zhao S, Li W, Zhang W, Qiu M, Muddassir Ali M. Identification of Six N7-Methylguanosine-Related miRNA Signatures to Predict the Overall Survival and Immune Landscape of Triple-Negative Breast Cancer through In Silico Analysis. Journal of Oncology 2022; 2022:1-16. [PMID: 36199792 PMCID: PMC9529398 DOI: 10.1155/2022/2735251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
Triple-negative breast cancer (TNBC) is a widely prevalent breast cancer, with a mortality rate of up to 25%. TNBC has a lower survival rate, and the significance of N7-methylguanosine (m7G) modification in TNBC remains unclear. Thus, this study is aimed at investigating m7G-related miRNAs in TNBC patients through in silico analysis. In our research, RNA sequencing and clinical data were obtained from The Cancer Genome Atlas (TCGA) database. The miRNAs targeting typical m7G modification regulators Methyltransferase-like 1 (METTL1) and WD repeat domain 4 (WDR4) were predicted on the TargetScan website. A miRNA risk model was built, and its prognostic value was evaluated by R soft packages. Single-sample gene set enrichment analysis was used to assess immune infiltration, and further expression of immune checkpoints was investigated. As a result, miR-421, miR-5001-3p, miR-4326, miR-1915-3p, miR-3177-5p, and miR-4505 were identified to create the risk model. A nomogram consisting of the stage N and risk model predicted overall survival effectively among TNBC patients. Treg and TIL were shown to be strongly linked to the risk model, and the high-risk group had higher levels of four immune checkpoints expression (CD28, CTLA-4, ICOS, and TNFRSF9). A risk model consisting of m7G-related miRNAs was constructed. The findings of the current study could be used as a prognostic biomarker and can provide a novel immunotherapy insight for TNBC patients.
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Liao H, Gaur A, McConie H, Shekar A, Wang K, Chang JT, Breton G, Denicourt C. Human NOP2/NSUN1 regulates ribosome biogenesis through non-catalytic complex formation with box C/D snoRNPs. Nucleic Acids Res 2022; 50:10695-10716. [PMID: 36161484 PMCID: PMC9561284 DOI: 10.1093/nar/gkac817] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022] Open
Abstract
5-Methylcytosine (m5C) is a base modification broadly found on various RNAs in the human transcriptome. In eukaryotes, m5C is catalyzed by enzymes of the NSUN family composed of seven human members (NSUN1-7). NOP2/NSUN1 has been primarily characterized in budding yeast as an essential ribosome biogenesis factor required for the deposition of m5C on the 25S ribosomal RNA (rRNA). Although human NOP2/NSUN1 has been known to be an oncogene overexpressed in several types of cancer, its functions and substrates remain poorly characterized. Here, we used a miCLIP-seq approach to identify human NOP2/NSUN1 RNA substrates. Our analysis revealed that NOP2/NSUN1 catalyzes the deposition of m5C at position 4447 on the 28S rRNA. We also find that NOP2/NSUN1 binds to the 5′ETS region of the pre-rRNA transcript and regulates pre-rRNA processing through non-catalytic complex formation with box C/D snoRNAs. We provide evidence that NOP2/NSUN1 facilitates the recruitment of U3 and U8 snoRNAs to pre-90S ribosomal particles and their stable assembly into snoRNP complexes. Remarkably, expression of both WT and catalytically inactive NOP2/NSUN1 in knockdown background rescues the rRNA processing defects and the stable assembly of box C/D snoRNP complexes, suggesting that NOP2/NSUN1-mediated deposition of m5C on rRNA is not required for ribosome synthesis.
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Affiliation(s)
- Han Liao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Anushri Gaur
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Hunter McConie
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Amirtha Shekar
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Karen Wang
- Wiess College, Rice University, Houston, TX 77251, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Ghislain Breton
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
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Abstract
As one of the prevalent posttranscriptional modifications of RNA, N7-methylguanosine (m7G) plays essential roles in RNA processing, metabolism, and function, mainly regulated by the methyltransferase-like 1 (METTL1) and WD repeat domain 4 (WDR4) complex. Emerging evidence suggests that the METTL1/WDR4 complex promoted or inhibited the processes of many tumors, including head and neck, lung, liver, colon, bladder cancer, and teratoma, dependent on close m7G methylation modification of tRNA or microRNA (miRNA). Therefore, METTL1 and m7G modification can be used as biomarkers or potential intervention targets, providing new possibilities for early diagnosis and treatment of tumors. This review will mainly focus on the mechanisms of METTL1/WDR4 via m7G in tumorigenesis and the corresponding detection methods.
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Affiliation(s)
- Wenli Cheng
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Aili Gao
- Guangzhou Institution of Dermatology, Guangzhou, Guangdong 510095, P.R. China
| | - Hui Lin
- Department of Radiation Oncology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P. R. China
| | - Wenjuan Zhang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
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Feng Q, Wang D, Xue T, Lin C, Gao Y, Sun L, Jin Y, Liu D. The role of RNA modification in hepatocellular carcinoma. Front Pharmacol 2022; 13:984453. [PMID: 36120301 PMCID: PMC9479111 DOI: 10.3389/fphar.2022.984453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/11/2022] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly mortal type of primary liver cancer. Abnormal epigenetic modifications are present in HCC, and RNA modification is dynamic and reversible and is a key post-transcriptional regulator. With the in-depth study of post-transcriptional modifications, RNA modifications are aberrantly expressed in human cancers. Moreover, the regulators of RNA modifications can be used as potential targets for cancer therapy. In RNA modifications, N6-methyladenosine (m6A), N7-methylguanosine (m7G), and 5-methylcytosine (m5C) and their regulators have important regulatory roles in HCC progression and represent potential novel biomarkers for the confirmation of diagnosis and treatment of HCC. This review focuses on RNA modifications in HCC and the roles and mechanisms of m6A, m7G, m5C, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and pseudouridine (ψ) on its development and maintenance. The potential therapeutic strategies of RNA modifications are elaborated for HCC.
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Affiliation(s)
- Qiang Feng
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Tianyi Xue
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Chao Lin
- School of Grain Science and Technology, Jilin Business and Technology College, Changchun, China
| | - Yongjian Gao
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Liqun Sun
- Department of Pediatrics, First Hospital of Jilin University, Changchun, China
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Dianfeng Liu
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Dianfeng Liu,
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Chen J, Yao S, Sun Z, Wang Y, Yue J, Cui Y, Yu C, Xu H, Li L. The pattern of expression and prognostic value of key regulators for m7G RNA methylation in hepatocellular carcinoma. Front Genet 2022; 13:894325. [PMID: 36118897 PMCID: PMC9478798 DOI: 10.3389/fgene.2022.894325] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
N7-methylguanosine (m7G) modification on internal RNA positions plays a vital role in several biological processes. Recent research shows m7G modification is associated with multiple cancers. However, in hepatocellular carcinoma (HCC), its implications remain to be determined. In this place, we need to interrogate the mRNA patterns for 29 key regulators of m7G RNA modification and assess their prognostic value in HCC. Initial, the details from The Cancer Genome Atlas (TCGA) database concerning transcribed gene data and clinical information of HCC patients were inspected systematically. Second, according to the mRNA profiles of 29 m7G RNA methylation regulators, two clusters (named 1 and 2, respectively) were identified by consensus clustering. Furthermore, robust risk signature for seven m7G RNA modification regulators was constructed. Last, we used the Gene Expression Omnibus (GEO) dataset to validate the prognostic associations of the seven-gene risk signature. We figured out that 24/29 key regulators of m7G RNA modification varied remarkably in their grades of expression between the HCC and the adjacent tumor control tissues. Cluster one compared with cluster two had a substandard prognosis and was also positively correlated with T classification (T), pathological stage, and vital status (fustat) significantly. Consensus clustering results suggested the expression pattern of m7G RNA modification regulators was correlated with the malignancy of HCC strongly. In addition, cluster one was extensively enriched in metabolic-related pathways. Seven optimal genes (METTL1, WDR4, NSUN2, EIF4E, EIF4E2, NCBP1, and NCBP2) were selected to establish the risk model for HCC. Indicating by further analyses and validation, the prognostic model has fine anticipating command and this probability signature might be a self supporting presage factor for HCC. Finally, a new prognostic nomogram based on age, gender, pathological stage, histological grade, and prospects were established to forecast the prognosis of HCC patients accurately. In essence, we detected association of HCC severity and expression levels of m7G RNA modification regulators, and developed a risk score model for predicting prognosis of HCC patients’ progression.
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Affiliation(s)
- Jianxing Chen
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shibin Yao
- Department of Emergency, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Zhijuan Sun
- International Education School, Chifeng University, Chifeng, China
| | - Yanjun Wang
- Department of Pediatrics, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Jili Yue
- Department of General Surgery, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Yongkang Cui
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chengping Yu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Haozhi Xu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Linqiang Li
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin Medical University, Harbin, China
- *Correspondence: Linqiang Li,
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Wang S, Li H, Lian Z, Deng S. The Role of RNA Modification in HIV-1 Infection. Int J Mol Sci 2022; 23:7571. [PMID: 35886919 PMCID: PMC9317671 DOI: 10.3390/ijms23147571] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 01/25/2023] Open
Abstract
RNA plays an important role in biology, and more than 170 RNA modifications have been identified so far. Post-transcriptional modification of RNA in cells plays a crucial role in the regulation of its stability, transport, processing, and gene expression. So far, the research on RNA modification and the exact role of its enzymes is becoming more and more comprehensive. Human immunodeficiency virus 1 (HIV-1) is an RNA virus and the causative agent of acquired immunodeficiency syndrome (AIDS), which is one of the most devastating viral pandemics in history. More and more studies have shown that HIV has RNA modifications and regulation of its gene expression during infection and replication. This review focuses on several RNA modifications and their regulatory roles as well as the roles that different RNA modifications play during HIV-1 infection, in order to find new approaches for the development of anti-HIV-1 therapeutics.
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Mariasina SS, Chang CF, Navalayeu TL, Chugunova AA, Efimov SV, Zgoda VG, Ivlev VA, Dontsova OA, Sergiev PV, Polshakov VI. Williams-Beuren Syndrome Related Methyltransferase WBSCR27: From Structure to Possible Function. Front Mol Biosci 2022; 9:865743. [PMID: 35782865 PMCID: PMC9240639 DOI: 10.3389/fmolb.2022.865743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Williams-Beuren syndrome (WBS) is a genetic disorder associated with the hemizygous deletion of several genes in chromosome 7, encoding 26 proteins. Malfunction of these proteins induce multisystemic failure in an organism. While biological functions of most proteins are more or less established, the one of methyltransferase WBSCR27 remains elusive. To find the substrate of methylation catalyzed by WBSCR27 we constructed mouse cell lines with a Wbscr27 gene knockout and studied the obtained cells using several molecular biology and mass spectrometry techniques. We attempted to pinpoint the methylation target among the RNAs and proteins, but in all cases neither a direct substrate has been identified nor the protein partners have been detected. To reveal the nature of the putative methylation substrate we determined the solution structure and studied the conformational dynamic properties of WBSCR27 in apo state and in complex with S-adenosyl-L-homocysteine (SAH). The protein core was found to form a canonical Rossman fold common for Class I methyltransferases. N-terminus of the protein and the β6–β7 loop were disordered in apo-form, but binding of SAH induced the transition of these fragments to a well-formed substrate binding site. Analyzing the structure of this binding site allows us to suggest potential substrates of WBSCR27 methylation to be probed in further research.
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Affiliation(s)
- Sofia S. Mariasina
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia
- Institute of Functional Genomics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | - Sergey V. Efimov
- NMR Laboratory, Institute of Physics, Kazan Federal University, Kazan, Russia
| | | | | | - Olga A. Dontsova
- Chemical Department, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Petr V. Sergiev
- Institute of Functional Genomics, M.V. Lomonosov Moscow State University, Moscow, Russia
- Chemical Department, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vladimir I. Polshakov
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia
- *Correspondence: Vladimir I. Polshakov,
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Liu Y, Zhu T, Jiang Y, Bu J, Zhu X, Gu X. The Key Role of RNA Modification in Breast Cancer. Front Cell Dev Biol 2022; 10:885133. [PMID: 35721510 PMCID: PMC9198488 DOI: 10.3389/fcell.2022.885133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/25/2022] [Indexed: 12/09/2022] Open
Abstract
The modulation of the function and expression of epigenetic regulators of RNA modification has gradually become the hotspot of cancer research. Studies have shown that alteration of epigenetic modifications can promote the development and metastasis of breast cancer. This review highlights the progress in characterization of the link between RNA modification and the prognosis, carcinogenesis and treatment of breast cancer, which may provide a new theoretical basis for development of effective strategies for monitoring of breast cancer based on epigenetics.
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Liang W, Yi H, Mao C, Meng Q, Wu X, Li S, Xue J. Research Progress of RNA Methylation Modification in Colorectal Cancer. Front Pharmacol 2022; 13:903699. [PMID: 35614935 PMCID: PMC9125385 DOI: 10.3389/fphar.2022.903699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 12/24/2022] Open
Abstract
Accumulating evidence indicates that RNA methylation, as the most common modification of mRNA, is of great significance in tumor progression and metastasis. Colorectal cancer is a common malignant tumor of the digestive system that seriously affects the health of middle-aged and elderly people. Although there have been many studies on the biological mechanism of the occurrence and development of colorectal cancer, there are still major deficiencies in the diagnosis and prognosis of colorectal cancer. With the deep study of RNA methylation, it was found that RNA modification is highly related to colorectal cancer tumorigenesis, development and prognosis. Here, we will highlight various RNA chemical modifications including N6-methyladenosine, 5-methylcytosine, N1-methyladenosine, 7-methylguanine, pseudouridine and their modification enzymes followed by summarizing their functions in colorectal cancer.
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Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Hongyang Yi
- The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Chenyu Mao
- School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States
| | - Qingxue Meng
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Xueliang Wu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Shanliang Li
- Department of Pharmacology, Guangxi University of Chinese Medicine, Nanning, China
| | - Jun Xue
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
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Abstract
N7-methylguanosine (m7G), one of the most prevalent RNA modifications, has recently attracted significant attention. The m7G modification actively participates in biological and pathological functions by affecting the metabolism of various RNA molecules, including messenger RNA, ribosomal RNA, microRNA, and transfer RNA. Increasing evidence indicates a critical role for m7G in human disease development, especially cancer, and aberrant m7G levels are closely associated with tumorigenesis and progression via regulation of the expression of multiple oncogenes and tumor suppressor genes. Currently, the underlying molecular mechanisms of m7G modification in cancer are not comprehensively understood. Here, we review the current knowledge regarding the potential function of m7G modifications in cancer and discuss future m7G-related diagnostic and therapeutic strategies.
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Affiliation(s)
- Yuejun Luo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuxin Yao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Wu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaohui Zi
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China. .,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China. .,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Ming J, Wang C. N7-Methylguanosine-Related lncRNAs: Integrated Analysis Associated With Prognosis and Progression in Clear Cell Renal Cell Carcinoma. Front Genet 2022; 13:871899. [PMID: 35495133 PMCID: PMC9043611 DOI: 10.3389/fgene.2022.871899] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/29/2022] [Indexed: 01/07/2023] Open
Abstract
N7-Methylguanosine (m7G) and long non-coding RNAs (lncRNAs) have been widely reported to play an important role in cancer. However, there is little known about the relationship between m7G-related lncRNAs and clear cell renal cell carcinoma (ccRCC). To find new potential biomarkers and construct an m7G-related lncRNA prognostic signature for ccRCC, we retrieved transcriptome data and clinical data from The Cancer Genome Atlas (TCGA), and divided the entire set into train set and test set with the ratio of 1:1 randomly. The m7G-related lncRNAs were identified by Pearson correlation analysis (|coefficients| > 0.4, and p < 0.001). Then we performed the univariate Cox regression and least absolute shrinkage and selection operator (LASSO) Cox regression analysis to construct a 12 m7G-related lncRNA prognostic signature. Next, principal component analysis (PCA), the Kaplan–Meier method, time-dependent receiver operating characteristics (ROC) were made to verify and evaluate the risk signature. A nomogram based on the risk signature and clinical parameters was developed and showed high accuracy and reliability for predicting the overall survival (OS). Functional enrichment analysis (GO, KEGG and GSEA) was used to investigate the potential biological pathways. We also performed the analysis of tumor mutation burden (TMB), immunological analysis including immune scores, immune cell infiltration (ICI), immune function, tumor immune escape (TIE) and immunotherapeutic drug in our study. In conclusion, using the 12 m7G-related lncRNA risk signature as a prognostic indicator may offer us insight into the oncogenesis and treatment response prediction of ccRCC.
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