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Li B, Zhou Q, Cai L, Li L, Xie C, Li D, Zhu F, Li X, Zhao X, Liu X, Shen L, Xu T, He C. TMK4-mediated FIP37 phosphorylation regulates auxin-triggered N 6-methyladenosine modification of auxin biosynthetic genes in Arabidopsis. Cell Rep 2024; 43:114597. [PMID: 39106180 DOI: 10.1016/j.celrep.2024.114597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 03/20/2024] [Accepted: 07/23/2024] [Indexed: 08/09/2024] Open
Abstract
The dynamics of N6-methyladenosine (m6A) mRNA modification are tightly controlled by the m6A methyltransferase complex and demethylases. Here, we find that auxin treatment alters m6A modification on auxin-responsive genes. Mechanically, TRANSMEMBRANE KINASE 4 (TMK4), a component of the auxin signaling pathway, interacts with and phosphorylates FKBP12-INTERACTING PROTEIN 37 (FIP37), a core component of the m6A methyltransferase complex, in an auxin-dependent manner. Phosphorylation of FIP37 enhances its interaction with RNA, thereby increasing m6A modification on its target genes, such as NITRILASE 1 (NIT1), a gene involved in indole-3-acetic acid (IAA) biosynthesis. 1-Naphthalacetic acid (NAA) treatment accelerates the mRNA decay of NIT1, in a TMK4- and FIP37-dependent manner, which leads to inhibition of auxin biosynthesis. Our findings identify a regulatory mechanism by which auxin modulates m6A modification through the phosphorylation of FIP37, ultimately affecting mRNA stability and auxin biosynthesis in plants.
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Affiliation(s)
- Bin Li
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410082, China
| | - Qiting Zhou
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China
| | - Linjun Cai
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China
| | - Lan Li
- School of Pharmacy, Xiangnan University, Chenzhou, Hunan 423000, China
| | - Chong Xie
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China
| | - Donghao Li
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China
| | - Fan Zhu
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China
| | - Xiushan Li
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China
| | - Xiaoying Zhao
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China
| | - Xuanming Liu
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China
| | - Lisha Shen
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Tongda Xu
- FAFU-Joint Center, Horticulture and Metabolic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chongsheng He
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China.
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Zheng Z, Ling X, Li Y, Qiao S, Zhang S, Wu J, Ma Z, Li M, Guo X, Li Z, Feng Y, Liu X, Goodfellow IG, Zheng H, Xiao S. Host cells reprogram lipid droplet synthesis through YY1 to resist PRRSV infection. mBio 2024; 15:e0154924. [PMID: 38953350 PMCID: PMC11323570 DOI: 10.1128/mbio.01549-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024] Open
Abstract
Metabolism in host cells can be modulated after viral infection, favoring viral survival or clearance. Here, we report that lipid droplet (LD) synthesis in host cells can be modulated by yin yang 1 (YY1) after porcine reproductive and respiratory syndrome virus (PRRSV) infection, resulting in active antiviral activity. As a ubiquitously distributed transcription factor, there was increased expression of YY1 upon PRRSV infection both in vitro and in vivo. YY1 silencing promoted the replication of PRRSV, whereas YY1 overexpression inhibited PRRSV replication. PRRSV infection led to a marked increase in LDs, while YY1 knockout inhibited LD synthesis, and YY1 overexpression enhanced LD accumulation, indicating that YY1 reprograms PRRSV infection-induced intracellular LD synthesis. We also showed that the viral components do not colocalize with LDs during PRRSV infection, and the effect of exogenously induced LD synthesis on PRRSV replication is nearly lethal. Moreover, we demonstrated that YY1 affects the synthesis of LDs by regulating the expression of lipid metabolism genes. YY1 negatively regulates the expression of fatty acid synthase (FASN) to weaken the fatty acid synthesis pathway and positively regulates the expression of peroxisome proliferator-activated receptor gamma (PPARγ) to promote the synthesis of LDs, thus inhibiting PRRSV replication. These novel findings indicate that YY1 plays a crucial role in regulating PRRSV replication by reprogramming LD synthesis. Therefore, our study provides a novel mechanism of host resistance to PRRSV and suggests potential new antiviral strategies against PRRSV infection.IMPORTANCEPorcine reproductive and respiratory virus (PRRSV) has caused incalculable economic damage to the global pig industry since it was first discovered in the 1980s. However, conventional vaccines do not provide satisfactory protection. It is well known that viruses are parasitic pathogens, and the completion of their replication life cycle is highly dependent on host cells. A better understanding of host resistance to PRRSV infection is essential for developing safe and effective strategies to control PRRSV. Here, we report a crucial host antiviral molecule, yin yang 1 (YY1), which is induced to be expressed upon PRRSV infection and subsequently inhibits virus replication by reprogramming lipid droplet (LD) synthesis through transcriptional regulation. Our work provides a novel antiviral mechanism against PRRSV infection and suggests that targeting YY1 could be a new strategy for controlling PRRSV.
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Affiliation(s)
- Zifang Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xue Ling
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yang Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shuang Qiao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuangquan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jie Wu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Zhiqian Ma
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Mingyu Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuyang Guo
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhiwei Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yingtong Feng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiao Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ian G. Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shuqi Xiao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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Hangyu W, Panpan L, Jie S, Hongyan W, Linmiao W, Kangning H, Yichen S, Shuai W, Cheng W. Advancements in Antiviral Drug Development: Comprehensive Insights into Design Strategies and Mechanisms Targeting Key Viral Proteins. J Microbiol Biotechnol 2024; 34:1376-1384. [PMID: 38934770 PMCID: PMC11294656 DOI: 10.4014/jmb.2403.03008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 06/28/2024]
Abstract
Viral infectious diseases have always been a threat to human survival and quality of life, impeding the stability and progress of human society. As such, researchers have persistently focused on developing highly efficient, low-toxicity antiviral drugs, whether for acute or chronic infectious diseases. This article presents a comprehensive review of the design concepts behind virus-targeted drugs, examined through the lens of antiviral drug mechanisms. The intention is to provide a reference for the development of new, virus-targeted antiviral drugs and guide their clinical usage.
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Affiliation(s)
- Wang Hangyu
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Li Panpan
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Shen Jie
- School of Medical Laboratory, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Wang Hongyan
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Wei Linmiao
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Han Kangning
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Shi Yichen
- School of Stomatology, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Wang Shuai
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia 010050, P.R. China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, Inner Mongolia 010110, P.R. China
| | - Wang Cheng
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia 010050, P.R. China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, Inner Mongolia 010110, P.R. China
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Sun M, Ren J, Qu X. In situ bioorthogonal-modulation of m 6A RNA methylation in macrophages for efficient eradication of intracellular bacteria. Chem Sci 2024; 15:11657-11666. [PMID: 39055012 PMCID: PMC11268468 DOI: 10.1039/d4sc03629h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
N6-Methyladenosine (m6A) methylation plays a critical role in controlling the RNA fate. Emerging evidence has demonstrated that aberrant m6A methylation in immune cells such as macrophages could alter cell homeostasis and function, which can be a promising target for disease treatment. Despite tremendous progress in regulating the level of m6A methylation, the current methods suffer from the time-consuming operation and annoying off-target effect, which hampers the in situ manipulation of m6A methylation. Here, a bioorthogonal in situ modulation strategy of m6A methylation was proposed. Well-designed covalent organic framework (COF) dots (CIDM) could deprotect the agonist prodrug of m6A methyltransferase, resulting in a considerable hypermethylation of m6A modification. Simultaneously, the bioorthogonal catalyst CIDM showed oxidase (OXD)-mimic activity that further promoted the level of m6A methylation. Ultimately, the potential therapeutic effect of bioorthogonal controllable regulation of m6A methylation was demonstrated through intracellular bacteria eradication. The remarkable antimicrobial outcomes indicate that upregulating m6A methylation in macrophages could reprogram them into the M1 phenotype with high bactericidal activity. We believe that our bioorthogonal chemistry-controlled epigenetics regulatory strategy will provide a unique insight into the development of controllable m6A methylation.
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Affiliation(s)
- Mengyu Sun
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
- University of Science and Technology of China Hefei Anhui 230029 China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
- University of Science and Technology of China Hefei Anhui 230029 China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
- University of Science and Technology of China Hefei Anhui 230029 China
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5
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Liang G, Hu JY, Liu RJ, Chao YP, Hu YF, Zheng H, Pan XY, Li YJ, Gong YH, Lin C, Lin JH, Wang JD, Li TX, Pan JP, Guo DY. α-Ketoglutarate plays an inflammatory inhibitory role by regulating scavenger receptor class a expression through N6-methyladenine methylation during sepsis. Eur J Immunol 2024:e2350655. [PMID: 38973083 DOI: 10.1002/eji.202350655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 07/09/2024]
Abstract
Sepsis arises from an uncontrolled inflammatory response triggered by infection or stress, accompanied by alteration in cellular energy metabolism, and a strong correlation exists between these factors. Alpha-ketoglutarate (α-KG), an intermediate product of the TCA cycle, has the potential to modulate the inflammatory response and is considered a crucial link between energy metabolism and inflammation. The scavenger receptor (SR-A5), a significant pattern recognition receptor, assumes a vital function in anti-inflammatory reactions. In the current investigation, we have successfully illustrated the ability of α-KG to mitigate inflammatory factors in the serum of septic mice and ameliorate tissue damage. Additionally, α-KG has been shown to modulate metabolic reprogramming and macrophage polarization. Moreover, our findings indicate that the regulatory influence of α-KG on sepsis is mediated through SR-A5. We also elucidated the mechanism by which α-KG regulates SR-A5 expression and found that α-KG reduced the N6-methyladenosine level of macrophages by up-regulating the m6A demethylase ALKBH5. α-KG plays a crucial role in inhibiting inflammation by regulating SR-A5 expression through m6A demethylation during sepsis. The outcomes of this research provide valuable insights into the relationship between energy metabolism and inflammation regulation, as well as the underlying molecular regulatory mechanism.
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Affiliation(s)
- Gang Liang
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
- Zhejiang University school of medicine, Hangzhou, P. R. China
| | - Jia-Yan Hu
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Rou-Jun Liu
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Yu-Peng Chao
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Yi-Fan Hu
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Hong Zheng
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Xin-Yu Pan
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Yuan-Jing Li
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Yang-Hui Gong
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Chi Lin
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Jia-Hao Lin
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Jia-Dong Wang
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Tong-Xin Li
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
| | - Jian-Ping Pan
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
- Institute of Translational Medicine, Hangzhou City University, Hangzhou, P.R. China
| | - Dong-Yang Guo
- Department of Clinical Medicine, Hangzhou City University School of Medicine, Hangzhou, P.R. China
- Institute of Translational Medicine, Hangzhou City University, Hangzhou, P.R. China
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Huang B, Bopp T, Li G. 8th Sino-German symposium on immunology: fostering mutual trust and collaborative endeavors for advancing immunological science. Cell Mol Immunol 2024; 21:798-799. [PMID: 38822078 PMCID: PMC11214616 DOI: 10.1038/s41423-024-01173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/02/2024] Open
Affiliation(s)
- Bo Huang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Department of Biochemistry & Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Tobias Bopp
- Institute for Immunology, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany.
| | - Guideng Li
- National Key Laboratory of Immunity and Inflammation, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China.
- Key Laboratory of Synthetic Biology Regulatory Element, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China.
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Liu X, Chen W, Li K, Sheng J. RNA N6-methyladenosine methylation in influenza A virus infection. Front Microbiol 2024; 15:1401997. [PMID: 38957616 PMCID: PMC11217485 DOI: 10.3389/fmicb.2024.1401997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024] Open
Abstract
Influenza A virus (IAV) is a negative-sense single-stranded RNA virus that causes acute lung injury and acute respiratory distress syndrome, posing a serious threat to both animal and human health. N6-methyladenosine (m6A), a prevalent and abundant post-transcriptional methylation of RNA in eukaryotes, plays a crucial regulatory role in IAV infection by altering viral RNA and cellular transcripts to affect viral infection and the host immune response. This review focuses on the molecular mechanisms underlying m6A modification and its regulatory function in the context of IAV infection and the host immune response. This will provide a better understanding of virus-host interactions and offer insights into potential anti-IAV strategies.
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Affiliation(s)
- Xueer Liu
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Weiqiang Chen
- Department of Neurosurgery, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Kangsheng Li
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Jiangtao Sheng
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
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Li S, Tan XY, He Z, Shen C, Li YL, Qin L, Zhao CQ, Luo GH, Fang JC, Ji R. The dynamics of N 6-methyladenine RNA modification in resistant and susceptible rice varieties responding to rice stem borer damage. INSECT SCIENCE 2024. [PMID: 38831720 DOI: 10.1111/1744-7917.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024]
Abstract
N6-methyladenosine (m6A) is the most prevalent modification in cellular RNA which orchestrates diverse physiological and pathological processes during stress response. However, the differential m6A modifications that cope with herbivore stress in resistant and susceptible crop varieties remain unclear. Here, we found that rice stem borer (RSB) larvae grew better on indica rice (e.g., MH63, IR64, Nanjing 11) than on japonica rice varieties (e.g., Nipponbare, Zhonghua 11, Xiushui 11). Then, transcriptome-wide m6A profiling of representative resistant (Nipponbare) and susceptible (MH63) rice varieties were performed using a nanopore direct RNA sequencing approach, to reveal variety-specific m6A modifications against RSB. Upon RSB infestation, m6A methylation occurred in actively expressed genes in Nipponbare and MH63, but the number of methylation sites decreased across rice chromosomes. Integrative analysis showed that m6A methylation levels were closely associated with transcriptional regulation. Genes involved in herbivorous resistance related to mitogen-activated protein kinase, jasmonic acid (JA), and terpenoid biosynthesis pathways, as well as JA-mediated trypsin protease inhibitors, were heavily methylated by m6A, and their expression was more pronounced in RSB-infested Nipponbare than in RSB-infested MH63, which may have contributed to RSB resistance in Nipponbare. Therefore, dynamics of m6A modifications act as the main regulatory strategy for expression of genes involved in plant-insect interactions, which is attributed to differential responses of resistant and susceptible rice varieties to RSB infestation. These findings could contribute to developing molecular breeding strategies for controlling herbivorous pests.
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Affiliation(s)
- Shuai Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Xin-Yang Tan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhen He
- School of Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chen Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ya-Li Li
- Wuhan Benagen Technology Company Limited, Wuhan, China
| | - Lang Qin
- School of Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chun-Qing Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guang-Hua Luo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Ji-Chao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, Jiangsu Province, China
| | - Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, Jiangsu Province, China
- School of Life Sciences, Anhui Normal University/Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Wuhu, Anhui Province, China
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Ye L, Tong X, Pan K, Shi X, Xu B, Yao X, Zhuo L, Fang S, Tang S, Jiang Z, Xue X, Lu W, Guo G. Identification of potential novel N6-methyladenosine effector-related lncRNA biomarkers for serous ovarian carcinoma: a machine learning-based exploration in the framework of 3P medicine. Front Pharmacol 2024; 15:1351929. [PMID: 38895621 PMCID: PMC11185051 DOI: 10.3389/fphar.2024.1351929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/04/2024] [Indexed: 06/21/2024] Open
Abstract
Background Serous ovarian carcinoma (SOC) is considered the most lethal gynecological malignancy. The current lack of reliable prognostic biomarkers for SOC reduces the efficacy of predictive, preventive, and personalized medicine (PPPM/3PM) in patients with SOC, leading to unsatisfactory therapeutic outcomes. N6-methyladenosine (m6A) modification-associated long noncoding RNAs (lncRNAs) are effective predictors of SOC. In this study, an effective risk prediction model for SOC was constructed based on m6A modification-associated lncRNAs. Methods Transcriptomic data and clinical information of patients with SOC were downloaded from The Cancer Genome Atlas. Candidate lncRNAs were identified using univariate and multivariate and least absolute shrinkage and selection operator-penalized Cox regression analyses. The molecular mechanisms of m6A effector-related lncRNAs were explored via Gene Ontology, pathway analysis, gene set enrichment analysis, and gene set variation analysis (GSVA). The extent of immune cell infiltration was assessed using various algorithms, including CIBERSORT, Microenvironment Cell Populations counter, xCell, European Prospective Investigation into Cancer and Nutrition, and GSVA. The calcPhenotype algorithm was used to predict responses to the drugs commonly used in ovarian carcinoma therapy. In vitro experiments, such as migration and invasion Transwell assays, wound healing assays, and dot blot assays, were conducted to elucidate the functional roles of candidate lncRNAs. Results Six m6A effector-related lncRNAs that were markedly associated with prognosis were used to establish an m6A effector-related lncRNA risk model (m6A-LRM) for SOC. Immune microenvironment analysis suggested that the high-risk group exhibited a proinflammatory state and displayed increased sensitivity to immunotherapy. A nomogram was constructed with the m6A effector-related lncRNAs to assess the prognostic value of the model. Sixteen drugs potentially targeting m6A effector-related lncRNAs were identified. Furthermore, we developed an online web application for clinicians and researchers (https://leley.shinyapps.io/OC_m6A_lnc/). Overexpression of the lncRNA RP11-508M8.1 promoted SOC cell migration and invasion. METTL3 is an upstream regulator of RP11-508M8.1. The preliminary regulatory axis METTL3/m6A/RP11-508M8.1/hsa-miR-1270/ARSD underlying SOC was identified via a combination of in vitro and bioinformatic analyses. Conclusion In this study, we propose an innovative prognostic risk model and provide novel insights into the mechanism underlying the role of m6A-related lncRNAs in SOC. Incorporating the m6A-LRM into PPPM may help identify high-risk patients and personalize treatment as early as possible.
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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, Zhejiang, China
- Women’s Reproductive Health Laboratory of Zhejiang Province, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 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, Zhejiang, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xinyu Shi
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Binbing Xu
- First Clinical College, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xuyang Yao
- First Clinical College, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Linpei Zhuo
- Haiyuan College, Kunming Medical University, Kunming, Yunnan, 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, Zhejiang, China
| | - Sangsang Tang
- Women’s Reproductive Health Laboratory of Zhejiang Province, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhuofeng Jiang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, 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, Zhejiang, China
| | - Weiguo Lu
- Women’s Reproductive Health Laboratory of Zhejiang Province, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Gynecologic Oncology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Center of Uterine Cancer Diagnosis and Therapy of Zhejiang Province, Hangzhou, Zhejiang, 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, Zhejiang, China
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10
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Liang L, Wang X, Wei S, Lei Y, Zhang S, Zhai H, Hu Y, Lv Y. m 6A methyltransferase AflIme4 orchestrates mycelial growth, development and aflatoxin B 1 biosynthesis in Aspergillus flavus. Microbiol Res 2024; 283:127710. [PMID: 38593581 DOI: 10.1016/j.micres.2024.127710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/20/2024] [Accepted: 03/30/2024] [Indexed: 04/11/2024]
Abstract
Aflatoxin B1 (AFB1), a highly toxic secondary metabolite produced by Aspergillus flavus, poses a severe threat to agricultural production, food safety and human health. The methylation of mRNA m6A has been identified as a regulator of both the growth and AFB1 production of A. flavus. However, its intracellular occurrence and function needs to be elucidated. Here, we identified and characterized a m6A methyltransferase, AflIme4, in A. flavus. The enzyme was localized in the cytoplasm, and knockout of AflIme4 significantly reduced the methylation modification level of mRNA. Compared with the control strains, ΔAflIme4 exhibited diminished growth, conidial formation, mycelial hydrophobicity, sclerotium yield, pathogenicity and increased sensitivity to CR, SDS, NaCl and H2O2. Notably, AFB1 production was markedly inhibited in the A. flavus ΔAflIme4 strain. RNA-Seq coupled with RT-qPCR validation showed that the transcriptional levels of genes involved in the AFB1 biosynthesis pathway including aflA, aflG, aflH, aflK, aflL, aflO, aflS, aflV and aflY were significantly upregulated. Methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) analysis demonstrated a significant increase in m6A methylation modification levels of these pathway-specific genes, concomitant with a decrease in mRNA stability. These results suggest that AflIme4 attenuates the mRNA stability of genes in AFB1 biosynthesis by enhancing their mRNA m6A methylation modification, leading to impaired AFB1 biosynthesis. Our study identifies a novel m6A methyltransferase AflIme4 and highlights it as a potential target to control A. flavus growth, development and aflatoxin pollution.
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Affiliation(s)
- Liuke Liang
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Xiaoyan Wang
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shan Wei
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yang Lei
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shuaibing Zhang
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Huanchen Zhai
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yuansen Hu
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yangyong Lv
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China.
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11
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Liu X, Xie B, Wang S, Wu Y, Zhang Y, Ruan L. Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum. PeerJ 2024; 12:e17376. [PMID: 38784389 PMCID: PMC11114121 DOI: 10.7717/peerj.17376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
Background Condyloma acuminatum (CA) is caused by low-risk human papillomavirus, and is characterized by high recurrence after treatment. The RNA modification N6-methyladenosine (m6A) plays an important role during diverse viral infections, including high-risk HPV infection in cervical cancer. However, it is unclear whether low-risk HPV infection changes the RNA m6A methylation in CA. Methods High-throughputm6A-sequencing was performed to profile the transcriptome-wide mRNA modifications of CA tissues infected by LR-HPVs and the paired normal tissues from CA patients. We further investigated the regulation of alternative splicing by RNA binding proteins (RBPs) with altered m6A modification and constructed a regulatory network among these RBPs, regulated alternative splicing events (RASEs) and regulated alternative splicing genes (RASGs) in CA. Results The results show that the m6A level in CA tissues differed from that in the paired controls. Furthermore, cell cycle- and cell adhesion- associated genes with m6A modification were differentially expressed in CA tissues compared to the paired controls. In particular, seven RNA binding protein genes with specific m6A methylated sites, showed a higher or lower expression at the mRNA level in CA tissues than in the paired normal tissues. In addition, these differentially expressed RNA binding protein genes would regulate the alternative splicing pattern of apoptotic process genes in CA tissue. Conclusions Our study reveals a sophisticated m6A modification profile in CA tissue that affects the response of host cells to HPV infection, and provides cues for the further exploration of the roles of m6A and the development of a novel treatment strategy for CA.
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Affiliation(s)
- Xiaoyan Liu
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bo Xie
- Department of Urology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Su Wang
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinhua Wu
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu Zhang
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Liming Ruan
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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12
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Wang L, Liu Y, Pang R, Guo Y, Ren Y, Wu Y, Cao Z. The Tick Saliva Peptide HIDfsin2 TLR4-Dependently Inhibits the Tick-Borne Severe Fever with Thrombocytopenia Syndrome Virus in Mouse Macrophages. Antibiotics (Basel) 2024; 13:449. [PMID: 38786177 PMCID: PMC11117380 DOI: 10.3390/antibiotics13050449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Ticks transmit a variety of pathogens to their hosts by feeding on blood. The interactions and struggle between tick pathogens and hosts have evolved bilaterally. The components of tick saliva can directly or indirectly trigger host biological responses in a manner that promotes pathogen transmission; however, host cells continuously develop strategies to combat pathogen infection and transmission. Moreover, it is still unknown how host cells develop their defense strategies against tick-borne viruses during tick sucking. Here, we found that the tick saliva peptide HIDfsin2 enhanced the antiviral innate immunity of mouse macrophages by activating the Toll-like receptor 4 (TLR4) signaling pathway, thereby restricting tick-borne severe fever with thrombocytopenia syndrome virus (SFTSV) replication. HIDfsin2 was identified to interact with lipopolysaccharide (LPS), a ligand of TLR4, and then depolymerize LPS micelles into smaller particles, effectively enhancing the activation of the nuclear factor kappa-B (NF-κB) and type I interferon (IFN-I) signaling pathways, which are downstream of TLR4. Expectedly, TLR4 knockout completely eliminated the promotion effect of HIDfsin2 on NF-κB and type I interferon activation. Moreover, HIDfsin2 enhanced SFTSV replication in TLR4-knockout mouse macrophages, which is consistent with our recent report that HIDfsin2 hijacked p38 mitogen-activated protein kinase (MAPK) to promote the replication of tick-borne SFTSV in A549 and Huh7 cells (human cell lines) with low expression of TLR4. Together, these results provide new insights into the innate immune mechanism of host cells following tick bites. Our study also shows a rare molecular event relating to the mutual antagonism between tick-borne SFTSV and host cells mediated by the tick saliva peptide HIDfsin2 at the tick-host-virus interface.
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Affiliation(s)
- Luyao Wang
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China;
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.L.); (R.P.); (Y.G.); (Y.R.); (Y.W.)
- Shenzhen Research Institute, Wuhan University, Shenzhen 518057, China
| | - Yishuo Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.L.); (R.P.); (Y.G.); (Y.R.); (Y.W.)
| | - Rui Pang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.L.); (R.P.); (Y.G.); (Y.R.); (Y.W.)
| | - Yiyuan Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.L.); (R.P.); (Y.G.); (Y.R.); (Y.W.)
| | - Yingying Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.L.); (R.P.); (Y.G.); (Y.R.); (Y.W.)
| | - Yingliang Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.L.); (R.P.); (Y.G.); (Y.R.); (Y.W.)
| | - Zhijian Cao
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China;
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.L.); (R.P.); (Y.G.); (Y.R.); (Y.W.)
- Shenzhen Research Institute, Wuhan University, Shenzhen 518057, China
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13
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Liufu C, Luo L, Pang T, Zheng H, Yang L, Lu L, Chang S. Integration of multi-omics summary data reveals the role of N6-methyladenosine in neuropsychiatric disorders. Mol Psychiatry 2024:10.1038/s41380-024-02574-w. [PMID: 38684796 DOI: 10.1038/s41380-024-02574-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
N6-methyladenosine (m6A) methylation regulates gene expression/protein by influencing numerous aspects of mRNA metabolism and contributes to neuropsychiatric diseases. Here, we integrated multi-omics data and genome-wide association study summary data of schizophrenia (SCZ), bipolar disorder (BP), attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), major depressive disorder (MDD), Alzheimer's disease (AD), and Parkinson's disease (PD) to reveal the role of m6A in neuropsychiatric disorders by using transcriptome-wide association study (TWAS) tool and Summary-data-based Mendelian randomization (SMR). Our investigation identified 86 m6A sites associated with seven neuropsychiatric diseases and then revealed 7881 associations between m6A sites and gene expressions. Based on these results, we discovered 916 significant m6A-gene associations involving 82 disease-related m6A sites and 606 genes. Further integrating the 58 disease-related genes from TWAS and SMR analysis, we obtained 61, 8, 7, 3, and 2 associations linking m6A-disease, m6A-gene, and gene-disease for SCZ, BP, AD, MDD, and PD separately. Functional analysis showed the m6A mapped genes were enriched in "response to stimulus" pathway. In addition, we also analyzed the effect of gene expression on m6A and the post-transcription effect of m6A on protein. Our study provided new insights into the genetic component of m6A in neuropsychiatric disorders and unveiled potential pathogenic mechanisms where m6A exerts influences on disease through gene expression/protein regulation.
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Affiliation(s)
- Chao Liufu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Lingxue Luo
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Tao Pang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Haohao Zheng
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Li Yang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Lin Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- Research Units of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China
| | - Suhua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China.
- Research Units of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China.
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14
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Berggren KA, Schwartz RE, Kleiner RE, Ploss A. The impact of epitranscriptomic modifications on liver disease. Trends Endocrinol Metab 2024; 35:331-346. [PMID: 38212234 DOI: 10.1016/j.tem.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
RNA modifications have emerged as important mechanisms of gene regulation. Developmental, metabolic, and cell cycle regulatory processes are all affected by epitranscriptomic modifications, which control gene expression in a dynamic manner. The hepatic tissue is highly metabolically active and has an impressive ability to regenerate after injury. Cell proliferation, differentiation, and metabolism, which are all essential to the liver response to injury and regeneration, are regulated via RNA modification. Two such modifications, N6-methyladenosine (m6A)and 5-methylcytosine (m5C), have been identified as prognostic disease markers and potential therapeutic targets for liver diseases. Here, we describe progress in understanding the role of RNA modifications in liver biology and disease and discuss specific areas where unexpected results could lead to improved future understanding.
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Affiliation(s)
- Keith A Berggren
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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15
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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] [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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16
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Zhuang T, Chen MH, Wu RX, Wang J, Hu XD, Meng T, Wu AH, Li Y, Yang YF, Lei Y, Hu DH, Li YX, Zhang L, Sun AJ, Lu W, Zhang GN, Zuo JL, Ruan CC. ALKBH5-mediated m6A modification of IL-11 drives macrophage-to-myofibroblast transition and pathological cardiac fibrosis in mice. Nat Commun 2024; 15:1995. [PMID: 38443404 PMCID: PMC10914760 DOI: 10.1038/s41467-024-46357-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/24/2024] [Indexed: 03/07/2024] Open
Abstract
Cardiac macrophage contributes to the development of cardiac fibrosis, but factors that regulate cardiac macrophages transition and activation during this process remains elusive. Here we show, by single-cell transcriptomics, lineage tracing and parabiosis, that cardiac macrophages from circulating monocytes preferentially commit to macrophage-to-myofibroblast transition (MMT) under angiotensin II (Ang II)-induced hypertension, with accompanying increased expression of the RNA N6-methyladenosine demethylases, ALKBH5. Meanwhile, macrophage-specific knockout of ALKBH5 inhibits Ang II-induced MMT, and subsequently ameliorates cardiac fibrosis and dysfunction. Mechanistically, RNA immunoprecipitation sequencing identifies interlukin-11 (IL-11) mRNA as a target for ALKBH5-mediated m6A demethylation, leading to increased IL-11 mRNA stability and protein levels. By contrast, overexpression of IL11 in circulating macrophages reverses the phenotype in ALKBH5-deficient mice and macrophage. Lastly, targeted delivery of ALKBH5 or IL-11 receptor α (IL11RA1) siRNA to monocytes/macrophages attenuates MMT and cardiac fibrosis under hypertensive stress. Our results thus suggest that the ALKBH5/IL-11/IL11RA1/MMT axis alters cardiac macrophage and contributes to hypertensive cardiac fibrosis and dysfunction in mice, and thereby identify potential targets for cardiac fibrosis therapy in patients.
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Affiliation(s)
- Tao Zhuang
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China
| | - Mei-Hua Chen
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China
- Institute of Metabolism and Regenerative Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruo-Xi Wu
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China
| | - Jing Wang
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China
| | - Xi-De Hu
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China
| | - Ting Meng
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China
| | - Ai-Hua Wu
- Minhang Hospital and School of Pharmacy, Key Laboratory of Smart Drug Delivery Ministry of Education, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Yan Li
- Department of Cardiology, RuiJin Hospital/LuWan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong-Feng Yang
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China
| | - Yu Lei
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China
| | - Dong-Hua Hu
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China
| | - Yan-Xiu Li
- Department of Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Zhang
- Department of Cardiology and Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ai-Jun Sun
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Wei Lu
- Minhang Hospital and School of Pharmacy, Key Laboratory of Smart Drug Delivery Ministry of Education, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China.
| | - Guan-Nan Zhang
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Jun-Li Zuo
- Department of Geriatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Cheng-Chao Ruan
- Department of Physiology and Pathophysiology, Shanghai Key Laboratory of Bioactive Small Molecules, State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, and Jinshan Hospital, Fudan University, Shanghai, China.
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17
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Fitzsimmons CM, Mandler MD, Lunger JC, Chan D, Maligireddy S, Schmiechen A, Gamage S, Link C, Jenkins L, Chan K, Andresson T, Crooks D, Meier J, Linehan W, Batista P. Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma. NAR Cancer 2024; 6:zcae004. [PMID: 38328795 PMCID: PMC10849186 DOI: 10.1093/narcan/zcae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of an aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxoglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively affects the levels of N6-methyladenosine (m6A), while the levels of 5-formylcytosine (f5C) in mitochondrial tRNA are unaffected. This supports the hypothesis of a differential impact of fumarate accumulation on distinct RNA demethylases. The observation that metabolites modulate specific subsets of RNA-modifying enzymes offers new insights into the intersection between metabolism and the epitranscriptome.
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Affiliation(s)
- Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Judith C Lunger
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dalen Chan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddhardha S Maligireddy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra C Schmiechen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Courtney Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - King Chan
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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18
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Chen J, Song HX, Hu JH, Bai JS, Li XH, Sun RC, Zhao BQ, Li MZ, Zhou B. Classical swine fever virus non-structural protein 5B hijacks host METTL14-mediated m6A modification to counteract host antiviral immune response. PLoS Pathog 2024; 20:e1012130. [PMID: 38551978 PMCID: PMC11006178 DOI: 10.1371/journal.ppat.1012130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/10/2024] [Accepted: 03/17/2024] [Indexed: 04/11/2024] Open
Abstract
Classical Swine Fever (CSF), caused by the Classical Swine Fever Virus (CSFV), inflicts significant economic losses on the global pig industry. A key factor in the challenge of eradicating this virus is its ability to evade the host's innate immune response, leading to persistent infections. In our study, we elucidate the molecular mechanism through which CSFV exploits m6A modifications to circumvent host immune surveillance, thus facilitating its proliferation. We initially discovered that m6A modifications were elevated both in vivo and in vitro upon CSFV infection, particularly noting an increase in the expression of the methyltransferase METTL14. CSFV non-structural protein 5B was found to hijack HRD1, the E3 ubiquitin ligase for METTL14, preventing METTL14 degradation. MeRIP-seq analysis further revealed that METTL14 specifically targeted and methylated TLRs, notably TLR4. METTL14-mediated regulation of TLR4 degradation, facilitated by YTHDF2, led to the accelerated mRNA decay of TLR4. Consequently, TLR4-mediated NF-κB signaling, a crucial component of the innate immune response, is suppressed by CSFV. Collectively, these data effectively highlight the viral evasion tactics, shedding light on potential antiviral strategies targeting METTL14 to curb CSFV infection.
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Affiliation(s)
- Jing Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hui-xin Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jia-huan Hu
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Ji-shan Bai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiao-han Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Rui-cong Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Bing-qian Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Mei-zhen Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Bin Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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19
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Zhu M, Wu N, Zhong J, Chen C, Liu W, Ren Y, Wang X, Jin H. N 6-methyladenosine modification of the mRNA for a key gene in purine nucleotide metabolism regulates virus proliferation in an insect vector. Cell Rep 2024; 43:113821. [PMID: 38368611 DOI: 10.1016/j.celrep.2024.113821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 02/20/2024] Open
Abstract
The titer of viruses that persist and propagate in their insect vector must be high enough for transmission yet not harm the insect, but the mechanism of this dynamic balance is unclear. Here, expression of inosine monophosphate dehydrogenase (LsIMPDH), a rate-limiting enzyme for guanosine triphosphate (GTP) synthesis, is shown to be downregulated by increased levels of N6-methyladenosine (m6A) on LsIMPDH mRNA in rice stripe virus (RSV)-infected small brown planthoppers (SBPHs; Laodelphax striatellus), the RSV vector, which decreases GTP content, thus limiting viral proliferation. Moreover, planthopper methyltransferase-like protein 3 (LsMETTL3) and m6A reader protein LsYTHDF3 are found to catalyze and recognize the m6A on LsIMPDH mRNA, respectively, and cooperate in destabilizing LsIMPDH transcripts. Co-silencing assays show that negative regulation of viral proliferation by both LsMETTL3 and LsYTHDF3 is partially dependent on LsIMPDH. This distinct mechanism limits virus replication in an insect vector, providing a potential gene target to block viral transmission.
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Affiliation(s)
- Mengjie Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiayi Zhong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chen Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingdang Ren
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huaibing Jin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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20
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Li Y, Guo M, Qiu Y, Li M, Wu Y, Shen M, Wang Y, Zhang F, Shao J, Xu X, Zhang Z, Zheng S. Autophagy activation is required for N6-methyladenosine modification to regulate ferroptosis in hepatocellular carcinoma. Redox Biol 2024; 69:102971. [PMID: 38056309 PMCID: PMC10749285 DOI: 10.1016/j.redox.2023.102971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/18/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND & AIMS Although ferroptosis holds promise as a new strategy for treating hepatocellular carcinoma (HCC), there are several obstacles that need to be overcome. One major challenge is the lack of understanding about the mechanisms underlying ferroptosis. Additionally, while the m6A modification has been shown to regulate various forms of cell death, its role in regulating ferroptosis in HCC has been largely overlooked. Bridging this knowledge gap, our study aimed to elucidate the regulatory influence of m6A modification on HCC ferroptosis. MATERIALS Dot blot and EpiQuik m6A RNA Methylation Quantitative kit detected changes in overall m6A modification level during ferroptosis in HCC. MeRIP-qPCR and RIP-qPCR identified that the m6A modification of ATG5 mRNA was significant changed. BALB/c nude mice were used to construct xenograft tumor models to verify the phenotypes upon YTHDC2 silencing. In addition, patient-derived organoid models were used to demonstrate that induction of ferroptosis was an effective strategy against HCC. RESULTS Our study has shown that inducing ferroptosis is a promising strategy for combatting HCC. Specifically, we have found a significant correlation between ferroptosis and high levels of m6A modification in HCC. Notably, we discovered that the elevation of ATG5 mRNA m6A modification mediated by WTAP is dependent on the reading protein YTHDC2. Importantly, inhibition of either WTAP or YTHDC2 effectively prevented ferroptosis and suppressed HCC development in both in vitro and in vivo models. CONCLUSION Our study revealed that WTAP upregulates ATG5 expression post-transcriptionally in an m6A-YTHDC2-dependent manner, thereby promoting the translation of ATG5 mRNA during ferroptosis in HCC. These findings have significant implications for the development of innovative and effective therapeutic approaches for HCC treatment.
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Affiliation(s)
- Yujia Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mei Guo
- School of Nursing, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yangling Qiu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mengran Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yang Wu
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210023, China
| | - Min Shen
- Department of Biochemistry and Molecular Biology, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Yingqian Wang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Feng Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiangjuan Shao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xuefen Xu
- Department of Pharmacology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine.
| | - Zili Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Shizhong Zheng
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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21
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Jiang J, Song B, Meng J, Zhou J. Tissue-specific RNA methylation prediction from gene expression data using sparse regression models. Comput Biol Med 2024; 169:107892. [PMID: 38171264 DOI: 10.1016/j.compbiomed.2023.107892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
N6-methyladenosine (m6A) is a highly prevalent and conserved post-transcriptional modification observed in mRNA and long non-coding RNA (lncRNA). Identifying potential m6A sites within RNA sequences is crucial for unraveling the potential influence of the epitranscriptome on biological processes. In this study, we introduce Exp2RM, a novel approach that formulates single-site-based tissue-specific elastic net models for predicting tissue-specific methylation levels utilizing gene expression data. The resulting ensemble model demonstrates robust predictive performance for tissue-specific methylation levels, with an average R-squared value of 0.496 and a median R-squared value of 0.482 across all 22 human tissues. Since methylation distribution varies among tissues, we trained the model to incorporate similar patterns, significantly improves accuracy with the median R-squared value increasing to 0.728. Additonally, functional analysis reveals Exp2RM's ability to capture coefficient genes in relevant biological processes. This study emphasizes the importance of tissue-specific methylation distribution in enhancing prediction accuracy and provides insights into the functional implications of methylation sites.
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Affiliation(s)
- Jie Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, United Kingdom
| | - Bowen Song
- Department of Public Health, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China; AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, United Kingdom
| | - Jingxian Zhou
- School of AI and Advanced Computing, Xi'an Jiaotong-Liverpool University Entrepreneur College (Taicang), Taicang, Suzhou, Jiangsu Province, 215400, China; Department of Computer Science, University of Liverpool, L69 7ZB, Liverpool, United Kingdom.
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22
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Aufgebauer CJ, Bland KM, Horner SM. Modifying the antiviral innate immune response by selective writing, erasing, and reading of m 6A on viral and cellular RNA. Cell Chem Biol 2024; 31:100-109. [PMID: 38176419 PMCID: PMC10872403 DOI: 10.1016/j.chembiol.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
Viral infection and the antiviral innate immune response are regulated by the RNA modification m6A. m6A directs nearly all aspects of RNA metabolism by recruiting RNA-binding proteins that mediate the fate of m6A-containing RNA. m6A controls the antiviral innate immune response in diverse ways, including shielding viral RNA from detection by antiviral sensors and influencing the expression of cellular mRNAs encoding antiviral signaling proteins, cytokines, and effector proteins. While m6A and the m6A machinery are important for the antiviral response, the precise mechanisms that determine how the m6A machinery selects specific viral or cellular RNA molecules for modification during infection are not fully understood. In this review, we highlight recent findings that shed light on how viral infection redirects the m6A machinery during the antiviral response. A better understanding of m6A targeting during viral infection could lead to new immunomodulatory and therapeutic strategies against viral infection.
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Affiliation(s)
- Caroline J Aufgebauer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katherine M Bland
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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23
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Tsukuda S, Harris JM, Magri A, Balfe P, Siddiqui A, Wing PA, McKeating JA. The N6-methyladenosine demethylase ALKBH5 regulates the hypoxic HBV transcriptome. PLoS Pathog 2024; 20:e1011917. [PMID: 38227578 PMCID: PMC10817175 DOI: 10.1371/journal.ppat.1011917] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/26/2024] [Accepted: 12/20/2023] [Indexed: 01/18/2024] Open
Abstract
Chronic hepatitis B is a global health problem and current treatments only suppress hepatitis B virus (HBV) infection, highlighting the need for new curative treatments. Oxygen levels influence HBV replication and we previously reported that hypoxia inducible factors (HIFs) activate the basal core promoter (BCP). Here we show that the hypoxic-dependent increase in BCP-derived transcripts is dependent on N6-methyladenosine (m6A) modifications in the 5' stem loop that regulate RNA half-life. Application of a probe-enriched long-read sequencing method to accurately map the HBV transcriptome showed an increased abundance of pre-genomic RNA under hypoxic conditions. Mapping the transcription start sites of BCP-RNAs identified a role for hypoxia to regulate pre-genomic RNA splicing that is dependent on m6A modification. Bioinformatic analysis of published single cell RNA-seq of murine liver showed an increased expression of the RNA demethylase ALKBH5 in the peri-central low oxygen region. In vitro studies with a human hepatocyte derived HepG2-NTCP cell line showed increased ALKBH5 gene expression under hypoxic conditions and a concomitant reduction in m6A-modified HBV BCP-RNA and host RNAs. Silencing the demethylase reduced the level of BCP-RNAs and host gene (CA9, NDRG1, VEGFA, BNIP3, FUT11, GAP and P4HA1) transcripts and this was mediated via reduced HIFα expression. In summary, our study highlights a previously unrecognized role for ALKBH5 in orchestrating viral and cellular transcriptional responses to low oxygen.
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Affiliation(s)
- Senko Tsukuda
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - James M. Harris
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Andrea Magri
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Peter Balfe
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Aleem Siddiqui
- Department of Medicine, University of California, California, United States of America
| | - Peter A.C. Wing
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, United Kingdom
| | - Jane A. McKeating
- Nuffield Department of Medicine, University of Oxford, United Kingdom
- Department of Medicine, University of California, California, United States of America
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24
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Zhang Y, Ling Y, Zhou Y, Shi X, Shen F, Zhou J, Chen Y, Yang F, Gu Y, Wang J. Research Advances in the Roles of N6-Methyladenosine Modification in Ovarian Cancer. Cancer Control 2024; 31:10732748241256819. [PMID: 38755968 PMCID: PMC11102699 DOI: 10.1177/10732748241256819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecological tumor, characterized by its insidious and frequently recurring metastatic progression. Owing to limited early screening methods, over 70% of OC cases are diagnosed at advanced stages, typically stage III or IV. Recently, N6-methyladenosine (m6A) modification has emerged as a hotspot of epigenetic research, representing a significant endogenous RNA modification in higher eukaryotes. Numerous studies have reported that m6A-related regulatory factors play pivotal roles in tumor development through diverse mechanisms. Moreover, recent studies have indicated the aberrant expression of multiple regulatory factors in OC. Therefore, this paper comprehensively reviews research advancements concerning m6A in OC, aiming to elucidate the regulatory mechanism of m6A-associated regulators on pivotal aspects, such as proliferation, invasion, metastasis, and drug resistance, in OC. Furthermore, it discusses the potential of m6A-associated regulators as early diagnostic markers and therapeutic targets, thus contributing to the diagnosis and treatment of OC.
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Affiliation(s)
- Yuhong Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology of Soochow University, Suzhou, China
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yufeng Ling
- Affiliated Hospital of Medical School, Nanjing University, Nanjing Stomatological Hospital, Nanjing, China
| | - Ying Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology of Soochow University, Suzhou, China
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiu Shi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fangrong Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jinhua Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Youguo Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fan Yang
- Department of Gynecology and Obstetrics, West China Second Hospital, University of Sichuan, Chengdu, China
- Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second Hospital, University of Sichuan, Chengdu, China
| | - Yanzheng Gu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Juan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
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25
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Liu Y, Song R, Lu Z, Zhao L, Zhan X, Li Y, Cao X. The RNA m 6A demethylase ALKBH5 drives emergency granulopoiesis and neutrophil mobilization by upregulating G-CSFR expression. Cell Mol Immunol 2024; 21:6-18. [PMID: 38114747 PMCID: PMC10757716 DOI: 10.1038/s41423-023-01115-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
Emergency granulopoiesis and neutrophil mobilization that can be triggered by granulocyte colony-stimulating factor (G-CSF) through its receptor G-CSFR are essential for antibacterial innate defense. However, the epigenetic modifiers crucial for intrinsically regulating G-CSFR expression and the antibacterial response of neutrophils remain largely unclear. N6-methyladenosine (m6A) RNA modification and the related demethylase alkB homolog 5 (ALKBH5) are key epigenetic regulators of immunity and inflammation, but their roles in neutrophil production and mobilization are still unknown. We used cecal ligation and puncture (CLP)-induced polymicrobial sepsis to model systemic bacterial infection, and we report that ALKBH5 is required for emergency granulopoiesis and neutrophil mobilization. ALKBH5 depletion significantly impaired the production of immature neutrophils in the bone marrow of septic mice. In addition, Alkbh5-deficient septic mice exhibited higher retention of mature neutrophils in the bone marrow and defective neutrophil release into the circulation, which led to fewer neutrophils at the infection site than in their wild-type littermates. During bacterial infection, ALKBH5 imprinted production- and mobilization-promoting transcriptome signatures in both mouse and human neutrophils. Mechanistically, ALKBH5 erased m6A methylation on the CSF3R mRNA to increase the mRNA stability and protein expression of G-CSFR, consequently upregulating cell surface G-CSFR expression and downstream STAT3 signaling in neutrophils. The RIP-qPCR results confirmed the direct binding of ALKBH5 to the CSF3R mRNA, and the binding strength declined upon bacterial infection, accounting for the decrease in G-CSFR expression on bacteria-infected neutrophils. Considering these results collectively, we define a new role of ALKBH5 in intrinsically driving neutrophil production and mobilization through m6A demethylation-dependent posttranscriptional regulation, indicating that m6A RNA modification in neutrophils is a potential target for treating bacterial infections and neutropenia.
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Affiliation(s)
- Yang Liu
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin, China.
| | - Renjie Song
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhike Lu
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Lu Zhao
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinyi Zhan
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yini Li
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Xuetao Cao
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin, China
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Chen Y, Wang W, Zhang W, He M, Li Y, Qu G, Tong J. Emerging roles of biological m 6A proteins in regulating virus infection: A review. Int J Biol Macromol 2023; 253:126934. [PMID: 37722640 DOI: 10.1016/j.ijbiomac.2023.126934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent chemical modifications of intracellular RNA, which recently emerging as a multifaceted effector of viral genomic RNA. As a dynamic process, three groups of biological proteins control the levels of m6A modification in eukaryocyte, designed as m6A writers, erasers, and readers. The m6A writers comprising of methyltransferases complex initiate the modification process. On the contrary, the m6A erasers ALKBH5 or FTO abolish the modification through three-step demethylation: m6A to N6-hydroxymethyl adenosine (hm6A), then hm6A to N6-methyladenosine (f6A), and finally f6A to adenosine. The known m6A readers include the YTH family and the hnRNP family. As m6A modification regulates RNA nuclear exportation, stability, and translation, m6A proteins commonly participate in virus infection by regulating viral genomic RNA synthesis. Moreover, m6A proteins establish molecular linkages between virus genome/viral encode proteins and host cells proteins via their multifunctional roles in cellular RNA metabolism. The m6A writers and erasers directly impact interferon expression and macrophage innate immune responses, facilitating them to act as anti-/pro-viral factors. The m6A readers enable to alter cell metabolism and stress granules (SGs) production to regulate virus-host interactions. Here, the latest progress of m6A proteins in regulating viral infection is reviewed. Demonstrating the roles of m6A proteins will enhance the understanding of epigenetic regulation of virus infection and stimulate the development of novel antiviral strategies.
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Affiliation(s)
- Yuran Chen
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Wenjing Wang
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Mei He
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yuming Li
- School of Public Health, Shandong First Medical University, Shandong Academy of Medical Sciences, Ji'nan 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, Shandong Academy of Medical Sciences, Tai'an 271000, China.
| | - Guosheng Qu
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
| | - Jie Tong
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
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Wang A, Huang H, Shi JH, Yu X, Ding R, Zhang Y, Han Q, Ni ZY, Li X, Zhao R, Zou Q. USP47 inhibits m6A-dependent c-Myc translation to maintain regulatory T cell metabolic and functional homeostasis. J Clin Invest 2023; 133:e169365. [PMID: 37788092 PMCID: PMC10688989 DOI: 10.1172/jci169365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 09/27/2023] [Indexed: 10/05/2023] Open
Abstract
The functional integrity of Tregs is interwoven with cellular metabolism; however, the mechanisms governing Treg metabolic programs remain elusive. Here, we identified that the deubiquitinase USP47 inhibited c-Myc translation mediated by the RNA N6-methyladenosine (m6A) reader YTHDF1 to maintain Treg metabolic and functional homeostasis. USP47 positively correlated with the tumor-infiltrating Treg signature in samples from patients with colorectal cancer and gastric cancer. USP47 ablation compromised Treg homeostasis and function in vivo, resulting in the development of inflammatory disorders, and boosted antitumor immune responses. USP47 deficiency in Tregs triggered the accumulation of the c-Myc protein and in turn exacerbated hyperglycolysis. Mechanistically, USP47 prevented YTHDF1 ubiquitination to attenuate the association of YTHDF1 with translation initiation machinery, thereby decreasing m6A-based c-Myc translation efficiency. Our findings reveal that USP47 directs m6A-dependent metabolic programs to orchestrate Treg homeostasis and suggest novel approaches for selective immune modulation in cancer and autoimmune diseases by targeting of USP47.
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Affiliation(s)
- Aiting Wang
- Department of General Surgery, Ruijin Hospital, and
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Center for Cancer Immunology, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Haiyan Huang
- Department of General Surgery, Ruijin Hospital, and
| | - Jian-Hong Shi
- Central Laboratory, Hebei Collaborative Innovation Center of Tumor Microecological Metabolism Regulation, Affiliated Hospital of Hebei University, Baoding, Hebei Province, China
| | - Xiaoyan Yu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Ding
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuerong Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiaoqiao Han
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Yu Ni
- Central Laboratory, Hebei Collaborative Innovation Center of Tumor Microecological Metabolism Regulation, Affiliated Hospital of Hebei University, Baoding, Hebei Province, China
| | - Xia Li
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital, and
| | - Qiang Zou
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhao L, Song R, Liu Y. Glycolytic metabolite phosphoenolpyruvate protects host from viral infection through promoting AATK expression. Eur J Immunol 2023; 53:e2350536. [PMID: 37724936 DOI: 10.1002/eji.202350536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/23/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
Viral infections can result in metabolism rewiring of host cells, which in turn affects the viral lifecycle. Phosphoenolpyruvate (PEP), a metabolic intermediate in the glycolytic pathway, plays important roles in several biological processes including anti-tumor T cell immunity. However, whether PEP might participate in modulating viral infection remains largely unknown. Here, we demonstrate that PEP generally inhibits viral replication via upregulation of apoptosis-associated tyrosine kinase (AATK) expression. Targeted metabolomic analyses have shown that the intracellular level of PEP was increased upon viral infection. PEP treatment significantly restricted viral infection and hence declined subsequent inflammatory response both in vitro and in vivo. Besides, PEP took inhibitory effect on the stage of viral replication and also decreased the mortality of mice with viral infection. Mechanistically, PEP significantly promoted the expression of AATK. Knockdown of AATK led to enhanced viral replication and consequent increased levels of cytokines. Moreover, AATK deficiency disabled the antiviral effect of PEP. Together, our study reveals a previously unknown role of PEP in broadly inhibiting viral replication by promoting AATK expression, highlighting the potential application of activation or upregulation of the PEP-AATK axis in controlling viral infections.
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Affiliation(s)
- Lu Zhao
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Renjie Song
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Liu
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
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29
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Wang H, Feng J, Zeng C, Liu J, Fu Z, Wang D, Wang Y, Zhang L, Li J, Jiang A, He M, Cao Y, Yan K, Tang H, Guo D, Xu K, Zhou X, Zhou L, Lan K, Zhou Y, Chen Y. NSUN2-mediated M 5c methylation of IRF3 mRNA negatively regulates type I interferon responses during various viral infections. Emerg Microbes Infect 2023; 12:2178238. [PMID: 36748584 PMCID: PMC9946332 DOI: 10.1080/22221751.2023.2178238] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
5-Methylcytosine (m5C) is a widespread post-transcriptional RNA modification and is reported to be involved in manifold cellular responses and biological processes through regulating RNA metabolism. However, its regulatory role in antiviral innate immunity has not yet been elucidated. Here, we report that NSUN2, a typical m5C methyltransferase, negatively regulates type I interferon responses during various viral infections, including SARS-CoV-2. NSUN2 specifically mediates m5C methylation of IRF3 mRNA and accelerates its degradation, resulting in low levels of IRF3 and downstream IFN-β production. Knockout or knockdown of NSUN2 enhanced type I interferon and downstream ISGs during various viral infection in vitro. And in vivo, the antiviral innate response is more dramatically enhanced in Nsun2+/- mice than in Nsun2+/+ mice. The highly m5C methylated cytosines in IRF3 mRNA were identified, and their mutation enhanced cellular IRF3 mRNA levels. Moreover, infection with Sendai virus (SeV), vesicular stomatitis virus (VSV), herpes simplex virus 1 (HSV-1), or Zika virus (ZIKV) resulted in a reduction of endogenous NSUN2 levels. Especially, SARS-CoV-2 infection (WT strain and BA.1 omicron variant) also decreased endogenous levels of NSUN2 in COVID-19 patients and K18-hACE2 KI mice, further increasing type I interferon and downstream ISGs. Together, our findings reveal that NSUN2 serves as a negative regulator of interferon response by accelerating the fast turnover of IRF3 mRNA, while endogenous NSUN2 levels decrease during SARS-CoV-2 and various viral infections to boost antiviral responses for effective elimination of viruses.
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Affiliation(s)
- Hongyun Wang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Jiangpeng Feng
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Cong Zeng
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China,College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jiejie Liu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Zhiying Fu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Dehe Wang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Lu Zhang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Jiali Li
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Ao Jiang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Miao He
- School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yuanyuan Cao
- Department of Microbiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, People’s Republic of China
| | - Kun Yan
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Hao Tang
- Heart Center of Henan Provincial People’s Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Deyin Guo
- School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Ke Xu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Li Zhou
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China,Animal Bio-Safety Level III Laboratory at Center for Animal Experiment, Wuhan University, Wuhan, People’s Republic of China
| | - Ke Lan
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yu Zhou
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yu Chen
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China, Yu Chen State Key Laboratory of Virology, Modern Virology Research Center, RNA Institute, College of Life Sciences, Wuhan University, Wuhan430072, People’s Republic of China
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30
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Liang Y, Yang R, Shang J, Zhong D, Yang Q, Su Y, Shi Y, Huang X. Lung immune prognostic index‑based nomogram for recurrence of hepatocellular carcinoma after postoperative adjuvant TACE. J Cancer Res Clin Oncol 2023; 149:16461-16471. [PMID: 37707573 DOI: 10.1007/s00432-023-05413-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Transarterial chemoembolization (TACE), one of the most commonly used postoperative adjuvant therapy for HCC, has achieved satisfactory outcomes. This study aimed to explore the prognostic value of lung immune prognostic index (LIPI) and develop a novel nomogram for recurrence-free survival (RFS) of HCC patients received postoperative adjuvant TACE (PA-TACE). METHODS The prognostic value of LIPI was evaluated by C-index, receiver operating characteristic (ROC) analysis, and Kaplan-Meier survival curve. An effective nomogram based on preoperative prognostic factors was established from multivariate analysis and validated in the validation cohort. RESULTS The ROC and survival analysis demonstrated that the LIPI exhibited better prediction performance of HCC recurrence than other inflammatory biomarkers. According to univariate and multivariate analysis, LIPI, followed by AFP, MVI and age, were significant independent predictors for HCC recurrence and were utilized to construct the nomogram. The C-indexes of the nomogram were 0.746 (95% CI 0.721-0.770) and 0.738 (95% CI 0.701-0.775) in the training and validation cohort, respectively. The AUCs for the 1-, 2-, and 3-year RFS were 0.799, 0.867 and 0.884 in the training cohort and 0.798, 0.779 and 0.770 in the validation cohort, respectively. The calibration curves presented good consistencies. Moreover, compared with the LIPI and other clinical staging system, the established nomogram presented better prognostic performance. CONCLUSION Preoperative LIPI might be a powerful predictor for RFS in HCC patients received PA-TACE. The LIPI-based nomogram could further effectively predict the risk of recurrence and help clinicians formulate personalized follow-up strategies and adjuvant therapy to improve patient outcomes.
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Affiliation(s)
- Yuxin Liang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruoyi Yang
- School of Stomatology, Guizhou Medical University, Guiyang, China
- Department of Head and Neck Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jin Shang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Deyuan Zhong
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Qinyan Yang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuhao Su
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ying Shi
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
| | - Xiaolun Huang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
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31
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Sun Y, Gong W, Zhang S. METTL3 promotes colorectal cancer progression through activating JAK1/STAT3 signaling pathway. Cell Death Dis 2023; 14:765. [PMID: 38001065 PMCID: PMC10673931 DOI: 10.1038/s41419-023-06287-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
The role of METTL3-mediated N6-methyladenosine (m6A) modification has been elucidated in several cancers, but the concrete mechanism underlying its function in colorectal cancer is still obscure. Here, we revealed that upregulated methyltransferase-like 3 (METTL3) in colorectal cancer exerted both methyltransferase activity-dependent and -independent functions in gene regulation. METTL3 deposited m6A on the 3' untranslated region of the JAK1 transcript to promote JAK1 translation relying on YTHDF1 recognition. Besides, METTL3 was redistributed to the STAT3 promoter and worked in concert with NF-κB to facilitate STAT3 transcription, which was achieved independently on METTL3 methyltransferase activity. The increased JAK1 and STAT3 corporately contributed to the activation of the p-STAT3 signaling pathway and further upregulated downstream effectors expressions, including VEGFA and CCND1, which finally resulted in enhanced cancer cell proliferation and metastasis in vitro and in vivo. Collectively, our study revealed the unappreciated dual role of METTL3 as an m6A writer and a transcription regulator, which worked together in the same signaling pathway to drive colorectal cancer malignancy.
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Affiliation(s)
- Yuechao Sun
- Ningbo Institute of Life and Health Industry, Chinese Academy of Sciences, Ningbo, Zhejiang, The People's Republic of China
| | - Weipeng Gong
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, The People's Republic of China
| | - Song Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University Affiliated Tumor Hospital, Jinan, Shandong, The People's Republic of China.
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32
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Yang Q, Liang Y, Shi Y, Shang J, Huang X. The ALKBH5/SOX4 axis promotes liver cancer stem cell properties via activating the SHH signaling pathway. J Cancer Res Clin Oncol 2023; 149:15499-15510. [PMID: 37646828 DOI: 10.1007/s00432-023-05309-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Hepatocellular carcinoma (HCC), featured with high prevalence and poor prognosis, is the major cause of cancer-related deaths worldwide. As a subgroup of liver cancer cells capable of differentiation, tumorigenesis and self-renewal, liver cancer stem cells (LCSCs) serve as one of the reasons leading to HCC progression and therapeutic resistance. Therefore, in-depth exploration of novel molecular biomarkers related to LSCSs is of great necessity. In our study, we found that human AlkB homolog H5 (ALKBH5) expression was enriched in LCSCs, which could foster proliferation, invasion and migration of the HCC cells. Mechanically, ALKBH5 positively mediated the expression of SOX4 via demethylation, and SOX4 promoted SHH expression at the transcriptional level to activate sonic hedgehog (SHH) signaling pathway. Furthermore, exosomes derived from CD133+ HCC cells could transmit ALKBH5 into THP-1 cells, which might be associated with M2 polarization of macrophages. In summary, the ALKBH5/SOX4 axis plays a significant role in exacerbating LCSC properties via activating SHH signaling pathway, and ALKBH5 could be a critical effector related to macrophage M2 polarization. These findings might provide a promising new biomarker for HCC diagnosis and treatment.
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Affiliation(s)
- Qinyan Yang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuxin Liang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ying Shi
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jin Shang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
| | - Xiaolun Huang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
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33
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Tsukuda S, Harris JM, Magri A, Balfe P, Wing PAC, Siddiqui A, McKeating JA. The N6-methyladenosine demethylase ALKBH5 regulates the hypoxic HBV transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564956. [PMID: 37961409 PMCID: PMC10634982 DOI: 10.1101/2023.10.31.564956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Chronic hepatitis B is a global health problem and current treatments only suppress hepatitis B virus (HBV) infection, highlighting the need for new curative treatments. Oxygen levels influence HBV replication and we previously reported that hypoxia inducible factors (HIFs) activate the basal core promoter to transcribe pre-genomic RNA. Application of a probe-enriched long-read sequencing method to map the HBV transcriptome showed an increased abundance of all viral RNAs under low oxygen or hypoxic conditions. Importantly, the hypoxic-associated increase in HBV transcripts was dependent on N6-methyladenosine (m6A) modifications and an m6A DRACH motif in the 5' stem loop of pre-genomic RNA defined transcript half-life under hypoxic conditions. Given the essential role of m6A modifications in the viral transcriptome we assessed the oxygen-dependent expression of RNA demethylases and bioinformatic analysis of published single cell RNA-seq of murine liver showed an increased expression of the RNA demethylase ALKBH5 in the peri-central low oxygen region. In vitro studies with a human hepatocyte derived HepG2 cell line showed increased ALKBH5 gene expression under hypoxic conditions. Silencing the demethylase reduced the levels of HBV pre-genomic RNA and host gene (CA9, NDRG1, VEGFA, BNIP3, FUT11, GAP and P4HA1) transcripts and this was mediated via reduced HIFα expression. In summary, our study highlights a previously unrecognized role for ALKBH5 in orchestrating viral and cellular transcriptional responses to low oxygen.
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Affiliation(s)
- Senko Tsukuda
- Nuffield Department of Medicine, University of Oxford, UK
| | - James M Harris
- Nuffield Department of Medicine, University of Oxford, UK
| | - Andrea Magri
- Nuffield Department of Medicine, University of Oxford, UK
| | - Peter Balfe
- Nuffield Department of Medicine, University of Oxford, UK
| | - Peter AC Wing
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, UK
| | - Aleem Siddiqui
- Division of Infectious Diseases and Global Public Health, University of California, CA, USA
| | - Jane A McKeating
- Nuffield Department of Medicine, University of Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, UK
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34
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Gao Y, Zimmer JT, Vasic R, Liu C, Gbyli R, Zheng SJ, Patel A, Liu W, Qi Z, Li Y, Nelakanti R, Song Y, Biancon G, Xiao AZ, Slavoff S, Kibbey RG, Flavell RA, Simon MD, Tebaldi T, Li HB, Halene S. ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m 6A modification-mediated RNA stability control. Cell Rep 2023; 42:113163. [PMID: 37742191 PMCID: PMC10636609 DOI: 10.1016/j.celrep.2023.113163] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/01/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
N6-methyladenosine (m6A) RNA modification controls numerous cellular processes. To what extent these post-transcriptional regulatory mechanisms play a role in hematopoiesis has not been fully elucidated. We here show that the m6A demethylase alkB homolog 5 (ALKBH5) controls mitochondrial ATP production and modulates hematopoietic stem and progenitor cell (HSPC) fitness in an m6A-dependent manner. Loss of ALKBH5 results in increased RNA methylation and instability of oxoglutarate-dehydrogenase (Ogdh) messenger RNA and reduction of OGDH protein levels. Limited OGDH availability slows the tricarboxylic acid (TCA) cycle with accumulation of α-ketoglutarate (α-KG) and conversion of α-KG into L-2-hydroxyglutarate (L-2-HG). L-2-HG inhibits energy production in both murine and human hematopoietic cells in vitro. Impaired mitochondrial energy production confers competitive disadvantage to HSPCs and limits clonogenicity of Mll-AF9-induced leukemia. Our study uncovers a mechanism whereby the RNA m6A demethylase ALKBH5 regulates the stability of metabolic enzyme transcripts, thereby controlling energy metabolism in hematopoiesis and leukemia.
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Affiliation(s)
- Yimeng Gao
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Joshua T Zimmer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Radovan Vasic
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Medicine, University of Toronto, Toronto, ON M5S3H2, Canada
| | - Chengyang Liu
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rana Gbyli
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shu-Jian Zheng
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Wei Liu
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zhihong Qi
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yaping Li
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Raman Nelakanti
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yuanbin Song
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Andrew Z Xiao
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sarah Slavoff
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Richard G Kibbey
- Department of Internal Medicine, Yale University, New Haven, CT 06520, USA; Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
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Zhu J, Liu S, Fang J, Cui Z, Wang B, Wang Y, Liu L, Wang Q, Cao X. Enzymolysis-based RNA pull-down identifies YTHDC2 as an inhibitor of antiviral innate response. Cell Rep 2023; 42:113192. [PMID: 37776518 DOI: 10.1016/j.celrep.2023.113192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 06/06/2023] [Accepted: 09/15/2023] [Indexed: 10/02/2023] Open
Abstract
The innate immune response must be terminated in a timely manner at the late stage of infection to prevent unwanted inflammation. The role of m6A-modified RNAs and their binding partners in this process is not well known. Here, we develop an enzymolysis-based RNA pull-down (eRP) method that utilizes the immunoglobulin G-degrading enzyme of Streptococcus pyogenes (IdeS) to fish out m6A-modified RNA-associated proteins. We apply eRP to capture the methylated single-stranded RNA (ssRNA) probe-associated proteins and identify YT521-B homology domain-containing 2 (YTHDC2) as the m6A-modified interferon β (IFN-β) mRNA-binding protein. YTHDC2, induced in macrophages at the late stage of virus infection, recruits IFN-stimulated exonuclease ISG20 (IFN-stimulated exonuclease gene 20) to degrade IFN-β mRNA, consequently inhibiting antiviral innate immune response. In vitro and in vivo deficiency of YTHDC2 increases IFN-β production at the late stage of viral infection. Our findings establish an eRP method to effectively identify RNA-protein interactions and add mechanistic insight to the termination of innate response for maintaining homeostasis.
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Affiliation(s)
- Jun Zhu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuo Liu
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jiali Fang
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zenghui Cui
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Bingjing Wang
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yuzhou Wang
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lin Liu
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Qingqing Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xuetao Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China; Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; Chinese Academy of Medical Sciences Oxford Institute, Chinese Academy of Medical Sciences, Beijing 100005, China.
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36
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Zeng S, Zhu W, Luo Z, Wu K, Lu Z, Li X, Wang W, Hu W, Qin Y, Chen W, Yi L, Fan S, Chen J. Role of OGDH in Atophagy-IRF3-IFN-β pathway during classical swine fever virus infection. Int J Biol Macromol 2023; 249:126443. [PMID: 37604413 DOI: 10.1016/j.ijbiomac.2023.126443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Classical swine fever (CSF) is a severe infectious disease caused by the classical swine fever virus (CSFV) that poses significant challenges to the swine industry. α-ketoglutarate dehydrogenase (OGDH), the first rate-limiting enzyme of the tricarboxylic acid (TCA) cycle, catalyzes α-ketoglutarate (α-KG) to succinyl-CoA, playing a crucial role in glycometabolism. Our previous studies showed that CSFV disrupts the TCA cycle, resulting in α-KG accumulation. However, the interplay between CSFV and OGDH remains unclear. In this study, we found that CSFV significantly reduces OGDH protein levels and promotes α-KG secretion through OGDH in PK-15 cells. Furthermore, we observed CSFV C protein interacts with OGDH and revealed that CSFV utilizes NDP52/NBR1 to target OGDH protein degradation in the autophagy-lysosome pathway. We also unveiled that OGDH overexpression inhibits CSFV proliferation, whereas OGDH knockdown increases CSFV proliferation. Further investigation into the mechanisms of OGDH on CSFV replication revealed that OGDH regulates the AMPK-mTOR-autophagy pathway. Additionally, using the autophagy agonist/inhibitor, rapamycin/3-MA, we observed that OGDH modulates autophagy to regulate the IRF3-IFN-β network and CSFV replication. These findings shed light on the role of OGDH in CSFV infection and host metabolism, promoting the development of innovative strategies for combating CSFV and other viral infections via targeting metabolic pathways.
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Affiliation(s)
- Sen Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Wenhui Zhu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Zipeng Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Zhimin Lu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Weijun Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Wenshuo Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Yuwei Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China.
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China.
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37
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Zhu L, Zhang H, Zhang X, Xia L. RNA m6A methylation regulators in sepsis. Mol Cell Biochem 2023:10.1007/s11010-023-04841-w. [PMID: 37659034 DOI: 10.1007/s11010-023-04841-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
N6-methyladenosine (m6A) modification is a class of epitope modifications that has received significant attention in recent years, particularly in relation to its role in various diseases, including sepsis. Epigenetic research has increasingly focused on m6A modifications, which is influenced by the dynamic regulation of three protein types: ‟Writers" (such as METTL3/METTL14/WTAP)-responsible for m6A modification; ‟Erasers" (FTO and ALKBH5)-involved in m6A de-modification; and ‟Readers" (YTHDC1/2, YTHDF1/2/3)-responsible for m6A recognition. Sepsis, a severe and fatal infectious disease, has garnered attention regarding the crucial effect of m6A modifications on its development. In this review, we attempted to summarize the recent studies on the involvement of m6A and its regulators in sepsis, as well as the significance of m6A modifications and their regulators in the development of novel drugs and clinical treatment. The potential value of m6A modifications and modulators in the diagnosis, treatment, and prognosis of sepsis has also been discussed.
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Affiliation(s)
- Lin Zhu
- School of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Hairong Zhang
- Department of Obstetrics and Gynecology, Shandong Provincial Third Hospital, Jinan, 250031, People's Republic of China.
| | - Xiaoyu Zhang
- School of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Lei Xia
- Department of Pathology, Shandong University of Traditional Chinese Medicine, Jinan, 250355, People's Republic of China.
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Wu R, Liu J, Tang D, Kang R. The Dual Role of ACOD1 in Inflammation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:518-526. [PMID: 37549395 DOI: 10.4049/jimmunol.2300101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/27/2023] [Indexed: 08/09/2023]
Abstract
Immunometabolism is an interdisciplinary field that focuses on the relationship between metabolic pathways and immune responses. Dysregulated immunometabolism contributes to many pathological settings, such as cytokine storm or immune tolerance. Aconitate decarboxylase 1 (ACOD1, also known as immunoresponsive gene 1), the mitochondrial enzyme responsible for catalyzing itaconate production, was originally identified as a bacterial LPS-inducible gene involved in innate immunity in mouse macrophages. We now know that the upregulation of ACOD1 expression in immune or nonimmune cells plays a context-dependent role in metabolic reprogramming, signal transduction, inflammasome regulation, and protein modification. The emerging function of ACOD1 in inflammation and infection is a double-edged sword. In this review, we discuss how ACOD1 regulates anti-inflammatory or proinflammatory responses in an itaconate-dependent or -independent manner. Further understanding of ACOD1 expression and function may pave the way for the development of precision therapies for inflammatory diseases.
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Affiliation(s)
- Runliu Wu
- Department of Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiao Liu
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX
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Wang Y, Zhou X. N 6-methyladenosine and Its Implications in Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:695-706. [PMID: 35835441 PMCID: PMC10787122 DOI: 10.1016/j.gpb.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 12/27/2022]
Abstract
N6-methyladenine (m6A) is the most abundant RNA modification in mammalian messenger RNAs (mRNAs), which participates in and regulates many important biological activities, such as tissue development and stem cell differentiation. Due to an improved understanding of m6A, researchers have discovered that the biological function of m6A can be linked to many stages of mRNA metabolism and that m6A can regulate a variety of complex biological processes. In addition to its location on mammalian mRNAs, m6A has been identified on viral transcripts. m6A also plays important roles in the life cycle of many viruses and in viral replication in host cells. In this review, we briefly introduce the detection methods of m6A, the m6A-related proteins, and the functions of m6A. We also summarize the effects of m6A-related proteins on viral replication and infection. We hope that this review provides researchers with some insights for elucidating the complex mechanisms of the epitranscriptome related to viruses, and provides information for further study of the mechanisms of other modified nucleobases acting on processes such as viral replication. We also anticipate that this review can stimulate collaborative research from different fields, such as chemistry, biology, and medicine, and promote the development of antiviral drugs and vaccines.
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Affiliation(s)
- Yafen Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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40
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Ribeiro DR, Nunes A, Ribeiro D, Soares AR. The hidden RNA code: implications of the RNA epitranscriptome in the context of viral infections. Front Genet 2023; 14:1245683. [PMID: 37614818 PMCID: PMC10443596 DOI: 10.3389/fgene.2023.1245683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023] Open
Abstract
Emerging evidence highlights the multifaceted roles of the RNA epitranscriptome during viral infections. By modulating the modification landscape of viral and host RNAs, viruses enhance their propagation and elude host surveillance mechanisms. Here, we discuss how specific RNA modifications, in either host or viral RNA molecules, impact the virus-life cycle and host antiviral responses, highlighting the potential of targeting the RNA epitranscriptome for novel antiviral therapies.
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41
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Zhang X, Liu J, Cheng Y, Chen K, Chen Y, Zhu H, Li Z, Liu S, Cao X. Metabolic enzyme Suclg2 maintains tolerogenicity of regulatory dendritic cells diffDCs by suppressing Lactb succinylation. J Autoimmun 2023; 138:103048. [PMID: 37216870 DOI: 10.1016/j.jaut.2023.103048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
Metabolic reprogramming plays a pivotal role in the differentiation and function of immune cells including dendritic cells (DCs). Regulatory DCs can be generated in regional tissue niches like splenic stroma and act as an important part of stromal control of immune response for the maintenance of immune tolerance. However, the metabolic alterations during splenic stroma-driven regulatory DCs differentiation and the metabolic enzyme involved in regulatory DCs function remain poorly understood. By combining metabolomic, transcriptomic, and functional investigations of mature DCs (maDCs) and diffDCs (regulatory DCs differentiated from activated mature DCs through coculturing with splenic stroma), here we identified succinate-CoA ligase subunit beta Suclg2 as a key metabolic enzyme that reprograms the proinflammatory status of mature DCs into a tolerogenic phenotype via preventing NF-κB signaling activation. diffDCs downregulate succinic acid levels and increase the Suclg2 expression along with their differentiation from mature DCs. Suclg2-interference impaired the tolerogenic function of diffDCs in inducing T cell apoptosis and enhanced activation of NF-κB signaling and expression of inflammatory genes CD40, Ccl5, and Il12b in diffDCs. Furthermore, we identified Lactb as a new positive regulator of NF-κB signaling in diffDCs whose succinylation at the lysine 288 residue was inhibited by Suclg2. Our study reveals that the metabolic enzyme Suclg2 is required to maintain the immunoregulatory function of diffDCs, adding mechanistic insights into the metabolic regulation of DC-based immunity and tolerance.
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Affiliation(s)
- Xiaomin Zhang
- National Key Laboratory of Medical Immunology, Institute of Immunology, Second Military Medical University, Shanghai, 200433, China
| | - Juan Liu
- National Key Laboratory of Medical Immunology, Institute of Immunology, Second Military Medical University, Shanghai, 200433, China.
| | - Yujie Cheng
- National Key Laboratory of Medical Immunology, Institute of Immunology, Second Military Medical University, Shanghai, 200433, China
| | - Kun Chen
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Yali Chen
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Ha Zhu
- National Key Laboratory of Medical Immunology, Institute of Immunology, Second Military Medical University, Shanghai, 200433, China
| | - Zhiqing Li
- National Key Laboratory of Medical Immunology, Institute of Immunology, Second Military Medical University, Shanghai, 200433, China
| | - Shuxun Liu
- National Key Laboratory of Medical Immunology, Institute of Immunology, Second Military Medical University, Shanghai, 200433, China
| | - Xuetao Cao
- National Key Laboratory of Medical Immunology, Institute of Immunology, Second Military Medical University, Shanghai, 200433, China; Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China; Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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42
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Wang S, Chen S, Sun J, Han P, Xu B, Li X, Zhong Y, Xu Z, Zhang P, Mi P, Zhang C, Li L, Zhang H, Xia Y, Li S, Heikenwalder M, Yuan D. m 6A modification-tuned sphingolipid metabolism regulates postnatal liver development in male mice. Nat Metab 2023; 5:842-860. [PMID: 37188818 DOI: 10.1038/s42255-023-00808-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Different organs undergo distinct transcriptional, epigenetic and physiological alterations that guarantee their functional maturation after birth. However, the roles of epitranscriptomic machineries in these processes have remained elusive. Here we demonstrate that expression of RNA methyltransferase enzymes Mettl3 and Mettl14 gradually declines during postnatal liver development in male mice. Liver-specific Mettl3 deficiency causes hepatocyte hypertrophy, liver injury and growth retardation. Transcriptomic and N6-methyl-adenosine (m6A) profiling identify the neutral sphingomyelinase, Smpd3, as a target of Mettl3. Decreased decay of Smpd3 transcripts due to Mettl3 deficiency results in sphingolipid metabolism rewiring, characterized by toxic ceramide accumulation and leading to mitochondrial damage and elevated endoplasmic reticulum stress. Pharmacological Smpd3 inhibition, Smpd3 knockdown or Sgms1 overexpression that counteracts Smpd3 can ameliorate the abnormality of Mettl3-deficent liver. Our findings demonstrate that Mettl3-N6-methyl-adenosine fine-tunes sphingolipid metabolism, highlighting the pivotal role of an epitranscriptomic machinery in coordination of organ growth and the timing of functional maturation during postnatal liver development.
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Affiliation(s)
- Shiguan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shanze Chen
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Jianfeng Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Pan Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bowen Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xinying Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Youquan Zhong
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Hubei Jiangxia Laboratory, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Zaichao Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Hubei Jiangxia Laboratory, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Peng Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ping Mi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for Digestive Disease, Jinan, China
| | - Haiyan Zhang
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Hubei Jiangxia Laboratory, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China.
| | - Shiyang Li
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, China.
- Advanced Medical Research Institute, Shandong University, Jinan, China.
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany.
- The M3 Research Institute, Eberhard Karls University Tübingen, Tübingen, Germany.
| | - Detian Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Shandong Provincial Clinical Research Center for Digestive Disease, Jinan, China.
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Zong G, Wang X, Guo X, Zhao Q, Wang C, Shen S, Xiao W, Yang Q, Jiang W, Shen J, Wan R. NAT10-mediated AXL mRNA N4-acetylcytidine modification promotes pancreatic carcinoma progression. Exp Cell Res 2023; 428:113620. [PMID: 37156457 DOI: 10.1016/j.yexcr.2023.113620] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/10/2023]
Abstract
Although the patient's survival time in various cancers has significantly increased in recent decades, the overall 5-year survival rate of pancreatic ductal adenocarcinoma (PDAC) has remained virtually unchanged due to rapid progression and metastasis. While N-acetyltransferase 10 (NAT10) has been identified as a regulator of mRNA acetylation in many malignancies, its role in PDAC remains unclear. Here, we found that NAT10 mRNA and protein levels were upregulated in PDAC tissues. Increased NAT10 protein expression was significantly correlated with poor prognosis in PDAC patients. Through our experiments, we demonstrated that NAT10 acted as an oncogene to promote PDAC tumorigenesis and metastasis in vitro and in vivo. Mechanistically, NAT10 exerts its oncogenic effects by promoting mRNA stability of receptor tyrosine kinase AXL in an ac4C-dependent manner leading to increased AXL expression and further promoting PDAC cell proliferation and metastasis. Together, our findings highlight the critical of NAT10 in PDAC progression and reveal a novel epigenetic mechanism by which modified mRNA acetylation promotes PDAC metastasis.
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Affiliation(s)
- Guanzhao Zong
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing Wang
- First Affiliated Hospital of Jiangxi Medical College, China
| | - Xingya Guo
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiuyan Zhao
- Department of Gastroenterology, Henan Provincial People's Hospital, Zhengzhou University, Zhengzhou, China
| | - Chuanyang Wang
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shien Shen
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqin Xiao
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingqing Yang
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiliang Jiang
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Shen
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Rong Wan
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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44
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Ge Y, Tang S, Xia T, Shi C. Research progress on the role of RNA N6-methyladenosine methylation in HCV infection. Virology 2023; 582:35-42. [PMID: 36996690 DOI: 10.1016/j.virol.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
Hepatitis C virus (HCV) is a positive-stranded RNA virus causing chronic liver diseases. The chemical modification of RNA is a research hotspot in related fields in recent years, including the methylation and acetylation of adenine, guanine, cytosine and other bases, among which methylation is the most important modification form. m6A (N6-methyladenosine), as the most abundant RNA modification form, plays an important role in HCV virus infection by modifying viral RNA and cell transcripts. This review aims to summarize the current knowledge on the roles of m6A modification in HCV infection, and discuss the research prospect.
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Abstract
Characterization of RNA modifications has identified their distribution features and molecular functions. Dynamic changes in RNA modification on various forms of RNA are essential for the development and function of the immune system. In this review, we discuss the value of innovative RNA modification profiling technologies to uncover the function of these diverse, dynamic RNA modifications in various immune cells within healthy and diseased contexts. Further, we explore our current understanding of the mechanisms whereby aberrant RNA modifications modulate the immune milieu of the tumor microenvironment and point out outstanding research questions.
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Affiliation(s)
- Dali Han
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Meng Michelle Xu
- Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, Beijing, China;
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Li Z, Liu Y, Zhang L, Tian J, Wang H, Ding H, Nie J, Pi H, Wang B, Liu D. N 6-methyladenosine modification contributes to respiratory syncytial virus infection. Heliyon 2023; 9:e15307. [PMID: 37089388 PMCID: PMC10114233 DOI: 10.1016/j.heliyon.2023.e15307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023] Open
Abstract
Background Respiratory syncytial virus (RSV) is the second leading cause of death due to lower respiratory tract infections. Effective prevention and treatment measures are lacking, posing a huge socioeconomic burden to the world. N 6-methyladenosine (m6A) is the most common internal modification in messenger RNA and noncoding RNA. Numerous recent studies have shown that the dysregulation of m6A modification is associated with diseases caused by pathogenic viruses. Methods The changes in m6A modification were evaluated using m6A RNA methylation assay. The differences in gene expression levels of various m6A-modifying enzymes were observed using Quantitative Real-time PCR (qRT-PCR) during RSV infection. The autophagosomes were observed using transmission electron microscopy, and the expression of autophagy-associated protein Microtubule Associated Protein 1 Light Chain 3 Beta Ⅱ/Ⅰ (LC3B Ⅱ/Ⅰ) and Beclin1 in Human Normal Lung Epithelial Cells (BEAS-2B) cells using Western blot during RSV infection. The significantly differentially expressed genes were screened guided by bioinformatics. Their relationship with m6A-modifying enzymes was analyzed through protein-protein interaction network and expression correlation analysis. Results The m6A abundance decreased and demethylase Fat Mass and Obesity- Associated Protein (FTO) significantly increased during RSV infection after 24 h. We also found that the DNA Damage-Inducible Transcript 3 Protein (DDIT3) level significantly increased during RSV infection after 24 h and observed autophagosomes in BEAS-2B cells. In addition, RSV infection could cause the upregulation of LC3B Ⅱ/Ⅰ and Beclin1. The expression correlation analysis showed that DDIT3 levels were positively correlated with the FTO level, and Methyltransferase Like 3 (METTL3), RNA Binding Motif Protein 15B (RBM15B), YTH Domain-Containing Family Protein 1 (YTHDF1), and levels were negatively correlated with the DDIT3 level. Conclusions We uncovered a significant role for m6A modification during RSV infection. Also, a correlation was found between m6A and autophagy, providing new ideas for therapeutic advancements in RSV treatment.
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Affiliation(s)
- Zhu Li
- Medical College of Soochow University, 215000, Suzhou, China
- Department of Respiratory Medicine, The First People's Hospital of Zunyi, (The Third Affiliated Hospital of Zunyi Medical University), 563000, Guizhou, China
| | - Yi Liu
- Zhuhai Campus of Zunyi Medical University, Zhuhai, 519000, Guangdong, China
| | - Ling Zhang
- Department of Respiratory Medicine, The First People's Hospital of Zunyi, (The Third Affiliated Hospital of Zunyi Medical University), 563000, Guizhou, China
- Zhuhai Campus of Zunyi Medical University, Zhuhai, 519000, Guangdong, China
| | - Jiahua Tian
- The Affiliated Hospital of Zunyi Medical University, 563000, Guizhou, China
| | - Hongping Wang
- Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Hongwei Ding
- Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Jin Nie
- The Affiliated Hospital of Zunyi Medical University, 563000, Guizhou, China
| | - Hang Pi
- Zhuhai Campus of Zunyi Medical University, Zhuhai, 519000, Guangdong, China
| | - Bingyao Wang
- Zhuhai Campus of Zunyi Medical University, Zhuhai, 519000, Guangdong, China
| | - Daishun Liu
- Medical College of Soochow University, 215000, Suzhou, China
- Zunyi Medical University, Zunyi, 563000, Guizhou, China
- Corresponding author. Medical College of Soochow University, 215000, Suzhou, China.
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Luo S, Liao C, Zhang L, Ling C, Zhang X, Xie P, Su G, Chen Z, Zhang L, Lai T, Tang J. METTL3-mediated m6A mRNA methylation regulates neutrophil activation through targeting TLR4 signaling. Cell Rep 2023; 42:112259. [PMID: 36920907 DOI: 10.1016/j.celrep.2023.112259] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/20/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
N6-methyladenosine (m6A) modification accounts for the most prevalent mRNA internal modification and has emerged as a widespread regulatory mechanism in multiple physiological processes. We address a role of methyltransferase-like protein 3 (METTL3) in neutrophil activation. METTL3 controls neutrophil release from bone marrow to circulation through surface expression of CXC chemokine receptor 2 (CXCR2) in a Toll-like receptor 4 (TLR4) signaling-dependent manner in lipopolysaccharide (LPS)-induced endotoxemia. We show that the mRNA of TLR4 is modified by m6A, exhibiting increased translation and slowed degradation simultaneously, leading to elevated protein levels of TLR4, which eventually promotes the TLR4 signaling activation of neutrophil. The reduced expression of TLR4 lowers cytokine secretion in METTL3-deleted neutrophils upon LPS stimulation through TLR4/Myd88/nuclear factor κB (NF-κB) signaling. Collectively, these data demonstrate that METTL3 modulation of TLR4 expression is a critical determinant of neutrophil activation in endotoxemia.
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Affiliation(s)
- Shuhua Luo
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China; Guangdong Medical University, Zhanjiang 524000, Guangdong, China
| | - Chaoxiong Liao
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China; Guangdong Medical University, Zhanjiang 524000, Guangdong, China
| | - Lina Zhang
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China; Guangdong Medical University, Zhanjiang 524000, Guangdong, China
| | - Chunxiu Ling
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China; Guangdong Medical University, Zhanjiang 524000, Guangdong, China
| | - Xuedi Zhang
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China; Guangdong Medical University, Zhanjiang 524000, Guangdong, China
| | - Pengyun Xie
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China
| | - Guomei Su
- Guangdong Medical University, Zhanjiang 524000, Guangdong, China; Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China
| | - Zhanghui Chen
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang 524000, Guangdong, China
| | - Liangqing Zhang
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China.
| | - Tianwen Lai
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China.
| | - Jing Tang
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China.
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Zhao J, Ding C, Li HB. N 6 - Methyladenosine defines a new checkpoint in γδ T cell development. Bioessays 2023; 45:e2300002. [PMID: 36942692 DOI: 10.1002/bies.202300002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
T cells, which are derived from hematopoietic stem cells (HSCs), are the most important components of adaptive immune system. Based on the expression of αβ and γδ receptors, T cells are mainly divided into αβ and γδ T cells. In the thymus, they share common progenitor cells, while undergoing a series of well-characterized and different developmental processes. N6 -Methyladenosine (m6 A), one of the most abundant modifications in mRNAs, plays critical roles in cell development and maintenance of function. Recently, we have demonstrated that the depletion of m6 A demethylase ALKBH5 in lymphocytes specifically induces an expansion of γδ T cells through the regulation of Jag1/Notch2 signaling, but not αβ T cells, indicating a checkpoint role of ALKBH5 and m6 A modification in the early development of γδ T cells. Based on previous studies, many key pathway molecules, which exert dominant roles in γδ T cell fate determination, have been identified as the targets regulated by m6 A modification. In this review, we mainly summarize the potential regulation between m6 A modification and these key signaling molecules in the γδ T cell lineage commitment, to provide new perspectives in the checkpoint of γδ T cell development.
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Affiliation(s)
- Jiachen Zhao
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenbo Ding
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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The Role of m 6A Modifications in B-Cell Development and B-Cell-Related Diseases. Int J Mol Sci 2023; 24:ijms24054721. [PMID: 36902149 PMCID: PMC10003095 DOI: 10.3390/ijms24054721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
B cells are a class of professional antigen-presenting cells that produce antibodies to mediate humoral immune response and participate in immune regulation. m6A modification is the most common RNA modification in mRNA; it involves almost all aspects of RNA metabolism and can affect RNA splicing, translation, stability, etc. This review focuses on the B-cell maturation process as well as the role of three m6A modification-related regulators-writer, eraser, and reader-in B-cell development and B-cell-related diseases. The identification of genes and modifiers that contribute to immune deficiency may shed light on regulatory requirements for normal B-cell development and the underlying mechanism of some common diseases.
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Abstract
N6-Methyladenosine (m6A) is one of the most abundant modifications of the epitranscriptome and is found in cellular RNAs across all kingdoms of life. Advances in detection and mapping methods have improved our understanding of the effects of m6A on mRNA fate and ribosomal RNA function, and have uncovered novel functional roles in virtually every species of RNA. In this Review, we explore the latest studies revealing roles for m6A-modified RNAs in chromatin architecture, transcriptional regulation and genome stability. We also summarize m6A functions in biological processes such as stem-cell renewal and differentiation, brain function, immunity and cancer progression.
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Affiliation(s)
- Konstantinos Boulias
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
| | - Eric Lieberman Greer
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA.
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