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Wang C, Tanizawa H, Hill C, Havas A, Zhang Q, Liao L, Hao X, Lei X, Wang L, Nie H, Qi Y, Tian B, Gardini A, Kossenkov AV, Goldman A, Berger SL, Noma KI, Adams PD, Zhang R. METTL3-mediated chromatin contacts promote stress granule phase separation through metabolic reprogramming during senescence. Nat Commun 2024; 15:5410. [PMID: 38926365 PMCID: PMC11208586 DOI: 10.1038/s41467-024-49745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
METTL3 is the catalytic subunit of the methyltransferase complex, which mediates m6A modification to regulate gene expression. In addition, METTL3 regulates transcription in an enzymatic activity-independent manner by driving changes in high-order chromatin structure. However, how these functions of the methyltransferase complex are coordinated remains unknown. Here we show that the methyltransferase complex coordinates its enzymatic activity-dependent and independent functions to regulate cellular senescence, a state of stable cell growth arrest. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 expression through the three-dimensional chromatin organization during senescence. Elevated Hexokinase 2 expression subsequently promotes liquid-liquid phase separation, manifesting as stress granule phase separation, by driving metabolic reprogramming. This correlates with an impairment of translation of cell-cycle related mRNAs harboring polymethylated m6A sites. In summary, our results report a coordination of m6A-dependent and -independent function of the methyltransferase complex in regulating senescence through phase separation driven by metabolic reprogramming.
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Affiliation(s)
- Chen Wang
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hideki Tanizawa
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
- Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Connor Hill
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Aaron Havas
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Qiang Zhang
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Liping Liao
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xue Hao
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xue Lei
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Lu Wang
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hao Nie
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yuan Qi
- Department of Bioinformatics & Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Bin Tian
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Alessandro Gardini
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Andrew V Kossenkov
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Aaron Goldman
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Shelley L Berger
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ken-Ichi Noma
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
- Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Rugang Zhang
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.
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Liu XW, Xu HW, Yi YY, Zhang SB, Chang SJ, Pan W, Wang SJ. Inhibition of Mettl3 ameliorates osteoblastic senescence by mitigating m6A modifications on Slc1a5 via Igf2bp2-dependent mechanisms. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167273. [PMID: 38844111 DOI: 10.1016/j.bbadis.2024.167273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/25/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024]
Abstract
Age-related osteoporosis is characterized by a marked decrease in the number of osteoblasts, which has been partly attributed to the senescence of cells of the osteoblastic lineage. Epigenetic studies have provided new insights into the mechanisms of current osteoporosis treatments and bone repair pathophysiology. N6-methyladenosine (m6A) is a novel transcript modification that plays a major role in cellular senescence and is essential for skeletal development and internal environmental stability. Bioinformatics analysis revealed that the expression of the m6A reading protein Igf2bp2 was significantly higher in osteoporosis patients. However, the role of Igf2bp2 in osteoblast senescence has not been elucidated. In this study, we found that Igf2bp2 levels are increased in ageing osteoblasts induced by multiple repetition and H2O2. Increasing Igf2bp2 expression promotes osteoblast senescence by increasing the stability of Slc1a5 mRNA and inhibiting cell cycle progression. Additionally, Mettl3 was identified as Slc1a5 m6A-methylated protein with increased m6A modification. The knockdown of Mettl3 in osteoblasts inhibits the reduction of senescence, whereas the overexpression of Mettl3 promotes the senescence of osteoblasts. We found that administering Cpd-564, a specific inhibitor of Mettl3, induced increased bone mass and decreased bone marrow fat accumulation in aged rats. Notably, in an OVX rat model, Igf2bp2 small interfering RNA delivery also induced an increase in bone mass and decreased fat accumulation in the bone marrow. In conclusion, our study demonstrated that the Mettl3/Igf2bp2-Slc1a5 axis plays a key role in the promotion of osteoblast senescence and age-related bone loss.
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Affiliation(s)
- Xiao-Wei Liu
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Hao-Wei Xu
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yu-Yang Yi
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Shu-Bao Zhang
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Sheng-Jie Chang
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Wei Pan
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Shan-Jin Wang
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China.
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3
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Li S, Mehal WZ, Ouyang X. RNA modifications in the progression of liver diseases: from fatty liver to cancer. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2494-x. [PMID: 38809498 DOI: 10.1007/s11427-023-2494-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/24/2023] [Indexed: 05/30/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has emerged as a prominent global health concern associated with high risk of metabolic syndrome, and has impacted a substantial segment of the population. The disease spectrum ranges from simple fatty liver to non-alcoholic steatohepatitis (NASH), which can progress to cirrhosis and hepatocellular carcinoma (HCC) and is increasingly becoming a prevalent indication for liver transplantation. The existing therapeutic options for NAFLD, NASH, and HCC are limited, underscoring the urgent need for innovative treatment strategies. Insights into gene expression, particularly RNA modifications such as N6 methyladenosine (m6A), hold promising avenues for interventions. These modifications play integral roles in RNA metabolism and cellular functions, encompassing the entire NAFLD-NASH-HCC progression. This review will encompass recent insights on diverse RNA modifications, including m6A, pseudouridine (ψ), N1-methyladenosine (m1A), and 5-methylcytidine (m5C) across various RNA species. It will uncover their significance in crucial aspects such as steatosis, inflammation, fibrosis, and tumorigenesis. Furthermore, prospective research directions and therapeutic implications will be explored, advancing our comprehensive understanding of the intricate interconnected nature of these pathological conditions.
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Affiliation(s)
- Simiao Li
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Wajahat Z Mehal
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Xinshou Ouyang
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, 06520, USA.
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Chu LX, Wang WJ, Gu XP, Wu P, Gao C, Zhang Q, Wu J, Jiang DW, Huang JQ, Ying XW, Shen JM, Jiang Y, Luo LH, Xu JP, Ying YB, Chen HM, Fang A, Feng ZY, An SH, Li XK, Wang ZG. Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine. Mil Med Res 2024; 11:31. [PMID: 38797843 PMCID: PMC11129507 DOI: 10.1186/s40779-024-00537-4] [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: 12/15/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Aging and regeneration represent complex biological phenomena that have long captivated the scientific community. To fully comprehend these processes, it is essential to investigate molecular dynamics through a lens that encompasses both spatial and temporal dimensions. Conventional omics methodologies, such as genomics and transcriptomics, have been instrumental in identifying critical molecular facets of aging and regeneration. However, these methods are somewhat limited, constrained by their spatial resolution and their lack of capacity to dynamically represent tissue alterations. The advent of emerging spatiotemporal multi-omics approaches, encompassing transcriptomics, proteomics, metabolomics, and epigenomics, furnishes comprehensive insights into these intricate molecular dynamics. These sophisticated techniques facilitate accurate delineation of molecular patterns across an array of cells, tissues, and organs, thereby offering an in-depth understanding of the fundamental mechanisms at play. This review meticulously examines the significance of spatiotemporal multi-omics in the realms of aging and regeneration research. It underscores how these methodologies augment our comprehension of molecular dynamics, cellular interactions, and signaling pathways. Initially, the review delineates the foundational principles underpinning these methods, followed by an evaluation of their recent applications within the field. The review ultimately concludes by addressing the prevailing challenges and projecting future advancements in the field. Indubitably, spatiotemporal multi-omics are instrumental in deciphering the complexities inherent in aging and regeneration, thus charting a course toward potential therapeutic innovations.
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Affiliation(s)
- Liu-Xi Chu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xin-Pei Gu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Ping Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Quan Zhang
- Integrative Muscle Biology Laboratory, Division of Regenerative and Rehabilitative Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Jia Wu
- Key Laboratory for Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Da-Wei Jiang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jun-Qing Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China
| | - Xin-Wang Ying
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jia-Men Shen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi Jiang
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Hua Luo
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 324025, Zhejiang, China
| | - Jun-Peng Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi-Bo Ying
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao-Man Chen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ao Fang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zun-Yong Feng
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.
| | - Shu-Hong An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China.
| | - Xiao-Kun Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Zhou-Guang Wang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.
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Han J, Wang C, Yang H, Luo J, Zhang X, Zhang XA. Novel Insights into the Links between N6-Methyladenosine and Regulated Cell Death in Musculoskeletal Diseases. Biomolecules 2024; 14:514. [PMID: 38785921 PMCID: PMC11117795 DOI: 10.3390/biom14050514] [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: 03/29/2024] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 05/25/2024] Open
Abstract
Musculoskeletal diseases (MSDs), including osteoarthritis (OA), osteosarcoma (OS), multiple myeloma (MM), intervertebral disc degeneration (IDD), osteoporosis (OP), and rheumatoid arthritis (RA), present noteworthy obstacles associated with pain, disability, and impaired quality of life on a global scale. In recent years, it has become increasingly apparent that N6-methyladenosine (m6A) is a key regulator in the expression of genes in a multitude of biological processes. m6A is composed of 0.1-0.4% adenylate residues, especially at the beginning of 3'-UTR near the translation stop codon. The m6A regulator can be classified into three types, namely the "writer", "reader", and "eraser". Studies have shown that the epigenetic modulation of m6A influences mRNA processing, nuclear export, translation, and splicing. Regulated cell death (RCD) is the autonomous and orderly death of cells under genetic control to maintain the stability of the internal environment. Moreover, distorted RCDs are widely used to influence the course of various diseases and receiving increasing attention from researchers. In the past few years, increasing evidence has indicated that m6A can regulate gene expression and thus influence different RCD processes, which has a central role in the etiology and evolution of MSDs. The RCDs currently confirmed to be associated with m6A are autophagy-dependent cell death, apoptosis, necroptosis, pyroptosis, ferroptosis, immunogenic cell death, NETotic cell death and oxeiptosis. The m6A-RCD axis can regulate the inflammatory response in chondrocytes and the invasive and migratory of MM cells to bone remodeling capacity, thereby influencing the development of MSDs. This review gives a complete overview of the regulatory functions on the m6A-RCD axis across muscle, bone, and cartilage. In addition, we also discuss recent advances in the control of RCD by m6A-targeted factors and explore the clinical application prospects of therapies targeting the m6A-RCD in MSD prevention and treatment. These may provide new ideas and directions for understanding the pathophysiological mechanism of MSDs and the clinical prevention and treatment of these diseases.
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Affiliation(s)
- Juanjuan Han
- College of Exercise and Health, Shenyang Sport University, Shenyang 110100, China; (J.H.); (C.W.)
| | - Cuijing Wang
- College of Exercise and Health, Shenyang Sport University, Shenyang 110100, China; (J.H.); (C.W.)
| | - Haolin Yang
- College of Pharmacy, Jilin University, Changchun 132000, China;
| | - Jiayi Luo
- College of Exercise and Health, Shenyang Sport University, Shenyang 110100, China; (J.H.); (C.W.)
| | - Xiaoyi Zhang
- College of Second Clinical Medical, China Medical University, Shenyang 110100, China;
| | - Xin-An Zhang
- College of Exercise and Health, Shenyang Sport University, Shenyang 110100, China; (J.H.); (C.W.)
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Li SR, Kang NN, Wang RR, Li MD, Chen LH, Zhou P, Xu DX, Zhao H, Fu L. ALKBH5 SUMOylation-mediated FBXW7 m6A modification regulates alveolar cells senescence during 1-nitropyrene-induced pulmonary fibrosis. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133704. [PMID: 38364577 DOI: 10.1016/j.jhazmat.2024.133704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 02/18/2024]
Abstract
Our previous study revealed that 1-nitropyrene (1-NP) exposure evoked pulmonary fibrosis in mice. However, the exact mechanism remained elusive. We found that 1-NP induced telomere damage and cellular senescence in mice lungs, and two alveolar epithelial cells lines. 1-NP downregulated telomere repeat binding factor 2 (TRF2), and upregulated FBXW7. Mechanistically, 1-NP-caused TRF2 ubiquitination and proteasomal degradation depended on E3 ubiquitin ligase activity of FBXW7. Moreover, 1-NP upregulated FBXW7 m6A modification via an ALKBH5-YTHDF1-dependent manner. Further analysis suggested 1-NP promoted ALKBH5 SUMOylation and subsequent proteasomal degradation. Additionally, 1-NP evoked mitochondrial reactive oxygen species (mtROS) overproduction. Mito-TEMPO, a mitochondrial-targeted antioxidant, mitigated 1-NP-caused mtROS overproduction, ALKBH5 SUMOylation, FBXW7 m6A modification, TRF2 degradation, cellular senescence, and pulmonary fibrosis. Taken together, mtROS-initiated ALKBH5 SUMOylation and subsequent FBXW7 m6A modification is indispensable for TRF2 degradation and cellular senescence in alveolar epithelial cells during 1-NP-induced pulmonary fibrosis. Our study provides target intervention measures towards 1-NP-evoked pulmonary fibrosis.
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Affiliation(s)
- Se-Ruo Li
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China; Institute of Respiratory Diseases, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China
| | - Ning-Ning Kang
- Department of Thoracic Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Rong-Rong Wang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China; Institute of Respiratory Diseases, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China
| | - Meng-Die Li
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China; Institute of Respiratory Diseases, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China
| | - Li-Hong Chen
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China; Institute of Respiratory Diseases, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China
| | - Peng Zhou
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China; Institute of Respiratory Diseases, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China
| | - De-Xiang Xu
- Department of Toxicology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Hui Zhao
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China; Institute of Respiratory Diseases, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China.
| | - Lin Fu
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China; Institute of Respiratory Diseases, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, China; Department of Toxicology, Anhui Medical University, Hefei, Anhui 230032, China.
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7
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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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8
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Yu C, Zhao J, Cheng F, Chen J, Chen J, Xu H, Shi K, Xia K, Ding S, Wang K, Wang R, Chen Y, Li Y, Li H, Chen Q, Yu X, Shao F, Liang C, Li F. Silencing circATXN1 in Aging Nucleus Pulposus Cell Alleviates Intervertebral Disc Degeneration via Correcting Progerin Mislocalization. RESEARCH (WASHINGTON, D.C.) 2024; 7:0336. [PMID: 38533181 PMCID: PMC10964222 DOI: 10.34133/research.0336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
Circular RNAs (circRNAs) play a critical regulatory role in degenerative diseases; however, their functions and therapeutic applications in intervertebral disc degeneration (IVDD) have not been explored. Here, we identified that a novel circATXN1 highly accumulates in aging nucleus pulposus cells (NPCs) accountable for IVDD. CircATXN1 accelerates cellular senescence, disrupts extracellular matrix organization, and inhibits mitochondrial respiration. Mechanistically, circATXN1, regulated by heterogeneous nuclear ribonucleoprotein A2B1-mediated splicing circularization, promotes progerin translocation from the cell nucleus to the cytoplasm and inhibits the expression of insulin-like growth factor 1 receptor (IGF-1R). To demonstrate the therapeutic potential of circATXN1, siRNA targeting the backsplice junction of circATNX1 was screened and delivered by tetrahedral framework nucleic acids (tFNAs) due to their unique compositional and tetrahedral structural features. Our siRNA delivery system demonstrates superior abilities to transfect aging cells, clear intracellular ROS, and enhanced biological safety. Using siRNA-tFNAs to silence circATXN1, aging NPCs exhibit reduced mislocalization of progerin in the cytoplasm and up-regulation of IGF-1R, thereby demonstrating a rejuvenated cellular phenotype and improved mitochondrial function. In vivo, administering an aging cell-adapted siRNA nucleic acid framework delivery system to progerin pathologically expressed premature aging mice (zmpste24-/-) can ameliorate the cellular matrix in the nucleus pulposus tissue, effectively delaying IVDD. This study not only identified circATXN1 functioning as a cell senescence promoter in IVDD for the first time, but also successfully demonstrated its therapeutic potential via a tFNA-based siRNA delivery strategy.
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Affiliation(s)
- Chao Yu
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Jing Zhao
- Department of Chemistry,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
| | - Feng Cheng
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Jiangjie Chen
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Jinyang Chen
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Haibin Xu
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Kesi Shi
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Kaishun Xia
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Siwen Ding
- Westlake Street Community Health Service Center, Hangzhou 310009, Zhejiang, PR China
| | - Kanbin Wang
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Ronghao Wang
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Yazhou Chen
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Yi Li
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Hao Li
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Qixin Chen
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Xiaohua Yu
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Fangwei Shao
- Zhejiang University-University of Illinois at Urbana-Champaign Institute,
Zhejiang University, Haining 314400, Zhejiang, PR China
- Biomedical and Health Translational Research Centre,
Zhejiang University, Haining 314400, Zhejiang, PR China
| | - Chengzhen Liang
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
| | - Fangcai Li
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Orthopedics Research Institute of Zhejiang University,
Zhejiang University, Hangzhou 310009, Zhejiang, PR China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
- Clinical Research Center of Motor System Disease of Zhejiang Province, Hangzhou 310009, Zhejiang, PR China
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9
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Kang J, Rhee J, Wang C, Yang Y, Li G, Li H. Unlocking the dark matter: noncoding RNAs and RNA modifications in cardiac aging. Am J Physiol Heart Circ Physiol 2024; 326:H832-H844. [PMID: 38305752 PMCID: PMC11221808 DOI: 10.1152/ajpheart.00532.2023] [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: 08/30/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Cardiac aging is a multifaceted process that encompasses structural and functional alterations culminating in heart failure. As the elderly population continues to expand, there is a growing urgent need for interventions to combat age-related cardiac functional decline. Noncoding RNAs have emerged as critical regulators of cellular and biochemical processes underlying cardiac disease. This review summarizes our current understanding of how noncoding RNAs function in the heart during aging, with particular emphasis on mechanisms of RNA modification that control their activity. Targeting noncoding RNAs as potential novel therapeutics in cardiac aging is also discussed.
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Affiliation(s)
- Jiayi Kang
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - James Rhee
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts, United States
| | - Chunyan Wang
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Yolander Yang
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Guoping Li
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts, United States
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Haobo Li
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts, United States
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10
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Ji Q, Jiang X, Wang M, Xin Z, Zhang W, Qu J, Liu GH. Multimodal Omics Approaches to Aging and Age-Related Diseases. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:56-71. [PMID: 38605908 PMCID: PMC11003952 DOI: 10.1007/s43657-023-00125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 04/13/2024]
Abstract
Aging is associated with a progressive decline in physiological capacities and an increased risk of aging-associated disorders. An increasing body of experimental evidence shows that aging is a complex biological process coordinately regulated by multiple factors at different molecular layers. Thus, it is difficult to delineate the overall systematic aging changes based on single-layer data. Instead, multimodal omics approaches, in which data are acquired and analyzed using complementary omics technologies, such as genomics, transcriptomics, and epigenomics, are needed for gaining insights into the precise molecular regulatory mechanisms that trigger aging. In recent years, multimodal omics sequencing technologies that can reveal complex regulatory networks and specific phenotypic changes have been developed and widely applied to decode aging and age-related diseases. This review summarizes the classification and progress of multimodal omics approaches, as well as the rapidly growing number of articles reporting on their application in the field of aging research, and outlines new developments in the clinical treatment of age-related diseases based on omics technologies.
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Affiliation(s)
- Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Minxian Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zijuan Xin
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100190 China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100190 China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053 China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
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11
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Wu Z, Zhang W, Qu J, Liu GH. Emerging epigenetic insights into aging mechanisms and interventions. Trends Pharmacol Sci 2024; 45:157-172. [PMID: 38216430 DOI: 10.1016/j.tips.2023.12.002] [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: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Epigenetic dysregulation emerges as a critical hallmark and driving force of aging. Although still an evolving field with much to explore, it has rapidly gained significance by providing valuable insights into the mechanisms of aging and potential therapeutic opportunities for age-related diseases. Recent years have witnessed remarkable strides in our understanding of the epigenetic landscape of aging, encompassing pivotal elements, such as DNA methylation, histone modifications, RNA modifications, and noncoding (nc) RNAs. Here, we review the latest discoveries that shed light on new epigenetic mechanisms and critical targets for predicting and intervening in aging and related disorders. Furthermore, we explore burgeoning interventions and exemplary clinical trials explicitly designed to foster healthy aging, while contemplating the potential ramifications of epigenetic influences.
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Affiliation(s)
- Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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12
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Wu Z, Qu J, Zhang W, Liu GH. Stress, epigenetics, and aging: Unraveling the intricate crosstalk. Mol Cell 2024; 84:34-54. [PMID: 37963471 DOI: 10.1016/j.molcel.2023.10.006] [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: 08/22/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023]
Abstract
Aging, as a complex process involving multiple cellular and molecular pathways, is known to be exacerbated by various stresses. Because responses to these stresses, such as oxidative stress and genotoxic stress, are known to interplay with the epigenome and thereby contribute to the development of age-related diseases, investigations into how such epigenetic mechanisms alter gene expression and maintenance of cellular homeostasis is an active research area. In this review, we highlight recent studies investigating the intricate relationship between stress and aging, including its underlying epigenetic basis; describe different types of stresses that originate from both internal and external stimuli; and discuss potential interventions aimed at alleviating stress and restoring epigenetic patterns to combat aging or age-related diseases. Additionally, we address the challenges currently limiting advancement in this burgeoning field.
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Affiliation(s)
- Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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13
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Wei H, Xu Y, Lin L, Li Y, Zhu X. A review on the role of RNA methylation in aging-related diseases. Int J Biol Macromol 2024; 254:127769. [PMID: 38287578 DOI: 10.1016/j.ijbiomac.2023.127769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Senescence is the underlying mechanism of organism aging and is robustly regulated at the post-transcriptional level. This regulation involves the chemical modifications, of which the RNA methylation is the most common. Recently, a rapidly growing number of studies have demonstrated that methylation is relevant to aging and aging-associated diseases. Owing to the rapid development of detection methods, the understanding on RNA methylation has gone deeper. In this review, we summarize the current understanding on the influence of RNA modification on cellular senescence, with a focus on mRNA methylation in aging-related diseases, and discuss the emerging potential of RNA modification in diagnosis and therapy.
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Affiliation(s)
- Hong Wei
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Department of Neurology, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuhao Xu
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Li Lin
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuefeng Li
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China.
| | - Xiaolan Zhu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China.
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14
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Jiang M, Ren J, Belmonte JCI, Liu GH. Hepatocyte reprogramming in liver regeneration: Biological mechanisms and applications. FEBS J 2023; 290:5674-5688. [PMID: 37556833 DOI: 10.1111/febs.16930] [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: 05/15/2023] [Revised: 07/17/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023]
Abstract
The liver is one of the few organs that retain the capability to regenerate in adult mammals. This regeneration process is mainly facilitated by the dynamic behavior of hepatocytes, which are the major functional constituents in the liver. In response to liver injury, hepatocytes undergo remarkable alterations, such as reprogramming, wherein they lose their original identity and acquire properties from other cells. This phenomenon of hepatocyte reprogramming, coupled with hepatocyte expansion, plays a central role in liver regeneration, and its underlying mechanisms are complex and multifaceted. Understanding the fate of reprogrammed hepatocytes and the mechanisms of their conversion has significant implications for the development of innovative therapeutics for liver diseases. Herein, we review the plasticity of hepatocytes in response to various forms of liver injury, with a focus on injury-induced hepatocyte reprogramming. We provide a comprehensive summary of current knowledge on the molecular and cellular mechanisms governing hepatocyte reprogramming, specifically in the context of liver regeneration, providing insight into potential applications of this process in the treatment of liver disorders, including chronic liver diseases and liver cancer.
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Affiliation(s)
- Mengmeng Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jie Ren
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
- Aging Biomarker Consortium, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | | | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Aging Biomarker Consortium, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, China
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15
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Li Q, Lin Y, Liang G, Xiao N, Zhang H, Yang X, Yang J, Liu A. Autophagy and Senescence: The Molecular Mechanisms and Implications in Liver Diseases. Int J Mol Sci 2023; 24:16880. [PMID: 38069199 PMCID: PMC10706096 DOI: 10.3390/ijms242316880] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The liver is the primary organ accountable for complex physiological functions, including lipid metabolism, toxic chemical degradation, bile acid synthesis, and glucose metabolism. Liver function homeostasis is essential for the stability of bodily functions and is involved in the complex regulation of the balance between cell proliferation and cell death. Cell proliferation-halting mechanisms, including autophagy and senescence, are implicated in the development of several liver diseases, such as cholestasis, viral hepatitis, nonalcoholic fatty liver disease, liver fibrosis, and hepatocellular carcinoma. Among various cell death mechanisms, autophagy is a highly conserved and self-degradative cellular process that recycles damaged organelles, cellular debris, and proteins. This process also provides the substrate for further metabolism. A defect in the autophagy machinery can lead to premature diseases, accelerated aging, inflammatory state, tumorigenesis, and cellular senescence. Senescence, another cell death type, is an active player in eliminating premalignant cells. At the same time, senescent cells can affect the function of neighboring cells by secreting the senescence-associated secretory phenotype and induce paracrine senescence. Autophagy can promote and delay cellular senescence under different contexts. This review decodes the roles of autophagy and senescence in multiple liver diseases to achieve a better understanding of the regulatory mechanisms and implications of autophagy and senescence in various liver diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Anding Liu
- Experimental Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan 430100, China; (Q.L.); (Y.L.); (G.L.); (N.X.); (H.Z.); (X.Y.); (J.Y.)
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16
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Hartstock K, Kueck NA, Spacek P, Ovcharenko A, Hüwel S, Cornelissen NV, Bollu A, Dieterich C, Rentmeister A. MePMe-seq: antibody-free simultaneous m 6A and m 5C mapping in mRNA by metabolic propargyl labeling and sequencing. Nat Commun 2023; 14:7154. [PMID: 37935679 PMCID: PMC10630376 DOI: 10.1038/s41467-023-42832-z] [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: 03/04/2022] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Internal modifications of mRNA have emerged as widespread and versatile regulatory mechanism to control gene expression at the post-transcriptional level. Most of these modifications are methyl groups, making S-adenosyl-L-methionine (SAM) a central metabolic hub. Here we show that metabolic labeling with a clickable metabolic precursor of SAM, propargyl-selenohomocysteine (PSH), enables detection and identification of various methylation sites. Propargylated A, C, and G nucleosides form at detectable amounts via intracellular generation of the corresponding SAM analogue. Integration into next generation sequencing enables mapping of N6-methyladenosine (m6A) and 5-methylcytidine (m5C) sites in mRNA with single nucleotide precision (MePMe-seq). Analysis of the termination profiles can be used to distinguish m6A from 2'-O-methyladenosine (Am) and N1-methyladenosine (m1A) sites. MePMe-seq overcomes the problems of antibodies for enrichment and sequence-motifs for evaluation, which was limiting previous methodologies. Metabolic labeling via clickable SAM facilitates the joint evaluation of methylation sites in RNA and potentially DNA and proteins.
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Affiliation(s)
- Katja Hartstock
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nadine A Kueck
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Spacek
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Amarnath Bollu
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany.
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17
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Jing Y, Jiang X, Ji Q, Wu Z, Wang W, Liu Z, Guillen-Garcia P, Esteban CR, Reddy P, Horvath S, Li J, Geng L, Hu Q, Wang S, Belmonte JCI, Ren J, Zhang W, Qu J, Liu GH. Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation. Cell Stem Cell 2023; 30:1452-1471.e10. [PMID: 37832549 DOI: 10.1016/j.stem.2023.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 08/04/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Our understanding of the molecular basis for cellular senescence remains incomplete, limiting the development of strategies to ameliorate age-related pathologies by preventing stem cell senescence. Here, we performed a genome-wide CRISPR activation (CRISPRa) screening using a human mesenchymal precursor cell (hMPC) model of the progeroid syndrome. We evaluated targets whose activation antagonizes cellular senescence, among which SOX5 outperformed as a top hit. Through decoding the epigenomic landscapes remodeled by overexpressing SOX5, we uncovered its role in resetting the transcription network for geroprotective genes, including HMGB2. Mechanistically, SOX5 binding elevated the enhancer activity of HMGB2 with increased levels of H3K27ac and H3K4me1, raising HMGB2 expression so as to promote rejuvenation. Furthermore, gene therapy with lentiviruses carrying SOX5 or HMGB2 rejuvenated cartilage and alleviated osteoarthritis in aged mice. Our study generated a comprehensive list of rejuvenators, pinpointing SOX5 as a potent driver for rejuvenation both in vitro and in vivo.
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Affiliation(s)
- Yaobin Jing
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Wei Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Pedro Guillen-Garcia
- Department of Traumatology and Research Unit, Clinica CEMTRO, 28035 Madrid, Spain
| | - Concepcion Rodriguez Esteban
- Altos Labs, Inc., San Diego, CA 94022, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Pradeep Reddy
- Altos Labs, Inc., San Diego, CA 94022, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Steve Horvath
- Altos Labs, Inc., San Diego, CA 94022, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 10833, USA
| | - Jingyi Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Lingling Geng
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Qinchao Hu
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510060, China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510060, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Chongqing Renji Hospital, University of Chinese Academy of Sciences, Chongqing 400062, China
| | - Juan Carlos Izpisua Belmonte
- Altos Labs, Inc., San Diego, CA 94022, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jie Ren
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Weiqi Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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18
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Imbriano C, Moresi V, Belluti S, Renzini A, Cavioli G, Maretti E, Molinari S. Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives. Int J Mol Sci 2023; 24:15161. [PMID: 37894843 PMCID: PMC10606696 DOI: 10.3390/ijms242015161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Epitranscriptomics refers to post-transcriptional regulation of gene expression via RNA modifications and editing that affect RNA functions. Many kinds of modifications of mRNA have been described, among which are N6-methyladenosine (m6A), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), and 5-methylcytidine (m5C). They alter mRNA structure and consequently stability, localization and translation efficiency. Perturbation of the epitranscriptome is associated with human diseases, thus opening the opportunity for potential manipulations as a therapeutic approach. In this review, we aim to provide an overview of the functional roles of epitranscriptomic marks in the skeletal muscle system, in particular in embryonic myogenesis, muscle cell differentiation and muscle homeostasis processes. Further, we explored high-throughput epitranscriptome sequencing data to identify RNA chemical modifications in muscle-specific genes and we discuss the possible functional role and the potential therapeutic applications.
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Affiliation(s)
- Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Viviana Moresi
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy;
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Giorgia Cavioli
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Eleonora Maretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Susanna Molinari
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
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19
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Xie L, Zhang X, Xie J, Xu Y, Li XJ, Lin L. Emerging Roles for DNA 6mA and RNA m6A Methylation in Mammalian Genome. Int J Mol Sci 2023; 24:13897. [PMID: 37762200 PMCID: PMC10531503 DOI: 10.3390/ijms241813897] [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] [Revised: 08/25/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Epigenetic methylation has been shown to play an important role in transcriptional regulation and disease pathogenesis. Recent advancements in detection techniques have identified DNA N6-methyldeoxyadenosine (6mA) and RNA N6-methyladenosine (m6A) as methylation modifications at the sixth position of adenine in DNA and RNA, respectively. While the distributions and functions of 6mA and m6A have been extensively studied in prokaryotes, their roles in the mammalian brain, where they are enriched, are still not fully understood. In this review, we provide a comprehensive summary of the current research progress on 6mA and m6A, as well as their associated writers, erasers, and readers at both DNA and RNA levels. Specifically, we focus on the potential roles of 6mA and m6A in the fundamental biological pathways of the mammalian genome and highlight the significant regulatory functions of 6mA in neurodegenerative diseases.
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Affiliation(s)
| | | | | | | | | | - Li Lin
- Guangdong Key Laboratory of Non-Human Primate Research, Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China; (L.X.); (X.Z.); (J.X.); (Y.X.); (X.-J.L.)
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20
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Zhang H, Li J, Yu Y, Ren J, Liu Q, Bao Z, Sun S, Liu X, Ma S, Liu Z, Yan K, Wu Z, Fan Y, Sun X, Zhang Y, Ji Q, Cheng F, Wei PH, Ma X, Zhang S, Xie Z, Niu Y, Wang YJ, Han JDJ, Jiang T, Zhao G, Ji W, Izpisua Belmonte JC, Wang S, Qu J, Zhang W, Liu GH. Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging. Cell Rep 2023; 42:112593. [PMID: 37261950 DOI: 10.1016/j.celrep.2023.112593] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/10/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
The primate frontal lobe (FL) is sensitive to aging-related neurocognitive decline. However, the aging-associated molecular mechanisms remain unclear. Here, using physiologically aged non-human primates (NHPs), we depicted a comprehensive landscape of FL aging with multidimensional profiling encompassing bulk and single-nucleus transcriptomes, quantitative proteome, and DNA methylome. Conjoint analysis across these molecular and neuropathological layers underscores nuclear lamina and heterochromatin erosion, resurrection of endogenous retroviruses (ERVs), activated pro-inflammatory cyclic GMP-AMP synthase (cGAS) signaling, and cellular senescence in post-mitotic neurons of aged NHP and human FL. Using human embryonic stem-cell-derived neurons recapitulating cellular aging in vitro, we verified the loss of B-type lamins inducing resurrection of ERVs as an initiating event of the aging-bound cascade in post-mitotic neurons. Of significance, these aging-related cellular and molecular changes can be alleviated by abacavir, a nucleoside reverse transcriptase inhibitor, either through direct treatment of senescent human neurons in vitro or oral administration to aged mice.
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Affiliation(s)
- Hui Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yu
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China; Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Liu
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zhaoshi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Chinese Glioma Genome Atlas Network & Asian Glioma Genome Atlas Network, Beijing 100070, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Cheng
- University of Chinese Academy of Sciences, Beijing 100049, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng-Hu Wei
- Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China; MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xibo Ma
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiqiang Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Zhengwei Xie
- Peking University International Cancer Institute, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yan-Jiang Wang
- Department of Neurology, Daping Hospital, Third Military Medical University, Chongqing 400042, China; State Key Laboratory of Trauma, Burn and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Beijing 100070, China; Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Chinese Glioma Genome Atlas Network & Asian Glioma Genome Atlas Network, Beijing 100070, China
| | - Guoguang Zhao
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Clinical Research Center for Epilepsy Capital Medical University, Beijing 100053, China; Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | | | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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