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Li Y, Xue J, Ma Y, Ye K, Zhao X, Ge F, Zheng F, Liu L, Gao X, Wang D, Xia Q. The complex roles of m 6 A modifications in neural stem cell proliferation, differentiation, and self-renewal and implications for memory and neurodegenerative diseases. Neural Regen Res 2025; 20:1582-1598. [PMID: 38845217 DOI: 10.4103/nrr.nrr-d-23-01872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/25/2024] [Indexed: 08/07/2024] Open
Abstract
N6-methyladenosine (m 6 A), the most prevalent and conserved RNA modification in eukaryotic cells, profoundly influences virtually all aspects of mRNA metabolism. mRNA plays crucial roles in neural stem cell genesis and neural regeneration, where it is highly concentrated and actively involved in these processes. Changes in m 6 A modification levels and the expression levels of related enzymatic proteins can lead to neurological dysfunction and contribute to the development of neurological diseases. Furthermore, the proliferation and differentiation of neural stem cells, as well as nerve regeneration, are intimately linked to memory function and neurodegenerative diseases. This paper presents a comprehensive review of the roles of m 6 A in neural stem cell proliferation, differentiation, and self-renewal, as well as its implications in memory and neurodegenerative diseases. m 6 A has demonstrated divergent effects on the proliferation and differentiation of neural stem cells. These observed contradictions may arise from the time-specific nature of m 6 A and its differential impact on neural stem cells across various stages of development. Similarly, the diverse effects of m 6 A on distinct types of memory could be attributed to the involvement of specific brain regions in memory formation and recall. Inconsistencies in m 6 A levels across different models of neurodegenerative disease, particularly Alzheimer's disease and Parkinson's disease, suggest that these disparities are linked to variations in the affected brain regions. Notably, the opposing changes in m 6 A levels observed in Parkinson's disease models exposed to manganese compared to normal Parkinson's disease models further underscore the complexity of m 6 A's role in neurodegenerative processes. The roles of m 6 A in neural stem cell proliferation, differentiation, and self-renewal, and its implications in memory and neurodegenerative diseases, appear contradictory. These inconsistencies may be attributed to the time-specific nature of m 6 A and its varying effects on distinct brain regions and in different environments.
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Affiliation(s)
- Yanxi Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jing Xue
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yuejia Ma
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Ke Ye
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xue Zhao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Fangliang Ge
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Feifei Zheng
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lulu Liu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xu Gao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- Basic Medical Institute, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang Province, China
- Key Laboratory of Heilongjiang Province for Genetically Modified Animals, Harbin Medical University, Harbin, Heilongjiang Province, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang Province, China
| | - Dayong Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- College of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang Province, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang Province, China
| | - Qing Xia
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
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Liu Y, Koo JS, Zhang H. Chronic intermittent ethanol exposure-induced m6A modifications around mRNA stop codons of opioid receptor genes. Epigenetics 2024; 19:2294515. [PMID: 38118075 PMCID: PMC10761033 DOI: 10.1080/15592294.2023.2294515] [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: 08/05/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Chronic alcohol consumption may alter mRNA methylation and expression levels of genes related to addiction and reward in the brain, potentially contributing to alcohol tolerance and dependence. Neuron-like (SH-SY5Y) and non-neuronal (SW620) cells were utilized as models to examine chronic intermittent ethanol (CIE) exposure-induced global m6A RNA methylation changes, as well as m6A mRNA methylation changes around the stop codon of three opioid receptor genes (OPRM1, OPRD1, and OPRK1), which are known to regulate pain, reward, and addiction behaviours. CIE exposure for three weeks significantly increased global RNA methylation levels in both SH-SY5Y (t = 3.98, P = 0.007) and SW620 (t = 2.24, P = 0.067) cells. However, a 3-week CIE exposure resulted in hypomethylation around mRNA stop codon regions of OPRM1 and OPRD1 in both cell lines [OPRM1(SH-SY5Y): t = -5.05, P = 0.0005; OPRM1(SW620): t = -3.19, P = 0.013; OPRD1(SH-SY5Y): t = -13.43, P < 0.00001; OPRD1(SW620): t = -4.00, P = 0.003]. Additionally, mRNA expression levels of OPRM1, OPRD1, and OPRK1 were downregulated (corresponding to mRNA hypomethylation) in both SH-SY5Y and SW620 cells after a 3-week CIE exposure. The present study demonstrated that chronic ethanol exposure altered global RNA methylation levels, as well as mRNA methylation and expression levels of opioid receptor genes in both neuron-like and non-neuronal cells. Our findings suggest a potential epitranscriptomic mechanism by which chronic alcohol consumption remodels the expression of reward-related and alcohol responsive genes in the brain, thus increasing the risk of alcohol use disorder development.Abbreviations: OPRM1: the μ-opioid receptor; OPRD1: the δ-opioid receptor; OPRK1: the κ-opioid receptor; CIE: chronic intermittent ethanol exposure; CIE+WD: chronic intermittent ethanol exposure followed by a 24-hr withdrawal; SH-SY5Y: human neuroblastoma cell Line; SW620: human colon carcinoma cell line; RT-qPCR: reverse transcription followed by quantitative polymerase reaction; MazF-RT-qPCR: MazF digestion followed by RT-qPCR.
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Affiliation(s)
- Ying Liu
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Ji Sun Koo
- Department of Biology, Boston University, Boston, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
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Li F, Wang F, Wang L, Wang J, Wei S, Meng J, Li Y, Feng L, Jiang P. m6A reader YTHDC2 mediates NCOA4 mRNA stability affecting ferritinophagy to alleviate secondary injury after intracerebral haemorrhage. Epigenetics 2024; 19:2326868. [PMID: 38465865 PMCID: PMC10936596 DOI: 10.1080/15592294.2024.2326868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/01/2024] [Indexed: 03/12/2024] Open
Abstract
Oxidative stress and neuronal dysfunction caused by intracerebral haemorrhage (ICH) can lead to secondary injury. The m6A modification has been implicated in the progression of ICH. This study aimed to investigate the role of the m6A reader YTHDC2 in ICH-induced secondary injury. ICH models were established in rats using autologous blood injection, and neuronal cell models were induced with Hemin. Experiments were conducted to overexpress YTH domain containing 2 (YTHDC2) and examine its effects on neuronal dysfunction, brain injury, and neuronal ferritinophagy. RIP-qPCR and METTL3 silencing were performed to investigate the regulation of YTHDC2 on nuclear receptor coactivator 4 (NCOA4). Finally, NCOA4 overexpression was used to validate the regulatory mechanism of YTHDC2 in ICH. The study found that YTHDC2 expression was significantly downregulated in the brain tissues of ICH rats. However, YTHDC2 overexpression improved neuronal dysfunction and reduced brain water content and neuronal death after ICH. Additionally, it reduced levels of ROS, NCOA4, PTGS2, and ATG5 in the brain tissues of ICH rats, while increasing levels of FTH and FTL. YTHDC2 overexpression also decreased levels of MDA and Fe2+ in the serum, while promoting GSH synthesis. In neuronal cells, YTHDC2 overexpression alleviated Hemin-induced injury, which was reversed by Erastin. Mechanistically, YTHDC2-mediated m6A modification destabilized NCOA4 mRNA, thereby reducing ferritinophagy and alleviating secondary injury after ICH. However, the effects of YTHDC2 were counteracted by NCOA4 overexpression. Overall, YTHDC2 plays a protective role in ICH-induced secondary injury by regulating NCOA4-mediated ferritinophagy.
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Affiliation(s)
- Fengfeng Li
- Department of Neurosurgery, Tengzhou Central People’s Hospital, Jining Medical University, Tengzhou, China
| | - Fang Wang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Lei Wang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Jianhua Wang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Shanshan Wei
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Junjun Meng
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Yanan Li
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Lei Feng
- Department of Neurosurgery, Jining First People’s Hospital, Shandong First Medical University, Jining, China
| | - Pei Jiang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
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Mi J, Wang Y, He S, Qin X, Li Z, Zhang T, Huang W, Wang R. LncRNA HOTAIRM1 promotes radioresistance in nasopharyngeal carcinoma by modulating FTO acetylation-dependent alternative splicing of CD44. Neoplasia 2024; 56:101034. [PMID: 39128424 PMCID: PMC11367117 DOI: 10.1016/j.neo.2024.101034] [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: 02/05/2024] [Revised: 07/17/2024] [Accepted: 07/28/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND Radiotherapy is the primary treatment for patients with nasopharyngeal carcinoma (NPC); however, almost 20% of patients experience treatment failure due to radioresistance. Therefore, understanding the mechanisms of radioresistance is imperative. HOTAIRM1 is deregulated in various human cancers, yet its role in NPC radioresistance are largely unclear. METHODS This study investigated the association between HOTAIRM1 and radioresistance using CCK8, flow cytometry, and comet assays. Additionally, xenograft mice and patient-derived xenografts (PDX) models were employed to elucidate the biological functions of HOTAIRM1, and transcriptomic RNA sequencing was utilized to identify its target genes. RESULTS Our study revealed an upregulation of HOTAIRM1 levels in radioresistant NPC cell lines and tissues. Furthermore, a positive correlation was noted between high HOTAIRM1 expression and increased NPC cell proliferation, reduced apoptosis, G2/M cell cycle arrest, and diminished cellular DNA damage following radiotherapy. HOTAIRM1 modulates the acetylation and stability of the FTO protein, and inhibiting FTO elevates the m6A methylation level of CD44 precursor transcripts in NPC cells. Additionally, silencing the m6A reading protein YTHDC1 was found to increase the expression of CD44V. HOTAIRM1 enhances NPC cell resistance to ferroptosis and irradiation through the HOTAIRM1-FTO-YTHDC1-CD44 axis. Mechanistically, HOTAIRM1 interacts with the FTO protein and induces m6A demethylation of the CD44 transcript. The absence of m6A modification in the CD44 transcript prevents its recognition by YTHDC1, resulting in the transition from CD44S to CD44V. An abundance of CD44V suppresses ferroptosis induced by irradiation and contributes to NPC radioresistance. CONCLUSIONS In conclusion, the results in this study support the idea that HOTAIRM1 stimulates CD44 alternative splicing via FTO-mediated demethylation, thereby attenuating ferroptosis induced by irradiation and promoting NPC radioresistance.
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Affiliation(s)
- Jinglin Mi
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China; Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi 530021, China; Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumors (Guangxi Medical University), Ministry of Education, Nanning, Guangxi 530021, China
| | - Yiru Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China; Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi 530021, China; Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumors (Guangxi Medical University), Ministry of Education, Nanning, Guangxi 530021, China
| | - Siyi He
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China; Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi 530021, China; Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumors (Guangxi Medical University), Ministry of Education, Nanning, Guangxi 530021, China
| | - Xinling Qin
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China; Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi 530021, China; Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumors (Guangxi Medical University), Ministry of Education, Nanning, Guangxi 530021, China
| | - Zhixun Li
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China; Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi 530021, China; Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumors (Guangxi Medical University), Ministry of Education, Nanning, Guangxi 530021, China
| | - Tingting Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China; Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi 530021, China; Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumors (Guangxi Medical University), Ministry of Education, Nanning, Guangxi 530021, China
| | - Weimei Huang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China; Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi 530021, China; Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumors (Guangxi Medical University), Ministry of Education, Nanning, Guangxi 530021, China.
| | - Rensheng Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China; Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi 530021, China; Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumors (Guangxi Medical University), Ministry of Education, Nanning, Guangxi 530021, China.
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Liu ZY, You QY, Liu ZY, Lin LC, Yang JJ, Tao H. m6A control programmed cell death in cardiac fibrosis. Life Sci 2024; 353:122922. [PMID: 39032691 DOI: 10.1016/j.lfs.2024.122922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/29/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
N6-methyladenosine (m6A) modification is closely related to cardiac fibrosis. As the most common and abundant form of mRNA modification in eukaryotes, m6A is deposited by methylases ("writers"), recognized and effected by RNA-binding proteins ("readers"), and removed by demethylases ("erasers"), achieving highly dynamic reversibility. m6A modification is involved in regulating the entire biological process of target RNA, including transcription, processing and splicing, export from the nucleus to the cytoplasm, and enhancement or reduction of stability and translation. Programmed cell death (PCD) comprises many forms and pathways, with apoptosis and autophagy being the most common. Other forms include pyroptosis, ferroptosis, necroptosis, mitochondrial permeability transition (MPT)-dependent necrosis, and parthanatos. In recent years, increasing evidence suggests that m6A modification can mediate PCD, affecting cardiac fibrosis. Since the correlation between some PCD types and m6A modification is not yet clear, this article mainly introduces the relationship between four common PCD types (apoptosis, autophagy, pyroptosis, and ferroptosis) and m6A modification, as well as their role and influence in cardiac fibrosis.
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Affiliation(s)
- Zhen-Yu Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Qing-Ye You
- Anhui Women and Children's Medical Center, Hefei 230001, PR China
| | - Zhi-Yan Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Li-Chan Lin
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Jing-Jing Yang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China.
| | - Hui Tao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China; Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China.
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Deng T, Ma J. Structures and mechanisms of the RNA m 6A writer. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39238441 DOI: 10.3724/abbs.2024152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024] Open
Abstract
N 6-methyladenosine (m 6A) is the most prevalent epigenetic modification found in eukaryotic mRNAs and plays a crucial role in regulating gene expression by influencing numerous aspects of mRNA metabolism. The m 6A writer for mRNAs and long non-coding RNAs consists of the catalytic subunit m 6A-METTL complex (MTC) (including METTL3/METTL14) and the regulatory subunit m 6A-METTL-associated complex (MACOM) (including HAKAI, WTAP, VIRMA, ZC3H13, and RBM15/15B). In this review, we focus on recent advances in our understanding of the structural and functional properties of m 6A writers and the possible mechanism by which they recognize RNA substrates and perform selective m 6A modifications.
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Yan Z, Zhang Y, Nan N, Ji S, Lan S, Qin G, Sang N. YTHDC2 mediated RNA m 6A modification contributes to PM 2.5-induced hepatic steatosis. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135004. [PMID: 38943883 DOI: 10.1016/j.jhazmat.2024.135004] [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: 04/01/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/01/2024]
Abstract
Exposure to fine particulate matter (PM2.5) is a significant risk factor for hepatic steatosis. The N6-methyladenosine (m6A) is implicated in metabolic disturbances triggered by exogenous environmental factors. However, the role of m6A in mediating PM2.5-induced hepatic steatosis remains unclear. Herein, male C57BL/6J mice were subjected to PM2.5 exposure throughout the entire heating season utilizing a real-ambient PM2.5 whole-body inhalation exposure system. Concurrently, HepG2 cell models exposed to PM2.5 were developed to delve the role of m6A methylation modification. Following PM2.5 exposure, significant hepatic lipid accumulation and elevated global m6A level were observed both in vitro and in vivo. The downregulation of YTHDC2, an m6A-binding protein, might contribute to this alteration. In vitro studies revealed that lipid-related genes CEPT1 and YWHAH might be targeted by m6A modification. YTHDC2 could bind to CDS region of them and increase their stability. Exposure to PM2.5 shortened mRNA lifespan and suppressed the expression of CEPT1 and YWHAH, which were reversed to baseline or higher level upon the enforced expression of YTHDC2. Consequently, our findings indicate that PM2.5 induces elevated m6A methylation modification of CEPT1 and YWHAH by downregulating YTHDC2, which in turn mediates the decrease in the mRNA stabilization and expression of these genes, ultimately resulting in hepatic steatosis.
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Affiliation(s)
- Zhipeng Yan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Shanxi 030006, PR China
| | - Yaru Zhang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Shanxi 030006, PR China
| | - Nan Nan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Shanxi 030006, PR China
| | - Shaoyang Ji
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Shanxi 030006, PR China
| | - Siyi Lan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Shanxi 030006, PR China
| | - Guohua Qin
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Shanxi 030006, PR China.
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Shanxi 030006, PR China
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Xu J, Wang Q, Tang X, Feng X, Zhang X, Liu T, Wu F, Wang Q, Feng X, Tang Q, Lisch D, Lu Y. Drought-induced circular RNAs in maize roots: Separating signal from noise. PLANT PHYSIOLOGY 2024; 196:352-367. [PMID: 38669308 DOI: 10.1093/plphys/kiae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024]
Abstract
Circular RNAs (circRNAs) play an important role in diverse biological processes; however, their origin and functions, especially in plants, remain largely unclear. Here, we used 2 maize (Zea mays) inbred lines, as well as 14 of their derivative recombination inbred lines with different drought sensitivity, to systematically characterize 8,790 circRNAs in maize roots under well-watered (WW) and water-stress (WS) conditions. We found that a diverse set of circRNAs expressed at significantly higher levels under WS. Enhanced expression of circRNAs was associated with longer flanking introns and an enrichment of long interspersed nuclear element retrotransposable elements. The epigenetic marks found at the back-splicing junctions of circRNA-producing genes were markedly different from canonical splicing, characterized by increased levels of H3K36me3/H3K4me1, as well as decreased levels of H3K9Ac/H3K27Ac. We found that genes expressing circRNAs are subject to relaxed selection. The significant enrichment of trait-associated sites along their genic regions suggested that genes giving rise to circRNAs were associated with plant survival rate under drought stress, implying that circRNAs play roles in plant drought responses. Furthermore, we found that overexpression of circMED16, one of the drought-responsive circRNAs, enhances drought tolerance in Arabidopsis (Arabidopsis thaliana). Our results provide a framework for understanding the intricate interplay of epigenetic modifications and how they contribute to the fine-tuning of circRNA expression under drought stress.
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Affiliation(s)
- Jie Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Sichuan Agricultural University, Sichuan 611130, China
| | - Qi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xin Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xiaoju Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xiaoyue Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Tianhong Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Fengkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Qingjun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Qi Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
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9
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Onchan W, Attakitbancha C, Uttamapinant C. An expanded molecular and systems toolbox for imaging, mapping, and controlling local translation. Curr Opin Chem Biol 2024; 82:102523. [PMID: 39226865 DOI: 10.1016/j.cbpa.2024.102523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/28/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
Abstract
Localized protein translation occurs through trafficking of mRNAs and protein translation machineries to different compartments of the cell, leading to rapid on-site synthesis of proteins in response to signaling cues. The spatiotemporally precise nature of the local translation process necessitates continual developments of technologies reviewed herein to visualize and map biomolecular components and the translation process with better spatial and temporal resolution and with fewer artifacts. We also discuss approaches to control local translation, which can serve as a design paradigm for subcellular genetic devices for eukaryotic synthetic biology.
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Affiliation(s)
- Warunya Onchan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chadaporn Attakitbancha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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10
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Xu GE, Zhao X, Li G, Gokulnath P, Wang L, Xiao J. The landscape of epigenetic regulation and therapeutic application of N 6-methyladenosine modifications in non-coding RNAs. Genes Dis 2024; 11:101045. [PMID: 38988321 PMCID: PMC11233902 DOI: 10.1016/j.gendis.2023.06.015] [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: 11/17/2022] [Revised: 05/18/2023] [Accepted: 06/04/2023] [Indexed: 07/12/2024] Open
Abstract
RNA N6-methyladenosine (m6A) methylation is the most abundant and conserved RNA modification in eukaryotes. It participates in the regulation of RNA metabolism and various pathophysiological processes. Non-coding RNAs (ncRNAs) are defined as small or long transcripts which do not encode proteins and display numerous biological regulatory functions. Similar to mRNAs, m6A deposition is observed in ncRNAs. Studying RNA m6A modifications on ncRNAs is of great importance specifically to deepen our understanding of their biological roles and clinical implications. In this review, we summarized the recent research findings regarding the mutual regulation between RNA m6A modification and ncRNAs (with a specific focus on microRNAs, long non-coding RNAs, and circular RNAs) and their functions. We also discussed the challenges of m6A-containing ncRNAs and RNA m6A as therapeutic targets in human diseases and their future perspective in translational roles.
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Affiliation(s)
- Gui-E Xu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong) and School of Life Sciences, Shanghai University, Nantong, Jiangsu 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Xuan Zhao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong) and School of Life Sciences, Shanghai University, Nantong, Jiangsu 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Priyanka Gokulnath
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Lijun Wang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong) and School of Life Sciences, Shanghai University, Nantong, Jiangsu 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong) and School of Life Sciences, Shanghai University, Nantong, Jiangsu 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
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11
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Zhao Z, Yan W, Weng X. RNA modifications identification based on chemical reactions. Bioorg Med Chem 2024; 111:117861. [PMID: 39079454 DOI: 10.1016/j.bmc.2024.117861] [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: 05/29/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/24/2024]
Abstract
RNA modification identification is an emerging field in epigenetics due to its indispensable regulatory role in the cell life cycle. With advancements in identification methods, an increasing number of RNA modifications has been discovered, thereby driving the development of more efficient and accurate techniques for localizing modified RNAs and elucidating their functions. High-throughput sequencing approaches for modified RNA detection can be categorized into antibody-based, enzymatic-based, and chemical-labeling-based methods. Given the intrinsic chemical reactions involved in all biochemical processes, we provide a comprehensive review of recent advancements in artificial chemical labeling and transformations of ten distinct RNA modifications and their applications in sequencing. Our aim is to contribute to a deeper understanding of the mechanisms underlying these modifications. We focus on the chemical reactions associated with RNA modifications and briefly compare the advantages and disadvantages of detection methods based on these reactions. Additionally, we introduce several approaches that identify multiple modifications through chemical labeling. As the field of RNA modification research continues to expand, we anticipate that the techniques and insights presented in this review will serve as a valuable resource for future studies aimed at further elucidating the functional roles of RNA modifications in biological processes.
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Affiliation(s)
- Zhengjia Zhao
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, China; College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan 430072, China
| | - Weikai Yan
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, China; College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan 430072, China
| | - Xiaocheng Weng
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, China; College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan 430072, China.
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12
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Zhang J, Tong L, Liu Y, Li X, Wang J, Lin R, Zhou Z, Chen Y, Chen Y, Liu Y, Chen D. The regulatory role of m 6A modification in the maintenance and differentiation of embryonic stem cells. Genes Dis 2024; 11:101199. [PMID: 38947741 PMCID: PMC11214295 DOI: 10.1016/j.gendis.2023.101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/28/2023] [Accepted: 11/11/2023] [Indexed: 07/02/2024] Open
Abstract
As the most prevalent and reversible internal epigenetic modification in eukaryotic mRNAs, N 6-methyladenosine (m6A) post-transcriptionally regulates the processing and metabolism of mRNAs involved in diverse biological processes. m6A modification is regulated by m6A writers, erasers, and readers. Emerging evidence suggests that m6A modification plays essential roles in modulating the cell-fate transition of embryonic stem cells. Mechanistic investigation of embryonic stem cell maintenance and differentiation is critical for understanding early embryonic development, which is also the premise for the application of embryonic stem cells in regenerative medicine. This review highlights the current knowledge of m6A modification and its essential regulatory contribution to the cell fate transition of mouse and human embryonic stem cells.
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Affiliation(s)
- Jin Zhang
- Center for Reproductive Medicine of the Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Lingling Tong
- Center for Reproductive Medicine of the Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yuchen Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Xiang Li
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Jiayi Wang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Ruoxin Lin
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Ziyu Zhou
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yunbing Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yanxi Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yirong Liu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
| | - Di Chen
- Center for Reproductive Medicine of the Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
- National Key Laboratory of Biobased Transportation Fuel Technology, Haining, Zhejiang 314400, China
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13
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Guarnacci M, Zhang PH, Kanchi M, Hung YT, Lin H, Shirokikh NE, Yang L, Preiss T. Substrate diversity of NSUN enzymes and links of 5-methylcytosine to mRNA translation and turnover. Life Sci Alliance 2024; 7:e202402613. [PMID: 38986569 PMCID: PMC11235314 DOI: 10.26508/lsa.202402613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Maps of the RNA modification 5-methylcytosine (m5C) often diverge markedly not only because of differences in detection methods, data depand analysis pipelines but also biological factors. We re-analysed bisulfite RNA sequencing datasets from five human cell lines and seven tissues using a coherent m5C site calling pipeline. With the resulting union list of 6,393 m5C sites, we studied site distribution, enzymology, interaction with RNA-binding proteins and molecular function. We confirmed tRNA:m5C methyltransferases NSUN2 and NSUN6 as the main mRNA m5C "writers," but further showed that the rRNA:m5C methyltransferase NSUN5 can also modify mRNA. Each enzyme recognises mRNA features that strongly resemble their canonical substrates. By analysing proximity between mRNA m5C sites and footprints of RNA-binding proteins, we identified new candidates for functional interactions, including the RNA helicases DDX3X, involved in mRNA translation, and UPF1, an mRNA decay factor. We found that lack of NSUN2 in HeLa cells affected both steady-state levels of, and UPF1-binding to, target mRNAs. Our studies emphasise the emerging diversity of m5C writers and readers and their effect on mRNA function.
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Affiliation(s)
- Marco Guarnacci
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Pei-Hong Zhang
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Molecular Medicine, Children's Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Madhu Kanchi
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Yu-Ting Hung
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Hanrong Lin
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Nikolay E Shirokikh
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Thomas Preiss
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Sydney, Australia
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14
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Li W, Liu Y, Xu R, Zong Y, He L, Hu J, Li G. M 6A modification in cardiovascular disease: With a focus on programmed cell death. Genes Dis 2024; 11:101039. [PMID: 38988324 PMCID: PMC11233881 DOI: 10.1016/j.gendis.2023.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/11/2023] [Accepted: 05/25/2023] [Indexed: 07/12/2024] Open
Abstract
N6-methyladenosine (m6A) methylation is one of the most predominant internal RNA modifications in eukaryotes and has become a hot spot in the field of epigenetics in recent years. Cardiovascular diseases (CVDs) are a leading cause of death globally. Emerging evidence demonstrates that RNA modifications, such as the m6A modification, are associated with the development and progression of many diseases, including CVDs. An increasing body of studies has indicated that programmed cell death (PCD) plays a vital role in CVDs. However, the molecular mechanisms underlying m6A modification and PCD in CVDs remain poorly understood. Herein, elaborating on the highly complex connections between the m6A mechanisms and different PCD signaling pathways and clarifying the exact molecular mechanism of m6A modification mediating PCD have significant meaning in developing new strategies for the prevention and therapy of CVDs. There is great potential for clinical application.
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Affiliation(s)
- Wen Li
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Department of Pathophysiology, MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yao Liu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Ruiyan Xu
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Department of Pathophysiology, MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yuan Zong
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Department of Pathophysiology, MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Lu He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Jun Hu
- Department of Cardiovascular Surgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Guohua Li
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Department of Pathophysiology, MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
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15
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Wang S, Zhang W, Wang Z, Liu Z, Yi X, Wu J. Mettl3-m6A-YTHDF1 axis promotion of mitochondrial dysfunction in metabolic dysfunction-associated steatotic liver disease. Cell Signal 2024; 121:111303. [PMID: 39019337 DOI: 10.1016/j.cellsig.2024.111303] [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: 05/18/2024] [Revised: 07/09/2024] [Accepted: 07/14/2024] [Indexed: 07/19/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) mRNA modification and mitochondrial function hold paramount importance in the advancement of metabolic dysfunction-associated steatotic liver disease (MASLD). AIM The aim of this study was to elucidate the impact of m6A on hepatic mitochondrial dysfunction and provide a novel perspective for a more comprehensive understanding of the pathogenesis of MASLD. METHODS High-throughput screening methods were used to identify the underlying transcriptome and proteome changes in MASLD model mice. Western blotting, blue native gel electrophoresis (BNGE), dot blot, and Seahorse analyses were conducted to identify and validate the underlying regulatory mechanisms of m6A on mitochondria. RESULTS In vivo, abnormal m6A modification in MASLD was attributed to the upregulation of methyltransferase like 3 (Mettl3) and the downregulation of YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) induced by high-fat foods. In vitro, knockdown of Mettl3 inhibited hepatic oxidative phosphorylation (OXPHOS) and the mitochondrial respiratory chain (MRC), while overexpression of Mettl3 promoted these processes. However, knockout of the reader protein YTHDF1, which plays a crucial role in the m6A modification process, counteracted the effect of Mettl3 and suppressed mitochondrial OXPHOS. CONCLUSIONS In MASLD, damage to the MRC may be regulated by the Mettl3-m6A-YTHDF1 axis, particularly by the role of YTHDF1. Modulation of the Mettl3-m6A-YTHDF1 axis has the potential to improve mitochondrial function, alleviate MASLD symptoms, and decrease the likelihood of disease progression.
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Affiliation(s)
- Shuowen Wang
- Beijing Tongren Hospital, Capital Medical University, Beijing 100176, China; Capital Institute of Pediatrics, Beijing 100020, China
| | - Wanyu Zhang
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Zijun Wang
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Zhuo Liu
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Xiaoyu Yi
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Jianxin Wu
- Beijing Tongren Hospital, Capital Medical University, Beijing 100176, China; Capital Institute of Pediatrics, Beijing 100020, China.
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16
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Liu L, Yu L, Wang Y, Zhou L, Liu Y, Pan X, Huang J. Unravelling the impact of RNA methylation genetic and epigenetic machinery in the treatment of cardiomyopathy. Pharmacol Res 2024; 207:107305. [PMID: 39002868 DOI: 10.1016/j.phrs.2024.107305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Cardiomyopathy (CM) represents a heterogeneous group of diseases primarily affecting cardiac structure and function, with genetic and epigenetic dysregulation playing a pivotal role in its pathogenesis. Emerging evidence from the burgeoning field of epitranscriptomics has brought to light the significant impact of various RNA modifications, notably N6-methyladenosine (m6A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N1-methyladenosine (m1A), 2'-O-methylation (Nm), and 6,2'-O-dimethyladenosine (m6Am), on cardiomyocyte function and the broader processes of cardiac and vascular remodelling. These modifications have been shown to influence key pathological mechanisms including mitochondrial dysfunction, oxidative stress, cardiomyocyte apoptosis, inflammation, immune response, and myocardial fibrosis. Importantly, aberrations in the RNA methylation machinery have been observed in human CM cases and animal models, highlighting the critical role of RNA methylating enzymes and their potential as therapeutic targets or biomarkers for CM. This review underscores the necessity for a deeper understanding of RNA methylation processes in the context of CM, to illuminate novel therapeutic avenues and diagnostic tools, thereby addressing a significant gap in the current management strategies for this complex disease.
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Affiliation(s)
- Li Liu
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Youjiang Medical University for Nationalities, Baise 533000, China; Laboratory of the Atherosclerosis and Ischemic Cardiovascular Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Linxing Yu
- Graduate School of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Yubo Wang
- Graduate School of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Liufang Zhou
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Yan Liu
- Laboratory of the Atherosclerosis and Ischemic Cardiovascular Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China; Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Xingshou Pan
- Laboratory of the Atherosclerosis and Ischemic Cardiovascular Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China; Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China.
| | - Jianjun Huang
- Youjiang Medical University for Nationalities, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China.
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17
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Akgül B, Akçaöz-Alasar A, Sağlam B. RNA m 6A methylation at the juxtaposition of apoptosis and RNA therapeutics. Trends Cell Biol 2024:S0962-8924(24)00159-4. [PMID: 39218733 DOI: 10.1016/j.tcb.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/19/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Targeting RNA m6A marks in apoptosis-related transcripts holds promise for RNA therapeutics. However, pathway-specific RNA m6A sites on pro- or antiapoptotic transcripts have not been fully unveiled, let alone characterized. This article summarizes the current knowledge and gaps in the cellular response modulated by apoptotic stimulus-specific RNA m6A marks.
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Affiliation(s)
- Bünyamin Akgül
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey.
| | - Azime Akçaöz-Alasar
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Buket Sağlam
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
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18
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Wang CH, Zhou H. Discovery of a new inhibitor for YTH domain-containing m 6A RNA readers. RSC Chem Biol 2024; 5:914-923. [PMID: 39211476 PMCID: PMC11353026 DOI: 10.1039/d4cb00105b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
N 6-methyladenosine (m6A) is an abundant modification in mammalian mRNAs and plays important regulatory roles in gene expression, primarily mediated through specific recognition by "reader" proteins. YTH family proteins are one major family of known m6A readers, which specifically recognize m6A-modified transcripts via the YTH domains. Despite the significant relevance of YTH-m6A recognition in biology and diseases, few small molecule inhibitors are available for specifically perturbing this interaction. Here we report the discovery of a new inhibitor ("N-7") for YTH-m6A RNA recognition, from the screening of a nucleoside analogue library against the YTH domain of the YTHDF1 protein. N-7 is characterized to be a pan-inhibitor in vitro against five YTH domains from human YTHDF1, YTHDF2, YTHDF3, YTHDC1, and YTHDC2 proteins, with IC50 values in the range of 30-48 μM measured using a fluorescence polarization competition assay. We demonstrated that N-7 directly interacts with the YTH domain proteins via a thermal shift assay. N-7 expands the chemical structure landscape of the m6A YTH domain-containing reader inhibitors and potentiates future inhibitor development for reader functional studies and therapeutic efforts in targeting the epitranscriptome.
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Affiliation(s)
- Chuan-Hui Wang
- Department of Chemistry, Merkert Chemistry Center, Boston College Chestnut Hill MA 02467 USA
| | - Huiqing Zhou
- Department of Chemistry, Merkert Chemistry Center, Boston College Chestnut Hill MA 02467 USA
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19
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Ma J, Zhang L, Zhang X, Zhang L, Zhang H, Zhu Y, Huang X, Zhang T, Tang X, Wang Y, Chen L, Pu Q, Yang L, Cao Z, Ding BS. Inhibiting endothelial Rhoj blocks profibrotic vascular intussusception and angiocrine factors to sustain lung regeneration. Sci Transl Med 2024; 16:eado5266. [PMID: 39196961 DOI: 10.1126/scitranslmed.ado5266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 08/07/2024] [Indexed: 08/30/2024]
Abstract
Lung regeneration after fibrosis requires formation of functional new vasculature, which is essential for gas exchange and cellular cross-talk with other lung cells. It remains unknown how the lung vasculature can be regenerated without fibrosis. Here, we tested the role of N6-methyladenosine (m6A) modification of forkhead box protein O1 (Foxo1) mRNA in lung regeneration after pneumonectomy (PNX) in mice, a model for lung regrowth after surgical resection. Endothelial cell (EC)-specific knockout of methyltransferase-like 3 (Mettl3) and Foxo1 caused nonproductive intussusceptive angiogenesis (IA), which impaired regeneration and enhanced fibrosis. This nonproductive IA was characterized by enhanced endothelial proliferation and increased vascular splitting with increased numbers of pillar ECs. Endothelial-selective knockout of Mettl3 in mice stimulated nonproductive IA and up-regulation of profibrotic factors after PNX, promoting regeneration to fibrotic transition. EC-specific mutation of m6A modification sites in the Foxo1 gene in mice revealed that endothelial Mettl3 modified A504 and A2035 sites in the Foxo1 mRNA to maintain pro-regenerative endothelial glycolysis, ensuring productive IA and lung regeneration without fibrosis. Suppression of Mettl3-Foxo1 signaling stimulated a subset of hyperglycolytic and hyperproliferative 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (Pfkfb3)+, Ras homolog family member J (Rhoj)+, and platelet-derived growth factor subunit B (Pdgfb)+ ECs in both human and mouse lungs with fibrosis. Inhibiting this Pfkfb3+Rhoj+Pdgfb+ EC subset normalized IA, alleviated fibrosis, and restored regeneration in bleomycin (BLM)-injured mouse lungs. We found that m6A modification of Foxo1 in the mouse vasculature promoted lung regeneration over fibrosis after PNX and BLM injury.
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Affiliation(s)
- Jie Ma
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Liyin Zhang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Xu Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin 150081, China
| | - Lanlan Zhang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
- Department of Respiratory and Critical Care Medicine, Department of Thoracic Surgery and Institute of Thoracic Oncology, and Laboratory of Liver Transplantation, West China Hospital, Chengdu 610041, China
| | - Hua Zhang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Yulei Zhu
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Xingming Huang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Ting Zhang
- Department of Respiratory and Critical Care Medicine, Department of Thoracic Surgery and Institute of Thoracic Oncology, and Laboratory of Liver Transplantation, West China Hospital, Chengdu 610041, China
| | - Xiangdong Tang
- Department of Respiratory and Critical Care Medicine, Department of Thoracic Surgery and Institute of Thoracic Oncology, and Laboratory of Liver Transplantation, West China Hospital, Chengdu 610041, China
| | - Yuan Wang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Lu Chen
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Qiang Pu
- Department of Respiratory and Critical Care Medicine, Department of Thoracic Surgery and Institute of Thoracic Oncology, and Laboratory of Liver Transplantation, West China Hospital, Chengdu 610041, China
| | - Liming Yang
- Department of Pathophysiology, Harbin Medical University, Harbin 150081, China
| | - Zhongwei Cao
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Bi-Sen Ding
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
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20
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Tan L, Guo Z, Shao Y, Ye L, Wang M, Deng X, Chen S, Li R. Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing. Nucleic Acids Res 2024; 52:8746-8762. [PMID: 39011882 PMCID: PMC11347139 DOI: 10.1093/nar/gkae601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/28/2024] [Indexed: 07/17/2024] Open
Abstract
Bacterial gene expression is a complex process involving extensive regulatory mechanisms. Along with growing interests in this field, Nanopore Direct RNA Sequencing (DRS) provides a promising platform for rapid and comprehensive characterization of bacterial RNA biology. However, the DRS of bacterial RNA is currently deficient in the yield of mRNA-mapping reads and has yet to be exploited for transcriptome-wide RNA modification mapping. Here, we showed that pre-processing of bacterial total RNA (size selection followed by ribosomal RNA depletion and polyadenylation) guaranteed high throughputs of sequencing data and considerably increased the amount of mRNA reads. This way, complex transcriptome architectures were reconstructed for Escherichia coli and Staphylococcus aureus and extended the boundaries of 225 known E. coli operons and 89 defined S. aureus operons. Utilizing unmodified in vitro-transcribed (IVT) RNA libraries as a negative control, several Nanopore-based computational tools globally detected putative modification sites in the E. coli and S. aureus transcriptomes. Combined with Next-Generation Sequencing-based N6-methyladenosine (m6A) detection methods, 75 high-confidence m6A candidates were identified in the E. coli protein-coding transcripts, while none were detected in S. aureus. Altogether, we demonstrated the potential of Nanopore DRS in systematic and convenient transcriptome and epitranscriptome analysis.
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Affiliation(s)
- Lu Tan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Zhihao Guo
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yanwen Shao
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Miaomiao Wang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Xin Deng
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hong Kong, China
| | - Runsheng Li
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, 518057, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
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21
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Li L, Liu Z. SRF Facilitates Transcriptional Inhibition of Gem Expression by m6A Methyltransferase METTL3 to Suppress Neuronal Damage in Epilepsy. Mol Neurobiol 2024:10.1007/s12035-024-04396-x. [PMID: 39190265 DOI: 10.1007/s12035-024-04396-x] [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: 11/01/2023] [Accepted: 07/21/2024] [Indexed: 08/28/2024]
Abstract
A bioinformatics analysis was conducted to screen for relevant expression datasets of the transcription factor SRF knockout mice. The aim was to investigate the relationship between SRF and m6A-related genes, predict how SRF regulates the m6A modification of GEM genes mediated by METTL3, and explore potential molecular mechanisms associated with neurotrauma. Disease gene databases such as GeneCards, DisGeNET, and Phenolyzer, and transcription factor databases TFDB and TRRUST, were used to obtain epilepsy-related genes and transcription factors. The intersection was then selected. Expression data of SRF knockout epilepsy mice were obtained from the GEO database and used to filter differentially expressed genes. Important module genes related to the disease were selected through WGCNA co-expression analysis. The intersection between these genes and the differentially expressed genes was performed, followed by PPI network analysis and GO/KEGG enrichment analysis. Furthermore, the core genes were selected using the cytoHubba plugin of the Cytoscape software. Differential expression analysis was performed on m6A-related factors in the GEO dataset, and the relationship between SRF and m6A-related factors and core genes was analyzed. The m6A binding sites of SRF with the METTL3 promoter and target gene Gem were predicted using the AnimalTFDB and SRAMP websites, respectively. We found that the transcription factor SRF may be a key gene in epilepsy during neuronal development. Further WGCNA analysis showed that 129 module genes were associated with SRF knockout epilepsy, and these differentially expressed genes were mainly enriched in the neuroactive ligand-receptor interaction pathway. The final results indicate that knocking out SRF may inhibit the transcription of METTL3, thereby inhibiting the m6A modification of Gem and leading to upregulation of Gem expression, thereby playing an important role in neuronal damage. Knocking out the SRF gene may inhibit the transcription of m6A methyltransferase METTL3, thereby inhibiting the m6A modification of GEM genes mediated by METTL3, promoting GEM gene expression, and leading to the occurrence of epilepsy-related neuron injury. Further investigation revealed that SRF overexpression can potentially enhance the transcription of METTL3, thus promoting m6A modification of GEM, resulting in downregulation of GEM expression. This process regulates oxidative stress in epileptic mouse neurons, suppresses inflammatory responses, and mitigates associated damage. Additionally, an in vitro neuronal epileptic model was established, and experimental techniques such as qRT-PCR and WB were employed to assess the expression of SRF, METTL3, and GEM in hippocampal tissues and neurons. The experimental results were consistent with our predictions, demonstrating that overexpression of SRF can inhibit the development of epilepsy-related neuronal damage. This study reveals that knockout of the SRF gene may suppress the transcription of m6A methyltransferase METTL3, thereby inhibiting m6A modification of the GEM gene mediated by METTL3 and subsequently promoting the expression of the GEM gene, leading to the occurrence of epilepsy-related neuronal damage.
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Affiliation(s)
- Lianling Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan Province, P. R. China.
| | - Zhiguo Liu
- Department of Neurosurgery, Centtal Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, P. R. China
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22
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Jin H, Shi Z, Zhou T, Xie S. Regulation of m6Am RNA modification and its implications in human diseases. J Mol Cell Biol 2024; 16:mjae012. [PMID: 38509021 PMCID: PMC11345611 DOI: 10.1093/jmcb/mjae012] [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: 08/11/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024] Open
Abstract
N 6,2'-O-dimethyladenosine (m6Am) is a prevalent modification frequently found at the 5' cap-adjacent adenosine of messenger RNAs (mRNAs) and small nuclear RNAs (snRNAs) and the internal adenosine of snRNAs. This dynamic and reversible modification is under the regulation of methyltransferases phosphorylated CTD interacting factor 1 and methyltransferase-like protein 4, along with the demethylase fat mass and obesity-associated protein. m6Am RNA modification plays a crucial role in the regulation of pre-mRNA splicing, mRNA stability, and translation, thereby influencing gene expression. In recent years, there has been growing interest in exploring the functions of m6Am and its relevance to human diseases. In this review, we provide a comprehensive overview of the current knowledge concerning m6Am, with a focus on m6Am-modifying enzymes, sequencing approaches for its detection, and its impacts on pre-mRNA splicing, mRNA stability, and translation regulation. Furthermore, we highlight the roles of m6Am in the context of obesity, viral infections, and cancers, unravelling its underlying regulatory mechanisms.
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Affiliation(s)
- Hao Jin
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhouyuanjing Shi
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310020, China
| | - Tianhua Zhou
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310020, China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou 310020, China
| | - Shanshan Xie
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
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23
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Chen S, Han J, Wu S, Guo S, Tang Y, Zheng Y, Hu L, Zhang X, Zhang P, Zhang H, Ren G, Gao S. From non-coding RNAs to histone modification: The epigenetic mechanisms in tomato fruit ripening and quality regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109070. [PMID: 39191041 DOI: 10.1016/j.plaphy.2024.109070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/28/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
Ripening is one of the most important stages of fruit development and determines the fruit quality. Various factors play a role in this process, with epigenetic mechanisms emerging as important players. Epigenetic regulation encompasses DNA methylation, histone modifications and variants, chromatin remodeling, RNA modifications, and non-coding RNAs. Over the past decade, studies using tomato as a model have made considerable progress in understanding the impact of epigenetic regulation on fleshy fruit ripening and quality. In this paper, we provide an overview of recent advancements in the epigenetic regulation of tomato fruit ripening and quality regulation, focusing on three main mechanisms: DNA/RNA modifications, non-coding RNAs, and histone modifications. Furthermore, we highlight the unresolved issues and challenges within this research field, offering perspectives for future investigations to drive agricultural innovation.
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Affiliation(s)
- Shengbo Chen
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jiazhen Han
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shu Wu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shangjing Guo
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Yufei Tang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yujing Zheng
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Lei Hu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xingxing Zhang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peng Zhang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Shuai Gao
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China.
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24
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Shu W, Huang Q, Chen R, Lan H, Yu L, Cui K, He W, Zhu S, Chen M, Li L, Jiang D, Xu G. Complicated role of ALKBH5 in gastrointestinal cancer: an updated review. Cancer Cell Int 2024; 24:298. [PMID: 39182071 PMCID: PMC11344947 DOI: 10.1186/s12935-024-03480-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024] Open
Abstract
Gastrointestinal cancer is the most common malignancy in humans, often accompanied by poor prognosis. N6-methyladenosine (m6A) modification is widely present in eukaryotic cells as the most abundant RNA modification. It plays a crucial role in RNA splicing and processing, nuclear export, translation, and stability. Human AlkB homolog 5 (ALKBH5) is a type of RNA demethylase exhibiting abnormal expression in various gastrointestinal cancers.It is closely related to the tumorigenesis, proliferation, migration, and other biological functions of gastrointestinal cancer. However, recent studies indicated that the role and mechanism of ALKBH5 in gastrointestinal cancer are complicated and even controversial. Thus, this review summarizes recent advances in elucidating the role of ALKBH5 as a tumor suppressor or promoter in gastrointestinal cancer. It examines the biological functions of ALKBH5 and its potential as a therapeutic target, providing new perspectives and insights for gastrointestinal cancer research.
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Affiliation(s)
- Weitong Shu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Qianying Huang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Rui Chen
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Huatao Lan
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Luxin Yu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Kai Cui
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Wanjun He
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Songshan Zhu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Mei Chen
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Li Li
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Dan Jiang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China.
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China.
| | - Guangxian Xu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China.
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China.
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25
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Chen H, Xuan A, Shi X, Fan T, Xue S, Ruan J, Wang X, Tang S, Qi W, Sun H, Liu C, He S, Ding C, Zhu Z. RNA N6-methyladenosine modification in arthritis: New insights into pathogenesis. Mod Rheumatol 2024:roae080. [PMID: 39235765 DOI: 10.1093/mr/roae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 08/15/2024] [Indexed: 09/06/2024]
Abstract
The commonest type of eukaryotic RNA modification, N6-methyladenosine (m6A), has drawn increased scrutiny in the context of pathological functioning as well as relevance in determination of RNA stability, splicing, transportation, localization, and translation efficiency. The m6A modification plays an important role in several types of arthritis, especially osteoarthritis and rheumatoid arthritis. Recent studies have reported that m6A modification regulates arthritis pathology in cells, such as chondrocytes and synoviocytes via immune responses and inflammatory responses through functional proteins classified as writers, erasers, and readers. The aim of this review was to highlight recent advances relevant to m6A modification in the context of arthritis pathogenesis and detail underlying molecular mechanisms, regulatory functions, clinical applications, and future perspectives of m6A in arthritis with the aim of providing a foundation for future research directions.
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Affiliation(s)
- Haowei Chen
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Anran Xuan
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaorui Shi
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Tianxiang Fan
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Song Xue
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Rheumatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jianzhao Ruan
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoshuai Wang
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Su'an Tang
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Weizhong Qi
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Haitao Sun
- Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Canzhao Liu
- Department of Cardiovascular Medicine, Translational Medicine Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shuai He
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Changhai Ding
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Rheumatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Zhaohua Zhu
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Rheumatology, Royal North Shore Hospital and Sydney Musculoskeletal Health, Kolling Institute, University of Sydney, Sydney, Australia
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26
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Mu S, Zhao K, Zhong S, Wang Y. The Role of m6A Methylation in Tumor Immunity and Immune-Associated Disorder. Biomolecules 2024; 14:1042. [PMID: 39199429 PMCID: PMC11353047 DOI: 10.3390/biom14081042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/11/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
N6-methyladenosine (m6A) represents the most prevalent and significant internal modification in mRNA, with its critical role in gene expression regulation and cell fate determination increasingly recognized in recent research. The immune system, essential for defense against infections and maintaining internal stability through interactions with other bodily systems, is significantly influenced by m6A modification. This modification acts as a key post-transcriptional regulator of immune responses, though its effects on different immune cells vary across diseases. This review delineates the impact of m6A modification across major system-related cancers-including those of the respiratory, digestive, endocrine, nervous, urinary reproductive, musculoskeletal system malignancies, as well as acute myeloid leukemia and autoimmune diseases. We explore the pathogenic roles of m6A RNA modifications within the tumor immune microenvironment and the broader immune system, highlighting how RNA modification regulators interact with immune pathways during disease progression. Furthermore, we discuss how the expression patterns of these regulators can influence disease susceptibility to immunotherapy, facilitating the development of diagnostic and prognostic models and pioneering new therapeutic approaches. Overall, this review emphasizes the challenges and prospective directions of m6A-related immune regulation in various systemic diseases throughout the body.
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Affiliation(s)
- Siyu Mu
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang 110000, China; (S.M.); (S.Z.)
| | - Kaiyue Zhao
- Department of Hepatology, Beijing Tsinghua Changgeng Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China;
| | - Shanshan Zhong
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang 110000, China; (S.M.); (S.Z.)
| | - Yanli Wang
- Department of Infectious Diseases, The First Affiliated Hospital of China Medical University, Shenyang 110000, China
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27
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Yang Y, Li G, Pang K, Cao W, Zhang Z, Li X. Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2407013. [PMID: 39159140 DOI: 10.1002/advs.202407013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/23/2024] [Indexed: 08/21/2024]
Abstract
The 3' untranslated regions (3'UTRs) of messenger RNAs contain many important cis-regulatory elements that are under functional and evolutionary constraints. It is hypothesized that these constraints are similar to grammars and syntaxes in human languages and can be modeled by advanced natural language techniques such as Transformers, which has been very effective in modeling complex protein sequence and structures. Here 3UTRBERT is described, which implements an attention-based language model, i.e., Bidirectional Encoder Representations from Transformers (BERT). 3UTRBERT is pre-trained on aggregated 3'UTR sequences of human mRNAs in a task-agnostic manner; the pre-trained model is then fine-tuned for specific downstream tasks such as identifying RBP binding sites, m6A RNA modification sites, and predicting RNA sub-cellular localizations. Benchmark results show that 3UTRBERT generally outperformed other contemporary methods in each of these tasks. More importantly, the self-attention mechanism within 3UTRBERT allows direct visualization of the semantic relationship between sequence elements and effectively identifies regions with important regulatory potential. It is expected that 3UTRBERT model can serve as the foundational tool to analyze various sequence labeling tasks within the 3'UTR fields, thus enhancing the decipherability of post-transcriptional regulatory mechanisms.
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Affiliation(s)
- Yuning Yang
- School of Information Science and Technology, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Gen Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kuan Pang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Wuxinhao Cao
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, Jilin, 130012, China
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Cao Y, Ren Q, Chang S, Cui W, Zhao P, Wang Y. N6-methyladenosine RNA methylation modification regulates the transcription of viral-derived E (XSR) miRNAs to promote ALV-J replication. Vet Microbiol 2024; 298:110218. [PMID: 39159504 DOI: 10.1016/j.vetmic.2024.110218] [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: 04/24/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024]
Abstract
The E (XSR) element located in the 3'UTR of the ALV-J genome has the capability to transcribe and generate viral-derived E (XSR) miRNA. However, the biological function and transcriptional regulation mechanism of this process remain unclear. In this study, the impact of E (XSR) miRNA on ALV-J replication and the regulatory effect of N6-methyladenosine (m6A) methylation on its transcription were investigated. The results demonstrated that E (XSR) miRNA could stimulate ALV-J replication and suppress apoptosis in DF-1 cells in vitro. E (XSR) miRNA's promotion of ALV-J replication was not associated with the type I interferon pathway, but achieved by suppressing the expression of the host GPC5 gene. The transcription of E (XSR) miRNA could be promoted by m6A methylation modification, where m6A modification was found at the A6880 and A7016 sites of ALV-J gRNA. This study provides a new perspective on the transcription of ALV-J E (XSR) miRNA and its regulatory function in ALV-J replication.
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Affiliation(s)
- Yuqing Cao
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China; Shandong Provincial Key Laboratory of Zoonoses, Tai'an, China
| | - Qingling Ren
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China; Shandong Provincial Key Laboratory of Zoonoses, Tai'an, China
| | - Shuang Chang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China; Shandong Provincial Key Laboratory of Zoonoses, Tai'an, China
| | - Wenping Cui
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China; Shandong Provincial Key Laboratory of Zoonoses, Tai'an, China
| | - Peng Zhao
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China; Shandong Provincial Key Laboratory of Zoonoses, Tai'an, China.
| | - Yixin Wang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China; Shandong Provincial Key Laboratory of Zoonoses, Tai'an, China.
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29
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Barone S, Cerchia C, Summa V, Brindisi M. Methyl-Transferase-Like Protein 16 (METTL16): The Intriguing Journey of a Key Epitranscriptomic Player Becoming an Emerging Biological Target. J Med Chem 2024. [PMID: 39150226 DOI: 10.1021/acs.jmedchem.4c01247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Key epitranscriptomic players have been increasingly characterized for their structural features and their involvement in several diseases. Accordingly, the design and synthesis of novel epitranscriptomic modulators have started opening a glimmer for drug discovery. m6A is a reversible modification occurring on a specific site and is catalyzed by three sets of proteins responsible for opposite functions. Writers (e.g., methyl-transferase-like protein (METTL) 3/METTL14 complex and METTL16) introduce the methyl group on adenosine N-6, by transferring the methyl group from the methyl donor S-adenosyl-methionine (SAM) to the substrate. Despite the rapidly advancing drug discovery progress on METTL3/METTL14, the METTL16 m6A writer has been marginally explored so far. We herein provide the first comprehensive overview of structural and biological features of METTL16, highlighting the state of the art in the field of its biological and structural characterization. We also showcase initial efforts in the identification of structural templates and preliminary structure-activity relationships for METTL16 modulators.
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Affiliation(s)
- Simona Barone
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Carmen Cerchia
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Vincenzo Summa
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Margherita Brindisi
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
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30
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Palos K, Nelson Dittrich AC, Lyons EH, Gregory BD, Nelson ADL. Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants. BMC PLANT BIOLOGY 2024; 24:768. [PMID: 39134938 PMCID: PMC11318313 DOI: 10.1186/s12870-024-05486-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND In recent years, covalent modifications on RNA nucleotides have emerged as pivotal moieties influencing the structure, function, and regulatory processes of RNA Polymerase II transcripts such as mRNAs and lncRNAs. However, our understanding of their biological roles and whether these roles are conserved across eukaryotes remains limited. RESULTS In this study, we leveraged standard polyadenylation-enriched RNA-sequencing data to identify and characterize RNA modifications that introduce base-pairing errors into cDNA reads. Our investigation incorporated data from three Poaceae (Zea mays, Sorghum bicolor, and Setaria italica), as well as publicly available data from a range of stress and genetic contexts in Sorghum and Arabidopsis thaliana. We uncovered a strong enrichment of RNA covalent modifications (RCMs) deposited on a conserved core set of nuclear mRNAs involved in photosynthesis and translation across these species. However, the cohort of modified transcripts changed based on environmental context and developmental program, a pattern that was also conserved across flowering plants. We determined that RCMs can partly explain accession-level differences in drought tolerance in Sorghum, with stress-associated genes receiving a higher level of RCMs in a drought tolerant accession. To address function, we determined that RCMs are significantly enriched near exon junctions within coding regions, suggesting an association with splicing. Intriguingly, we found that these base-pair disrupting RCMs are associated with stable mRNAs, are highly correlated with protein abundance, and thus likely associated with facilitating translation. CONCLUSIONS Our data point to a conserved role for RCMs in mRNA stability and translation across the flowering plant lineage.
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Affiliation(s)
- Kyle Palos
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY, 14853, USA
| | | | - Eric H Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D L Nelson
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY, 14853, USA.
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31
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Huo M, Zhang M, Zhang J, Wang Y, Hu T, Ma T, Wang Y, Yuan B, Qin H, Teng X, Yu H, Huang W, Wang Y. Prognostic analysis of patients with gastric cancer based on N 6-methyladenosine modification patterns and tumor microenvironment characterization. Front Pharmacol 2024; 15:1445321. [PMID: 39185313 PMCID: PMC11341457 DOI: 10.3389/fphar.2024.1445321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/24/2024] [Indexed: 08/27/2024] Open
Abstract
Background Cancers arise from genetic and epigenetic abnormalities that affect oncogenes and tumor suppressor genes, compounded by gene mutations. The N6-methyladenosine (m6A) RNA modification, regulated by methylation regulators, has been implicated in tumor proliferation, differentiation, tumorigenesis, invasion, and metastasis. However, the role of m6A modification patterns in the tumor microenvironment of gastric cancer (GC) remains poorly understood. Materials and methods In this study, we analyzed m6A modification patterns in 267 GC samples utilizing 31 m6A regulators. Using consensus clustering, we identified two unique subgroups of GC. Patients with GC were segregated into high- and low-infiltration cohorts to evaluate the infiltration proportions of the five prognostically significant immune cell types. Leveraging the differential genes in GC, we identified a "green" module via Weighted Gene Co-expression Network Analysis. A risk prediction model was established using the LASSO regression method. Results The "green" module was connected to both the m6A RNA methylation cluster and immune infiltration patterns. Based on "Module Membership" and "Gene Significance", 37 hub genes were identified, and a risk prediction model incorporating nine hub genes was established. Furthermore, methylated RNA immunoprecipitation and RNA Immunoprecipitation assays revealed that YTHDF1 elevated the expression of DNMT3B, which synergistically promoted the initiation and development of GC. We elucidated the molecular mechanism underlying the regulation of DNMT3B by YTHDF1 and explored the crosstalk between m6A and 5mC modification. Conclusion m6A RNA methylation regulators are instrumental in malignant progression and the dynamics of tumor microenvironment infiltration of GC. Assessing m6A modification patterns and tumor microenvironment infiltration characteristics in patients with GC holds promise as a valuable prognostic biomarker.
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Affiliation(s)
- Miaomiao Huo
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Min Zhang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingyao Zhang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Wang
- Department of Ultrasound, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Hu
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianyu Ma
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yinuo Wang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baowen Yuan
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Qin
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xu Teng
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Hefen Yu
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Wei Huang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yan Wang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Sun W, Fang X, Zhang H, Lu Y, Wang P, Li J, Li M. Endogenous RBM4 prevents Ang II-induced cardiomyocyte hypertrophy via downregulating the expression of PTBP1. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39118568 DOI: 10.3724/abbs.2024103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
Aberrant gene expression in cardiomyocyte has been revealed to be the fundamental essence of pathological cardiac hypertrophy. However, the detailed mechanisms are not fully understood. The underlying regulators of gene expression involved in cardiac hypertrophy remain to be further identified. Here, we report that the RNA-binding protein RNA-binding motif protein 4 (RBM4) functions as an endogenic protector that is able to fight against cardiomyocyte hypertrophy in vitro. Under pro-hypertrophic stimulation of angiotensin II (Ang II), the protein level of RBM4 in cardiomyocyte and myocardium is elevated. Knockdown of RBM4 can further aggravate cardiomyocyte hypertrophy, while over-expression of RBM4 represses cardiomyocyte hypertrophy. Mechanistically, RBM4 is localized in the nucleus and down-regulates the expression of polypyrimidine tract-binding protein 1 (PTBP1), which has been shown to aggravate cardiomyocyte hypertrophy. In addition, we suggest that the up-regulation of RBM4 in cardiomyocyte hypertrophy is caused by N6-methyladenosine (m6A). Ang II induces m6A methylation of RBM4 mRNA, which further enhances the YTH domain-containing family protein 1 (YTHDF1)-mediated translation of RBM4. Thus, our results reveal a novel pathway consisting of m6A, RBM4 and PTBP1, which is involved in cardiomyocyte hypertrophy.
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Wang S, Liu Q. Research progress on m6A demethylase FTO and its role in gynecological tumors. Front Oncol 2024; 14:1413505. [PMID: 39175477 PMCID: PMC11338917 DOI: 10.3389/fonc.2024.1413505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/22/2024] [Indexed: 08/24/2024] Open
Abstract
Recent advances in genomic research have increasingly focused on the fat mass- and obesity-associated (FTO) gene due to its notable correlation with obesity. Initially explored for its contribution to increased body weight, FTO was later discovered to function as an m6A demethylase. This pivotal role enhances our understanding of its broader implications across various pathologies. Epigenetic modifications, such as m6A, have been implicated in gynecological cancers, including ovarian, endometrial, and cervical malignancies. However, the precise mechanisms by which FTO influences the development of gynecological cancers remain largely unknown. This analysis underscores the growing relevance of investigations into the FTO gene in elucidating the mechanisms underlying gynecological cancers and exploring potential therapeutic avenues.
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Affiliation(s)
- SiYuan Wang
- Jiangsu University School of Medicine, Jiangsu University School, Zhenjiang, Jiangsu, China
| | - Qin Liu
- Gynecology, KunShan Affiliated Hospital of Jiangsu University, Jiangsu University, Suzhou, Jiangsu, China
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Hu B, Lin D, Liu Z, Chen R, Liu J, Wu Y, Wang T. Identification of RBM15 as a prognostic biomarker in prostate cancer involving the regulation of prognostic m6A-related lncRNAs. Eur J Med Res 2024; 29:411. [PMID: 39118157 PMCID: PMC11312177 DOI: 10.1186/s40001-024-02000-5] [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: 03/18/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) and N6-methyladenosine (m6A) modification of RNA play pivotal roles in tumorigenesis and cancer progression. However, knowledge regarding the expression patterns of m6A-related lncRNAs and their corresponding m6A regulators in prostate cancer (PCa) is limited. This study aimed to delineate the landscape of m6A-related lncRNAs, develop a predictive model, and identify the critical m6A regulators of prognostic lncRNAs in PCa. METHODS Clinical and transcriptome data of PCa patients were downloaded from The Cancer Genome Atlas (TCGA) database. Prognostic m6A-related lncRNAs were subsequently identified through Pearson correlation and univariate Cox regression analyses. The prognostic lncRNAs were clustered into two groups by consensus clustering analysis, and a risk signature model was constructed using least absolute shrinkage and selection operator (LASSO) regression analysis of the lncRNAs. This model was evaluated using survival, clinicopathological, and immunological analyses. Furthermore, based on the constructed lncRNA-m6A regulatory network and RT-qPCR results, RBM15 was identified as a critical regulator of m6A-related lncRNAs. The biological roles of RBM15 in PCa were explored through bioinformatics analysis and biological experiments. RESULTS Thirty-four prognostic m6A-related lncRNAs were identified and categorized into two clusters with different expression patterns and survival outcomes in PCa patients. Seven m6A lncRNAs (AC105345.1, AL354989.1, AC138028.4, AC022211.1, AC020558.2, AC004076.2, and LINC02666) were selected to construct a risk signature with robust predictive ability for overall survival and were correlated with clinicopathological characteristics and the immune microenvironment of PCa patients. Among them, LINC02666 and AC022211.1 were regulated by RBM15. In addition, RBM15 expression correlated with PCa progression, survival, and the immune response. Patients with elevated RBM15 expression were more susceptible to the drug AMG-232. Moreover, silencing RBM15 decreased the viability of PCa cells and promoted apoptosis. CONCLUSION RBM15 is involved in the regulation of prognostic lncRNAs in the risk signature and has a robust predictive ability for PCa, making it a promising biomarker in PCa.
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Affiliation(s)
- Bintao Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, China
| | - Dongxu Lin
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhicheng Liu
- Department of Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ruibao Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yue Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, China.
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Chen X, Wei Q, Yang Z, Chen X, Guo S, Jiang M, Wang M. Structural basis for RNA recognition by the C-terminal RRM domain of human RBM45. J Biol Chem 2024; 300:107640. [PMID: 39122006 DOI: 10.1016/j.jbc.2024.107640] [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: 02/08/2024] [Revised: 07/08/2024] [Accepted: 07/18/2024] [Indexed: 08/12/2024] Open
Abstract
RBM45 is an RNA-binding protein with roles in neural development by regulating RNA splicing. Its dysfunction and aggregation are associated with neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). RBM45 harbors three RRM domains that potentially bind RNA. While the recognitions of RNA by its N-terminal tandem RRM domains (RRM1 and RRM2) have been well understood, the RNA-binding property of its C-terminal RRM (RRM3) remains unclear. In this work, we identified that the RRM3 of the RBM45 sequence specifically binds RNA with a GACG sequence, similar but not identical to those recognized by the RRM1 and RRM2. Further, we determined the crystal structure of RBM45RRM3 in complex with a GACG sequence-containing single-stranded DNA. Our structural results, together with the RNA-binding assays of mutants at key amino acid residues, revealed the molecular mechanism by which RBM45RRM3 recognizes an RNA sequence. Our finding on the RNA-binding property of the individual RRM module of RBM45 provides the foundation for unraveling the RNA-binding characteristics of full-length RBM45 and for understanding the biological functions of RBM45.
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Affiliation(s)
- Xi Chen
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Qinghao Wei
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Zhongmei Yang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xiaolei Chen
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Shuoxuan Guo
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Meiyu Jiang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China.
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36
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Cun Y, Guo W, Ma B, Okuno Y, Wang J. Decoding the specificity of m 6A RNA methylation and its implication in cancer therapy. Mol Ther 2024; 32:2461-2469. [PMID: 38796701 DOI: 10.1016/j.ymthe.2024.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024] Open
Abstract
N6-methyladenosine (m6A) is the most abundant endogenous modification in eukaryotic RNAs. It plays important roles in various biological processes and diseases, including cancers. More and more studies have revealed that the deposition of m6A is specifically regulated in a context-dependent manner. Here, we review the diverse mechanisms that determine the topology of m6A along RNAs and the cell-type-specific m6A methylomes. The exon junction complex (EJC) as well as histone modifications play important roles in determining the topological distribution of m6A along nascent RNAs, while the transcription factors and RNA-binding proteins, which usually bind specific DNAs and RNAs in a cell-type-specific manner, largely account for the cell-type-specific m6A methylomes. Due to the lack of specificity of m6A writers and readers, there are still challenges to target the core m6A machinery for cancer therapies. Therefore, understanding the mechanisms underlying the specificity of m6A modifications in cancers would be important for future cancer therapies through m6A intervention.
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Affiliation(s)
- Yixian Cun
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangdong 510080, China
| | - Wenbing Guo
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangdong 510080, China
| | - Biao Ma
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasushi Okuno
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Jinkai Wang
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangdong 510080, China.
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37
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Harrahill NJ, Hadden MK. Small molecules that regulate the N 6-methyladenosine RNA modification as potential anti-cancer agents. Eur J Med Chem 2024; 274:116526. [PMID: 38805939 DOI: 10.1016/j.ejmech.2024.116526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Epitranscriptomics, the field of post-translational RNA modifications, is a burgeoning domain of research that has recently received significant attention for its role in multiple diseases, including cancer. N6-methyladenosine (m6A) is the most prominent post-translational RNA modification and plays a critical role in RNA transcription, processing, translation, and metabolism. The m6A modification is controlled by three protein classes known as writers (methyltransferases), erasers (demethylases), and readers (m6A-binding proteins). Each class of m6A regulatory proteins has been implicated in cancer initiation and progression. As such, many of these proteins have been identified as potential targets for anti-cancer chemotherapeutics. In this work, we provide an overview of the role m6A-regulating proteins play in cancer and discuss the current state of small molecule therapeutics targeting these proteins.
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Affiliation(s)
- Noah J Harrahill
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT, 06269-3092, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT, 06269-3092, United States.
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Liu C, Yu M, Wang M, Yang S, Fu Y, Zhang L, Zhu C, Zhang H. PCAF-mediated acetylation of METTL3 impairs mRNA translation efficiency in response to oxidative stress. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2535-x. [PMID: 39096338 DOI: 10.1007/s11427-023-2535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/08/2024] [Accepted: 08/01/2024] [Indexed: 08/05/2024]
Abstract
METTL3 methylates RNA and regulates the fate of mRNA through its methyltransferase activity. METTL3 enhances RNA translation independently of its catalytic activity. However, the underlying mechanism is still elusive. Here, we report that METTL3 is both interacted with and acetylated at lysine 177 by the acetyltransferase PCAF and deacetylated by SIRT3. Neither the methyltransferase activity nor the stability of METTL3 is affected by its acetylation at K177. Importantly, acetylation of METTL3 blocks its interaction with EIF3H, a subunit of the translation initiation factor, thereby reducing mRNA translation efficiency. Interestingly, acetylation of METTL3 responds to oxidative stress. Mechanistically, oxidative stress enhances the interaction of PCAF with METTL3, increases METTL3 acetylation, and suppresses the interaction of METTL3 with EIF3H, thereby decreasing the translation efficiency of ribosomes and inhibiting cell proliferation. Altogether, we suggest a mechanism by which oxidative stress regulates RNA translation efficiency by the modulation of METTL3 acetylation mediated by PCAF.
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Affiliation(s)
- Cheng Liu
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Miao Yu
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Mengyuan Wang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Siyuan Yang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Yenan Fu
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Lei Zhang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Chaoyang Zhu
- Department of General Surgery and Urological Surgery, Huaihe Hospital, Henan University, Kaifeng, 100084, China.
| | - Hongquan Zhang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China.
- Department of Human Anatomy, Histology, and Embryology, Shenzhen University School of Medicine, Shenzhen, 518055, China.
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Sethi AJ, Acera Mateos P, Hayashi R, Shirokikh NE, Eyras E. R2Dtool: integration and visualization of isoform-resolved RNA features. Bioinformatics 2024; 40:btae495. [PMID: 39110520 PMCID: PMC11338438 DOI: 10.1093/bioinformatics/btae495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/06/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
MOTIVATION Long-read RNA sequencing enables the mapping of RNA modifications, structures, and protein-interaction sites at the resolution of individual transcript isoforms. To understand the functions of these RNA features, it is critical to analyze them in the context of transcriptomic and genomic annotations, such as open reading frames and splice junctions. RESULTS We have developed R2Dtool, a bioinformatics tool that integrates transcript-mapped information with transcript and genome annotations, allowing for the isoform-resolved analytics and graphical representation of RNA features in their genomic context. We illustrate R2Dtool's capability to integrate and expedite RNA feature analysis using epitranscriptomics data. R2Dtool facilitates the comprehensive analysis and interpretation of alternative transcript isoforms. AVAILABILITY AND IMPLEMENTATION R2Dtool is freely available under the MIT license at github.com/comprna/R2Dtool.
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Affiliation(s)
- Aditya J Sethi
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
- Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Acton ACT 2601, Australia
| | - Pablo Acera Mateos
- Children’s Cancer Institute, Lowy Cancer Centre, University of New South Wales, Sydney, Kensington NSW 2033, Australia
| | - Rippei Hayashi
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
| | - Nikolay E Shirokikh
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
| | - Eduardo Eyras
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
- Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Acton ACT 2601, Australia
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40
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Xu X, Wu S, Zhang Y, Fan W, Lin X, Chen K, Lin X. m6A modification of VEGFA mRNA by RBM15/YTHDF2/IGF2BP3 contributes to angiogenesis of hepatocellular carcinoma. Mol Carcinog 2024. [PMID: 39092767 DOI: 10.1002/mc.23802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Vascular endothelial growth factor A (VEGFA) plays a critical role as a potent angiogenesis factor and is highly expressed in hepatocellular carcinoma (HCC). Although the expression of VEGFA has been strongly linked to the aggressive nature of HCC, the specific posttranscriptional modifications that might contribute to VEGFA expression and HCC angiogenesis are not yet well understood. In this study, we aimed to investigate the epitranscriptome regulation of VEGFA in HCC. A comprehensive analysis integrating MeRIP-seq, RNA-seq, and crosslinking-immunprecipitation-seq data revealed that VEGFA was hypermethylated in HCC and identified the potential m6A regulators of VEGFA including a m6A methyltransferase complex component RBM15 and the two readers, YTHDF2 and IGF2BP3. Through rigorous cell and molecular biology experiments, RBM15 was validated as a key component of methyltransferase complex responsible for m6A methylation of VEGFA, which was subsequently recognized and stabilized by IGF2BP3 and YTHDF2, leading to enhanced VEGFA expression and VEGFA-related functions such as human umbilical vascular endothelial cells (HUVEC) migration and tube formation. In the HCC xenograft model, knockdown of RBM15, IGF2BP3, or YTHDF2 resulted in reduced expression of VEGFA, accompanied by significant inhibition of tumor growth closely associated with VEGFA expression and angiogenesis. Furthermore, our analysis of HCC clinical samples identified positive correlations between the expression levels of VEGFA and the regulators RBM15, IGF2BP3, and YTHDF2. Collectively, these findings offer novel insights into the posttranscriptional modulation of VEGFA and provide potential avenues for alternative approaches to antiangiogenesis therapy targeting VEGFA.
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Affiliation(s)
- Xiaoxin Xu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
| | - Shuxiang Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
| | - Yi Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
| | - Weijie Fan
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
| | - Xinjian Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
| | - Kunqi Chen
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
| | - Xu Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fuzhou, China
- Department of Medical Microbiology, Fujian Key Laboratory of Tumor Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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Lin H, Cui Z, E T, Xu H, Wang D, Wang P, Ruan X, Liu L, Xue Y. M6A-methylated circPOLR2B forms an R-loop and regulates the biological behavior of glioma stem cells through positive feedback loops. Cell Death Dis 2024; 15:554. [PMID: 39090090 PMCID: PMC11294345 DOI: 10.1038/s41419-024-06946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Glioma is the most common primary brain tumor, and targeting glioma stem cells (GSCs) has become a key aspect of glioma treatment. In this study, we discovered a molecular network in which circRNA forms an R-loop structure with its parental gene to regulate the biological behavior of GSCs. Genes with abnormal expression in GSCs were screened using RNA-seq and circRNA microarray analyses. The study results showed that high expression of YTHDC1 in GSCs promoted the transportation of N6-methyladenosine (m6A)-modified circPOLR2B from the nucleus to the cytoplasm. Decreased circPOLR2B levels in the nucleus resulted in fewer R-loop structures formed with its parental gene POLR2B. This reduction in R-loop structures relieved the inhibitory effect on POLR2B transcription and upregulated PBX1 expression through alternative polyadenylation (APA) action, thereby promoting the malignant biological behavior of GSCs. Knockdown of YTHDC1, POLR2B, and PBX1 reduced xenograft tumor volume and prolonged the survival of nude mice. The YTHDC1/circPOLR2B/POLR2B/PBX1 axis plays a regulatory role in the biological behavior of GSCs, offering potential targets and novel strategies for the treatment of glioma.
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Affiliation(s)
- Hongda Lin
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Zheng Cui
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Tiange E
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Hailing Xu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Ping Wang
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Xuelei Ruan
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Libo Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Yixue Xue
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China.
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China.
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Horner SM, Reaves JV. Recent insights into N 6-methyladenosine during viral infection. Curr Opin Genet Dev 2024; 87:102213. [PMID: 38901100 DOI: 10.1016/j.gde.2024.102213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/15/2024] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
The RNA modification of N6-methyladenosine (m6A) controls many aspects of RNA function that impact biological processes, including viral infection. In this review, we highlight recent work that shapes our current understanding of the diverse mechanisms by which m6A can regulate viral infection by acting on viral or cellular mRNA molecules. We focus on emerging concepts and understanding, including how viral infection alters the localization and function of m6A machinery proteins, how m6A regulates antiviral innate immunity, and the multiple roles of m6A in regulating specific viral infections. We also summarize the recent studies on m6A during SARS-CoV-2 infection, focusing on points of convergence and divergence. Ultimately, this review provides a snapshot of the latest research on m6A during viral infection.
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Affiliation(s)
- Stacy M Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Jordan V Reaves
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
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Liu D, Ren L, Liu J. METTL14 promotes chondrocyte ferroptosis in osteoarthritis via m6A modification of GPX4. Int J Rheum Dis 2024; 27:e15297. [PMID: 39175261 DOI: 10.1111/1756-185x.15297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/19/2024] [Accepted: 08/11/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND Ferroptosis is caused by iron-dependent peroxidation of membrane phospholipids and chondrocyte ferroptosis contributes to osteoarthritis (OA) progression. Glutathione peroxidase 4 (GPX4) plays a master role in blocking ferroptosis. N6-methyladenosine (m6A) is an epigenetic modification among mRNA post-transcriptional modifications. This study investigated the effect of methyltransferase-like 14 (METTL14), the key component of the m6A methyltransferase, on chondrocyte ferroptosis via m6A modification. METHODS An OA rat model was established through an intra-articular injection of monosodium iodoacetate in the right knee. OA cartilages in rat models were used for gene expression analysis. Primary mouse chondrocytes or ADTC5 cells were stimulated with IL-1β or erastin. The m6A RNA methylation quantification kit was used to measure m6A level. The effect of METTL14 and GPX4 on ECM degradation and ferroptosis was investigated through western blotting, fluorescence immunostaining, propidium iodide staining, and commercially available kits. The mechanism of METTL14 action was explored through MeRIP-qPCR assays. RESULTS METTL14 and m6A expression was upregulated in osteoarthritic cartilages and IL-1β-induced chondrocytes. METTL14 depletion repressed the IL-1β or erastin-stimulated ECM degradation and ferroptosis in mouse chondrocytes. METTL14 inhibited GPX4 gene through m6A methylation modification. GPX4 knockdown reversed the si-METTL14-mediated protection in IL-1β-induced chondrocytes. CONCLUSION METTL14 depletion inhibits ferroptosis and ECM degradation by suppressing GPX4 mRNA m6A modification in injured chondrocytes.
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Affiliation(s)
- Dawei Liu
- Tianjin University, Tianjin, China
- Specialized Orthopedics Construction Office, Tianjin Nankai Hospital, Tianjin, China
| | - Liang Ren
- Department of Ultrasound medicine, Yichang Yiling People's Hospital, Yichang, China
| | - Jun Liu
- Knee-joint Department, Tianjin Hospital, Tianjin, China
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Cui L, Shen G, Yu Y, Yan Z, Zeng H, Ye X, Xu K, Zhu C, Li Y, Shen Z, Zhang B, Wu L. Gubi decoction mitigates knee osteoarthritis via promoting chondrocyte autophagy through METTL3-mediated ATG7 m 6A methylation. J Cell Mol Med 2024; 28:e70019. [PMID: 39164798 PMCID: PMC11335466 DOI: 10.1111/jcmm.70019] [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: 02/02/2024] [Revised: 07/23/2024] [Accepted: 08/05/2024] [Indexed: 08/22/2024] Open
Abstract
Knee osteoarthritis (KOA) is a chronic joint disease that significantly affects the health of the elderly. As an herbal remedy, Gubi decoction (GBD) has been traditionally used for the treatment of osteoarthritis-related syndromes. However, the anti-KOA efficacy and mechanism of GBD remain unclear. This study aimed to experimentally investigate the anti-KOA efficacy and the underlying mechanism of GBD. The medial meniscus (DMM) mice model and IL-1β-stimulated chondrocytes were, respectively, constructed as in vivo and in vitro models of KOA to evaluate the osteoprotective effect and molecular mechanism of GBD. The UPLC-MS/MS analysis showed that GBD mainly contained pinoresinol diglucoside, rehmannioside D, hesperidin, liquiritin, baohuoside I, glycyrrhizic acid, kaempferol and tangeretin. Animal experiment showed that GBD could alleviate articular cartilage destruction and recover histopathological alterations in DMM mice. In addition, GBD inhibited chondrocyte apoptosis and restored DMM-induced dysregulated autophagy evidenced by the upregulation of ATG7 and LC3 II/LC3 I but decreased P62 level. Mechanistically, METTL3-mediated m6A modification decreased the expression of ATG7 in DMM mice, as it could be significantly attenuated by GBD. METTL3 overexpression significantly counteracted the protective effect of GBD on chondrocyte autophagy. Further research showed that GBD promoted proteasome-mediated ubiquitination degradation of METLL3. Our findings suggest that GBD could act as a protective agent against KOA. The protective effect of GBD may result from its promotion on chondrocyte autophagy by suppressing METTL3-dependent ATG7 m6A methylation.
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Affiliation(s)
- Longkang Cui
- The Second Clinical CollegeZhejiang Chinese Medical UniversityHangzhouChina
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Gaobo Shen
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Yang Yu
- The Second Clinical CollegeZhejiang Chinese Medical UniversityHangzhouChina
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Zheng Yan
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Hanbing Zeng
- The Second Clinical CollegeZhejiang Chinese Medical UniversityHangzhouChina
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Xiaoang Ye
- The Second Clinical CollegeZhejiang Chinese Medical UniversityHangzhouChina
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Kuangying Xu
- The Second Clinical CollegeZhejiang Chinese Medical UniversityHangzhouChina
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Chaojin Zhu
- The Second Clinical CollegeZhejiang Chinese Medical UniversityHangzhouChina
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Yanan Li
- The Second Clinical CollegeZhejiang Chinese Medical UniversityHangzhouChina
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Zhe Shen
- The Second Clinical CollegeZhejiang Chinese Medical UniversityHangzhouChina
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Bingbing Zhang
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
| | - Lianguo Wu
- The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhouChina
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Zhao L, Wei X, Chen F, Yuan L, Chen B, Li R. N6-methyladenosine RNA methyltransferase CpMTA1 mediates CpAphA mRNA stability through a YTHDF1-dependent m6A modification in the chestnut blight fungus. PLoS Pathog 2024; 20:e1012476. [PMID: 39159278 PMCID: PMC11361730 DOI: 10.1371/journal.ppat.1012476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 08/29/2024] [Accepted: 08/04/2024] [Indexed: 08/21/2024] Open
Abstract
In eukaryotic cells, N6-methyladenosine (m6A) is the most prevalent RNA epigenetic modification that plays crucial roles in multiple biological processes. Nevertheless, the functions and regulatory mechanisms of m6A in phytopathogenic fungi are poorly understood. Here, we showed that CpMTA1, an m6A methyltransferase in Cryphonectria parasitica, plays a crucial role in fungal phenotypic traits, virulence, and stress tolerance. Furthermore, the acid phosphatase gene CpAphA was implicated to be a target of CpMTA1 by integrated analysis of m6A-seq and RNA-seq, as in vivo RIP assay data confirmed that CpMTA1 directly interacts with CpAphA mRNA. Deletion of CpMTA1 drastically lowered the m6A level of CpAphA and reduced its mRNA expression. Moreover, we found that an m6A reader protein CpYTHDF1 recognizes CpAphA mRNA and increases its stability. Typically, the levels of CpAphA mRNA and protein exhibited a positive correlation with CpMTA1 and CpYTHDF1. Importantly, site-specific mutagenesis demonstrated that the m6A sites, A1306 and A1341, of CpAphA mRNA are important for fungal phenotypic traits and virulence in C. parasitica. Together, our findings demonstrate the essential role of the m6A methyltransferase CpMTA1 in C. parasitica, thereby advancing our understanding of fungal gene regulation through m6A modification.
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Affiliation(s)
- Lijiu Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xiangyu Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Fengyue Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Luying Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
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Chen XH, Guo KX, Li J, Xu SH, Zhu H, Yan GR. Regulations of m 6A and other RNA modifications and their roles in cancer. Front Med 2024; 18:622-648. [PMID: 38907157 DOI: 10.1007/s11684-024-1064-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/17/2024] [Indexed: 06/23/2024]
Abstract
RNA modification is an essential component of the epitranscriptome, regulating RNA metabolism and cellular functions. Several types of RNA modifications have been identified to date; they include N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), N4-acetylcytidine (ac4C), etc. RNA modifications, mediated by regulators including writers, erasers, and readers, are associated with carcinogenesis, tumor microenvironment, metabolic reprogramming, immunosuppression, immunotherapy, chemotherapy, etc. A novel perspective indicates that regulatory subunits and post-translational modifications (PTMs) are involved in the regulation of writer, eraser, and reader functions in mediating RNA modifications, tumorigenesis, and anticancer therapy. In this review, we summarize the advances made in the knowledge of different RNA modifications (especially m6A) and focus on RNA modification regulators with functions modulated by a series of factors in cancer, including regulatory subunits (proteins, noncoding RNA or peptides encoded by long noncoding RNA) and PTMs (acetylation, SUMOylation, lactylation, phosphorylation, etc.). We also delineate the relationship between RNA modification regulator functions and carcinogenesis or cancer progression. Additionally, inhibitors that target RNA modification regulators for anticancer therapy and their synergistic effect combined with immunotherapy or chemotherapy are discussed.
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Affiliation(s)
- Xin-Hui Chen
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Kun-Xiong Guo
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Jing Li
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Shu-Hui Xu
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Huifang Zhu
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Guang-Rong Yan
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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Xie Y, Xiao J, Ying Y, Liu J, Zhang L, Zeng X. Bioinformatic identification reveals a m6A-binding protein, IGF2BP2, as a novel tumor-promoting gene signature in thyroid carcinoma. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:5663-5676. [PMID: 38289368 DOI: 10.1007/s00210-024-02961-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/15/2024] [Indexed: 08/18/2024]
Abstract
N6-methyladenosine (m6A) modification plays a crucial role in thyroid carcinoma (THCA). Insulin-like growth factor 2 binding protein 2 (IGF2BP2) is a m6A-binding protein. We aimed to explore the effect of IGF2BP2 on the development of THCA. Differentially expressed genes (DEGs) were screened from GSE50901 and GSE60542 datasets. LinkedOmics, Genebank, and Sequence-based RNA Adenosine Methylation Site Predictor databases were employed to find potential m6A modification sites. Protein-protein interaction network and receiver-operating characteristic curves were applied to determine hub genes of THCA. ESTIMATE revealed the effect of IGF2BP2 on tumor immunity. The mRNA expression of IGF2BP2 was detected using real-time quantitative polymerase chain reaction. The viability, migration, and invasion were assessed by Cell Counting Kit-8, wound healing, and transwell assays. A total of 166 common DEGs were identified from GSE50901 and GSE60542 datasets. One m6A-related gene, IGF2BP2, was differentially expressed in THCA and selected as the research target. The hub genes (CD44, DCN, CXCL12, ICAM1, SDC4, KIT, CTGF, and FMOD) were identified with high prediction values for THCA. Subsequently, the target genes of IGF2BP2, SDC4, and ICAM1, which had potential m6A modification sites, were screened out based on the hub genes. IGF2BP2 was upregulated in THCA and IGF2BP2 expression was positively correlated with immune infiltration in THCA. Additionally, knockdown of IGF2BP2 inhibited the proliferation, invasion, and migration of THCA cells. IGF2BP2 has a contributory effect on the progression of THCA, which is a novel biomarker and a therapeutic target for THCA.
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Affiliation(s)
- Yang Xie
- Suzhou Medical College of Soochow University, Suzhou, China
- Department of Thyroid and Hernia Surgery, The First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Zhanggong District, Ganzhou, 341000, Jiangxi Province, China
- Institute of Thyroid Diseases, Gannan Medical University, Ganzhou, China
- Ganzhou Key Laboratory of Thyroid Tumor, Ganzhou, China
| | - Junqi Xiao
- Department of Vascular Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yong Ying
- Department of Thyroid and Hernia Surgery, The First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Zhanggong District, Ganzhou, 341000, Jiangxi Province, China
| | - Jiafeng Liu
- Department of Thyroid and Hernia Surgery, The First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Zhanggong District, Ganzhou, 341000, Jiangxi Province, China
| | - Leiying Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xiangtai Zeng
- Suzhou Medical College of Soochow University, Suzhou, China.
- Department of Thyroid and Hernia Surgery, The First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Zhanggong District, Ganzhou, 341000, Jiangxi Province, China.
- Institute of Thyroid Diseases, Gannan Medical University, Ganzhou, China.
- Ganzhou Key Laboratory of Thyroid Tumor, Ganzhou, China.
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Li F, Zeng C, Liu J, Wang L, Yuan X, Yuan L, Xia X, Huang W. The YTH domain-containing protein family: Emerging players in immunomodulation and tumour immunotherapy targets. Clin Transl Med 2024; 14:e1784. [PMID: 39135292 PMCID: PMC11319238 DOI: 10.1002/ctm2.1784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND The modification of N6-methyladenosine (m6A) plays a pivotal role in tumor by altering both innate and adaptive immune systems through various pathways, including the regulation of messenger RNA. The YTH domain protein family, acting as "readers" of m6A modifications, affects RNA splicing, stability, and immunogenicity, thereby playing essential roles in immune regulation and antitumor immunity. Despite their significance, the impact of the YTH domain protein family on tumor initiation and progression, as well as their involvement in tumor immune regulation and therapy, remains underexplored and lacks comprehensive review. CONCLUSION This review introduces the molecular characteristics of the YTH domain protein family and their physiological and pathological roles in biological behavior, emphasizing their mechanisms in regulating immune responses and antitumor immunity. Additionally, the review discusses the roles of the YTH domain protein family in immune-related diseases and tumor resistance, highlighting that abnormal expression or dysfunction of YTH proteins is closely linked to tumor resistance. KEY POINTS This review provides an in-depth understanding of the YTH domain protein family in immune regulation and antitumor immunity, suggesting new strategies and directions for immunotherapy of related diseases. These insights not only deepen our comprehension of m6A modifications and YTH protein functions but also pave the way for future research and clinical applications.
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Affiliation(s)
- Fenghe Li
- Department of Gynaecology and ObstetricsSecond Xiangya HospitalCentral South UniversityChangshaChina
| | - Chong Zeng
- Department of Respiratory and Critical Care MedicineThe Seventh Affiliated Hospital, Hengyang Medical School, University of South ChinaChangshaHunanChina
| | - Jie Liu
- Department of PathologyThe Affiliated Changsha Central Hospital, Hengyang Medical School, University of South ChinaChangshaHunanChina
| | - Lei Wang
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research Institute, School of Basic Medical Science, Central South UniversityChangshaHunanChina
| | - Xiaorui Yuan
- Department of Gynaecology and ObstetricsSecond Xiangya HospitalCentral South UniversityChangshaChina
| | - Li Yuan
- Department of Nuclear MedicineThe Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xiaomeng Xia
- Department of Gynaecology and ObstetricsSecond Xiangya HospitalCentral South UniversityChangshaChina
| | - Wei Huang
- Department of OncologyXiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center of Geriatric DisordersXiangya HospitalCentral South UniversityChangshaChina
- Research Center of Carcinogenesis and Targeted TherapyXiangya HospitalCentral South UniversityChangshaChina
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Zha X, Gao Z, Li M, Xia X, Mao Z, Wang S. Insight into the regulatory mechanism of m 6A modification: From MAFLD to hepatocellular carcinoma. Biomed Pharmacother 2024; 177:116966. [PMID: 38906018 DOI: 10.1016/j.biopha.2024.116966] [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: 04/10/2024] [Revised: 06/05/2024] [Accepted: 06/15/2024] [Indexed: 06/23/2024] Open
Abstract
In recent years, there has been a significant increase in the incidence of metabolic-associated fatty liver disease (MAFLD), which has been attributed to the increasing prevalence of type 2 diabetes mellitus (T2DM) and obesity. MAFLD affects more than one-third of adults worldwide, making it the most prevalent liver disease globally. Moreover, MAFLD is considered a significant risk factor for hepatocellular carcinoma (HCC), with MAFLD-related HCC cases increasing. Approximately 1 in 6 HCC patients are believed to have MAFLD, and nearly 40 % of these HCC patients do not progress to cirrhosis, indicating direct transformation from MAFLD to HCC. N6-methyladenosine (m6A) is commonly distributed in eukaryotic mRNA and plays a crucial role in normal development and disease progression, particularly in tumors. Numerous studies have highlighted the close association between abnormal m6A modification and cellular metabolic alterations, underscoring its importance in the onset and progression of MAFLD. However, the specific impact of m6A modification on the progression of MAFLD to HCC remains unclear. Can targeting m6A effectively halt the progression of MAFLD-related HCC? In this review, we investigated the pivotal role of abnormal m6A modification in the transition from MAFLD to HCC, explored the potential of m6A modification as a therapeutic target for MAFLD-related HCC, and proposed possible directions for future investigations.
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Affiliation(s)
- Xuan Zha
- Department of Laboratory Medicine, the Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zewei Gao
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Min Li
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xueli Xia
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zhenwei Mao
- Department of Laboratory Medicine, Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.
| | - Shengjun Wang
- Department of Laboratory Medicine, the Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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50
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Shen J, Wang L, Zhang W, Gong X, Li S, Zou X, Chen C, Xia R, Zhang D, Xu S, Xu J, Wang S, Jiang Y, Sun H, Wang C, Wang SL. Effects of Naphtho[2,1- a]pyrene Exposure on CYP1A1 Expression: An in Vivo and in Vitro Mechanistic Study Exploring the Role of m6A Posttranscriptional Modification. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:87003. [PMID: 39133094 PMCID: PMC11318572 DOI: 10.1289/ehp14055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 06/28/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND Currently, many emerging polycyclic aromatic hydrocarbons (PAHs) have been found to be widely present in the environment. However, little has been reported about their toxicity, particularly in relation to CYP1A1. OBJECTIVES This study aimed to explore the toxicity of naphtho[2,1-a]pyrene (N21aP) and elucidate the mechanism underlying N21aP-induced expression of CYP1A1. METHODS The concentration and sources of N21aP were detected and analyzed by gas chromatography-triple quadrupole mass spectrometry (GC-MS/MS) and diagnostic ratio analysis. Then the effects of CYP1A1 on the toxicity of N21aP were conducted in male wild-type (WT) and Cyp1a1 knockout mice exposed to N21aP (0.02, 0.2, and 2 mg / kg ) through intratracheal instillation. Further, the aryl hydrocarbon receptor (AhR) pathway was examined through luciferase and chromatin immunoprecipitation (ChIP) assays. N 6 -methyladenosine (m 6 A ) modification levels were measured on global RNA and specifically on CYP1A1 mRNA using dot blotting and methylated RNA immunoprecipitation-quantitative real-time polymerase chain reaction (MeRIP qRT-PCR), with validation by m 6 A inhibitors, DAA and SAH. m 6 A sites on CYP1A1 were identified by bioinformatics and luciferase assays, and CYP1A1 mRNA's interaction with IGF2BP3 was confirmed by RNA pull-down, luciferase, and RNA binding protein immunoprecipitation (RIP) assays. RESULTS N21aP was of the same environmental origin as benzo[a]pyrene (BaP) but was more stably present in the environment. N21aP could be metabolically activated by CYP1A1 to produce epoxides, causing DNA damage and further leading to lung inflammation. Importantly, in addition to the classical AhR pathway (i.e., BaP), N21aP also induced CYP1A1 expression with a posttranscriptional modification of m 6 A in CYP1A1 mRNA via the METTL14-IGF2BP3-CYP1A1 axis. Specifically, in the two recognition sites of METTL14 on the CYP1A1 mRNA transcript (position at 2700 and 5218), a methylation site (position at 5218) in the 3'-untranslated region (UTR) was recognized by IGF2BP3, enhanced the stability of CYP1A1 mRNA, and finally resulted in an increase in CYP1A1 expression. DISCUSSION This study systematically demonstrated that in addition to AhR-mediated transcriptional regulation, N21aP, had a new additional mechanism of m 6 A -mediated posttranscriptional modification, jointly contributing to CYP1A1 expression. Given that PAHs are the metabolic substrates of CYP1A1, this study not only helps to understand the significance of environment-genetic interactions for the toxicity of PAHs but also helps to better understand the health risks of the emerging PAHs at environmental exposure levels. https://doi.org/10.1289/EHP14055.
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Affiliation(s)
- Jiemiao Shen
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Li Wang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wen Zhang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xing Gong
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- State Key Lab of Reproductive Medicine and Offspring Health, Institute of Toxicology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Sheng Li
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xuyan Zou
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chao Chen
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Rong Xia
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Di Zhang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shuyu Xu
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- State Key Lab of Reproductive Medicine and Offspring Health, Institute of Toxicology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiayi Xu
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- State Key Lab of Reproductive Medicine and Offspring Health, Institute of Toxicology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shaozhuo Wang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- State Key Lab of Reproductive Medicine and Offspring Health, Institute of Toxicology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yinyue Jiang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hong Sun
- Institute of Environment and Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Chao Wang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- State Key Lab of Reproductive Medicine and Offspring Health, Institute of Toxicology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shou-Lin Wang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- State Key Lab of Reproductive Medicine and Offspring Health, Institute of Toxicology, Nanjing Medical University, Nanjing, Jiangsu, China
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