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Wu X, Cai W, He J, Zhang S, Wang S, Huang L, Zhang H, Sun X, Zhou J, Liu XM. YTHDF2 suppresses the 2C-like state in mouse embryonic stem cells via the DUX-ZSCAN4 molecular circuit. J Biol Chem 2025; 301:108479. [PMID: 40188945 DOI: 10.1016/j.jbc.2025.108479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Revised: 03/21/2025] [Accepted: 03/31/2025] [Indexed: 05/01/2025] Open
Abstract
Mouse embryonic stem cells (ESCs) consist of a rare population of heterogeneous 2-cell-like cells (2CLCs). These cells transiently recapitulate the transcriptional and epigenetic features of the 2-cell embryos, serving as a unique model for studying totipotency acquisition and embryonic development. Accumulating evidence has demonstrated that transcription factors and epigenetic modifications exert crucial functions in the transition of ESCs to 2CLCs. However, the roles of RNA modification in the regulation of the 2C-like state remain elusive. Using a DUX-induced 2CLCs system, we examine N6-methyladenosine (m6A) modification landscape transcriptome-wide and observe dynamic regulation of m6A during DUX-driven 2C-like reprogramming. Notably, many core 2C transcripts like Dux and Zscan4 are highly methylated. We identify the m6A reader protein YTHDF2 as a critical regulator of 2C-like state. Depletion of YTHDF2 facilitates robust expression of 2C-signature genes and ESCs-to-2CLCs transition. Intriguingly, YTHDF2 binds to a subset of m6A-modified 2C transcripts and promotes their decay. We further demonstrate that YTHDF2 suppresses the 2C-like program in a manner that is dependent on both m6A and the DUX-ZSCAN4 molecular circuit. Mechanistically, YTHDF2 interacts with CNOT1, a key component of the RNA deadenylase complex. Consistently, silencing of CNOT1 upregulates the 2C program and promotes ESCs-to-2CLCs transition. Collectively, our findings reveal novel insights into the epitranscriptomic regulation of the 2C-like state in mouse ESCs.
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Affiliation(s)
- Xiang Wu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Wanting Cai
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Junjie He
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Shiyin Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Lingci Huang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Haotian Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Xiaoyan Sun
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Jun Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.
| | - Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.
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2
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Koopmans T, van Rooij E. Molecular gatekeepers of endogenous adult mammalian cardiomyocyte proliferation. Nat Rev Cardiol 2025:10.1038/s41569-025-01145-y. [PMID: 40195566 DOI: 10.1038/s41569-025-01145-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2025] [Indexed: 04/09/2025]
Abstract
Irreversible cardiac fibrosis, cardiomyocyte death and chronic cardiac dysfunction after myocardial infarction pose a substantial global health-care challenge, with no curative treatments available. To regenerate the injured heart, cardiomyocytes must proliferate to replace lost myocardial tissue - a capability that adult mammals have largely forfeited to adapt to the demanding conditions of life. Using various preclinical models, our understanding of cardiomyocyte proliferation has progressed remarkably, leading to the successful reactivation of cell cycle induction in adult animals, with functional recovery after cardiac injury. Central to this success is the targeting of key pathways and structures that drive cardiomyocyte maturation after birth - nucleation and ploidy, sarcomere structure, developmental signalling, chromatin and epigenetic regulation, the microenvironment and metabolic maturation - forming a complex regulatory framework that allows efficient cellular contraction but restricts cardiomyocyte proliferation. In this Review, we explore the molecular pathways underlying these core mechanisms and how their manipulation can reactivate the cell cycle in cardiomyocytes, potentially contributing to cardiac repair.
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Affiliation(s)
- Tim Koopmans
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Eva van Rooij
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands.
- Department of Cardiology, University Medical Center Utrecht, Utrecht, Netherlands.
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3
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Zhang F, Evans T. Stage-specific DNA methylation dynamics in mammalian heart development. Epigenomics 2025; 17:359-371. [PMID: 39980349 PMCID: PMC11970762 DOI: 10.1080/17501911.2025.2467024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 02/10/2025] [Indexed: 02/22/2025] Open
Abstract
Cardiac development is a precisely regulated process governed by both genetic and epigenetic mechanisms. Among these, DNA methylation is one mode of epigenetic regulation that plays a crucial role in controlling gene expression at various stages of heart development and maturation. Understanding stage-specific DNA methylation dynamics is critical for unraveling the molecular processes underlying heart development from specification of early progenitors, formation of a primitive and growing heart tube from heart fields, heart morphogenesis, organ function, and response to developmental and physiological signals. This review highlights research that has explored profiles of DNA methylation that are highly dynamic during cardiac development and maturation, exploring stage-specific roles and the key molecular players involved. By exploring recent insights into the changing methylation landscape, we aim to highlight the complex interplay between DNA methylation and stage-specific cardiac gene expression, differentiation, and maturation.
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Affiliation(s)
- Fangfang Zhang
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Hartman Institute for Therapeutic Organ Regeneration, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
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Pilala KM, Panoutsopoulou K, Papadimitriou MA, Soureas K, Scorilas A, Avgeris M. Exploring the methyl-verse: Dynamic interplay of epigenome and m6A epitranscriptome. Mol Ther 2025; 33:447-464. [PMID: 39659016 PMCID: PMC11852398 DOI: 10.1016/j.ymthe.2024.12.003] [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: 07/23/2024] [Revised: 11/19/2024] [Accepted: 12/05/2024] [Indexed: 12/12/2024] Open
Abstract
The orchestration of dynamic epigenetic and epitranscriptomic modifications is pivotal for the fine-tuning of gene expression. However, these modifications are traditionally examined independently. Recent compelling studies have disclosed an interesting communication and interplay between m6A RNA methylation (m6A epitranscriptome) and epigenetic modifications, enabling the formation of feedback circuits and cooperative networks. Intriguingly, the interaction between m6A and DNA methylation machinery, coupled with the crosstalk between m6A RNA and histone modifications shape the transcriptional profile and translational efficiency. Moreover, m6A modifications interact also with non-coding RNAs, modulating their stability, abundance, and regulatory functions. In the light of these findings, m6A imprinting acts as a versatile checkpoint, linking epigenetic and epitranscriptomic layers toward a multilayer and time-dependent control of gene expression and cellular homeostasis. The scope of the present review is to decipher the m6A-coordinated circuits with DNA imprinting, chromatin architecture, and non-coding RNAs networks in normal physiology and carcinogenesis. Ultimately, we summarize the development of innovative CRISPR-dCas engineering platforms fused with m6A catalytic components (m6A writers or erasers) to achieve transcript-specific editing of m6A epitranscriptomes that can create new insights in modern RNA therapeutics.
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Affiliation(s)
- Katerina-Marina Pilala
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Panoutsopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria-Alexandra Papadimitriou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Soureas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece; Laboratory of Clinical Biochemistry - Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece; Laboratory of Clinical Biochemistry - Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, Athens, Greece.
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Shi K, Chen Y, Liu R, Fu X, Guo H, Gao T, Wang S, Dou L, Wang J, Wu Y, Yu J, Yu H. NFIC mediates m6A mRNA methylation to orchestrate transcriptional and post-transcriptional regulation to represses malignant phenotype of non-small cell lung cancer cells. Cancer Cell Int 2024; 24:223. [PMID: 38943137 PMCID: PMC11212411 DOI: 10.1186/s12935-024-03414-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/22/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Multiple genetic and epigenetic regulatory mechanisms are crucial in the development and tumorigenesis process. Transcriptional regulation often involves intricate relationships and networks with post-transcriptional regulatory molecules, impacting the spatial and temporal expression of genes. However, the synergistic relationship between transcription factors and N6-methyladenosine (m6A) modification in regulating gene expression, as well as their influence on the mechanisms underlying the occurrence and progression of non-small cell lung cancer (NSCLC), requires further investigation. The present study aimed to investigate the synergistic relationship between transcription factors and m6A modification on NSCLC. METHODS The transcription factor NFIC and its potential genes was screened by analyzing publicly available datasets (ATAC-seq, DNase-seq, and RNA-seq). The association of NFIC and its potential target genes were validated through ChIP-qPCR and dual-luciferase reporter assays. Additionally, the roles of NFIC and its potential genes in NSCLC were detected in vitro and in vivo through silencing and overexpression assays. RESULTS Based on multi-omics data, the transcription factor NFIC was identified as a potential tumor suppressor of NSCLC. NFIC was significantly downregulated in both NSCLC tissues and cells, and when NFIC was overexpressed, the malignant phenotype and total m6A content of NSCLC cells was suppressed, while the PI3K/AKT pathway was inactivated. Additionally, we discovered that NFIC inhibits the expression of METTL3 by directly binding to its promoter region, and METTL3 regulates the expression of KAT2A, a histone acetyltransferase, by methylating the m6A site in the 3'UTR of KAT2A mRNA in NSCLC cells. Intriguingly, NFIC was also found to negatively regulate the expression of KAT2A by directly binding to its promoter region. CONCLUSIONS Our findings demonstrated that NFIC suppresses the malignant phenotype of NSCLC cells by regulating gene expression at both the transcriptional and post-transcriptional levels. A deeper comprehension of the genetic and epigenetic regulatory mechanisms in tumorigenesis would be beneficial for the development of personalized treatment strategies.
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Affiliation(s)
- Kesong Shi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Yani Chen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Ruihua Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Xinyao Fu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Hua Guo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Tian Gao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Shu Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Le Dou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Jiemin Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Yuan Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Jiale Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China.
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Wang Y, Wang S, Meng Z, Liu XM, Mao Y. Determinant of m6A regional preference by transcriptional dynamics. Nucleic Acids Res 2024; 52:3510-3521. [PMID: 38452220 DOI: 10.1093/nar/gkae169] [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: 01/28/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant chemical modification occurring on eukaryotic mRNAs, and has been reported to be involved in almost all stages of mRNA metabolism. The distribution of m6A sites is notably asymmetric along mRNAs, with a strong preference toward the 3' terminus of the transcript. How m6A regional preference is shaped remains incompletely understood. In this study, by performing m6A-seq on chromatin-associated RNAs, we found that m6A regional preference arises during transcription. Nucleosome occupancy is remarkedly increased in the region downstream of m6A sites, suggesting an intricate interplay between m6A methylation and nucleosome-mediated transcriptional dynamics. Notably, we found a remarkable slowdown of Pol-II movement around m6A sites. In addition, inhibiting Pol-II movement increases nearby m6A methylation levels. By analyzing massively parallel assays for m6A, we found that RNA secondary structures inhibit m6A methylation. Remarkably, the m6A sites associated with Pol-II pausing tend to be embedded within RNA secondary structures. These results suggest that Pol-II pausing could affect the accessibility of m6A motifs to the methyltransferase complex and subsequent m6A methylation by mediating RNA secondary structure. Overall, our study reveals a crucial role of transcriptional dynamics in the formation of m6A regional preference.
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Affiliation(s)
- Yalan Wang
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Zhen Meng
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yuanhui Mao
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
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Liu ZY, Lin LC, Liu ZY, Yang JJ, Tao H. m6A epitranscriptomic and epigenetic crosstalk in cardiac fibrosis. Mol Ther 2024; 32:878-889. [PMID: 38311850 PMCID: PMC11163196 DOI: 10.1016/j.ymthe.2024.01.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/27/2023] [Accepted: 01/31/2024] [Indexed: 02/06/2024] Open
Abstract
Cardiac fibrosis, a crucial pathological characteristic of various cardiac diseases, presents a significant treatment challenge. It involves the deposition of the extracellular matrix (ECM) and is influenced by genetic and epigenetic factors. Prior investigations have predominantly centered on delineating the substantial influence of epigenetic and epitranscriptomic mechanisms in driving the progression of fibrosis. Recent studies have illuminated additional avenues for modulating the progression of fibrosis, offering potential solutions to the challenging issues surrounding fibrosis treatment. In the context of cardiac fibrosis, an intricate interplay exists between m6A epitranscriptomic and epigenetics. This interplay governs various pathophysiological processes: mitochondrial dysfunction, mitochondrial fission, oxidative stress, autophagy, apoptosis, pyroptosis, ferroptosis, cell fate switching, and cell differentiation, all of which affect the advancement of cardiac fibrosis. In this comprehensive review, we meticulously analyze pertinent studies, emphasizing the interplay between m6A epitranscriptomics and partial epigenetics (including histone modifications and noncoding RNA), aiming to provide novel insights for cardiac fibrosis treatment.
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Affiliation(s)
- Zhi-Yan Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, P.R. China
| | - Li-Chan Lin
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, P.R. China
| | - Zhen-Yu Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, P.R. China
| | - Jing-Jing Yang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, P.R. China.
| | - Hui Tao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, P.R. China; Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, P.R. China; Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China.
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Tan Y, Qiao J, Yang S, Wang Q, Liu H, Liu Q, Feng W, Yang B, Li Z, Cui L. ARID5B-mediated LINC01128 epigenetically activated pyroptosis and apoptosis by promoting the formation of the BTF3/STAT3 complex in β2GPI/anti-β2GPI-treated monocytes. Clin Transl Med 2024; 14:e1539. [PMID: 38224186 PMCID: PMC10788880 DOI: 10.1002/ctm2.1539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Alterations of the trimethylation of histone 3 lysine 4 (H3K4me3) mark in monocytes are implicated in the development of autoimmune diseases. Therefore, the purpose of our study was to elucidate the role of H3K4me3-mediated epigenetics in the pathogenesis of antiphospholipid syndrome (APS). METHODS H3K4me3 Cleavage Under Targets and Tagmentation and Assay for Transposase-Accessible Chromatin were performed to determine the epigenetic profiles. Luciferase reporter assay, RNA immunoprecipitation, RNA pull-down, co-immunoprecipitation and chromatin immunoprecipitation were performed for mechanistic studies. Transmission electron microscopy and propidium iodide staining confirmed cell pyroptosis. Primary monocytes from patients with primary APS (PAPS) and healthy donors were utilised to test the levels of key molecules. A mouse model mimicked APS was constructed with beta2-glycoprotein I (β2GPI) injection. Blood velocity was detected using murine Doppler ultrasound. RESULTS H3K4me3 signal and open chromatin at the ARID5B promoter were increased in an in vitro model of APS. The epigenetic factor ARID5B directly activated LINC01128 transcription at its promoter. LINC01128 promoted the formation of the BTF3/STAT3 complex to enhance STAT3 phosphorylation. Activated STAT3 interacted with the NLRP3 promoter and subsequently stimulated pyroptosis and apoptosis. ARID5B or BTF3 depletion compensated for LINC01128-induced pyroptosis and apoptosis by inhibiting STAT3 phosphorylation. In mice with APS, β2GPI exposure elevated the levels of key proteins of pyroptosis and apoptosis pathways in bone marrow-derived monocytes, reduced the blood velocity of the ascending aorta, increased the thrombus size of the carotid artery, and promoted the release of interleukin (IL)-18, IL-1β and tissue factor. Patients with PAPS had the high-expressed ARID5B and LINC01128, especially those with triple positivity for antiphospholipid antibodies. Moreover, there was a positive correlation between ARID5B and LINC01128 expression. CONCLUSION This study indicated that ARID5B/LINC01128 was synergistically upregulated in APS, and they aggravated disease pathogenesis by enhancing the formation of the BTF3/STAT3 complex and boosting p-STAT3-mediated pyroptosis and apoptosis, thereby providing candidate therapeutic targets for APS. HIGHLIGHTS The H3K4me3 mark and chromatin accessibility at the ARID5B promoter are increased in vitro model mimicked APS. ARID5B-mediated LINC01128 induces pyroptosis and apoptosis via p-STAT3 by binding to BTF3. ARID5B is high- expressed in patients with primary APS and positively correlated with LINC01128 expression. OICR-9429 treatment mitigates pyroptosis and related inflammation in vivo and in vitro models mimicked APS.
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Affiliation(s)
- Yuan Tan
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Jiao Qiao
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Shuo Yang
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Qingchen Wang
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Hongchao Liu
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Qi Liu
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Weimin Feng
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Boxin Yang
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Zhongxin Li
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Liyan Cui
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
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9
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Zeng Y, Wang F, Li S, Song B. Regulatory Network of Methyltransferase-Like 3 in Stem Cells: Mechanisms and Medical Implications. Cell Transplant 2024; 33:9636897241282792. [PMID: 39466679 PMCID: PMC11528761 DOI: 10.1177/09636897241282792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/23/2024] [Accepted: 08/25/2024] [Indexed: 10/30/2024] Open
Abstract
Stem cells have the potential to replace defective cells in several human diseases by depending on their self-renewal and differentiation capacities that are controlled by genes. Currently, exploring the regulation mechanism for stem cell capacities from the perspective of methyltransferase-like 3 (METTL3)-mediated N6-methyladenosine modification has obtained great advance, which functions by regulating target genes post-transcriptionally. However, reviews that interpret the regulatory network of METTL3 in stem cells are still lacking. In this review, we systematically analyze the available publications that report the role and mechanisms of METTL3 in stem cells, including embryonic stem cells, pluripotent stem cells, mesenchymal stem cells, and cancer stem cells. The analysis of such publications suggests that METTL3 controls stem cell fates and is indispensable for maintaining its normal capacities. However, its dysfunction induces various pathologies, particularly cancers. To sum up, this review suggests METTL3 as a key regulator for stem cell capacities, with further exploration potential in translational and clinical fields. In conclusion, this review promotes the understanding of how METTL3 functions in stem cells, which provides a valuable reference for further fundamental studies and clinical applications.
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Affiliation(s)
- Yan Zeng
- Department of Pediatrics, People’s Hospital of Deyang City, Affiliated Hospital of Chengdu Medical College, Deyang, China
| | - Fengyang Wang
- Department of Pediatrics, People’s Hospital of Deyang City, Affiliated Hospital of Chengdu Medical College, Deyang, China
| | - Silu Li
- Department of Pediatrics, People’s Hospital of Deyang City, Affiliated Hospital of Chengdu Medical College, Deyang, China
| | - Bin Song
- Department of Nephrology, People’s Hospital of Deyang City, Affiliated Hospital of Chengdu Medical College, Deyang, China
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10
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Zhigalova NA, Oleynikova KY, Ruzov AS, Ermakov AS. The Functions of N 6-Methyladenosine in Nuclear RNAs. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:159-172. [PMID: 38467552 DOI: 10.1134/s0006297924010103] [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: 07/23/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 03/13/2024]
Abstract
N6-methyladenosine (m6A) is one of the most common modifications in both eukaryotic and prokaryotic mRNAs. It has been experimentally confirmed that m6A methylation is involved in the regulation of stability and translation of various mRNAs. Until recently, the majority of m6A-related studies have been focused on the cytoplasmic functions of this modification. Here, we review new data on the role of m6A in several key biological processes taking place in the cell nucleus, such as transcription, chromatin organization, splicing, nuclear-cytoplasmic transport, and R-loop metabolism. Based on analysis of these data, we suggest that m6A methylation of nuclear RNAs is another level of gene expression regulation which, together with DNA methylation and histone modifications, controls chromatin structure and functioning in various biological contexts.
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Affiliation(s)
- Nadezhda A Zhigalova
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Katerina Yu Oleynikova
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Alexey S Ruzov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Alexander S Ermakov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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11
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Shi K, Sa R, Dou L, Wu Y, Dong Z, Fu X, Yu H. METTL3 exerts synergistic effects on m6A methylation and histone modification to regulate the function of VGF in lung adenocarcinoma. Clin Epigenetics 2023; 15:153. [PMID: 37742030 PMCID: PMC10517543 DOI: 10.1186/s13148-023-01568-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Multiple genetic and epigenetic regulatory mechanisms play a vital role in tumorigenesis and development. Understanding the interplay between different epigenetic modifications and its contribution to transcriptional regulation in cancer is essential for precision medicine. Here, we aimed to investigate the interplay between N6-methyladenosine (m6A) modifications and histone modifications in lung adenocarcinoma (LUAD). RESULTS Based on the data from public databases, including chromatin property data (ATAC-seq, DNase-seq), methylated RNA immunoprecipitation sequencing (MeRIP-seq), and gene expression data (RNA-seq), a m6A-related differentially expressed gene nerve growth factor inducible (VGF) was identified between LUAD tissues and normal lung tissues. VGF was significantly highly expressed in LUAD tissues and cells, and was associated with a worse prognosis for LUAD, silencing of VGF inhibited the malignant phenotype of LUAD cells by inactivating the PI3K/AKT/mTOR pathway. Through the weighted correlation network analysis (WGCNA) and integration of TCGA-LUAD RNA-seq and m6A methyltransferase METTL3-knockdown RNA-seq data, a significant positive correlation between METTL3 and VGF was observed. By using the MeRIP-qPCR and dual-luciferase reporter assays, we demonstrated that METTL3 knockdown decreased m6A modification level of VGF coding sequences in LUAD cells, the colorimetric m6A quantification assay also showed that METTL3 knockdown significantly decreased global m6A modification level in LUAD cells. Interestingly, we found that METTL3 knockdown also reduced VGF expression by increasing H3K36me3 modification at the VGF promoter. Further research revealed that METTL3 knockdown upregulated the expression of histone methylase SETD2, the major H3K36me3 methyltransferase, by methylating the m6A site in the 3'UTR of SETD2 mRNA in LUAD cells. CONCLUSIONS Overall, our results reveal that the expression of VGF in LUAD cells is regulated spatio-temporally by METTL3 through both transcriptional (via histone modifications) and post-transcriptional (via m6A modifications) mechanisms. The synergistic effect of these multiple epigenetic mechanisms provides new opportunities for the diagnosis and precision treatment of tumors.
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Affiliation(s)
- Kesong Shi
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Rula Sa
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Le Dou
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Yuan Wu
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Zhiqiang Dong
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Xinyao Fu
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China.
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Dong S, Sun Y, Liu C, Li Y, Yu S, Zhang Q, Xu Y. Stage-specific requirement for m 6A RNA methylation during cardiac differentiation of pluripotent stem cells. Differentiation 2023; 133:77-87. [PMID: 37506593 DOI: 10.1016/j.diff.2023.07.001] [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: 02/23/2023] [Revised: 06/16/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
Precise spatiotemporal control of gene expression patterns is critical for normal development. Pluripotent stem cells, including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), with the ability of unlimited self-renewal and differentiation into any cell type, provide a unique tool for understanding the underlying mechanism of development and disease in a dish. N6-methyl-adenosine (m6A) modification is the most extensive internal mRNA modification, which regulates almost all aspects of mRNA metabolism and thus extensively participates in gene expression regulation. However, the role of m6A during cardiogenesis still needs to be fully elucidated. Here, we found that core components of m6A methyltransferase decreased during cardiomyocyte differentiation. Impeding m6A deposition, by either deleting the m6A methyltransferase Mettl3 or overexpressing m6A demethylase alkB homolog 5 (Alkbh5), at early stages of cardiac differentiation of mouse pluripotent stem cells, led to inhibition of cardiac gene activation and retardation of the outgrowth of embryoid bodies, whereas interfering m6A modification at later stages of differentiation had minimal effects. Consistently, stage-specific inhibition of METTL3 with METTL3 inhibitor STM2457 during human ESCs (hESCs) cardiac differentiation demonstrated a similarly pivotal role of METTL3 for the induction of mesodermal cells while dispensable function for later stages. In summary, our study reveals a stage-specific requirement of m6A on the cardiac differentiation of pluripotent stem cells and demonstrates that precise tuning of m6A level is critical for cardiac differentiation.
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Affiliation(s)
- Shuai Dong
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuetong Sun
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chang Liu
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanli Li
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shanshan Yu
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qi Zhang
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Cell-gene Therapy Translational Medicine Research Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Xu
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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