1
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Bhattarai PY, Kim G, Lim SC, Choi HS. METTL3-STAT5B interaction facilitates the co-transcriptional m 6A modification of mRNA to promote breast tumorigenesis. Cancer Lett 2024; 603:217215. [PMID: 39218290 DOI: 10.1016/j.canlet.2024.217215] [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: 05/20/2024] [Revised: 08/07/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Enhanced expression of methyltransferase-like 3 (METTL3) promotes the m6A modification of specific mRNAs, contributing to breast tumorigenesis. While the mRNA substrates targeted by METTL3 are well characterized, the factors dictating the selection of these specific mRNA remain elusive. This study aimed to examine the regulatory role of the transcription factor STAT5B in METTL3-induced m6A modification. METTL3 specifically interacts with STAT5B in response to mitogenic stimulation by epidermal growth factor (EGF). Chromatin immunoprecipitation and CRISPR/Cas9 mutagenesis showed that STAT5B recruits METTL3 to gene promoters like CCND1, where METTL3 interacts with RPB1, dependent on CDK9-mediated RPB1 (Ser2) phosphorylation during transcription elongation. Inhibition and depletion of either STAT5B or CDK9 prevented the EGF-induced m6A modification of CCND1. The translation efficiency of CCND1 was increased following m6A modification, thereby increasing cell proliferation. STAT5B facilitated METTL3-induced tumor formation by increasing CCND1 expression in an orthotopic mouse model. In clinical context, a positive correlation was observed between p-STAT5B and METTL3 expression in high-grade breast tumors. This study elucidates a novel mechanism that underlies the specificity of m6A modification in breast cancer cells, thereby underscoring its potential therapeutic value.
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Affiliation(s)
- Poshan Yugal Bhattarai
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chosun University, Gwangju, 61452, Republic of Korea
| | - Garam Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chosun University, Gwangju, 61452, Republic of Korea
| | - Sung-Chul Lim
- Department of Pathology, School of Medicine, Chosun University, Gwangju, 61452, Republic of Korea
| | - Hong Seok Choi
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chosun University, Gwangju, 61452, Republic of Korea.
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2
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Shi Y, Yin L, Li JY, Zhou SM, Wang N, Chen HQ, Zeng Y, Li YW, Liu WB. FTO mediates bisphenol F-induced blood-testis barrier impairment through regulating ferroptosis via YTHDF1/TfRc and YTHDF2/SLC7A11 signal axis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124531. [PMID: 38996995 DOI: 10.1016/j.envpol.2024.124531] [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: 05/08/2024] [Revised: 06/30/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Bisphenol F (BPF) has been extensively utilized in daily life, which brings new hazards to male reproductive health. However, the specific functional mechanism is still unclear. Both cell and animal models were utilized for exploring the role of RNA methylation and ferroptosis and its underlying mechanisms in male reproductive injury induced by BPF. In animal model, BPF severely destroyed the integrity of the blood-testis barrier (BTB) and induced ferroptosis. Furthermore, BPF significantly affected the barrier function of TM4 cells and promoted ferroptosis. Importantly, ChIP assays revealed that BPF inhibited AR transcriptional regulation of FTO and FTO expression was downregulated in TM4 cells. Overexpression of FTO prevented the impairment of BTB by inhibiting ferroptosis in TM4 cells. Mechanistically, FTO could significantly down-regulate the m6A modification level of TfRc and SLC7A11 mRNA through MeRIP experiment. RIP experiments showed that YTHDF1 can bind to TfRc mRNA and promote its translation while YTHDF2 could bind to SLC7A11 mRNA and reduce its mRNA stability. Therefore, our results suggest that FTO plays a key role in BPF induced male reproductive toxicity through YTHDF1-TfRc axis and YTHDF2-SLC7A11 axis and may provide new ideas and methods for the prevention and treatment of male reproductive diseases associated with environmental pollutants.
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Affiliation(s)
- Yu Shi
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Li Yin
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Jiang-Ying Li
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Shi-Meng Zhou
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China; Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Na Wang
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China; School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 561113, China
| | - Hong-Qiang Chen
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yong Zeng
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Ya-Wen Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China; School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 561113, China
| | - Wen-Bin Liu
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China; Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
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3
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Patke R, Harris AE, Woodcock CL, Thompson R, Santos R, Kumari A, Allegrucci C, Archer N, Gudas LJ, Robinson BD, Persson JL, Fray R, Jeyapalan J, Rutland CS, Rakha E, Madhusudan S, Emes RD, Muyangwa-Semenova M, Alsaleem M, de Brot S, Green W, Ratan H, Mongan NP, Lothion-Roy J. Epitranscriptomic mechanisms of androgen signalling and prostate cancer. Neoplasia 2024; 56:101032. [PMID: 39033689 PMCID: PMC11295630 DOI: 10.1016/j.neo.2024.101032] [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: 05/31/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Prostate cancer (PCa) is the second most common cancer diagnosed in men. While radical prostatectomy and radiotherapy are often successful in treating localised disease, post-treatment recurrence is common. As the androgen receptor (AR) and androgen hormones play an essential role in prostate carcinogenesis and progression, androgen deprivation therapy (ADT) is often used to deprive PCa cells of the pro-proliferative effect of androgens. ADTs act by either blocking androgen biosynthesis (e.g. abiraterone) or blocking AR function (e.g. bicalutamide, enzalutamide, apalutamide, darolutamide). ADT is often effective in initially suppressing PCa growth and progression, yet emergence of castrate-resistant PCa and progression to neuroendocrine-like PCa following ADT are major clinical challenges. For this reason, there is an urgent need to identify novel approaches to modulate androgen signalling to impede PCa progression whilst also preventing or delaying therapy resistance. The mechanistic convergence of androgen and epitranscriptomic signalling offers a potential novel approach to treat PCa. The epitranscriptome involves covalent modifications of mRNA, notably, in the context of this review, the N(6)-methyladenosine (m6A) modification. m6A is involved in the regulation of mRNA splicing, stability, and translation, and has recently been shown to play a role in PCa and androgen signalling. The m6A modification is dynamically regulated by the METTL3-containing methyltransferase complex, and the FTO and ALKBH5 RNA demethylases. Given the need for novel approaches to treat PCa, there is significant interest in new therapies that target m6A that modulate AR expression and androgen signalling. This review critically summarises the potential benefit of such epitranscriptomic therapies for PCa patients.
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Affiliation(s)
- Rodhan Patke
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK
| | - Anna E Harris
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK
| | - Corinne L Woodcock
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK
| | - Rachel Thompson
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK
| | - Rute Santos
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK
| | - Amber Kumari
- Biodiscovery Institute, University of Nottingham, UK
| | - Cinzia Allegrucci
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK
| | - Nathan Archer
- School of Veterinary Medicine and Science, University of Nottingham, UK
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Brian D Robinson
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Jenny L Persson
- Department of Molecular Biology, Umea University, Umea, Sweden
| | - Rupert Fray
- School of Biosciences, University of Nottingham, UK
| | - Jennie Jeyapalan
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK
| | - Catrin S Rutland
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK
| | - Emad Rakha
- School of Medicine, University of Nottingham, UK; Nottingham University NHS Trust, Nottingham, UK
| | - Srinivasan Madhusudan
- School of Medicine, University of Nottingham, UK; Nottingham University NHS Trust, Nottingham, UK
| | - Richard D Emes
- Research and Innovation, Nottingham Trent University, UK
| | | | - Mansour Alsaleem
- Biodiscovery Institute, University of Nottingham, UK; Unit of Scientific Research, Applied College, Qassim University, Qassim, Saudi Arabia
| | - Simone de Brot
- Institute of Animal Pathology, University of Bern, Switzerland
| | - William Green
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Hari Ratan
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Nigel P Mongan
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK; Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
| | - Jennifer Lothion-Roy
- Biodiscovery Institute, University of Nottingham, UK; School of Veterinary Medicine and Science, University of Nottingham, UK.
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4
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Park D, Cenik C. Long-read RNA sequencing reveals allele-specific N 6-methyladenosine modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602538. [PMID: 39026828 PMCID: PMC11257478 DOI: 10.1101/2024.07.08.602538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Long-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA promises the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNA. We utilized human and mouse cells with known genetic variants to assign allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses revealed the importance of sequences adjacent to the DRACH-motif in determining m6A deposition, in addition to allelic differences that directly alter the motif. Moreover, we discovered allele-specific m6A modification (ASM) events with no genetic variants in close proximity to the differentially modified nucleotide, demonstrating the unique advantage of using long reads and surpassing the capabilities of antibody-based short-read approaches. This technological advancement promises to advance our understanding of the role of genetics in determining mRNA modifications.
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Affiliation(s)
- Dayea Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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5
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Bove G, Del Gaudio N, Altucci L. Epitranscriptomics and epigenetics: two sides of the same coin? Clin Epigenetics 2024; 16:121. [PMID: 39252109 PMCID: PMC11386089 DOI: 10.1186/s13148-024-01729-4] [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: 07/30/2024] [Accepted: 08/12/2024] [Indexed: 09/11/2024] Open
Abstract
Gene expression is an intricate biological process that bridges gap between the genotype and the phenotype. Canonical and hereditable epigenetic mechanisms, such as histone and DNA modifications, regulate the release of genetic information encoded in DNA without altering the underlying sequence. Many other non-canonical players, such as chromatin regulators and noncoding RNAs, are also involved in regulating gene expression. Recently, RNA modifications (epitranscriptomics) have been shown to hold enormous potential in shaping cellular transcriptomes. However, their co-transcriptional nature and uncertain heritability mean that they fall outside the current definition of epigenetics, sparking an ongoing debate in the field. Here we will discuss the relationship between canonical and non-canonical epigenetic mechanisms that govern gene expression and offer our perspective on whether (or not) epitranscriptomic modifications can be classified as epigenetic mechanisms.
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Affiliation(s)
- Guglielmo Bove
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. de Crecchio 7, Naples, Italy
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. de Crecchio 7, Naples, Italy.
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. de Crecchio 7, Naples, Italy.
- BIOGEM, Via Camporeale, Ariano Irpino, Italy.
- UP Medical Epigenetics, AOU Vanvitelli, Naples, Italy.
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6
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Wang C, Wang Y. Meiosis requires m 6A modification for selection of targets in plants. THE NEW PHYTOLOGIST 2024. [PMID: 39223876 DOI: 10.1111/nph.20089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Affiliation(s)
- Cong Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Institute for Soybean Innovation Research, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yingxiang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Institute for Soybean Innovation Research, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, China
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7
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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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8
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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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9
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Zhang L, Wang J, Liu X, Xiao X, Liu Y, Huang Q, Li J, Li G, Yang P. Regulation of SETD2 maintains immune regulatory function in macrophages to suppress airway allergy. Immunology 2024; 173:185-195. [PMID: 38859694 DOI: 10.1111/imm.13823] [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: 03/15/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024] Open
Abstract
SET domain-containing 2 (SETD2) is a histone methyltransferase. It regulates the activity of H3K36me3 to enhance gene transcription. Macrophages (Mϕs) are one of the cell types involved in immune response. The purpose of this study is to clarify the role of SETD2 in regulating the immune property of Mϕ. The Mφs were isolated from the bronchoalveolar lavage fluid (BALF) and analysed through flow cytometry and RNA sequencing. A mouse strain carrying Mφs deficient in SETD2 was used. A mouse model of airway allergy was established with the ovalbumin/alum protocol. Less expression of SETD2 was observed in airway Mϕs in patients with allergic asthma. SETD2 of M2 cells was associated with the asthmatic clinical response. Sensitization reduced the expression of SETD2 in mouse respiratory tract M2 cells, which is associated with the allergic reaction. Depletion of SETD2 in Mφs resulted in Th2 pattern inflammation in the lungs. SETD2 maintained the immune regulatory ability in airway M2 cells. SETD2 plays an important role in the maintenance of immune regulatory property of airway Mφs.
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Affiliation(s)
- Lei Zhang
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Junyi Wang
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Xiaoyu Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen, China
- State Key Laboratory of Respiratory Disease Allergy Division at Shenzhen University, Institute of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Xiaojun Xiao
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen, China
- State Key Laboratory of Respiratory Disease Allergy Division at Shenzhen University, Institute of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Yu Liu
- Department of General Medicine Practice and Respirology, Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qinmiao Huang
- Department of General Medicine Practice and Respirology, Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jing Li
- Department of Allergy, First Affiliated Hospital, Guangzhou Medial University, Guangzhou, China
| | - Guoping Li
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Pingchang Yang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen, China
- State Key Laboratory of Respiratory Disease Allergy Division at Shenzhen University, Institute of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China
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10
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Hong Y, Ma H, Yang H, Zhu Y, Wei Y, Xu Z, Zhang Y, Jin D, Chen Z, Song W, Li J. Ouabain-mediated downregulation of ALKBH5 and IGF2BP2 inhibits the malignant progression of DLBCL. Front Pharmacol 2024; 15:1447830. [PMID: 39281280 PMCID: PMC11392878 DOI: 10.3389/fphar.2024.1447830] [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: 06/12/2024] [Accepted: 08/19/2024] [Indexed: 09/18/2024] Open
Abstract
m6A modification is a crucial epigenetic regulatory mechanism in diffuse large B-cell lymphoma (DLBCL). Low-dose cardiotonic drugs have been shown to induce apoptosis in DLBCL cells through epigenetic modulation. However, the involvement of the cardiotonic drug ouabain in the malignant progression of DLBCL remains unclear. Our study revealed that ouabain indeed contributes to the malignant progression of DLBCL through m6A modification. Through qPCR analysis, we observed a negative correlation between ouabain concentration and the expression levels of the demethylase ALKBH5 and the m6A-binding protein IGF2BP2 in DLBCL cells. Furthermore, high expression levels of ALKBH5 and IGF2BP2 were identified in both the GEO database and DLBCL patient tissue samples. Notably, elevated ALKBH5 and IGF2BP2 promoted cell proliferation both in vitro and in vivo. Inhibition of their expression rendered DLBCL cells more sensitive to ouabain treatment, resulting in significant suppression of cell proliferation, G1/S phase cell cycle arrest, and increased apoptosis. In summary, our results clarify that the demethylase ALKBH5 and the m6A-binding protein IGF2BP2 are involved in the malignant progression of DLBCL, and that the cardiotonic drug ouabain can inhibit the proliferation of DLBCL cells by inhibiting the expression of ALKBH5 and IGF2BP2, which provides new insights into the targeted treatment of DLBCL.
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Affiliation(s)
- Yuxin Hong
- Department of Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Hehua Ma
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Haoyi Yang
- Department of Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuning Zhu
- Department of Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuan Wei
- Department of Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhenzhen Xu
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuwen Zhang
- Department of Phase I Clinical Trials Unit, China Pharmaceutical University Nanjing Drum Tower Hospital, Nanjing, China
| | - Dandan Jin
- Department of Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhiyou Chen
- Department of Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Song
- Department of Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Phase I Clinical Trials Unit, China Pharmaceutical University Nanjing Drum Tower Hospital, Nanjing, China
| | - Juan Li
- Department of Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Phase I Clinical Trials Unit, China Pharmaceutical University Nanjing Drum Tower Hospital, Nanjing, China
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11
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Shan Y, Zhang Y, Wei Y, Zhang C, Lin H, He J, Wang J, Guo W, Li H, Chen Q, Zhou T, Xing Q, Liu Y, Chen J, Pan G. METTL3/METTL14 maintain human nucleoli integrity by mediating SUV39H1/H2 degradation. Nat Commun 2024; 15:7186. [PMID: 39169036 PMCID: PMC11339338 DOI: 10.1038/s41467-024-51742-7] [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: 01/26/2024] [Accepted: 08/14/2024] [Indexed: 08/23/2024] Open
Abstract
Nucleoli are fundamentally essential sites for ribosome biogenesis in cells and formed by liquid-liquid phase separation (LLPS) for a multilayer condensate structure. How the nucleoli integrity is maintained remains poorly understood. Here, we reveal that METTL3/METTL14, the typical methyltransferase complex catalyzing N6-methyladnosine (m6A) on mRNAs maintain nucleoli integrity in human embryonic stem cells (hESCs). METTL3/METTL14 deficiency impairs nucleoli and leads to the complete loss of self-renewal in hESCs. We further show that SUV39H1/H2 protein, the methyltransferases catalyzing H3K9me3 were dramatically elevated in METTL3/METTL14 deficient cells, which causes an accumulation and infiltration of H3K9me3 across the whole nucleolus and impairs the LLPS. Mechanistically, METTL3/METTL14 complex serves as an essential adapter for CRL4 E3 ubiquitin ligase targeting SUV39H1/H2 for polyubiquitination and proteasomal degradation and therefore prevents H3K9me3 accumulation in nucleoli. Together, these findings uncover a previously unknown role of METTL3/METTL14 to maintain nucleoli integrity by facilitating SUV39H1/H2 degradation in human cells.
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Affiliation(s)
- Yongli Shan
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.
- Nanfang Hospital, Southern Medical University, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Yanqi Zhang
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanxing Wei
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Cong Zhang
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Huaisong Lin
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | - Junwei Wang
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Wenjing Guo
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Heying Li
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qianyu Chen
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tiancheng Zhou
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qi Xing
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yancai Liu
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jiekai Chen
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Guangjin Pan
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, Hong Kong.
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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12
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Li C, Chen K, Fang Q, Shi S, Nan J, He J, Yin Y, Li X, Li J, Hou L, Hu X, Kellis M, Han X, Xiong X. Crosstalk between epitranscriptomic and epigenomic modifications and its implication in human diseases. CELL GENOMICS 2024; 4:100605. [PMID: 38981476 PMCID: PMC11406187 DOI: 10.1016/j.xgen.2024.100605] [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: 01/10/2024] [Revised: 04/17/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
Crosstalk between N6-methyladenosine (m6A) and epigenomes is crucial for gene regulation, but its regulatory directionality and disease significance remain unclear. Here, we utilize quantitative trait loci (QTLs) as genetic instruments to delineate directional maps of crosstalk between m6A and two epigenomic traits, DNA methylation (DNAme) and H3K27ac. We identify 47 m6A-to-H3K27ac and 4,733 m6A-to-DNAme and, in the reverse direction, 106 H3K27ac-to-m6A and 61,775 DNAme-to-m6A regulatory loci, with differential genomic location preference observed for different regulatory directions. Integrating these maps with complex diseases, we prioritize 20 genome-wide association study (GWAS) loci for neuroticism, depression, and narcolepsy in brain; 1,767 variants for asthma and expiratory flow traits in lung; and 249 for coronary artery disease, blood pressure, and pulse rate in muscle. This study establishes disease regulatory paths, such as rs3768410-DNAme-m6A-asthma and rs56104944-m6A-DNAme-hypertension, uncovering locus-specific crosstalk between m6A and epigenomic layers and offering insights into regulatory circuits underlying human diseases.
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Affiliation(s)
- Chengyu Li
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Kexuan Chen
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Qianchen Fang
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Shaohui Shi
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Jiuhong Nan
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Jialin He
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Yafei Yin
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaoyu Li
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingyun Li
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Lei Hou
- Department of Medicine, Biomedical Genetics Section, Boston University, Boston, MA 02118, USA
| | - Xinyang Hu
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China; The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xikun Han
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Xushen Xiong
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China.
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13
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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 PMCID: PMC11405154 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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14
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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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15
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Chen K, Nan J, Xiong X. Genetic regulation of m 6A RNA methylation and its contribution in human complex diseases. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1591-1600. [PMID: 38764000 DOI: 10.1007/s11427-024-2609-8] [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: 01/08/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
N6-methyladenosine (m6A) has been established as the most prevalent chemical modification in message RNA (mRNA), playing an essential role in determining the fate of RNA molecules. Dysregulation of m6A has been revealed to lead to abnormal physiological conditions and cause various types of human diseases. Recent studies have delineated the genetic regulatory maps for m6A methylation by mapping the quantitative trait loci of m6A (m6A-QTLs), thereby building up the regulatory circuits linking genetic variants, m6A, and human complex traits. Here, we review the recent discoveries concerning the genetic regulatory maps of m6A, describing the methodological and technical details of m6A-QTL identification, and introducing the key findings of the cis- and trans-acting drivers of m6A. We further delve into the tissue- and ethnicity-specificity of m6A-QTL, the association with other molecular phenotypes in light of genetic regulation, the regulators underlying m6A genetics, and importantly, the functional roles of m6A in mediating human complex diseases. Lastly, we discuss potential research avenues that can accelerate the translation of m6A genetics studies toward the development of therapies for human genetic diseases.
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Affiliation(s)
- Kexuan Chen
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Jiuhong Nan
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Xushen Xiong
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China.
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China.
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16
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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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17
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Tang P, Yang J, Chen Z, Du C, Yang Y, Zhao H, Huang L, Li G, Liu F, Dong B, Shan T, Bao X, Zhou Y. Nuclear retention coupled with sequential polyadenylation dictates post-transcriptional m 6A modification in the nucleus. Mol Cell 2024:S1097-2765(24)00593-8. [PMID: 39127036 DOI: 10.1016/j.molcel.2024.07.017] [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: 01/09/2023] [Revised: 06/28/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024]
Abstract
N6-methyladenosine (m6A) modification is deemed to be co-transcriptionally installed on pre-mRNAs, thereby influencing various downstream RNA metabolism events. However, the causal relationship between m6A modification and RNA processing is often unclear, resulting in premature or even misleading generalizations on the function of m6A modification. Here, we develop 4sU-coupled m6A-level and isoform-characterization sequencing (4sU-m6A-LAIC-seq) and 4sU-GLORI to quantify the m6A levels for both newly synthesized and steady-state RNAs at transcript and single-base-resolution levels, respectively, which enable dissecting the relationship between m6A modification and alternative RNA polyadenylation. Unexpectedly, our results show that many m6A addition events occur post-transcriptionally, especially on transcripts with high m6A levels. Importantly, we find higher m6A levels on shorter 3' UTR isoforms, which likely result from sequential polyadenylation of longer 3' UTR isoforms with prolonged nuclear dwelling time. Therefore, m6A modification can also take place post-transcriptionally to intimately couple with other key RNA metabolism processes to establish and dynamically regulate epi-transcriptomics in mammalian cells.
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Affiliation(s)
- Peng Tang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jiayi Yang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Zonggui Chen
- Institute of Advanced Studies, Wuhan University, Wuhan, China
| | - Chen Du
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Yang Yang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China; Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Haiping Zhao
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Li Huang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Guangnan Li
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Feiyan Liu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Bei Dong
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ting Shan
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Xichen Bao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China; Institute of Advanced Studies, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China.
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18
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Jayakrishnan M, Havlová M, Veverka V, Regnard C, Becker P. Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers. Nucleic Acids Res 2024; 52:7627-7649. [PMID: 38813825 PMCID: PMC11260483 DOI: 10.1093/nar/gkae449] [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: 01/24/2024] [Revised: 05/03/2024] [Accepted: 05/28/2024] [Indexed: 05/31/2024] Open
Abstract
Methylation of histone H3 at lysine 36 (H3K36me3) marks active chromatin. The mark is interpreted by epigenetic readers that assist transcription and safeguard the integrity of the chromatin fiber. The chromodomain protein MSL3 binds H3K36me3 to target X-chromosomal genes in male Drosophila for dosage compensation. The PWWP-domain protein JASPer recruits the JIL1 kinase to active chromatin on all chromosomes. Unexpectedly, depletion of K36me3 had variable, locus-specific effects on the interactions of those readers. This observation motivated a systematic and comprehensive study of K36 methylation in a defined cellular model. Contrasting prevailing models, we found that K36me1, K36me2 and K36me3 each contribute to distinct chromatin states. A gene-centric view of the changing K36 methylation landscape upon depletion of the three methyltransferases Set2, NSD and Ash1 revealed local, context-specific methylation signatures. Set2 catalyzes K36me3 predominantly at transcriptionally active euchromatin. NSD places K36me2/3 at defined loci within pericentric heterochromatin and on weakly transcribed euchromatic genes. Ash1 deposits K36me1 at regions with enhancer signatures. The genome-wide mapping of MSL3 and JASPer suggested that they bind K36me2 in addition to K36me3, which was confirmed by direct affinity measurement. This dual specificity attracts the readers to a broader range of chromosomal locations and increases the robustness of their actions.
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Affiliation(s)
- Muhunden Jayakrishnan
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Magdalena Havlová
- Institute of Organic Chemistry and Biochemistry (IOCB) of the Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry (IOCB) of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Catherine Regnard
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
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19
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Guo X, Hong P, Xiong S, Yan Y, Xie H, Guan JS. Kdm4a is an activity downregulated barrier to generate engrams for memory separation. Nat Commun 2024; 15:5887. [PMID: 39003305 PMCID: PMC11246488 DOI: 10.1038/s41467-024-50218-y] [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: 12/20/2023] [Accepted: 07/01/2024] [Indexed: 07/15/2024] Open
Abstract
Memory engrams are a subset of learning activated neurons critical for memory recall, consolidation, extinction and separation. While the transcriptional profile of engrams after learning suggests profound neural changes underlying plasticity and memory formation, little is known about how memory engrams are selected and allocated. As epigenetic factors suppress memory formation, we developed a CRISPR screening in the hippocampus to search for factors controlling engram formation. We identified histone lysine-specific demethylase 4a (Kdm4a) as a negative regulator for engram formation. Kdm4a is downregulated after neural activation and controls the volume of mossy fiber boutons. Mechanistically, Kdm4a anchors to the exonic region of Trpm7 gene loci, causing the stalling of nascent RNAs and allowing burst transcription of Trpm7 upon the dismissal of Kdm4a. Furthermore, the YTH domain containing protein 2 (Ythdc2) recruits Kdm4a to the Trpm7 gene and stabilizes nascent RNAs. Reducing the expression of Kdm4a in the hippocampus via genetic manipulation or artificial neural activation facilitated the ability of pattern separation in rodents. Our work indicates that Kdm4a is a negative regulator of engram formation and suggests a priming state to generate a separate memory.
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Affiliation(s)
- Xiuxian Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Pengfei Hong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Songhai Xiong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yuze Yan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hong Xie
- Institute of Photonic Chips, School of Artificial Intelligence Science and Technology, University of Shanghai for Science and Technology, Shanghai, China.
| | - Ji-Song Guan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, China.
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20
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Yi C. DDX21 is a new player in co-transcriptional RNA modification and functions. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2626-7. [PMID: 38995490 DOI: 10.1007/s11427-024-2626-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/16/2024] [Indexed: 07/13/2024]
Affiliation(s)
- Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, China.
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21
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Hu J, Xu T, Kang H. Crosstalk between RNA m 6A modification and epigenetic factors in plant gene regulation. PLANT COMMUNICATIONS 2024:101037. [PMID: 38971972 DOI: 10.1016/j.xplc.2024.101037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/04/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant modification observed in eukaryotic mRNAs. Advances in transcriptome-wide m6A mapping and sequencing technologies have enabled the identification of several conserved motifs in plants, including the RRACH (R = A/G and H = A/C/U) and UGUAW (W = U or A) motifs. However, the mechanisms underlying deposition of m6A marks at specific positions in the conserved motifs of individual transcripts remain to be clarified. Evidence from plant and animal studies suggests that m6A writer or eraser components are recruited to specific genomic loci through interactions with particular transcription factors, 5-methylcytosine DNA methylation marks, and histone marks. In addition, recent studies in animal cells have shown that microRNAs play a role in depositing m6A marks at specific sites in transcripts through a base-pairing mechanism. m6A also affects the biogenesis and function of chromatin-associated regulatory RNAs and long noncoding RNAs. Although we have less of an understanding of the link between m6A modification and epigenetic factors in plants than in animals, recent progress in identifying the proteins that interact with m6A writer or eraser components has provided insights into the crosstalk between m6A modification and epigenetic factors, which plays a crucial role in transcript-specific methylation and regulation of m6A in plants.
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Affiliation(s)
- Jianzhong Hu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Tao Xu
- Jiangsu Key Laboratory of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province 221116, China.
| | - Hunseung Kang
- Jiangsu Key Laboratory of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province 221116, China; Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea.
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22
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Du B, Wang P, Wei L, Qin K, Pei Z, Zheng J, Wang J. Unraveling the independent role of METTL3 in m6A modification and tumor progression in esophageal squamous cell carcinoma. Sci Rep 2024; 14:15398. [PMID: 38965238 PMCID: PMC11224396 DOI: 10.1038/s41598-024-64517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
METTL3 and METTL14 are traditionally posited to assemble the m6A methyltransferase complex in a stoichiometric 1:1 ratio, modulating mRNA fate via m6A modifications. Nevertheless, recent investigations reveal inconsistent expression levels and prognostic significance of METTL3 and METTL14 across various tumor types, challenging their consistent functional engagement in neoplastic contexts. A pan-cancer analysis leveraging The Cancer Genome Atlas (TCGA) data has identified pronounced disparities in the expression patterns, functional roles, and correlations with tumor burden between METTL3 and METTL14, particularly in esophageal squamous cell carcinoma (ESCC). Knockdown experiments of METTL3 in EC109 cells markedly suppress cell proliferation both in vitro and in vivo, whereas METTL14 knockdown shows a comparatively muted effect on proliferation and does not significantly alter METTL3 protein levels. mRNA sequencing indicates that METTL3 singularly governs the expression of 1615 genes, with only 776 genes co-regulated with METTL14. Additionally, immunofluorescence co-localization studies suggest discrepancies in cellular localization between METTL3 and METTL14. High-performance liquid chromatography-mass spectrometry (HPLC-MS) analyses demonstrate that METTL3 uniquely associates with the Nop56p-linked pre-rRNA complex and mRNA splicing machinery, independent of METTL14. Preliminary bioinformatics and multi-omics investigations reveal that METTL3's autonomous role in modulating tumor cell proliferation and its involvement in mRNA splicing are potentially pivotal molecular mechanisms. Our study lays both experimental and theoretical groundwork for a deeper understanding of the m6A methyltransferase complex and the development of targeted tumor therapies focusing on METTL3.
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Affiliation(s)
- Bin Du
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Pu Wang
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Lingyu Wei
- Central Laboratory of Clinical Research, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, 047500, China
| | - Kai Qin
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Zhen Pei
- Department of Physiology, Changzhi Medical College, Changzhi, 047500, China
| | - Jinping Zheng
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Jia Wang
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China.
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23
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Liu S, Cao Y, Zhang Y. Regulatory roles of RNA methylation in vascular lesions in ocular and cardiopulmonary diseases. Crit Rev Clin Lab Sci 2024:1-15. [PMID: 38957015 DOI: 10.1080/10408363.2024.2370267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
RNA methylation is a widespread regulatory mechanism that controls gene expression in physiological processes. In recent years, the mechanisms and functions of RNA methylation under diseased conditions have been increasingly unveiled by RNA sequencing technologies with large scale and high resolution. In this review, the fundamental concept of RNA methylation is introduced, and the common types of transcript methylation and their machineries are described. Then, the regulatory roles of RNA methylation, particularly N6-methyladenosine and 5-methylcytosine, in the vascular lesions of ocular and cardiopulmonary diseases are discussed and compared. The ocular diseases include corneal neovascularization, retinopathy of prematurity, diabetic retinopathy, and pathologic myopia; whereas the cardiopulmonary ailments involve atherosclerosis and pulmonary hypertension. This review hopes to shed light on the common regulatory mechanisms underlying the vascular lesions in these ocular and cardiopulmonary diseases, which may be conducive to developing therapeutic strategies in clinical practice.
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Affiliation(s)
- Siyi Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Yunshan Cao
- Department of Cardiology, Gansu Provincial Hospital, Lanzhou, China
| | - Yan Zhang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
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24
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Shi C, Zou W, Liu X, Zhang H, Li X, Fu G, Fei Q, Qian Q, Shang L. Programmable RNA N 6-methyladenosine editing with CRISPR/dCas13a in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1867-1880. [PMID: 38363049 PMCID: PMC11182597 DOI: 10.1111/pbi.14307] [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: 04/12/2023] [Revised: 10/07/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
N6-methyladenonsine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) and plays critical roles in mRNA processing and metabolism. However, perturbation of individual m6A modification to reveal its function and the phenotypic effects is still lacking in plants. Here, we describe the construction and characterization of programmable m6A editing tools by fusing the m6A writers, the core catalytic domain of the MTA and MTB complex, and the AlkB homologue 5 (ALKBH5) eraser, to catalytically dead Cas13a (dCas13a) to edit individual m6A sites on mRNAs. We demonstrated that our m6A editors could efficiently and specifically deposit and remove m6A modifications on specific RNA transcripts in both Nicotiana benthamiana and Arabidopsis thaliana. Moreover, we found that targeting SHORT-ROOT (SHR) transcripts with a methylation editor could significantly increase its m6A levels with limited off-target effects and promote its degradation. This leads to a boost in plant growth with enlarged leaves and roots, increased plant height, plant biomass, and total grain weight in Arabidopsis. Collectively, these findings suggest that our programmable m6A editing tools can be applied to study the functions of individual m6A modifications in plants, and may also have potential applications for future crop improvement.
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Affiliation(s)
- Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Wenli Zou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Xiangpei Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Hong Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Xiaofang Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- Zhengzhou Research Base, State Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
| | - Guiling Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- College of AgricultureShanxi Agricultural UniversityTaiyuanShanxiChina
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouZhejiangChina
- Yazhouwan National LaboratorySanya CityHainan ProvinceChina
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- Yazhouwan National LaboratorySanya CityHainan ProvinceChina
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25
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Qi J, Xia C, Zhang Y, Ding R, Zhang Y, Cao W, Duan C, Yao Z, Qin H, Ye Y, Qu P, Li Y, Liu E. Impact of high-fat diet on ovarian epigenetics: Insights from altered intestinal butyric acid levels. Heliyon 2024; 10:e33170. [PMID: 39021996 PMCID: PMC11252756 DOI: 10.1016/j.heliyon.2024.e33170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
Objective To investigate the effects of a high-fat diet (HFD) on the gut bacterium Roseburia intestinalis and butyric acid levels, and to assess their impact on ovarian function and epigenetic markers in mice. Methods A total of 20 female ICR mice aged 4 weeks were randomly assigned to two groups and fed either a control diet (CD) or an HFD for 36 weeks. Post-intervention, ileal contents were analyzed for the quantification of butyric acid using ELISA, while feces were obtained for Roseburia intestinalis expression assessment via qPCR. Histological evaluations of intestinal and ovarian tissues included H&E and Alcian Blue-Periodic Acid Schiff (AB-PAS) staining, alongside immunohistochemical analysis for F4/80, and immunofluorescent detection of Occludin, ZO-1, 5 mC, and H3K36me3. Ovarian health was assessed through follicle counts and morphological evaluations. Statistical analyses were performed using GraphPad Prism 8.0, with P < 0.05 considered significant. Results After 36 weeks, the HFD group showed significantly higher body weight compared to the CD group (P < 0.01). The HFD led to a decrease in Roseburia intestinalis and butyric acid levels, a reduction in intestinal goblet cells, and an increase in intestinal inflammation. Histological analyses revealed impaired ovarian follicular development and enhanced inflammation in the HFD mice, with immunofluorescent staining showing downregulation of the ovarian epigenetic markers 5 mC and H3K36me3. Conclusion Our study demonstrates that long-term HFD negatively impacts ovarian function and epigenetic regulation. We found decreased levels of the gut bacterium Roseburia intestinalis and its metabolite, butyric acid, which contribute to these adverse effects. Additionally, the associated intestinal inflammation and compromised mucosal barrier may contribute to these adverse outcomes on female reproductive health.
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Affiliation(s)
- Jia Qi
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
| | - Congcong Xia
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
| | - Yulin Zhang
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
| | - Ruike Ding
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
| | - Yanru Zhang
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
| | - Wenbin Cao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
| | - Chenjing Duan
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
| | - Zijing Yao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
| | - Hongyu Qin
- Central Laboratory, The First Affiliated Hospital of Xi'an Medical University, Xi'an, China
| | - Yun Ye
- Central Laboratory, The First Affiliated Hospital of Xi'an Medical University, Xi'an, China
| | - Pengxiang Qu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
| | - Yandong Li
- Xi'an International Medical Center Hospital, Xi'an, China
| | - Enqi Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, China
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26
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Li Y, Jin H, Li Q, Shi L, Mao Y, Zhao L. The role of RNA methylation in tumor immunity and its potential in immunotherapy. Mol Cancer 2024; 23:130. [PMID: 38902779 PMCID: PMC11188252 DOI: 10.1186/s12943-024-02041-8] [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: 12/24/2023] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
RNA methylation, a prevalent post-transcriptional modification, has garnered considerable attention in research circles. It exerts regulatory control over diverse biological functions by modulating RNA splicing, translation, transport, and stability. Notably, studies have illuminated the substantial impact of RNA methylation on tumor immunity. The primary types of RNA methylation encompass N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N7-methylguanosine (m7G), and 3-methylcytidine (m3C). Compelling evidence underscores the involvement of RNA methylation in regulating the tumor microenvironment (TME). By affecting RNA translation and stability through the "writers", "erasers" and "readers", RNA methylation exerts influence over the dysregulation of immune cells and immune factors. Consequently, RNA methylation plays a pivotal role in modulating tumor immunity and mediating various biological behaviors, encompassing proliferation, invasion, metastasis, etc. In this review, we discussed the mechanisms and functions of several RNA methylations, providing a comprehensive overview of their biological roles and underlying mechanisms within the tumor microenvironment and among immunocytes. By exploring how these RNA modifications mediate tumor immune evasion, we also examine their potential applications in immunotherapy. This review aims to provide novel insights and strategies for identifying novel targets in RNA methylation and advancing cancer immunotherapy efficacy.
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Affiliation(s)
- Yan Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haoer Jin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Qingling Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Liangrong Shi
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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27
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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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Wang J, Wang S, Yang H, Wang R, Shi K, Liu Y, Dou L, Yu H. Methyltransferase like-14 suppresses growth and metastasis of non-small-cell lung cancer by decreasing LINC02747. Cancer Sci 2024. [PMID: 38888105 DOI: 10.1111/cas.16254] [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: 02/29/2024] [Revised: 05/29/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
Multiple epigenetic regulatory mechanisms exert critical roles in tumor development, and understanding the interactions and impact of diverse epigenetic modifications on gene expression in cancer is crucial for the development of precision medicine. We found that methyltransferase-like 14 (METTL14) was significantly downregulated in non-small-cell lung cancer (NSCLC) tissues. Functional experiments demonstrated that overexpression of METTL14 inhibited the proliferation and migration of NSCLC cells both in vivo and in vitro, and the colorimetric m6A quantification assay also showed that knockdown of METTL14 notably reduced global m6A modification levels in NSCLC cells. By using the methylated-RNA immunoprecipitation-qPCR and dual-luciferase reporter assays, we verified that long noncoding RNA LINC02747 was a target of METTL14 and was regulated by METTL14-mediated m6A modification, and silencing LINC02747 inhibited the malignant progression of NSCLC by modulating the PI3K/Akt and CDK4/Cyclin D1 signaling pathway. Further studies revealed that overexpression of METTL14 promoted m6A methylation and accelerated the decay of LINC02747 mRNA via increased recognition of the "GAACU" binding site by YTHDC2. Additionally, histone demethylase lysine-specific histone demethylase 5B (KDM5B) mediated the demethylation of histone H3 lysine 4 tri-methylation (H3K4me3) in the METTL14 promoter region and repressed its transcription. In summary, KDM5B downregulated METTL14 expression at the transcriptional level in a H3K4me3-dependent manner, while METTL14 modulated LINC02747 expression via m6A modification. Our results demonstrate a synergy of multiple mechanisms in regulating the malignant phenotype of NSCLC, revealing the complex regulation involved in the occurrence and development of cancer.
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Affiliation(s)
- Jiemin Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Shu Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Haopeng Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Ruixuan Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Kesong Shi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Yueshi Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Le Dou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China
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29
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Liu D, Zhou X, Zhao J. Prognostic signature and immune efficacy of m 1A-, m 5C-, m 6A-, m 7G-, and DNA methylation-related regulators in hepatocellular carcinoma. J Cancer 2024; 15:4287-4300. [PMID: 38947378 PMCID: PMC11212094 DOI: 10.7150/jca.95730] [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: 02/27/2024] [Accepted: 05/19/2024] [Indexed: 07/02/2024] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is the main type of primary liver cancer, and its related death ranks third worldwide. The curative methods and progress prediction markers of HCC are not sufficient enough. Nevertheless, little progress has been made in the signature of m1A-, m5C-, m6A-, m7G-, and DNA methylation of HCC. Results: We calibrated a risk gene signature model that can be used to categorize HCC patients based on univariate, multivariate, and LASSO Cox regression analysis. This gene signature classified the patients into high- and low-risk subgroups. Patients in the high-risk group showed significantly reduced overall survival (OS) compared with patients in the low-risk group. The gene set variation analysis (GSVA), immune infiltration, and immunotherapy response were analyzed. The results demonstrated that an immunosuppressive environment was exited and the high-risk group had higher sensitivity to 5-fluorouracil, cisplatin, sorafenib, tamoxifen, and epirubicin. These results indicated personalized therapy should be taken into consideration. Conclusions: Our findings enriched our understanding of the molecular heterogeneity, tumor microenvironment (TME), and drug susceptibility of HCC. m1A-, m5C-, m6A-, m7G-, and DNA methylation-related regulators may be promising biomarkers for future research.
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Affiliation(s)
- Donghong Liu
- Department of Special Medical Care, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, 200438, China
| | - Xinyu Zhou
- Department of Epidemiology, Naval Medical University, Shanghai, 200433, China
| | - Jun Zhao
- Department of Special Medical Care, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, 200438, China
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30
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Khan FA, Nsengimana B, Awan UA, Ji XY, Ji S, Dong J. Regulatory roles of N6-methyladenosine (m 6A) methylation in RNA processing and non-communicable diseases. Cancer Gene Ther 2024:10.1038/s41417-024-00789-1. [PMID: 38839892 DOI: 10.1038/s41417-024-00789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
Post-transcriptional RNA modification is an emerging epigenetic control mechanism in cells that is important in many different cellular and organismal processes. N6-methyladenosine (m6A) is one of the most prevalent, prolific, and ubiquitous internal transcriptional alterations in eukaryotic mRNAs, making it an important topic in the field of Epigenetics. m6A methylation acts as a dynamical regulatory process that regulates the activity of genes and participates in multiple physiological processes, by supporting multiple aspects of essential mRNA metabolic processes, including pre-mRNA splicing, nuclear export, translation, miRNA synthesis, and stability. Extensive research has linked aberrations in m6A modification and m6A-associated proteins to a wide range of human diseases. However, the impact of m6A on mRNA metabolism and its pathological connection between m6A and other non-communicable diseases, including cardiovascular disease, neurodegenerative disorders, liver diseases, and cancer remains in fragmentation. Here, we review the existing understanding of the overall role of mechanisms by which m6A exerts its activities and address new discoveries that highlight m6A's diverse involvement in gene expression regulation. We discuss m6A deposition on mRNA and its consequences on degradation, translation, and transcription, as well as m6A methylation of non-coding chromosomal-associated RNA species. This study could give new information about the molecular process, early detection, tailored treatment, and predictive evaluation of human non-communicable diseases like cancer. We also explore more about new data that suggests targeting m6A regulators in diseases may have therapeutic advantages.
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Affiliation(s)
- Faiz Ali Khan
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan.
| | - Bernard Nsengimana
- Department of Hepatobiliary Surgery, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Usman Ayub Awan
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xin-Ying Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
| | - Shaoping Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Jingcheng Dong
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
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31
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Xu W, Shen H. m 6A regulates heterochromatin in mammalian embryonic stem cells. Curr Opin Genet Dev 2024; 86:102196. [PMID: 38669774 DOI: 10.1016/j.gde.2024.102196] [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: 01/14/2024] [Revised: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
As the most well-studied modification in mRNA, m6A has been shown to regulate multiple biological processes, including RNA degradation, processing, and translation. Recent studies showed that m6A modification is enriched in chromatin-associated RNAs and nascent RNAs, suggesting m6A might play regulatory roles in chromatin contexts. Indeed, in the past several years, a number of studies have clarified how m6A and its modulators regulate different types of chromatin states. Specifically, in the past 2-3 years, several studies discovered the roles of m6A and/or its modulators in regulating constitutive and facultative heterochromatin, shedding interesting lights on RNA-dependent heterochromatin formation in mammalian cells. This review will summarize and discuss the mechanisms underlying m6A's regulation in different types of heterochromatin, with a specific emphasis on the regulation in mammalian embryonic stem cells, which exhibit distinct features of multiple heterochromatin marks.
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Affiliation(s)
- Wenqi Xu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Hongjie Shen
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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32
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Bussey-Sutton CR, Ward A, Fox JA, Turner AMW, Peterson JJ, Emery A, Longoria AR, Gomez-Martinez I, Jones C, Hepperla A, Margolis DM, Strahl BD, Browne EP. The histone methyltransferase SETD2 regulates HIV expression and latency. PLoS Pathog 2024; 20:e1012281. [PMID: 38848441 PMCID: PMC11189200 DOI: 10.1371/journal.ppat.1012281] [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: 01/05/2024] [Revised: 06/20/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the mechanisms that drive HIV expression and latency is a key goal for achieving an HIV cure. Here we investigate the role of the SETD2 histone methyltransferase, which deposits H3K36 trimethylation (H3K36me3), in HIV infection. We show that prevention of H3K36me3 by a potent and selective inhibitor of SETD2 (EPZ-719) leads to reduced post-integration viral gene expression and accelerated emergence of latently infected cells. CRISPR/Cas9-mediated knockout of SETD2 in primary CD4 T cells confirmed the role of SETD2 in HIV expression. Transcriptomic profiling of EPZ-719-exposed HIV-infected cells identified numerous pathways impacted by EPZ-719. Notably, depletion of H3K36me3 prior to infection did not prevent HIV integration but resulted in a shift of integration sites from highly transcribed genes to quiescent chromatin regions and to polycomb repressed regions. We also observed that SETD2 inhibition did not apparently affect HIV RNA levels, indicating a post-transcriptional mechanism affecting HIV expression. Viral RNA splicing was modestly reduced in the presence of EPZ-719. Intriguingly, EPZ-719 exposure enhanced responsiveness of latent HIV to the HDAC inhibitor vorinostat, suggesting that H3K36me3 can contribute to a repressive chromatin state at the HIV locus. These results identify SETD2 and H3K36me3 as novel regulators of HIV integration, expression and latency.
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Affiliation(s)
- Cameron R. Bussey-Sutton
- Department of Biochemistry, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Airlie Ward
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joshua A. Fox
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Anne-Marie W. Turner
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jackson J. Peterson
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ann Emery
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Arturo R. Longoria
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ismael Gomez-Martinez
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin Jones
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Austin Hepperla
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David M. Margolis
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Brian D. Strahl
- Department of Biochemistry, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Edward P. Browne
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
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Zhao Q, Yang S, Hao S, Chen Z, Tang L, Wu Z, Wu J, Xu M, Ma Z, Zhou L, Xu J, Qin Q. Identification of transcriptionally-active human papillomavirus integrants through nanopore sequencing reveals viable targets for gene therapy against cervical cancer. J Med Virol 2024; 96:e29769. [PMID: 38932482 DOI: 10.1002/jmv.29769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Integration of the human papillomavirus (HPV) genome into the cellular genome is a key event that leads to constitutive expression of viral oncoprotein E6/E7 and drives the progression of cervical cancer. However, HPV integration patterns differ on a case-by-case basis among related malignancies. Next-generation sequencing technologies still face challenges for interrogating HPV integration sites. In this study, utilizing Nanopore long-read sequencing, we identified 452 and 108 potential integration sites from the cervical cancer cell lines (CaSki and HeLa) and five tissue samples, respectively. Based on long Nanopore chimeric reads, we were able to analyze the methylation status of the HPV long control region (LCR), which controls oncogene E6/E7 expression, and to identify transcriptionally-active integrants among the numerous integrants. As a proof of concept, we identified an active HPV integrant in between RUNX2 and CLIC5 on chromosome 6 in the CaSki cell line, which was supported by ATAC-seq, H3K27Ac ChIP-seq, and RNA-seq analysis. Knockout of the active HPV integrant, by the CRISPR/Cas9 system, dramatically crippled cell proliferation and induced cell senescence. In conclusion, identifying transcriptionally-active HPV integrants with Nanopore sequencing can provide viable targets for gene therapy against HPV-associated cancers.
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Affiliation(s)
- Qianqian Zhao
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College, Shantou, China
| | - Shuaibing Yang
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Shijia Hao
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Zejia Chen
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Lihua Tang
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Zhaoting Wu
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jiaxin Wu
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Mingqian Xu
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Zebiao Ma
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Li Zhou
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jianzhen Xu
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College, Shantou, China
| | - Qingsong Qin
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
- International Science and Technology Collaboration Center for Emerging Infectious Diseases, Shantou University Medical College, Shantou, China
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Li X, Uslu VV, Chen Y, Han X, Berr A, Zhang W, Dong Y. Specific chromatin states and m6A modifications are associated with mRNA mobility in planta. HORTICULTURE RESEARCH 2024; 11:uhae101. [PMID: 38863994 PMCID: PMC11165156 DOI: 10.1093/hr/uhae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 06/13/2024]
Affiliation(s)
- Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Veli Vural Uslu
- RLP AgroScience GmbH, Neustadt an der Weinstraße 67435, Germany
- MAPS, Center for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Ying Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Xiao Han
- College of Biology Science and Engineering, Fuzhou University, Fuzhou, China
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Yihan Dong
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
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35
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Wang Y, Huang H, Chen J, Weng H. Crosstalk between histone/DNA modifications and RNA N 6-methyladenosine modification. Curr Opin Genet Dev 2024; 86:102205. [PMID: 38776766 DOI: 10.1016/j.gde.2024.102205] [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: 12/28/2023] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal RNA modification in eukaryotic messenger RNAs (mRNAs), regulating gene expression at the transcription and post-transcription levels. Complex interplay between m6A and other well-studied epigenetic modifications, including histone modifications and DNA modification, has been extensively reported in recent years. The crosstalk between RNA m6A modification and histone/DNA modifications plays a critical role in establishing the chromatin state for the precise and specific fine-tuning of gene expression and undoubtedly has profound impacts on both physiological and pathological processes. In this review, we discuss the crosstalk between RNA m6A modification and histone/DNA modifications, emphasizing their sophisticated communications and the mechanisms underlying to gain a comprehensive view of the biological relevance of m6A-based epigenetic network.
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Affiliation(s)
- Yushuai Wang
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Gehr Family Center for Leukemia Research & City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA.
| | - Hengyou Weng
- Guangzhou National Laboratory, Guangzhou 510005, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China; The First Affiliated Hospital, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou 510005, China.
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Liu S, Liu M, Li Y, Song Q. N6-methyladenosine-dependent signaling in colorectal cancer: Functions and clinical potential. Crit Rev Oncol Hematol 2024; 198:104360. [PMID: 38615872 DOI: 10.1016/j.critrevonc.2024.104360] [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: 10/30/2023] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024] Open
Abstract
Colorectal cancer (CRC) ranks as the third most prevalent malignancy worldwide. Despite the gradual expansion of therapeutic options for CRC, its clinical management remains a formidable challenge. And, because of the current dearth of technical means for early CRC screening, most patients are diagnosed at an advanced stage. Therefore, it is imperative to develop novel diagnostic and therapeutic tools for this disease. N6-methyladenosine (m6A), the predominant RNA modification in eukaryotes, can be recognized by m6A-specific methylated reading proteins to modulate gene expression. Studies have revealed that CRC disrupts m6A homeostasis through various mechanisms, thereby sustaining aberrant signal transduction and promoting its own progression. Consequently, m6A-based diagnostic and therapeutic strategies have garnered widespread attention. Although utilizing m6A as a biomarker and drug target has demonstrated promising feasibility, existing observations primarily stem from preclinical models; henceforth necessitating further investigation and resolution of numerous outstanding issues.
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Affiliation(s)
- Shaojun Liu
- Department of Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese medicine, Suzhou, Jiangsu, China
| | - Min Liu
- Department of Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese medicine, Suzhou, Jiangsu, China
| | - Yuxuan Li
- Department of Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese medicine, Suzhou, Jiangsu, China
| | - Qing Song
- Department of Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese medicine, Suzhou, Jiangsu, China.
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37
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Pinello N, Song R, Lee Q, Calonne E, Duan KL, Wong E, Tieng J, Mehravar M, Rong B, Lan F, Roediger B, Ma CJ, Yuan BF, Rasko JEJ, Larance M, Ye D, Fuks F, Wong JJL. Dynamic changes in RNA m 6A and 5 hmC influence gene expression programs during macrophage differentiation and polarisation. Cell Mol Life Sci 2024; 81:229. [PMID: 38780787 PMCID: PMC11116364 DOI: 10.1007/s00018-024-05261-9] [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: 02/06/2024] [Revised: 04/27/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications regulate the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear. While m6A has been widely studied, other RNA modifications, including 5 hmC, remain poorly characterised. We profiled m6A and 5 hmC epitranscriptomes, transcriptomes, translatomes and proteomes of monocytes and macrophages at rest and pro- and anti-inflammatory states. Transcriptome-wide mapping of m6A and 5 hmC reveals enrichment of m6A and/or 5 hmC on specific categories of transcripts essential for macrophage differentiation. Our analyses indicate that m6A and 5 hmC modifications are present in transcripts with critical functions in pro- and anti-inflammatory macrophages. Notably, we also discover the co-occurrence of m6A and 5 hmC on alternatively-spliced isoforms and/or opposing ends of the untranslated regions (UTR) of mRNAs with key roles in macrophage biology. In specific examples, RNA 5 hmC controls the decay of transcripts independently of m6A. This study provides (i) a comprehensive dataset to interrogate the role of RNA modifications in a plastic system (ii) a resource for exploring different layers of gene expression regulation in the context of human monocyte-to-macrophage differentiation and polarisation, (iii) new insights into RNA modifications as central regulators of effector cells in innate immunity.
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Affiliation(s)
- Natalia Pinello
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
| | - Renhua Song
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Quintin Lee
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Kun-Long Duan
- The Molecular and Cell Biology Lab, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Emilie Wong
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Jessica Tieng
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Majid Mehravar
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Bowen Rong
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ben Roediger
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Skin Inflammation Group, Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Autoimmunity, Transplantation and Inflammation (ATI) Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Cheng-Jie Ma
- School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Bi-Feng Yuan
- School of Public Health, Wuhan University, Wuhan, 430071, China
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Gene and Stem Cell Therapy Program, Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, NSW, Australia
| | - Mark Larance
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Charles Perkins Centre, School of Medical Sciences, University of Sydney, Sydney, 2006, Australia
| | - Dan Ye
- The Molecular and Cell Biology Lab, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Justin J-L Wong
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.
- Charles Perkins Centre, School of Medical Sciences, University of Sydney, Sydney, 2006, Australia.
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Feng G, Wu Y, Hu Y, Shuai W, Yang X, Li Y, Ouyang L, Wang G. Small molecule inhibitors targeting m 6A regulators. J Hematol Oncol 2024; 17:30. [PMID: 38711100 PMCID: PMC11075261 DOI: 10.1186/s13045-024-01546-5] [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: 02/07/2024] [Accepted: 04/23/2024] [Indexed: 05/08/2024] Open
Abstract
As the most common form of epigenetic regulation by RNA, N6 methyladenosine (m6A) modification is closely involved in physiological processes, such as growth and development, stem cell renewal and differentiation, and DNA damage response. Meanwhile, its aberrant expression in cancer tissues promotes the development of malignant tumors, as well as plays important roles in proliferation, metastasis, drug resistance, immunity and prognosis. This close association between m6A and cancers has garnered substantial attention in recent years. An increasing number of small molecules have emerged as potential agents to target m6A regulators for cancer treatment. These molecules target the epigenetic level, enabling precise intervention in RNA modifications and efficiently disrupting the survival mechanisms of tumor cells, thus paving the way for novel approaches in cancer treatment. However, there is currently a lack of a comprehensive review on small molecules targeting m6A regulators for anti-tumor. Here, we have comprehensively summarized the classification and functions of m6A regulators, elucidating their interactions with the proliferation, metastasis, drug resistance, and immune responses in common cancers. Furthermore, we have provided a comprehensive overview on the development, mode of action, pharmacology and structure-activity relationships of small molecules targeting m6A regulators. Our aim is to offer insights for subsequent drug design and optimization, while also providing an outlook on future prospects for small molecule development targeting m6A.
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Affiliation(s)
- Guotai Feng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yongya Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yuan Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, China
| | - Wen Shuai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Xiao Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yong Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Liang Ouyang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
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Hao JD, Liu QL, Liu MX, Yang X, Wang LM, Su SY, Xiao W, Zhang MQ, Zhang YC, Zhang L, Chen YS, Yang YG, Ren J. DDX21 mediates co-transcriptional RNA m 6A modification to promote transcription termination and genome stability. Mol Cell 2024; 84:1711-1726.e11. [PMID: 38569554 DOI: 10.1016/j.molcel.2024.03.006] [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: 06/14/2023] [Revised: 02/09/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
N6-methyladenosine (m6A) is a crucial RNA modification that regulates diverse biological processes in human cells, but its co-transcriptional deposition and functions remain poorly understood. Here, we identified the RNA helicase DDX21 with a previously unrecognized role in directing m6A modification on nascent RNA for co-transcriptional regulation. DDX21 interacts with METTL3 for co-recruitment to chromatin through its recognition of R-loops, which can be formed co-transcriptionally as nascent transcripts hybridize onto the template DNA strand. Moreover, DDX21's helicase activity is needed for METTL3-mediated m6A deposition onto nascent RNA following recruitment. At transcription termination regions, this nexus of actions promotes XRN2-mediated termination of RNAPII transcription. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination that can induce DNA damage. Therefore, we propose that the R-loop-DDX21-METTL3 nexus forges the missing link for co-transcriptional modification of m6A, coordinating transcription termination and genome stability.
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Affiliation(s)
- Jin-Dong Hao
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian-Lan Liu
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Meng-Xia Liu
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xing Yang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liu-Ming Wang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Yi Su
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Xiao
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Qi Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Chang Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lan Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yu-Sheng Chen
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun-Gui Yang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jie Ren
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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40
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Hong Y, Bie L, Zhang T, Yan X, Jin G, Chen Z, Wang Y, Li X, Pei G, Zhang Y, Hong Y, Gong L, Li P, Xie W, Zhu Y, Shen X, Liu N. SAFB restricts contact domain boundaries associated with L1 chimeric transcription. Mol Cell 2024; 84:1637-1650.e10. [PMID: 38604171 DOI: 10.1016/j.molcel.2024.03.021] [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: 10/31/2023] [Revised: 02/05/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024]
Abstract
Long interspersed element-1 (LINE-1 or L1) comprises 17% of the human genome, continuously generates genetic variations, and causes disease in certain cases. However, the regulation and function of L1 remain poorly understood. Here, we uncover that L1 can enrich RNA polymerase IIs (RNA Pol IIs), express L1 chimeric transcripts, and create contact domain boundaries in human cells. This impact of L1 is restricted by a nuclear matrix protein scaffold attachment factor B (SAFB) that recognizes transcriptionally active L1s by binding L1 transcripts to inhibit RNA Pol II enrichment. Acute inhibition of RNA Pol II transcription abolishes the domain boundaries associated with L1 chimeric transcripts, indicating a transcription-dependent mechanism. Deleting L1 impairs domain boundary formation, and L1 insertions during evolution have introduced species-specific domain boundaries. Our data show that L1 can create RNA Pol II-enriched regions that alter genome organization and that SAFB regulates L1 and RNA Pol II activity to preserve gene regulation.
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Affiliation(s)
- Yaqiang Hong
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Luyao Bie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tao Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohan Yan
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangpu Jin
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo Chen
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yang Wang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiufeng Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yongyan Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Liang Gong
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Pilong Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yanfen Zhu
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu 322000, China
| | - Xiaohua Shen
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Nian Liu
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Jang J, Accornero F, Li D. Epigenetic determinants and non-myocardial signaling pathways contributing to heart growth and regeneration. Pharmacol Ther 2024; 257:108638. [PMID: 38548089 DOI: 10.1016/j.pharmthera.2024.108638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Congenital heart disease is the most common birth defect worldwide. Defective cardiac myogenesis is either a major presentation or associated with many types of congenital heart disease. Non-myocardial tissues, including endocardium and epicardium, function as a supporting hub for myocardial growth and maturation during heart development. Recent research findings suggest an emerging role of epigenetics in nonmyocytes supporting myocardial development. Understanding how growth signaling pathways in non-myocardial tissues are regulated by epigenetic factors will likely identify new disease mechanisms for congenital heart diseases and shed lights for novel therapeutic strategies for heart regeneration.
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Affiliation(s)
- Jihyun Jang
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH 43215, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA.
| | - Federica Accornero
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Deqiang Li
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH 43215, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA.
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42
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Zhang M, Zhai Y, An X, Li Q, Zhang D, Zhou Y, Zhang S, Dai X, Li Z. DNA methylation regulates RNA m 6A modification through transcription factor SP1 during the development of porcine somatic cell nuclear transfer embryos. Cell Prolif 2024; 57:e13581. [PMID: 38095020 PMCID: PMC11056710 DOI: 10.1111/cpr.13581] [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: 10/05/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Epigenetic modifications play critical roles during somatic cell nuclear transfer (SCNT) embryo development. Whether RNA N6-methyladenosine (m6A) affects the developmental competency of SCNT embryos remains unclear. Here, we showed that porcine bone marrow mesenchymal stem cells (pBMSCs) presented higher RNA m6A levels than those of porcine embryonic fibroblasts (pEFs). SCNT embryos derived from pBMSCs had higher RNA m6A levels, cleavage, and blastocyst rates than those from pEFs. Compared with pEFs, the promoter region of METTL14 presented a hypomethylation status in pBMSCs. Mechanistically, DNA methylation regulated METTL14 expression by affecting the accessibility of transcription factor SP1 binding, highlighting the role of the DNA methylation/SP1/METTL14 pathway in donor cells. Inhibiting the DNA methylation level in donor cells increased the RNA m6A level and improved the development efficiency of SCNT embryos. Overexpression of METTL14 significantly increased the RNA m6A level in donor cells and the development efficiency of SCNT embryos, whereas knockdown of METTL14 suggested the opposite result. Moreover, we revealed that RNA m6A-regulated TOP2B mRNA stability, translation level, and DNA damage during SCNT embryo development. Collectively, our results highlight the crosstalk between RNA m6A and DNA methylation, and the crucial role of RNA m6A during nuclear reprogramming in SCNT embryo development.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Yanhui Zhai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Daoyu Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Yongfeng Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Xiangpeng Dai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
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43
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Wang Z, Zhang YX, Shi JZ, Yan Y, Zhao LL, Kou JJ, He YY, Xie XM, Zhang SJ, Pang XB. RNA m6A methylation and regulatory proteins in pulmonary arterial hypertension. Hypertens Res 2024; 47:1273-1287. [PMID: 38438725 DOI: 10.1038/s41440-024-01607-9] [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: 07/17/2023] [Revised: 11/12/2023] [Accepted: 01/27/2024] [Indexed: 03/06/2024]
Abstract
m6A (N6‑methyladenosine) is the most common and abundant apparent modification in mRNA of eukaryotes. The modification of m6A is regulated dynamically and reversibly by methyltransferase (writer), demethylase (eraser), and binding protein (reader). It plays a significant role in various processes of mRNA metabolism, including regulation of transcription, maturation, translation, degradation, and stability. Pulmonary arterial hypertension (PAH) is a malignant cardiopulmonary vascular disease characterized by abnormal proliferation of pulmonary artery smooth muscle cells. Despite the existence of several effective and targeted therapies, there is currently no cure for PAH and the prognosis remains poor. Recent studies have highlighted the crucial role of m6A modification in cardiovascular diseases. Investigating the role of RNA m6A methylation in PAH could provide valuable insights for drug development. This review aims to explore the mechanism and function of m6A in the pathogenesis of PAH and discuss the potential targeting of RNA m6A methylation modification as a treatment for PAH.
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Affiliation(s)
- Zhe Wang
- School of Pharmacy, Henan University, Henan, China
| | - Yi-Xuan Zhang
- Department of Anesthesiology, Huaihe Hospital of Henan University, Henan, China
| | - Jun-Zhuo Shi
- School of Pharmacy, Henan University, Henan, China
| | - Yi Yan
- Heart Center and Shanghai Institute of Pediatric Congenital Heart Disease, Shanghai Children's Medical Center, National Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu-Ling Zhao
- School of Pharmacy, Henan University, Henan, China
| | - Jie-Jian Kou
- Department of Pharmacy, Huaihe Hospital of Henan University, Henan, China
| | - Yang-Yang He
- School of Pharmacy, Henan University, Henan, China
| | - Xin-Mei Xie
- School of Pharmacy, Henan University, Henan, China.
| | - Si-Jin Zhang
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
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Baek A, Lee GE, Golconda S, Rayhan A, Manganaris AA, Chen S, Tirumuru N, Yu H, Kim S, Kimmel C, Zablocki O, Sullivan MB, Addepalli B, Wu L, Kim S. Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m 6As. Nat Microbiol 2024; 9:1340-1355. [PMID: 38605174 PMCID: PMC11087264 DOI: 10.1038/s41564-024-01638-5] [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: 03/10/2023] [Accepted: 02/15/2024] [Indexed: 04/13/2024]
Abstract
Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N6-methyladenosine (m6A) modifications near the 3' end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m6As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m6A ensembles, and maintaining multiple of these m6As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.
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Affiliation(s)
- Alice Baek
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Ga-Eun Lee
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Sarah Golconda
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Asif Rayhan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Anastasios A Manganaris
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
- Department of Computer Science and Engineering, Ohio State University, Columbus, OH, USA
| | - Shuliang Chen
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Nagaraja Tirumuru
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Hannah Yu
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Shihyoung Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Christopher Kimmel
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Matthew B Sullivan
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sanggu Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA.
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA.
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA.
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, Ohio State University, Columbus, OH, USA.
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45
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Zhuang S, Yang Z, Cui Z, Zhang Y, Che F. Epigenetic alterations and advancement of lymphoma treatment. Ann Hematol 2024; 103:1435-1454. [PMID: 37581713 DOI: 10.1007/s00277-023-05395-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/29/2023] [Indexed: 08/16/2023]
Abstract
Lymphomas, complex and heterogeneous malignant tumors, originate from the lymphopoietic system. These tumors are notorious for their high recurrence rates and resistance to treatment, which leads to poor prognoses. As ongoing research has shown, epigenetic modifications like DNA methylation, histone modifications, non-coding RNA regulation, and RNA modifications play crucial roles in lymphoma pathogenesis. Epigenetic modification-targeting drugs have exhibited therapeutic efficacy and tolerability in both monotherapy and combination lymphoma therapy. This review discusses pathogenic mechanisms and potential epigenetic therapeutic targets in common lymphomas, offering new avenues for lymphoma diagnosis and treatment. We also discuss the shortcomings of current lymphoma treatments, while suggesting potential areas for future research, in order to improve the prediction and prognosis of lymphoma.
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Affiliation(s)
- Shuhui Zhuang
- Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China
| | - Zhaobo Yang
- Spine Surgery, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China
| | - Zhuangzhuang Cui
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China
| | - Yuanyuan Zhang
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China.
- Department of Hematology, Shandong Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, People's Republic of China.
| | - Fengyuan Che
- Department of Neurology, Central Laboratory and Key Laboratory of Neurophysiology, Linyi People's Hospital, Shandong University, Linyi, 276000, China.
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46
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Wei G. RNA m6A modification, signals for degradation or stabilisation? Biochem Soc Trans 2024; 52:707-717. [PMID: 38629637 PMCID: PMC11088905 DOI: 10.1042/bst20230574] [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: 12/01/2023] [Revised: 03/24/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The RNA modification N6-methyladenosine (m6A) is conserved across eukaryotes, and profoundly influences RNA metabolism, including regulating RNA stability. METTL3 and METTL14, together with several accessory components, form a 'writer' complex catalysing m6A modification. Conversely, FTO and ALKBH5 function as demethylases, rendering m6A dynamic. Key to understanding the functional significance of m6A is its 'reader' proteins, exemplified by YTH-domain-containing proteins (YTHDFs) canonical reader and insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) non-canonical reader. These proteins play a crucial role in determining RNA stability: YTHDFs mainly promote mRNA degradation through different cytoplasmic pathways, whereas IGF2BPs function to maintain mRNA stability. Additionally, YTHDC1 functions within the nucleus to degrade or protect certain m6A-containing RNAs, and other non-canonical readers also contribute to RNA stability regulation. Notably, m6A regulates retrotransposon LINE1 RNA stability and/or transcription via multiple mechanisms. However, conflicting observations underscore the complexities underlying m6A's regulation of RNA stability depending upon the RNA sequence/structure context, developmental stage, and/or cellular environment. Understanding the interplay between m6A and other RNA regulatory elements is pivotal in deciphering the multifaceted roles m6A plays in RNA stability regulation and broader cellular biology.
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Affiliation(s)
- Guifeng Wei
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
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47
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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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48
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Song P, Cai Z, Jia G. Principles, functions, and biological implications of m 6A in plants. RNA (NEW YORK, N.Y.) 2024; 30:491-499. [PMID: 38531642 PMCID: PMC11019739 DOI: 10.1261/rna.079951.124] [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: 01/14/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Over the past decade, N 6-methyladenosine (m6A) has emerged as a prevalent and dynamically regulated modification across the transcriptome; it has been reversibly installed, removed, and interpreted by specific binding proteins, and has played crucial roles in molecular and biological processes. Within this scope, we consolidate recent advancements of m6A research in plants regarding gene expression regulation, diverse physiologic and pathogenic processes, as well as crop trial implications, to guide discussions on challenges associated with and leveraging epitranscriptome editing for crop improvement.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- PKU-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
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49
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Horner SM, Thompson MG. Challenges to mapping and defining m 6A function in viral RNA. RNA (NEW YORK, N.Y.) 2024; 30:482-490. [PMID: 38531643 PMCID: PMC11019751 DOI: 10.1261/rna.079959.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Viral RNA molecules contain multiple layers of regulatory information. This includes features beyond the primary sequence, such as RNA structures and RNA modifications, including N6-methyladenosine (m6A). Many recent studies have identified the presence and location of m6A in viral RNA and have found diverse regulatory roles for this modification during viral infection. However, to date, viral m6A mapping strategies have limitations that prevent a complete understanding of the function of m6A on individual viral RNA molecules. While m6A sites have been profiled on bulk RNA from many viruses, the resulting m6A maps of viral RNAs described to date present a composite picture of m6A across viral RNA molecules in the infected cell. Thus, for most viruses, it is unknown if unique viral m6A profiles exist throughout infection, nor if they regulate specific viral life cycle stages. Here, we describe several challenges to defining the function of m6A in viral RNA molecules and provide a framework for future studies to help in the understanding of how m6A regulates viral infection.
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Affiliation(s)
- Stacy M Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Matthew G Thompson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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50
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Li X, Cai P, Tang X, Wu Y, Zhang Y, Rong X. Lactylation Modification in Cardiometabolic Disorders: Function and Mechanism. Metabolites 2024; 14:217. [PMID: 38668345 PMCID: PMC11052226 DOI: 10.3390/metabo14040217] [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] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Cardiovascular disease (CVD) is recognized as the primary cause of mortality and morbidity on a global scale, and developing a clear treatment is an important tool for improving it. Cardiometabolic disorder (CMD) is a syndrome resulting from the combination of cardiovascular, endocrine, pro-thrombotic, and inflammatory health hazards. Due to their complex pathological mechanisms, there is a lack of effective diagnostic and treatment methods for cardiac metabolic disorders. Lactylation is a type of post-translational modification (PTM) that plays a regulatory role in various cellular physiological processes by inducing changes in the spatial conformation of proteins. Numerous studies have reported that lactylation modification plays a crucial role in post-translational modifications and is closely related to cardiac metabolic diseases. This article discusses the molecular biology of lactylation modifications and outlines the roles and mechanisms of lactylation modifications in cardiometabolic disorders, offering valuable insights for the diagnosis and treatment of such conditions.
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Affiliation(s)
- Xu Li
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Pingdong Cai
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xinyuan Tang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yingzi Wu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yue Zhang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xianglu Rong
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
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