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Wang Y, Peng L, Wang F. M6A-mediated molecular patterns and tumor microenvironment infiltration characterization in nasopharyngeal carcinoma. Cancer Biol Ther 2024; 25:2333590. [PMID: 38532632 DOI: 10.1080/15384047.2024.2333590] [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: 08/02/2023] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
N6-methyladenosine (m6A) is the most predominant RNA epigenetic regulation in eukaryotic cells. Numerous evidence revealed that m6A modification exerts a crucial role in the regulation of tumor microenvironment (TME) cell infiltration in several tumors. Nevertheless, the potential role and mechanism of m6A modification in nasopharyngeal carcinoma (NPC) remains unknown. mRNA expression data and clinical information from GSE102349, and GSE53819 datasets obtained from Gene Expression Omnibus (GEO) was used for differential gene expression and subsequent analysis. Consensus clustering was used to identify m6A-related molecular patterns of 88 NPC samples based on prognostic m6A regulators using Univariate Cox analysis. The TME cell-infiltrating characteristics of each m6A-related subclass were explored using single-sample gene set enrichment (ssGSEA) algorithm and CIBERSORT algotithm. DEGs between two m6A-related subclasses were screened using edgeR package. The prognostic signature and predicated nomogram were constructed based on the m6A-related DEGs. The cell infiltration and expression of prognostic signature in NPC was determined using immunohistochemistry (IHC) analysis. Chi-square test was used to analysis the significance of difference of the categorical variables. And survival analysis was performed using Kaplan-Meier plots and log-rank tests. The NPC samples were divided into two m6A-related subclasses. The TME cell-infiltrating characteristics analyses indicated that cluster 1 is characterized by immune-related and metabolism pathways activation, better response to anit-PD1 and anti-CTLA4 treatment and chemotherapy. And cluster 2 is characterized by stromal activation, low expression of HLA family and immune checkpoints, and a worse response to anti-PD1 and anti-CTLA4 treatment and chemotherapy. Furthermore, we identified 1558 DEGs between two m6A-related subclasses and constructed prognostic signatures to predicate the progression-free survival (PFS) for NPC patients. Compared to non-tumor samples, REEP2, TMSB15A, DSEL, and ID4 were upregulated in NPC samples. High expression of REEP2 and TMSB15A showed poor survival in NPC patients. The interaction between REEP2, TMSB15A, DSEL, ID4, and m6A regulators was detected. Our finding indicated that m6A modification plays an important role in the regulation of TME heterogeneity and complexity.
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Affiliation(s)
- Yong Wang
- Department of Radiotherapy, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Lisha Peng
- Department of Radiotherapy, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Feng Wang
- Department of Radiotherapy, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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Tan Z, Hei F, Ma K, Lv Z, Zhang H, Sun N, Guo W, Song M. m 6A reader YTHDF2 orchestrates CD8 + T cell infiltration to promote pancreatic cancer progression and predicts clinical outcome. Int Immunopharmacol 2024; 142:113079. [PMID: 39288628 DOI: 10.1016/j.intimp.2024.113079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 08/31/2024] [Accepted: 09/01/2024] [Indexed: 09/19/2024]
Abstract
Pancreatic cancer has emerged as one of the most lethal malignancies, characterized by rising morbidity and mortality rates. Research has demonstrated that N6-methyladenosine (m6A) modification of RNA significantly influences RNA metabolism, and dysregulation of m6A is implicated in various human diseases. A clearer picture of how the divergent m6A methylation patterns affect immunological microenvironment in pancreatic cancer is still unknown. Based on an analysis of RNA-sequencing (RNA-seq) data from the TCGA, GEO, and GTEx databases, we predicted and validated the expression of YTHDF2. Apoptosis and cell cycle analyses of YTHDF2 were conducted using flow cytometry, and a subcutaneous transplantation tumor model was established in BALB/c nude mice. The immune infiltration status and Weighted Gene Co-expression Network Analysis (WGCNA) were employed to evaluate cellular immunity and identify downstream target genes associated with the CD8+ T cell module. Additionally, machine learning-based integrative approaches were utilized to generate a predictive signature. The Western blot technique was employed to quantify YTHDF2 expression levels in PDAC cell lines and tissues. WGCNA and PPI unveiled TFG as the core gene regulation network conducting the function of the CD8+ T cell. Quantitative reverse transcription PCR (qRT-PCR) assays were conducted to confirm the reduction in TFG expression subsequent to YTHDF2 knockdown. Integrative analyses using large-scale genomic data sets were conducted to reveal that YTHDF2 could affect pancreatic cancer cell apoptosis and the cell cycle, promote malignant biologic processes, and gene regulation in immune cells. YTHDF2 potentially modulates crucial molecular subgroups of immune checkpoint molecules in CD8+ T cells, thereby enhancing tumor immunogenicity and promoting anti-tumor immune responses.
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Affiliation(s)
- Zhen Tan
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China; Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Faxian Hei
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Kai Ma
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ziqiang Lv
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Haowen Zhang
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ning Sun
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Weidong Guo
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Mengqi Song
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.
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Zhong Z, Ye Y, Xia L, Na N. Identification of RNA-binding protein genes associated with renal rejection and graft survival. Ren Fail 2024; 46:2360173. [PMID: 38874084 PMCID: PMC11182075 DOI: 10.1080/0886022x.2024.2360173] [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: 12/07/2023] [Accepted: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
Rejection is one of the major factors affecting the long-term prognosis of kidney transplantation, and timely recognition and aggressive treatment of rejection is essential to prevent disease progression. RBPs are proteins that bind to RNA to form ribonucleoprotein complexes, thereby affecting RNA stability, processing, splicing, localization, transport, and translation, which play a key role in post-transcriptional gene regulation. However, their role in renal transplant rejection and long-term graft survival is unclear. The aim of this study was to comprehensively analyze the expression of RPBs in renal rejection and use it to construct a robust prediction strategy for long-term graft survival. The microarray expression profiles used in this study were obtained from GEO database. In this study, a total of eight hub RBPs were identified, all of which were upregulated in renal rejection samples. Based on these RBPs, the renal rejection samples could be categorized into two different clusters (cluster A and cluster B). Inflammatory activation in cluster B and functional enrichment analysis showed a strong association with rejection-related pathways. The diagnostic prediction model had a high diagnostic accuracy for T cell mediated rejection (TCMR) in renal grafts (area under the curve = 0.86). The prognostic prediction model effectively predicts the prognosis and survival of renal grafts (p < .001) and applies to both rejection and non-rejection situations. Finally, we validated the expression of hub genes, and patient prognosis in clinical samples, respectively, and the results were consistent with the above analysis.
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Affiliation(s)
- Zhaozhong Zhong
- Department of Kidney Transplantation, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yongrong Ye
- Department of Kidney Transplantation, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Liubing Xia
- Department of Kidney Transplantation, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ning Na
- Department of Kidney Transplantation, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Zhang Z, Zhang L, Li J, Feng R, Li C, Liu Y, Sun G, Xiao F, Zhang C. Comprehensive analysis of m 6A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing. Comput Struct Biotechnol J 2024; 23:1144-1153. [PMID: 38510975 PMCID: PMC10950754 DOI: 10.1016/j.csbj.2024.02.029] [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: 01/15/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
N6 adenosine methylation (m6A), one of the most prevalent internal modifications on mammalian RNAs, regulates RNA transcription, stabilization, and splicing. Growing evidence has focused on the functional role of m6A regulators on acute myeloid leukemia (AML). However, the global m6A levels after azacytidine (AZA) plus venetoclax (VEN) treatment in AML patients remain unclear. In our present study, bone marrow (BM) sample pairs (including pre-treatment [AML] and post-treatment [complete remission (CR)] samples) were harvested from three AML patients who had achieved CR after AZA plus VEN treatment for Nanopore direct RNA sequencing. Notably, the amount of m6A sites and the m6A levels in CR BMs was significantly lower than those in the AML BMs. Such a significant reduction in the m6A levels was also detected in AZA-treated HL-60 cells. Thirteen genes with decreased m6A and expression levels were identified, among which three genes (HPRT1, SNRPC, and ANP32B) were closely related to the prognosis of AML. Finally, we speculated the mechanism via which m6A modifications affected the mRNA stability of these three genes. In conclusion, we illustrated for the first time the global landscape of m6A levels in AZA plus VEN treated AML (CR) patients and revealed that AZA had a significant demethylation effect at the RNA level in AML patients. In addition, we identified new biomarkers for AZA plus VEN-treated AML via Nanopore sequencing technology in RNA epigenetics.
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Affiliation(s)
- Zaifeng Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology of National Health Commission, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing 100730, China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiangtao Li
- Department of Hematology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ru Feng
- Department of Hematology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Chang Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology of National Health Commission, Beijing, China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology of National Health Commission, Beijing, China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Gaoyuan Sun
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Xiao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology of National Health Commission, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing 100730, China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Chunli Zhang
- Department of Hematology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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Tao X, Kang N, Zheng Z, Zhu Z, Ma J, He W. The regulatory mechanisms of N6-methyladenosine modification in ferroptosis and its implications in disease pathogenesis. Life Sci 2024; 355:123011. [PMID: 39181316 DOI: 10.1016/j.lfs.2024.123011] [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: 05/06/2024] [Revised: 07/30/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
HEADING AIMS Based on the current knowledge of the molecular mechanisms by which m6A influences ferroptosis, our objective is to underscore the intricate and interdependent relationships between m6A and the principal regulatory pathways of ferroptosis, as well as other molecules, emphasizing its relevance to diseases associated with this cell death mode. MATERIALS AND METHODS We conducted a literature search using the keywords "m6A and ferroptosis" across PubMed, Web of Science, and Medline. The search was limited to English-language publications from 2017 to 2024. Retrieved articles were managed using Endnote software. Two authors independently screened the search results and reviewed the full texts of selected articles. KEY FINDINGS Abnormal m6A levels are often identified as critical regulators of ferroptosis. Specifically, "writers", "readers" and "erasers" that dynamically modulate m6A function regulate various pathways in ferroptosis including iron metabolism, lipid metabolism and antioxidant system. Additionally, we provide an overview of the role of m6A-mediated ferroptosis in multiple diseases and summarize the potential applications of m6A-mediated ferroptosis, including its use as a therapeutic target for diseases and as diagnostic as well as prognostic biomarkers. SIGNIFICANCE N6-methyladenosine (m6A) modification, a prevalent RNA modification in eukaryotic cells, is crucial in regulating various aspects of RNA metabolism. Notably, accumulating evidence has implicated m6A modification in ferroptosis, a form of iron-dependent cell death characterized by elevated iron levels and lipid peroxide accumulation. Overall, this review sheds light on the potential diagnostic and therapeutic applications of m6A regulators in addressing conditions associated with ferroptosis.
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Affiliation(s)
- Xiao Tao
- Department of Clinical Medicine, The First School of Clinical Medicine, Anhui Medical University, Hefei, Anhui 230032, PR China
| | - Ningning Kang
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230000, PR China
| | - Zongqin Zheng
- Department of Anesthesiology, The Second School of Clinical Medicine, Anhui Medical University, Hefei, Anhui 230032, PR China
| | - Ziyi Zhu
- Department of Clinical Medicine, The First School of Clinical Medicine, Anhui Medical University, Hefei, Anhui 230032, PR China
| | - Junting Ma
- Department of Immunology and Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, PR China.
| | - Wei He
- Department of Immunology and Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, PR China.
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Xing H, Gu X, Liu Y, Xu L, He Y, Xue C. NSUN2 regulates Wnt signaling pathway depending on the m5C RNA modification to promote the progression of hepatocellular carcinoma. Oncogene 2024:10.1038/s41388-024-03184-0. [PMID: 39375506 DOI: 10.1038/s41388-024-03184-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/26/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024]
Abstract
5-Methylcytosine (m5C) RNA modification is a highly abundant and important epigenetic modification in mammals. As an important RNA m5C methyltransferase, NOP2/Sun-domain family member 2 (NSUN2)-mediated m5C RNA modification plays an important role in the regulation of the biological functions in many cancers. However, little is known about the biological role of NSUN2 in hepatocellular carcinoma (HCC). In this study, we found that the expression of NSUN2 was significantly upregulated in HCC, and the HCC patients with higher expression of NSUN2 had a poorer prognosis than those with lower expression of NSUN2. NSUN2 could affect the tumor immune regulation of HCC in several ways. In vitro and in vivo experiments confirmed that NSUN2 knockdown significantly decreased the abilities of proliferation, colony formation, migration and invasion of HCC cells. The methylated RNA immunoprecipitation-sequencing (MeRIP-seq) showed NSUN2 knockdown significantly affected the abundance, distribution, and composition of m5C RNA modification in HCC cells. Functional enrichment analyses and in vitro experiments suggested that NSUN2 could promote the HCC cells to proliferate, migrate and invade by regulating Wnt signaling pathway. SARS2 were identified via the RNA immunoprecipitation-sequencing (RIP-Seq) and MeRIP-seq as downstream target of NSUN2, which may play an important role in tumor-promoting effect of NSUN2-mediated m5C RNA modification in HCC. In conclusion, NSUN2 promotes HCC progression by regulating Wnt signaling pathway and SARS2 in an m5C-dependent manner.
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Affiliation(s)
- Huiwu Xing
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, China
| | - Yingru Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lixia Xu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Chen Xue
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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7
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Mishra T, Phillips S, Zhao Y, Wilms B, He C, Wu L. Epitranscriptomic m 6A modifications during reactivation of HIV-1 latency in CD4 + T cells. mBio 2024:e0221424. [PMID: 39373537 DOI: 10.1128/mbio.02214-24] [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: 08/23/2024] [Accepted: 09/16/2024] [Indexed: 10/08/2024] Open
Abstract
Despite effective antiretroviral therapy reducing HIV-1 viral loads to undetectable levels, the presence of latently infected CD4+ T cells poses a major barrier to HIV-1 cure. N6-methyladenosine (m6A) modification of viral and cellular RNA has a functional role in regulating HIV-1 infection. m6A modification of HIV-1 RNA can affect its stability, translation, and splicing in cells and suppresses type-I interferon induction in macrophages. However, the function of m6A modification in regulating HIV-1 latency reactivation remains unknown. We used the Jurkat T cell line-derived HIV-1 latency model (J-Lat cells) to investigate changes in m6A levels of cellular RNA in response to latency reversal. We observed a significant increase in m6A levels of total cellular RNA upon reactivation of latent HIV-1 in J-Lat cells. This increase in m6A levels was transient and returned to steady-state levels despite continued high levels of viral gene expression in reactivated cells compared to control cells. Upregulation of m6A levels occurred without significant changes in the protein expression of m6A writers or erasers that add or remove m6A, respectively. Knockdown of m6A writers in J-Lat cells significantly reduced HIV-1 reactivation. Treatment with an m6A writer inhibitor reduced cellular RNA m6A levels, along with a reduction in HIV-1 reactivation. Furthermore, using m6A-specific sequencing, we identified cellular RNAs that are differentially m6A-modified during HIV-1 reactivation in J-Lat cells. Knockdown of identified m6A-modified RNA validates these results with an established primary CD4+ T cell model of HIV-1 latency. These results show the importance of m6A RNA modification in HIV-1 latency reversal. IMPORTANCE RNA m6A modification is important for regulating gene expression and innate immune responses to HIV-1 infection. However, the functional significance of m6A modification during HIV-1 latency reactivation is unknown. To address this important question, in this study, we used established cellular models of HIV-1 latency, m6A-specific sequencing at single-base resolution, and functional assays. We demonstrate that HIV-1 latency reversal leads to increased levels of cellular m6A modification, correlates with cellular m6A levels, and is dependent on the catalytic activity of the m6A methyltransferase enzyme. We also identified cellular genes that are differentially m6A-modified during HIV-1 reactivation, as well as the sites of m6A within HIV-1 RNA. Our novel findings point toward a significant role for m6A modification in HIV-1 latency reversal.
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Affiliation(s)
- Tarun Mishra
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Stacia Phillips
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Yutao Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Bethany Wilms
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
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Zhang RK, Li Y, Sun FL, Zhou ZH, Xie YX, Liu WJ, Wang W, Qiu JG, Jiang BH, Wang L. RNA methyltransferase NSUN2-mediated m5C methylation promotes Cr(VI)-induced malignant transformation and lung cancer by accelerating metabolism reprogramming. ENVIRONMENT INTERNATIONAL 2024; 192:109055. [PMID: 39395236 DOI: 10.1016/j.envint.2024.109055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 10/03/2024] [Accepted: 10/03/2024] [Indexed: 10/14/2024]
Abstract
Hexavalent chromium [Cr(VI)], one common environmental contaminant, has long been recognized as a carcinogen associated with lung cancer, but roles and mechanisms of Cr(VI)-induced epigenetic dysregulations in carcinogenesis remain to be investigated. In this study, we identified that RNA m5C methyltransferase NSUN2 was significantly upregulated in Cr(VI)-transformed cells and lung tissues of Cr(VI)-exposed mice. Inhibition of NSUN2 reduced cell proliferation, migration, colony formation and tube formation abilities. We found NSUN2-mediated m5C modification induced metabolic reprogramming and cell cycle by promoting the mRNA stabilities of ME1, GLUT3 and CDK2. In addition, knockdown of NSUN2 attenuated tumorigenesis and angiogenesis in vivo. RNA m5C reader ALYREF was identified to be involved in NSUN2-mediated m5C modification in Cr (VI)-induced carcinogenesis. Further study showed that EP300 induced NSUN2 upregulation through transcriptional activation by inducing histone modification at H3K27ac site for regulating Cr(VI) carcinogenesis. Our findings demonstrated novel role and mechanism of NSUN2 and epigenetic changes by increasing the RNA m5C modification that are important for Cr (VI)-induced carcinogenesis through NSUN2/ALYREF pathway. NSUN2, ALYREF, ME1, GLUT3 or/and CDK2 may be used as potential new biomarkers or/and therapeutic target(s) in the future.
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Affiliation(s)
- Rui-Ke Zhang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Yan Li
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Fan-Li Sun
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Zhi-Hao Zhou
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Yun-Xia Xie
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Wen-Jing Liu
- The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Wei Wang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Jian-Ge Qiu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Bing-Hua Jiang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China.
| | - Lin Wang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China.
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Cui L, Wu Y, Chen Z, Li B, Cai J, Chang Z, Xiao W, Wang Y, Yang N, Wang Y, Yu Z, Yao L, Ma R, Wang X, Chen Y, Chen Q, Mei H, Lan Z, Yu Y, Chen R, Wu X, Yu Q, Lu J, Yu N, Zhang X, Liu J, Zhang L, Lai Y, Gao S, Gao Y, Guo C, Shi Y. N6-methyladenosine modification-tuned lipid metabolism controls skin immune homeostasis via regulating neutrophil chemotaxis. SCIENCE ADVANCES 2024; 10:eadp5332. [PMID: 39356764 PMCID: PMC11446281 DOI: 10.1126/sciadv.adp5332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 08/27/2024] [Indexed: 10/04/2024]
Abstract
Disrupted N6-methyladenosine (m6A) modification modulates various inflammatory disorders. However, the role of m6A in regulating cutaneous inflammation remains elusive. Here, we reveal that the m6A and its methyltransferase METTL3 are down-regulated in keratinocytes in inflammatory skin diseases. Inducible deletion of Mettl3 in murine keratinocytes results in spontaneous skin inflammation and increases susceptibility to cutaneous inflammation with activation of neutrophil recruitment. Therapeutically, restoration of m6A alleviates the disease phenotypes in mice and suppresses inflammation in human biopsy specimens. We support a model in which m6A modification stabilizes the mRNA of the lipid-metabolizing enzyme ELOVL6 via the m6A reader IGF2BP3, leading to a rewiring of fatty acid metabolism with a reduction in palmitic acid accumulation and, consequently, suppressing neutrophil chemotaxis in cutaneous inflammation. Our findings highlight a previously unrecognized epithelial-intrinsic m6A modification-lipid metabolism pathway that is essential for maintaining epidermal and immune homeostasis and lay the basis for potential therapeutic targeting of m6A modulators to attenuate inflammatory skin diseases.
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Affiliation(s)
- Lian Cui
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - You Wu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Zeyu Chen
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Bingjie Li
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiangluyi Cai
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Zhanhe Chang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Weide Xiao
- 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
| | - Yuanyuan Wang
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Nan Yang
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Yu Wang
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Zengyang Yu
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
- Department of Dermatology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lingling Yao
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Rui Ma
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Xin Wang
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Youdong Chen
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
- Department of Dermatology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qianyu Chen
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Hao Mei
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
- Department of Dermatology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhiyi Lan
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
- Department of Dermatology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yingyuan Yu
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Rongfen Chen
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Xingbiao Wu
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qian Yu
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
- Department of Dermatology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiajing Lu
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Ning Yu
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Xilin Zhang
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Jun Liu
- 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
| | - Lingjuan Zhang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Yuping Lai
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Shaorong Gao
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Yawei Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Chunyuan Guo
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Yuling Shi
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
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10
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Xu Z, Zheng X, Fan J, Jiao Y, Huang S, Xie Y, Xu S, Lu Y, Liu A, Liu R, Yang Y, Luo GZ, Pan T, Wang X. Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing. Cell Rep 2024; 43:114798. [PMID: 39365698 DOI: 10.1016/j.celrep.2024.114798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/10/2024] [Accepted: 09/10/2024] [Indexed: 10/06/2024] Open
Abstract
It has been widely recognized that the microbiota has the capacity to shape host gene expression and physiological functions. However, there remains a paucity of comprehensive study revealing the host transcriptional landscape regulated by the microbiota. Here, we comprehensively examined mRNA landscapes in mouse tissues (brain and cecum) from specific-pathogen-free and germ-free mice using nanopore direct RNA sequencing. Our results show that the microbiome has global influence on a host's RNA modifications (m6A, m5C, Ψ), isoform generation, poly(A) tail length, and transcript abundance in both brain and cecum tissues. Moreover, the microbiome exerts tissue-specific effects on various post-transcriptional regulatory processes. In addition, the microbiome impacts the coordination of multiple RNA modifications in host brain and cecum tissues. In conclusion, we establish the relationship between microbial regulation and gene expression. Our results help the understanding of the mechanisms by which the microbiome reprograms host gene expression.
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Affiliation(s)
- Zihe Xu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaoqi Zheng
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jiajun Fan
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yuting Jiao
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Sihao Huang
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Yingyuan Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shunlan Xu
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yi Lu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Anrui Liu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Runzhou Liu
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Ying Yang
- 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
| | - Guan-Zheng Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaoyun Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Hu S, Tian G, Bai Y, Qu A, He Q, Chen L, Xu P. Alternative splicing dynamically regulates common carp embryogenesis under thermal stress. BMC Genomics 2024; 25:918. [PMID: 39358679 PMCID: PMC11448050 DOI: 10.1186/s12864-024-10838-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 09/26/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Thermal stress is a major environmental factor affecting fish development and survival. Common carp (Cyprinus carpio) are susceptible to heat stress in their embryonic and larval phases, but the thermal stress response of alternative splicing during common carp embryogenesis remains poorly understood. RESULTS Using RNA-seq data from eight developmental stages and four temperatures, we constructed a comprehensive profile of alternative splicing (AS) during the embryogenesis of common carp, and found that AS genes and events are widely distributed among all stages. A total of 5,835 developmental stage-specific AS (SAS) genes, 21,368 temperature-specific differentially expressed genes (TDEGs), and 2,652 temperature-specific differentially AS (TDAS) genes were identified. Hub TDAS genes in each developmental stage, such as taf2, hnrnpa1, and drg2, were identified through protein-protein interaction (PPI) network analysis. The early developmental stages may be more sensitive to temperature, with thermal stress leading to a massive increase in the number of expressed transcripts, TDEGs, and TDAS genes in the morula stage, followed by the gastrula stage. GO and KEGG analyses showed that from the morula stage to the neurula stage, TDAS genes were more involved in intracellular transport, protein modification, and localization processes, while from the optic vesicle stage to one day post-hatching, they participated more in biosynthetic processes. Further subgenomic analysis revealed that the number of AS genes and events in subgenome B was generally higher than that in subgenome A, and the homologous AS genes were significantly enriched in basic life activity pathways, such as mTOR signaling pathway, p53 signaling pathway, and MAPK signaling pathway. Additionally, lncRNAs can play a regulatory role in the response to thermal stress by targeting AS genes such as lmnl3, affecting biological processes such as apoptosis and axon guidance. CONCLUSIONS In short, thermal stress can affect alternative splicing regulation during common carp embryogenesis at multiple levels. Our work complemented some gaps in the study of alternative splicing at both levels of embryogenesis and thermal stress in C. carpio and contributed to the comprehension of environmental adaptation formation in polyploid fishes during embryogenesis.
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Affiliation(s)
- Shuimu Hu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Guopeng Tian
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ang Qu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Qian He
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lin Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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12
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Wang N, Shi B, Ding L, Zhang X, Ma X, Guo S, Qiao X, Wang L, Ma D, Cao J. FMRP protects breast cancer cells from ferroptosis by promoting SLC7A11 alternative splicing through interacting with hnRNPM. Redox Biol 2024; 77:103382. [PMID: 39388855 DOI: 10.1016/j.redox.2024.103382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 09/27/2024] [Accepted: 10/01/2024] [Indexed: 10/12/2024] Open
Abstract
Ferroptosis is a unique modality of regulated cell death that is driven by iron-dependent phospholipid peroxidation. N6-methyladenosine (m6A) RNA modification participates in varieties of cellular processes. However, it remains elusive whether m6A reader Fragile X Mental Retardation Protein (FMRP) are involved in the modulation of ferroptosis in breast cancer (BC). In this study, we found that FMRP expression was elevated and associated with poor prognosis and pathological stage in BC patients. Overexpression of FMRP induced ferroptosis resistance and exerted oncogenic roles by positively regulating a critical ferroptosis defense gene SLC7A11. Mechanistically, upregulated FMRP catalyzes m6A modification of SLC7A11 mRNA and further influences the SLC7A11 translation through METTL3-dependent manner. Further studies revealed that FMRP interacts with splicing factor hnRNPM to recognize the splice site and then modulated the exon skip splicing event of SLC7A11 transcript. Interestingly, SLC7A11-S splicing variant can effectively promote FMRP overexpression-induced ferroptosis resistance in BC cells. Moreover, our clinical data suggested that FMRP/hnRNPM/SLC7A11 expression were significantly increased in the tumor tissues, and this signal axis was important evaluation factors closely related to the worse survival and prognosis of BC patients. Overall, our results uncovered a novel regulatory mechanism by which high FMRP expression protects BC cells from undergoing ferroptosis. Targeting the FMRP-SLC7A11 axis has a dual effect of inhibiting ferroptosis resistance and tumor growth, which could be a promising therapeutic target for treating BC.
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Affiliation(s)
- Nan Wang
- Department of Surgery Laboratory, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, China; Department of Medical Oncology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Bin Shi
- Department of Emergency, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Lu Ding
- Department of Surgery Laboratory, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Xu Zhang
- Department of Surgery Laboratory, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Xiaolan Ma
- Department of Surgery Laboratory, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, China; Department of Medical Oncology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Songlin Guo
- Department of Surgery Laboratory, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Xia Qiao
- Department of Surgery Laboratory, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Libin Wang
- Department of Neurosurgery, Huazhong University of Science and Technology Union Shenzhen Hospital/Shenzhen Nanshan Hospital, Shenzhen, China.
| | - Duan Ma
- Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Jia Cao
- Department of Surgery Laboratory, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, China.
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13
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Dong QQ, Yang Y, Tao H, Lu C, Yang JJ. m6A epitranscriptomic and epigenetic crosstalk in liver fibrosis: Special emphasis on DNA methylation and non-coding RNAs. Cell Signal 2024; 122:111302. [PMID: 39025344 DOI: 10.1016/j.cellsig.2024.111302] [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: 05/30/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
Liver fibrosis is a pathological process caused by a variety of chronic liver diseases. Currently, therapeutic options for liver fibrosis are very limited, highlighting the urgent need to explore new treatment approaches. Epigenetic modifications and epitranscriptomic modifications, as reversible regulatory mechanisms, are involved in the development of liver fibrosis. In recent years, researches in epitranscriptomics and epigenetics have opened new perspectives for understanding the pathogenesis of liver fibrosis. Exploring the epigenetic mechanisms of liver fibrosis may provide valuable insights into the development of new therapies for chronic liver diseases. This review primarily focus on the regulatory mechanisms of N6-methyladenosine (m6A) modification, non-coding RNA, and DNA methylation in organ fibrosis. It discusses the interactions between m6A modification and DNA methylation, as well as between m6A modification and non-coding RNA, providing a reference for understanding the interplay between epitranscriptomics and epigenetics.
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Affiliation(s)
- Qi-Qi Dong
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Yang Yang
- Department of General Surgery, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou 215153, China
| | - Hui Tao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.
| | - Chao Lu
- First Affiliated Hospital, Anhui University of Science & Technology, Huainan 232001, China.
| | - Jing-Jing Yang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.
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14
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Han J, Song Y, Xie J, Tano V, Shen H, Gan WL, Ng L, Ng BYL, Ng VHE, Sui X, Tang SJ, Chen L. Modulation of m 6A RNA modification by DAP3 in cancer cells. Proc Natl Acad Sci U S A 2024; 121:e2404509121. [PMID: 39316047 PMCID: PMC11459197 DOI: 10.1073/pnas.2404509121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 08/23/2024] [Indexed: 09/25/2024] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is a prevalent RNA modification that significantly impacts RNA metabolism and cancer development. Maintaining the global m6A levels in cancer cells relies on RNA accessibility to methyltransferases and the availability of the methyl donor S-adenosylmethionine (SAM). Here, we reveal that death associated protein 3 (DAP3) plays a crucial role in preserving m6A levels through two distinct mechanisms. First, although DAP3 is not a component of the m6A writer complex, it directly binds to m6A target regions, thereby facilitating METTL3 binding. Second, DAP3 promotes MAT2A's last intron splicing, increasing MAT2A protein, cellular SAM, and m6A levels. Silencing DAP3 hinders tumorigenesis, which can be rescued by MAT2A overexpression. This evidence suggests DAP3's role in tumorigenesis, partly through m6A regulation. Our findings unveil DAP3's complex role as an RNA-binding protein and tumor promoter, impacting RNA processing, splicing, and m6A modification in cancer transcriptomes.
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Affiliation(s)
- Jian Han
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Jinghe Xie
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Vincent Tano
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Wei Liang Gan
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Larry Ng
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | | | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Xiaohui Sui
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
- National University of Singapore (NUS) Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117594, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117594, Singapore
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15
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Wu S, Liu K, Cui Y, Zhou B, Zhao H, Xiao X, Zhou Q, Ma D, Li X. N6-methyladenosine dynamics in placental development and trophoblast functions, and its potential role in placental diseases. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167290. [PMID: 38866113 DOI: 10.1016/j.bbadis.2024.167290] [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: 12/20/2023] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant modification controlling RNA metabolism and cellular functions, but its roles in placental development are still poorly understood. Here, we characterized the synchronization of m6A modifications and placental functions by mapping the m6A methylome in human placentas (n = 3, each trimester), revealing that the dynamic patterns of m6A were associated with gene expression homeostasis and different biological pathways in placental development. Then, we generated trophoblast-specific knockout mice of Wtap, a critical component of methyltransferase complex, and demonstrated that Wtap was essential for trophoblast proliferation, placentation and perinatal growth. Further in vitro experiments which includes cell viability assays and series molecular binding assays demonstrated that WTAP-m6A-IGF2BP3 axis regulated the RNA stability and translation of Anillin (ANLN) and VEGFA, promoting trophoblast proliferation and secretion. Dysregulation of this regulatory axis was observed in placentas from pregnancies with fetal growth restriction (FGR) or preeclampsia, revealing the pathogenic effects of imbalanced m6A modifications. Therefore, our findings provide novel insights into the functions and regulatory mechanisms of m6A modifications in placental development and placental-related gestational diseases.
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Affiliation(s)
- Suwen Wu
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ketong Liu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yutong Cui
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Bingyan Zhou
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, China
| | - Huanqiang Zhao
- Shenzhen Maternity and Children Health Care Hospital, Shenzhen, China
| | - Xirong Xiao
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Qiongjie Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China; Shenzhen Maternity and Children Health Care Hospital, Shenzhen, China.
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16
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Zhang S, Sun S, Zhang Y, Liu J, Wu Y, Zhang X. Comprehensive Analysis of N6-Methyladenosine RNA Methylation Regulators in the Diagnosis and Subtype Classification of Rheumatoid Arthritis. Biochem Genet 2024; 62:3467-3484. [PMID: 38112894 DOI: 10.1007/s10528-023-10610-7] [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: 04/11/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023]
Abstract
m6A modification is the most abundant mRNA modifications and plays an integral role in various biological processes in eukaryotes. However, the role of m6A regulators in rheumatoid arthritis remains unknown. To determine the expression of m6A RNA methylation regulators in rheumatoid arthritis and their possible functional and prognostic value. In this study, we performed differential analysis in the comprehensive gene expression database GSE93272 dataset between non-rheumatoid arthritis patients and rheumatoid arthritis patients to obtain 15 important m6A regulators. A random forest model and lasso regression were used to screen the five most important m6A regulators to predict the risk of developing rheumatoid arthritis. After further validation using in vitro qPCR experiments, a nomogram model was developed based on the four most important m6A regulators (ELAVL1, WTAP, YTHDF1, and ALKBH5). Immuno-infiltration analysis and consensus clustering analysis were then performed. An analysis of the decision curve showed that the nomogram model could be beneficial to patients. According to selected important m6A regulators, patients with rheumatoid arthritis were classified into two m6A models (ClusterA and ClusterB) via consensus approach. Activated B cells, CD56dim natural killer cells, immature B cells, monocytes, natural killer T cells, and T lymphocytes were associated with ClusterA in immune infiltration analysis. Importantly, immune infiltration in patients with high ELAVL1 expression was strikingly similar to ClusterA. m6A regulators play a non-negligible role in the development of rheumatoid arthritis. A study of m6A patterns may provide future therapeutic options for rheumatoid arthritis.
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Affiliation(s)
- Shaoxiong Zhang
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Shuo Sun
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | | | - Jianping Liu
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Yuhuai Wu
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China.
| | - Xiguang Zhang
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China.
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17
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Liufu C, Luo L, Pang T, Zheng H, Yang L, Lu L, Chang S. Integration of multi-omics summary data reveals the role of N6-methyladenosine in neuropsychiatric disorders. Mol Psychiatry 2024; 29:3141-3150. [PMID: 38684796 DOI: 10.1038/s41380-024-02574-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
N6-methyladenosine (m6A) methylation regulates gene expression/protein by influencing numerous aspects of mRNA metabolism and contributes to neuropsychiatric diseases. Here, we integrated multi-omics data and genome-wide association study summary data of schizophrenia (SCZ), bipolar disorder (BP), attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), major depressive disorder (MDD), Alzheimer's disease (AD), and Parkinson's disease (PD) to reveal the role of m6A in neuropsychiatric disorders by using transcriptome-wide association study (TWAS) tool and Summary-data-based Mendelian randomization (SMR). Our investigation identified 86 m6A sites associated with seven neuropsychiatric diseases and then revealed 7881 associations between m6A sites and gene expressions. Based on these results, we discovered 916 significant m6A-gene associations involving 82 disease-related m6A sites and 606 genes. Further integrating the 58 disease-related genes from TWAS and SMR analysis, we obtained 61, 8, 7, 3, and 2 associations linking m6A-disease, m6A-gene, and gene-disease for SCZ, BP, AD, MDD, and PD separately. Functional analysis showed the m6A mapped genes were enriched in "response to stimulus" pathway. In addition, we also analyzed the effect of gene expression on m6A and the post-transcription effect of m6A on protein. Our study provided new insights into the genetic component of m6A in neuropsychiatric disorders and unveiled potential pathogenic mechanisms where m6A exerts influences on disease through gene expression/protein regulation.
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Affiliation(s)
- Chao Liufu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Lingxue Luo
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Tao Pang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Haohao Zheng
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Li Yang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Lin Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- Research Units of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China
| | - Suhua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China.
- Research Units of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China.
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18
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Ouyang W, Huang Z, Wan K, Nie T, Chen H, Yao H. RNA ac 4C modification in cancer: Unraveling multifaceted roles and promising therapeutic horizons. Cancer Lett 2024; 601:217159. [PMID: 39128536 DOI: 10.1016/j.canlet.2024.217159] [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: 03/21/2024] [Revised: 06/18/2024] [Accepted: 08/03/2024] [Indexed: 08/13/2024]
Abstract
RNA modifications play a crucial role in cancer development, profoundly influencing various stages of the RNA lifecycle. These stages encompass nuclear processing, nuclear export, splicing, and translation in the cytoplasm. Among RNA modifications, RNA ac4C modification, also known as N4-acetylcytidine, stands out for its unique role in acetylation processes. Specific proteins regulate RNA ac4C modification, maintaining the dynamic and reversible nature of these changes. This review explores the molecular mechanisms and biological functions of RNA ac4C modification. It examines the intricate ways in which RNA ac4C modification influences the pathogenesis and progression of cancer. Additionally, the review provides an integrated overview of the current methodologies for detecting RNA ac4C modification. Exploring the potential applications of manipulating this modification suggests avenues for novel therapeutic strategies, potentially leading to more effective cancer treatments in the future.
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Affiliation(s)
- Wenhao Ouyang
- Department of Oncology, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510120, China
| | - Zhenjun Huang
- Department of Oncology, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510120, China
| | - Keyu Wan
- The First Clinical Medical College, Nanchang University, Nanchang, 330006, China
| | - Tiantian Nie
- The First Clinical Medical College, Nanchang University, Nanchang, 330006, China
| | - Haizhu Chen
- Department of Oncology, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510120, China.
| | - Herui Yao
- Department of Oncology, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510120, China.
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19
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Su K, Liu J, Chen J, Wu H, Tang W, Sun S, Lin J, Zhan G, Hsu CH. Bisphenol C Induces Cardiac Developmental Defects by Disrupting m 6A Homeostasis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:17259-17269. [PMID: 39208335 PMCID: PMC11447910 DOI: 10.1021/acs.est.4c04373] [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: 05/07/2024] [Revised: 08/16/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Bisphenol A (BPA) is a commonly used plastic additive. Since BPA has been banned in maternal and infant food containers in many countries, BPA substitutes have been widely introduced to replace it. By systematically assessing the potential developmental toxicity of BPA substitutes, we observed that the 41-150 nM in vivo BPC exposure (around the reported concentration detected in infant urine: 6-186 nM) induced cardiac defects in zebrafish. Mechanistically, BPC disrupted m6A homeostasis by downregulation of the key m6A methyltransferase, Mettl3, thereby causing the m6A reader, Igf2bp2b, to fail in recognizing and stabilizing the inefficiently m6A-modified acox1 and tnnt2d mRNA. Then, downregulation of Acox1 (a regulator in cardiac fatty acid metabolism) and Tnnt2d (a component of cardiac troponin for muscle contraction) led to cardiac defects. Indeed, the dual cardiac functional axes regulated by the same m6A reader in response to BPC provided new insight into the regulatory mechanisms of epitranscriptomics and cardiac development. Collectively, our study not only presented evidence showing that the internal exposure levels of BPC in humans could lead to cardiac developmental defects but also demonstrated the underlying mechanism of BPC-mediated defects by disrupting the Mettl3-m6A-Igf2bp2b-Acox1/Tnnt2d pathways, which provided potential molecular markers associated with BPC exposure.
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Affiliation(s)
- Kunhui Su
- The
Fourth Affiliated Hospital, Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang 310058, China
- Institute
of Genetics, International School of Medicine, Zhejiang University, Zhejiang 310058, China
| | - Jinfeng Liu
- The
Fourth Affiliated Hospital, Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang 310058, China
- Institute
of Genetics, International School of Medicine, Zhejiang University, Zhejiang 310058, China
| | - Jiafeng Chen
- The
Fourth Affiliated Hospital, Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang 310058, China
- Institute
of Genetics, International School of Medicine, Zhejiang University, Zhejiang 310058, China
| | - Hengyu Wu
- The
Fourth Affiliated Hospital, Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang 310058, China
- Institute
of Genetics, International School of Medicine, Zhejiang University, Zhejiang 310058, China
| | - Wenbin Tang
- The
Fourth Affiliated Hospital, Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang 310058, China
- Institute
of Genetics, International School of Medicine, Zhejiang University, Zhejiang 310058, China
| | - Siqi Sun
- The
Fourth Affiliated Hospital, Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang 310058, China
- Institute
of Genetics, International School of Medicine, Zhejiang University, Zhejiang 310058, China
| | - Jiebo Lin
- The
Fourth Affiliated Hospital, Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang 310058, China
- Institute
of Genetics, International School of Medicine, Zhejiang University, Zhejiang 310058, China
| | - Guankai Zhan
- The
Fourth Affiliated Hospital, Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang 310058, China
- Institute
of Genetics, International School of Medicine, Zhejiang University, Zhejiang 310058, China
| | - Chih-Hung Hsu
- The
Fourth Affiliated Hospital, Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang 310058, China
- Institute
of Genetics, International School of Medicine, Zhejiang University, Zhejiang 310058, China
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20
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Gervason S, Sen S, Fontecave M, Golinelli-Pimpaneau B. [4Fe-4S]-dependent enzymes in non-redox tRNA thiolation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119807. [PMID: 39106920 DOI: 10.1016/j.bbamcr.2024.119807] [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: 12/26/2023] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 08/09/2024]
Abstract
Post-transcriptional modification of nucleosides in transfer RNAs (tRNAs) is an important process for accurate and efficient translation of the genetic information during protein synthesis in all domains of life. In particular, specific enzymes catalyze the biosynthesis of sulfur-containing nucleosides, such as the derivatives of 2-thiouridine (s2U), 4-thiouridine (s4U), 2-thiocytidine (s2C), and 2-methylthioadenosine (ms2A), within tRNAs. Whereas the mechanism that has prevailed for decades involved persulfide chemistry, more and more tRNA thiolation enzymes have now been shown to contain a [4Fe-4S] cluster. This review summarizes the information over the last ten years concerning the biochemical, spectroscopic and structural characterization of [4Fe-4S]-dependent non-redox tRNA thiolation enzymes.
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Affiliation(s)
- Sylvain Gervason
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris cedex 05, France
| | - Sambuddha Sen
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris cedex 05, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris cedex 05, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris cedex 05, France.
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21
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Xia W, Liu Y, Lu J, Cheung HH, Meng Q, Huang B. RNA methylation in neurodevelopment and related diseases. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39344412 DOI: 10.3724/abbs.2024159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024] Open
Abstract
Biological development and genetic information transfer are governed by genetic, epigenetic, transcriptional, and posttranscriptional mechanisms. RNA methylation, the attachment of methyl (-CH 3) groups to RNA molecules, is a posttranscriptional modification that has gained increasing attention in recent years because of its role in RNA epitranscriptomics. RNA modifications (RMs) influence various aspects of RNA metabolism and are involved in the regulation of diverse biological processes and diseases. Neural cell types emerge at specific stages of brain development, and recent studies have revealed that neurodevelopment, aging, and disease are tightly linked to transcriptome dysregulation. In this review, we discuss the roles of N6-methyladenine (m6A) and 5-methylcytidine (m5C) RNA modifications in neurodevelopment, physiological functions, and related diseases.
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Affiliation(s)
- Wenjuan Xia
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Yue Liu
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Jiafeng Lu
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Hoi-Hung Cheung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Qingxia Meng
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Boxian Huang
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
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22
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Gong Y, Lin Z, Sun H, Yu C, Qiu M, Xiong X, Yin L, Zhang D, Wang Y, Yang C, Liu Y. miR-24-3p inhibits lipid synthesis and progesterone secretion in chicken granulosa cells via ERK1/2 signaling pathway. Theriogenology 2024; 230:250-262. [PMID: 39348732 DOI: 10.1016/j.theriogenology.2024.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 09/19/2024] [Accepted: 09/26/2024] [Indexed: 10/02/2024]
Abstract
Normal follicular development is the basis for ovulation in poultry. Our previous sequencing analysis revealed a high expression of miR-24-3p in chicken follicles from degenerated ovaries, suggesting that miR-24-3p may modulate follicular development. Hence, this study investigated the specific mechanisms of miR-24-3p in regulating chicken follicular development. The results revealed that the proliferation, lipid synthesis, and progesterone secretion were significantly inhibited after miR-24-3p overexpression in chicken granulosa cells, vice versa by miR-24-3p knockdown. Dual-specificity phosphatase 16 (DUSP16) and thousand and one amino acid kinase 1 (TAOK1) were identified as potential target genes of miR-24-3p. Further validation revealed that knockdown of DUSP16 and TAOK1 suppressed proliferation, lipid synthesis, and progesterone secretion in chicken granulosa cells. Moreover, we observed that miR-24-3p, along with knockdown of DUSP16 and TAOK1, increased the phosphorylation levels of extracellular signal-regulated kinases 1 and 2 (ERK1/2). Our previous study proved that activation of ERK1/2 inhibited lipid synthesis and progesterone secretion of chicken granulosa cells. In summary, we demonstrated that miR-24-3p targeting DUSP16 and TAOK1 disrupts lipid synthesis and progesterone secretion via ERK1/2 signaling pathway in chicken granulosa cells in vitro. These results may provide a new theoretical basis for resolving miRNAs regulation on reproductive performance of chickens.
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Affiliation(s)
- Yanrong Gong
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhongzhen Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hao Sun
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chunlin Yu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Mohan Qiu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xia Xiong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Lingqian Yin
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Donghao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China.
| | - Yiping Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
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23
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Nabeel-Shah S, Pu S, Burke GL, Ahmed N, Braunschweig U, Farhangmehr S, Lee H, Wu M, Ni Z, Tang H, Zhong G, Marcon E, Zhang Z, Blencowe BJ, Greenblatt JF. Recruitment of the m 6A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48. Genome Biol 2024; 25:246. [PMID: 39300486 PMCID: PMC11414060 DOI: 10.1186/s13059-024-03392-7] [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: 06/04/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A), the most abundant internal modification on eukaryotic mRNA, and N6, 2'-O-dimethyladenosine (m6Am), are epitranscriptomic marks that function in multiple aspects of posttranscriptional regulation. Fat mass and obesity-associated protein (FTO) can remove both m6A and m6Am; however, little is known about how FTO achieves its substrate selectivity. RESULTS Here, we demonstrate that ZBTB48, a C2H2-zinc finger protein that functions in telomere maintenance, associates with FTO and binds both mRNA and the telomere-associated regulatory RNA TERRA to regulate the functional interactions of FTO with target transcripts. Specifically, depletion of ZBTB48 affects targeting of FTO to sites of m6A/m6Am modification, changes cellular m6A/m6Am levels and, consequently, alters decay rates of target RNAs. ZBTB48 ablation also accelerates growth of HCT-116 colorectal cancer cells and modulates FTO-dependent regulation of Metastasis-associated protein 1 (MTA1) transcripts by controlling the binding to MTA1 mRNA of the m6A reader IGF2BP2. CONCLUSIONS Our findings thus uncover a previously unknown mechanism of posttranscriptional regulation in which ZBTB48 co-ordinates RNA-binding of the m6A/m6Am demethylase FTO to control expression of its target RNAs.
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Affiliation(s)
- Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
| | - Giovanni L Burke
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Nujhat Ahmed
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | | | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Computer Sciences, University of Toronto, Toronto, M5S 1A8, Canada
| | - Mingkun Wu
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Zuyao Ni
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
| | - Hua Tang
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
| | - Guoqing Zhong
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, Canada
| | - Zhaolei Zhang
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
- Department of Computer Sciences, University of Toronto, Toronto, M5S 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada.
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24
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Xu C, Wang S, Sun Y. The role of KRT7 in metastasis and prognosis of pancreatic cancer. Cancer Cell Int 2024; 24:321. [PMID: 39300449 DOI: 10.1186/s12935-024-03500-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 09/05/2024] [Indexed: 09/22/2024] Open
Abstract
PURPOSE The aim of this study is to delve into the value of N6-Methyladenosine (m6A)-associated genes (MAGs) in pancreatic cancer (PC) prognosis. METHODS PC sequencing data and corresponding clinicopathological information were retrieved from GEO and TCGA databases. We filtered 19 MAGs in PC specimens and implemented functional annotation in biology. Later, the m6A modification pattern was stratified into m6Acluster A-B according to MAG expression levels, and further categorized into genecluster A-C based on differentially expressed genes between m6Acluster A and B. Next, a MAG-based prognostic prediction model was established by the least absolute shrinkage and selection operator (LASSO) regression analysis and multivariate Cox regression analysis. At last, the role of KRT7 in PC were explored. RESULTS We found m6Acluster A pattern presented enrichment pathways associated with cell apoptosis, proliferation, migration, and cancer pathways. Additionally, high-risk group displayed more dismal prognosis and a higher programmed death-ligand 1 expression. The survival prediction ability of the model was verified in three independent PC GEO datasets. KRT7 is the most momentous risk gene in the established prognostic model. Among 18 clinical samples, the KRT7 protein in the surviving patient samples is lower than that in the deceased patient samples. We also identified elevated expression of KRT7 in PC tumor tissues compared to normal tissues using GEPIA 2. Then, the metastasis of PC cells was promoted by overexpressed KRT7 in vitro and in vivo. And IGF2BP3 upregulated KRT7 by increasing the mRNA stability of KRT7. CONCLUSIONS The PPM built based on CXCL5, LY6K and KRT7 is an encouraging biomarker to define the prognosis. Additionally, IGF2BP3 promoted KRT7 by stabilizing mRNA of KRT7. And KRT7 promoted the metastasis of PC cells by promoting EMT.
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Affiliation(s)
- Chao Xu
- Department of General Surgery, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, 223300, Jiangsu, China.
| | - Shuming Wang
- Department of General Surgery, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, 223300, Jiangsu, China
| | - Yong Sun
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, China
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25
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Zhu M, Huang F, Sun H, Liu K, Chen Z, Yu B, Hao H, Liu H, Ding S, Zhang X, Liu L, Zhang K, Ren J, Liu Y, Liu H, Shan C, Guan W. Characterization of ACTN4 as a novel antiviral target against SARS-CoV-2. Signal Transduct Target Ther 2024; 9:243. [PMID: 39289355 PMCID: PMC11408661 DOI: 10.1038/s41392-024-01956-4] [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: 11/01/2023] [Revised: 08/13/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024] Open
Abstract
The various mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pose a substantial challenge in mitigating the viral infectivity. The identification of novel host factors influencing SARS-CoV-2 replication holds potential for discovering new targets for broad-spectrum antiviral drugs that can combat future viral mutations. In this study, potential host factors regulated by SARS-CoV-2 infection were screened through different high-throughput sequencing techniques and further identified in cells. Subsequent analysis and experiments showed that the reduction of m6A modification level on ACTN4 (Alpha-actinin-4) mRNA leads to a decrease in mRNA stability and translation efficiency, ultimately inhibiting ACTN4 expression. In addition, ACTN4 was demonstrated to target nsp12 for binding and characterized as a competitor for SARS-CoV-2 RNA and the RNA-dependent RNA polymerase complex, thereby impeding viral replication. Furthermore, two ACTN4 agonists, YS-49 and demethyl-coclaurine, were found to dose-dependently inhibit SARS-CoV-2 infection in both Huh7 cells and K18-hACE2 transgenic mice. Collectively, this study unveils the pivotal role of ACTN4 in SARS-CoV-2 infection, offering novel insights into the intricate interplay between the virus and host cells, and reveals two potential candidates for future anti-SARS-CoV-2 drug development.
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Affiliation(s)
- Miao Zhu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Huang
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China
| | - Huize Sun
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kunpeng Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Baocheng Yu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haojie Hao
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Haizhou Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Shuang Ding
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Xueyan Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Lishi Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kui Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jierao Ren
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Liu
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China
| | - Haibin Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China
| | - Chao Shan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China
| | - Wuxiang Guan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China.
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Yin Z, Ma L, Tian X, Sun Q, Zhang C, Wang Y, Miao Y, Xue X, Wang Y, Wang J, Zhang X, Hou X. Downregulation of the m 6A reader YTHDC2 upregulates exosome content in lung adenocarcinoma via inhibiting IFIT and OAS family members. J Biol Chem 2024; 300:107783. [PMID: 39303913 DOI: 10.1016/j.jbc.2024.107783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 08/01/2024] [Accepted: 08/28/2024] [Indexed: 09/22/2024] Open
Abstract
N6-Methyladenosine (m6A) is the most prevalent mRNA modification. Its biological function primarily relies on its "Reader" protein, such as YTHDC2. Previous studies have shown that YTHDC2 downregulation is a procarcinogenic phenomenon in lung adenocarcinoma (LUAD). However, further investigation is needed to understand the molecular mechanisms of downstream genes and the associated biological phenomena following YTHDC2 downregulation. Here, we found that YTHDC2 knockout upregulated exosome content in LUAD. Following YTHDC2 knockout, the mRNA levels of OAS family members (OASs) and IFIT family members (IFITs) also decreased; and inhibition of OASs and IFITs could promote exosome content. Several m6A modification sites on the NT domain of OASs and the TPR12 domain of IFITs were found to increase the stability of OASs and IFITs in a YTHDC2-dependent manner. OASs and IFITs affected exosome content through target genes including RAB5A, RAB7, and RAB11A, and three arginine (R) amino acids on IFITs were critical for combination IFITs with targeted RAB mRNAs and subsequent degradation. Simultaneously, OASs degraded targeted RABs through RNAseL. Additionally, mutual bindings between OASs and IFITs were critical for their target gene degradation. Collectively, the above findings might provide a theoretical basis for the treatment of LUAD patients with low YTHDC2 expression.
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Affiliation(s)
- Zhixin Yin
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoting Tian
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Sun
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Congcong Zhang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yikun Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yayou Miao
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangfei Xue
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongjie Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xumin Hou
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Huang H, Lin Y, Xin J, Sun N, Zhao Z, Wang H, Duan L, Zhou Y, Liu X, Fang J, Jing B, Pan K, Zeng Y, Zeng D, Li H, Ma H, Bai Y, Wei L, Ni X. Fluoride exposure-induced gut microbiota alteration mediates colonic ferroptosis through N 6-methyladenosine (m 6A) mediated silencing of SLC7A11. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116816. [PMID: 39096685 DOI: 10.1016/j.ecoenv.2024.116816] [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: 02/08/2024] [Revised: 07/24/2024] [Accepted: 07/27/2024] [Indexed: 08/05/2024]
Abstract
Fluoride exposure is widespread worldwide and poses a significant threat to organisms, particularly to their gastrointestinal tracts. However, due to limited knowledge of the mechanism of fluoride induced intestinal injury, it has been challenging to develop an effective treatment. To address this issue, we used a series of molecular biology in vitro and in vivo experiments. NaF triggered m6A mediated ferroptosis to cause intestinal damage. Mechanistically, NaF exposure increased the m6A level of SLC7A11 mRNA, promoted YTHDF2 binding to m6A-modified SLC7A11 mRNA, drove the degradation of SLC7A11 mRNA, and led to a decrease in its protein expression, which eventually triggers ferroptosis. Moreover, NaF aggravated ferroptosis of the colon after antibiotics destroyed the composition of gut microbiota. 16 S rRNA sequencing and SPEC-OCCU plots, Zi-Pi relationships, and Spearman correlation coefficients verified that Lactobacillus murinus (ASV54, ASV58, and ASV82) plays a key role in the response to NaF-induced ferroptosis. Collectively, NaF-induced gut microbiota alteration mediates severe intestinal cell injury by inducing m6A modification-mediated ferroptosis. Our results highlight a key mechanism of the gut in response to NaF exposure and suggest a valuable theoretical basis for its prevention and treatment.
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Affiliation(s)
- Haonan Huang
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu Lin
- Department of Gastroenterology, Southern Medical University Hospital of Integrative Chinese and Western Medicine, Southern Medical University, Guangzhou, China
| | - Jinge Xin
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ning Sun
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhifang Zhao
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, Medical College of Guizhou University, Guiyang, Guizhou, China
| | - Hesong Wang
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lixiao Duan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanxi Zhou
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xingmei Liu
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Fang
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Jing
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hao Li
- Plateau Brain Science Research Center, Tibet University, Lhasa, Tibet 850000, China
| | - Hailin Ma
- Plateau Brain Science Research Center, Tibet University, Lhasa, Tibet 850000, China
| | - Yang Bai
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Limin Wei
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Medical and Pharmaceutical College, Chongqing 401331, China.
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.
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Fan J, Sah SK, Lemes Jorge G, Blanford J, Xie D, Yu L, Thelen J, Shanklin J, Xu C. Arabidopsis trigalactosyldiacylglycerol1 mutants reveal a critical role for phosphtidylcholine remodeling in lipid homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39276345 DOI: 10.1111/tpj.17020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 08/08/2024] [Accepted: 08/27/2024] [Indexed: 09/17/2024]
Abstract
Lipid remodeling plays a critical role in plant response to abiotic stress and metabolic perturbations. Key steps in this process involve modifications of phosphatidylcholine (PC) acyl chains mediated by lysophosphatidylcholine: acyl-CoA acyltransferases (LPCATs) and phosphatidylcholine: diacylglycerol cholinephosphotransferase (ROD1). To assess their importance in lipid homeostasis, we took advantage of the trigalactosyldiacylglycerol1 (tgd1) mutant that exhibits marked increases in fatty acid synthesis and fatty acid flux through PC due to a block in inter-organelle lipid trafficking. Here, we showed that the increased fatty acid synthesis in tgd1 is due to posttranslational activation of the plastidic acetyl-coenzyme A carboxylase. Genetic analysis showed that knockout of LPCAT1 and 2 resulted in a lethal phenotype in tgd1. In addition, plants homozygous for lpcat2 and heterozygous for lpcat1 in the tgd1 background showed reduced levels of PC and triacylglycerols (TAG) and alterations in their fatty acid profiles. We further showed that disruption of ROD1 in tgd1 resulted in changes in fatty acid composition of PC and TAG, decreased leaf TAG content and reduced seedling growth. Together, our results reveal a critical role of LPCATs and ROD1 in maintaining cellular lipid homeostasis under conditions, in which fatty acid production largely exceeds the cellular demand for membrane lipid synthesis.
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Affiliation(s)
- Jilian Fan
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Saroj Kumar Sah
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Gabriel Lemes Jorge
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, 1201 E Rollins, Columbia, Missouri, 65211, USA
| | - Jantana Blanford
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Dongling Xie
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Linhui Yu
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Jay Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, 1201 E Rollins, Columbia, Missouri, 65211, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Changcheng Xu
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
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Yu X, Xu J, Song B, Zhu R, Liu J, Liu YF, Ma YJ. The role of epigenetics in women's reproductive health: the impact of environmental factors. Front Endocrinol (Lausanne) 2024; 15:1399757. [PMID: 39345884 PMCID: PMC11427273 DOI: 10.3389/fendo.2024.1399757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/28/2024] [Indexed: 10/01/2024] Open
Abstract
This paper explores the significant role of epigenetics in women's reproductive health, focusing on the impact of environmental factors. It highlights the crucial link between epigenetic modifications-such as DNA methylation and histones post-translational modifications-and reproductive health issues, including infertility and pregnancy complications. The paper reviews the influence of pollutants like PM2.5, heavy metals, and endocrine disruptors on gene expression through epigenetic mechanisms, emphasizing the need for understanding how dietary, lifestyle choices, and exposure to chemicals affect gene expression and reproductive health. Future research directions include deeper investigation into epigenetics in female reproductive health and leveraging gene editing to mitigate epigenetic changes for improving IVF success rates and managing reproductive disorders.
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Affiliation(s)
- Xinru Yu
- College Of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Jiawei Xu
- College Of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine School, Jinan, Shandong, China
| | - Bihan Song
- College Of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine School, Jinan, Shandong, China
| | - Runhe Zhu
- College Of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine School, Jinan, Shandong, China
| | - Jiaxin Liu
- College Of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yi Fan Liu
- Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Ying Jie Ma
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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Huang Z, Yoo KH, Li D, Yu Q, Ye L, Wei W. Pan-cancer analysis of m1A writer gene RRP8: implications for immune infiltration and prognosis in human cancers. Discov Oncol 2024; 15:437. [PMID: 39266915 PMCID: PMC11393379 DOI: 10.1007/s12672-024-01299-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Ribosomal RNA Processing 8 (RRP8) is a gene associated with RNA modification and has been implicated in the development of several types of tumors in recent research. Nevertheless, the biological importance of RRP8 in pan-cancer has not yet been thoroughly and comprehensively investigated. METHODS In this study, we conducted an analysis of various public databases to investigate the biological functions of RRP8. Our analysis included examining its correlation with pan-cancer prognosis, heterogeneity, stemness, immune checkpoint genes, and immune cell infiltration. Furthermore, we utilized the GDSC and CTRP databases to assess the sensitivity of RRP8 to small molecule drugs. RESULTS Our findings indicate that RRP8 exhibits differential expression between tumor and normal samples, particularly impacting the prognosis of various cancers such as Adrenocortical carcinoma (ACC) and Kidney Chromophobe (KICH). The expression of RRP8 is intricately linked to tumor heterogeneity and stemness markers. Additionally, RRP8 shows a positive correlation with the presence of tumor-infiltrating cells, with TP53 being the predominant mutated gene in these malignancies. CONCLUSION Our findings suggest that RRP8 may serve as a potential prognostic marker and therapeutic target in a variety of cancer types.
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Affiliation(s)
- Zhihui Huang
- Operating Room, West China Hospital, Sichuan University, Chengdu, China
- West China School of Nursing, Sichuan University, Chengdu, China
- West China Tianfu Hospital, Sichuan University, Chengdu, China
| | - Koo Han Yoo
- Department of Urology, Kyung Hee University, Seoul, South Korea
| | - Duohui Li
- Department of Pharmacy Management, Anqing Municipal Hospital, Anqing, 246000, Anhui, China.
| | - Qingxin Yu
- Department of Pathology, Ningbo Clinical Pathology Diagnosis Center, Ningbo, 315211, Zhejiang, China.
- Department of pathology, Ningbo Medical Centre Lihuili Hospital, Ningbo, China.
| | - Luxia Ye
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China.
| | - Wuran Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Zhu C, Cheng Y, Yu Y, Zhang Y, Ren G. VIRMA promotes the progression of head and neck squamous cell carcinoma by regulating UBR5 mRNA and m6A levels. BIOMOLECULES & BIOMEDICINE 2024; 24:1244-1257. [PMID: 38577917 PMCID: PMC11379021 DOI: 10.17305/bb.2024.10358] [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: 02/09/2024] [Revised: 03/23/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a globally prevalent and lethal cancer form which precise mechanisms remain incompletely understood. Increasing evidence suggests that N6-methyladenosine (m6A) plays a crucial role in cancer progression. This study aimed to explore the biological function of m6A modification and vir-like m6A methyltransferase associated (VIRMA) in HNSCC. We conducted an analysis of VIRMA expression in HNSCC cells using The Cancer Genome Atlas (TCGA) database and employed reverse transcription quantitative polymerase chain reaction (RT-qPCR) and western blotting to assess its expression levels in HNSCC cell lines. Additionally, m6A levels in HNSCC cells were quantified, and the correlation between VIRMA expression levels and the clinical and pathological features of other genes was analyzed. Upon knocking down VIRMA levels, we assessed HNSCC cell proliferation, migration, and invasion and validated downstream genes using RT-qPCR and western blot. Our findings suggested that VIRMA, as an m6A-related regulator, may significantly influence HNSCC progression by regulating ubiquitin protein ligase E3 component N-recognin 5 (UBR5) through m6A modification. Therefore, VIRMA may serve as a prognostic biomarker.
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Affiliation(s)
- Chunyu Zhu
- Department of Oral and Maxillofacial Surgery, School of Stomatology and Stomatological Hospital, Hebei Medical University, Shijiazhuang, China
| | - Yameng Cheng
- The Key Laboratory of Oral Medicine in Hebei Province, School of Stomatology and Stomatological Hospital, Hebei Medical University, Shijiazhuang, China
| | - Yao Yu
- Hebei Provincial Clinical Research Center for Oral Diseases, Shijiazhuang, China
| | - Yanning Zhang
- The Key Laboratory of Oral Medicine in Hebei Province, School of Stomatology and Stomatological Hospital, Hebei Medical University, Shijiazhuang, China
| | - Guiyun Ren
- Department of Oral and Maxillofacial Surgery, School of Stomatology and Stomatological Hospital, Hebei Medical University, Shijiazhuang, China
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Su Y, Wu Z, Liu Y, Liu X, Kang J, Jia J, Zhang L. Increased m6A RNA methylation and METTL3 expression may contribute to the synovitis progression of rheumatoid arthritis. Exp Cell Res 2024; 442:114237. [PMID: 39245197 DOI: 10.1016/j.yexcr.2024.114237] [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: 01/31/2024] [Revised: 08/21/2024] [Accepted: 09/04/2024] [Indexed: 09/10/2024]
Abstract
OBJECTIVE Rheumatoid arthritis (RA) is an autoimmune disease characterized by synovial hyperplasia and progressive bone destruction. The tumor-like growth of fibroblast-like synoviocytes (FLSs) plays a crucial role in the pathogenesis of RA. The N6 methyladenine (m6A) mRNA methylation modification, regulated by methyltransferases (METTL3) and demethylation enzymes, is a novel epigenetic regulator in the development of RA. However, there is limited research on m6A methylation modifications in RA synovitis and a lack of mechanistic studies on their impact on the function of RA-FLSs. METHODS This study utilized clinical synovial tissue specimens and FLSs as research subjects. The m6A methylation level and the expression of methyltransferases and demethylation enzymes were detected. RNA interference and gene overexpression methods were employed to investigate the mechanism of METTL3 in RA-FLSs. The study also examined the proliferation, apoptosis, migration, invasion, and cytokine levels of RA-FLSs, as well as the expression of METTL3 in RA animal models. RESULTS In this study, we found that m6A methylation levels were elevated in synovial tissues and FLSs of RA patients. Immunohistochemical staining showed that METTL3 and METTL14 levels were up-regulated in synovial tissues of RA, the mRNA levels of METTL3, METTL14, WTAP, FTO, and ALKBH5 were significantly higher in synovial tissues and FLSs of RA patients. Overexpression of METTL3 could promote the proliferation, migration, and secretion of IL-6, RANKL of RA-FLSs; inhibition of METTL3 expression could inhibit the abnormal proliferation, migration, invasion, and secretion of IL-6, RANKL, at the same time promoted the apoptosis and secretion of OPG, thus inhibited RA-FLSs tumor-like growth. In CIA mice, the use of MTX and STM2457 reduced METTL3 expression, synovial hyperplasia and bone destruction. CONCLUSION Abnormal modification of m6A methylation exists in synovial tissues and FLSs of RA patients, and inhibition of METTL3 can reduce synovitis and bone destruction. Our findings suggest that m6A methylation might control FLS-mediated tumor-like phenotype, and be a novel target for RA treatment.
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Affiliation(s)
- Yazhen Su
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China; Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic diseases), Taiyuan, China
| | - Zewen Wu
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China; Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic diseases), Taiyuan, China
| | - Yang Liu
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China; Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic diseases), Taiyuan, China
| | - Xinling Liu
- Third Clinical College, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Jie Kang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China; Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic diseases), Taiyuan, China
| | - Junqing Jia
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Liyun Zhang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China; Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic diseases), Taiyuan, China.
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Xu J, Wang Q, Tang X, Feng X, Zhang X, Liu T, Wu F, Wang Q, Feng X, Tang Q, Lisch D, Lu Y. Drought-induced circular RNAs in maize roots: Separating signal from noise. PLANT PHYSIOLOGY 2024; 196:352-367. [PMID: 38669308 DOI: 10.1093/plphys/kiae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024]
Abstract
Circular RNAs (circRNAs) play an important role in diverse biological processes; however, their origin and functions, especially in plants, remain largely unclear. Here, we used 2 maize (Zea mays) inbred lines, as well as 14 of their derivative recombination inbred lines with different drought sensitivity, to systematically characterize 8,790 circRNAs in maize roots under well-watered (WW) and water-stress (WS) conditions. We found that a diverse set of circRNAs expressed at significantly higher levels under WS. Enhanced expression of circRNAs was associated with longer flanking introns and an enrichment of long interspersed nuclear element retrotransposable elements. The epigenetic marks found at the back-splicing junctions of circRNA-producing genes were markedly different from canonical splicing, characterized by increased levels of H3K36me3/H3K4me1, as well as decreased levels of H3K9Ac/H3K27Ac. We found that genes expressing circRNAs are subject to relaxed selection. The significant enrichment of trait-associated sites along their genic regions suggested that genes giving rise to circRNAs were associated with plant survival rate under drought stress, implying that circRNAs play roles in plant drought responses. Furthermore, we found that overexpression of circMED16, one of the drought-responsive circRNAs, enhances drought tolerance in Arabidopsis (Arabidopsis thaliana). Our results provide a framework for understanding the intricate interplay of epigenetic modifications and how they contribute to the fine-tuning of circRNA expression under drought stress.
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Affiliation(s)
- Jie Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Sichuan Agricultural University, Sichuan 611130, China
| | - Qi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xin Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xiaoju Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xiaoyue Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Tianhong Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Fengkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Qingjun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Qi Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
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Wang N, Chen HQ, Zeng Y, Shi Y, Zhang Z, Li JY, Zhou SM, Li YW, Deng SW, Han X, Zhou ZY, Yao ML, Liu WB. Benzo(a)pyrene promotes the malignant progression of malignant-transformed BEAS-2B cells by regulating YTH N6-methyladenosine RNA binding protein 1 to inhibit ferroptosis. Toxicology 2024; 507:153886. [PMID: 39002880 DOI: 10.1016/j.tox.2024.153886] [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: 04/23/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Benzo[a]pyrene (BaP) is associated with the development of lung cancer, but the underlying mechanism has not been completely clarified. Here, we used 10 μM BaP to induce malignant transformation of human bronchial epithelial BEAS-2B cells, named BEAS-2B-T. Results indicated that BaP (6.25, 12.5 and 25 μM) treatment significantly promoted the migration and invasion of BEAS-2B-T cells. Meanwhile, BaP exposure inhibited ferroptosis in BEAS-2B-T, ferroptosis-related indexes Fe2+, malondialdehyde (MDA), lipid peroxidation (LPO) and reactive oxygen species (ROS) decreased significantly. The protein level of ferroptosis-related molecule transferrin receptor (TFRC) decreased significantly, while solute carrier family 7 membrane 11 (SLC7A11), ferritin heavy chain 1 (FTH1) and glutathione peroxidase 4 (GPX4) increased significantly. The intervention of ferroptosis dramatically effected the migration and invasion of BEAS-2B-T induced by BaP. Furthermore, the expression of YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) was markedly increased after BaP exposure. YTHDF1 knockdown inhibited BEAS-2B-T migration and invasion by promoting ferroptosis. In the meantime, the contents of Fe2+, MDA, LPO and ROS increased significantly, TFRC was markedly increased, and SLC7A11, FTH1, and GPX4 were markedly decreased. Moreover, overexpression of YTHDF1 promoted BEAS-2B-T migration and invasion by inhibiting ferroptosis. Importantly, knockdown of YTHDF1 promoted ferroptosis and reduced BEAS-2B-T migration and invasion during BaP exposure, and overexpression of YTHDF1 increased migration and invasion of BEAS-2B-T by inhibiting ferroptosis during BaP exposure. RNA immunoprecipitation assays indicated that the binding of YTHDF1 to SLC7A11 and FTH1 markedly increased after YTHDF1 overexpression. Therefore, we concluded that BaP promotes the malignant progression of BEAS-2B-T cells through YTHDF1 upregulating SLC7A11 and FTH1 to inhibit ferroptosis. This study reveals new epigenetic and ferroptosis markers for preventing and treating lung cancer induced by environmental carcinogens.
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Affiliation(s)
- Na Wang
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, 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
| | - Yu Shi
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China; College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Zhe Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, China
| | - Jiang-Ying Li
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China; College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Shi-Meng Zhou
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Ya-Wen Li
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Shuang-Wu Deng
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xue Han
- Department of Traditional Chinese Medicine Health and Preventive Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou 510006, China
| | - Zi-Yuan Zhou
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Mao-Lin Yao
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China.
| | - Wen-Bin Liu
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; 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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He D, He X, Shen D, Liu L, Yang X, Hao M, Wang Y, Li Y, Liu Q, Liu M, Wang J, Zhang X, Cui L. Loss-of-function variants in RNA binding motif protein X-linked induce neuronal defects contributing to amyotrophic lateral sclerosis pathogenesis. MedComm (Beijing) 2024; 5:e712. [PMID: 39263607 PMCID: PMC11387721 DOI: 10.1002/mco2.712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 06/19/2024] [Accepted: 06/27/2024] [Indexed: 09/13/2024] Open
Abstract
Despite being one of the most prevalent RNA modifications, the role of N6-methyladenosine (m6A) in amyotrophic lateral sclerosis (ALS) remains ambiguous. In this investigation, we explore the contribution of genetic defects of m6A-related genes to ALS pathogenesis. We scrutinized the mutation landscape of m6A genes through a comprehensive analysis of whole-exome sequencing cohorts, encompassing 508 ALS patients and 1660 population-matched controls. Our findings reveal a noteworthy enrichment of RNA binding motif protein X-linked (RBMX) variants among ALS patients, with a significant correlation between pathogenic m6A variants and adverse clinical outcomes. Furthermore, Rbmx knockdown in NSC-34 cells overexpressing mutant TDP43Q331K results in cell death mediated by an augmented p53 response. Similarly, RBMX knockdown in ALS motor neurons derived from induced pluripotent stem cells (iPSCs) manifests morphological defects and activation of the p53 pathway. Transcriptional analysis using publicly available single-cell sequencing data from the primary motor cortex indicates that RBMX-regulated genes selectively influence excitatory neurons and exhibit enrichment in ALS-implicated pathways. Through integrated analyses, our study underscores the emerging roles played by RBMX in ALS, suggesting a potential nexus between the disease and dysregulated m6A-mediated mRNA metabolism.
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Affiliation(s)
- Di He
- Department of Neurology Beijing Tiantan Hospital, Capital Medical University Beijing China
- Department of Neurology Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
| | - Xinyi He
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute Fudan University Shanghai China
| | - Dongchao Shen
- Department of Neurology Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
| | - Liyang Liu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College Beijing China
| | - Xunzhe Yang
- Department of Neurology Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
| | - Meng Hao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute Fudan University Shanghai China
| | - Yi Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute Fudan University Shanghai China
| | - Yi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute Fudan University Shanghai China
| | - Qing Liu
- Department of Neurology Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
| | - Mingsheng Liu
- Department of Neurology Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute Fudan University Shanghai China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases Chinese Academy of Medical Sciences (2019RU058) Shanghai China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College Beijing China
- Neuroscience Center Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS) Beijing China
| | - Liying Cui
- Department of Neurology Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
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Zhang F, Zhang B, Cui T, Chen S, Zhang C, Wang Z, Liu X. The novel roles of RNA m6A modification in regulating the development, infection, and oxidative DNA damage repair of Phytophthora sojae. PLoS Pathog 2024; 20:e1012553. [PMID: 39312577 PMCID: PMC11449341 DOI: 10.1371/journal.ppat.1012553] [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: 07/03/2024] [Revised: 10/03/2024] [Accepted: 08/30/2024] [Indexed: 09/25/2024] Open
Abstract
N6-methyladenosine (m6A), a vital post-transcriptional regulator, is among the most prevalent RNA modifications in eukaryotes. Nevertheless, the biological functions of m6A in oomycetes remain poorly understood. Here, we showed that the PsMTA1 and PsMTA2 genes are orthologs of human METTL4, while the PsMET16 gene is an ortholog of human METTL16. These genes are implicated in m6A modification and play a critical role in the production of sporangia and oospores, the release of zoospores, and the virulence of Phytophthora sojae. In P. sojae, m6A modifications are predominantly enriched in the coding sequence and the 3' untranslated region. Notably, the PsMTA1 knockout mutant exhibited reduced virulence, attributed to impaired tolerance to host defense-generated ROS stress. Mechanistically, PsMTA1-mediated m6A modification positively regulates the mRNA lifespan of DNA damage response (DDR) genes in reaction to plant ROS stress during infection. Consequently, the mRNA abundance of the DDR gene PsRCC1 was reduced in the single m6A site mutant ΔRCC1/RCC1A2961C, resulting in compromised DNA damage repair and reduced ROS adaptation-associated virulence in P. sojae. Overall, these results indicate that m6A-mediated RNA metabolism is associated with the development and pathogenicity of P. sojae, underscoring the roles of epigenetic markers in the adaptive flexibility of Phytophthora during infection.
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Affiliation(s)
- Fan Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Borui Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Tongshan Cui
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shanshan Chen
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Can Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhiwen Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xili Liu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
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Wang S, Zhang W, Wang Z, Liu Z, Yi X, Wu J. Mettl3-m6A-YTHDF1 axis promotion of mitochondrial dysfunction in metabolic dysfunction-associated steatotic liver disease. Cell Signal 2024; 121:111303. [PMID: 39019337 DOI: 10.1016/j.cellsig.2024.111303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/09/2024] [Accepted: 07/14/2024] [Indexed: 07/19/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) mRNA modification and mitochondrial function hold paramount importance in the advancement of metabolic dysfunction-associated steatotic liver disease (MASLD). AIM The aim of this study was to elucidate the impact of m6A on hepatic mitochondrial dysfunction and provide a novel perspective for a more comprehensive understanding of the pathogenesis of MASLD. METHODS High-throughput screening methods were used to identify the underlying transcriptome and proteome changes in MASLD model mice. Western blotting, blue native gel electrophoresis (BNGE), dot blot, and Seahorse analyses were conducted to identify and validate the underlying regulatory mechanisms of m6A on mitochondria. RESULTS In vivo, abnormal m6A modification in MASLD was attributed to the upregulation of methyltransferase like 3 (Mettl3) and the downregulation of YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) induced by high-fat foods. In vitro, knockdown of Mettl3 inhibited hepatic oxidative phosphorylation (OXPHOS) and the mitochondrial respiratory chain (MRC), while overexpression of Mettl3 promoted these processes. However, knockout of the reader protein YTHDF1, which plays a crucial role in the m6A modification process, counteracted the effect of Mettl3 and suppressed mitochondrial OXPHOS. CONCLUSIONS In MASLD, damage to the MRC may be regulated by the Mettl3-m6A-YTHDF1 axis, particularly by the role of YTHDF1. Modulation of the Mettl3-m6A-YTHDF1 axis has the potential to improve mitochondrial function, alleviate MASLD symptoms, and decrease the likelihood of disease progression.
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Affiliation(s)
- Shuowen Wang
- Beijing Tongren Hospital, Capital Medical University, Beijing 100176, China; Capital Institute of Pediatrics, Beijing 100020, China
| | - Wanyu Zhang
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Zijun Wang
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Zhuo Liu
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Xiaoyu Yi
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Jianxin Wu
- Beijing Tongren Hospital, Capital Medical University, Beijing 100176, China; Capital Institute of Pediatrics, Beijing 100020, China.
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38
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Chen D, Gu X, Nurzat Y, Xu L, Li X, Wu L, Jiao H, Gao P, Zhu X, Yan D, Li S, Xue C. Writers, readers, and erasers RNA modifications and drug resistance in cancer. Mol Cancer 2024; 23:178. [PMID: 39215288 PMCID: PMC11363509 DOI: 10.1186/s12943-024-02089-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
Drug resistance in cancer cells significantly diminishes treatment efficacy, leading to recurrence and metastasis. A critical factor contributing to this resistance is the epigenetic alteration of gene expression via RNA modifications, such as N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 7-methylguanosine (m7G), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I) editing. These modifications are pivotal in regulating RNA splicing, translation, transport, degradation, and stability. Governed by "writers," "readers," and "erasers," RNA modifications impact numerous biological processes and cancer progression, including cell proliferation, stemness, autophagy, invasion, and apoptosis. Aberrant RNA modifications can lead to drug resistance and adverse outcomes in various cancers. Thus, targeting RNA modification regulators offers a promising strategy for overcoming drug resistance and enhancing treatment efficacy. This review consolidates recent research on the role of prevalent RNA modifications in cancer drug resistance, with a focus on m6A, m1A, m5C, m7G, Ψ, and A-to-I editing. Additionally, it examines the regulatory mechanisms of RNA modifications linked to drug resistance in cancer and underscores the existing limitations in this field.
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Affiliation(s)
- Di Chen
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Yeltai Nurzat
- State Key Laboratory of Respiratory Disease, Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lixia Xu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xueyuan Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Lixin Wu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Henan Jiao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Peng Gao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xuqiang Zhu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
| | - Dongming Yan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
| | - Shaohua Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
| | - Chen Xue
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
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Shu W, Huang Q, Chen R, Lan H, Yu L, Cui K, He W, Zhu S, Chen M, Li L, Jiang D, Xu G. Complicated role of ALKBH5 in gastrointestinal cancer: an updated review. Cancer Cell Int 2024; 24:298. [PMID: 39182071 PMCID: PMC11344947 DOI: 10.1186/s12935-024-03480-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024] Open
Abstract
Gastrointestinal cancer is the most common malignancy in humans, often accompanied by poor prognosis. N6-methyladenosine (m6A) modification is widely present in eukaryotic cells as the most abundant RNA modification. It plays a crucial role in RNA splicing and processing, nuclear export, translation, and stability. Human AlkB homolog 5 (ALKBH5) is a type of RNA demethylase exhibiting abnormal expression in various gastrointestinal cancers.It is closely related to the tumorigenesis, proliferation, migration, and other biological functions of gastrointestinal cancer. However, recent studies indicated that the role and mechanism of ALKBH5 in gastrointestinal cancer are complicated and even controversial. Thus, this review summarizes recent advances in elucidating the role of ALKBH5 as a tumor suppressor or promoter in gastrointestinal cancer. It examines the biological functions of ALKBH5 and its potential as a therapeutic target, providing new perspectives and insights for gastrointestinal cancer research.
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Affiliation(s)
- Weitong Shu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Qianying Huang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Rui Chen
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Huatao Lan
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Luxin Yu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Kai Cui
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Wanjun He
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Songshan Zhu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Mei Chen
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Li Li
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Dan Jiang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China.
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China.
| | - Guangxian Xu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China.
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China.
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40
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Snyder LR, Koutmou KS. Studying the intersection of nucleoside modifications and SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted system. Methods Enzymol 2024; 705:81-109. [PMID: 39389674 DOI: 10.1016/bs.mie.2024.07.005] [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] [Indexed: 10/12/2024]
Abstract
There is growing recognition that viral RNA genomes possess enzymatically incorporated modified nucleosides. These small chemical changes are analogous to epigenomic modifications in DNA and have the potential to be similarly important modulators of viral transcription and evolution. However, the molecular level consequences of individual sites of modification remain to be broadly explored. Here we describe an in vitro assay to examine the impact of nucleoside modifications on the rate and fidelity of SARS-CoV-2 RNA transcription. Establishing the role of modified nucleotides in SARS-CoV-2 is of interest both for advancing fundamental knowledge of RNA modifications in viruses, and because modulating the modification-landscape of SARS-CoV-2 may represent a therapeutic strategy to interfere with viral RNA replication. Our approach can be used to assess the influence both of modifications present in a template RNA, as well nucleotide analog inhibitors. These methods provide a reproducible guide for generating active SARS-CoV-2 replication/transcription complexes capable of establishing how RNA modifications influence the pre-steady state rate constants of nucleotide addition by RNA-dependent RNA polymerases.
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Affiliation(s)
- Laura R Snyder
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States.
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41
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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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He L, Xiang Y. Interrogating the Presence of RNA Phosphorothioate in Nature by a Highly Selective and Sensitive Fluorescence Method. Anal Chem 2024. [PMID: 39138966 DOI: 10.1021/acs.analchem.4c01597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
In nature, DNA phosphorothioate (PT) is found in the genomic materials of some prokaryotes. In contrast, whether there is natural RNA PT is still a question under debate. A groundbreaking study reported the discovery of RNA PT in cellular RNA samples from both prokaryotes and eukaryotes at contents of >100 PT per million nucleotides (PPM-nt) according to liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis. However, this finding was challenged by a later work showing that other RNA modifications, such as 2'-O-methylation, could give almost the same LC-MS/MS signal patterns as RNA PT. As the LC-MS/MS technique led to contradicting conclusions, another independent method is thus needed to interrogate the presence of RNA PT in nature. In this work, we have developed a highly selective and sensitive fluorescence method for RNA PT quantification based on a new RNA PT-specific conversion reaction. It can detect as low as 2.8 PPM-nt in RNA without interference from RNA thiobases or protein cysteines. We measured the total RNA samples from some bacteria and human cells using this method. None of these samples gave any RNA PT signal above the detection limit (2.8 PPM-nt), suggesting that the widespread presence of natural RNA PT at the 100 PPM-nt level or above is highly unlikely. Nevertheless, due to the limited number of cell species tested in this work, the possible existence of natural RNA PT cannot be excluded. The fluorescence method reported here is simple and low-cost; therefore, it should be an ideal assay for broadly screening various types of cells to search for the clue of RNA PT in nature.
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Affiliation(s)
- Luo He
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Tsinghua University, Beijing 100084, China
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Ye Y, Tian Y, Chen J, Zhao J. Anoectochilusroxburghii extract down-regulates METTL3 to reduce RNA m 6A on WNT pathway and inhibit melanoma cancer cell metastasis. J Cancer 2024; 15:5140-5148. [PMID: 39247584 PMCID: PMC11375548 DOI: 10.7150/jca.92212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/03/2024] [Indexed: 09/10/2024] Open
Abstract
Characterized by high invasiveness and expansive growth, melanoma progression is intricately regulated, with RNA m6A modifications playing a pivotal role. Among these regulators, METTL3 modulates the migratory capabilities of melanoma cells, specifically by modifying the RNA m6A of UCK2. The extract of Anoectochilusroxburghii, a plant known for its broad-spectrum antitumour properties, has been shown to effectively curb the invasion and migration of melanoma cells and impede tumour growth. The primary mechanism involves the downregulation of METTL3 expression. By doing so, the Anoectochilus roxburghii extract reduces the m6A level on the mRNA of UCK2, accelerating UCK2 mRNA degradation and, consequently, decreasing UCK2 expression. This process, in turn, suppresses gene expression within the Wnt/β-catenin pathway, contributing to its antimelanoma effects.
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Affiliation(s)
- Yingyi Ye
- School of Medicine, Tongji University, Shanghai, 200092, China
- Dermatology department of Ningbo No.2 Hospital of Zhejiang Province, Ningbo, 315200, China
- Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, 315200, China
| | - Yazhi Tian
- Dermatology department of Ningbo No.2 Hospital of Zhejiang Province, Ningbo, 315200, China
| | - Jinchun Chen
- Dermatology department of Ningbo No.2 Hospital of Zhejiang Province, Ningbo, 315200, China
| | - Jingjun Zhao
- Department of Dermatology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Shi Z, Wen K, Zou Z, Fu W, Guo K, Sammudin NH, Ruan X, Sullere S, Wang S, Zhang X, Thinakaran G, He C, Zhuang X. YTHDF1 mediates translational control by m6A mRNA methylation in adaptation to environmental challenges. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.07.607063. [PMID: 39149343 PMCID: PMC11326287 DOI: 10.1101/2024.08.07.607063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Animals adapt to environmental challenges with long-term changes at the behavioral, circuit, cellular, and synaptic levels which often require new protein synthesis. The discovery of reversible N6-methyladenosine (m 6 A) modifications of mRNA has revealed an important layer of post-transcriptional regulation which affects almost every phase of mRNA metabolism and therefore translational control. Many in vitro and in vivo studies have demonstrated the significant role of m 6 A in cell differentiation and survival, but its role in adult neurons is understudied. We used cell-type specific gene deletion of Mettl14, which encodes one of the subunits of the m 6 A methyltransferase, and Ythdf1 , which encodes one of the cytoplasmic m 6 A reader proteins, in dopamine D1 receptor expressing or D2 receptor expressing neurons. Mettl14 or Ythdf1 deficiency blunted responses to environmental challenges at the behavioral, cellular, and molecular levels. In three different behavioral paradigms, gene deletion of either Mettl14 or Ythdf1 in D1 neurons impaired D1-dependent learning, whereas gene deletion of either Mettl14 or Ythdf1 in D2 neurons impaired D2-dependent learning. At the cellular level, modulation of D1 and D2 neuron firing in response to changes in environments was blunted in all three behavioral paradigms in mutant mice. Ythdf1 deletion resembled impairment caused by Mettl14 deletion in a cell type-specific manner, suggesting YTHDF1 is the main mediator of the functional consequences of m 6 A mRNA methylation in the striatum. At the molecular level, while striatal neurons in control mice responded to elevated cAMP by increasing de novo protein synthesis, striatal neurons in Ythdf1 knockout mice didn't. Finally, boosting dopamine release by cocaine drastically increased YTHDF1 binding to many mRNA targets in the striatum, especially those that encode structural proteins, suggesting the initiation of long-term neuronal and/or synaptic structural changes. While the m6A-YTHDF1 pathway has similar functional significance at cellular level, its cell type specific deficiency in D1 and D2 neurons often resulted in contrasting behavioral phenotypes, allowing us to cleanly dissociate the opposing yet cooperative roles of D1 and D2 neurons.
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45
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Teng S, Han C, Zhou J, He Z, Qian W. m 5C RNA methylation: a potential mechanism for infectious Alzheimer's disease. Front Cell Dev Biol 2024; 12:1440143. [PMID: 39175875 PMCID: PMC11338875 DOI: 10.3389/fcell.2024.1440143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder caused by a variety of factors, including age, genetic susceptibility, cardiovascular disease, traumatic brain injury, and environmental factors. The pathogenesis of AD is largely associated with the overproduction and accumulation of amyloid-β peptides and the hyperphosphorylation of tau protein in the brain. Recent studies have identified the presence of diverse pathogens, including viruses, bacteria, and parasites, in the tissues of AD patients, underscoring the critical role of central nervous system infections in inducing pathological changes associated with AD. Nevertheless, it remains unestablished about the specific mechanism by which infections lead to the occurrence of AD. As an important post-transcriptional RNA modification, RNA 5-methylcytosine (m5C) methylation regulates a wide range of biological processes, including RNA splicing, nuclear export, stability, and translation, therefore affecting cellular function. Moreover, it has been recently demonstrated that multiple pathogenic microbial infections are associated with the m5C methylation of the host. However, the role of m5C methylation in infectious AD is still uncertain. Therefore, this review discusses the mechanisms of pathogen-induced AD and summarizes research on the molecular mechanisms of m5C methylation in infectious AD, thereby providing new insight into exploring the mechanism underlying infectious AD.
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Affiliation(s)
- Sisi Teng
- Department of Neurology, Shangjinnanfu Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Cunqiao Han
- Department of Emergency, Shangjinnanfu Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian Zhou
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, Guangdong, China
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Zhenyan He
- Department of Neurosurgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Weiwei Qian
- Department of Emergency, Shangjinnanfu Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Emergency Medicine, Laboratory of Emergency Medicine, West China Hospital, and Disaster Medical Center, Sichuan University, Chengdu, Sichuan, China
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Wang S, Liu Q. Research progress on m6A demethylase FTO and its role in gynecological tumors. Front Oncol 2024; 14:1413505. [PMID: 39175477 PMCID: PMC11338917 DOI: 10.3389/fonc.2024.1413505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/22/2024] [Indexed: 08/24/2024] Open
Abstract
Recent advances in genomic research have increasingly focused on the fat mass- and obesity-associated (FTO) gene due to its notable correlation with obesity. Initially explored for its contribution to increased body weight, FTO was later discovered to function as an m6A demethylase. This pivotal role enhances our understanding of its broader implications across various pathologies. Epigenetic modifications, such as m6A, have been implicated in gynecological cancers, including ovarian, endometrial, and cervical malignancies. However, the precise mechanisms by which FTO influences the development of gynecological cancers remain largely unknown. This analysis underscores the growing relevance of investigations into the FTO gene in elucidating the mechanisms underlying gynecological cancers and exploring potential therapeutic avenues.
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Affiliation(s)
- SiYuan Wang
- Jiangsu University School of Medicine, Jiangsu University School, Zhenjiang, Jiangsu, China
| | - Qin Liu
- Gynecology, KunShan Affiliated Hospital of Jiangsu University, Jiangsu University, Suzhou, Jiangsu, China
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Huang M, Wang X, Zhang M, Liu Y, Chen YG. METTL3 restricts RIPK1-dependent cell death via the ATF3-cFLIP axis in the intestinal epithelium. CELL REGENERATION (LONDON, ENGLAND) 2024; 13:14. [PMID: 39093347 PMCID: PMC11297012 DOI: 10.1186/s13619-024-00197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
Intestinal epithelial cells (IECs) are pivotal for maintaining intestinal homeostasis through self-renewal, proliferation, differentiation, and regulated cell death. While apoptosis and necroptosis are recognized as distinct pathways, their intricate interplay remains elusive. In this study, we report that Mettl3-mediated m6A modification maintains intestinal homeostasis by impeding epithelial cell death. Mettl3 knockout induces both apoptosis and necroptosis in IECs. Targeting different modes of cell death with specific inhibitors unveils that RIPK1 kinase activity is critical for the cell death triggered by Mettl3 knockout. Mechanistically, this occurs via the m6A-mediated transcriptional regulation of Atf3, a transcription factor that directly binds to Cflar, the gene encoding the anti-cell death protein cFLIP. cFLIP inhibits RIPK1 activity, thereby suppressing downstream apoptotic and necroptotic signaling. Together, these findings delineate the essential role of the METTL3-ATF3-cFLIP axis in homeostatic regulation of the intestinal epithelium by blocking RIPK1 activity.
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Affiliation(s)
- Meimei Huang
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Guangzhou National Laboratory, Guangzhou, 510700, China
| | - Xiaodan Wang
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Mengxian Zhang
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuan Liu
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Ye-Guang Chen
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
- Guangzhou National Laboratory, Guangzhou, 510700, China.
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Wu S, Tu Q, Yuan H, Wu Z, Yang Y, Chen C, Huang C. Comprehensive Analysis for Predicting Prognoses and Immune Responses of m6A-Related lncRNAs in Women with Lung Adenocarcinoma. Biochem Genet 2024; 62:2702-2720. [PMID: 37999876 DOI: 10.1007/s10528-023-10572-w] [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: 06/18/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
During the past decade, the average 5-year survival rate of patients with Lung adenocarcinoma (LUAD) has remained < 20%, although the targeted therapies and novel immunotherapy approaches have held promise. Epigenetic modifications could provide prognostic value as molecular biomarkers, and we aimed to identify the independent risk of m6A-related lncRNAs to establish a risk model for the clinical prediction of prognoses in women with LUAD. In this study, we first assessed 31 N6-methyladenosine (m6A)-related lncRNAs associated with overall survival. Moreover, we evaluated the expression of the oncogenic driver and the tumor immune microenvironment (TIME) in two female LUAD subtypes (clusters 1 and 2) using consensus clustering. We also found 16 m6A-related lncRNAs as the independent prognostic indicator of women with LUAD and established a risk model developed from these lncRNAs. We comprehensively investigated the correlation between the TIME and m6A-related lncRNA and found that m6A-related lncRNA may significantly affect the immune cell infiltration level in LUAD. In conclusion, our study provides evidence on the prognostic prediction in women with LUAD and may help elucidate the processes and mechanisms of m6A-regulated lncRNAs.
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Affiliation(s)
- Sijie Wu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
| | - Qinxian Tu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
| | - Haoyong Yuan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
- Engineering Laboratory of Hunan Province for Cardiovascular Biomaterials, Changsha, 410008, Hunan, China
| | - Zhongshi Wu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
- Engineering Laboratory of Hunan Province for Cardiovascular Biomaterials, Changsha, 410008, Hunan, China
| | - Yifeng Yang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
| | - Chunyang Chen
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
- Engineering Laboratory of Hunan Province for Cardiovascular Biomaterials, Changsha, 410008, Hunan, China
| | - Can Huang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China.
- Engineering Laboratory of Hunan Province for Cardiovascular Biomaterials, Changsha, 410008, Hunan, China.
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Xie Y, Xiao J, Ying Y, Liu J, Zhang L, Zeng X. Bioinformatic identification reveals a m6A-binding protein, IGF2BP2, as a novel tumor-promoting gene signature in thyroid carcinoma. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:5663-5676. [PMID: 38289368 DOI: 10.1007/s00210-024-02961-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/15/2024] [Indexed: 08/18/2024]
Abstract
N6-methyladenosine (m6A) modification plays a crucial role in thyroid carcinoma (THCA). Insulin-like growth factor 2 binding protein 2 (IGF2BP2) is a m6A-binding protein. We aimed to explore the effect of IGF2BP2 on the development of THCA. Differentially expressed genes (DEGs) were screened from GSE50901 and GSE60542 datasets. LinkedOmics, Genebank, and Sequence-based RNA Adenosine Methylation Site Predictor databases were employed to find potential m6A modification sites. Protein-protein interaction network and receiver-operating characteristic curves were applied to determine hub genes of THCA. ESTIMATE revealed the effect of IGF2BP2 on tumor immunity. The mRNA expression of IGF2BP2 was detected using real-time quantitative polymerase chain reaction. The viability, migration, and invasion were assessed by Cell Counting Kit-8, wound healing, and transwell assays. A total of 166 common DEGs were identified from GSE50901 and GSE60542 datasets. One m6A-related gene, IGF2BP2, was differentially expressed in THCA and selected as the research target. The hub genes (CD44, DCN, CXCL12, ICAM1, SDC4, KIT, CTGF, and FMOD) were identified with high prediction values for THCA. Subsequently, the target genes of IGF2BP2, SDC4, and ICAM1, which had potential m6A modification sites, were screened out based on the hub genes. IGF2BP2 was upregulated in THCA and IGF2BP2 expression was positively correlated with immune infiltration in THCA. Additionally, knockdown of IGF2BP2 inhibited the proliferation, invasion, and migration of THCA cells. IGF2BP2 has a contributory effect on the progression of THCA, which is a novel biomarker and a therapeutic target for THCA.
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Affiliation(s)
- Yang Xie
- Suzhou Medical College of Soochow University, Suzhou, China
- Department of Thyroid and Hernia Surgery, The First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Zhanggong District, Ganzhou, 341000, Jiangxi Province, China
- Institute of Thyroid Diseases, Gannan Medical University, Ganzhou, China
- Ganzhou Key Laboratory of Thyroid Tumor, Ganzhou, China
| | - Junqi Xiao
- Department of Vascular Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yong Ying
- Department of Thyroid and Hernia Surgery, The First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Zhanggong District, Ganzhou, 341000, Jiangxi Province, China
| | - Jiafeng Liu
- Department of Thyroid and Hernia Surgery, The First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Zhanggong District, Ganzhou, 341000, Jiangxi Province, China
| | - Leiying Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xiangtai Zeng
- Suzhou Medical College of Soochow University, Suzhou, China.
- Department of Thyroid and Hernia Surgery, The First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Zhanggong District, Ganzhou, 341000, Jiangxi Province, China.
- Institute of Thyroid Diseases, Gannan Medical University, Ganzhou, China.
- Ganzhou Key Laboratory of Thyroid Tumor, Ganzhou, China.
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50
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Chen XH, Guo KX, Li J, Xu SH, Zhu H, Yan GR. Regulations of m 6A and other RNA modifications and their roles in cancer. Front Med 2024; 18:622-648. [PMID: 38907157 DOI: 10.1007/s11684-024-1064-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/17/2024] [Indexed: 06/23/2024]
Abstract
RNA modification is an essential component of the epitranscriptome, regulating RNA metabolism and cellular functions. Several types of RNA modifications have been identified to date; they include N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), N4-acetylcytidine (ac4C), etc. RNA modifications, mediated by regulators including writers, erasers, and readers, are associated with carcinogenesis, tumor microenvironment, metabolic reprogramming, immunosuppression, immunotherapy, chemotherapy, etc. A novel perspective indicates that regulatory subunits and post-translational modifications (PTMs) are involved in the regulation of writer, eraser, and reader functions in mediating RNA modifications, tumorigenesis, and anticancer therapy. In this review, we summarize the advances made in the knowledge of different RNA modifications (especially m6A) and focus on RNA modification regulators with functions modulated by a series of factors in cancer, including regulatory subunits (proteins, noncoding RNA or peptides encoded by long noncoding RNA) and PTMs (acetylation, SUMOylation, lactylation, phosphorylation, etc.). We also delineate the relationship between RNA modification regulator functions and carcinogenesis or cancer progression. Additionally, inhibitors that target RNA modification regulators for anticancer therapy and their synergistic effect combined with immunotherapy or chemotherapy are discussed.
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Affiliation(s)
- Xin-Hui Chen
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Kun-Xiong Guo
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Jing Li
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Shu-Hui Xu
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Huifang Zhu
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Guang-Rong Yan
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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