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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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2
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Wu Y, He H, Zheng K, Qin Z, Cai N, Zuo S, Zhu X. RNA M6A modification shaping cutaneous melanoma tumor microenvironment and predicting immunotherapy response. Pigment Cell Melanoma Res 2024; 37:496-509. [PMID: 38624045 DOI: 10.1111/pcmr.13170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/13/2024] [Accepted: 04/04/2024] [Indexed: 04/17/2024]
Abstract
Recent years have seen rising mortality rates linked to cutaneous melanoma (SKCM), despite advances in immunotherapy. Understanding RNA N6-methyladenosine (M6A) significance in SKCM is crucial for prognosis, tumor microenvironment (TME), immune cell presence, and immunotherapy efficacy. We analyzed 23 M6A regulators using SKCM samples from TCGA and GEO databases, identifying three M6A modification patterns linked to TME cell infiltration. Principal component analysis (PCA) yielded an M6A score for individual tumors, utilizing patient gene expression profiles and CNV data from TCGA. M6A modification patterns play a crucial role in SKCM development and progression, influencing tumor attributes such as inflammatory stage, subtype, TME interstitial activity, and genetic mutations. The M6A score independently predicts patient outcomes and correlates with improved response to immunotherapy, validated across anti-PD-1 and anti-PD-L1 therapy cohorts. M6A modifications significantly impact the TME landscape, with the M6A score serving as a predictive marker for immunotherapy response. Integrating M6A-related information into clinical practice could revolutionize SKCM management and treatment strategies.
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Affiliation(s)
- Yanhong Wu
- School of Ocean and Tropical Medicine, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Hongying He
- Liuzhou Key Laboratory of Molecular Diagnosis, Guangxi Health Commission Key Laboratory of Molecular Diagnosis and Application, Affiliated Liutie Central Hospital of Guangxi Medical University, Liuzhou, China
| | - Kairong Zheng
- School of Ocean and Tropical Medicine, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Zhenxin Qin
- School of Ocean and Tropical Medicine, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Naikun Cai
- School of Ocean and Tropical Medicine, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Shuguang Zuo
- Liuzhou Key Laboratory of Molecular Diagnosis, Guangxi Health Commission Key Laboratory of Molecular Diagnosis and Application, Affiliated Liutie Central Hospital of Guangxi Medical University, Liuzhou, China
| | - Xiao Zhu
- School of Ocean and Tropical Medicine, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
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3
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Chen Y, Hou Y, Li S, Qin W, Zhang J. The N6-methyladenosine methylation landscape stratifies breast cancer into two subtypes with distinct immunological characteristics. Clin Exp Pharmacol Physiol 2024; 51:e13875. [PMID: 38797522 DOI: 10.1111/1440-1681.13875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
N6-methyladenosine (m6A) methylation modification affects the tumorigenesis and metastasis of breast cancer (BC). This study investigated the association between m6A regulator-mediated methylation modification patterns and characterization of the tumour microenvironment in BC, as well as their prognostic importance. Public gene expression data and clinical annotations were collected from The Cancer Genome Atlas (TCGA) database, the Gene Expression Omnibus website and the METABRIC program. We analysed the genetic expression, gene-gene interactions, gene mutations and copy number variations using R software. The data were screened for risk genes using the Cox risk regression model, and we developed an algorithm for risk score and its predictive value. Compared to adjacent normal tissue, we identified 16 differentially expressed m6A regulators in BC, including six writers and 10 readers. Under unsupervised clustering, two distinguished modification patterns were identified, cluster C1 and C2. Compared to m6A cluster C2, cluster C1 was found to be more involved in immune-related pathways, with a relatively higher immune score and stromal score (P < 0.05). Patients were divided into two groups based on their risk scores for survival analysis. The patients in the high-risk score group had significantly worse overall survival than patients in the low-risk score group, (P < 0.0001). The TCGA database validation revealed the same prognostic tendency. In summary, our study showed distinct m6A regulator modification patterns contribute to the immunological heterogeneity and diversity of BC. The development of m6A gene signatures and the m6A score aid in the prognostic prediction of patients with BC.
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Affiliation(s)
- Yang Chen
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yijiang Hou
- School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Shuguang Li
- School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Wenxing Qin
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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4
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Wu J, Huang H, Yang W, Xue T, Wang W, Zheng GD. TRPM4 mRNA stabilization by METTL3-mediated m6A modification promotes calcific aortic valve inflammation. Heliyon 2024; 10:e31871. [PMID: 38868032 PMCID: PMC11167295 DOI: 10.1016/j.heliyon.2024.e31871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
Background Transient receptor potential melastatin 4 (TRPM4) affects immune responses by regulating calcium homeostasis, but its role in calcific aortic valve inflammation remains unclear. This study aimed to assess the expression and function of TRPM4 in patients with or without calcific aortic valve disease (CAVD). Methods The mRNA and protein expression levels of TRPM4 and related factors in calcified and noncalcified tissues were measured using qRT-PCR and Western blot. The proteins interacting with TRPM4 were confirmed by RNA pull-down and RNA immunoprecipitation assays. Dual-Luciferase Reporter Assay was performed to confirm the m6A site of TRPM4. Results The mRNA expression levels of TRPM4, TLR4, IL-6, MCP-1, TNF-α, and NF-κB p65 were significantly higher in calcified aortic valve tissues than in noncalcified tissues, and TRPM4 was significantly positively correlated with inflammation-related factors. The protein expression level of TRPM4, TLR4 and NF-κB p65 were significantly higher in calcified aortic valve tissues than in noncalcified tissues. N6-methyladenosine (m6A) modification of TRPM4 mRNA by METTL3-YTHDF1 up-regulated its expression in CAVD. And TRPM4 promoted the level of inflammation via activation of the JNK-MAPK signaling pathway, after knockdown TRPM4, the production of proinflammatory cytokines was significantly suppressed. Conclusion The results indicate the pivotal role of TRPM4 in CAVD and highlight METTL3-mediated m6A modification of TRPM4 in promoting inflammation through JNK-MAPK signaling pathway. This work provides potential therapeutic strategy to impede inflammation in CAVD.
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Affiliation(s)
- Jianguo Wu
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Haozong Huang
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Wenkai Yang
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Tufeng Xue
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Wenjuan Wang
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Guang-Di Zheng
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
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Hwang HJ, Kim YK. Molecular mechanisms of circular RNA translation. Exp Mol Med 2024:10.1038/s12276-024-01220-3. [PMID: 38871818 DOI: 10.1038/s12276-024-01220-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 06/15/2024] Open
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs without a 5' cap structure and a 3' poly(A) tail typically present in linear mRNAs of eukaryotic cells. CircRNAs are predominantly generated through a back-splicing process within the nucleus. CircRNAs have long been considered non-coding RNAs seemingly devoid of protein-coding potential. However, many recent studies have challenged this idea and have provided substantial evidence that a subset of circRNAs can associate with polysomes and indeed be translated. Therefore, in this review, we primarily highlight the 5' cap-independent internal initiation of translation that occurs on circular RNAs. Several molecular features of circRNAs, including the internal ribosome entry site, N6-methyladenosine modification, and the exon junction complex deposited around the back-splicing junction after back-splicing event, play pivotal roles in their efficient internal translation. We also propose a possible relationship between the translatability of circRNAs and their stability, with a focus on nonsense-mediated mRNA decay and nonstop decay, both of which are well-characterized mRNA surveillance mechanisms. An in-depth understanding of circRNA translation will reshape and expand our current knowledge of proteomics.
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Affiliation(s)
- Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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Zhu DH, Su KK, Ou-Yang XX, Zhang YH, Yu XP, Li ZH, Ahmadi-Nishaboori SS, Li LJ. Mechanisms and clinical landscape of N6-methyladenosine (m6A) RNA modification in gastrointestinal tract cancers. Mol Cell Biochem 2024:10.1007/s11010-024-05040-x. [PMID: 38856795 DOI: 10.1007/s11010-024-05040-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/18/2024] [Indexed: 06/11/2024]
Abstract
Epigenetics encompasses reversible and heritable chemical modifications of non-nuclear DNA sequences, including DNA and RNA methylation, histone modifications, non-coding RNA modifications, and chromatin rearrangements. In addition to well-studied DNA and histone methylation, RNA methylation has emerged as a hot topic in biological sciences over the past decade. N6-methyladenosine (m6A) is the most common and abundant modification in eukaryotic mRNA, affecting all RNA stages, including transcription, translation, and degradation. Advances in high-throughput sequencing technologies made it feasible to identify the chemical basis and biological functions of m6A RNA. Dysregulation of m6A levels and associated modifying proteins can both inhibit and promote cancer, highlighting the importance of the tumor microenvironment in diverse biological processes. Gastrointestinal tract cancers, including gastric, colorectal, and pancreatic cancers, are among the most common and deadly malignancies in humans. Growing evidence suggests a close association between m6A levels and the progression of gastrointestinal tumors. Global m6A modification levels are substantially modified in gastrointestinal tumor tissues and cell lines compared to healthy tissues and cells, possibly influencing various biological behaviors such as tumor cell proliferation, invasion, metastasis, and drug resistance. Exploring the diagnostic and therapeutic potential of m6A-related proteins is critical from a clinical standpoint. Developing more specific and effective m6A modulators offers new options for treating these tumors and deeper insights into gastrointestinal tract cancers.
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Affiliation(s)
- Dan-Hua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Kun-Kai Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xiao-Xi Ou-Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yan-Hong Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xiao-Peng Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Zu-Hong Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | | | - Lan-Juan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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Chen A, Zhang VX, Zhang Q, Sze KMF, Tian L, Huang H, Wang X, Lee E, Lu J, Lyu X, Lee MFJ, Wong CM, Ho DWH, Ng IOL. Targeting the oncogenic m6A demethylase FTO suppresses tumourigenesis and potentiates immune response in hepatocellular carcinoma. Gut 2024:gutjnl-2024-331903. [PMID: 38839271 DOI: 10.1136/gutjnl-2024-331903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
OBJECTIVE Fat mass and obesity-associated protein (FTO), an eraser of N 6-methyadenosine (m6A), plays oncogenic roles in various cancers. However, its role in hepatocellular carcinoma (HCC) is unclear. Furthermore, small extracellular vesicles (sEVs, or exosomes) are critical mediators of tumourigenesis and metastasis, but the relationship between FTO-mediated m6A modification and sEVs in HCC is unknown. DESIGN The functions and mechanisms of FTO and glycoprotein non-metastatic melanoma protein B (GPNMB) in HCC progression were investigated in vitro and in vivo. Neutralising antibody of syndecan-4 (SDC4) was used to assess the significance of sEV-GPNMB. FTO inhibitor CS2 was used to examine the effects on anti-PD-1 and sorafenib treatment. RESULTS FTO expression was upregulated in patient HCC tumours. Functionally, FTO promoted HCC cell proliferation, migration and invasion in vitro, and tumour growth and metastasis in vivo. FTO knockdown enhanced the activation and recruitment of tumour-infiltrating CD8+ T cells. Furthermore, we identified GPNMB to be a downstream target of FTO, which reduced the m6A abundance of GPNMB, hence, stabilising it from degradation by YTH N 6-methyladenosine RNA binding protein F2. Of note, GPNMB was packaged into sEVs derived from HCC cells and bound to the surface receptor SDC4 of CD8+ T cells, resulting in the inhibition of CD8+ T cell activation. A potential FTO inhibitor, CS2, suppresses the oncogenic functions of HCC cells and enhances the sensitivity of anti-PD-1 and sorafenib treatment. CONCLUSION Targeting the FTO/m6A/GPNMB axis could significantly suppress tumour growth and metastasis, and enhance immune activation, highlighting the potential of targeting FTO signalling with effective inhibitors for HCC therapy.
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Affiliation(s)
- Ao Chen
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
- Department of Biology, Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei Province, China
| | - Vanilla Xin Zhang
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Qingyang Zhang
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Karen Man-Fong Sze
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Lu Tian
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Hongyang Huang
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Xia Wang
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Eva Lee
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jingyi Lu
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Xueying Lyu
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Man-Fong Joyce Lee
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chun Ming Wong
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Daniel Wai-Hung Ho
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Irene Oi-Lin Ng
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
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Khan FA, Nsengimana B, Awan UA, Ji XY, Ji S, Dong J. Regulatory roles of N6-methyladenosine (m 6A) methylation in RNA processing and non-communicable diseases. Cancer Gene Ther 2024:10.1038/s41417-024-00789-1. [PMID: 38839892 DOI: 10.1038/s41417-024-00789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
Post-transcriptional RNA modification is an emerging epigenetic control mechanism in cells that is important in many different cellular and organismal processes. N6-methyladenosine (m6A) is one of the most prevalent, prolific, and ubiquitous internal transcriptional alterations in eukaryotic mRNAs, making it an important topic in the field of Epigenetics. m6A methylation acts as a dynamical regulatory process that regulates the activity of genes and participates in multiple physiological processes, by supporting multiple aspects of essential mRNA metabolic processes, including pre-mRNA splicing, nuclear export, translation, miRNA synthesis, and stability. Extensive research has linked aberrations in m6A modification and m6A-associated proteins to a wide range of human diseases. However, the impact of m6A on mRNA metabolism and its pathological connection between m6A and other non-communicable diseases, including cardiovascular disease, neurodegenerative disorders, liver diseases, and cancer remains in fragmentation. Here, we review the existing understanding of the overall role of mechanisms by which m6A exerts its activities and address new discoveries that highlight m6A's diverse involvement in gene expression regulation. We discuss m6A deposition on mRNA and its consequences on degradation, translation, and transcription, as well as m6A methylation of non-coding chromosomal-associated RNA species. This study could give new information about the molecular process, early detection, tailored treatment, and predictive evaluation of human non-communicable diseases like cancer. We also explore more about new data that suggests targeting m6A regulators in diseases may have therapeutic advantages.
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Affiliation(s)
- Faiz Ali Khan
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan.
| | - Bernard Nsengimana
- Department of Hepatobiliary Surgery, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Usman Ayub Awan
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xin-Ying Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
| | - Shaoping Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Jingcheng Dong
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
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9
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Li S, Tan XY, He Z, Shen C, Li YL, Qin L, Zhao CQ, Luo GH, Fang JC, Ji R. The dynamics of N 6-methyladenine RNA modification in resistant and susceptible rice varieties responding to rice stem borer damage. INSECT SCIENCE 2024. [PMID: 38831720 DOI: 10.1111/1744-7917.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024]
Abstract
N6-methyladenosine (m6A) is the most prevalent modification in cellular RNA which orchestrates diverse physiological and pathological processes during stress response. However, the differential m6A modifications that cope with herbivore stress in resistant and susceptible crop varieties remain unclear. Here, we found that rice stem borer (RSB) larvae grew better on indica rice (e.g., MH63, IR64, Nanjing 11) than on japonica rice varieties (e.g., Nipponbare, Zhonghua 11, Xiushui 11). Then, transcriptome-wide m6A profiling of representative resistant (Nipponbare) and susceptible (MH63) rice varieties were performed using a nanopore direct RNA sequencing approach, to reveal variety-specific m6A modifications against RSB. Upon RSB infestation, m6A methylation occurred in actively expressed genes in Nipponbare and MH63, but the number of methylation sites decreased across rice chromosomes. Integrative analysis showed that m6A methylation levels were closely associated with transcriptional regulation. Genes involved in herbivorous resistance related to mitogen-activated protein kinase, jasmonic acid (JA), and terpenoid biosynthesis pathways, as well as JA-mediated trypsin protease inhibitors, were heavily methylated by m6A, and their expression was more pronounced in RSB-infested Nipponbare than in RSB-infested MH63, which may have contributed to RSB resistance in Nipponbare. Therefore, dynamics of m6A modifications act as the main regulatory strategy for expression of genes involved in plant-insect interactions, which is attributed to differential responses of resistant and susceptible rice varieties to RSB infestation. These findings could contribute to developing molecular breeding strategies for controlling herbivorous pests.
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Affiliation(s)
- Shuai Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Xin-Yang Tan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhen He
- School of Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chen Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ya-Li Li
- Wuhan Benagen Technology Company Limited, Wuhan, China
| | - Lang Qin
- School of Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chun-Qing Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guang-Hua Luo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Ji-Chao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, Jiangsu Province, China
| | - Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, Jiangsu Province, China
- School of Life Sciences, Anhui Normal University/Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Wuhu, Anhui Province, China
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10
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Li R, Yan X, Xiao C, Wang T, Li X, Hu Z, Liang J, Zhang J, Cai J, Sui X, Liu Q, Wu M, Xiao J, Chen H, Liu Y, Jiang C, Lv G, Chen G, Zhang Y, Yao J, Zheng J, Yang Y. FTO deficiency in older livers exacerbates ferroptosis during ischaemia/reperfusion injury by upregulating ACSL4 and TFRC. Nat Commun 2024; 15:4760. [PMID: 38834654 PMCID: PMC11150474 DOI: 10.1038/s41467-024-49202-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 05/24/2024] [Indexed: 06/06/2024] Open
Abstract
Older livers are more prone to hepatic ischaemia/reperfusion injury (HIRI), which severely limits their utilization in liver transplantation. The potential mechanism remains unclear. Here, we demonstrate older livers exhibit increased ferroptosis during HIRI. Inhibiting ferroptosis significantly attenuates older HIRI phenotypes. Mass spectrometry reveals that fat mass and obesity-associated gene (FTO) expression is downregulated in older livers, especially during HIRI. Overexpressing FTO improves older HIRI phenotypes by inhibiting ferroptosis. Mechanistically, acyl-CoA synthetase long chain family 4 (ACSL4) and transferrin receptor protein 1 (TFRC), two key positive contributors to ferroptosis, are FTO targets. For ameliorative effect, FTO requires the inhibition of Acsl4 and Tfrc mRNA stability in a m6A-dependent manner. Furthermore, we demonstrate nicotinamide mononucleotide can upregulate FTO demethylase activity, suppressing ferroptosis and decreasing older HIRI. Collectively, these findings reveal an FTO-ACSL4/TFRC regulatory pathway that contributes to the pathogenesis of older HIRI, providing insight into the clinical translation of strategies related to the demethylase activity of FTO to improve graft function after older donor liver transplantation.
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Affiliation(s)
- Rong Li
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Xijing Yan
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China
| | - Cuicui Xiao
- Department of Anesthesiology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Tingting Wang
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China
| | - Xuejiao Li
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhongying Hu
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Jinliang Liang
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Jiebin Zhang
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China
| | - Jianye Cai
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China
| | - Xin Sui
- Surgical ICU, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Qiuli Liu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Manli Wu
- Department of ultrasound, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jiaqi Xiao
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China
| | - Haitian Chen
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China
| | - Yasong Liu
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China
| | - Chenhao Jiang
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China
| | - Guo Lv
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Guihua Chen
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China
| | - Yingcai Zhang
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China.
| | - Jia Yao
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China.
| | - Jun Zheng
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China.
| | - Yang Yang
- Guangdong Provincial Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou, 510630, China.
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11
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Liu Y, Sun X, Gou Z, Deng Z, Zhang Y, Zhao P, Sun W, Bai Y, Jing Y. Epigenetic modifications in abdominal aortic aneurysms: from basic to clinical. Front Cardiovasc Med 2024; 11:1394889. [PMID: 38895538 PMCID: PMC11183338 DOI: 10.3389/fcvm.2024.1394889] [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: 03/11/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Abdominal Aortic Aneurysm (AAA) is a disease characterized by localized dilation of the abdominal aorta, involving multiple factors in its occurrence and development, ultimately leading to vessel rupture and severe bleeding. AAA has a high mortality rate, and there is a lack of targeted therapeutic drugs. Epigenetic regulation plays a crucial role in AAA, and the treatment of AAA in the epigenetic field may involve a series of related genes and pathways. Abnormal expression of these genes may be a key factor in the occurrence of the disease and could potentially serve as promising therapeutic targets. Understanding the epigenetic regulation of AAA is of significant importance in revealing the mechanisms underlying the disease and identifying new therapeutic targets. This knowledge can contribute to offering AAA patients better clinical treatment options beyond surgery. This review systematically explores various aspects of epigenetic regulation in AAA, including DNA methylation, histone modification, non-coding RNA, and RNA modification. The analysis of the roles of these regulatory mechanisms, along with the identification of relevant genes and pathways associated with AAA, is discussed comprehensively. Additionally, a comprehensive discussion is provided on existing treatment strategies and prospects for epigenetics-based treatments, offering insights for future clinical interventions.
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Affiliation(s)
- YuChen Liu
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - XiaoYun Sun
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Zhen Gou
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - ZhenKun Deng
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - YunRui Zhang
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - PingPing Zhao
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Wei Sun
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Yang Bai
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - YuChen Jing
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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12
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Chen JJ, Lu TZ, Wang T, Yan WH, Zhong FY, Qu XH, Gong XC, Li JG, Tou FF, Jiang LP, Han XJ. The m6A reader HNRNPC promotes glioma progression by enhancing the stability of IRAK1 mRNA through the MAPK pathway. Cell Death Dis 2024; 15:390. [PMID: 38830885 PMCID: PMC11148022 DOI: 10.1038/s41419-024-06736-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/04/2024] [Accepted: 05/09/2024] [Indexed: 06/05/2024]
Abstract
Glioma is the most common and aggressive type of primary malignant brain tumor. The N6-methyladenosine (m6A) modification widely exists in eukaryotic cells and plays an important role in the occurrence and development of human tumors. However, the function and mechanism of heterogeneous nuclear ribonucleoprotein C (HNRNPC), an RNA-binding protein and m6A reader in gliomas remains to be comprehensively and extensively explored. Herein, we found that HNRNPC mRNA and protein overexpression were associated with a poor prognosis for patients with gliomas, based on the data from TCGA, the CGGA, and the TMAs. Biologically, HNRNPC knockdown markedly repressed malignant phenotypes of glioma in vitro and in vivo, whereas ectopic HNRNPC expression had the opposite effect. Integrative RNA sequencing and MeRIP sequencing analyses identified interleukin-1 receptor-associated kinase 1 (IRAK1) as a downstream target of HNRNPC. The glioma public datasets and tissue microarrays (TMAs) data indicated that IRAK1 overexpression was associated with poor prognosis, and IRAK1 knockdown significantly repressed malignant biological behavior in vitro. Mechanistically, HNRNPC maintains the mRNA stability of IRAK1 in an m6A-dependent manner, resulting in activation of the mitogen-activated protein kinase (MAPK) signaling pathway, which was necessary for the malignant behavior of glioma. Our findings demonstrate the HNRNPC-IRAK1-MAPK axis as a crucial carcinogenic factor for glioma and the novel underlying mechanism of IRAK1 upregulation, which provides a rationale for therapeutically targeting epitranscriptomic modulators in glioma.
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Affiliation(s)
- Jun-Jun Chen
- Department of Pharmacology, School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
- Institute of Geriatrics, Jiangxi Provincial People's Hospital & The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Tian-Zhu Lu
- NHC Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
| | - Tao Wang
- Institute of Geriatrics, Jiangxi Provincial People's Hospital & The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Wen-Hui Yan
- Department of Pharmacology, School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
- Institute of Geriatrics, Jiangxi Provincial People's Hospital & The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Fang-Yan Zhong
- NHC Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
| | - Xin-Hui Qu
- The Second Department of Neurology, Jiangxi Provincial People's Hospital & the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Xiao-Chang Gong
- NHC Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
| | - Jin-Gao Li
- NHC Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
| | - Fang-Fang Tou
- Department of Oncology, Jiangxi Provincial People's Hospital & the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Li-Ping Jiang
- Department of Pharmacology, School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
- Key Laboratory of Drug Targets and Drug Screening of Jiangxi Province, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Xiao-Jian Han
- Institute of Geriatrics, Jiangxi Provincial People's Hospital & The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China.
- Key Laboratory of Drug Targets and Drug Screening of Jiangxi Province, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China.
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13
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Gu T, Guo R, Fang Y, Xiao Y, Chen L, Li N, Ge XK, Shi Y, Wu J, Yan M, Yu J, Li Z. METTL3-mediated pre-miR-665/DLX3 m 6A methylation facilitates the committed differentiation of stem cells from apical papilla. Exp Mol Med 2024:10.1038/s12276-024-01245-8. [PMID: 38825638 DOI: 10.1038/s12276-024-01245-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 01/16/2024] [Accepted: 03/11/2024] [Indexed: 06/04/2024] Open
Abstract
Methyltransferase-like 3 (METTL3) is a crucial element of N6-methyladenosine (m6A) modifications and has been extensively studied for its involvement in diverse biological and pathological processes. In this study, we explored how METTL3 affects the differentiation of stem cells from the apical papilla (SCAPs) into odonto/osteoblastic lineages through gain- and loss-of-function experiments. The m6A modification levels were assessed using m6A dot blot and activity quantification experiments. In addition, we employed Me-RIP microarray experiments to identify specific targets modified by METTL3. Furthermore, we elucidated the molecular mechanism underlying METTL3 function through dual-luciferase reporter gene experiments and rescue experiments. Our findings indicated that METTL3+/- mice exhibited significant root dysplasia and increased bone loss. The m6A level and odonto/osteoblastic differentiation capacity were affected by the overexpression or inhibition of METTL3. This effect was attributed to the acceleration of pre-miR-665 degradation by METTL3-mediated m6A methylation in cooperation with the "reader" protein YTHDF2. Additionally, the targeting of distal-less homeobox 3 (DLX3) by miR-665 and the potential direct regulation of DLX3 expression by METTL3, mediated by the "reader" protein YTHDF1, were demonstrated. Overall, the METTL3/pre-miR-665/DLX3 pathway might provide a new target for SCAP-based tooth root/maxillofacial bone tissue regeneration.
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Affiliation(s)
- Tingjie Gu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University and Department of Stomatology, Nanjing Medical University, Nanjing, China
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Rong Guo
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University and Department of Stomatology, Nanjing Medical University, Nanjing, China
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yuxin Fang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University and Department of Stomatology, Nanjing Medical University, Nanjing, China
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Ya Xiao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University and Department of Stomatology, Nanjing Medical University, Nanjing, China
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Luyao Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University and Department of Stomatology, Nanjing Medical University, Nanjing, China
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Na Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University and Department of Stomatology, Nanjing Medical University, Nanjing, China
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Xingyun Kelesy Ge
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR, China
| | - Yijia Shi
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University and Department of Stomatology, Nanjing Medical University, Nanjing, China
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Jintao Wu
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Ming Yan
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Jinhua Yu
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
| | - Zehan Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University and Department of Stomatology, Nanjing Medical University, Nanjing, China.
- Department of Endodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
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14
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Song D, Dai X, Fu M, Sun Y, Wu X, Zhou Q, Bi W, Sun J, Yang F, Yu Y. Insights into the role of the N6-methyladenosine reader IGF2BP3 in the progression of oral squamous cell carcinoma and its connection to cell-cycle control. Transl Oncol 2024; 44:101932. [PMID: 38492500 PMCID: PMC10959721 DOI: 10.1016/j.tranon.2024.101932] [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: 11/06/2023] [Revised: 02/17/2024] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
The genome of oral squamous cell carcinoma (OSCC) has been extensively characterized via bulk sequencing, revealing a multitude of genetic changes. The gene IGF2BP3, which encodes for the insulin-like growth factor 2 mRNA-binding protein 3, has been observed to be highly expressed in several types of cancer. This finding suggests that IGF2BP3 may play a significant role in the initiation and advancement of cancer. Nevertheless, the mechanisms by which IGF2BP3 contribute to OSCC are yet to be fully understood. In this study, we have observed that IGF2BP3 exhibits overexpression in OSCC. Based on our findings from bulk sequencing analysis, we have concluded that IGF2BP3 could potentially serve as a biomarker for predicting poor prognosis in OSCC. Moreover, it has been demonstrated that IGF2BP3 exhibits a significant association with the initiation and advancement of tumors both in vivo and in vitro. The evaluation of IGF2BP3 expression levels in relation to the cell cycle stage was conducted using single-cell RNA sequencing data. Tumor cells characterized by elevated IGF2BP3 expression demonstrated a higher percentage of cells in the G2/M transition phase. This study presents new findings indicating that the molecular target IGF2BP3 can serve as a prognostic indicator for tumors and has an impact on the development and progression of OSCC by influencing the regulation of the cell cycle.
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Affiliation(s)
- Dandan Song
- Department of Stomatology, Zhongshan Hospital, Fudan University, No.180, Fenglin Road, Shanghai 200032, China
| | - Xiaofeng Dai
- Department of Stomatology, Shanghai Jing-An Dental Clinic, Shanghai 200040, China
| | - Minna Fu
- Department of Stomatology, Zhongshan Hospital, Fudan University, No.180, Fenglin Road, Shanghai 200032, China
| | - Yang Sun
- Department of Stomatology, Zhongshan Hospital, Fudan University, No.180, Fenglin Road, Shanghai 200032, China
| | - Xingwen Wu
- Department of Stomatology, Zhongshan Hospital, Fudan University, No.180, Fenglin Road, Shanghai 200032, China
| | - Qianrong Zhou
- Department of Stomatology, Zhongshan Hospital, Fudan University, No.180, Fenglin Road, Shanghai 200032, China
| | - Wei Bi
- Department of Stomatology, Zhongshan Hospital, Fudan University, No.180, Fenglin Road, Shanghai 200032, China
| | - Jian Sun
- Department of Stomatology, Zhongshan Hospital, Fudan University, No.180, Fenglin Road, Shanghai 200032, China
| | - Fei Yang
- Department of Stomatology, Zhongshan Hospital, Fudan University, No.180, Fenglin Road, Shanghai 200032, China.
| | - Youcheng Yu
- Department of Stomatology, Zhongshan Hospital, Fudan University, No.180, Fenglin Road, Shanghai 200032, China.
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15
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Fu M, Chen Y, Shi X. ZC3H13 Accelerates Keloid Formation by Mediating N 6-methyladenosine Modification of HIPK2. Biochem Genet 2024; 62:1857-1871. [PMID: 37752292 DOI: 10.1007/s10528-023-10514-6] [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: 06/24/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
Keloids are fibroproliferative skin disorders caused by the improper healing of wounded skin. A growing body of evidence suggests the involvement of N6-Methyladenosine (m6A) modification in various bioprocesses; however, its role in keloid formation has not yet been investigated. The aim of this study was to determine the effect of the m6A regulator zinc finger CCCH domain containing protein 13 (ZC3H13) on the pathogenesis of keloid formation. ZC3H13 and homeodomain-interacting protein kinase 2 (HIPK2) expression was evaluated in healthy skin and keloid tissues, as well as in human dermal fibroblasts and human keloid fibroblasts (HKF), using qRT-PCR and western blotting. The effects of ZC3H13 overexpression and knockdown on the cell function of HKFs were assessed using CCK8, transwell, and flow cytometry. Furthermore, the influence of ZC3H13 on HIPK2 m6A modification was assessed using MeRIP-qPCR and mRNA stability assays. Both ZC3H13 expression and m6A RNA methylation were upregulated in keloid tissues and HKFs. Silencing of ZC3H13 inhibited proliferation and migration, while enhancing apoptosis in HKFs, whereas overexpression had the opposite effect. Furthermore, HIPK2 levels were high in keloid tissues and HKFs, and a positive correlation was observed between ZC3H13 and HIPK2. In HKFs, ZC3H13 overexpression elevated the m6A levels of HIPK2 mRNA and reduced the rate of HIPK2 mRNA degradation. Mechanically, ZC3H13-induced m6A modifications significantly improved HIPK2 mRNA stability. Collectively, ZC3H13 accelerated keloid formation by mediating the m6A modification of HIPK2 mRNA and maintaining its stability.
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Affiliation(s)
- Manni Fu
- Department of dermatology, Huangshi Central Hospital, No.293, Hospital Street, Xisai District, Huangshi, 435000, Hubei, China
| | - Yongjun Chen
- Department of dermatology, Huangshi Central Hospital, No.293, Hospital Street, Xisai District, Huangshi, 435000, Hubei, China
| | - Xian Shi
- Department of dermatology, Huangshi Central Hospital, No.293, Hospital Street, Xisai District, Huangshi, 435000, Hubei, China.
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16
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Liu X, Xie X, Sui C, Liu X, Song M, Luo Q, Zhan P, Feng J, Liu J. Unraveling the cross-talk between N6-methyladenosine modification and non-coding RNAs in breast cancer: Mechanisms and clinical implications. Int J Cancer 2024; 154:1877-1889. [PMID: 38429857 DOI: 10.1002/ijc.34900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
In recent years, breast cancer (BC) has surpassed lung cancer as the most common malignant tumor worldwide and remains the leading cause of cancer death in women. The etiology of BC usually involves dysregulation of epigenetic mechanisms and aberrant expression of certain non-coding RNAs (ncRNAs). N6-methyladenosine (m6A), the most prevalent RNA modification in eukaryotes, widely exists in ncRNAs to affect its biosynthesis and function, and is an important regulator of tumor-related signaling pathways. Interestingly, ncRNAs can also regulate or target m6A modification, playing a key role in cancer progression. However, the m6A-ncRNAs regulatory network in BC has not been fully elucidated, especially the regulation of m6A modification by ncRNAs. Therefore, in this review, we comprehensively summarize the interaction mechanisms and biological significance of m6A modifications and ncRNAs in BC. Meanwhile, we also focused on the clinical application value of m6A modification in BC diagnosis and prognosis, intending to explore new biomarkers and potential therapeutic targets.
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Affiliation(s)
- Xuan Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Xuelong Xie
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Chentao Sui
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Xuexue Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Miao Song
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Qing Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Ping Zhan
- Department of Obstetrics, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jia Feng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
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17
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Nasimi Shad A, Fanoodi A, Maharati A, Akhlaghipour I, Bina AR, Saburi E, Forouzanfar F, Moghbeli M. Role of microRNAs in tumor progression by regulation of kinesin motor proteins. Int J Biol Macromol 2024; 270:132347. [PMID: 38754673 DOI: 10.1016/j.ijbiomac.2024.132347] [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: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
Aberrant cell proliferation is one of the main characteristics of tumor cells that can be affected by many cellular processes and signaling pathways. Kinesin superfamily proteins (KIFs) are motor proteins that are involved in cytoplasmic transportations and chromosomal segregation during cell proliferation. Therefore, regulation of the KIF functions as vital factors in chromosomal stability is necessary to maintain normal cellular homeostasis and proliferation. KIF deregulations have been reported in various cancers. MicroRNAs (miRNAs) and signaling pathways are important regulators of KIF proteins. MiRNAs have key roles in regulation of the cell proliferation, migration, and apoptosis. In the present review, we discussed the role of miRNAs in tumor biology through the regulation of KIF proteins. It has been shown that miRNAs have mainly a tumor suppressor function via the KIF targeting. This review can be an effective step to introduce the miRNAs/KIFs axis as a probable therapeutic target in tumor cells.
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Affiliation(s)
- Arya Nasimi Shad
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Fanoodi
- Student Research Committee, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Iman Akhlaghipour
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Reza Bina
- Student Research Committee, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Ehsan Saburi
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Forouzanfar
- Clinical Research Development Unit, Imam Reza Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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18
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He B, Chen Y, Yi C. Quantitative mapping of the mammalian epitranscriptome. Curr Opin Genet Dev 2024; 87:102212. [PMID: 38823337 DOI: 10.1016/j.gde.2024.102212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/04/2024] [Accepted: 05/17/2024] [Indexed: 06/03/2024]
Abstract
The epitranscriptome encompasses a diverse array of dynamic and reversible RNA modifications, affecting both coding and noncoding RNAs. Over 170 types of RNA chemical modifications have been identified, underscoring the need for innovative detection methods to deepen our understanding of RNA modification roles and mechanisms. In particular, the base resolution and quantitative information on RNA modifications are critical for understanding the regulation and functions of RNA modifications. Based on detection throughput and principles, existing quantitative RNA modification detection methods can be categorized into two groups, including next-generation sequencing and nanopore direct RNA sequencing. In this review, we focus on methodologies for elucidating the base resolution and stoichiometric information of RNA modifications. In addition, we further discuss the challenges and the potential prospects of the quantitative RNA modification detection methods.
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Affiliation(s)
- Bo He
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yuting Chen
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China
| | - Chengqi Yi
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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19
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Zhang J, Yao S, Cheng X, Zhao Y, Yu W, Ren X, Ji K, Yu Q. Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing RNA-Binding Protein Family in Cinnamomum camphora. Int J Mol Sci 2024; 25:5960. [PMID: 38892149 PMCID: PMC11173211 DOI: 10.3390/ijms25115960] [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: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
N6-methyladenosine (m6A) is one of the most abundant chemical modifications on mRNA in eukaryotes. RNA-binding proteins containing the YT521-B (YTH) domain play crucial roles in post-transcriptional regulation of plant growth, development, and stress response by reading the m6A mark. However, the YTH domain-containing RNA-binding protein family has not been studied in a valuable and medicinal tree such as Cinnamomum camphora (C. camphora) yet. In this study, we identified 10 YTH genes in C. camphora, located on eight out of 12 chromosomes. Phylogenetic analysis revealed that these genes can be classified into two major classes, YTHDF (CcDF) and YTHDC (CcDC). Closely related CcYTHs within the same class exhibited a similar distribution of conserved motifs and domain organization, suggesting functional similarities among these closely related CcYTHs. All CcYTH proteins possessed a highly conserved YTH domain, with CcDC1A containing an additional CCCH domain. The liquid-liquid phase separation (LLPS) predictions indicate that CcDC1A, CcDF1A, CcDF1C, CcDF3C, CcDF4C, and CcDF5C may undergo phase transitions. Quantitative expression analysis revealed that tissue-specific expression was observed fo CcYTHs. Notably, there were two genes, CcDF1A and CcDF5C; both exhibited significantly higher expression levels in various tissues than other genes, indicating that the m6A-YTH regulatory network in C. camphora might be quite distinct from that in most plants such as Arabidopsis thaliana (A. thaliana) with only one abundant YTH protein. According to the analysis of the up-stream cis-regulatory elements of these YTH genes, these genes could be closely related to stress, hormones, and development. The following stress response experiments further verified that their expression levels indeed changed under both PEG and NaCl treatments. These findings not only provide a foundation for future functional analysis of CcYTHs in C. camphora, but also provide insights into the functions of epigenetic mark m6A in forest trees.
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Affiliation(s)
- Jingjing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yulu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenya Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xingyue Ren
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qiong Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
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20
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Gu N, Shen Y, He Y, Li C, Xiong W, Hu Y, Qiu Z, Peng F, Han W, Li C, Long X, Zhao R, Zhao Y, Shi B. Loss of m6A demethylase ALKBH5 alleviates hypoxia-induced pulmonary arterial hypertension via inhibiting Cyp1a1 mRNA decay. J Mol Cell Cardiol 2024:S0022-2828(24)00087-7. [PMID: 38821243 DOI: 10.1016/j.yjmcc.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Hypoxia-induced pulmonary artery hypertension (HPH) is a complication of chronic hypoxic lung disease and the third most common type of pulmonary artery hypertension (PAH). Epigenetic mechanisms play essential roles in the pathogenesis of HPH. N6-methyladenosine (m6A) is an important modified RNA nucleotide involved in a variety of biological processes and an important regulator of epigenetic processes. To date, the precise role of m6A and regulatory molecules in HPH remains unclear. METHODS HPH model and pulmonary artery smooth muscle cells (PASMCs) were constructed from which m6A changes were observed and screened for AlkB homolog 5 (Alkbh5). Alkbh5 knock-in (KI) and knock-out (KO) mice were constructed to observe the effects on m6A and evaluate right ventricular systolic pressure (RVSP), left ventricular and septal weight [RV/(LV + S)], and pulmonary vascular remodeling in the context of HPH. Additionally, the effects of Alkbh5 knockdown using adenovirus were examined in vitro on m6A, specifically in PASMCs with regard to proliferation, migration and cytochrome P450 1A1 (Cyp1a1) mRNA stability. RESULTS In both HPH mice lung tissues and hypoxic PASMCs, a decrease in m6A was observed, accompanied by a significant up-regulation of Alkbh5 expression. Loss of Alkbh5 attenuated the proliferation and migration of hypoxic PASMCs in vitro, with an associated increase in m6A modification. Furthermore, Alkbh5 KO mice exhibited reduced RVSP, RV/(LV + S), and attenuated vascular remodeling in HPH mice. Mechanistically, loss of Alkbh5 inhibited Cyp1a1 mRNA decay and increased its expression through an m6A-dependent post-transcriptional mechanism, which hindered the proliferation and migration of hypoxic PASMCs. CONCLUSION The current study highlights the loss of Alkbh5 impedes the proliferation and migration of PASMCs by inhibiting post-transcriptional Cyp1a1 mRNA decay in an m6A-dependent manner.
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Affiliation(s)
- Ning Gu
- College of Medicine, Soochow University, Suzhou, China; Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Youcheng Shen
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yuanjie He
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Chaofu Li
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Weidong Xiong
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yiqing Hu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Zhimei Qiu
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Fengli Peng
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Weiyu Han
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Chaozhong Li
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xianping Long
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Ranzun Zhao
- College of Medicine, Soochow University, Suzhou, China; Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yongchao Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China; Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China.
| | - Bei Shi
- College of Medicine, Soochow University, Suzhou, China; Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China.
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21
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Yang K, Zhong Z, Zou J, Liao JY, Chen S, Zhou S, Zhao Y, Li J, Yin D, Huang K, Li Y. Glycolysis and tumor progression promoted by the m 6A writer VIRMA via m 6A-dependent upregulation of STRA6 in pancreatic ductal adenocarcinoma. Cancer Lett 2024; 590:216840. [PMID: 38604311 DOI: 10.1016/j.canlet.2024.216840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal malignancies, highlighting the urgent need to elucidate the underlying oncogenic mechanisms. VIRMA is a classic isoform of methyltransferases that participates in epigenetic transcriptomic modification in eukaryotic mRNAs. However, the exact roles of VIRMA in PDAC remain unclear. Here, we identified that VIRMA is highly expressed in PDAC, and histone modifications of the promoter may partly account for this dysregulation. Moreover, VIRMA is closely related to glycolysis and poor prognosis in PDAC. We further determined that STRA6 is a direct downstream target of VIRMA in PDAC by RNA sequencing (RNA-seq) and m6A sequencing (m6A-seq). VIRMA is involved in gene expression regulation via 3' UTR targeting of STRA6 mRNA. Furthermore, the m6A reader IGF2BP2 was shown to critically contribute to the stability of STRA6 mRNA. We describe the role of VIRMA in promoting signaling via the STRA6/STAT3 axis, which results in increased levels of HIF-1α, a key activator of glycolysis. In vivo and in vitro experiments reveal that the VIRMA-STRA6-STAT3-HIF-1α axis plays an instrumental role in glycolysis and tumor progression in PDAC. In conclusion, we demonstrate that VIRMA can increase glycolysis in PDAC by upregulating STRA6, a cell surface membrane protein that stimulates the STAT3 pathway, thereby activating HIF-1α and leading to pancreatic cancer malignancy. Overall, our data strongly suggest that the VIRMA-STRA6-STAT3-HIF-1α axis is a viable therapeutic target in PDAC.
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Affiliation(s)
- Kege Yang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Ziyi Zhong
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Jinmao Zou
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Jian-You Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Shaojie Chen
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Shurui Zhou
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Yue Zhao
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Jiajia Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. Guangdong, PR China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Kaihong Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China.
| | - Yaqing Li
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China.
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22
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Yang S, Xu L, Zhuang H, Li F, Lu Y. A new perspective on hematological malignancies: m6A modification in immune microenvironment. Front Immunol 2024; 15:1374390. [PMID: 38868768 PMCID: PMC11168112 DOI: 10.3389/fimmu.2024.1374390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Immunotherapy for hematological malignancies is a rapidly advancing field that has gained momentum in recent years, primarily encompassing chimeric antigen receptor T-cell (CAR-T) therapies, immune checkpoint inhibitors, and other modalities. However, its clinical efficacy remains limited, and drug resistance poses a significant challenge. Therefore, novel immunotherapeutic targets and agents need to be identified. Recently, N6-methyladenosine (m6A), the most prevalent RNA epitope modification, has emerged as a pivotal factor in various malignancies. Reportedly, m6A mutations influence the immunological microenvironment of hematological malignancies, leading to immune evasion and compromising the anti-tumor immune response in hematological malignancies. In this review, we comprehensively summarize the roles of the currently identified m6A modifications in various hematological malignancies, with a particular focus on their impact on the immune microenvironment. Additionally, we provide an overview of the research progress made in developing m6A-targeted drugs for hematological tumor therapy, to offer novel clinical insights.
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Affiliation(s)
- Shiyu Yang
- Department of Hematology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Institute of Hematology, Ningbo University, Ningbo, China
| | - Liping Xu
- Department of Hematology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Institute of Hematology, Ningbo University, Ningbo, China
| | - Haihui Zhuang
- Department of Hematology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Institute of Hematology, Ningbo University, Ningbo, China
| | - Fenglin Li
- Department of Hematology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Institute of Hematology, Ningbo University, Ningbo, China
| | - Ying Lu
- Department of Hematology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Institute of Hematology, Ningbo University, Ningbo, China
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23
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Dabrowski KR, Daws SE. Morphine-Driven m6A Epitranscriptomic Neuroadaptations in Primary Cortical Cultures. Mol Neurobiol 2024:10.1007/s12035-024-04219-z. [PMID: 38780720 DOI: 10.1007/s12035-024-04219-z] [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: 10/04/2023] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Opioid overdose is the leading cause of accidental death in the United States and remains a major public health concern, despite significant resources aimed at combating opioid misuse. Neurobiological research to elucidate molecular and cellular consequences of opioid exposure is required to define avenues to explore for reversal of opioid-induced neuroadaptations. Opioids impart well-documented regulation of the transcriptome and epigenetic modifications in the brain, but opioid-induced epitranscriptomic posttranscriptional regulation of RNA is vastly understudied. N6-methyladenosine (m6A) RNA methylation is significantly enriched in the brain and involved in learning, memory, and reward. m6A modifications have not been studied in opioid use disorder, despite being the most common RNA modification. We detected significant regulation of m6A-modifying enzymes in rat primary cortical cultures following morphine treatment, including AlkB Homolog 5 (Alkbh5). The m6a demethylase ALKBH5 functions as an m6A eraser, removing m6A modifications from mRNA. We hypothesized that chronic opioid treatment regulates m6A modifications through modulation of Alkbh5 and profiled m6A modifications in primary cortical cultures following chronic morphine treatment and Alkbh5 knock-down. We observed differential regulation of m6A modifications for a common set of transcripts following morphine or Alkbh5 knock-down, and the two treatments elicited concordant m6A epitranscriptomic profiles, suggesting that a subset of morphine-driven m6A modifications may be mediated through downregulation of Alkbh5 in cortical cultures. Gene Ontology terms of commonly regulated transcripts included serotonin secretion, synapse disassembly, neuron remodeling, and immune response. Thus, we conclude that morphine can drive epitranscriptomic changes, a subset of which may occur in an Alkbh5-dependent manner.
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Affiliation(s)
- Konrad R Dabrowski
- Center for Substance Abuse Research, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Stephanie E Daws
- Center for Substance Abuse Research, Temple University, Philadelphia, PA, USA.
- Department of Neural Sciences, Temple University, Philadelphia, PA, USA.
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24
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Mishra T, Phillips S, Maldonado C, Stapleton JT, Wu L. Antiretroviral Therapy Suppresses RNA N6-Methyladenosine Modification in Peripheral Blood Mononuclear Cells from HIV-1-Infected Individuals. AIDS Res Hum Retroviruses 2024. [PMID: 38753726 DOI: 10.1089/aid.2024.0003] [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] [Indexed: 05/18/2024] Open
Abstract
RNA N6-methyladenosine (m6A) modification is important for regulating gene expression and innate immune responses to viral infection. HIV-1 in vitro infection induces a significant increase in m6A modification of cellular RNA; however, whether m6A levels of cellular RNA are affected by HIV-1 replication or by antiretroviral therapy (ART) in infected individuals remains unknown. Using dot blot or enzyme-linked immunosorbent assay, we measured RNA m6A levels of peripheral blood mononuclear cells (PBMCs) from healthy donors or HIV-1-infected individuals with or without ART. Using a reverse transcription-quantitative polymerase chain reaction array, we quantified expression levels of 84 type-I interferon (IFN-I)-responsive genes in PBMCs from some individuals of these three groups. RNA m6A levels in PBMCs from HIV-1 viremic patients (n = 10) were significantly higher (p ≤ .0001) compared with ART-treated individuals (n = 22) or 1.5-fold higher compared with healthy donors (n = 14). However, the increase in RNA m6A levels did not correlate with changes in the expression of 10 m6A-regulatory genes. We found significant upregulation and downregulation in the expression of several IFN-I-responsive genes from HIV-1 viremic patients (n = 4) and ART-treated patients (n = 6) compared with healthy donors (n = 5), respectively. Our results suggest that post-transcriptional m6A modification may contribute to the regulation of IFN-I-responsive gene expression during HIV-1 infection and ART.
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Affiliation(s)
- Tarun Mishra
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Stacia Phillips
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Crystal Maldonado
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Jack T Stapleton
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Division of Infectious Diseases, Department of Internal Medicine, Carver College of Medicine, University of Iowa, The Iowa City VA Healthcare System, Iowa City, Iowa, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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25
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Shi R, Zhao R, Shen Y, Wei S, Zhang T, Zhang J, Shu W, Cheng S, Teng H, Wang H. IGF2BP2-modified circular RNA circCHD7 promotes endometrial cancer progression via stabilizing PDGFRB and activating JAK/STAT signaling pathway. Cancer Gene Ther 2024:10.1038/s41417-024-00781-9. [PMID: 38778089 DOI: 10.1038/s41417-024-00781-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
Circular RNAs (circRNAs) represent a class of covalently closed, single-stranded RNAs and have been linked to cancer progression. N6-methyladenosine (m6A) methylation is a ubiquitous RNA modification in cancer cells. Increasing evidence suggests that m6A can mediate the effects of circRNAs in cancer biology. In contrast, the post-transcriptional systems of m6A and circRNA in the progression of endometrial cancer (EC) remain obscure. The current study identified a novel circRNA with m6A modification, hsa_circ_0084582 (circCHD7), which was upregulated in EC tissues. Functionally, circCHD7 was found to promote the proliferation of EC cells. Mechanistically, circCHD7 interacted with insulin-like growth factor 2 mRNA-binding protein (IGF2BP2) to amplify its enrichment. Moreover, circCHD7 increased the mRNA stability of platelet-derived growth factor receptor beta (PDGFRB) in an m6A-dependent manner, thereby enhancing its expression. In addition, the circCHD7/IGF2BP2/PDGFRB axis activated the JAK/STAT signaling pathway and promoted EC cell proliferation. In conclusion, these findings provide new insights into the regulation of circRNA-mediated m6A modification, and the new "circCHD7-PDGFRB" model of regulation offers new perspectives on circCHD7 as a potential target for EC therapy.
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Affiliation(s)
- Rui Shi
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China
| | - Yan Shen
- Health Management Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China
| | - Sitian Wei
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China
| | - Tangansu Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China
| | - Shuangshuang Cheng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China
| | - Hua Teng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China
| | - Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, PR China.
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Liu MH, Zhao NN, Yu WT, Qiu JG, Jiang BH, Zhang Y, Zhang CY. Construction of a label-free fluorescent biosensor for homogeneous detection of m 6A eraser FTO in breast cancer tissues. Talanta 2024; 272:125784. [PMID: 38364555 DOI: 10.1016/j.talanta.2024.125784] [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: 12/06/2023] [Revised: 01/24/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
Fat mass and obesity-associated protein (FTO) is a crucial eraser of RNA N6- methyladenosine (m6A) modification, and abnormal FTO expression level is implicated in pathogenesis of numerous cancers. Herein, we demonstrate the construction of a label-free fluorescent biosensor for homogeneous detection of m6A eraser FTO in breast cancer tissues. When FTO is present, it specifically erases the methyl group in m6A, inducing the cleavage of demethylated DNA by endonuclease DpnII and the generation of a single-stranded DNA (ssDNA) with a 3'-hydroxyl group. Subsequently, terminal deoxynucleotidyl transferase (TdT) promotes the incorporation of dTTPs into the ssDNA to obtain a long polythymidine (T) DNA sequence. The resultant long poly (T) DNA sequence can act as a template to trigger hyperbranched strand displacement amplification (HSDA), yielding numerous DNA fragments that may be stained by SYBR Gold to produce an enhanced fluorescence signal. This biosensor processes ultrahigh sensitivity with a detection limit of 1.65 × 10-10 mg/mL (2.6 fM), and it can detect the FTO activity in a single MCF-7 cell. Moreover, this biosensor can screen the FTO inhibitors, evaluate enzyme kinetic parameters, and discriminate the FTO expression levels in the tissues of breast cancer patients and healthy persons.
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Affiliation(s)
- Ming-Hao Liu
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China; College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China; College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China
| | - Ning-Ning Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Wan-Tong Yu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Jian-Ge Qiu
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Bing-Hua Jiang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Yan Zhang
- College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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Su Y, Hu Y, Qu B, Lei R, Guo G. METTL3 Promotes OSCC Progression by Down-Regulating WEE1 in a m6A-YTHDF2-Dependent Manner. Mol Biotechnol 2024:10.1007/s12033-024-01165-y. [PMID: 38744787 DOI: 10.1007/s12033-024-01165-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
Oral squamous cell carcinoma (OSCC) is a common and highly lethal epithelial cancer. This study aimed to confirm the role of METTL3 in promoting OSCC and investigate its specific underlying mechanisms. Expression of the METTL3, YTH domain-containing family 2 (YTHDF2), and WEE1 were examined in normal oral epithelial cells and OSCC cells. Cell functions were examined after overexpressing WEE1 in OSCC cells. MeRIP-qPCR analysis was used to detect WEE1 m6A levels in HOK, SCC25, and CAL27 cells. WEE1 and its m6A levels were evaluated in OSCC cells by knocking down METTL3/YTHDF2, assessing the interaction between METTL3/YTHDF2 and WEE1. The impact of METTL3 and YTHDF2 downregulation on WEE1 mRNA stability was also investigated. The tumor weight and volume in a nude mouse model of OSCC after overexpression of WEE1 and YTHDF2 were measured. Expression of Ki-67 and WEE1 in OSCC tissue was detected using immunohistochemistry. Compared to normal oral epithelial cells, METTL3 and YTHDF2 were upregulated in OSCC cells, while WEE1 was downregulated, and there was a negative correlation between WEE1 and METTL3/YTHDF2 expression. WEE1 overexpression inhibited proliferation, invasion, and migration while promoting apoptosis in OSCC cells. METTL3 and YTHDF2 bound to WEE1 mRNA. METTL3/YTHDF2 knockdown increased WEE1 levels and WEE1 mRNA stability. METTL3 inhibition reduced WEE1 m6A levels. Inhibition of METTL3 weakened the interaction between YTHDF2 and WEE1 mRNA. In vivo, overexpression of WEE1 suppressed OSCC development, which was reversed by overexpression of YTHDF2. METTL3 facilitates the progression of OSCC through m6A-YTHDF2-dependent downregulation of WEE1.
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Affiliation(s)
- Yongxu Su
- Department of Oral and Maxilofacial Sugery, Changsha Stomatological Hospital, Changsha, 410004, Hunan, China.
| | - Yanjia Hu
- Department of Oral and Maxilofacial Sugery, Xiangya Stomatological Hospital Central South University, Changsha, 410000, Hunan, China
| | - Binbin Qu
- Department of Oral and Maxilofacial Sugery, Changsha Stomatological Hospital, Changsha, 410004, Hunan, China
| | - Rongchang Lei
- Department of Oral and Maxilofacial Sugery, Changsha Stomatological Hospital, Changsha, 410004, Hunan, China
| | - Ge Guo
- Department of Oral and Maxilofacial Sugery, Changsha Stomatological Hospital, Changsha, 410004, Hunan, China
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Bai Y, Zhu Y, He X, Huang R, Xu X, Yang L, Wang Z, Zhu R. Size-Optimized Layered Double Hydroxide Nanoparticles Promote Neural Progenitor Cells Differentiation of Embryonic Stem Cells Through the Regulation of M 6A Methylation. Int J Nanomedicine 2024; 19:4181-4197. [PMID: 38766656 PMCID: PMC11100968 DOI: 10.2147/ijn.s463141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024] Open
Abstract
Purpose The committed differentiation fate regulation has been a difficult problem in the fields of stem cell research, evidence showed that nanomaterials could promote the differentiation of stem cells into specific cell types. Layered double hydroxide (LDH) nanoparticles possess the regulation function of stem cell fate, while the underlying mechanism needs to be investigated. In this study, the process of embryonic stem cells (ESCs) differentiate to neural progenitor cells (NPCs) by magnesium aluminum LDH (MgAl-LDH) was investigated. Methods MgAl-LDH with diameters of 30, 50, and 100 nm were synthesized and characterized, and their effects on the cytotoxicity and differentiation of NPCs were detected in vitro. Dot blot and MeRIP-qPCR were performed to detect the level of m6A RNA methylation in nanoparticles-treated cells. Results Our work displayed that LDH nanoparticles of three different sizes were biocompatible with NPCs, and the addition of MgAl-LDH could significantly promote the process of ESCs differentiate to NPCs. 100 nm LDH has a stronger effect on promoting NPCs differentiation compared to 30 nm and 50 nm LDH. In addition, dot blot results indicated that the enhanced NPCs differentiation by MgAl-LDH was closely related to m6A RNA methylation process, and the major modification enzyme in LDH controlled NPCs differentiation may be the m6A RNA methyltransferase METTL3. The upregulated METTL3 by LDH increased the m6A level of Sox1 mRNA, enhancing its stability. Conclusion This work reveals that MgAl-LDH nanoparticles can regulate the differentiation of ESCs into NPCs by increasing m6A RNA methylation modification of Sox1.
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Affiliation(s)
- Yuxin Bai
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, People’s Republic of China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Yanjing Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Xiaolie He
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Ruiqi Huang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, People’s Republic of China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Xu Xu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Li Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Zhaojie Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, People’s Republic of China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Rongrong Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, People’s Republic of China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200065, People’s Republic of China
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Wang P, Lin J, Zheng X, Xu X. RNase P: Beyond Precursor tRNA Processing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae016. [PMID: 38862431 DOI: 10.1093/gpbjnl/qzae016] [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: 09/26/2022] [Revised: 09/18/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
Ribonuclease P (RNase P) was first described in the 1970's as an endoribonuclease acting in the maturation of precursor transfer RNAs (tRNAs). More recent studies, however, have uncovered non-canonical roles for RNase P and its components. Here, we review the recent progress of its involvement in chromatin assembly, DNA damage response, and maintenance of genome stability with implications in tumorigenesis. The possibility of RNase P as a therapeutic target in cancer is also discussed.
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Affiliation(s)
- Peipei Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
| | - Juntao Lin
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Xiangyang Zheng
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine, Dehua Hospital, Dehua 362500, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
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Yang L, Liu J, Jin Y, Xing J, Zhang J, Chen X, Yu A. Synchronous profiling of mRNA N6-methyladenosine modifications and mRNA expression in high-grade serous ovarian cancer: a pilot study. Sci Rep 2024; 14:10427. [PMID: 38714753 PMCID: PMC11076553 DOI: 10.1038/s41598-024-60975-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 04/29/2024] [Indexed: 05/10/2024] Open
Abstract
This study aimed to synchronously determine epitranscriptome-wide RNA N6-methyladenosine (m6A) modifications and mRNA expression profile in high grade serous ovarian cancer (HGSOC). The methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to comprehensively examine the m6A modification profile and the RNA-sequencing (RNA-seq) was performed to analyze the mRNA expression profile in HGSOC and normal fallopian tube (FT) tissues. Go and KEGG analyses were carried out in the enrichment of those differentially methylated and expressed genes. MeRIP-seq data showed 53,794 m6A methylated peaks related to 19,938 genes in the HGSOC group and 51,818 m6A peaks representing 19,681 genes in the FT group. RNA-seq results revealed 2321 upregulated and 2486 downregulated genes in HGSOC. Conjoint analysis of MeRIP-seq and RNA-seq data identified differentially expressed genes in which 659 were hypermethylated (330 up- and 329 down-regulated) and 897 were hypomethylated (475 up- and 422 down-regulated). Functional enrichment analysis indicated that these differentially modulated genes are involved in pathways related to cancer development. Among methylation regulators, the m6A eraser (FTO) expression was significantly lower, but the m6A readers (IGF2BP2 and IGF2BP3) were higher in HGSOC, which was validated by the subsequent real-time PCR assay. Exploration through public databases further corroborated their possible clinical application of certain methylation regulators and differentially expressed genes. For the first time, our study screens the epitranscriptome-wide m6A modification and expression profiles of their modulated genes and signaling pathways in HGSOC. Our findings provide an alternative direction in exploring the molecular mechanisms of ovarian pathogenesis and potential biomarkers in the diagnosis and predicting the prognosis of the disease.
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Affiliation(s)
- Li Yang
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Jingfang Liu
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
- The Second Clinical Medical College, Wenzhou Medical University, Wenzhou, 325015, Zhejiang, China
| | - Yanlu Jin
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Jie Xing
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Jiejie Zhang
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Xin Chen
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
| | - Aijun Yu
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
- The Second Clinical Medical College, Wenzhou Medical University, Wenzhou, 325015, Zhejiang, China.
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Zhang P, Zhang F, Sui H, Yang X, Ji Y, Zheng S, Li W, Cheng K, Wang C, Jiao J, Zhang X, Cao Z, Zhang Y. Characterization of sexual maturity-associated N6-methyladenosine in boar testes. BMC Genomics 2024; 25:447. [PMID: 38714941 PMCID: PMC11075296 DOI: 10.1186/s12864-024-10343-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The health and size of the testes are crucial for boar fertility. Testicular development is tightly regulated by epigenetics. N6-methyladenosine (m6A) modification is a prevalent internal modification on mRNA and plays an important role in development. The mRNA m6A methylation in boar testicular development still needs to be investigated. RESULTS Using the MeRIP-seq technique, we identify and profile m6A modification in boar testes between piglets and adults. The results showed 7783 distinct m6A peaks in piglets and 6590 distinct m6A peaks in adults, with 2,471 peaks shared between the two groups. Enrichment of GO and KEGG analysis reveal dynamic m6A methylation in various biological processes and signalling pathways. Meanwhile, we conjointly analyzed differentially methylated and expressed genes in boar testes before and after sexual maturity, and reproductive related genes (TLE4, TSSK3, TSSK6, C11ORF94, PATZ1, PHLPP1 and PAQR7) were identified. Functional enrichment analysis showed that differential genes are associated with important biological functions, including regulation of growth and development, regulation of metabolic processes and protein catabolic processes. CONCLUSION The results demonstrate that m6A methylation, differential expression and the related signalling pathways are crucial for boar testicular development. These results suggest a role for m6A modification in boar testicular development and provided a resource for future studies on m6A function in boar testicular development.
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Affiliation(s)
- Pengfei Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China
| | - Fei Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China
| | - Heming Sui
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China
- National Animal Husbandry Service, Beijing, 100125, China
| | - Xingyu Yang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China
| | - Yiming Ji
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China
| | - Shenghao Zheng
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China
| | - Wei Li
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China
| | - Kun Cheng
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China
| | - Chonglong Wang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jun Jiao
- Anhui Haoyu Animal Husbandry Co., Ltd, Luan, 237451, China
| | - Xiaodong Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China.
| | - Zubing Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China.
| | - Yunhai Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, No.130 West Changjiang Road, Hefei, 230036, China.
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Liu X, Wang N, Gu S, He Z. Changes of RNA m 6A/m 5C Modification Regulatory Molecules in Ferroptosis of T2DM Rat Pancreas. Cell Biochem Biophys 2024:10.1007/s12013-024-01282-0. [PMID: 38709441 DOI: 10.1007/s12013-024-01282-0] [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] [Accepted: 04/17/2024] [Indexed: 05/07/2024]
Abstract
N6-methyladenine (m6A) and 5-methylcytosine (m5C) are two common forms of RNA methylation that play an important role in the epigenetics of type 2 diabetes mellitus (T2DM). One type of cell death, ferroptosis, has been implicated in islet β-cell damage in T2DM. Notably, RNA methylation, an upstream regulatory mechanism of mRNAs, can regulate the expression of ferroptosis signaling molecules, thereby affecting cell proliferation and death. Here, we found that the ferroptosis signaling pathway was activated in pancreas of T2DM rats, followed by significant changes in m6A/m5C modification regulatory molecules. These detection data together with the prediction results that m6A and m5C exist in the mRNAs of ferroptosis molecules, we speculate that m6A and m5C are probably involved in pancreatic cell damage by modifying of ferroptosis signaling molecules. In short, our findings provide a new research idea for future studies on the molecular mechanisms of pancreatic cell damage and point to a new direction for exploring the mechanisms of ferroptosis from the perspective of RNA methylation modification.
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Affiliation(s)
- Xiaoyu Liu
- Institute of Preventive Medicine, School of Public Health, Dali University, Dali, Yunnan, China
| | - Nan Wang
- Institute of Preventive Medicine, School of Public Health, Dali University, Dali, Yunnan, China
| | - Shiyan Gu
- Institute of Preventive Medicine, School of Public Health, Dali University, Dali, Yunnan, China.
| | - Zuoshun He
- Institute of Preventive Medicine, School of Public Health, Dali University, Dali, Yunnan, China.
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Wang Y, Sun N, He R, Wang Z, Jin J, Gao T, Qu J. Molecular characterization of m6A RNA methylation regulators with features of immune dysregulation in IgA nephropathy. Clin Exp Med 2024; 24:92. [PMID: 38693353 PMCID: PMC11062981 DOI: 10.1007/s10238-024-01346-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
The role of RNA N6-methyladenosine (m6A) modification in immunity is being elucidated. This study aimed to explore the potential association between m6A regulators and the immune microenvironment in IgA nephropathy (IgAN). The expression profiles of 24 m6A regulators in 107 IgAN patients were obtained from the Gene Expression Omnibus (GEO) database. The least absolute shrinkage and selection operator (LASSO) regression and logistic regression analysis were utilized to construct a model for distinguishing IgAN from control samples. Based on the expression levels of m6A regulators, unsupervised clustering was used to identify m6A-induced molecular clusters in IgAN. Gene set enrichment analysis (GSEA) and immunocyte infiltration among different clusters were examined. The gene modules with the highest correlation for each of the three clusters were identified by weighted gene co-expression network analysis (WGCNA). A model containing 10 m6A regulators was developed using LASSO and logistic regression analyses. Three molecular clusters were determined using consensus clustering of 24 m6A regulators. A decrease in the expression level of YTHDF2 in IgAN samples was significantly negatively correlated with an increase in resting natural killer (NK) cell infiltration and was positively correlated with the abundance of M2 macrophage infiltration. The risk scores calculated by the nomogram were significantly higher for cluster-3, and the expression levels of m6A regulators in this cluster were generally low. Immunocyte infiltration and pathway enrichment results for cluster-3 differed significantly from those for the other two clusters. Finally, the expression of YTHDF2 was significantly decreased in IgAN based on immunohistochemical staining. This study demonstrated that m6A methylation regulators play a significant role in the regulation of the immune microenvironment in IgAN. Based on m6A regulator expression patterns, IgAN can be classified into multiple subtypes, which might provide additional insights into novel therapeutic methods for IgAN.
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Affiliation(s)
- Yihao Wang
- Department of Nephrology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Nan Sun
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Rui He
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zida Wang
- Department of Emergency, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jingsi Jin
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ting Gao
- Department of Emergency, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Junwen Qu
- Department of Urology, Jiading Branch, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201899, China.
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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Zhang M, Zhai Y, An X, Li Q, Zhang D, Zhou Y, Zhang S, Dai X, Li Z. DNA methylation regulates RNA m 6A modification through transcription factor SP1 during the development of porcine somatic cell nuclear transfer embryos. Cell Prolif 2024; 57:e13581. [PMID: 38095020 PMCID: PMC11056710 DOI: 10.1111/cpr.13581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Epigenetic modifications play critical roles during somatic cell nuclear transfer (SCNT) embryo development. Whether RNA N6-methyladenosine (m6A) affects the developmental competency of SCNT embryos remains unclear. Here, we showed that porcine bone marrow mesenchymal stem cells (pBMSCs) presented higher RNA m6A levels than those of porcine embryonic fibroblasts (pEFs). SCNT embryos derived from pBMSCs had higher RNA m6A levels, cleavage, and blastocyst rates than those from pEFs. Compared with pEFs, the promoter region of METTL14 presented a hypomethylation status in pBMSCs. Mechanistically, DNA methylation regulated METTL14 expression by affecting the accessibility of transcription factor SP1 binding, highlighting the role of the DNA methylation/SP1/METTL14 pathway in donor cells. Inhibiting the DNA methylation level in donor cells increased the RNA m6A level and improved the development efficiency of SCNT embryos. Overexpression of METTL14 significantly increased the RNA m6A level in donor cells and the development efficiency of SCNT embryos, whereas knockdown of METTL14 suggested the opposite result. Moreover, we revealed that RNA m6A-regulated TOP2B mRNA stability, translation level, and DNA damage during SCNT embryo development. Collectively, our results highlight the crosstalk between RNA m6A and DNA methylation, and the crucial role of RNA m6A during nuclear reprogramming in SCNT embryo development.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Yanhui Zhai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Daoyu Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Yongfeng Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Xiangpeng Dai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
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Carvalho L, Lasek AW. It is not just about transcription: involvement of brain RNA splicing in substance use disorders. J Neural Transm (Vienna) 2024; 131:495-503. [PMID: 38396082 PMCID: PMC11055753 DOI: 10.1007/s00702-024-02740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 01/04/2024] [Indexed: 02/25/2024]
Abstract
Alternative splicing is a co-transcriptional process that significantly contributes to the molecular landscape of the cell. It plays a multifaceted role in shaping gene transcription, protein diversity, and functional adaptability in response to environmental cues. Recent studies demonstrate that drugs of abuse have a profound impact on alternative splicing patterns within different brain regions. Drugs like alcohol and cocaine modify the expression of genes responsible for encoding splicing factors, thereby influencing alternative splicing of crucial genes involved in neurotransmission, neurogenesis, and neuroinflammation. Notable examples of these alterations include alcohol-induced changes in splicing factors such as HSPA6 and PCBP1, as well as cocaine's impact on PTBP1 and SRSF11. Beyond the immediate effects of drug exposure, recent research has shed light on the role of alternative splicing in contributing to the risk of substance use disorders (SUDs). This is exemplified by exon skipping events in key genes like ELOVL7, which can elevate the risk of alcohol use disorder. Lastly, drugs of abuse can induce splicing alterations through epigenetic modifications. For example, cocaine exposure leads to alterations in levels of trimethylated lysine 36 of histone H3, which exhibits a robust association with alternative splicing and serves as a reliable predictor for exon exclusion. In summary, alternative splicing has emerged as a critical player in the complex interplay between drugs of abuse and the brain, offering insights into the molecular underpinnings of SUDs.
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Affiliation(s)
- Luana Carvalho
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 1220 E. Broad ST, Box 980613, Richmond, VA, 23298, USA.
| | - Amy W Lasek
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 1220 E. Broad ST, Box 980613, Richmond, VA, 23298, USA
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Li L, Xia X, Yang T, Sun Y, Liu X, Xu W, Lu M, Cui D, Wu Y. RNA methylation: A potential therapeutic target in autoimmune disease. Int Rev Immunol 2024; 43:160-177. [PMID: 37975549 DOI: 10.1080/08830185.2023.2280544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and inflammatory bowel disease (IBD) are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is unclear. Numerous studies have demonstrated that RNA methylation plays a key role in disease progression, which is essential for post-transcriptional regulation and has gradually become a broad regulatory mechanism that controls gene expression in various physiological processes, including RNA nuclear output, translation, splicing, and noncoding RNA processing. Here, we outline the writers, erasers, and readers of RNA methylation, including N6-methyladenosine (m6A), 2'-O-methylation (Nm), 2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytidine (m5C) and N7-methylguanosine (m7G). As the role of RNA methylation modifications in the immune system and diseases is explained, the potential treatment value of these modifications has also been demonstrated. This review reports the relationship between RNA methylation and autoimmune diseases, highlighting the need for future research into the therapeutic potential of RNA modifications.
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Affiliation(s)
- Lele Li
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaoping Xia
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Tian Yang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yuchao Sun
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xueke Liu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Wei Xu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mei Lu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Dawei Cui
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingping Wu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
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Qian W, Yang L, Li T, Li W, Zhou J, Xie S. RNA modifications in pulmonary diseases. MedComm (Beijing) 2024; 5:e546. [PMID: 38706740 PMCID: PMC11068158 DOI: 10.1002/mco2.546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 05/07/2024] Open
Abstract
Threatening public health, pulmonary disease (PD) encompasses diverse lung injuries like chronic obstructive PD, pulmonary fibrosis, asthma, pulmonary infections due to pathogen invasion, and fatal lung cancer. The crucial involvement of RNA epigenetic modifications in PD pathogenesis is underscored by robust evidence. These modifications not only shape cell fates but also finely modulate the expression of genes linked to disease progression, suggesting their utility as biomarkers and targets for therapeutic strategies. The critical RNA modifications implicated in PDs are summarized in this review, including N6-methylation of adenosine, N1-methylation of adenosine, 5-methylcytosine, pseudouridine (5-ribosyl uracil), 7-methylguanosine, and adenosine to inosine editing, along with relevant regulatory mechanisms. By shedding light on the pathology of PDs, these summaries could spur the identification of new biomarkers and therapeutic strategies, ultimately paving the way for early PD diagnosis and treatment innovation.
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Affiliation(s)
- Weiwei Qian
- Emergency Department of Emergency MedicineLaboratory of Emergency Medicine, West China Hospital, And Disaster Medical, Sichuan UniversityChengduSichuanChina
- Emergency DepartmentShangjinnanfu Hospital, West China Hospital, Sichuan UniversityChengduSichuanChina
| | - Lvying Yang
- The Department of Respiratory and Critical Care MedicineThe First Veterans Hospital of Sichuan ProvinceChengduSichuanChina
| | - Tianlong Li
- Department of Critical Care Medicine Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Wanlin Li
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's HospitalShenzhenGuangdongChina
| | - Jian Zhou
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National‐Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical SchoolShenzhenChina
- Department of ImmunologyInternational Cancer Center, Shenzhen University Health Science CenterShenzhenGuangdongChina
| | - Shenglong Xie
- Department of Thoracic SurgerySichuan Provincial People's Hospital, University of Electronic Science and Technology of ChinaChengduSichuanChina
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Zang Q, Ju Y, Liu S, Wu S, Zhu C, Liu L, Xu W, He Y. The significance of m6A RNA methylation regulators in diagnosis and subtype classification of HBV-related hepatocellular carcinoma. Hum Cell 2024; 37:752-767. [PMID: 38536633 DOI: 10.1007/s13577-024-01044-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/14/2024] [Indexed: 04/15/2024]
Abstract
In recent years, abnormal m6A alteration in hepatocellular carcinoma (HCC) has been a focus on investigating the biological implications. In this study, our objective is to determine whether m6A modification contributes to the progression of HBV-related HCC. To achieve this, we employed a random forest model to screen top 8 characteristic m6A regulators from 19 candidate genes. Subsequently, we developed a nomogram model that utilizes these 8 characteristic m6A regulators to predict the prevalence of HBV-related HCC. According to decision curve analysis, patients may benefit from the nomogram model. The clinical impact curves exhibited a robust predictive capability of the nomogram models. Additionally, consensus molecular subtyping was employed to identify m6A modification patterns and m6A-related gene signature. The quantification of immune cell subsets was accomplished through the implementation of ssGSEA algorithms. PCA algorithms were developed to compute the m6A score for individual tumors. Two distinct m6A modification patterns, namely cluster A and cluster B, exhibited significant correlations with distinct immune infiltration patterns and biological pathways. Notably, patients belonging to cluster B demonstrated higher m6A scores compared to those in cluster A, as determined by the m6A score metric. Furthermore, the expression of IGFBP3 proteins was validated through immunofluorescence, revealing their pronounced lower expression in tumor tissues. In summary, our study underscores the importance of m6A modification in the advancement of HBV-related HCC. This research has the potential to yield novel prognostic biomarkers and therapeutic targets for the identification of HBV-related HCC.
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Affiliation(s)
- Qijuan Zang
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta Road(W), Xi'an, 710061, Shaanxi, China
| | - Yalin Ju
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Siyi Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta Road(W), Xi'an, 710061, Shaanxi, China
| | - Shaobo Wu
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chengbin Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta Road(W), Xi'an, 710061, Shaanxi, China
| | - Liangru Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta Road(W), Xi'an, 710061, Shaanxi, China
| | - Weicheng Xu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta Road(W), Xi'an, 710061, Shaanxi, China
| | - Yingli He
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta Road(W), Xi'an, 710061, Shaanxi, China.
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Yang J, Ji Z, Gao F, Wu J, Du M, Zhang Z, Yuan L, Zheng R, Wang M. Cigarette smoking combined with genetic variation regulates the m 6A methylation of CRNKL1 and is associated with bladder cancer risk. ENVIRONMENTAL TOXICOLOGY 2024; 39:2782-2793. [PMID: 38270278 DOI: 10.1002/tox.24138] [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: 09/14/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/26/2024]
Abstract
Cigarette smoking was known to accelerate the occurrence and development of bladder cancer by regulating RNA modification. However, the association between the combination of cigarette smoking and RNA modification-related single nucleotide polymorphisms (RNAm-SNPs) and bladder cancer risk remains unclear. In this study, 1681 participants, including 580 cases and 1101 controls, were recruited for genetic association analysis. In total, 1 287 990 RNAm-SNPs involving nine RNA modifications (m6A, m1A, m6Am, 2'-O-Me, m5C, m7G, A-to-I, m5U, and pseudouridine modification) were obtained from the RMVar database. The interactive effect of cigarette smoking and RNAm-SNPs on bladder cancer risk was assessed through joint analysis. The susceptibility analysis revealed that 89 RNAm-SNPs involving m6A, m1A, and A-to-I modifications were associated with bladder cancer risk. Among them, m6A-related rs2273058 in CRNKL1 was associated with bladder cancer risk (odds ratios (OR) = 1.35, padj = 1.78 × 10-4), and CRNKL1 expression was increased in bladder cancer patients (p = 0.035). Cigarette smoking combined with the A allele of rs2273058 increased bladder cancer risk compared with nonsmokers with the G allele of rs2273058 (OR = 2.40, padj = 3.11 × 10-9). Mechanistically, the A allele of rs2273058 endowed CRNKL1 with an additional m6A motif, facilitating recognition by m6A reader IGF2BP1, thereby promoting CRNKL1 expression under cigarette smoking (r = 0.142, p = 0.017). Moreover, elevated CRNKL1 expression may accelerate cell cycle and proliferation, thereby increasing bladder cancer risk. In summary, our study demonstrated that cigarette smoking combined with RNAm-SNPs contributes to bladder cancer risk, which provides a potential target for bladder cancer prevention.
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Affiliation(s)
- Jialei Yang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Zihan Ji
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Fang Gao
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Jiajin Wu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Mulong Du
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Lin Yuan
- Department of Urology, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Rui Zheng
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
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40
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Wang F, Chen P, Ouyang S, Xiong K, Liu Z, Wang Y. Identification of prognostic m6A modification patterns and score system in melanoma patients. Medicine (Baltimore) 2024; 103:e37950. [PMID: 38669381 PMCID: PMC11049698 DOI: 10.1097/md.0000000000037950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
N6-methyladenosine (m6A) is the most common modification on RNAs and LncRNAs. It plays an important role in cancer stem cell differentiation, T cell differentiation, and immune homeostasis. In this study, we explored the potential roles of m6A modification of RNA in melanoma and investigated the immune cell infiltration in tumor microenvironment in diverse m6Aclusters and different m6Ascore groups. A consensus clustering algorithm determined m6A modification patterns based on 14 m6A regulators, and further explored the biological functions and the connection with TME. An m6A-related gene signature (m6Ascore) was constructed based on m6A-related genes using principal component analysis. Three m6A modification patterns were identified based on 14 m6A regulators, named as m6Aclusters A-C. The prognosis of m6Acluster A was more favorable than m6Aclusters B and C, and it was more closely associated with immune regulation. To quantify the m6A modification patterns of individual tumor, an m6Ascore was constructed, and patients were classified into high and low m6Ascore groups. The low m6Ascore group, which had a favorable prognosis, was more relevant to immunology. The expression of PD-L1 was higher and the immunophenoscore (IPS) revealed stronger response to immunotherapy in the low m6Ascore group. This study identified 3 m6A modification patterns with different immune characteristics and constructed an m6Ascore system to predict prognosis and immunogenicity of patients, which is conducive to clinical prognosis judgment and individual treatment.
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Affiliation(s)
- Feixiang Wang
- Medical Oncology Department, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Peijie Chen
- Medical Oncology Department, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Si Ouyang
- Medical Oncology Department, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Kaixin Xiong
- Medical Oncology Department, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Zichuan Liu
- Medical Oncology Department, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Yao Wang
- Medical Oncology Department, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangdong, Guangzhou, China
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41
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Martinez-Feduchi P, Jin P, Yao B. Epigenetic modifications of DNA and RNA in Alzheimer's disease. Front Mol Neurosci 2024; 17:1398026. [PMID: 38726308 PMCID: PMC11079283 DOI: 10.3389/fnmol.2024.1398026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder and the most common form of dementia. There are two main types of AD: familial and sporadic. Familial AD is linked to mutations in amyloid precursor protein (APP), presenilin-1 (PSEN1), and presenilin-2 (PSEN2). On the other hand, sporadic AD is the more common form of the disease and has genetic, epigenetic, and environmental components that influence disease onset and progression. Investigating the epigenetic mechanisms associated with AD is essential for increasing understanding of pathology and identifying biomarkers for diagnosis and treatment. Chemical covalent modifications on DNA and RNA can epigenetically regulate gene expression at transcriptional and post-transcriptional levels and play protective or pathological roles in AD and other neurodegenerative diseases.
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Affiliation(s)
| | | | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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Li TF, Xu Z, Zhang K, Yang X, Thakur A, Zeng S, Yan Y, Liu W, Gao M. Effects and mechanisms of N6-methyladenosine RNA methylation in environmental pollutant-induced carcinogenesis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 277:116372. [PMID: 38669875 DOI: 10.1016/j.ecoenv.2024.116372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/20/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
Environmental pollution, including air pollution, plastic contamination, and heavy metal exposure, is a pressing global issue. This crisis contributes significantly to pollution-related diseases and is a critical risk factor for chronic health conditions, including cancer. Mounting evidence underscores the pivotal role of N6-methyladenosine (m6A) as a crucial regulatory mechanism in pathological processes and cancer progression. Governed by m6A writers, erasers, and readers, m6A orchestrates alterations in target gene expression, consequently playing a vital role in a spectrum of RNA processes, covering mRNA processing, translation, degradation, splicing, nuclear export, and folding. Thus, there is a growing need to pinpoint specific m6A-regulated targets in environmental pollutant-induced carcinogenesis, an emerging area of research in cancer prevention. This review consolidates the understanding of m6A modification in environmental pollutant-induced tumorigenesis, explicitly examining its implications in lung, skin, and bladder cancer. We also investigate the biological mechanisms that underlie carcinogenesis originating from pollution. Specific m6A methylation pathways, such as the HIF1A/METTL3/IGF2BP3/BIRC5 network, METTL3/YTHDF1-mediated m6A modification of IL 24, METTL3/YTHDF2 dynamically catalyzed m6A modification of AKT1, METTL3-mediated m6A-modified oxidative stress, METTL16-mediated m6A modification, site-specific ATG13 methylation-mediated autophagy, and the role of m6A in up-regulating ribosome biogenesis, all come into play in this intricate process. Furthermore, we discuss the direction regarding the interplay between pollutants and RNA metabolism, particularly in immune response, providing new information on RNA modifications for future exploration.
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Affiliation(s)
- Tong-Fei Li
- Shiyan Key Laboratory of Natural Medicine Nanoformulation Research, Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Renmin road No. 30, Shiyan, Hubei 442000, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kui Zhang
- Pritzker School of Molecular Engineering, Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Xiaoxin Yang
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Abhimanyu Thakur
- Pritzker School of Molecular Engineering, Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Wangrui Liu
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
| | - Ming Gao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Han J, Wang C, Yang H, Luo J, Zhang X, Zhang XA. Novel Insights into the Links between N6-Methyladenosine and Regulated Cell Death in Musculoskeletal Diseases. Biomolecules 2024; 14:514. [PMID: 38785921 PMCID: PMC11117795 DOI: 10.3390/biom14050514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 05/25/2024] Open
Abstract
Musculoskeletal diseases (MSDs), including osteoarthritis (OA), osteosarcoma (OS), multiple myeloma (MM), intervertebral disc degeneration (IDD), osteoporosis (OP), and rheumatoid arthritis (RA), present noteworthy obstacles associated with pain, disability, and impaired quality of life on a global scale. In recent years, it has become increasingly apparent that N6-methyladenosine (m6A) is a key regulator in the expression of genes in a multitude of biological processes. m6A is composed of 0.1-0.4% adenylate residues, especially at the beginning of 3'-UTR near the translation stop codon. The m6A regulator can be classified into three types, namely the "writer", "reader", and "eraser". Studies have shown that the epigenetic modulation of m6A influences mRNA processing, nuclear export, translation, and splicing. Regulated cell death (RCD) is the autonomous and orderly death of cells under genetic control to maintain the stability of the internal environment. Moreover, distorted RCDs are widely used to influence the course of various diseases and receiving increasing attention from researchers. In the past few years, increasing evidence has indicated that m6A can regulate gene expression and thus influence different RCD processes, which has a central role in the etiology and evolution of MSDs. The RCDs currently confirmed to be associated with m6A are autophagy-dependent cell death, apoptosis, necroptosis, pyroptosis, ferroptosis, immunogenic cell death, NETotic cell death and oxeiptosis. The m6A-RCD axis can regulate the inflammatory response in chondrocytes and the invasive and migratory of MM cells to bone remodeling capacity, thereby influencing the development of MSDs. This review gives a complete overview of the regulatory functions on the m6A-RCD axis across muscle, bone, and cartilage. In addition, we also discuss recent advances in the control of RCD by m6A-targeted factors and explore the clinical application prospects of therapies targeting the m6A-RCD in MSD prevention and treatment. These may provide new ideas and directions for understanding the pathophysiological mechanism of MSDs and the clinical prevention and treatment of these diseases.
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Affiliation(s)
- Juanjuan Han
- College of Exercise and Health, Shenyang Sport University, Shenyang 110100, China; (J.H.); (C.W.)
| | - Cuijing Wang
- College of Exercise and Health, Shenyang Sport University, Shenyang 110100, China; (J.H.); (C.W.)
| | - Haolin Yang
- College of Pharmacy, Jilin University, Changchun 132000, China;
| | - Jiayi Luo
- College of Exercise and Health, Shenyang Sport University, Shenyang 110100, China; (J.H.); (C.W.)
| | - Xiaoyi Zhang
- College of Second Clinical Medical, China Medical University, Shenyang 110100, China;
| | - Xin-An Zhang
- College of Exercise and Health, Shenyang Sport University, Shenyang 110100, China; (J.H.); (C.W.)
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Cheng W, Tan L, Yu S, Song J, Li Z, Peng X, Wei Q, He Z, Zhang W, Yang X. Geniposide reduced oxidative stress-induced apoptosis in HK-2 cell through PI3K/AKT3/FOXO1 by m6A modification. Int Immunopharmacol 2024; 131:111820. [PMID: 38508092 DOI: 10.1016/j.intimp.2024.111820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024]
Abstract
Exogenous hydrogen peroxide (H2O2) may generate excessive oxidative stress, inducing renal cell apoptosis related with kidney dysfunction. Geniposide (GP) belongs to the iridoid compound with anti-inflammatory, antioxidant and anti-apoptotic effects. This study aimed to observe the intervention effect of GP on H2O2-induced apoptosis in human kidney-2 (HK-2) cells and to explore its potential mechanism in relation to N6-methyladenosine (m6A) RNA methylation. Cell viability, apotosis rate and cell cycle were tested separately after different treatments. The mRNA and protein levels of m6A related enzymes and phosphoinositide 3-kinase (PI3K)/a serine/threonine-specific protein kinase 3 (AKT3)/forkhead boxo 1 (FOXO1) and superoxide dismutase 2 (SOD2) were detected by reverse transcription-quantitative real-time PCR (RT-qPCR) and Western blot. The whole m6A methyltransferase activity and the m6A content were measured by ELISA-like colorimetric methods. The changes of m6A methylation levels of PI3K/AKT3/FOXO1 and SOD2 were determined by methylated RNA immunoprecipitation (MeRIP)-qPCR. Multiple comparisons were performed by ANOVA with Turkey's post hoc test. Exposed to 400 μmol/L H2O2, cells were arrested in G1 phase and the apoptosis rate increased, which were significantly alleviated by GP. Compared with the H2O2 apoptosis group, both the whole m6A RNA methyltransferase activity and the m6A contents were increased due to GP intervention. Besides, the SOD2 protein was increased, while PI3K and FOXO1 decreased. The m6A methylation level of AKT3 was negatively correlated with its protein level. Taken together, GP affects the global m6A methylation microenvironment and regulates the expression of PI3K/AKT3/FOXO1 signaling pathway via m6A modification, alleviating cell cycle arrest and apoptosis caused by oxidative stress in HK-2 cells with a good application prospect.
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Affiliation(s)
- Wenli Cheng
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China; Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Luyi Tan
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Susu Yu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Jia Song
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
| | - Ziyin Li
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
| | - Xinyue Peng
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Qinzhi Wei
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
| | - Zhini He
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
| | - Wenjuan Zhang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China.
| | - Xingfen Yang
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China.
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45
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Hu J, Wang S, Li X. A comprehensive review of m 6A research in cervical cancer. Epigenomics 2024:1-21. [PMID: 38639713 DOI: 10.2217/epi-2024-0002] [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: 01/03/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Cervical cancer (CC) remains one of the most common malignancies among women worldwide, posing a serious threat to women's health. N6-methyladenosine (m6A) modification, as the most abundant type of RNA methylation modification, and has been found to play a crucial role in various cancers. Current research suggests a close association between RNA m6A modification and the occurrence and progression of CC, encompassing disruptions in m6A levels and its regulatory machinery. This review summarizes the current status of m6A modification research in CC, explores the mechanisms underlying m6A levels and regulators (methyltransferases, demethylases, reader proteins) in CC and examines the application of small-molecule inhibitors of m6A regulators in disease treatment. The findings provide new insights into the future treatment of CC.
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Affiliation(s)
- Jing Hu
- Key Laboratory of Environmental Medicine & Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine & Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Xiuting Li
- Department of Public Health, Jiangsu Health Vocational College, Nanjing, 210000, China
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Yu P, Xu T, Ma W, Fang X, Bao Y, Xu C, Huang J, Sun Y, Li G. PRMT6-mediated transcriptional activation of ythdf2 promotes glioblastoma migration, invasion, and emt via the wnt-β-catenin pathway. J Exp Clin Cancer Res 2024; 43:116. [PMID: 38637831 PMCID: PMC11025288 DOI: 10.1186/s13046-024-03038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Protein arginine methyltransferase 6 (PRMT6) plays a crucial role in various pathophysiological processes and diseases. Glioblastoma (GBM; WHO Grade 4 glioma) is the most common and lethal primary brain tumor in adults, with a prognosis that is extremely poor, despite being less common than other systemic malignancies. Our current research finds PRMT6 upregulated in GBM, enhancing tumor malignancy. Yet, the specifics of PRMT6's regulatory processes and potential molecular mechanisms in GBM remain largely unexplored. METHODS PRMT6's expression and prognostic significance in GBM were assessed using glioma public databases, immunohistochemistry (IHC), and immunoblotting. Scratch and Transwell assays examined GBM cell migration and invasion. Immunoblotting evaluated the expression of epithelial-mesenchymal transition (EMT) and Wnt-β-catenin pathway-related proteins. Dual-luciferase reporter assays and ChIP-qPCR assessed the regulatory relationship between PRMT6 and YTHDF2. An in situ tumor model in nude mice evaluated in vivo conditions. RESULTS Bioinformatics analysis indicates high expression of PRMT6 and YTHDF2 in GBM, correlating with poor prognosis. Functional experiments show PRMT6 and YTHDF2 promote GBM migration, invasion, and EMT. Mechanistic experiments reveal PRMT6 and CDK9 co-regulate YTHDF2 expression. YTHDF2 binds and promotes the degradation of negative regulators APC and GSK3β mRNA of the Wnt-β-catenin pathway, activating it and consequently enhancing GBM malignancy. CONCLUSIONS Our results demonstrate the PRMT6-YTHDF2-Wnt-β-Catenin axis promotes GBM migration, invasion, and EMT in vitro and in vivo, potentially serving as a therapeutic target for GBM.
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Affiliation(s)
- Peng Yu
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang, Liaoning, 110001, China
| | - Tutu Xu
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang, Liaoning, 110001, China
| | - Wenmeng Ma
- Department of Immunology, Basic Medicine College, China Medical University, Shenyang, Liaoning, China
| | - Xiang Fang
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang, Liaoning, 110001, China
- Department of Neurosurgery, Central hospital affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yue Bao
- Department of Neurosurgery, Qingdao Municipal Hospital, Qingdao, Shandong, China
| | - Chengran Xu
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang, Liaoning, 110001, China
| | - Jinhai Huang
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang, Liaoning, 110001, China
| | - Yongqing Sun
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang, Liaoning, 110001, China
| | - Guangyu Li
- Department of Neurosurgery, the First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang, Liaoning, 110001, China.
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Shi Y, Li K, Yuan Y, Wang C, Yang Z, Zuo D, Niu Y, Qiu J, Li B, Yuan Y, He W. Comprehensive analysis of m6A modification in immune infiltration, metabolism and drug resistance in hepatocellular carcinoma. Cancer Cell Int 2024; 24:138. [PMID: 38627760 PMCID: PMC11022358 DOI: 10.1186/s12935-024-03307-3] [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: 08/09/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
N6-methyladenosine (m6A) is important in regulating mRNA stability, splicing, and translation, and it also contributes to tumor development. However, there is still limited understanding of the comprehensive effects of m6A modification patterns on the tumor immune microenvironment, metabolism, and drug resistance in hepatocellular carcinoma (HCC). In this study, we utilized unsupervised clustering based on the expression of 23 m6A regulators to identify m6A clusters. We identified differential m6A modification patterns and characterized m6A-gene-cluster A, which exhibited poorer survival rates, a higher abundance of Treg cells, and increased expression of TGFβ in the tumor microenvironment (TME). Additionally, m6A-gene-cluster A demonstrated higher levels of glycolysis activity, cholesterol metabolism, and fatty acid biosynthesis. We also found that the m6A score was associated with prognosis and drug resistance. Patients with a low m6A score experienced worse prognoses, which were linked to an abundance of Treg cells, upregulation of TGFβ, and increased metabolic activity. HCC patients with a higher m6A score showed improved prognosis following sorafenib treatment and immunotherapy. In conclusion, we reveals the association between m6A modification patterns and the tumor immune microenvironment, metabolism, and drug resistance in HCC. Furthermore, the m6A score holds potential as a predictive factor for the efficacy of targeted therapy and immunotherapy in HCC.
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Affiliation(s)
- Yunxing Shi
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat- sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kai Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yichuan Yuan
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, 651 Dongfeng Road E, 510060, Guangzhou, P.R. China
| | - Chenwei Wang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, 651 Dongfeng Road E, 510060, Guangzhou, P.R. China
| | - Zhiwen Yang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, 651 Dongfeng Road E, 510060, Guangzhou, P.R. China
| | - Dinglan Zuo
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, 651 Dongfeng Road E, 510060, Guangzhou, P.R. China
| | - Yi Niu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, 651 Dongfeng Road E, 510060, Guangzhou, P.R. China
| | - Jiliang Qiu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, 651 Dongfeng Road E, 510060, Guangzhou, P.R. China
| | - Binkui Li
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, 651 Dongfeng Road E, 510060, Guangzhou, P.R. China
| | - Yunfei Yuan
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, 651 Dongfeng Road E, 510060, Guangzhou, P.R. China
| | - Wei He
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, 651 Dongfeng Road E, 510060, Guangzhou, P.R. China.
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48
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Zhou KI, Pecot CV, Holley CL. 2'- O-methylation (Nm) in RNA: progress, challenges, and future directions. RNA (NEW YORK, N.Y.) 2024; 30:570-582. [PMID: 38531653 PMCID: PMC11019748 DOI: 10.1261/rna.079970.124] [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: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
RNA 2'-O-methylation (Nm) is highly abundant in noncoding RNAs including ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA), and occurs in the 5' cap of virtually all messenger RNAs (mRNAs) in higher eukaryotes. More recently, Nm has also been reported to occur at internal sites in mRNA. High-throughput methods have been developed for the transcriptome-wide detection of Nm. However, these methods have mostly been applied to abundant RNAs such as rRNA, and the validity of the internal mRNA Nm sites detected with these approaches remains controversial. Nonetheless, Nm in both coding and noncoding RNAs has been demonstrated to impact cellular processes, including translation and splicing. In addition, Nm modifications at the 5' cap and possibly at internal sites in mRNA serve to prevent the binding of nucleic acid sensors, thus preventing the activation of the innate immune response by self-mRNAs. Finally, Nm has been implicated in a variety of diseases including cancer, cardiovascular diseases, and neurologic syndromes. In this review, we discuss current challenges in determining the distribution, regulation, function, and disease relevance of Nm, as well as potential future directions for the field.
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Affiliation(s)
- Katherine I Zhou
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
| | - Chad V Pecot
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
- University of North Carolina RNA Discovery Center, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Christopher L Holley
- Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
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Li Y, Ma B, Wang Z, Chen Y, Dong Y. The Effect Mechanism of N6-adenosine Methylation (m6A) in Melatonin Regulated LPS-induced Colon Inflammation. Int J Biol Sci 2024; 20:2491-2506. [PMID: 38725850 PMCID: PMC11077364 DOI: 10.7150/ijbs.95316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/29/2024] [Indexed: 05/12/2024] Open
Abstract
Colon inflammation is characterized by disturbances in the intestinal microbiota and inflammation. Melatonin (Mel) can improve colon inflammation. However, the underlying mechanism remains unclear. Recent studies suggest that m6A methylation modification may play an important role in inflammatory responses. This study aimed to explore the effects of melatonin and LPS-mediated m6A methylation on colon inflammation. Our study found that melatonin inhibits M1 macrophages, activates M2 macrophages, inhibit the secretion of pro-inflammatory factors, maintain colon homeostasis and improves colon inflammation through MTNR1B. In addition, the increased methylation level of m6A is associated with the occurrence of colon inflammation, and melatonin can also reduce the level of colon methylation to improve colon inflammation. Among them, the main methylated protein METTL3 can be inhibited by melatonin through MTNR1B. In a word, melatonin regulates m6A methylation by improving abnormal METTL3 protein level to reshape the microflora and activate macrophages to improve colon inflammation, mainly through MTNR1B.
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Affiliation(s)
- Yuanyuan Li
- Laboratory of Neurobiology, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Baochen Ma
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing, People's Republic of China
| | - Zixu Wang
- Laboratory of Neurobiology, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yaoxing Chen
- Laboratory of Neurobiology, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yulan Dong
- Laboratory of Neurobiology, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
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50
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Yin J, Fu J, Xu J, Chen C, Zhu H, Wang B, Yu C, Yang X, Cai R, Li M, Ji K, Wu W, Zhao Y, Zheng Z, Pu Y, Zheng L. Integrated analysis of m6A regulator-mediated RNA methylation modification patterns and immune characteristics in Sjögren's syndrome. Heliyon 2024; 10:e28645. [PMID: 38596085 PMCID: PMC11002070 DOI: 10.1016/j.heliyon.2024.e28645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
The epigenetic modifier N6-methyladenosine (m6A), recognized as the most prevalent internal modification in messenger RNA (mRNA), has recently emerged as a pivotal player in immune regulation. Its dysregulation has been implicated in the pathogenesis of various autoimmune conditions. However, the implications of m6A modification within the immune microenvironment of Sjögren's syndrome (SS), a chronic autoimmune disorder characterized by exocrine gland dysfunction, remain unexplored. Herein, we leverage an integrative analysis combining public database resources and novel sequencing data to investigate the expression profiles of m6A regulatory genes in SS. Our cohort comprised 220 patients diagnosed with SS and 62 healthy individuals, enabling a comprehensive evaluation of peripheral blood at the transcriptomic level. We report a significant association between SS and altered expression of key m6A regulators, with these changes closely tied to the activation of CD4+ T cells. Employing a random forest (RF) algorithm, we identified crucial genes contributing to the disease phenotype, which facilitated the development of a robust diagnostic model via multivariate logistic regression analysis. Further, unsupervised clustering revealed two distinct m6A modification patterns, which were significantly associated with variations in immunocyte infiltration, immune response activity, and biological function enrichment in SS. Subsequently, we proceeded with a screening process aimed at identifying genes that were differentially expressed (DEGs) between the two groups distinguished by m6A modification. Leveraging these DEGs, we employed weight gene co-expression network analysis (WGCNA) to uncover sets of genes that exhibited strong co-variance and hub genes that were closely linked to m6A modification. Through rigorous analysis, we identified three critical m6A regulators - METTL3, ALKBH5, and YTHDF1 - alongside two m6A-related hub genes, COMMD8 and SRP9. These elements collectively underscore a complex but discernible pattern of m6A modification that appears to be integrally linked with SS's pathogenesis. Our findings not only illuminate the significant correlation between m6A modification and the immune microenvironment in SS but also lay the groundwork for a deeper understanding of m6A regulatory mechanisms. More importantly, the identification of these key regulators and hub genes opens new avenues for the diagnosis and treatment of SS, presenting potential targets for therapeutic intervention.
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Affiliation(s)
- Junhao Yin
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Jiayao Fu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Jiabao Xu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Changyu Chen
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Hanyi Zhu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Baoli Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Chuangqi Yu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Xiujuan Yang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Ruiyu Cai
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Mengyang Li
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Kaihan Ji
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanning Wu
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Yijie Zhao
- Department of Oral and Maxillofacial Surgery, Shanghai Stomatological Hospital, Fudan University, 1258 Fuxin Zhong Road, Shanghai 200031, China
| | - Zhanglong Zheng
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Yiping Pu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Lingyan Zheng
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
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