1
|
Qin J, Zou L, Lu F, Liu F, Min Q, Zhu L. METTL3 promotes immature dental pulp stem cells-induced angiogenesis by regulating ETS1 mRNA stability in an m 6A-HuR-dependent manner. Odontology 2024:10.1007/s10266-024-00977-3. [PMID: 38969870 DOI: 10.1007/s10266-024-00977-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/24/2024] [Indexed: 07/07/2024]
Abstract
Angiogenesis serves as the determinate element of pulp regeneration. Dental pulp stem cell (DPSC) implantation can promote the regeneration of dental pulp tissue. Herein, the role of m6A methyltransferase methyltransferase-like 3 (METTL3) in regulating DPSCs-induced angiogenesis during pulp regeneration therapy was investigated. Cell DPSC viability, HUVEC migration, and angiogenesis ability were analyzed by CCK-8 assay, wound healing, Transwell assay, and tube formation assay. The global and EST1 mRNA m6A levels were detected by m6A dot blot and Me-RIP. The interactions between E26 transformation-specific proto-oncogene 1(ETS1), human antigen R(HuR), and METTL3 were analyzed by RIP assay. The relationship between METTL3 and the m6A site of ETS1 was performed by dual-luciferase reporter assay. ETS1 mRNA stability was examined with actinomycin D. Herein, our results revealed that human immature DPSCs (hIDPSCs) showed stronger ability to induce angiogenesis than human mature DPSCs (hMDPSCs), which might be related to ETS1 upregulation. ETS1 knockdown inhibited DPSCs-induced angiogenesis. Our mechanistic experiments demonstrated that METTL3 increased ETS1 mRNA stability and expression level on DPSCs in an m6A-HuR-dependent manner. ETS1 upregulation abolished sh-METTL3's inhibition on DPSCs-induced angiogenesis. METTL3 upregulation promoted DPSCs-induced angiogenesis by enhancing ETS1 mRNA stability in an m6A-HuR-dependent manner. This study reveals a new mechanism by which m6A methylation regulates angiogenesis in DPSCs, providing new insights for stem cell-based tissue engineering.
Collapse
Affiliation(s)
- Jian Qin
- Department of Endodontics, Changsha Stomatological Hospital, Hunan Province, Changsha, 410005, People's Republic of China
| | - Li Zou
- Department of Endodontics, Changsha Stomatological Hospital, Hunan Province, Changsha, 410005, People's Republic of China
| | - Fachao Lu
- Department of Endodontics, Changsha Stomatological Hospital, Hunan Province, Changsha, 410005, People's Republic of China
| | - Fang Liu
- Department of Endodontics, Changsha Stomatological Hospital, Hunan Province, Changsha, 410005, People's Republic of China
| | - Qian Min
- Department of Endodontics, Changsha Stomatological Hospital, Hunan Province, Changsha, 410005, People's Republic of China
| | - Lilei Zhu
- Department of Periodontology, Changsha Stomatological Hospital, Hunan Province, No.389, Youyi Road, Changsha, 410005, People's Republic of China.
| |
Collapse
|
2
|
Liu S, Cao Y, Zhang Y. Regulatory roles of RNA methylation in vascular lesions in ocular and cardiopulmonary diseases. Crit Rev Clin Lab Sci 2024:1-15. [PMID: 38957015 DOI: 10.1080/10408363.2024.2370267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
RNA methylation is a widespread regulatory mechanism that controls gene expression in physiological processes. In recent years, the mechanisms and functions of RNA methylation under diseased conditions have been increasingly unveiled by RNA sequencing technologies with large scale and high resolution. In this review, the fundamental concept of RNA methylation is introduced, and the common types of transcript methylation and their machineries are described. Then, the regulatory roles of RNA methylation, particularly N6-methyladenosine and 5-methylcytosine, in the vascular lesions of ocular and cardiopulmonary diseases are discussed and compared. The ocular diseases include corneal neovascularization, retinopathy of prematurity, diabetic retinopathy, and pathologic myopia; whereas the cardiopulmonary ailments involve atherosclerosis and pulmonary hypertension. This review hopes to shed light on the common regulatory mechanisms underlying the vascular lesions in these ocular and cardiopulmonary diseases, which may be conducive to developing therapeutic strategies in clinical practice.
Collapse
Affiliation(s)
- Siyi Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Yunshan Cao
- Department of Cardiology, Gansu Provincial Hospital, Lanzhou, China
| | - Yan Zhang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| |
Collapse
|
3
|
Wei Q, Xue C, Li M, Wei J, Zheng L, Chen S, Duan Y, Deng H, Tang F, Xiong W, Zhou M. Ferroptosis: a critical mechanism of N 6-methyladenosine modification involved in carcinogenesis and tumor progression. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1119-1132. [PMID: 38811442 DOI: 10.1007/s11427-023-2474-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/23/2023] [Indexed: 05/31/2024]
Abstract
Ferroptosis is an iron-dependent regulatory cell necrosis induced by iron overload and lipid peroxidation. It occurs when multiple redox-active enzymes are ectopically expressed or show abnormal function. Hence, the precise regulation of ferroptosis-related molecules is mediated across multiple levels, including transcriptional, posttranscriptional, translational, and epigenetic levels. N6-methyladenosine (m6A) is a highly evolutionarily conserved epigenetic modification in mammals. The m6A modification is commonly linked to tumor proliferation, progression, and therapy resistance because it is involved in RNA metabolic processes. Intriguingly, accumulating evidence suggests that dysregulated ferroptosis caused by the m6A modification drives tumor development. In this review, we summarized the roles of m6A regulators in ferroptosis-mediated malignant tumor progression and outlined the m6A regulatory mechanism involved in ferroptosis pathways. We also analyzed the potential value and application strategies of targeting m6A/ferroptosis pathway in the clinical diagnosis and therapy of tumors.
Collapse
Affiliation(s)
- Qingqing Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Lemei Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Shipeng Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Yumei Duan
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Hongyu Deng
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Faqing Tang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China.
- Hunan Key Laboratory of Oncotarget Gene, Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
| |
Collapse
|
4
|
Liu X, Xie B, Wang S, Wu Y, Zhang Y, Ruan L. Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum. PeerJ 2024; 12:e17376. [PMID: 38784389 PMCID: PMC11114121 DOI: 10.7717/peerj.17376] [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: 12/26/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
Background Condyloma acuminatum (CA) is caused by low-risk human papillomavirus, and is characterized by high recurrence after treatment. The RNA modification N6-methyladenosine (m6A) plays an important role during diverse viral infections, including high-risk HPV infection in cervical cancer. However, it is unclear whether low-risk HPV infection changes the RNA m6A methylation in CA. Methods High-throughputm6A-sequencing was performed to profile the transcriptome-wide mRNA modifications of CA tissues infected by LR-HPVs and the paired normal tissues from CA patients. We further investigated the regulation of alternative splicing by RNA binding proteins (RBPs) with altered m6A modification and constructed a regulatory network among these RBPs, regulated alternative splicing events (RASEs) and regulated alternative splicing genes (RASGs) in CA. Results The results show that the m6A level in CA tissues differed from that in the paired controls. Furthermore, cell cycle- and cell adhesion- associated genes with m6A modification were differentially expressed in CA tissues compared to the paired controls. In particular, seven RNA binding protein genes with specific m6A methylated sites, showed a higher or lower expression at the mRNA level in CA tissues than in the paired normal tissues. In addition, these differentially expressed RNA binding protein genes would regulate the alternative splicing pattern of apoptotic process genes in CA tissue. Conclusions Our study reveals a sophisticated m6A modification profile in CA tissue that affects the response of host cells to HPV infection, and provides cues for the further exploration of the roles of m6A and the development of a novel treatment strategy for CA.
Collapse
Affiliation(s)
- Xiaoyan Liu
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bo Xie
- Department of Urology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Su Wang
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinhua Wu
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu Zhang
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Liming Ruan
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| |
Collapse
|
5
|
Zhang TH, Jo S, Zhang M, Wang K, Gao SJ, Huang Y. Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg. Brief Bioinform 2024; 25:bbae170. [PMID: 38622358 PMCID: PMC11018547 DOI: 10.1093/bib/bbae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/05/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024] Open
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation and splicing. Furthermore, it plays a critical role in the regulation of RNA degradation by primarily recruiting the YTHDF2 reader protein. However, the selective regulation of mRNA decay of the m6A-methylated mRNA through YTHDF2 binding is poorly understood. To improve our understanding, we developed m6A-BERT-Deg, a BERT model adapted for predicting YTHDF2-mediated degradation of m6A-methylated mRNAs. We meticulously assembled a high-quality training dataset by integrating multiple data sources for the HeLa cell line. To overcome the limitation of small training samples, we employed a pre-training-fine-tuning strategy by first performing a self-supervised pre-training of the model on 427 760 unlabeled m6A site sequences. The test results demonstrated the importance of this pre-training strategy in enabling m6A-BERT-Deg to outperform other benchmark models. We further conducted a comprehensive model interpretation and revealed a surprising finding that the presence of co-factors in proximity to m6A sites may disrupt YTHDF2-mediated mRNA degradation, subsequently enhancing mRNA stability. We also extended our analyses to the HEK293 cell line, shedding light on the context-dependent YTHDF2-mediated mRNA degradation.
Collapse
Affiliation(s)
- Ting-He Zhang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA,15261, USA
| | - Sumin Jo
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Michelle Zhang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA,15261, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| |
Collapse
|
6
|
Ma S, Chen F, Lin C, Sun W, Wang D, Zhou S, Chang S, Lu Z, Zhang D. MiR-186-5p prevents hepatocellular carcinoma progression by targeting methyltransferase-like 3 that regulates m6A-mediated stabilization of follistatin-like 5. Heliyon 2024; 10:e26767. [PMID: 38463829 PMCID: PMC10920164 DOI: 10.1016/j.heliyon.2024.e26767] [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: 06/28/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a multistep process involving sophisticated genetic, epigenetic, and transcriptional changes. However, studies on microRNA (miRNA)'s regulatory effects of N6-methyladenosine (m6A) modifications on HCC progression are limited. Methods Cell Counting Kit-8 (CCK-8), clone formation, and Transwell assays were used to investigate changes in cancer cell proliferation, invasion, and migration. RNA m6A levels were verified using methylated RNA immunoprecipitation. Luciferase reporter assay was used to study the potential binding between miRNAs and mRNA. A mouse tumor transplant model was established to study the changes in tumor progression. Results Follistatin-like 5 (FSTL5) was significantly downregulated in HCC and inhibited its further progression. Additionally, methyltransferase-like 3 (METTL3) reduced FSTL5 mRNA stability in an m6A-YTH domain family 2(YTHDF2)-dependent manner. Functional experiments revealed that METTL3 downregulation inhibited HCC progression by upregulating FSTL5 in vitro and in vivo. Luciferase reporter assay verified that miR-186-5p directly targets METTL3. Additionally, miR-186-5p inhibits the proliferation, migration, and invasion of HCC cells by downregulating METTL3 expression. Conclusions The miR-186-5p/METTL3/YTHDF2/FSTL5 axis may offer new directions for targeted HCC therapy.
Collapse
Affiliation(s)
- Shuoshuo Ma
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
- Liver Transplantation Center and Hepatobiliary and Pancreatic Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Fangfang Chen
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Chuanle Lin
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Wanliang Sun
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Dongdong Wang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Shuo Zhou
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - ShiRu Chang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Zheng Lu
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Dengyong Zhang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
- The University of Texas MD Anderson Cancer Center, Department of Translational Molecular Pathology, Houston, USA
| |
Collapse
|
7
|
Sun L, Chen X, Zhu S, Wang J, Diao S, Liu J, Xu J, Li X, Sun Y, Huang C, Meng X, Lv X, Li J. Decoding m 6A mRNA methylation by reader proteins in liver diseases. Genes Dis 2024; 11:711-726. [PMID: 37692496 PMCID: PMC10491919 DOI: 10.1016/j.gendis.2023.02.054] [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: 10/03/2022] [Accepted: 02/22/2023] [Indexed: 09/12/2023] Open
Abstract
N6-methyladenosine (m6A) is a dynamic and reversible epigenetic regulation. As the most prevalent internal post-transcriptional modification in eukaryotic RNA, it participates in the regulation of gene expression through various mechanisms, such as mRNA splicing, nuclear export, localization, translation efficiency, mRNA stability, and structural transformation. The involvement of m6A in the regulation of gene expression depends on the specific recognition of m6A-modified RNA by reader proteins. In the pathogenesis and treatment of liver disease, studies have found that the expression levels of key genes that promote or inhibit the development of liver disease are regulated by m6A modification, in which abnormal expression of reader proteins determines the fate of these gene transcripts. In this review, we introduce m6A readers, summarize the recognition and regulatory mechanisms of m6A readers on mRNA, and focus on the biological functions and mechanisms of m6A readers in liver cancer, viral hepatitis, non-alcoholic fatty liver disease (NAFLD), hepatic fibrosis (HF), acute liver injury (ALI), and other liver diseases. This information is expected to be of high value to researchers deciphering the links between m6A readers and human liver diseases.
Collapse
Affiliation(s)
- Lijiao Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xin Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Sai Zhu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- Department of Nephropathy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Jianan Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
| | - Shaoxi Diao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jinyu Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jinjin Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiaofeng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
| | - Yingyin Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiaoming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
| | - Xiongwen Lv
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| |
Collapse
|
8
|
Zhang TH, Jo S, Zhang M, Wang K, Gao SJ, Huang Y. Understanding YTHDF2-mediated mRNA Degradation By m 6A-BERT-Deg. ARXIV 2024:arXiv:2401.08004v1. [PMID: 38292306 PMCID: PMC10827231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation, and splicing. Furthermore, it plays a critical role in the regulation of RNA degradation by primarily recruiting the YTHDF2 reader protein. However, the selective regulation of mRNA decay of the m6A-methylated mRNA through YTHDF2 binding is poorly understood. To improve our understanding, we developed m6A-BERT-Deg, a BERT model adapted for predicting YTHDF2-mediated degradation of m6A-methylated mRNAs. We meticulously assembled a high-quality training dataset by integrating multiple data sources for the HeLa cell line. To overcome the limitation of small training samples, we employed a pre-training-fine-tuning strategy by first performing a self-supervised pre-training of the model on 427,760 unlabeled m6A site sequences. The test results demonstrated the importance of this pre-training strategy in enabling m6A-BERT-Deg to outperform other benchmark models. We further conducted a comprehensive model interpretation and revealed a surprising finding that the presence of co-factors in proximity to m6A sites may disrupt YTHDF2-mediated mRNA degradation, subsequently enhancing mRNA stability. We also extended our analyses to the HEK293 cell line, shedding light on the context-dependent YTHDF2-mediated mRNA degradation.
Collapse
Affiliation(s)
- Ting-He Zhang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sumin Jo
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelle Zhang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
9
|
Kudrin P, Rebane A. Do RNA modifications contribute to modulation of immune responses in allergic diseases? FRONTIERS IN ALLERGY 2023; 4:1277244. [PMID: 38026133 PMCID: PMC10679440 DOI: 10.3389/falgy.2023.1277244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
RNA modifications have emerged as a fundamental mechanism of post-transcriptional gene regulation, playing vital roles in cellular physiology and the development of various diseases. While the investigation of RNA modifications has seen significant advancements, the exploration of their implication in allergic diseases has been comparatively overlooked. Allergic reactions, including hay fever, asthma, eczema and food allergies, result from hypersensitive immune responses, affecting a considerable population worldwide. Despite the high prevalence, the molecular mechanisms underlying these responses remain partially understood. The potential role of RNA modifications in modulating the hypersensitive immune responses has yet to be fully elucidated. This mini-review seeks to shed light on potential connections between RNA modifications and allergy, highlighting recent findings and potential future research directions. By expanding our understanding of the complex interplay between RNA modifications and allergic responses, we hope to unlock new avenues for allergy diagnosis, prognosis, and therapeutic intervention.
Collapse
Affiliation(s)
- Pavel Kudrin
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | | |
Collapse
|
10
|
Feng M, Zhou X, Hu Y, Zhang J, Yang T, Chen Z, Yuan W. Comprehensive Transcriptomic Profiling of m6A Modification in Age-Related Hearing Loss. Biomolecules 2023; 13:1537. [PMID: 37892219 PMCID: PMC10605720 DOI: 10.3390/biom13101537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Age-related hearing loss (ARHL), also known as presbycusis, is one of the most common neurodegenerative disorders in elderly individuals and has a prevalence of approximately 70-80% among individuals aged 65 and older. As ARHL is an intricate and multifactorial disease, the exact pathogenesis of ARHL is not fully understood. There is evidence that transcriptional dysregulation mediated by epigenetic modifications is widespread in ARHL. However, the potential role of N6-methyladenosine (m6A) modification, as a crucial component of epigenetics, in ARHL progression remains unclear. In this study, we confirmed that the downregulation of m6A modification in cochlear tissues is related to ARHL and found that the expression of the m6A methylation regulators Wilms tumour suppressor-1-associated protein (WTAP), methyltransferase-like 3 (METTL3), ALKB homologous protein 5 (ALKBH5) and fat mass and obesity-associated protein (FTO) is decreased significantly at the mRNA and protein levels in ARHL mice. Then, we used methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and RNA sequencing (RNA-Seq) to identify the differentially m6A-methylated genes in the cochlear tissues of ARHL mice. A total of 3438 genes with differential m6A methylation were identified, of which 1332 genes were m6A-hypermethylated and 2106 genes were m6A-hypomethylated in the ARHL group compared to the control group according to MeRIP-seq. Further joint analysis of RNA-Seq and MeRIP-Seq data showed that 262 genes had significant differences in both mRNA expression and m6A methylation. GO and KEGG analyses indicated that 262 unique genes were enriched mainly in the PI3K-AKT signalling pathway. In conclusion, the results of this study reveal differential m6A methylation patterns in the cochlear tissues of ARHL mice, providing a theoretical basis for further study of the pathogenesis of ARHL and potential therapeutic strategies.
Collapse
Affiliation(s)
- Menglong Feng
- Chongqing Medical University, Chongqing 400016, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Department of Otolaryngology & Head and Neck, Chongqing General Hospital, Chongqing 401147, China
| | - Xiaoqing Zhou
- Department of Otolaryngology & Head and Neck, Chongqing General Hospital, Chongqing 401147, China
| | - Yaqin Hu
- Department of Otolaryngology & Head and Neck, Chongqing General Hospital, Chongqing 401147, China
| | - Juhong Zhang
- Department of Otolaryngology & Head and Neck, Chongqing General Hospital, Chongqing 401147, China
| | - Ting Yang
- Chongqing Medical University, Chongqing 400016, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Department of Otolaryngology & Head and Neck, Chongqing General Hospital, Chongqing 401147, China
| | - Zhiji Chen
- Department of Otolaryngology & Head and Neck, Chongqing General Hospital, Chongqing 401147, China
| | - Wei Yuan
- Chongqing Medical University, Chongqing 400016, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Department of Otolaryngology & Head and Neck, Chongqing General Hospital, Chongqing 401147, China
| |
Collapse
|
11
|
Hwang HJ, Park TL, Kim HI, Park Y, Kim G, Song C, Cho WK, Kim YK. YTHDF2 facilitates aggresome formation via UPF1 in an m 6A-independent manner. Nat Commun 2023; 14:6248. [PMID: 37803021 PMCID: PMC10558514 DOI: 10.1038/s41467-023-42015-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 09/27/2023] [Indexed: 10/08/2023] Open
Abstract
YTHDF2 has been extensively studied and typified as an RNA-binding protein that specifically recognizes and destabilizes RNAs harboring N6-methyladenosine (m6A), the most prevalent internal modification found in eukaryotic RNAs. In this study, we unravel the m6A-independent role of YTHDF2 in the formation of an aggresome, where cytoplasmic protein aggregates are selectively sequestered upon failure of protein homeostasis mediated by the ubiquitin-proteasome system. Downregulation of YTHDF2 in HeLa cells reduces the circularity of aggresomes and the rate of movement of misfolded polypeptides, inhibits aggresome formation, and thereby promotes cellular apoptosis. Mechanistically, YTHDF2 is recruited to a misfolded polypeptide-associated complex composed of UPF1, CTIF, eEF1A1, and DCTN1 through its interaction with UPF1. Subsequently, YTHDF2 increases the interaction between the dynein motor protein and the misfolded polypeptide-associated complex, facilitating the diffusion dynamics of the movement of misfolded polypeptides toward aggresomes. Therefore, our data reveal that YTHDF2 is a cellular factor involved in protein quality control.
Collapse
Affiliation(s)
- Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Tae Lim Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Hyeong-In Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yeonkyoung Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Geunhee Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Chiyeol Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Won-Ki Cho
- 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.
| |
Collapse
|
12
|
Che F, Ye X, Wang Y, Wang X, Ma S, Tan Y, Mao Y, Luo Z. METTL3 facilitates multiple myeloma tumorigenesis by enhancing YY1 stability and pri-microRNA-27 maturation in m 6A-dependent manner. Cell Biol Toxicol 2023; 39:2033-2050. [PMID: 35038059 DOI: 10.1007/s10565-021-09690-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022]
Abstract
Multiple myeloma (MM) is a pernicious plasma cell disorder and has a poor prognosis. N6-methyladenosine (m6A) is an abundant epigenetic RNA modification and is important in cancer progression. Nevertheless, the function of m6A and its regulator METTL3 in MM are rarely reported. Here, we identified the m6A "writers", METTL3, was enhanced in MM and found that Yin Yang 1 (YY1) and primary-miR-27a-3p were the potential target for METTL3. METTL3 promoted primary-miR-27a-3p maturation and YY1 mRNA stability in an m6A manner. YY1 also was found to facilitate miR-27a-3p transcription. METTL3 affected the growth, apoptosis, and stemness of MM cells through accelerating the stability of YY1 mRNA and the maturation of primary-miR-27a-3p in vitro and in vivo. Our results reveal the key function of the METTL3/YY1/miR-27a-3p axis in MM and may provide fresh insights into MM therapy.
Collapse
Affiliation(s)
- Feifei Che
- Department of Hematology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, No.32 West Second Section, First Ring Road, Chengdu, 610072, Sichuan, China.
| | - Xuemei Ye
- Department of Hematology, Dongli Medical District of Sichuan People's Hospital, Chengdu, 610051, Sichuan, China
| | - Yu Wang
- Department of Hematology, Dongli Medical District of Sichuan People's Hospital, Chengdu, 610051, Sichuan, China
| | - Xuemei Wang
- Department of Hematology, Dongli Medical District of Sichuan People's Hospital, Chengdu, 610051, Sichuan, China
| | - Shuyue Ma
- Department of Hematology, Dongli Medical District of Sichuan People's Hospital, Chengdu, 610051, Sichuan, China
| | - Yawen Tan
- Department of Hematology, Dongli Medical District of Sichuan People's Hospital, Chengdu, 610051, Sichuan, China
| | - Yan Mao
- Department of Hematology, Dongli Medical District of Sichuan People's Hospital, Chengdu, 610051, Sichuan, China
| | - Ziyue Luo
- Department of Hematology, Dongli Medical District of Sichuan People's Hospital, Chengdu, 610051, Sichuan, China
| |
Collapse
|
13
|
Nicastro G, Abis G, Klein P, Esteban-Serna S, Gallagher C, Chaves-Arquero B, Cai Y, Figueiredo AM, Martin SR, Patani R, Taylor IA, Ramos A. Direct m6A recognition by IMP1 underlays an alternative model of target selection for non-canonical methyl-readers. Nucleic Acids Res 2023; 51:8774-8786. [PMID: 37377445 PMCID: PMC10484666 DOI: 10.1093/nar/gkad534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
m6A methylation provides an essential layer of regulation in organismal development, and is aberrant in a range of cancers and neuro-pathologies. The information encoded by m6A methylation is integrated into existing RNA regulatory networks by RNA binding proteins that recognise methylated sites, the m6A readers. m6A readers include a well-characterised class of dedicated proteins, the YTH proteins, as well as a broader group of multi-functional regulators where recognition of m6A is only partially understood. Molecular insight in this recognition is essential to build a mechanistic understanding of global m6A regulation. In this study, we show that the reader IMP1 recognises the m6A using a dedicated hydrophobic platform that assembles on the methyl moiety, creating a stable high-affinity interaction. This recognition is conserved across evolution and independent from the underlying sequence context but is layered upon the strong sequence specificity of IMP1 for GGAC RNA. This leads us to propose a concept for m6A regulation where methylation plays a context-dependent role in the recognition of selected IMP1 targets that is dependent on the cellular concentration of available IMP1, differing from that observed for the YTH proteins.
Collapse
Affiliation(s)
- Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Giancarlo Abis
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Pierre Klein
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Sofia Esteban-Serna
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Christopher Gallagher
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Belen Chaves-Arquero
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Yuyang Cai
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Angelo Miguel Figueiredo
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Stephen R Martin
- Structural Biology Technology Platform, The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Rickie Patani
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andres Ramos
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| |
Collapse
|
14
|
Jin Z, Liu Y. The m6A reader YTHDC1-mediated lncRNA CTBP1-AS2 m6A modification accelerates cholangiocarcinoma progression. Heliyon 2023; 9:e19816. [PMID: 37809459 PMCID: PMC10559219 DOI: 10.1016/j.heliyon.2023.e19816] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Background Cholangiocarcinoma (CCA) is a serious malignancy originating from the bile ducts and the second most common primary liver cancer. Long non-coding RNA (lncRNA) is a functional lncRNA that plays an important role in human cancers. However, the role and underlying mechanisms of CTBP1-AS2 in CCA remain unknown. Purpose In this study, we investigated the functional role and mechanism of long-stranded non-coding RNA (lncRNA) C-terminal binding protein 1 antisense RNA 2 (CTBP1-AS2) in CCA progression. Result In the present study, the bioinformatics analysis revealed that YTHDC1 and CTBP1-AS2 were significantly upregulated, and it was confirmed in cholangiocarcinoma tissues from CCA patients. Meanwhile, we demonstrated that knockdown of YTHDC1 or lncRNA CTBP1-AS2 inhibited CCA cell proliferation, migration and invasion, blocked the cell cycle in G2/M phase and promoted apoptosis of CCA cells. In addition, lncRNA CTBP1-AS2-mediated N6-methyladenosine (m6A) methylation levels were significantly elevated in cholangiocarcinoma tissues, whereas knockdown of YTHDC1 resulted in a significant down-regulation of m6A methylation levels by lncRNA CTBP1-AS2. Conclusion Our results suggest that YTHDC1 affects cholangiocarcinoma progression by modifying the lncRNA CTBP1-AS2 m6A, and CTBP1-AS2 may be a promising therapeutic target for CCA.
Collapse
Affiliation(s)
- Zhe Jin
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Yahui Liu
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| |
Collapse
|
15
|
Yu F, Zhu AC, Liu S, Gao B, Wang Y, Khudaverdyan N, Yu C, Wu Q, Jiang Y, Song J, Jin L, He C, Qian Z. RBM33 is a unique m 6A RNA-binding protein that regulates ALKBH5 demethylase activity and substrate selectivity. Mol Cell 2023; 83:2003-2019.e6. [PMID: 37257451 PMCID: PMC10330838 DOI: 10.1016/j.molcel.2023.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/09/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023]
Abstract
Regulation of RNA substrate selectivity of m6A demethylase ALKBH5 remains elusive. Here, we identify RNA-binding motif protein 33 (RBM33) as a previously unrecognized m6A-binding protein that plays a critical role in ALKBH5-mediated mRNA m6A demethylation of a subset of mRNA transcripts by forming a complex with ALKBH5. RBM33 recruits ALKBH5 to its m6A-marked substrate and activates ALKBH5 demethylase activity through the removal of its SUMOylation. We further demonstrate that RBM33 is critical for the tumorigenesis of head-neck squamous cell carcinoma (HNSCC). RBM33 promotes autophagy by recruiting ALKBH5 to demethylate and stabilize DDIT4 mRNA, which is responsible for the oncogenic function of RBM33 in HNSCC cells. Altogether, our study uncovers the mechanism of selectively demethylate m6A methylation of a subset of transcripts during tumorigenesis that may explain demethylation selectivity in other cellular processes, and we showed its importance in the maintenance of tumorigenesis of HNSCC.
Collapse
Affiliation(s)
- Fang Yu
- Department of Medicine, UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; Department of Medicine and Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Allen C Zhu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Shun Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Boyang Gao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Yuzhi Wang
- Department of Medicine and Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Chunjie Yu
- Department of Medicine, UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Qiong Wu
- Department of Medicine, UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Yunhan Jiang
- Department of Molecular Medicine, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Lingtao Jin
- Department of Molecular Medicine, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
| | - Zhijian Qian
- Department of Medicine, UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; Department of Medicine and Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
| |
Collapse
|
16
|
Wang C, Danli Ma, Yu H, Zhuo Z, Ye Z. N6-methyladenosine (m6A) as a regulator of carcinogenesis and drug resistance by targeting epithelial-mesenchymal transition and cancer stem cells. Heliyon 2023; 9:e14001. [PMID: 36915498 PMCID: PMC10006539 DOI: 10.1016/j.heliyon.2023.e14001] [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: 09/08/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
Emergence of drug resistance to chemotherapeutic agents is the principal obstacle towards curative cancer treatment in human cancer patients. It is in an urgent to explore the underlying molecular mechanisms to overcome the drug resistance. N6-Methyladenosine (m6A) RNA modification is the most abundant reversible RNA modification and has emerged in recent years to regulate gene expression in eukaryotes. Recent evidence has identified m6A is associated with cancer pathogenesis and drug resistance, contributing to the self-renewal and differentiation of cancer stem cell, tumor epithelial-mesenchymal transition (EMT) and tumor metastasis. Here we reviewed up-to-date knowledge of the relationship between m6A modulation and drug resistance. Furthermore, we illustrated the underlying mechanisms of m6A modulation in drug resistance. Lastly, we discussed the regulation of m6A modulation in EMT and cancer stem cells. Hence, it will help to provide significant therapeutic strategies to overcome drug resistance for cancer patients by changing m6A-related proteins via targeting cancer stem cells and EMT-phenotypic cells.
Collapse
Affiliation(s)
- Chuhan Wang
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 31500, China.,Medical School of NingBo University, Ningbo, Zhejiang, 31500, China
| | - Danli Ma
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 31500, China
| | - Huimin Yu
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 31500, China
| | - Zhihong Zhuo
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 31500, China
| | - Zhiying Ye
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 31500, China
| |
Collapse
|
17
|
Yu PL, Wu R, Cao SJ, Wen YP, Huang XB, Zhao S, Lang YF, Zhao Q, Lin JC, Du SY, Yu SM, Yan QG. Pseudorabies virus exploits N 6-methyladenosine modification to promote viral replication. Front Microbiol 2023; 14:1087484. [PMID: 36819040 PMCID: PMC9936159 DOI: 10.3389/fmicb.2023.1087484] [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: 11/02/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction Pseudorabies virus (PRV) is the pathogenic virus of porcine pseudorabies (PR), belonging to the Herpesviridae family. PRV has a wide range of hosts and in recent years has also been reported to infect humans. N6-methyladenosine (m6A) modification is the major pathway of RNA post-transcriptional modification. Whether m6A modification participates in the regulation of PRV replication is unknown. Methods Here, we investigated that the m6A modification was abundant in the PRV transcripts and PRV infection affected the epitranscriptome of host cells. Knockdown of cellular m6A methyltransferases METTL3 and METTL14 and the specific binding proteins YTHDF2 and YTHDF3 inhibited PRV replication, while silencing of demethylase ALKBH5 promoted PRV output. The overexpression of METTL14 induced more efficient virus proliferation in PRV-infected PK15 cells. Inhibition of m6A modification by 3-deazaadenosine (3-DAA), a m6A modification inhibitor, could significantly reduce viral replication. Results and Discussion Taken together, m6A modification played a positive role in the regulation of PRV replication and gene expression. Our research revealed m6A modification sites in PRV transcripts and determined that m6A modification dynamically mediated the interaction between PRV and host.
Collapse
Affiliation(s)
- Pei-Lun Yu
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Rui Wu
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - San-Jie Cao
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yi-Ping Wen
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Bo Huang
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shan Zhao
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yi-Fei Lang
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ju-Chun Lin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sen-Yan Du
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shu-Min Yu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qi-Gui Yan
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,*Correspondence: Qi-Gui Yan, ✉
| |
Collapse
|
18
|
Petri BJ, Klinge CM. m6A readers, writers, erasers, and the m6A epitranscriptome in breast cancer. J Mol Endocrinol 2023; 70:JME-22-0110. [PMID: 36367225 PMCID: PMC9790079 DOI: 10.1530/jme-22-0110] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/11/2022] [Indexed: 11/13/2022]
Abstract
Epitranscriptomic modification of RNA regulates human development, health, and disease. The true diversity of the transcriptome in breast cancer including chemical modification of transcribed RNA (epitranscriptomics) is not well understood due to limitations of technology and bioinformatic analysis. N-6-methyladenosine (m6A) is the most abundant epitranscriptomic modification of mRNA and regulates splicing, stability, translation, and intracellular localization of transcripts depending on m6A association with reader RNA-binding proteins. m6A methylation is catalyzed by the METTL3 complex and removed by specific m6A demethylase ALKBH5, with the role of FTO as an 'eraser' uncertain. In this review, we provide an overview of epitranscriptomics related to mRNA and focus on m6A in mRNA and its detection. We summarize current knowledge on altered levels of writers, readers, and erasers of m6A and their roles in breast cancer and their association with prognosis. We summarize studies identifying m6A peaks and sites in genes in breast cancer cells.
Collapse
Affiliation(s)
- Belinda J. Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Carolyn M. Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS)
| |
Collapse
|
19
|
Fear stress promotes glioma progression through inhibition of ferroptosis by enhancing FSP1 stability. Clin Transl Oncol 2022; 25:1378-1388. [PMID: 36484954 DOI: 10.1007/s12094-022-03032-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE Patients diagnosed with cancer often suffer from emotional stressors, such as anxiety, depression, and fear of death. However, whether fear stress could influence the glioma progression is still unclear. METHODS Xenograft glioma animal models were established in nude mice. Tumor-bearing mice were subjected to fear stress by living closely with cats and then their depressive behaviors were measured using an open field test. Hematoxylin and eosin staining, the TUNEL staining and immunochemical staining were used to detect the histopathological changes of tumor tissues. Gene expression profiling was used to screen the aberrant gene expression. Methylated RNA immunoprecipitation was used to identify the RNA m6A level. Gene expression was measured by western blot and real-time PCR, respectively. RESULTS We found that fear stress promoted glioma tumor progression in mice. Fear stress-induced upregulation of METTL3 and FSP1, increased m6A level of glioma tumor tissues, and inhibited ferroptosis in glioma progression, which were reversed by knockdown of METTL3 and FSP1 in vivo. In addition, we found that when iFSP1 (a ferroptosis inducer by targeting inhibition of FSP1) was introduced to glioma cells, the cells viability of glioma significantly was decreased and ferroptosis was enhanced in glioma cells. CONCLUSIONS Fear stress-induced upregulation of METTL3 stabilized FSP1 mRNA by m6A modification, leading to tumor progression through inhibition of ferroptosis. Our study provides a new understanding of psychological effects on glioma development, and new insights for glioma therapy.
Collapse
|
20
|
RNA-Binding Proteins in the Regulation of Adipogenesis and Adipose Function. Cells 2022; 11:cells11152357. [PMID: 35954201 PMCID: PMC9367552 DOI: 10.3390/cells11152357] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/27/2023] Open
Abstract
The obesity epidemic represents a critical public health issue worldwide, as it is a vital risk factor for many diseases, including type 2 diabetes (T2D) and cardiovascular disease. Obesity is a complex disease involving excessive fat accumulation. Proper adipose tissue accumulation and function are highly transcriptional and regulated by many genes. Recent studies have discovered that post-transcriptional regulation, mainly mediated by RNA-binding proteins (RBPs), also plays a crucial role. In the lifetime of RNA, it is bound by various RBPs that determine every step of RNA metabolism, from RNA processing to alternative splicing, nucleus export, rate of translation, and finally decay. In humans, it is predicted that RBPs account for more than 10% of proteins based on the presence of RNA-binding domains. However, only very few RBPs have been studied in adipose tissue. The primary aim of this paper is to provide an overview of RBPs in adipogenesis and adipose function. Specifically, the following best-characterized RBPs will be discussed, including HuR, PSPC1, Sam68, RBM4, Ybx1, Ybx2, IGF2BP2, and KSRP. Characterization of these proteins will increase our understanding of the regulatory mechanisms of RBPs in adipogenesis and provide clues for the etiology and pathology of adipose-tissue-related diseases.
Collapse
|
21
|
Zhang L, Luo X, Qiao S. METTL14-mediated N6-methyladenosine modification of Pten mRNA inhibits tumour progression in clear-cell renal cell carcinoma. Br J Cancer 2022; 127:30-42. [PMID: 35249103 PMCID: PMC9276773 DOI: 10.1038/s41416-022-01757-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 01/24/2022] [Accepted: 02/10/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Clear-cell renal-cell carcinoma (ccRCC) is one of the leading causes of tumour-related death worldwide. Methyltransferase-like 14 (METTL14) is reported to regulate m6A modification in cancers. The aim of this study is to investigate the biological function and molecular mechanism of METTL14 in the pathogenesis of ccRCC. METHODS Quantitative real-time PCR (qRT-PCR), western blot and immunohistochemical (IHC) assays were used to detect the expression of METTL14 and Pten. METTL14 overexpression or knockdown was used in the in vitro and in vivo studies to investigate the biological functions of METTL14. m6A-RNA immunoprecipitation and RNA immunoprecipitation were used to investigate the m6A modification mediated by METTL14. RESULTS METTL14 expression was significantly down-regulated in ccRCC tissues. Functionally, upregulation of METTL14 inhibited ccRCC cells proliferation and migration in vitro. METTL14 overexpression significantly inhibited the activation of the phosphoinositide 3 kinase (PI3K)/AKT signalling pathway. Furthermore, phosphate and tension homology deleted on chromosome ten (Pten) is a target of METTL14. Overexpression of METTL14 increased the m6A enrichment of Pten, and promoted Pten expression. METTL14-enhanced Pten mRNA stability was dependent on YTHDF1. CONCLUSIONS METTL14-mediated m6A modification of Pten mRNA inhibited tumour progression, suggesting that METTL14 might be a potential prognostic biomarker and effective therapeutic target for ccRCC.
Collapse
Affiliation(s)
- Lili Zhang
- grid.413390.c0000 0004 1757 6938Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, 563003 Zunyi, P. R. China ,grid.417409.f0000 0001 0240 6969School of Laboratory Medicine, Zunyi Medical University, 563003 Zunyi, P. R. China
| | - Xiaofang Luo
- grid.417409.f0000 0001 0240 6969School of Laboratory Medicine, Zunyi Medical University, 563003 Zunyi, P. R. China
| | - Sen Qiao
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, 563003, Zunyi, P. R. China. .,School of Laboratory Medicine, Zunyi Medical University, 563003, Zunyi, P. R. China.
| |
Collapse
|
22
|
Zhang X, Deng S, Peng Y, Wei H, Tian Z. ALKBH5 inhibits TNF-α-induced apoptosis of HUVECs through Bcl-2 pathway. Open Med (Wars) 2022; 17:1092-1099. [PMID: 35799597 PMCID: PMC9202073 DOI: 10.1515/med-2022-0484] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 03/28/2022] [Accepted: 04/15/2022] [Indexed: 01/02/2023] Open
Abstract
Abstract
The dysfunction and apoptosis of vascular endothelial cells are the initiating links in the formation of atherosclerosis. N6-methyladenosine (m6A) is an extremely extensive RNA methylation modification and its abnormality leads to the occurrence of various human diseases. In this study, we explored the effects of demethylase α-ketoglutarate-dependent dioxygenase ALKB homolog 5 (ALKBH5) on TNF-α-induced apoptosis of human umbilical vein endothelial cells (HUVECs). In TNF-α-treated HUVECs, the expression of ALKBH5 was significantly decreased. ALKBH5 overexpression promoted the proliferation and inhibited the apoptosis in TNF-α-treated HUVECs, suggesting that ALKBH5 had a protective effect on cell damage induced by TNF-α. Importantly, ALKBH5 promoted the expression of Bcl-2 in HUVECs. Bcl2 overexpression reduced the expression of Gadd45, Bax, and p21, which are transcriptionally activated by p53. But the expression of p53 has not been significantly affected, indicating that Bcl2 might regulate the apoptosis by inhibiting p53 downstream targets. In addition, ALKBH5 overexpression significantly increased the level of pri-miR-7 and decreased the level of miR-7. In conclusion, ALKBH5 attenuated the TNF-α-induced cell injury via promoting Bcl2 expression. Our research expands the understanding of the progression mechanism of atherosclerosis and provides a potential strategy for the protection of vascular endothelial injury.
Collapse
Affiliation(s)
- Xiaoshan Zhang
- Department of Cardiology, First School of Clinical Medicine College, Yangtze University , Hubei , China
| | - ShiBing Deng
- Department of Cardiology, First School of Clinical Medicine College, Yangtze University , Hubei , China
| | - Yang Peng
- Department of Cardiology, First School of Clinical Medicine College, Yangtze University , Hubei , China
| | - Han Wei
- Department of Cardiology, First School of Clinical Medicine College, Yangtze University , Hubei , China
| | - Zhiming Tian
- Department of Cardiology, First School of Clinical Medicine College, Yangtze University , No. 8, Hangkong Road, Jingzhou 434000 , Hubei , China
| |
Collapse
|
23
|
RNA m6A reader YTHDF1 facilitates inflammation via enhancing NLRP3 translation. Biochem Biophys Res Commun 2022; 616:76-81. [PMID: 35649302 DOI: 10.1016/j.bbrc.2022.05.076] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 05/21/2022] [Indexed: 11/20/2022]
Abstract
N6-methyladenosine (m6A) modification of mRNAs is involved in multiple essential biological processes, dynamically regulated by m6A "writers", "erasers", and "readers". Yet, the detailed functional roles of RNA m6A reader proteins, such as YTHDFs, are largely unknown. Herein we show that YTHDF1 promotes pro-inflammatory IL-1β production in macrophages during bacterial infections. YTHDF1 overexpression promotes NLRP3 translation. In vivo knockdown of YTHDF1 facilitates survival in a mouse model of sepsis. Thus, YTHDF1 participates in inflammatory responses and subsequent injuries, serving as a new potential therapeutic target in clinical treatment of inflammatory diseases.
Collapse
|
24
|
Boo SH, Ha H, Lee Y, Shin MK, Lee S, Kim YK. UPF1 promotes rapid degradation of m 6A-containing RNAs. Cell Rep 2022; 39:110861. [PMID: 35613594 DOI: 10.1016/j.celrep.2022.110861] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 11/03/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification in eukaryotic mRNAs and affects RNA processing and metabolism. When YTHDF2, an m6A-recognizing protein, binds to m6A, it facilitates the destabilization of m6A-containing RNAs (m6A RNAs). Here, we demonstrate that upstream frameshift 1 (UPF1), a key factor for nonsense-mediated mRNA decay, interacts with YTHDF2, thereby triggering rapid degradation of m6A RNAs. The UPF1-mediated m6A RNA degradation depends on a specific interaction between UPF1 and N-terminal residues 101-168 of YTHDF2, UPF1 ATPase/helicase activities, and UPF1 interaction with proline-rich nuclear receptor coactivator 2 (PNRC2), a decapping-promoting factor preferentially involved in nonsense-mediated mRNA decay. Furthermore, transcriptome-wide analyses show that YTHDF2-bound mRNAs that are not substrates for HRSP12-RNase P/MRP-mediated endoribonucleolytic cleavage are destabilized with a higher dependency on UPF1. Collectively, our data indicate dynamic and multilayered regulation of the stability of m6A RNAs and highlight the multifaceted role of UPF1 in mRNA decay.
Collapse
Affiliation(s)
- Sung Ho Boo
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hongseok Ha
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yujin Lee
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Min-Kyung Shin
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sena Lee
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea.
| |
Collapse
|
25
|
Shan HJ, Gu WX, Duan G, Chen HL. Fat mass and obesity associated (FTO)-mediated N6-methyladenosine modification of Krüppel-like factor 3 (KLF3) promotes osteosarcoma progression. Bioengineered 2022; 13:8038-8050. [PMID: 35311620 PMCID: PMC9161850 DOI: 10.1080/21655979.2022.2051785] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N6-methyladenosine (m6A) methylation is the most common and abundant methylation modification of eukaryotic mRNAs, which is involved in tumor initiation and progression. The study aims to explore the potential role and the regulatory mechanism of fat mass and obesity associated (FTO) in osteosarcoma (OS) progression. In this study, we detected the expressions of Krüppel-like factor 3 (KLF3) in OS cells and tissues and found that the mRNA and protein levels of KLF3 were increased in OS cells and tissues and significantly related to tumor size, metastasis, and TNM stage and poor prognosis of OS patients. FTO promoted the proliferation and invasion and suppressed apoptosis of OS cells through cell experiments in vitro. Further mechanism dissection revealed that FTO and YTHDF2 enforced the decay of KLF3 mRNA and decreased its expression. FTO-mediated mRNA demethylation inhibited KLF3 expression in the YTHDF2-dependent manner. Moreover, KLF3 overexpression abrogated FTO-induced oncogenic effects on the proliferation and invasion of OS cells. Overall, our findings showed that FTO-mediated m6A modification of KLF3 promoted OS progression, which may provide a therapeutic target for OS.
Collapse
Affiliation(s)
- Hong-Jian Shan
- Department of Orthopedics, Institute of Orthopedics, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China.,Department of Orthopedics, the Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, 211100, P. R. China
| | - Wen-Xiang Gu
- Department of Orthopedics, Institute of Orthopedics, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| | - Gang Duan
- Department of Orthopedics, the Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221002, P. R. China
| | - Hong-Liang Chen
- Department of Orthopedics, Institute of Orthopedics, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| |
Collapse
|
26
|
Nie X, Tan J. N6-methyladenosine-related lncRNAs is a potential marker for predicting prognosis and immunotherapy in ovarian cancer. Hereditas 2022; 159:17. [PMID: 35303965 PMCID: PMC8933961 DOI: 10.1186/s41065-022-00222-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 12/02/2022] Open
Abstract
Background With a lack of specific symptoms, ovarian cancer (OV) is often diagnosed at an advanced stage. This coupled with inadequate prognostic indicators and treatments with limited therapeutic effect make OV the deadliest type of gynecological tumor. Recent research indicates that N6-methyladenosine (m6A) and long-chain non-coding RNA (lncRNA) play important roles in the prognosis of OV and the efficacy of immunotherapy. Results Using the Cancer Genome Atlas (TCGA) OV-related data set and the expression profiles of 21 m6A-related genes, we identified two m6A subtypes, and the differentially expressed genes between the two. Based on the differentially expressed lncRNAs in the two m6A subtypes and the lncRNAs co-expressed with the 21 m6A-related genes, single-factor cox and LASSO regression were used to further isolate the 13 major lncRNAs. Finally, multi-factor cox regression was used to construct a m6A-related lncRNA risk score model for OV, with good performance in patient prognosis. Using risk score, OV tumor samples are divided into with high- and low-score groups. We explored the differences in clinical characteristics, tumor mutational burden, and tumor immune cell infiltration between the two groups, and evaluated the risk score’s ability to predict the benefit of immunotherapy. Conclusion Our m6A-based lncRNA risk model could be used to predict the prognosis and immunotherapy response of future OV patients. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00222-3.
Collapse
Affiliation(s)
- Xin Nie
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, China
| | - Jichun Tan
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China. .,Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, China.
| |
Collapse
|
27
|
Zou Z, He T, Liu Y, Zheng L, Zhong Y, Mo Y, Peng S, Shuai C. Emerging role of m6A modification in osteogenesis of stem cells. J Bone Miner Metab 2022; 40:177-188. [PMID: 35091784 DOI: 10.1007/s00774-021-01297-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/20/2021] [Indexed: 12/19/2022]
Abstract
The differentiation of stem cells into osteoblasts is a key link in the treatment of bone defects and other orthopedic diseases. N6-methyladenosine (m6A) modification, an important post-transcriptional modification, is a methylation that occurs at the N6 site of RNA adenylate. The modification plays a regulatory role in the growth and development of biological individuals, the directional differentiation of stem cells and the occurrence of diseases. It is involved in various processes of the fate decision of stem cells. And it regulates the development and constant renewal of bone and keeps bone homeostasis by controlling and maintaining the balance between osteogenesis and adipogenesis. Meanwhile, it also affects the progress of orthopedic-associated diseases such as degenerative osteoporosis and bone tumor. In this review, we mainly summarize the new findings of three key molecules including Writers, Erasers and Readers which regulate m6A modification, and the emerging role of m6A modification in determining the fate and directed differentiation potential of stem cells, especially highlight the regulatory mechanism of osteogenic differentiation, the balance between osteogenesis and adipogenesis and the occurrence and development of bone-related diseases. It may provide some important ideas about finding new strategies to recover from bone defect and degenerative bone disease.
Collapse
Affiliation(s)
- Zi Zou
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Tiantian He
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Ying Liu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Leliang Zheng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Yancheng Zhong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Yuqing Mo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Shuping Peng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China.
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
| | - Cijun Shuai
- Institute of Additive Manufacturing, Jiangxi University of Science and Technology, Nanchang, 330013, China.
- State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha, 410083, China.
| |
Collapse
|
28
|
The Bright and the Dark Side of TGF-β Signaling in Hepatocellular Carcinoma: Mechanisms, Dysregulation, and Therapeutic Implications. Cancers (Basel) 2022; 14:cancers14040940. [PMID: 35205692 PMCID: PMC8870127 DOI: 10.3390/cancers14040940] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Transforming growth factor β (TGF-β) signaling is a preeminent regulator of diverse cellular and physiological processes. Frequent dysregulation of TGF-β signaling has been implicated in cancer. In hepatocellular carcinoma (HCC), the most prevalent form of primary liver cancer, the autocrine and paracrine effects of TGF-β have paradoxical implications. While acting as a potent tumor suppressor pathway in the early stages of malignancy, TGF-β diverts to a promoter of tumor progression in the late stages, reflecting its bright and dark natures, respectively. Within this context, targeting TGF-β represents a promising therapeutic option for HCC treatment. We discuss here the molecular properties of TGF-β signaling in HCC, attempting to provide an overview of its effects on tumor cells and the stroma. We also seek to evaluate the dysregulation mechanisms that mediate the functional switch of TGF-β from a tumor suppressor to a pro-tumorigenic signal. Finally, we reconcile its biphasic nature with the therapeutic implications. Abstract Hepatocellular carcinoma (HCC) is associated with genetic and nongenetic aberrations that impact multiple genes and pathways, including the frequently dysregulated transforming growth factor β (TGF-β) signaling pathway. The regulatory cytokine TGF-β and its signaling effectors govern a broad spectrum of spatiotemporally regulated molecular and cellular responses, yet paradoxically have dual and opposing roles in HCC progression. In the early stages of tumorigenesis, TGF-β signaling enforces profound tumor-suppressive effects, primarily by inducing cell cycle arrest, cellular senescence, autophagy, and apoptosis. However, as the tumor advances in malignant progression, TGF-β functionally switches to a pro-tumorigenic signal, eliciting aggressive tumor traits, such as epithelial–mesenchymal transition, tumor microenvironment remodeling, and immune evasion of cancer cells. On this account, the inhibition of TGF-β signaling is recognized as a promising therapeutic strategy for advanced HCC. In this review, we evaluate the functions and mechanisms of TGF-β signaling and relate its complex and pleiotropic biology to HCC pathophysiology, attempting to provide a detailed perspective on the molecular determinants underlying its functional diversion. We also address the therapeutic implications of the dichotomous nature of TGF-β signaling and highlight the rationale for targeting this pathway for HCC treatment, alone or in combination with other agents.
Collapse
|
29
|
Liu Q. Current Advances in N6-Methyladenosine Methylation Modification During Bladder Cancer. Front Genet 2022; 12:825109. [PMID: 35087575 PMCID: PMC8787278 DOI: 10.3389/fgene.2021.825109] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022] Open
Abstract
N6-methyladenosine (m6A) is a dynamic, reversible post-transcriptional modification, and the most common internal modification of eukaryotic messenger RNA (mRNA). Considerable evidence now shows that m6A alters gene expression, thereby regulating cell self-renewal, differentiation, invasion, and apoptotic processes. M6A methylation disorders are directly related to abnormal RNA metabolism, which may lead to tumor formation. M6A methyltransferase is the dominant catalyst during m6A modification; it removes m6A demethylase, promotes recognition by m6A binding proteins, and regulates mRNA metabolic processes. Bladder cancer (BC) is a urinary system malignant tumor, with complex etiology and high incidence rates. A well-differentiated or moderately differentiated pathological type at initial diagnosis accounts for most patients with BC. For differentiated superficial bladder urothelial carcinoma, the prognosis is normally good after surgery. However, due to poor epithelial cell differentiation, BC urothelial cell proliferation and infiltration may lead to invasive or metastatic BC, which lowers the 5-years survival rate and significantly affects clinical treatments in elderly patients. Here, we review the latest progress in m6A RNA methylation research and investigate its regulation on BC occurrence and development.
Collapse
Affiliation(s)
- Qiang Liu
- Department of Urology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| |
Collapse
|
30
|
Lo N, Xu X, Soares F, He HH. The Basis and Promise of Programmable RNA Editing and Modification. Front Genet 2022; 13:834413. [PMID: 35154288 PMCID: PMC8831800 DOI: 10.3389/fgene.2022.834413] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/07/2022] [Indexed: 12/14/2022] Open
Abstract
One key advantage of RNA over genomic editing is its temporary effects. Aside from current use of DNA-targeting CRISPR-Cas9, the more recently discovered CRISPR-Cas13 has been explored as a means of editing due to its RNA-targeting capabilities. Specifically, there has been a recent interest in identifying and functionally characterizing biochemical RNA modifications, which has spurred a new field of research known as “epitranscriptomics”. As one of the most frequently occurring transcriptome modifications, N6-methyladenosine (m6A) has generated much interest. The presence of m6A modifications is under the tight control of a series of regulators, and the ability of fusing these proteins or demethylases to catalytically inactive CRISPR proteins have resulted in a new wave of programmable RNA methylation tools. In addition, studies have been conducted to develop different CRISPR/Cas and base editor systems capable of more efficient editing, and some have explored the effects of in vivo editing for certain diseases. As well, the application of CRISPR and base editors for screening shows promise in revealing the phenotypic outcomes from m6A modification, many of which are linked to physiological, and pathological effects. Thus, the therapeutic potential of CRISPR/Cas and base editors for not only m6A related, but other RNA and DNA related disease has also garnered insight. In this review, we summarize/discuss the recent findings on RNA editing with CRISPR, base editors and non-CRISPR related tools and offer a perspective regarding future applications for basic and clinical research.
Collapse
Affiliation(s)
- Nicholas Lo
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Xin Xu
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Fraser Soares
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- *Correspondence: Fraser Soares, ; Housheng Hansen He,
| | - Housheng Hansen He
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Fraser Soares, ; Housheng Hansen He,
| |
Collapse
|
31
|
Wang N, Yao F, Liu D, Jiang H, Xia X, Xiong S. RNA N6-methyladenosine in nonocular and ocular disease. J Cell Physiol 2021; 237:1686-1710. [PMID: 34913163 DOI: 10.1002/jcp.30652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 10/27/2021] [Accepted: 11/12/2021] [Indexed: 12/23/2022]
Abstract
N6 -methyladenosine (m6 A), the sixth N methylation of adenylate (A) in RNA, is the most abundant transcriptome modification in eukaryotic messenger RNA (mRNAs). m6 A modification exists in both coding mRNA and noncoding RNAs, and its functions are controlled by methyltransferase, demethylase, and m6 A reading proteins. Methylation modification of m6 A can regulate RNA cleavage, transport, stability, and expression. This review summarizes the enzymes involved in RNA m6 A methylation and the commonly used detection methods. The role of m6 A modification in physiological processes is described, and its impact on tumorigenesis, viral infection, and diabetes is further highlighted. Moreover, up-to-date knowledge of the implications of RNA m6 A modification in ocular diseases such as uveal melanoma and diabetic retinopathy is introduced. Clarifying the mechanism of RNA m6 A methylation will help elucidate the pathogenesis of various diseases, providing options for subsequent treatment.
Collapse
Affiliation(s)
- Nan Wang
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Opthalmology, Central South University, Changsha, China
| | - Fei Yao
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Opthalmology, Central South University, Changsha, China
| | - Die Liu
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Opthalmology, Central South University, Changsha, China
| | - Haibo Jiang
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Opthalmology, Central South University, Changsha, China
| | - Xiaobo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Opthalmology, Central South University, Changsha, China
| | - Siqi Xiong
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Opthalmology, Central South University, Changsha, China
| |
Collapse
|
32
|
Meng L, Zhang Q, Huang X. Abnormal 5-methylcytosine lncRNA methylome is involved in human high-grade serous ovarian cancer. Am J Transl Res 2021; 13:13625-13639. [PMID: 35035702 PMCID: PMC8748087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Methylcytosine (m5C) is an important posttranscriptional RNA methylation modification. Studies have reported that aberrant RNA methylation can regulate tumorigenesis and development, indicating the importance of exploring the distribution and biological functions of m5C modification in human high-grade serous ovarian cancer (HGSOC) lncRNAs. In the current study, we identified 2,050 dysregulated m5C peaks, 1,767 of which were significantly upregulated, while 283 were significantly downregulated by performing methylated RNA immunoprecipitation sequencing on 3 pairs of human HGSOC tissues and paired normal tissues. GO enrichment analysis showed that genes altered by the m5C peak played a key role in phylogeny, protein metabolism, and gene mismatch repair. KEGG pathway analysis revealed that these genes were enriched in some important pathways in cancer regulation, such as the PI3K-Akt signalling pathway, transcriptional dysregulation in cancer, and mismatch repair pathways. In addition, through joint analysis of MeRIP-seq and RNA-seq data, we identified 1671 differentially methylated m5C peaks and synchronous differentially expressed genes. These genes play a key role in cell growth or maintenance, RNA metabolism and material transport. We analyzed expression of the m5C modification regulatory gene collagen type IV alpha 3 chain (COL4A3) in 80 HGSOC tissue samples by immunohistochemistry and found that high expression of COL4A3 was significantly correlated with CA125 level (P=0.016), lymph node metastasis (P<0.001), degree of interstitial invasion (P<0.001) and FIGO staging (P<0.001) and indicated a poorer prognosis. Our results revealed the critical role of m5C methylation of lncRNAs in HGSOC, and provided a reference for the prognostic stratification and treatment strategy of HGSOC.
Collapse
Affiliation(s)
- Li Meng
- Department of Gynecology, The Second Hospital of Hebei Medical University 215 Heping West Road, Shijiazhuang 050011, Hebei, China
| | - Qianqian Zhang
- Department of Gynecology, The Second Hospital of Hebei Medical University 215 Heping West Road, Shijiazhuang 050011, Hebei, China
| | - Xianghua Huang
- Department of Gynecology, The Second Hospital of Hebei Medical University 215 Heping West Road, Shijiazhuang 050011, Hebei, China
| |
Collapse
|
33
|
Yang H, Wu YF, Ding J, Liu W, Zhu DS, Shen XF, Guan YT. Comprehensive Analysis of N 6-Methyladenosine (m 6A) Methylation in Neuromyelitis Optica Spectrum Disorders. Front Genet 2021; 12:735454. [PMID: 34899833 PMCID: PMC8660110 DOI: 10.3389/fgene.2021.735454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Background: N6-Methyladenosine (m6A) methylation is the most prevalent internal posttranscriptional modification on mammalian mRNA. But its role in neuromyelitis optica spectrum disorders (NMOSD) is not known. Aims: To explore the mechanism of m6A in NMOSD patients. Methods: This study assessed the m6A methylation levels in blood from two groups: NMOSD patients and healthy controls. Methylated RNA immunoprecipitation Sequencing (MeRIP-seq) and RNA-seq were performed to assess differences in m6A methylation between NMOSD patients and healthy controls. Ultra-high performance liquid chromatography coupled with triple quadruple mass spectrometry (UPLC-QQQ-MS) method was performed to check m6A level. Differential m6A methylation genes were validated by MeRIP-qPCR. Results: Compared with that in the control group, the total m6A level was decreased in the NMOSD group. Genes with upregulated methylation were primarily enriched in processes associated with RNA splicing, mRNA processing, and innate immune response, while genes with downregulated methylation were enriched in processes associated with the regulation of transcription, DNA-templating, and the positive regulation of I-kappa B kinase/NF-kappa B signalling. Conclusion: These findings demonstrate that differential m6A methylation may act on functional genes to regulate immune homeostasis in NMOSD.
Collapse
Affiliation(s)
- Hong Yang
- Department of Neurology, The First Rehabilitation Hospital of Shanghai, Tongji University School of Medicine, Shanghai, China
| | - Yi-Fan Wu
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Ding
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Liu
- Department of Neurology, The First Rehabilitation Hospital of Shanghai, Tongji University School of Medicine, Shanghai, China
| | - De-Sheng Zhu
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xia-Feng Shen
- Department of Neurology, The First Rehabilitation Hospital of Shanghai, Tongji University School of Medicine, Shanghai, China
| | - Yang-Tai Guan
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Neurology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
34
|
Yang D, Chang S, Li F, Ma M, Yang J, Lv X, Huangfu L, Jia C. m 6 A transferase KIAA1429-stabilized LINC00958 accelerates gastric cancer aerobic glycolysis through targeting GLUT1. IUBMB Life 2021; 73:1325-1333. [PMID: 34409730 DOI: 10.1002/iub.2545] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 02/06/2023]
Abstract
Emerging evidence has demonstrated that N6 -methyladenosine (m6 A) and long noncoding RNAs (lncRNAs) are both crucial regulators in gastric cancer (GC) tumorigenesis. However, the interaction of m6 A and lncRNAs in GC progression are still unclear. Here, our team discovered that lncRNA LINC00958 expression up-regulated in GC tissue and cells. Clinically, high-expression of LINC00958 was clinically correlated to lower survival of GC patients. Functionally, in vitro assays demonstrated that LINC00958 promoted the GC cells' aerobic glycolysis. Mechanistically, methylated RNA immunoprecipitation sequencing (MeRIP-Seq) found that there were m6 A-modificated sites in LINC00958, and moreover m6 A methyltransferase KIAA1429 catalyzed the m6 A modification on LINC00958 loci. Moreover, LINC00958 interacted with GLUT1 mRNA via the m6 A-dependent manner to enhance GLUT1 mRNA transcript stability, thereby positively regulating the aerobic glycolysis of GC. In conclusion, our findings reveal the function and mechanism of KIAA1429-induced LINC00958 in GC, delineating novel understanding of m6 A-lncRNA in cancer biology.
Collapse
Affiliation(s)
- Desheng Yang
- Department of Geriatric Medicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Shuang Chang
- Department of Gastroenterology, Kaifeng People's Hospital, Kaifeng, Henan, China
| | - Fuchun Li
- Department of Medical Ultrasonics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Mingxiao Ma
- Department of Gastroenterology, Kaifeng People's Hospital, Kaifeng, Henan, China
- Henan University College of Medicine, Kaifeng, Henan, China
| | - Jiayao Yang
- Department of Gastroenterology, Kaifeng People's Hospital, Kaifeng, Henan, China
| | - Xun Lv
- Department of Geriatric Medicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Luxin Huangfu
- Department of Geriatric Medicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Changhe Jia
- Department of Geriatric Medicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| |
Collapse
|
35
|
Wang Z, Liu J, Yang Y, Xing C, Jing J, Yuan Y. Expression and prognostic potential of ribosome 18S RNA m 6A methyltransferase METTL5 in gastric cancer. Cancer Cell Int 2021; 21:569. [PMID: 34702266 PMCID: PMC8549223 DOI: 10.1186/s12935-021-02274-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/17/2021] [Indexed: 11/23/2022] Open
Abstract
Background Ribosomal RNA N6-methyltransferase METTL5 was reported to catalyze m6A in 18S rRNA. We aimed to investigate the expression and prognostic features of METTL5 in gastric cancer (GC). Methods In this study, 168 GC patients and their corresponding adjacent tissues were collected. Immunohistochemical staining was used to detect the expression of METTL5 protein. Univariate and multivariate Cox analysis were used to dertermine the prognostic role of METTL5 protein in GC, and a nomogram was constructed to evaluate GC patients’ prognosis based on METTL5 expression. Data from TCGA and GEO database were also used to validate the prognostic value of METTL5 in GC patients on mRNA level. We further performed GSEA enrichment analysis to explore the possible function and related pathways related to METTL5. Results METTL5 protein in gastric cancer tissues (GCTs) was significantly decreased compared with adjacent normal tissues (ANTs) and adjacent intestinal metaplasia tissues (AIMTs) (P < 0.001, respectively). Meanwhile, METTL5 expression was negatively correlated with clinicopathologic stage. According to multivariate Cox proportional hazards model analysis, METTL5 protein expression was a good independent predictor of GC prognosis (p < 0.05). Patients with high METTL5 expression had better prognosis. The nomogram constructed based on METTL5 expression could predict the prognosis of GC patients well. GSEA analysis showed that genes of METTL5 low expression group were enriched in some oncogenic signaling pathways such as ERBB, MAPK, JAK-STAT, Wnt, and mTOR, as well as some immune pathways, including Fc-gamma R mediated phagocytosis, Fc-epsilon Ri, chemokine, T cell receptor and B cell receptor signaling pathway. While the high expression group of METTL5 was mainly related to oxidative phosphorylation, nucleotide excision repair and mismatch repair. Conclusions METTL5 protein was decreased in GCTs compared with AIMTs and ANTs, and it may be a potential prognostic biomarker in GC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02274-3.
Collapse
Affiliation(s)
- Zhenshuang Wang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Jingwei Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, Liaoning Province, China
| | - Yi Yang
- Department of Neurosurgery of the First Hospital of China Medical University, Shenyang, 110001, China
| | - Chenzhong Xing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, Liaoning Province, China
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China. .,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First hospital of China Medical University, Shenyang, 110001, China. .,Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, Liaoning Province, China.
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China. .,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First hospital of China Medical University, Shenyang, 110001, China. .,Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, Liaoning Province, China.
| |
Collapse
|
36
|
Lee B, Lee S, Shim J. YTHDF2 Suppresses Notch Signaling through Post-transcriptional Regulation on Notch1. Int J Biol Sci 2021; 17:3776-3785. [PMID: 34671198 PMCID: PMC8495403 DOI: 10.7150/ijbs.61573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
YTH domain family 2 (YTHDF2) is an N6-methyladenosine (m6A) binding protein promoting mRNA degradation in various biological processes. Despite its essential roles, the role of YTHDF2 in determining cell fates has not been fully elucidated. Notch signaling plays a vital role in determining cell fates, such as proliferation, differentiation, and apoptosis. We investigated the effect of YTHDF2 on Notch signaling. Our results show that YTHDF2 inhibits Notch signaling by downregulating the Notch1, HES1, and HES5 mRNA levels. Analyzing YTHDF2 deletion mutants indicates that the YTH domain is critical in regulating the Notch signal by directly binding m6A of Notch1 mRNA. Recently, YTHDF2 nuclear translocation was reported under heat shock conditions, but its physiological function is unknown. In our study, the YTH domain is required for YTHDF2 nuclear translocation. In addition, under heat shock stress, the Notch signal was significantly restored due to the increased expression of the Notch1 targets. These results suggest that YTHDF2 in the cytoplasm may act as an intrinsic suppressor in Notch signaling by promoting Notch1 mRNA degradation under normal cellular conditions. Conversely, upon the extracellular stress such as heat shock, YTHDF2 nuclear translocation resulting in reduced Notch1 mRNA decay may contribute to the increasing of Notch intracellular domain (NICD) regulating the survival-related target genes.
Collapse
Affiliation(s)
- Byongsun Lee
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Seungjae Lee
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Jaekyung Shim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| |
Collapse
|
37
|
Klinge CM, Piell KM, Petri BJ, He L, Zhang X, Pan J, Rai SN, Andreeva K, Rouchka EC, Wahlang B, Beier JI, Cave MC. Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab008. [PMID: 34548932 PMCID: PMC8448424 DOI: 10.1093/eep/dvab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 08/10/2021] [Indexed: 05/30/2023]
Abstract
Exposure to a single dose of polychlorinated biphenyls (PCBs) and a 12-week high-fat diet (HFD) results in nonalcoholic steatohepatitis (NASH) in mice by altering intracellular signaling and inhibiting epidermal growth factor receptor signaling. Post-transcriptional chemical modification (PTM) of RNA regulates biological processes, but the contribution of epitranscriptomics to PCB-induced steatosis remains unknown. This study tested the hypothesis that PCB and HFD exposure alters the global RNA epitranscriptome in male mouse liver. C57BL/6J male mice were fed a HFD for 12 weeks and exposed to a single dose of Aroclor 1260 (20 mg/kg), PCB 126 (20 µg/kg), both Aroclor 1260 and PCB 126 or vehicle control after 2 weeks on HFD. Chemical RNA modifications were identified at the nucleoside level by liquid chromatography-mass spectrometry. From 22 PTM global RNA modifications, we identified 10 significant changes in RNA modifications in liver with HFD and PCB 126 exposure. Only two modifications were significantly different from HFD control liver in all three PCB exposure groups: 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A). Exposure to HFD + PCB 126 + Aroclor 1260 increased the abundance of N(6), O(2)-dimethyladenosine (m6Am), which is associated with the largest number of transcript changes. Increased m6Am and pseudouridine were associated with increased protein expression of the writers of these modifications: Phosphorylated CTD Interacting Factor 1 (PCIF1) and Pseudouridine Synthase 10 (PUS10), respectively, in HFD + PCB 126- + Aroclor 1260-exposed mouse liver. Increased N1-methyladenosine (m1A) and m6A were associated with increased transcript levels of the readers of these modifications: YTH N6-Methyladenosine RNA Binding Protein 2 (YTHDF2), YTH Domain Containing 2 (YTHDC2), and reader FMRP Translational Regulator 1 (FMR1) transcript and protein abundance. The results demonstrate that PCB exposure alters the global epitranscriptome in a mouse model of NASH; however, the mechanism for these changes requires further investigation.
Collapse
Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Belinda J Petri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Liqing He
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
| | - Jianmin Pan
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Shesh N Rai
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- Department of Bioinformatics and Biostatistics, University of Louisville School of Public Health and Information Sciences, Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
| | - Kalina Andreeva
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, JB Speed School of Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Banrida Wahlang
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Juliane I Beier
- Department of Medicine, Division of Gastroenterology, Hepatology & Nutrition, University of Pittsburgh, Louisville, KY 40292, USA
- Pittsburgh Liver Research Center (PLRC), Louisville, KY 40292, USA
- Department of Environmental and Occupational Health Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew C Cave
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA
| |
Collapse
|
38
|
Zhang Y, Zeng F, Zeng M, Han X, Cai L, Zhang J, Weng J, Gao Y. Identification and Characterization of Alcohol-related Hepatocellular Carcinoma Prognostic Subtypes based on an Integrative N6-methyladenosine methylation Model. Int J Biol Sci 2021; 17:3554-3572. [PMID: 34512165 PMCID: PMC8416726 DOI: 10.7150/ijbs.62168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/01/2021] [Indexed: 12/29/2022] Open
Abstract
Background: Alcohol consumption increases the risk of hepatocellular carcinoma (HCC), and associated with a high mortality rate and poor prognosis. N6-methyladenosine (m6A) methylations play key roles in tumorigenesis and progression. However, our current knowledge about m6A in alcohol-related HCC (A-HCC) remains elucidated. Herein, the authors construct an integrative m6A model based on A-HCC subtyping and mechanism exploration workflow. Methods: Based on the m6A expressions of A-HCC and in vivo experiment, different prognosis risk A-HCC subtypes are identified. Meanwhile, multiple interdependent indicators of prognosis including patient survival rate, clinical pathological prognosis and immunotherapy sensitivity. Results: The m6A model includes LRPPRC, YTHDF2, KIAA14219, and RBM15B, classified A-HCC patients into high/low-risk subtypes. The high-risk subtype compared to the low-risk subtype showed phenotypic malignancy, poor prognosis, immunosuppression, and activation of tumorigenesis and proliferation-related pathways, including the E2F target, DNA repair, and mTORC1 signalling pathways. The expression of Immunosuppressive cytokines DNMT1/EZH2 was up-regulated in A-HCC patients, and teniposide may be a potential therapeutic drug for A-HCC. Conclusion: Our model redefined A-HCC prognosis risk, identified potential m6As linking tumour progress and immune regulations and selected possible therapy target, thus promoting understanding and clinical applications about A-HCC.
Collapse
Affiliation(s)
- Yue Zhang
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, ZhuJiang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Fanhong Zeng
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, ZhuJiang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Min Zeng
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, ZhuJiang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Xu Han
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, ZhuJiang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Lei Cai
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, ZhuJiang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Jiajun Zhang
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, ZhuJiang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Jun Weng
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, ZhuJiang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Yi Gao
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, ZhuJiang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| |
Collapse
|
39
|
Huang K, Zhao W, Wang X, Qiu Y, Liu Z, Chen R, Liu W, Liu B. Akt Inhibition Enhanced the Growth Inhibition Effects of Low-Dose Heavy-Ion Radiation via the PI3K/Akt/p53 Signaling Pathway in C6 Glioblastoma Cells. Front Oncol 2021; 11:649176. [PMID: 33869050 PMCID: PMC8047659 DOI: 10.3389/fonc.2021.649176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/15/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Glioma has one of the highest mortality rates of all tumors of the nervous system and commonly used treatments almost always fail to achieve tumor control. Low-dose carbon-ion radiation can effectively target cancer and tumor cells, but the mechanisms of growth inhibition induced by heavy-ion radiation via the PI3K/Akt signaling pathway are unknown, and inhibition by heavy-ion radiation is minor in C6 cells. METHODS Carbon-ion radiation was used to investigate the effects of heavy-ion radiation on C6 cells, and suppression of Akt was performed using perifosine. MTT assays were used to investigate optimal perifosine treatment concentrations. Clone formation assays were used to investigate the growth inhibition effects of carbon-ion radiation and the effects of radiation with Akt inhibition. Lactate dehydrogenase release, superoxide dismutase activity, and malondialdehyde content were assessed to investigate oxidative stress levels. Expression levels of proteins in the PI3K/Akt/p53 signaling pathway were assessed via western blotting. RESULTS The 10% maximum inhibitory concentration of perifosine was 19.95 μM. In clone formation assays there was no significant inhibition of cell growth after treatment with heavy-ion irradiation, whereas perifosine enhanced inhibition. Heavy-ion radiation induced lactate dehydrogenase release, increased the level of malondialdehyde, and reduced superoxide dismutase activity. Akt inhibition promoted these processes. Heavy-ion radiation treatment downregulated Akt expression, and upregulated B-cell lymphoma-2 (Bcl-2) expression. p53 and Bcl-2 expression were significantly upregulated, and Bcl-2-associated X protein (Bax) expression was downregulated. The expression profiles of pAkt, Bcl-2, and Bax were reversed by perifosine treatment. Caspase 3 expression was upregulated in all radiation groups. CONCLUSIONS The growth inhibition effects of low-dose heavy-ion irradiation were not substantial in C6 cells, and Akt inhibition induced by perifosine enhanced the growth inhibition effects via proliferation inhibition, apoptosis, and oxidative stress. Akt inhibition enhanced the effects of heavy-ion radiation, and the PI3K/Akt/p53 signaling pathway may be a critical component involved in the process.
Collapse
Affiliation(s)
- Ke Huang
- School/Hospital of Stomatology, Lanzhou University, Lanzhou, China
| | - Wei Zhao
- Peking University People’s Hospital, Peking University, Beijing, China
| | - Xuqiao Wang
- School/Hospital of Stomatology, Lanzhou University, Lanzhou, China
| | - Yingfei Qiu
- School/Hospital of Stomatology, Lanzhou University, Lanzhou, China
| | - Zelin Liu
- School/Hospital of Stomatology, Lanzhou University, Lanzhou, China
| | - Rui Chen
- School/Hospital of Stomatology, Lanzhou University, Lanzhou, China
| | - Wei Liu
- Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
- The School of Nuclear Science and Technology, Lanzhou University, Lanzhou, China
| | - Bin Liu
- School/Hospital of Stomatology, Lanzhou University, Lanzhou, China
- The School of Nuclear Science and Technology, Lanzhou University, Lanzhou, China
| |
Collapse
|
40
|
Feng Z, Zhou F, Tan M, Wang T, Chen Y, Xu W, Li B, Wang X, Deng X, He ML. Targeting m6A modification inhibits herpes virus 1 infection. Genes Dis 2021; 9:1114-1128. [PMID: 35685469 PMCID: PMC9170584 DOI: 10.1016/j.gendis.2021.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/26/2021] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
The latent infection by herpes virus type 1 (HSV-1) may be lifelong in trigeminal ganglia and a suspected cause of Alzheimer's Disease (AD) and Amyotrophic lateral sclerosis (ALS). Whether and how N6-methyladenosine (m6A) modification of viral RNAs affects virus infection are poorly understood. Here, we report that HSV-1 infection enhanced the expression of m6A writers (METTL3, METTL14) and readers (YTHDF1/2/3) at the early infection stage and decreased their expression later on, while suppressed the erasers' (FTO, ALBKH5) expression immediately upon infection to facilitate viral replication. Inhibiting m6A modification by 3-deazaadenosine (DAA) significantly decreased viral replication and reduced viral reproduction over 1000 folds. More interestingly, depleting the writers and readers by siRNAs inhibited virus replication and reproduction; whereas depleting the erasers promoted viral replication and reproduction. Silencing YTHDF3 strikingly decreased viral replication by up to 90%, leading to reduction of up to 10-fold viral replication and over 100-fold virus reproduction, respectively. Depletion of m6A initiator METTL3 (by 60%–70%) by siRNA correlatedly decreased viral replication 60%–70%, and reduced virus yield over 30-fold. Consistently, ectopic expression of METTL3 largely increased virus yield. METTL3 knockdown suppressed the HSV-1 intermediate early and early genes (ICP0, ICP8 and UL23) and late genes (VP16, UL44, UL49 and ICP47); while ectopic expression of METTL3 upregulated these gene expression. Results from our study shed the lights on the importance for m6A modification to initiate HSV-1 early replication. The components of m6A modification machinery, particularly m6A initiator METTL3 and reader YTHDF3, would be potential important targets for combating HSV-1 infections.
Collapse
Affiliation(s)
- Zhuoying Feng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, PR China
| | - Fanghang Zhou
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, PR China
| | - Miaomiao Tan
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, PR China
| | - Tingting Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, PR China
| | - Ying Chen
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, PR China
| | - Wenwen Xu
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Bin Li
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, PR China
- Corresponding author.
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, PR China
- Corresponding author.
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, PR China
- CityU Shenzhen Research Institute, Shenzhen, Guangdong 518057, PR China
- Corresponding author. Department of Biomedical Science, City University of Hong Kong, Know loon, Hong Kong, PR China.
| |
Collapse
|
41
|
Hasan MM, Shoombuatong W, Kurata H, Manavalan B. Critical evaluation of web-based DNA N6-methyladenine site prediction tools. Brief Funct Genomics 2021; 20:258-272. [PMID: 33491072 DOI: 10.1093/bfgp/elaa028] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
Methylation of DNA N6-methyladenosine (6mA) is a type of epigenetic modification that plays pivotal roles in various biological processes. The accurate genome-wide identification of 6mA is a challenging task that leads to understanding the biological functions. For the last 5 years, a number of bioinformatics approaches and tools for 6mA site prediction have been established, and some of them are easily accessible as web application. Nevertheless, the accurate genome-wide identification of 6mA is still one of the challenging works that lead to understanding the biological functions. Especially in practical applications, these tools have implemented diverse encoding schemes, machine learning algorithms and feature selection methods, whereas few systematic performance comparisons of 6mA site predictors have been reported. In this review, 11 publicly available 6mA predictors evaluated with seven different species-specific datasets (Arabidopsis thaliana, Tolypocladium, Diospyros lotus, Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans and Escherichia coli). Of those, few species are close homologs, and the remaining datasets are distant sequences. Our independent, validation tests demonstrated that Meta-i6mA and MM-6mAPred models for A. thaliana, Tolypocladium, S. cerevisiae and D. melanogaster achieved excellent overall performance when compared with their counterparts. However, none of the existing methods were suitable for E. coli, C. elegans and D. lotus. A feasibility of the existing predictors is also discussed for the seven species. Our evaluation provides useful guidelines for the development of 6mA site predictors and helps biologists selecting suitable prediction tools.
Collapse
Affiliation(s)
| | - Watshara Shoombuatong
- Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics in the Kyushu Institute of Technology, Japan
| | | |
Collapse
|
42
|
Li K, Chen J, Lou X, Li Y, Qian B, Xu D, Wu Y, Ma S, Zhang D, Cui W. HNRNPA2B1 Affects the Prognosis of Esophageal Cancer by Regulating the miR-17-92 Cluster. Front Cell Dev Biol 2021; 9:658642. [PMID: 34277606 PMCID: PMC8278577 DOI: 10.3389/fcell.2021.658642] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/09/2021] [Indexed: 02/05/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotes. Accumulating evidence suggests that dysregulation of m6A modification significantly correlates with tumorigenesis and progression. In this study, we observed an increased expression and positive correlations of all 25 m6A regulators in esophageal cancer (ESCA) data obtained from the TCGA database. Through expression profiling of these regulators, a prognostic score model containing HNRNPA2B1, ALKBH5, and HNRNPG was established, and the high-risk subgroup exhibited strong positive correlations with ESCA progression and outcome. The risk score obtained from this model may represent an independent predictor of ESCA prognosis. Notably, the gene most frequently associated with increased risk was HNRNPA2B1; in ESCA, the increased expression of this gene alone predicted poor prognosis by affecting tumor-promoting signaling pathways through miR-17-92 cluster. An experimental study demonstrated that elevated HNRNPA2B1 expression was positively associated with distant metastasis and lymph node stage, and predicted the poor outcomes of ESCA patients. Knockdown of HNRNPA2B1 significantly decreased the expression of miR-17, miR-18a, miR-20a, miR-93, and miR-106b and inhibited the proliferation of ESCA cells. Therefore, our study indicated that the dynamic changes in 25 m6A regulators were associated with the clinical features and prognosis of patients with ESCA. Importantly, HNRNPA2B1 alone may affect the prognosis of patients with ESCA by regulating the miR-17-92 cluster.
Collapse
Affiliation(s)
- Kexin Li
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiongyu Chen
- Central Laboratory, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Xiaoying Lou
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yiling Li
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Benheng Qian
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Danfei Xu
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Wu
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shaohui Ma
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Donghong Zhang
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Wei Cui,
| | - Wei Cui
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Donghong Zhang,
| |
Collapse
|
43
|
Zhou M, Xiao MS, Li Z, Huang C. New progresses of circular RNA biology: from nuclear export to degradation. RNA Biol 2020; 18:1365-1373. [PMID: 33241761 DOI: 10.1080/15476286.2020.1853977] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Circular RNA, typically generated from backsplicing reaction, is a class of single-stranded and covalently linked RNA. Although most circular RNAs are lowly expressed, some of them are able to accumulate to high levels and even exceed their cognate mRNAs due to their longer half-lives. Once produced in the nucleus, the majority of circular RNAs are exported to the cytoplasm for their proper functions or degradation. In this review, we will summarize the biogenesis and classification of circular RNAs and highlight the recent advances in our understanding of circular RNA nuclear export and degradation.
Collapse
Affiliation(s)
- Min Zhou
- School of Life Sciences, Chongqing University, Chongqing, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Mei-Sheng Xiao
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| |
Collapse
|
44
|
Song T, Yang Y, Jiang S, Peng J. Novel Insights into Adipogenesis from the Perspective of Transcriptional and RNA N6-Methyladenosine-Mediated Post-Transcriptional Regulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001563. [PMID: 33173729 PMCID: PMC7610318 DOI: 10.1002/advs.202001563] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 05/09/2023]
Abstract
Obesity is a critical risk factor causing the development of metabolic diseases and cancers. Its increasing prevalence worldwide has aroused great concerns of the researchers on adipose development and metabolic function. During adipose expansion, adipogenesis is a way to store lipids as well as to avoid lipotoxicity in other tissues, and may be an approach to offset the negative metabolic effects of obesity. In this Review, the transcriptional regulation of adipogenesis is outlined to characterize numerous biological processes in research on the determination of adipocyte fate and regulation of adipogenic differentiation. Notably, one of the post-transcriptional modifications of mRNA, namely, N6-methyladenosine (m6A), has been recently found to play a role in adipogenesis. Here, the roles of m6A-related enzymes and proteins in adipogenesis, with a particular focus on how these m6A-related proteins function at different stages of adipogenesis, are mainly discussed. The Review also highlights the coordination role of the transcriptional and post-transcriptional (RNA m6A methylation) regulation in adipogenesis and related biological processes. In this context, a better understanding of adipogenesis at both the transcriptional and post-transcriptional levels may facilitate the development of novel strategies to improve metabolic health in obesity.
Collapse
Affiliation(s)
- Tongxing Song
- Department of Animal Nutrition and Feed ScienceCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- The Cooperative Innovation Center for Sustainable Pig ProductionWuhan430070China
| | - Yang Yang
- Department of Animal Nutrition and Feed ScienceCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- The Cooperative Innovation Center for Sustainable Pig ProductionWuhan430070China
| | - Siwen Jiang
- The Cooperative Innovation Center for Sustainable Pig ProductionWuhan430070China
- Key Laboratory of Animal GeneticsBreeding and Reproduction Ministry of EducationCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Jian Peng
- Department of Animal Nutrition and Feed ScienceCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- The Cooperative Innovation Center for Sustainable Pig ProductionWuhan430070China
| |
Collapse
|
45
|
Niu X, Xu J, Liu J, Chen L, Qiao X, Zhong M. Landscape of N 6-Methyladenosine Modification Patterns in Human Ameloblastoma. Front Oncol 2020; 10:556497. [PMID: 33178585 PMCID: PMC7592903 DOI: 10.3389/fonc.2020.556497] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/21/2020] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE To comprehensively analyze the global N6-methyladenosine (m6A) modification pattern in ameloblastoma. METHODS m6A peaks in ameloblastoma and normal oral tissues were detected by MeRIP-seq. Differentially methylated m6A sites within messenger RNAs (mRNAs), long no-coding RNA (lncRNAs) and circular RNA (circRNAs) were identified, followed by functional enrichment analysis. By comprehensively analyzing MeRIP-seq and RNA-seq data, differentially expressed mRNAs, lncRNAs and circRNAs containing differentially methylated sites were identified. RNA binding proteins (RBPs) were then identified for differentially methylated m6A sites. RESULTS In total, 3,673 differentially methylated m6A sites within coding genes were detected, of which 16.2% (704/3,673) were significantly upmethylated sites in ameloblastoma compared to normal oral tissues. Furthermore, 4,975 differentially methylated m6A sites within lncRNAs were identified, of which 29.4% (1,465/4,975) were upmethylated sites in ameloblastoma. We also found 364 differentially methylated m6A sites within circRNAs, of which 22.5% (82/364) were upmethylated sites in ameloblastoma. Differentially methylated m6A was most often harbored in the CDS (54.10%), followed by 5'UTR (21.71%). Functional enrichment analysis revealed that m6A modification could be involved in the development of ameloblastoma by organism developmental processes. A total of 158 RBPs within differentially methylated m6A sites were identified, which were significantly involved in mRNA metabolic process, mRNA processing, RNA processing, RNA splicing and RNA transport. CONCLUSION Our findings for the first time provide m6A landscape of human ameloblastoma, which expand the understanding of m6A modifications and uncover regulation of lncRNAs and circRNAs through m6A modification in ameloblastoma.
Collapse
Affiliation(s)
- Xing Niu
- Department of Stomatology, Xiang’an Hospital of Xiamen University, Xiamen, China
- Department of Oral Histopathology, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Jingping Xu
- Department of Stomatology, Xiang’an Hospital of Xiamen University, Xiamen, China
| | - Jinwen Liu
- Department of Oral Histopathology, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Lijie Chen
- Department of Stomatology, Xiang’an Hospital of Xiamen University, Xiamen, China
- Department of Oral Histopathology, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Xue Qiao
- Department of Central Laboratory, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Ming Zhong
- Department of Stomatology, Xiang’an Hospital of Xiamen University, Xiamen, China
- Department of Oral Histopathology, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| |
Collapse
|
46
|
Xu Z, Peng B, Cai Y, Wu G, Huang J, Gao M, Guo G, Zeng S, Gong Z, Yan Y. N6-methyladenosine RNA modification in cancer therapeutic resistance: Current status and perspectives. Biochem Pharmacol 2020; 182:114258. [PMID: 33017575 DOI: 10.1016/j.bcp.2020.114258] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 02/05/2023]
Abstract
Several strategies, including chemotherapy and radiotherapy, have improved therapeutic outcomes among cancer patients in clinical practice. However, due to their heterogeneity, cancer cells frequently display primary or acquired therapeutic resistance, thereby resulting in treatment failure. The mechanisms underlying cancer therapeutic resistance are complex and varied. Among them, N6-methyladenosine (m6A) RNA modification has gained increasing attention as a potential determinant of therapy resistance within various cancers. In this review, we primarily describe evidence for the effect of the m6A epitranscriptome on RNA homeostasis modulation, which has been shown to alter multiple cellular pathways in cancer research and treatment. Additionally, we discuss the profiles and biological implications of m6A RNA methylation, which is undergoing intensive investigation for its effect on the control of therapeutic resistance.
Collapse
Affiliation(s)
- Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| |
Collapse
|
47
|
Role of Viral Ribonucleoproteins in Human Papillomavirus Type 16 Gene Expression. Viruses 2020; 12:v12101110. [PMID: 33007936 PMCID: PMC7600041 DOI: 10.3390/v12101110] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 02/06/2023] Open
Abstract
Human papillomaviruses (HPVs) depend on the cellular RNA-processing machineries including alternative RNA splicing and polyadenylation to coordinate HPV gene expression. HPV RNA processing is controlled by cis-regulatory RNA elements and trans-regulatory factors since the HPV splice sites are suboptimal. The definition of HPV exons and introns may differ between individual HPV mRNA species and is complicated by the fact that many HPV protein-coding sequences overlap. The formation of HPV ribonucleoproteins consisting of HPV pre-mRNAs and multiple cellular RNA-binding proteins may result in the different outcomes of HPV gene expression, which contributes to the HPV life cycle progression and HPV-associated cancer development. In this review, we summarize the regulation of HPV16 gene expression at the level of RNA processing with focus on the interactions between HPV16 pre-mRNAs and cellular RNA-binding factors.
Collapse
|
48
|
Weiße J, Rosemann J, Krauspe V, Kappler M, Eckert AW, Haemmerle M, Gutschner T. RNA-Binding Proteins as Regulators of Migration, Invasion and Metastasis in Oral Squamous Cell Carcinoma. Int J Mol Sci 2020; 21:E6835. [PMID: 32957697 PMCID: PMC7555251 DOI: 10.3390/ijms21186835] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023] Open
Abstract
Nearly 7.5% of all human protein-coding genes have been assigned to the class of RNA-binding proteins (RBPs), and over the past decade, RBPs have been increasingly recognized as important regulators of molecular and cellular homeostasis. RBPs regulate the post-transcriptional processing of their target RNAs, i.e., alternative splicing, polyadenylation, stability and turnover, localization, or translation as well as editing and chemical modification, thereby tuning gene expression programs of diverse cellular processes such as cell survival and malignant spread. Importantly, metastases are the major cause of cancer-associated deaths in general, and particularly in oral cancers, which account for 2% of the global cancer mortality. However, the roles and architecture of RBPs and RBP-controlled expression networks during the diverse steps of the metastatic cascade are only incompletely understood. In this review, we will offer a brief overview about RBPs and their general contribution to post-transcriptional regulation of gene expression. Subsequently, we will highlight selected examples of RBPs that have been shown to play a role in oral cancer cell migration, invasion, and metastasis. Last but not least, we will present targeting strategies that have been developed to interfere with the function of some of these RBPs.
Collapse
Affiliation(s)
- Jonas Weiße
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| | - Julia Rosemann
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| | - Vanessa Krauspe
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| | - Matthias Kappler
- Department of Oral and Maxillofacial Plastic Surgery, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Alexander W. Eckert
- Department of Cranio Maxillofacial Surgery, Paracelsus Medical University, 90471 Nuremberg, Germany;
| | - Monika Haemmerle
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
| | - Tony Gutschner
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| |
Collapse
|
49
|
Wang YJ, Yang B, Lai Q, Shi JF, Peng JY, Zhang Y, Hu KS, Li YQ, Peng JW, Yang ZZ, Li YT, Pan Y, Koeffler HP, Liao JY, Yin D. Reprogramming of m 6A epitranscriptome is crucial for shaping of transcriptome and proteome in response to hypoxia. RNA Biol 2020; 18:131-143. [PMID: 32746693 DOI: 10.1080/15476286.2020.1804697] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Hypoxia causes a series of responses supporting cells to survive in harsh environments. Substantial post-transcriptional and translational regulation during hypoxia has been observed. However, detailed regulatory mechanism in response to hypoxia is still far from complete. RNA m6A modification has been proven to govern the life cycle of RNAs. Here, we reported that total m6A level of mRNAs was decreased during hypoxia, which might be mediated by the induction of m6A eraser, ALKBH5. Meanwhile, expression levels of most YTH family members of m6A readers were systematically down-regulated. Transcriptome-wide analysis of m6A revealed a drastic reprogramming of m6A epitranscriptome during cellular hypoxia. Integration of m6A epitranscriptome with either RNA-seq based transcriptome analysis or mass spectrometry (LC-MS/MS) based proteome analysis of cells upon hypoxic stress revealed that reprogramming of m6A epitranscriptome reshaped the transcriptome and proteome, thereby supporting efficient generation of energy for adaption to hypoxia. Moreover, ATP production was blocked when silencing an m6A eraser, ALKBH5, under hypoxic condition, demonstrating that m6A pathway is an important regulator during hypoxic response. Collectively, our studies indicate that crosstalk between m6A and HIF1 pathway is essential for cellular response to hypoxia, providing insights into the underlying molecular mechanisms during hypoxia.
Collapse
Affiliation(s)
- Yan-Jie Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Bing Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Qiao Lai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China.,Department of Science and Teaching, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University , Guangzhou, China
| | - Jun-Fang Shi
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China
| | - Jiang-Yun Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Kai-Shun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Ya-Qing Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China.,Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou P.R. China
| | - Jing-Wen Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Zhi-Zhi Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Yao-Ting Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Yue Pan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore , Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California Los Angeles School of Medicine , Los Angeles, CA, USA
| | - Jian-You Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| |
Collapse
|
50
|
Han B, Yao HH. N 6-methyladenosine as a Novel Regulator of Brain Physiology and Diseases. Curr Med Sci 2020; 40:401-406. [PMID: 32681245 DOI: 10.1007/s11596-020-2194-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/02/2020] [Indexed: 01/29/2023]
Abstract
N6-methyladenosine (m6A) is identified as the most widespread and abundant internal chemical modification of RNA in eukaryotes. A series of proteins including methyltransferases (also known as "writers"), demethylases (also known as "erasers"), and m6A-binding proteins (also known as "readers") were indicated to participate in the m6A methylation. m6A has emerged as a regulator of various cellular, developmental, and disease processes. Notably, there is highest abundance of m6A methylation in brain than in other organs, which indicates that m6A plays an essential role in brain functions. Here, we describe the general features, mechanisms, and functions of m6A in the brain, and discuss the emerging roles of m6A in brain physiology and diseases.
Collapse
Affiliation(s)
- Bing Han
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Hong-Hong Yao
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, 210009, China.
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210009, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226019, China.
| |
Collapse
|