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Song K, Cao Q, Yang Y, Zuo Y, Wu X. ALKBH5 modulates bone cancer pain in a rat model by suppressing NR2B expression. Biotechnol Appl Biochem 2024; 71:1105-1115. [PMID: 38764325 DOI: 10.1002/bab.2601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/21/2024]
Abstract
Currently, the clinical treatment of bone cancer pain (BCP) is mainly related to its pathogenesis. The aim of the present study was to elucidate the potential role of N6-methyladenosine (m6A) in BCP in the spinal cord dorsal root ganglia (DRG) of BCP rats and its specific regulatory mechanism in N-methyl-d-aspartate receptor subunit 2B (NR2B). A rat model of BCP was constructed by tibial injection of Walker256 cells, and ALKBH5 and NR2B expression in the spinal cord DRG was detected. ALKBH5 was silenced or overexpressed in PC12 cells to verify the regulatory effect of ALKBH5 on NR2B. The specific mechanism underlying the interaction between ALKBH5 and NR2B was investigated using methylated RNA immunoprecipitation and dual-luciferase reporter gene assays. The results showed increased expression of m6A, decreased expression of ALKBH5, and increased expression of NR2B in the DRG of the BCP rat model. Overexpression of ALKBH5 inhibited NR2B expression, whereas interference with ALKBH5 caused an increase in NR2B expression. In NR2B, interference with ALKBH5 caused an increase in m6A modification, which caused an increase in NR2B. Taken together, ALKBH5 affected the expression of NR2B by influencing the stability of the m6A modification site of central NR2B, revealing that ALKBH5 is a therapeutic target for BCP.
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Affiliation(s)
- Kun Song
- Department of Anesthesiology, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- Graduate school, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qionghua Cao
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yanping Yang
- Department of Anesthesiology, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- Graduate school, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuefen Zuo
- Department of Anesthesiology, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Xianping Wu
- Department of Anesthesiology, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
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Ma M, Duan Y, Peng C, Wu Y, Zhang X, Chang B, Wang F, Yang H, Zheng R, Cheng H, Cheng Y, He Y, Huang J, Lei J, Ma H, Li L, Wang J, Huang X, Tang F, Liu J, Li J, Ying R, Wang P, Sha W, Gao Y, Wang L, Ge B. Mycobacterium tuberculosis inhibits METTL14-mediated m 6A methylation of Nox2 mRNA and suppresses anti-TB immunity. Cell Discov 2024; 10:36. [PMID: 38548762 PMCID: PMC10978938 DOI: 10.1038/s41421-024-00653-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/29/2024] [Indexed: 04/01/2024] Open
Abstract
Internal N6-methyladenosine (m6A) modifications are among the most abundant modifications of messenger RNA, playing a critical role in diverse biological and pathological processes. However, the functional role and regulatory mechanism of m6A modifications in the immune response to Mycobacterium tuberculosis infection remains unknown. Here, we report that methyltransferase-like 14 (METTL14)-dependent m6A methylation of NAPDH oxidase 2 (Nox2) mRNA was crucial for the host immune defense against M. tuberculosis infection and that M. tuberculosis-secreted antigen EsxB (Rv3874) inhibited METTL14-dependent m6A methylation of Nox2 mRNA. Mechanistically, EsxB interacted with p38 MAP kinase and disrupted the association of TAB1 with p38, thus inhibiting the TAB1-mediated autophosphorylation of p38. Interaction of EsxB with p38 also impeded the binding of p38 with METTL14, thereby inhibiting the p38-mediated phosphorylation of METTL14 at Thr72. Inhibition of p38 by EsxB restrained liquid-liquid phase separation (LLPS) of METTL14 and its subsequent interaction with METTL3, preventing the m6A modification of Nox2 mRNA and its association with the m6A-binding protein IGF2BP1 to destabilize Nox2 mRNA, reduce ROS levels, and increase intracellular survival of M. tuberculosis. Moreover, deletion or mutation of the phosphorylation site on METTL14 impaired the inhibition of ROS level by EsxB and increased bacterial burden or histological damage in the lungs during infection in mice. These findings identify a previously unknown mechanism that M. tuberculosis employs to suppress host immunity, providing insights that may empower the development of effective immunomodulators that target M. tuberculosis.
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Affiliation(s)
- Mingtong Ma
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yongjia Duan
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Cheng Peng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - You Wu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xinning Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Boran Chang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Fei Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Hua Yang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
| | - Hongyu Cheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yuanna Cheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yifan He
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jingping Huang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jinming Lei
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Hanyu Ma
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Liru Li
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
| | - Xiaochen Huang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
| | - Fen Tang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jun Liu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ruoyan Ying
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Peng Wang
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Sha
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yawei Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Lin Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China.
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Key Laboratory of Pathogen-Host Interaction, Ministry of Education, Tongji University School of Medicine, Shanghai, China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China.
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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Zhang S, Wu M, Xue W. Decoding the role of m 6A Regulators in identifying and characterizing molecular subtypes of rosacea. Heliyon 2023; 9:e23310. [PMID: 38144308 PMCID: PMC10746518 DOI: 10.1016/j.heliyon.2023.e23310] [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: 05/09/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/26/2023] Open
Abstract
Rosacea is a common skin disease that predominantly affects individuals aged between 30 and 50 years. While the exact cause of the disease remains unclear, various factors have been shown to trigger or exacerbate its symptoms. N6-methyladenosine (m6A) modification is one of the most abundant epigenetic methylation modification in messenger RNA (mRNA) and non-coding RNA (ncRNA), plays a crucial role in RNA splicing, export, stability, and translation. In this study, we aimed to characterize m6A genes in rosacea, identify molecular subtypes based on m6A gene expression, characterize the immune features among subtypes, explore key molecules based on co-expression analysis, and identify potential targets and drugs. To achieve our objectives, we first compared the expression pattern and immune regulation of m6A genes between healthy and diseased groups. Then, we performed clustering to stratify disease samples into different subtypes and analyzed immune regulation and functional enrichment among the subtypes. Then, we conducted differential analysis between subtypes and applied weighted gene co-expression network analysis (WGCNA) in three subtypes. We found hub differential expression analysis (DEG) genes and their potential drug based on the WGCNA results and the drug-gene interaction database (DGIdb). Finally, in vivo and in vitro studies showed significant differences in m6A methyltransferase METTL3 levels in rosacea mice and control mice, as well as in the skin of rosacea patients and healthy people, while reducing METTL3 significantly inhibited the inflammatory response of human fibroblasts (HDFs) stimulated by LL37, suggesting that METTL3 may be associated with changes in overall m6A levels in rosacea. Taken together, our findings provide valuable insights into therapeutic targets and drug predictions for rosacea.
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Affiliation(s)
- Shuping Zhang
- Department of Dermatology, Postdoctoral Station of Clinical Medicine, The Third Xiangya Hospital of Central South University, Changsha 410013, Hunan, China
| | - Meng Wu
- Department of Dermatology, Postdoctoral Station of Clinical Medicine, The Third Xiangya Hospital of Central South University, Changsha 410013, Hunan, China
| | - Wenbo Xue
- Department of Surgery, The Third Xiangya Hospital of Central South University, Changsha 410013, Hunan, China
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Li H, Zhao J, Deng H, Zhong Y, Chen M, Chi L, Luo G, Cao C, Yu C, Liu H, Zhang X. N6-methyladenosine modification of PLOD2 causes spermatocyte damage in rats with varicocele. Cell Mol Biol Lett 2023; 28:72. [PMID: 37670228 PMCID: PMC10481479 DOI: 10.1186/s11658-023-00475-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/29/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND In recent years, N6-methyladenosine (m6A) methylation modification of mRNA has been studied extensively. It has been reported that m6A determines mRNA fate and participates in many cellular functions and reactions, including oxidative stress. The PLOD2 gene encodes a protein that plays a key role in tissue remodeling and fibrotic processes. METHODS The m6A methylation and expression levels of PLOD2 were determined by m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-quantitative polymerase chain reaction (qPCR) in the testes of varicocele rats compared with control. To determine whether IGF2BP2 had a targeted effect on the PLOD2 mRNA, RNA immunoprecipitation-qPCR (RIP-qPCR) and luciferase assays were performed. CRISPR/dCas13b-ALKBH5 could downregulate m6A methylation level of PLOD2, which plays an important role in PLOD2-mediated cell proliferation and apoptosis in GC-2 cells. RESULTS PLOD2 was frequently exhibited with high m6A methylation and expression level in the testes of varicocele rats compared with control. In addition, we found that IGF2BP2 binds to the m6A-modified 3' untranslated region (3'-UTR) of PLOD2 mRNA, thereby positively regulating its mRNA stability. Targeted specific demethylation of PLOD2 m6A by CRISPR/dCas13b-ALKBH5 system can significantly decrease the m6A and expression level of PLOD2. Furthermore, demethylation of PLOD2 mRNA dramatically promote GC-2 cell proliferation and inhibit cell apoptosis under oxidative stress. CONCLUSION As a result, we found that varicocele-induced oxidative stress promoted PLOD2 expression level via m6A methylation modification. In addition, targeting m6A demethylation of PLOD2 by CRISPR/dCas13b-ALKBH5 system can regulate GC-2 cell proliferation and apoptosis under oxidative stress. Taken together, our study has acquired a better understanding of the mechanisms underlying male infertility associated with oxidative stress, as well as a novel therapeutic target for male infertility.
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Affiliation(s)
- Huan Li
- Assisted Reproductive Technology Center, Foshan Maternal and Child Health Care Hospital, Foshan, China
| | - Jun Zhao
- Assisted Reproductive Technology Center, Foshan Maternal and Child Health Care Hospital, Foshan, China
| | - Hao Deng
- Assisted Reproductive Technology Center, Foshan Maternal and Child Health Care Hospital, Foshan, China
| | - YuCheng Zhong
- Assisted Reproductive Technology Center, Foshan Maternal and Child Health Care Hospital, Foshan, China
| | - Mian Chen
- Pharmacy Department, Foshan Maternal and Child Health Care Hospital, Foshan, China
| | - LinSheng Chi
- Assisted Reproductive Technology Center, Foshan Maternal and Child Health Care Hospital, Foshan, China
| | - GuoQun Luo
- Assisted Reproductive Technology Center, Foshan Maternal and Child Health Care Hospital, Foshan, China
| | - Cong Cao
- Assisted Reproductive Technology Center, Foshan Maternal and Child Health Care Hospital, Foshan, China
| | - Cong Yu
- Assisted Reproductive Technology Centre, Maternity and Child Healthcare Hospital of Meizhou, Meizhou, China
| | - Honghai Liu
- Assisted Reproductive Technology Centre, Maternity and Child Healthcare Hospital of Meizhou, Meizhou, China
| | - Xinzong Zhang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China.
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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: 16] [Impact Index Per Article: 16.0] [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.
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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)
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Zhang T, Tang X, Zhu Y, Wang C, Jiang Z, Yang N, Wang T, Shu L, Xu Y, Sun L. IGF2BP2 enhances LincRNA01116 stability via m 6 A: A potential biomarker and therapeutic target for patients with pre-eclampsia. J Cell Biochem 2023; 124:239-253. [PMID: 36538649 DOI: 10.1002/jcb.30358] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 02/24/2023]
Abstract
Pre-eclampsia (PE) is a serious complication in pregnant women characterized by failure of placental remodeling and is one of the primary causes of changes in the placental structure and function. The aberrant expression of long noncoding RNA is associated with the occurrence and progression of PE. This study found that linc01116 expression was significantly downregulated in PE patients and was related to poor uterine spiral artery remodeling. Knockdown of linc01116 remarkably decreased the angiogenesis of trophoblast cells in vitro and in vivo. Mechanistically, IGF2BP2 regulated linc01116 RNA stability via m6 A methylation. Bioinformatics and other experiments further revealed that linc01116 upregulates AAMP expression by adsorbing miR-210-3p in trophoblast cells. In conclusion, this study revealed the critical role of linc01116 in regulating trophoblast angiogenesis. Furthermore, the study provides new clues for detecting placental pathology in PE.
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Affiliation(s)
- Tingting Zhang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaotong Tang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yuanyuan Zhu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Cong Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Ziyan Jiang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Nana Yang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Tianjun Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lijun Shu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yetao Xu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lizhou Sun
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
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Qi F, Liu W, Tan B, Zhang J, Ma Y, Cao C, Ma F, Zhu B, Yang J, Liu X. BTG2 suppresses renal cell carcinoma progression through N6-methyladenosine. Front Oncol 2022; 12:1049928. [PMID: 36591524 PMCID: PMC9795213 DOI: 10.3389/fonc.2022.1049928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/01/2022] [Indexed: 12/15/2022] Open
Abstract
The biological functions of N6-methyladenosine (m6A) modification of mRNA have recently received a great deal of attention. In previous studies, m6A methylation modification has been shown to regulate mRNA fate and to be crucial for the progression and development of tumors. BTG2 (B-cell translocation gene 2) is a member of BTG/TOB anti-proliferative protein family. BTG2 could inhibit cell proliferation and migration and regulate the cell cycle progression. In this study, we confirm that BTG2 is frequently down-regulated in renal cell carcinoma (RCC) tissues and its low expression is associated with unfavorable prognosis and decreased m6A level. Moreover, we found that m6A methylation modifies the 5'UTR of BTG2 to promote its mRNA stability by binding to IGF2BP2. It has been shown that CRISPR/dCas13b-METLL3 can specifically increase BTG2 m6A modification to significantly increase its m6A and expression levels. Then m6A hypermethylation in BTG2 mRNA could dramatically inhibit RCC cells proliferation and migration, and induce cells apoptosis. Taken together, our data show that BTG2 functions as a tumor suppressor and is frequently silenced via m6A modification in RCC.
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Shao Y, Duan X, Zhao X, Lv Z, Li C. Global N 6-methyladenosine methylation analysis reveals the positive correlation between m 6A modification and mRNA abundance during Apostichopus japonicus disease development. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 133:104434. [PMID: 35562078 DOI: 10.1016/j.dci.2022.104434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
N6-methyladenosine (m6A), the most abundant epitranscriptomic modification in eukaryotic messenger RNA (mRNA), plays important roles in regulation of gene expression for fundamental biological processes and diverse physiological functions, including combating with pathogen infection. Here, we were first profile transcriptome-wide m6A sequencing in four stages of skin ulceration syndrome-diseased Apostichopus japonicus following Vibrio splendidus infection, including Control (healthy), Early (small ulcer), Later (extensive ulcer), and Resistant (no ulcer) groups. Our results revealed that three experimental groups were all extensively methylated by m6A and the proportion of the m6A modified genes were also significantly increased to 28.90% (Early), 27.97% (Later), and 29.98% (Resistant) when compared with Control group (15.15%), indicating m6A modification could be induced by V. splendidus infection. Intriguingly, we discovered a positive correlation between the m6A methylation level and mRNA abundance, indicating a positive regulatory role of m6A in sea cucumber gene expression during V. splendidus infection. Moreover, genes with specific and differentially expressed m6A methylation in Later group were both enriched in cell adhesion, while Early and Resistant groups were both mainly involved in DNA conformation change and chromosome organization when compared with Control, suggesting the higher-methylated m6A might serve as "conformational marker" and associated to the initiation of related anti-disease genes transcription in order to improve disease resistance of sea cucumber. Subsequently, we selected the pivotal genes enriched in cell adhesion pathway and found that the IggFc-binding protein (FcGBP) and Fibrocystin-L both had higher levels of m6A methylation and higher level of mRNA expressions in Later group. Conversely, Fibrinogen C domain-containing protein 1 (F1BCD1) gene presented as an antibacterial role in sea cucumber and showed higher mRNA expression and higher m6A methylation in Resistant group and lower mRNA level in Later group. The levels of m6A methylation and mRNA abundance of FcGBP and F1BCD1 genes indicates disease occurrence or disease resistant were also verified by MeRIP-qPCR. Overall, our study presents the first comprehensive characterize of dynamic m6A methylation modification in the different stages of disease in sea cucumber. These data provide an invaluable resource for future studies of function and biological significance of m6A in mRNA in marine invertebrates.
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Affiliation(s)
- Yina Shao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Xuemei Duan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Xuelin Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Zhimeng Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
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9
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Su Q, Chen N, Tang J, Wang J, Chou WC, Zheng F, Shao W, Yu G, Cai P, Guo Z, He M, Li H, Wu S. Paraquat-induced oxidative stress regulates N6-methyladenosine (m 6A) modification of long noncoding RNAs in Neuro-2a cells. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 237:113503. [PMID: 35453019 DOI: 10.1016/j.ecoenv.2022.113503] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Paraquat (PQ) is a ubiquitously applied herbicide. Long-term PQ exposure with low dose has been reported to induce abnormal expression of long non-coding RNAs (lncRNAs) in brain nerve cells, which could further lead to Parkinson's disease (PD). N6-methyladenosine (m6A) modification has recently been identified as having an important role in regulating the function of lncRNAs. However, how m6A modification regulates lncRNAs following PQ exposure remains largely unknown. Herein, this study reported m6A modification of lncRNAs in mouse neuroblastoma cells (Neuro-2a) following PQ induced reactive oxide species (ROS). M6A sequencing was performed to explore the m6A modificated pattern of lncRNAs in Neuro-2a cells which were treated with 200 μM PQ for 3 h. It was found that PQ hypermethylated total RNA and changed the expression of m6A methyltransferase and demethylase proteins, which leading to the alteration of m6A modification of lncRNAs. Furthermore, the functional analysis further revealed that N-acetyl-L-cysteine (NAC),a ROS scavengers, partly reversed PQ-induced distinct m6A modificated pattern of lncRNAs. In addition, tow specific m6A modified lncRNAs were identified: cell division cycle 5-like (lncRNA CDC5L) and signal transducer and activator of transcription 3 (lncRNA STAT3), which could influence downstream autophagy related biological function. In summary, this work could potentially contribute to the new insight of lncRNAs m6A modification mechanism in the field of environmental toxicology.
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Affiliation(s)
- Qianqian Su
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Nengzhou Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jianping Tang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Junxiang Wang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Wei-Chun Chou
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Fuli Zheng
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Wenya Shao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Guangxia Yu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Ping Cai
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Zhenkun Guo
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Minghua He
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Huangyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Siying Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
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10
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Li A, Cao C, Gan Y, Wang X, Wu T, Zhang Q, Liu Y, Yao L, Zhang Q. ZNF677 suppresses renal cell carcinoma progression through N6-methyladenosine and transcriptional repression of CDKN3. Clin Transl Med 2022; 12:e906. [PMID: 35678231 PMCID: PMC9178504 DOI: 10.1002/ctm2.906] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 11/06/2022] Open
Abstract
Background Studies on biological functions of N6‐methyladenosine (m6A) modification in mRNA have sprung up in recent years. Previous studies have reported m6A can determine mRNA fate and play a pivotal role in tumour development and progression. The zinc finger protein 677 (ZNF677) belongs to the zinc finger protein family and possesses transcription factor activity by binding sequence‐specific DNA. Methods The expression of ZNF677 and its clinicopathological impact were evaluated in renal cell carcinoma (RCC) patients. The m6A level of ZNF677 was determined by m6A methylated RNA immunoprecipitation‐sequencing (MeRIP‐seq) and MeRIP‐qPCR in RCC tissues and adjacent normal tissues. RNA immunoprecipitation‐qPCR (RIP‐qPCR) and luciferase assays were performed to identify the targeted effect of IGF2BP2 and YTHDF1 on ZNF677. RCC cells and subcutaneous models uncovered the role of ZNF677 methylated by CRISPR/dCas13b‐METTL3 in tumour growth. ZNF677‐binding sites in the CDKN3 promoter were investigated by chromatin immunoprecipitation (ChIP) and luciferase assays. Results ZNF677 is frequently downregulated in RCC tissues and its low expression is associated with unfavourable prognosis and decreased m6A modification level. Further, we find the m6A‐modified coding sequence (CDS) of ZNF677 positively regulates its translation and mRNA stability via binding with YTHDF1 and IGF2BP2, respectively. Targeted specific methylation of ZNF677 m6A by CRISPR/dCas13b‐METLL3 system can significantly increase the m6A and expression level of ZNF677, and dramatically inhibit cell proliferation and induce cell apoptosis of RCC cells. In addition, ZNF677 exerted its tumour suppressor functions in RCC cells through transcriptional repression of CDKN3 via binding to its promoter. In vitro and clinical data confirm the negative roles of ZNF677/CDKN3 in tumour growth and progression of RCC. Conclusion ZNF677 functions as a tumour suppressor and is frequently silenced via m6A modification in RCC, which may highlight m6A methylation‐based approach for RCC diagnosis and therapy.
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Affiliation(s)
- Aolin Li
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Congcong Cao
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ying Gan
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Xiaofei Wang
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Tianyu Wu
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Quan Zhang
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Yuchen Liu
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Qian Zhang
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
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11
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Ouyang M, Fang J, Wang M, Huang X, Lan J, Qu Y, Lai W, Xu Q. Advanced glycation end products alter the m 6A-modified RNA profiles in human dermal fibroblasts. Epigenomics 2022; 14:431-449. [PMID: 35285253 DOI: 10.2217/epi-2022-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: To explore advanced glycation end products (AGEs)-induced m6A modification in fibroblasts and its potential role in photoaging. Methods: We studied m6A modification in AGEs-bovine serum albumin-treated fibroblasts with m6A-mRNA & lncRNA epitranscriptomic microarray and bioinformatics analysis. The m6A modification level was also investigated in skin samples. Results: m6A methylation microarray analysis revealed m6A modification profiles in AGEs-treated fibroblasts. Gene ontology, Kyoto Encyclopedia of Genes and Genomes, protein-protein interaction and competing endogenous RNA network analysis indicated that the genes of differentially methylated mRNAs and lncRNAs were mainly related to inflammation processes. We also found that AGEs-bovine serum albumin dose-dependently increased the m6A level and METTL14 expression in both fibroblasts and sun-exposed skin. Conclusion: Our study provided novel information regarding alterations of m6A modifications in AGEs-induced dermal fibroblasts and potential targets for treatment of photoaging.
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Affiliation(s)
- Mengting Ouyang
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Jiaqi Fang
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Mengyao Wang
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Xianyin Huang
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Jingjing Lan
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Yingying Qu
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Wei Lai
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Qingfang Xu
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
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12
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Khan FA, Nsengimana B, Khan NH, Song Z, Ngowi EE, Wang Y, Zhang W, Ji S. Chimeric Peptides/Proteins Encoded by circRNA: An Update on Mechanisms and Functions in Human Cancers. Front Oncol 2022; 12:781270. [PMID: 35223470 PMCID: PMC8874284 DOI: 10.3389/fonc.2022.781270] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/10/2022] [Indexed: 12/30/2022] Open
Abstract
The discovery of circular RNAs and exploration of their biological functions are increasingly attracting attention in cell bio-sciences. Owing to their unique characteristics of being highly conserved, having a relatively longer half-life, and involvement in RNA maturation, transportation, epigenetic regulation, and transcription of genes, it has been accepted that circRNAs play critical roles in the variety of cellular processes. One of the critical importance of these circRNAs is the presence of small open reading frames that enable them to encode peptides/proteins. In particular, these encoded peptides/proteins mediate essential cellular activities such as proliferation, invasion, epithelial-mesenchymal transition, and apoptosis and develop an association with the development and progression of cancers by modulating diverse signaling pathways. In addition, these peptides have potential roles as biomarkers for the prognosis of cancer and are being used as drug targets against tumorigenesis. In the present review, we thoroughly discussed the biogenesis of circRNAs and their functional mechanisms along with a special emphasis on the reported chimeric peptides/proteins encoded by circRNAs. Additionally, this review provides a perspective regarding the opportunities and challenges to the potential use of circRNAs in cancer diagnosis and therapeutic targets in clinics.
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Affiliation(s)
- Faiz Ali Khan
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- School of Life Sciences, Henan University, Kaifeng, China
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Bernard Nsengimana
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Nazeer Hussain Khan
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Zhenhua Song
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Ebenezeri Erasto Ngowi
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yunyun Wang
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Weijuan Zhang
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Shaoping Ji
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
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13
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Gan Y, Li A, Liu J, Wang X, Zhang Z, Li Q, Ye X, Yao L, Zhang Q. m6A-mRNA Methylation Regulates Gene Expression and Programmable m6A Modification of Cellular RNAs With CRISPR-Cas13b in Renal Cell Carcinoma. Front Genet 2022; 12:795611. [PMID: 35126463 PMCID: PMC8815861 DOI: 10.3389/fgene.2021.795611] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/09/2021] [Indexed: 11/13/2022] Open
Abstract
Background: N6-methyladenosine (m6A) is the most extensive messenger RNA modification. Despite recent advances in the biological roles of m6A, its role in the development and progression of renal cell carcinoma (RCC) remains unclear. Methods: In this study, we gained the transcriptome-wide m6A profile and gene expression pattern in RCC and paired adjacent peritumoral tissues by meRIP-seq and RNA-seq. m6A modifications of mRNAs were validated by meRIP-qPCR in tissues, and targeted methylation or demethylation was validated by using a CRISPR-Cas13b-based tool in RCC cell lines. Results: Our findings showed that there were 13,805 m6A peaks among 5,568 coding gene transcripts (mRNAs) in adjacent tissues and 24,730 m6A peaks among 6,866 mRNAs in tumor tissues. Furthermore, m6A modification sites were usually located in the coding sequences (CDS), and some near the start and stop codons. Gene Ontology analysis revealed that coding genes had differential N6-methyladenosine sites and were enriched in kidney development and cancer-related signaling pathways. We also found that different levels of m6A modifications could regulate gene expression. Conclusion: In summary, our results provided evidence for studying the potential function of RNA m6A modification and m6A-mediated gene expression regulation in human RCC.
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Affiliation(s)
- Ying Gan
- Department of Urology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Aolin Li
- Department of Urology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Jun Liu
- Urology and Lithotripsy Center, Peking University People’s Hospital, Peking University, Beijing, China
- Peking University Applied Lithotripsy Institute, Peking University, Beijing, China
| | - Xiaofei Wang
- Department of Urology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Zhenan Zhang
- Department of Urology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Qinhan Li
- Department of Urology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Xiongjun Ye
- Urology and Lithotripsy Center, Peking University People’s Hospital, Peking University, Beijing, China
- Peking University Applied Lithotripsy Institute, Peking University, Beijing, China
- *Correspondence: Lin Yao, ; Xiongjun Ye, ; Qian Zhang,
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
- *Correspondence: Lin Yao, ; Xiongjun Ye, ; Qian Zhang,
| | - Qian Zhang
- Department of Urology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
- *Correspondence: Lin Yao, ; Xiongjun Ye, ; Qian Zhang,
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14
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Jin C, Li R, Deng T, Li J, Yang Y, Li H, Chen K, Xiong H, Chen G, Wang Y. Identification and Validation of a Prognostic Prediction Model of m6A Regulator-Related LncRNAs in Hepatocellular Carcinoma. Front Mol Biosci 2022; 8:784553. [PMID: 34988119 PMCID: PMC8721125 DOI: 10.3389/fmolb.2021.784553] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/08/2021] [Indexed: 01/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly invasive malignancy prone to recurrence, and patients with HCC have a low 5-year survival rate. Long non-coding RNAs (lncRNAs) play a vital role in the occurrence and development of HCC. N6-methyladenosine methylation (m6A) is the most common modification influencing cancer development. Here, we used the transcriptome of m6A regulators and lncRNAs, along with the complete corresponding clinical HCC patient information obtained from The Cancer Genome Atlas (TCGA), to explore the role of m6A regulator-related lncRNA (m6ARlnc) as a prognostic biomarker in patients with HCC. The prognostic m6ARlnc was selected using Pearson correlation and univariate Cox regression analyses. Moreover, three clusters were obtained via consensus clustering analysis and further investigated for differences in immune infiltration, immune microenvironment, and prognosis. Subsequently, nine m6ARlncs were identified with Lasso-Cox regression analysis to construct the prognostic signature m6A-9LPS for patients with HCC in the training cohort (n = 226). Based on m6A-9LPS, the risk score for each case was calculated. Patients were then divided into high- and low-risk subgroups based on the cutoff value set by the X-tile software. m6A-9LPS showed a strong prognosis prediction ability in the validation cohort (n = 116), the whole cohort (n = 342), and even clinicopathological stratified survival analysis. Combining the risk score and clinical characteristics, we established a nomogram for predicting the overall survival (OS) of patients. To further understand the mechanism underlying the m6A-9LPS-based classification of prognosis differences, KEGG and GO enrichment analyses, competitive endogenous RNA (ceRNA) network, chemotherapeutic agent sensibility, and immune checkpoint expression level were assessed. Taken together, m6A-9LPS could be used as a precise prediction model for the prognosis of patients with HCC, which will help in individualized treatment of HCC.
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Affiliation(s)
- Chen Jin
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Rui Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Tuo Deng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jialiang Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yan Yang
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Haoqi Li
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Kaiyu Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Gang Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yi Wang
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
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15
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Dong G, Yu J, Shan G, Su L, Yu N, Yang S. N6-Methyladenosine Methyltransferase METTL3 Promotes Angiogenesis and Atherosclerosis by Upregulating the JAK2/STAT3 Pathway via m6A Reader IGF2BP1. Front Cell Dev Biol 2021; 9:731810. [PMID: 34950654 PMCID: PMC8689138 DOI: 10.3389/fcell.2021.731810] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/19/2021] [Indexed: 01/15/2023] Open
Abstract
Atherosclerosis (AS) is a life-threatening vascular disease. RNA N6-methyladenosine (m6A) modification level is dysregulated in multiple pathophysiologic processes including AS. In this text, the roles and molecular mechanisms of m6A writer METTL3 in AS progression were explored in vitro and in vivo. In the present study, cell proliferative, migratory, and tube formation capacities were assessed through CCK-8, Transwell migration, and tube formation assays, respectively. RNA m6A level was examined through a commercial kit. RNA and protein levels of genes were measured through RT-qPCR and western blot assays, respectively. VEGF secretion level was tested through ELISA assay. JAK2 mRNA stability was detected through actinomycin D assay. The relationship of METTL3, IGF2BP1, and JAK2 was investigated through bioinformatics analysis, MeRIP, RIP, RNA pull-down, and luciferase reporter assays. An AS mouse model was established to examine the effect of METTL3 knockdown on AS development in vivo. The angiogenetic activity was examined through chick chorioallantoic membrane assay in vivo. The results showed that METTL3 was highly expressed in ox-LDL-induced dysregulated HUVECs. METTL3 knockdown inhibited cell proliferation, migration, tube formation, and VEGF expression/secretion in ox-LDL-treated HUVECs, hampered AS process in vivo, and prevented in vivo angiogenesis of developing embryos. METTL3 positively regulated JAK2 expression and JAK2/STAT3 pathway in an m6A dependent manner in HUVECs. IGF2BP1 positively regulated JAK2 expression through directly binding to an m6A site within JAK2 mRNA in HUVECs. METTL3 knockdown weakened the interaction of JAK2 and IGF2BP1. METTL3 exerted its functions through JAK2/STAT3 pathway. In conclusion, METTL3 knockdown prevented AS progression by inhibiting JAK2/STAT3 pathway via IGF2BP1.
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Affiliation(s)
- Guo Dong
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiangbo Yu
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Gaojun Shan
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lide Su
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Nannan Yu
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shusen Yang
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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16
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Zhang G, Lv Z, Diao S, Liu H, Duan A, He C, Zhang J. Unique features of the m 6A methylome and its response to drought stress in sea buckthorn ( Hippophae rhamnoides Linn.). RNA Biol 2021; 18:794-803. [PMID: 34806556 DOI: 10.1080/15476286.2021.1992996] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In plants, recent studies have revealed that N6-methyladenosine (m6A) methylation of mRNA has potential regulatory functions of this mRNA modification in many biological processes. m6A methyltransferase, m6A demethylase and m6A-binding proteins can cause differential phenotypes, indicating that m6A may have critical roles in the plant. In this study, we depicted the m6A map of sea buckthorn (Hippophae rhamnoides Linn.) transcriptome. Similar to A. thaliana, m6A sites of sea buckthorn transcriptome is significantly enriched around the stop codon and within 3'-untranslated regions (3'UTR). Gene ontology analysis shows that the m6A modification genes are associated with metabolic biosynthesis. In addition, we identified 13,287 different m6A peaks (DMPs) between leaf under drought (TR) and control (CK) treatment. It reveals that m6A has a high level of conservation and has a positive correlation with mRNA abundance in plants. GO and KEGG enrichment results showed that DMP modification DEGs in TR were particularly associated with ABA biosynthesis. Interestingly, our results showed three m6A demethylase (HrALKBH10B, HrALKBH10C and HrALKBH10D) genes were significantly increased following drought stress, which indicated that it may contributed the decreased m6A levels. This exhaustive m6A map provides a basis and resource for the further functional study of mRNA m6A modification in abiotic stress.
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Affiliation(s)
- Guoyun Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Zhongrui Lv
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Songfeng Diao
- Non-timber Forestry Research and Development Center, Chinese Academy of Forestry & Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Hong Liu
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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17
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Zhou Y, Yang J, Tian Z, Zeng J, Shen W. Research progress concerning m 6A methylation and cancer. Oncol Lett 2021; 22:775. [PMID: 34589154 PMCID: PMC8442141 DOI: 10.3892/ol.2021.13036] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A) methylation is a type of methylation modification on RNA molecules, which was first discovered in 1974, and has become a hot topic in life science in recent years. m6A modification is an epigenetic regulation similar to DNA and histone modification and is dynamically reversible in mammalian cells. This chemical marker of RNA is produced by m6A 'writers' (methylase) and can be degraded by m6A 'erasers' (demethylase). Methylated reading protein is the 'reader', that can recognize the mRNA containing m6A and regulate the expression of downstream genes accordingly. m6A methylation is involved in all stages of the RNA life cycle, including RNA processing, nuclear export, translation and regulation of RNA degradation, indicating that m6A plays a crucial role in RNA metabolism. Recent studies have shown that m6A modification is a complicated regulatory network in different cell lines, tissues and spatio-temporal models, and m6A methylation is associated with the occurrence and development of tumors. The present review describes the regulatory mechanism and physiological functions of m6A methylation, and its research progress in several types of human tumor, to provide novel approaches for early diagnosis and targeted treatment of cancer.
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Affiliation(s)
- Yang Zhou
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Jie Yang
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Zheng Tian
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Jing Zeng
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Weigan Shen
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
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Zhang S, Dong J, Li Y, Xiao H, Shang Y, Wang B, Chen Z, Zhang M, Fan S, Cui M. Gamma-irradiation fluctuates the mRNA N 6-methyladenosine (m 6A) spectrum of bone marrow in hematopoietic injury. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117509. [PMID: 34380217 DOI: 10.1016/j.envpol.2021.117509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/25/2021] [Accepted: 05/30/2021] [Indexed: 06/13/2023]
Abstract
Humans benefit from nuclear technologies but consequently experience nuclear disasters or side effects of iatrogenic radiation. Hematopoietic system injury first arises upon radiation exposure. As an intricate new layer of genetic control, the posttranscriptional m6A modification of RNA has recently come under investigation and has been demonstrated to play pivotal roles in multiple physiological and pathological processes. However, how the m6A methylome functions in the hematopoietic system after irradiation remains ambiguous. Here, we uncovered the time-varying epitranscriptome-wide m6A methylome and transcriptome alterations in γ-ray-exposed mouse bone marrow. 4 Gy γ-irradiation rapidly (5 min and 2 h) and severely impaired the mouse hematopoietic system, including spleen and thymus weight, blood components, tissue inflammation and malondialdehyde (MDA) levels. The m6A content and expression of m6A related enzymes were altered. Gamma-irradiation triggered dynamic and reversible m6A modification profiles and altered mRNA expression, where both m6A fold-enrichment and mRNA expression most followed the (5 min_up/2 h_down) pattern. The CDS enrichment region preferentially upregulated m6A peaks at 5 min. Moreover, the main GO and KEGG pathways were closely related to metabolism and the classical radiation response. Finally, m6A modifications correlated with transcriptional regulation of genes in multiple aspects. Blocking the expression of m6A demethylases FTO and ALKBH5 mitigated radiation hematopoietic toxicity. Together, our findings present the comprehensive landscape of mRNA m6A methylation in the mouse hematopoietic system in response to γ-irradiation, shedding light on the significance of m6A modifications in mammalian radiobiology. Regulation of the epitranscriptome may be exploited as a strategy against radiation damage.
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Affiliation(s)
- Shuqin Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Jiali Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Yuan Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Huiwen Xiao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Yue Shang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Bin Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Zhiyuan Chen
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Mengran Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Ming Cui
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China.
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19
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METTL14 facilitates global genome repair and suppresses skin tumorigenesis. Proc Natl Acad Sci U S A 2021; 118:2025948118. [PMID: 34452996 DOI: 10.1073/pnas.2025948118] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Global genome repair (GGR), a subpathway of nucleotide excision repair, corrects bulky helix-distorting DNA lesions across the whole genome and is essential for preventing mutagenesis and skin cancer. Here, we show that METTL14 (methyltransferase-like 14), a critical component of the N6-methyladenosine (m6A) RNA methyltransferase complex, promotes GGR through regulating m6A mRNA methylation-mediated DDB2 translation and suppresses ultraviolet B (UVB) radiation-induced skin tumorigenesis. UVB irradiation down-regulates METTL14 protein through NBR1-dependent selective autophagy. METTL14 knockdown decreases GGR and DDB2 abundance. Conversely, overexpression of wild-type METTL14 but not its enzymatically inactive mutant increases GGR and DDB2 abundance. METTL14 knockdown decreases m6A methylation and translation of the DDB2 transcripts. Adding DDB2 reverses the GGR repair defect in METTL14 knockdown cells, indicating that METTL14 facilitates GGR through regulating DDB2 m6A methylation and translation. Similarly, knockdown of YTHDF1, an m6A reader promoting translation of m6A-modified transcripts, decreases DDB2 protein levels. Both METTL14 and YTHDF1 bind to the DDB2 transcript. In mice, skin-specific heterozygous METTL14 deletion increases UVB-induced skin tumorigenesis. Furthermore, METTL14 as well as DDB2 is down-regulated in human and mouse skin tumors and by chronic UVB irradiation in mouse skin, and METTL14 level is associated with the DDB2 level, suggesting a tumor-suppressive role of METTL14 in UVB-associated skin tumorigenesis in association with DDB2 regulation. Taken together, these findings demonstrate that METTL14 is a target for selective autophagy and acts as a critical epitranscriptomic mechanism to regulate GGR and suppress UVB-induced skin tumorigenesis.
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Li Z, Qi J, Liu H, Tang Y, Liu J, Sun C. Abnormal m6A modification in non-alcoholic fatty liver disease. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021; 46:785-792. [PMID: 34565720 PMCID: PMC10929970 DOI: 10.11817/j.issn.1672-7347.2021.210264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Non-alcoholic fatty liver disease has seriously affected people's health. Recent studies have found that N6-methyladenosine (m6A) methylation is involved in the lipid metabolism process of the body, but the study on the level of m6A modification in NAFLD is still not available. This study aims to explore the changes in the level of RNA m6A methylation modification in NAFLD liver tissues, and to provide experimental and theoretical basis for in-depth study on the role of RNA m6A methylation in the occurrence and development of NAFLD. METHODS Changes in the m6A level in NAFLD liver tissues were measured by liquid chromatography-mass spectrometry (LC-MS). Total RNA was extracted from liver tissues of NAFLD patients or normal control individuals and subjected to methylated RNA immunoprecipitation (MeRIP) with microarray analysis (including 44 122 mRNAs and 12 496 lncRNAs) to determine the changes in m6A modification levels across the entire transcriptome. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to annotate the differentially modified mRNAs. Finally, 4 mRNAs and 4 lncRNAs were randomly selected to verify the microarray results by MeRIP and real-time transcription polymerase chain reaction. RESULTS A total of 176 mRNAs and 44 lncRNAs were found to be differentially m6A-modified in the NAFLD group compared with the control group. Among them, 15 mRNAs and 7 lncRNAs were hypermethylated in NAFLD, while 161 mRNAs and 37 lncRNAs were hypomethylated in NAFLD. GO and pathway analysis showed that the differentially modified mRNAs were enriched mainly in biological processes such as carboxylic acid metabolism and transcriptional regulation. CONCLUSIONS The m6A modification profile is changed in NAFLD liver tissues compared with normal liver tissues, which may functionally impact the pathophysiological progress in NAFLD.
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Affiliation(s)
- Zhenzhou Li
- Department of Emergency, Third Xiangya Hospital, Central South University, Changsha 410013, China.
| | - Jing Qi
- Department of Emergency, Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Huaizheng Liu
- Department of Emergency, Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Yishu Tang
- Department of Emergency, Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Jun Liu
- Department of Emergency, Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Chuanzheng Sun
- Department of Emergency, Third Xiangya Hospital, Central South University, Changsha 410013, China.
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21
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Luo J, Yu J, Peng X. Could partial nonstarch polysaccharides ameliorate cancer by altering m 6A RNA methylation in hosts through intestinal microbiota? Crit Rev Food Sci Nutr 2021; 62:8319-8334. [PMID: 34036843 DOI: 10.1080/10408398.2021.1927975] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
There is a growing scientific view that the improvement of cancer by nonstarch polysaccharides (NSPs) is mediated by intestinal microbiota. Intestinal bacteria affect the supply of methyl donor substances and influence N6-methyladenosine (m6A) RNA methylation. As one of the epigenetic/epitranscriptomic modifications, m6A RNA methylation is closely related to the initiation and progression of cancers. This review summarizes the cancer-improving effects of NSPs through modulation of intestinal microbiota. It also summarizes the relationship between intestinal bacteria and the supply of methyl donor substances. Moreover, it also provides a summary of the effects of m6A RNA methylation on various types of cancer. The proposed mechanism is that, dietary consumed NSPs are utilized by specific intestinal bacteria and further reshape the microbial structure. Methyl donor substances will be directly or indirectly generated by the reshaped-microbiota, and affect the m6A RNA methylation of cancer-related and pro-carcinogenic inflammatory cytokine genes. Therefore, NSPs may change the m6A RNA methylation by affecting the methyl donor supply produced by intestinal microbiota and ameliorate cancer. This review discussed the possibility of cancer improvement of bioactive NSPs achieved by impacting RNA methylation via the intestinal microbiota, and it will offer new insights for the application of NSPs toward specific cancer prevention.
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Affiliation(s)
- Jianming Luo
- Department of Food Science and Engineering, Jinan University, Guangzhou, Guangdong, China
| | - Juntong Yu
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Xichun Peng
- Department of Food Science and Engineering, Jinan University, Guangzhou, Guangdong, China
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m 6A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms. Int J Mol Sci 2020; 21:ijms21207508. [PMID: 33053767 PMCID: PMC7589960 DOI: 10.3390/ijms21207508] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 01/08/2023] Open
Abstract
Circadian regulations are essential for enabling organisms to synchronize physiology with environmental light-dark cycles. Post-transcriptional RNA modifications still represent an understudied level of gene expression regulation in plants, although they could play crucial roles in environmental adaptation. N6-methyl-adenosine (m6A) is the most prevalent mRNA modification, established by "writer" and "eraser" proteins. It influences the clockwork in several taxa, but only few studies have been conducted in plants and none in marine plants. Here, we provided a first inventory of m6A-related genes in seagrasses and investigated daily changes in the global RNA methylation and transcript levels of writers and erasers in Cymodocea nodosa and Zostera marina. Both species showed methylation peaks during the dark period under the same photoperiod, despite exhibiting asynchronous changes in the m6A profile and related gene expression during a 24-h cycle. At contrasting latitudes, Z. marina populations displayed overlapping daily patterns of the m6A level and related gene expression. The observed rhythms are characteristic for each species and similar in populations of the same species with different photoperiods, suggesting the existence of an endogenous circadian control. Globally, our results indicate that m6A RNA methylation could widely contribute to circadian regulation in seagrasses, potentially affecting the photo-biological behaviour of these plants.
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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.
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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.
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24
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Protein-Related Circular RNAs in Human Pathologies. Cells 2020; 9:cells9081841. [PMID: 32781555 PMCID: PMC7463956 DOI: 10.3390/cells9081841] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) are a distinct family of RNAs derived from alternative splicing which play a crucial role in regulating gene expression by acting as microRNA (miRNA) and RNA binding protein (RBP) sponges. However, recent studies have also reported the multifunctional potential of these particles. Under different conditions, circRNAs not only regulate protein synthesis, destination, and degradation but can serve as protein scaffolds or recruiters and are also able to produce short peptides with active biological functions. circRNAs are under ongoing investigation because of their close association with the development of diseases. Some circRNAs are reportedly expressed in a tissue- and development stage-specific manner. Furthermore, due to other features of circRNAs, including their stability, conservation, and high abundance in bodily fluids, they are believed to be potential biomarkers for various diseases, including cancers. In this review, we focus on providing a summary of the current knowledge on circRNA-protein interactions. We present the properties and functions of circRNAs, the possible mechanisms of their translation abilities, and the emerging functions of circRNA-derived peptides in human pathologies.
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25
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Yang J, Chen J, Fei X, Wang X, Wang K. N6-methyladenine RNA modification and cancer. Oncol Lett 2020; 20:1504-1512. [PMID: 32724392 DOI: 10.3892/ol.2020.11739] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) in messenger RNA (mRNA) is regulated by m6A methyltransferases and demethylases. Modifications of m6A are dynamic and reversible, may regulate gene expression levels and serve vital roles in numerous life processes, such as cell cycle regulation, cell fate decision and cell differentiation. In recent years, m6A modifications have been reported to exhibit functions in human cancers via regulation of RNA stability, microRNA processing, mRNA splicing and mRNA translation, including lung cancer, breast tumor and acute myeloid leukemia. In the present review, the roles of m6A modifications in the onset and progression of cancer were summarized. These modifications display an oncogenic role in certain types of cancer, whereas in other types of cancer they exhibit a tumor suppressor role. Therefore, understanding the biological functions performed by m6A in different types of tumors and identifying pivotal m6A target genes to deduce the potential mechanisms underlying the progression of cancer may assist in the development of novel therapeutics.
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Affiliation(s)
- Jun Yang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Junwen Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Xiang Fei
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
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Miao R, Dai CC, Mei L, Xu J, Sun SW, Xing YL, Wu LS, Wang MH, Wei JF. KIAA1429 regulates cell proliferation by targeting c-Jun messenger RNA directly in gastric cancer. J Cell Physiol 2020; 235:7420-7432. [PMID: 32052427 DOI: 10.1002/jcp.29645] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/04/2020] [Indexed: 12/13/2022]
Abstract
N6-methyladenosine (m6A) modification regulatory proteins are involved in the development of many types of cancer. KIAA1429 serves as a scaffold in bridging the catalytic core components of the m6A methyltransferase complex. The role of KIAA1429 in gastric cancer and its related mechanism has not been reported upon. The expression of KIAA1429 was detected in human gastric cancer tissues and cell lines by quantitative real-time polymerase chain reaction and western blot. The effects of KIAA1429 on gastric cancer proliferation were evaluated by cell counting kit assays, colony formation assays, flow cytometry assay, and in vivo experiments with nude mice. And messenger RNA (mRNA) high-throughput sequencing, RNA immunoprecipitation assay (RIP), luciferase assay, and a rescue experiment were used to identify the relationship between KIAA1429 and its specific targeted gene, c-Jun. We found that KIAA1429 was upregulated in gastric cancer tissues, and expressed lower in adjacent tissues. The upregulated KIAA1429 promoted proliferation and downregulated KIAA1429 was proved to inhibit proliferation of gastric cancer in vitro and in vivo. Then, we identified the potential KIAA1429 regulating gene as c-Jun by mRNAs high-throughput sequencing and RIP assay. By luciferase assay, we verified that KIAA1429 regulated the expression of c-Jun in an m6A-independent manner. Finally, the overexpression of c-Jun rescued the inhibition of proliferation caused by KIAA1429 knockdown in gastric cancer cells. KIAA1429 could act as an oncogene in gastric cancer by stabilizing c-Jun mRNA in an m6A-independent manner. This highlights the functional role for KIAA1429 as a potential prognostic biomarker and therapeutic target in gastric cancer.
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Affiliation(s)
- Ran Miao
- Department of General Surgery, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Cong-Cong Dai
- Department of General Surgery, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Lin Mei
- Department of General Surgery, The First Affiliated Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Jun Xu
- Department of Oncology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shan-Wen Sun
- Department of Oncology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yun-Long Xing
- Department of General Surgery, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Li-Sheng Wu
- Department of General Surgery, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Ming-Hai Wang
- Department of General Surgery, The First Affiliated Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
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Yang S, Wei J, Cui YH, Park G, Shah P, Deng Y, Aplin AE, Lu Z, Hwang S, He C, He YY. m 6A mRNA demethylase FTO regulates melanoma tumorigenicity and response to anti-PD-1 blockade. Nat Commun 2019; 10:2782. [PMID: 31239444 PMCID: PMC6592937 DOI: 10.1038/s41467-019-10669-0] [Citation(s) in RCA: 449] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Melanoma is one of the most deadly and therapy-resistant cancers. Here we show that N6-methyladenosine (m6A) mRNA demethylation by fat mass and obesity-associated protein (FTO) increases melanoma growth and decreases response to anti-PD-1 blockade immunotherapy. FTO level is increased in human melanoma and enhances melanoma tumorigenesis in mice. FTO is induced by metabolic starvation stress through the autophagy and NF-κB pathway. Knockdown of FTO increases m6A methylation in the critical protumorigenic melanoma cell-intrinsic genes including PD-1 (PDCD1), CXCR4, and SOX10, leading to increased RNA decay through the m6A reader YTHDF2. Knockdown of FTO sensitizes melanoma cells to interferon gamma (IFNγ) and sensitizes melanoma to anti-PD-1 treatment in mice, depending on adaptive immunity. Our findings demonstrate a crucial role of FTO as an m6A demethylase in promoting melanoma tumorigenesis and anti-PD-1 resistance, and suggest that the combination of FTO inhibition with anti-PD-1 blockade may reduce the resistance to immunotherapy in melanoma.
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Affiliation(s)
- Seungwon Yang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA
| | - Jiangbo Wei
- Departments of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, 60637, USA
| | - Yan-Hong Cui
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA
| | - Gayoung Park
- Department of Pathology, University of Chicago, Chicago, IL, 60637, USA
| | - Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA
- Committee on Molecular Pathogenesis and Molecular Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Yu Deng
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Laoning, 110122, China
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Zhike Lu
- Departments of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, 60637, USA
| | - Seungmin Hwang
- Department of Pathology, University of Chicago, Chicago, IL, 60637, USA
| | - Chuan He
- Departments of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA.
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA.
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Cheng X, Li M, Rao X, Zhang W, Li X, Wang L, Huang G. KIAA1429 regulates the migration and invasion of hepatocellular carcinoma by altering m6A modification of ID2 mRNA. Onco Targets Ther 2019; 12:3421-3428. [PMID: 31118692 PMCID: PMC6510231 DOI: 10.2147/ott.s180954] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Purpose N6-methyladenosine (m6A), the most abundant mRNA modification in mammals, is involved in various biological processes. KIAA1429 is an important methyltransferase participating in m6A modification. However, the role of KIAA1429 in hepatocellular carcinoma (HCC) is still not well understood. Here, we aimed to investigate the function of KIAA1429 and its corresponding regulation mechanisms in HCC. Patients and methods HCC-related genes were analyzed by clinical and expression data of HCC patients in The Cancer Genome Atlas (TCGA) database. Expression of KIAA1429 was verified by quantitative reverse-transcription PCR, and interference efficiency was obtained using small interfering RNA (siRNA). Cell proliferation, migration, and invasion were assessed by cell counting kit-8 and transwell assays, and the m6A modification was detected by methylated RNA immunoprecipitation-PCR (MeRIP-PCR). Results We found a difference in the expression of KIAA1429 between HCC and normal hepatic tissues by analyzing data from the TCGA database. Comparing HCC cell lines (HepG2, Huh-7, HepG2.2.15) with normal hepatic cells (HL-7702), we observed an identically significant difference in KIAA1429 expression. KIAA1429 significantly enhanced proliferation, migration, and invasion of HepG2 cells. Moreover, Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and correlation analysis revealed a significant negative correlation between KIAA1429 and ID2. In the subsequent MeRIP-PCR assay, downregulation of KIAA1429 inhibited m6A modification of ID2 mRNA. Conclusion KIAA1429 facilitated migration and invasion of HCC by inhibiting ID2 via upregulating m6A modification of ID2 mRNA.
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Affiliation(s)
- Xiaoyu Cheng
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, JiangXi, China
| | - Ming Li
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, JiangXi, China
| | - Xi Rao
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, JiangXi, China
| | - Wenfeng Zhang
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, JiangXi, China
| | - Xiaopeng Li
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, JiangXi, China
| | - Liang Wang
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, JiangXi, China
| | - Guanjun Huang
- Department of Endocrinology, Shangrao People's Hospital, Shangrao, JiangXi, China,
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