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Jiang N, Wang C, Xie B, Xie H, Wu A, Kong X, Gu L, Jiang Y, Peng J. Identification of endoplasmic reticulum stress genes in human stroke based on bioinformatics and machine learning. Neurobiol Dis 2024; 199:106583. [PMID: 38942324 DOI: 10.1016/j.nbd.2024.106583] [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: 05/28/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 06/30/2024] Open
Abstract
After ischemic stroke (IS), secondary injury is intimately linked to endoplasmic reticulum (ER) stress and body-brain crosstalk. Nonetheless, the underlying mechanism systemic immune disorder mediated ER stress in human IS remains unknown. In this study, 32 candidate ER stress-related genes (ERSRGs) were identified by overlapping MSigDB ER stress pathway genes and DEGs. Three Key ERSRGs (ATF6, DDIT3 and ERP29) were identified using LASSO, random forest, and SVM-RFE. IS patients with different ERSRGs profile were clustered into two groups using consensus clustering and the difference between 2 group was further explored by GSVA. Through immune cell infiltration deconvolution analysis, and middle cerebral artery occlusion (MCAO) mouse scRNA analysis, we found that the expression of 3 key ERSRGs were closely related with peripheral macrophage cell ER stress in IS and this was further confirmed by RT-qPCR experiment. These ERS genes might be helpful to further accurately regulate the central nervous system and systemic immune response through ER stress and have potential application value in clinical practice in IS.
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Affiliation(s)
- Nan Jiang
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital, Southwest Medical University, Luzhou, China; Institute of Brain Science, Southwest Medical University, Luzhou, China
| | - Chuying Wang
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital, Southwest Medical University, Luzhou, China; Department of Neurosurgery, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Bingqing Xie
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital, Southwest Medical University, Luzhou, China; Institute of Brain Science, Southwest Medical University, Luzhou, China
| | - Huangfan Xie
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital, Southwest Medical University, Luzhou, China; Institute of Brain Science, Southwest Medical University, Luzhou, China
| | - Anguo Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xi Kong
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital, Southwest Medical University, Luzhou, China; Institute of Brain Science, Southwest Medical University, Luzhou, China
| | - Long Gu
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital, Southwest Medical University, Luzhou, China; Institute of Brain Science, Southwest Medical University, Luzhou, China
| | - Yong Jiang
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital, Southwest Medical University, Luzhou, China; Institute of Brain Science, Southwest Medical University, Luzhou, China; Department of Neurosurgery, The Affiliated Hospital, Southwest Medical University, Luzhou, China; Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital, Southwest Medical University, Luzhou, China.
| | - Jianhua Peng
- Institute of Brain Science, Southwest Medical University, Luzhou, China; Department of Neurosurgery, The Affiliated Hospital, Southwest Medical University, Luzhou, China; Sichuan Clinical Research Center for Neurosurgery, The Affiliated Hospital, Southwest Medical University, Luzhou, China.
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2
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Zha X, Gao Z, Li M, Xia X, Mao Z, Wang S. Insight into the regulatory mechanism of m 6A modification: From MAFLD to hepatocellular carcinoma. Biomed Pharmacother 2024; 177:116966. [PMID: 38906018 DOI: 10.1016/j.biopha.2024.116966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/05/2024] [Accepted: 06/15/2024] [Indexed: 06/23/2024] Open
Abstract
In recent years, there has been a significant increase in the incidence of metabolic-associated fatty liver disease (MAFLD), which has been attributed to the increasing prevalence of type 2 diabetes mellitus (T2DM) and obesity. MAFLD affects more than one-third of adults worldwide, making it the most prevalent liver disease globally. Moreover, MAFLD is considered a significant risk factor for hepatocellular carcinoma (HCC), with MAFLD-related HCC cases increasing. Approximately 1 in 6 HCC patients are believed to have MAFLD, and nearly 40 % of these HCC patients do not progress to cirrhosis, indicating direct transformation from MAFLD to HCC. N6-methyladenosine (m6A) is commonly distributed in eukaryotic mRNA and plays a crucial role in normal development and disease progression, particularly in tumors. Numerous studies have highlighted the close association between abnormal m6A modification and cellular metabolic alterations, underscoring its importance in the onset and progression of MAFLD. However, the specific impact of m6A modification on the progression of MAFLD to HCC remains unclear. Can targeting m6A effectively halt the progression of MAFLD-related HCC? In this review, we investigated the pivotal role of abnormal m6A modification in the transition from MAFLD to HCC, explored the potential of m6A modification as a therapeutic target for MAFLD-related HCC, and proposed possible directions for future investigations.
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Affiliation(s)
- Xuan Zha
- Department of Laboratory Medicine, the Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zewei Gao
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Min Li
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xueli Xia
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zhenwei Mao
- Department of Laboratory Medicine, Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.
| | - Shengjun Wang
- Department of Laboratory Medicine, the Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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3
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Wang J, Fan P, Shen P, Fan C, Zhao P, Yao Shen, Dong K, Ling R, Chen S, Zhang J. XBP1s activates METTL3/METTL14 for ER-phagy and paclitaxel sensitivity regulation in breast cancer. Cancer Lett 2024; 596:216846. [PMID: 38582397 DOI: 10.1016/j.canlet.2024.216846] [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: 11/21/2023] [Revised: 03/25/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Cancer cells employ the unfolded protein response (UPR) or induce autophagy, especially selective removal of certain ER domains via reticulophagy (termed ER-phagy), to mitigate endoplasmic reticulum (ER) stress for ER homeostasis when encountering microenvironmental stress. N6-methyladenosine (m6A) is one of the most abundant epitranscriptional modifications and plays important roles in various biological processes. However, the molecular mechanism of m6A modification in the ER stress response is poorly understood. In this study, we first found that ER stress could dramatically elevate m6A methylation levels through XBP1s-dependent transcriptional upregulation of METTL3/METTL14 in breast cancer (BC) cells. Further MeRIP sequencing and relevant validation results confirmed that ER stress caused m6A methylation enrichment on target genes for ER-phagy. Mechanistically, METTL3/METTL14 increased ER-phagy machinery formation by promoting m6A modification of the ER-phagy regulators CALCOCO1 and p62, thus enhancing their mRNA stability. Of note, we further confirmed that the chemotherapeutic drug paclitaxel (PTX) could induce ER stress and increase m6A methylation for ER-phagy. Furthermore, the combination of METTL3/METTL14 inhibitors with PTX demonstrated a significant synergistic therapeutic effect in both BC cells and xenograft mice. Thus, our data built a novel bridge on the crosstalk between ER stress, m6A methylation and ER-phagy. Most importantly, our work provides novel evidence of METTL3 and METTL14 as potential therapeutic targets for PTX sensitization in breast cancer.
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Affiliation(s)
- Jiajia Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Pengyu Fan
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Peng Shen
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Cong Fan
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Pan Zhao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yao Shen
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Kewei Dong
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Rui Ling
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Suning Chen
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Jian Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China.
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4
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Yang B, Wang Z, Wang S, Li X. Unveiling the Hub Genes Involved in Cadmium-Induced Hepatotoxicity. Biol Trace Elem Res 2024:10.1007/s12011-024-04307-0. [PMID: 39012411 DOI: 10.1007/s12011-024-04307-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/08/2024] [Indexed: 07/17/2024]
Abstract
Cadmium (Cd) is a highly toxic heavy metal that can cause severe liver damage in both humans and animals. However, the specific genes responsible for Cd-induced hepatotoxicity are still not fully understood. Therefore, the aim of this study was to identify the key genes associated with Cd-induced liver damage. To achieve this, we utilized the GSE19662 dataset from the Gene Expression Omnibus (GEO), which consisted of rat hepatocyte samples treated with cadmium chloride (CdCl2) as well as control groups. By focusing on rat hepatocytes treated with 0.10 ppm of CdCl2, the study identified 851 differentially expressed genes (DEGs), with 438 genes being upregulated and 413 genes being downregulated. Gene Ontology (GO) analysis revealed that these DEGs were primarily involved in inflammatory responses, xenobiotic metabolic processes, and the response to drugs and xenobiotic stimuli. Finally, the study identified several hub genes, including CYP2E1, CYP3A62, CYP2C11, CYP2C13, CYP2B3, HSP90B1, HSP90AA1, GSTA2, and MAPK8, which were associated with CdCl2-induced liver damage. Furthermore, pathway analysis demonstrated that these hub genes were mainly linked to pathways involved in chemical carcinogenesis, metabolic processes, steroid hormone biosynthesis, retinol metabolism, linoleic acid metabolism, arachidonic acid metabolism, inflammatory mediator regulation, Ras, and protein processing in the endoplasmic reticulum. In conclusion, this study provides important insights into the molecular mechanisms underlying Cd-induced liver damage.
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Affiliation(s)
- Bing Yang
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
| | - Zhongyuan Wang
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
| | - Shujuan Wang
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
| | - Xiaofeng Li
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China.
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5
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Jin Y, Wu A, Bian S, Teng J. Icariin upregulates methyltransferase-like 14-mediated prolyl 4-hydroxylase beta subunit m6A modification to promote osteogenic differentiation of bone marrow stem cells. Exp Cell Res 2024; 440:114138. [PMID: 38906316 DOI: 10.1016/j.yexcr.2024.114138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Prolyl 4-hydroxylase beta subunit (P4HB) plays a vital role in bone formation. This study intends to clarify the role of P4HB in the therapeutic effect of Icariin (ICA) on osteoporosis. Herein, in vivo and in vitro models were constructed by performing ovariectomy (OVX) in rats and inducing osteogenic differentiation in bone marrow stem cells (BMSCs), respectively. Hematoxylin and eosin staining and micro-computed tomography analysis were performed to evaluate osteoporosis in OVX rats. Alizarin Red staining, alkaline phosphatase staining, and the ALP activity test were employed to assess osteogenesis. m6A dot blotting and methylated RNA immunoprecipitation were used to determine m6A modification. We found that P4HB was downregulated in bone tissues of patients with osteoporosis and OVX rats. P4HB facilitated osteogenic differentiation of BMSCs. What's more, ICA upregulated P4HB expression, promoted osteogenic differentiation of BMSCs, and alleviated osteoporosis in OVX rats, which were reversed by knocking down P4HB. ICA enhanced the stability and m6A modification of P4HB. METTL14 mediated m6A modification of P4HB mRNA. In addition, METTL14 knockdown overturned the promotive effects of ICA on P4HB m6A level and BMSC osteogenic differentiation. To sum up, ICA elevated the METTL14-mediated m6A modification of P4HB to facilitate BMSC osteogenic differentiation.
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Affiliation(s)
- Yao Jin
- The First Clinical Medical College of Shandong University of Chinese Medicine, Jinan, 250014, Shandong Province, PR China
| | - Ao Wu
- The First Clinical Medical College of Shandong University of Chinese Medicine, Jinan, 250014, Shandong Province, PR China
| | - Sishan Bian
- Department of Minimally Invasive Orthopedics, Affiliated Hospital of Shandong Traditional Chinese Medicine University, Jinan, 250014, Shandong Province, PR China
| | - Jiawen Teng
- Department of Microscopic Orthopaedics, Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, 250014, Shandong Province, PR China.
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6
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Berggren KA, Sinha S, Lin AE, Schwoerer MP, Maya S, Biswas A, Cafiero TR, Liu Y, Gertje HP, Suzuki S, Berneshawi AR, Carver S, Heller B, Hassan N, Ali Q, Beard D, Wang D, Cullen JM, Kleiner RE, Crossland NA, Schwartz RE, Ploss A. Liver-specific Mettl14 deletion induces nuclear heterotypia and dysregulates RNA export machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599413. [PMID: 38948765 PMCID: PMC11212911 DOI: 10.1101/2024.06.17.599413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Modification of RNA with N6-methyladenosine (m6A) has gained attention in recent years as a general mechanism of gene regulation. In the liver, m6A, along with its associated machinery, has been studied as a potential biomarker of disease and cancer, with impacts on metabolism, cell cycle regulation, and pro-cancer state signaling. However these observational data have yet to be causally examined in vivo. For example, neither perturbation of the key m6A writers Mettl3 and Mettl14, nor the m6A readers Ythdf1 and Ythdf2 have been thoroughly mechanistically characterized in vivo as they have been in vitro. To understand the functions of these machineries, we developed mouse models and found that deleting Mettl14 led to progressive liver injury characterized by nuclear heterotypia, with changes in mRNA splicing, processing and export leading to increases in mRNA surveillance and recycling.
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Affiliation(s)
- Keith A Berggren
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Saloni Sinha
- Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Aaron E Lin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Stephanie Maya
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Abhishek Biswas
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Research Computing, Office of Information Technology, Princeton University, Princeton, NJ, 08544, USA
| | - Thomas R Cafiero
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yongzhen Liu
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Saori Suzuki
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Sebastian Carver
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brigitte Heller
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nora Hassan
- Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Qazi Ali
- Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Daniel Beard
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Danyang Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - John M Cullen
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medicine, NY, USA
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, NY, USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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7
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Li S, Mehal WZ, Ouyang X. RNA modifications in the progression of liver diseases: from fatty liver to cancer. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2494-x. [PMID: 38809498 DOI: 10.1007/s11427-023-2494-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/24/2023] [Indexed: 05/30/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has emerged as a prominent global health concern associated with high risk of metabolic syndrome, and has impacted a substantial segment of the population. The disease spectrum ranges from simple fatty liver to non-alcoholic steatohepatitis (NASH), which can progress to cirrhosis and hepatocellular carcinoma (HCC) and is increasingly becoming a prevalent indication for liver transplantation. The existing therapeutic options for NAFLD, NASH, and HCC are limited, underscoring the urgent need for innovative treatment strategies. Insights into gene expression, particularly RNA modifications such as N6 methyladenosine (m6A), hold promising avenues for interventions. These modifications play integral roles in RNA metabolism and cellular functions, encompassing the entire NAFLD-NASH-HCC progression. This review will encompass recent insights on diverse RNA modifications, including m6A, pseudouridine (ψ), N1-methyladenosine (m1A), and 5-methylcytidine (m5C) across various RNA species. It will uncover their significance in crucial aspects such as steatosis, inflammation, fibrosis, and tumorigenesis. Furthermore, prospective research directions and therapeutic implications will be explored, advancing our comprehensive understanding of the intricate interconnected nature of these pathological conditions.
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Affiliation(s)
- Simiao Li
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Wajahat Z Mehal
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Xinshou Ouyang
- Department of Internal Medicine, Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, 06520, USA.
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8
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Berggren KA, Schwartz RE, Kleiner RE, Ploss A. The impact of epitranscriptomic modifications on liver disease. Trends Endocrinol Metab 2024; 35:331-346. [PMID: 38212234 DOI: 10.1016/j.tem.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
RNA modifications have emerged as important mechanisms of gene regulation. Developmental, metabolic, and cell cycle regulatory processes are all affected by epitranscriptomic modifications, which control gene expression in a dynamic manner. The hepatic tissue is highly metabolically active and has an impressive ability to regenerate after injury. Cell proliferation, differentiation, and metabolism, which are all essential to the liver response to injury and regeneration, are regulated via RNA modification. Two such modifications, N6-methyladenosine (m6A)and 5-methylcytosine (m5C), have been identified as prognostic disease markers and potential therapeutic targets for liver diseases. Here, we describe progress in understanding the role of RNA modifications in liver biology and disease and discuss specific areas where unexpected results could lead to improved future understanding.
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Affiliation(s)
- Keith A Berggren
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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9
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Xue M, Dong L, Zhang H, Li Y, Qiu K, Zhao Z, Gao M, Han L, Chan AKN, Li W, Leung K, Wang K, Pokharel SP, Qing Y, Liu W, Wang X, Ren L, Bi H, Yang L, Shen C, Chen Z, Melstrom L, Li H, Timchenko N, Deng X, Huang W, Rosen ST, Tian J, Xu L, Diao J, Chen CW, Chen J, Shen B, Chen H, Su R. METTL16 promotes liver cancer stem cell self-renewal via controlling ribosome biogenesis and mRNA translation. J Hematol Oncol 2024; 17:7. [PMID: 38302992 PMCID: PMC10835888 DOI: 10.1186/s13045-024-01526-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND While liver cancer stem cells (CSCs) play a crucial role in hepatocellular carcinoma (HCC) initiation, progression, recurrence, and treatment resistance, the mechanism underlying liver CSC self-renewal remains elusive. We aim to characterize the role of Methyltransferase 16 (METTL16), a recently identified RNA N6-methyladenosine (m6A) methyltransferase, in HCC development/maintenance, CSC stemness, as well as normal hepatogenesis. METHODS Liver-specific Mettl16 conditional KO (cKO) mice were generated to assess its role in HCC pathogenesis and normal hepatogenesis. Hydrodynamic tail-vein injection (HDTVi)-induced de novo hepatocarcinogenesis and xenograft models were utilized to determine the role of METTL16 in HCC initiation and progression. A limiting dilution assay was utilized to evaluate CSC frequency. Functionally essential targets were revealed via integrative analysis of multi-omics data, including RNA-seq, RNA immunoprecipitation (RIP)-seq, and ribosome profiling. RESULTS METTL16 is highly expressed in liver CSCs and its depletion dramatically decreased CSC frequency in vitro and in vivo. Mettl16 KO significantly attenuated HCC initiation and progression, yet only slightly influenced normal hepatogenesis. Mechanistic studies, including high-throughput sequencing, unveiled METTL16 as a key regulator of ribosomal RNA (rRNA) maturation and mRNA translation and identified eukaryotic translation initiation factor 3 subunit a (eIF3a) transcript as a bona-fide target of METTL16 in HCC. In addition, the functionally essential regions of METTL16 were revealed by CRISPR gene tiling scan, which will pave the way for the development of potential inhibitor(s). CONCLUSIONS Our findings highlight the crucial oncogenic role of METTL16 in promoting HCC pathogenesis and enhancing liver CSC self-renewal through augmenting mRNA translation efficiency.
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Affiliation(s)
- Meilin Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, 7539, USA
| | - Honghai Zhang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Yangchan Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Kangqiang Qiu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Zhicong Zhao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Gao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Li Han
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- School of Pharmacy, China Medical University, Shenyang, 110001, Liaoning, China
| | - Anthony K N Chan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Keith Leung
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Kitty Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Sheela Pangeni Pokharel
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Wei Liu
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Xueer Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Lili Ren
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Hongjie Bi
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Laleh Melstrom
- Division of Surgical Oncology, Department of Surgery, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Hongzhi Li
- Department of Molecular Medicine, City of Hope National Medical Center, Duarte, CA, 91016, USA
| | - Nikolai Timchenko
- Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Graduate School of Biological Science, City of Hope, Duarte, CA, 91010, USA
| | - Steven T Rosen
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
| | - Jingyan Tian
- State Key Laboratory of Medical Genomics, Clinical Trial Center, Shanghai Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, 7539, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, 91010, USA
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA.
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10
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Lu T, Xie F, Huang C, Zhou L, Lai K, Gong Y, Li Z, Li L, Liang J, Cong Q, Li W, Ju R, Zhang SX, Jin C. ERp29 Attenuates Nicotine-Induced Endoplasmic Reticulum Stress and Inhibits Choroidal Neovascularization. Int J Mol Sci 2023; 24:15523. [PMID: 37958506 PMCID: PMC10649101 DOI: 10.3390/ijms242115523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023] Open
Abstract
Nicotine-induced endoplasmic reticulum (ER) stress in retinal pigment epithelium (RPE) cells is thought to be one pathological mechanism underlying age-related macular degeneration (AMD). ERp29 attenuates tobacco extract-induced ER stress and mitigates tight junction damage in RPE cells. Herein, we aimed to further investigate the role of ERp29 in nicotine-induced ER stress and choroidal neovascularization (CNV). We found that the expression of ERp29 and GRP78 in ARPE-19 cells was increased in response to nicotine exposure. Overexpression of ERp29 decreased the levels of GRP78 and the C/EBP homologous protein (CHOP). Knockdown of ERp29 increased the levels of GRP78 and CHOP while reducing the viability of ARPE-19 cells under nicotine exposure conditions. In the ARPE-19 cell/macrophage coculture system, overexpression of ERp29 decreased the levels of M2 markers and increased the levels of M1 markers. The viability, migration and tube formation of human umbilical vein endothelial cells (HUVECs) were inhibited by conditioned medium from the ERp29-overexpressing group. Moreover, overexpression of ERp29 inhibits the activity and growth of CNV in mice exposed to nicotine in vivo. Taken together, our results revealed that ERp29 attenuated nicotine-induced ER stress, regulated macrophage polarization and inhibited CNV.
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Affiliation(s)
- Tu Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Fangfang Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Chuangxin Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Lijun Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Kunbei Lai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yajun Gong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zijing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Longhui Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jiandong Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Qifeng Cong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Weihua Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Rong Ju
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Sarah X. Zhang
- Department of Ophthalmology and Ross Eye Institute, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
- SUNY Eye Institute, State University of New York, Buffalo, NY 14203, USA
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
| | - Chenjin Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
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11
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Chen L, Zhen H, Chen Z, Huang M, Mak DW, Jin W, Zou Y, Chen M, Zheng M, Xie Q, Zhou Z, Jin G. Deciphering m6A dynamics at a single-base level during planarian anterior-posterior axis specification. Comput Struct Biotechnol J 2023; 21:4567-4579. [PMID: 37790241 PMCID: PMC10542940 DOI: 10.1016/j.csbj.2023.09.018] [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: 03/30/2023] [Revised: 09/04/2023] [Accepted: 09/16/2023] [Indexed: 10/05/2023] Open
Abstract
Background The establishment of the anterior-posterior (A-P) axis is a crucial step during tissue repair and regeneration. Despite the association reported recently of N6-methyladenosine (m6A) with regeneration, the mechanism underlying the regulation of m6A in A-P axis specification during regeneration remains unknown. Herein, we deciphered the m6A landscape at a single-base resolution at multiple time points during A-P axis regeneration and constructed the de novo transcriptome assembly of the Dugesia japonica planarian. Results Immunofluorescence staining and comparative analysis revealed that m6A is widespread across the planarian and dynamically regulated during regeneration along the A-P axis, exhibiting a strong spatiotemporal feature. The resulting datasets of m6A-modified genes identified 80 anterior-specific genes and 13 posterior-specific genes, respectively. In addition, we showed that YTHDC1 serves as the primary m6A reader to be involved in the m6A-mediated specification of A-P axis during regeneration in Dugesia japonica planarian. Conclusions Our study provides an RNA epigenetic explanation for the specification of the A-P axis during tissue regeneration in planarian.
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Affiliation(s)
- Liqian Chen
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Hui Zhen
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Zixin Chen
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Mujie Huang
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Daniel W. Mak
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wei Jin
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Yuxiu Zou
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Mingjie Chen
- Shanghai NewCore Biotechnology Co., Ltd., Room 309, Building C, No.154, Lane 953, Jianchuan Road, Minhang District, Shanghai, China
| | - Mingyue Zheng
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Qingqiang Xie
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Zhongjun Zhou
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Guoxiang Jin
- Guangdong Cardiovascular Institute, Medical Research Institute, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
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12
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Du J, Liao W, Wang H, Hou G, Liao M, Xu L, Huang J, Yuan K, Chen X, Zeng Y. MDIG-mediated H3K9me3 demethylation upregulates Myc by activating OTX2 and facilitates liver regeneration. Signal Transduct Target Ther 2023; 8:351. [PMID: 37709738 PMCID: PMC10502063 DOI: 10.1038/s41392-023-01575-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 09/16/2023] Open
Abstract
The mineral dust-induced gene (MDIG) comprises a conserved JmjC domain and has the ability to demethylate histone H3 lysine 9 trimethylation (H3K9me3). Previous studies have indicated the significance of MDIG in promoting cell proliferation by modulating cell-cycle transition. However, its involvement in liver regeneration has not been extensively investigated. In this study, we generated mice with liver-specific knockout of MDIG and applied partial hepatectomy or carbon tetrachloride mouse models to investigate the biological contribution of MDIG in liver regeneration. The MDIG levels showed initial upregulation followed by downregulation as the recovery progressed. Genetic MDIG deficiency resulted in dramatically impaired liver regeneration and delayed cell cycle progression. However, the MDIG-deleted liver was eventually restored over a long latency. RNA-seq analysis revealed Myc as a crucial effector downstream of MDIG. However, ATAC-seq identified the reduced chromatin accessibility of OTX2 locus in MDIG-ablated regenerating liver, with unaltered chromatin accessibility of Myc locus. Mechanistically, MDIG altered chromatin accessibility to allow transcription by demethylating H3K9me3 at the OTX2 promoter region. As a consequence, the transcription factor OTX2 binding at the Myc promoter region was decreased in MDIG-deficient hepatocytes, which in turn repressed Myc expression. Reciprocally, Myc enhanced MDIG expression by regulating MDIG promoter activity, forming a positive feedback loop to sustain hepatocyte proliferation. Altogether, our results prove the essential role of MDIG in facilitating liver regeneration via regulating histone methylation to alter chromatin accessibility and provide valuable insights into the epi-transcriptomic regulation during liver regeneration.
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Affiliation(s)
- Jinpeng Du
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Wenwei Liao
- Department of Thoracic Surgery, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510630, China
| | - Haichuan Wang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Guimin Hou
- Department of Hepato-Biliary-Pancreatic Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, The Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, Sichuan, 610041, China
| | - Min Liao
- Department of Medical Ultrasound, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lin Xu
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiwei Huang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kefei Yuan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiangzheng Chen
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Yong Zeng
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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13
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Hou X, Li Y, Song J, Peng L, Zhang W, Liu R, Yuan H, Feng T, Li J, Li W, Zhu C. METTL14 reverses liver fibrosis by inhibiting NOVA2 through an m6A-YTHDF2-dependent mechanism. Hepatol Commun 2023; 7:e0199. [PMID: 37534933 PMCID: PMC10409442 DOI: 10.1097/hc9.0000000000000199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/15/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A), the most prevalent internal RNA modification in eukaryotic cells, is dynamically regulated in response to a wide range of physiological and pathological states. Nonetheless, the involvement of METTL14-induced m6A in liver fibrosis (LF) has yet to be established. METHODS In vitro, HSC cell lines with knock-down and overexpression of METTL14 were constructed, and the effects of METTL14 gene on the phenotypic function of activated HSCs were observed. The proliferation rate was measured by CCK8 and EDU, the cell proliferation cycle was measured by flow detector, the migration rate was measured by Transwell, and the contractility of F-actin was observed after phalloidin staining. The downstream target gene NOVA2 of METTL14 was screened by combined sequencing of MeRIP-seq and RNA-seq, combined with signal analysis. Adeno-associated virus (AAV) was injected into the tail vein in vivo to knock down the expression of METTL14, so as to further observe the role of METTL14 in the progress of LF. RESULTS our research showed that the methylase METTL14 content was decreased in hepatic tissue from patients with LF, leading to a lowered degree of m6A modification. Functionally, we discovered that knocking down m6A methyltransferase METTL14 led to increased HSC activation and a substantial worsening of LF. Mechanically, as shown in a multiomics study of HSCs, depleting METTL14 levels decreased m6A deposition onNOVA2 mRNA transcripts, which prompted the activation of YTHDF2 to detect and degrade the decrease of NOVA2 mRNA. CONCLUSIONS METTL14 functioned as a profibrotic gene by suppressing NOVA2 activity in a mechanism dependent on m6A-YTHDF2. Moreover, knocking down METTL14 exacerbated LF, while NOVA2 prevented its development and partly reversed the damage.
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Affiliation(s)
- Xiaoxue Hou
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuwen Li
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiali Song
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Linya Peng
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wen Zhang
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Liu
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Hui Yuan
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tiantong Feng
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jieying Li
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Wenting Li
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Chuanlong Zhu
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
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14
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Zhou J, Liao S, Zhang C, Luo J, Li G, Li H. Expression profiling of N6-methyladenosine-modified mRNA in PC12 cells in response to unconjugated bilirubin. Mol Biol Rep 2023; 50:6703-6715. [PMID: 37378749 PMCID: PMC10374823 DOI: 10.1007/s11033-023-08576-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND Abnormal methylation of N6-methyladenosine (m6A) is reportedly associated with central nervous system disorders. However, the role of m6A mRNA methylation in unconjugated bilirubin (UCB) neurotoxicity requires further research. METHODS Rat pheochromocytoma PC12 cells treated with UCB were used as in vitro models. After the PC12 cells were treated with UCB (0, 12, 18, and 24 µM) for 24 h, the total RNA m6A levels were measured using an m6A RNA methylation quantification kit. The expression of m6A demethylases and methyltransferases was detected through western blotting. We determined the m6A mRNA methylation profile in PC12 cells exposed to UCB (0 and 18 µM) for 24 h using methylated RNA immunoprecipitation sequencing (MeRIP-seq). RESULTS Compared with the control group, UCB (18 and 24 µM) treatment decreased the expression of the m6A demethylase ALKBH5 and increased the expression of the methyltransferases METTL3 and METTL14, which resulted in an increase in the total m6A levels in PC12 cells. Furthermore, 1533 m6A peaks were significantly elevated and 1331 peaks were reduced in the UCB (18 µM)-treated groups compared with those in the control group. Genes with differential m6A peaks were mainly enriched in protein processing in the endoplasmic reticulum, ubiquitin-mediated proteolysis, cell cycle, and endocytosis. Through combined analysis of the MeRIP-seq and RNA sequencing data, 129 genes with differentially methylated m6A peaks and differentially expressed mRNA levels were identified. CONCLUSION Our study suggests that the modulation of m6A methylation modifications plays a significant role in UCB neurotoxicity.
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Affiliation(s)
- Jinfu Zhou
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, Fujian Province, China
| | - Sining Liao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China
| | - Chenran Zhang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China
| | - Jinying Luo
- Obstetrics and Gynecology Department, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, Fujian Province, China
| | - Guilin Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China
| | - Huangyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China.
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China.
- Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian Province, China.
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15
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Lv Z, Ran R, Yang Y, Xiang M, Su H, Huang J. The interplay between N6-methyladenosine and precancerous liver disease: molecular functions and mechanisms. Discov Oncol 2023; 14:78. [PMID: 37227534 DOI: 10.1007/s12672-023-00695-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023] Open
Abstract
N6-methyladenosine(m6A) is one of the most abundant modifications of mammalian cellular RNAs. m6A regulates various biological functions in epitranscriptomic ways, including RNA stability, decay, splicing, translation and nuclear export. Recent studies have indicated the growing importance of m6A modification in precancerous disease, influencing viral replication, immune escape, and carcinogenesis. Here, we review the role of m6A modification in HBV/HCV infection, NAFLD and liver fibrosis, and its function in liver disease pathogenesis. Our review will provide a new sight for the innovative treatment strategy for precancerous liver disease.
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Affiliation(s)
- Zhihua Lv
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Ruoxi Ran
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Yuting Yang
- Department of General Office, School of Stomatology, Wuhan University, Wuhan, China
| | - Meixian Xiang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China
| | - Hanwen Su
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Jingtao Huang
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
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16
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Wang S, Gao S, Ye W, Li Y, Luan J, Lv X. The emerging importance role of m6A modification in liver disease. Biomed Pharmacother 2023; 162:114669. [PMID: 37037093 DOI: 10.1016/j.biopha.2023.114669] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
N6-methyladenosine (m6A) modification, as one of the most common types of inner RNA modification in eukaryotes, plays a multifunctional role in normal and abnormal biological processes. This type of modification is modulated by m6A writer, eraser and reader, which in turn impact various processes of RNA metabolism, such as RNA processing, translation, nuclear export, localization and decay. The current academic view holds that m6A modification exerts a crucial role in the post-transcriptional modulation of gene expression, and is involved in multiple cellular functions, developmental and disease processes. However, the potential molecular mechanism and specific role of m6A modification in the development of liver disease have not been fully elucidated. In our review, we summarized the latest research progress on m6A modification in liver disease, and explored how these novel findings reshape our knowledge of m6A modulation of RNA metabolism. In addition, we also illustrated the effect of m6A on liver development and regeneration to prompt further exploration of the mechanism and role of m6A modification in liver physiology and pathology, providing new insights and references for the search of potential therapeutic targets for liver disease.
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Affiliation(s)
- Sheng Wang
- Department of Pharmacy, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui Province, China; The Key Laboratory of Anti-inflammatory and Immune medicines, Ministry of Education, Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Institute for Liver Disease of Anhui Medical University, Hefei, Anhui Province, China
| | - Songsen Gao
- Department of Orthopedics (Spinal Surgery), The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Wufei Ye
- Department of Pharmacy, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui Province, China
| | - Yueran Li
- Department of Pharmacy, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui Province, China
| | - Jiajie Luan
- Department of Pharmacy, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui Province, China
| | - Xiongwen Lv
- The Key Laboratory of Anti-inflammatory and Immune medicines, Ministry of Education, Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Institute for Liver Disease of Anhui Medical University, Hefei, Anhui Province, China.
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17
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Li D, Guo M, Lv Z, Shao Y, Liang W, Li C. METTL3 activates PERK-eIF2α dependent coelomocyte apoptosis by targeting the endoplasmic reticulum degradation-related protein SEL1L in echinoderms. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194927. [PMID: 36933883 DOI: 10.1016/j.bbagrm.2023.194927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
N6-methyladenosine (m6A) plays an important role in regulating many physiological and disease processes in vertebrates, in which methyltransferase-like 3 (METTL3) is the best-known m6A methyltransferase. However, the functional roles of invertebrate METTL3 have not yet been highlighted. In this study, we found that METTL3 from Apostichopus japonicus (AjMETTL3) was significantly induced in coelomocytes accompanied by higher levels of m6A modification in response to Vibrio splendidus challenge. Overexpression or silencing of AjMETTL3 in coelomocytes increased or decreased the m6A levels and promoted or inhibited V. splendidus-induced coelomocyte apoptosis, respectively. To further explore the molecular mechanism of AjMETTL3-mediated coelomic immunity, m6A-seq analysis revealed that the endoplasmic reticulum-related degradation (ERAD) pathway was significantly enriched, in which suppressor/enhancer of Lin-12-like (AjSEL1L) was suggested to be a target of AjMETTL3 in a negative regulatory manner. Functional analysis revealed that the increased AjMETTL3 reduced the stability of AjSEL1L mRNA by targeting the m6A modification site of 2004 bp-GGACA-2008 bp. The decreased AjSEL1L was further confirmed to be involved in AjMETTL3-mediated coelomocyte apoptosis. Mechanistically, the inhibited AjSEL1L increased the transcription of AjOS9 and Ajp97 in the EARD pathway to promote ubiquitin protein accumulation and ER stress, which further activated AjPERK-AjeIF2α pathway dependent coelomocyte apoptosis, but not the AjIRE1 or AjATF6 pathway. Taken together, our results supported invertebrate METTL3-mediated coelomocyte apoptosis by regulating the PERK-eIF2α pathway.
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Affiliation(s)
- Dongdong Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Ming Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Zhimeng Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Yina Shao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Weikang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, 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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18
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Huang ZC, Huang J, Huang CK, Hou Y, Zhu B. Euchromatic histone lysine methyltransferase 2 facilitates radioresistance in prostate cancer by repressing endoplasmic reticulum protein 29 transcription. Kaohsiung J Med Sci 2023. [PMID: 36825520 DOI: 10.1002/kjm2.12661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/12/2023] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
Prostate cancer is one of the most common cancers in men. This study was conducted to investigate the role of euchromatic histone lysine methyltransferase 2 (EHMT2) and endoplasmic reticulum protein 29 (ERP29) in the progression of radioresistance in prostate cancer. The expression of EHMT2 and ERP29 in prostate cancer cells and during the progression of radioresistance was detected using quantitative reverse transcription-polymerase chain reaction and western blotting, and the interaction between EHMT2 and ERP29 was investigated. The proliferation of transfected cells under x-ray irradiation was determined using the methyl thiazolyl tetrazolium and colony formation assays. Flow cytometry was used to analyze the apoptosis of the transfected cells under x-ray irradiation. Nude mice were subcutaneously injected with prostate cancer (DU145) cells stably transfected with sh-ERP29 or sh-NC. The effect of ERP29 expression on radioresistance in nude mice was assessed by x-ray irradiation. The expression of EHMT2 was upregulated and that of ERP29 was downregulated in prostate cancer cells during radioresistance progression. EHMT2 downregulation suppressed radioresistance in DU145 and androgen-sensitive prostate cancer (LNCaP) cells. In irradiated DU145 cells, EHMT2 inhibition decreased the number of colonies and accelerated apoptosis. The transcription of ERP29 was suppressed by EHMT2 by upregulating H3K9me2 and downregulating H3K4me3, thereby regulating radioresistance in prostate cancer cells. In addition, the downregulation of ERP29 promoted the progression of radioresistance in prostate cancer cells in nude mice. EHMT2 promotes radioresistance in prostate cancer cells by repressing ERP29 transcription.
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Affiliation(s)
- Zhi-Chao Huang
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Jun Huang
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Chang-Kun Huang
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Yi Hou
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Bin Zhu
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
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19
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Chen Y, Liu X, Li L, He X, Zheng F, Zhang Y, Gao H, Jin Z, Wu D, Wang Q, Tao H, Zhao Y, Liu W, Zou L. Methyltransferase-like 3 aggravates endoplasmic reticulum stress in preeclampsia by targeting TMBIM6 in YTHDF2-dependent manner. Mol Med 2023; 29:19. [PMID: 36747144 PMCID: PMC9901113 DOI: 10.1186/s10020-023-00604-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 01/06/2023] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND With the increasing morbidity and mortality of preeclampsia (PE), it has posed a huge challenge to public health. Previous studies have reported endoplasmic reticulum (ER) stress could contribute to trophoblastic dysfunction which was associated with the N6-methyladenosine (m6A) modification by methyltransferase-like 3 (METTL3), resulting in PE. However, little was known about the relationship between METTL3 and ER stress in PE. Thus, in vitro and in vivo studies were performed to clarify the mechanism about how METTL3 affects the trophoblasts under ER stress in PE and to explore a therapeutic approach for PE. METHODS An ER stress model in HTR-8/SVneo cells and a preeclamptic rat model were used to study the mechanism and explore a therapeutic approach for PE. Western blot, immunohistochemistry, quantitative reverse transcription-polymerase chain reaction (qRT-PCR), and methylated RNA immunoprecipitation (MeRIP)-qPCR were performed to detect the protein, RNA, and methylated transmembrane BAX inhibitor motif containing 6 (TMBIM6) expression levels. The m6A colorimetric and mRNA stability assays were used to measure the m6A levels and TMBIM6 stability, respectively. Short hairpin RNAs (shRNAs) were used to knockdown METTL3 and YTH N6-methyladenosine RNA binding protein 2 (YTHDF2). Flow cytometry and Transwell assays were performed to evaluate the apoptosis and invasion abilities of trophoblasts. RESULTS Upregulated METTL3 and m6A levels and downregulated TMBIM6 levels were observed in preeclamptic placentas under ER stress. The ER stress model was successfully constructed, and knockdown of METTL3 had a beneficial effect on HTR-8/SVneo cells under ER stress as it decreased the levels of methylated TMBIM6 mRNA. Moreover, overexpression of TMBIM6 was beneficial to HTR-8/SVneo cells under ER stress as it could neutralize the harmful effects of METTL3 overexpression. Similar to the knockdown of METTL3, downregulation of YTHDF2 expression resulted in the increased expression and mRNA stability of TMBIM6. Finally, improved systemic symptoms as well as protected placentas and fetuses were demonstrated in vivo. CONCLUSIONS METTL3/YTHDF2/TMBIM6 axis exerts a significant role in trophoblast dysfunction resulting in PE while inhibiting METTL3 may provide a novel therapeutic approach for PE.
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Affiliation(s)
- Yangyang Chen
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xiaoxia Liu
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Lun Li
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xiyang He
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Fanghui Zheng
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Yang Zhang
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Hui Gao
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Zhishan Jin
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Di Wu
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Qianhua Wang
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Hui Tao
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Yin Zhao
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Weifang Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Li Zou
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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20
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Yang I, Oh SY, Jang S, Kim IY, Sung YM, Seong JK. Mettl14 mutation restrains liver regeneration by attenuating mitogens derived from non-parenchymal liver cells. BMB Rep 2022; 55:633-638. [PMID: 36284441 PMCID: PMC9813429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Indexed: 12/29/2022] Open
Abstract
Liver regeneration is a well-known systemic homeostatic phenomenon. The N6-methyladenosine (m6A) modification pathway has been associated with liver regeneration and hepatocellular carcinoma. m6A methyltransferases, such as methyltransferase 3 (METTL3) and methyltransferase 14 (METTL14), are involved in the hepatocyte-specific-regenerative pathway. To illustrate the role of METTL14, secreted from non-parenchymal liver cells, in the initiation phase of liver regeneration, we performed 70% partial hepatectomy (PH) in Mettl14 heterozygous (HET) and wild-type (WT) mice. Next, we analyzed the ratio of liver weight to body weight and the expression of mitogenic stimulators derived from non-parenchymal liver cells. Furthermore, we evaluated the expression of cell cycle-related genes and the hepatocyte proliferation rate via MKI67-immunostaining. During regeneration after PH, the weight ratio was lower in Mettl14 HET mice compared to WT mice. The expressions of hepatocyte growth factor (HGF) and tumor necrosis factor (TNF)-α, mitogens derived from non-parenchymal liver cells that stimulate the cell cycle, as well as the expressions of cyclin B1 and D1, which regulate the cell cycle, and the number of MKI67-positive cells, which indicate proliferative hepatocyte in the late G1-M phase, were significantly reduced in Mettl14 HET mice 72 h after PH. Our findings demonstrate that global Mettl14 mutation may interrupt the homeostasis of liver regeneration after an acute injury like PH by restraining certain mitogens, such as HGF and TNF-α, derived from sinusoidal endothelial cells, stellate cells, and Kupffer cells. These results provide new insights into the role of METTL14 in the clinical treatment strategies of liver disease. [BMB Reports 2022; 55(12): 633-638].
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Affiliation(s)
- Insook Yang
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Seung Yeon Oh
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea
| | - Suin Jang
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea
| | - Il Yong Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea,Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea
| | - You Me Sung
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea,Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea,Interdisciplinary Program for Bioinformatics and BIO-MAX Institute, Seoul National University, Seoul 08826, Korea,Corresponding author. Tel: +82-2-885-8395; Fax: +82-2-885-8397; E-mail:
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21
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The m 6A methyltransferase Mettl3 deficiency attenuates hepatic stellate cell activation and liver fibrosis. Mol Ther 2022; 30:3714-3728. [PMID: 35923112 PMCID: PMC9734030 DOI: 10.1016/j.ymthe.2022.07.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/21/2022] [Accepted: 07/30/2022] [Indexed: 12/14/2022] Open
Abstract
Activation of hepatic stellate cells (HSCs) is a central driver of liver fibrosis. Previous investigations have identified various altered epigenetic landscapes during the cellular progression of HSC activation. N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic cells and is dynamically regulated under various physiological and pathophysiological conditions. However, the functional role of Mettl3-mediated m6A in liver fibrosis remains elusive. Here, we found that the HSC-specific knockout of m6A methyltransferase Mettl3 suppressed HSC activation and significantly alleviated liver fibrosis. Multi-omics analysis of HSCs showed that Mettl3 depletion reduced m6A deposition on mRNA transcripts of Lats2 (a central player of the Hippo/YAP signaling pathway) and slowed down their degradation. Elevated Lats2 increased phosphorylation of the downstream transcription factor YAP, suppressed YAP nuclear translocation, and decreased pro-fibrotic gene expression. Overexpressing YAP mutant resistant to phosphorylation by Lats2 partially rescued the activation and pro-fibrotic gene expression of Mettl3-deficient HSCs. Our study revealed that disruption of Mettl3 in HSCs mitigated liver fibrosis by controlling the Hippo/YAP signaling pathway, providing potential therapeutic strategies to alleviate liver fibrosis by targeting epitranscriptomic machinery.
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22
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Yang I, Oh SY, Jang S, Kim IY, Sung YM, Seong JK. Mettl14 mutation restrains liver regeneration by attenuating mitogens derived from non-parenchymal liver cells. BMB Rep 2022; 55:633-638. [PMID: 36284441 PMCID: PMC9813429 DOI: 10.5483/bmbrep.2022.55.12.140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/10/2022] [Accepted: 10/24/2022] [Indexed: 08/27/2023] Open
Abstract
Liver regeneration is a well-known systemic homeostatic phenomenon. The N6-methyladenosine (m6A) modification pathway has been associated with liver regeneration and hepatocellular carcinoma. m6A methyltransferases, such as methyltransferase 3 (METTL3) and methyltransferase 14 (METTL14), are involved in the hepatocyte-specific-regenerative pathway. To illustrate the role of METTL14, secreted from non-parenchymal liver cells, in the initiation phase of liver regeneration, we performed 70% partial hepatectomy (PH) in Mettl14 heterozygous (HET) and wild-type (WT) mice. Next, we analyzed the ratio of liver weight to body weight and the expression of mitogenic stimulators derived from non-parenchymal liver cells. Furthermore, we evaluated the expression of cell cycle-related genes and the hepatocyte proliferation rate via MKI67-immunostaining. During regeneration after PH, the weight ratio was lower in Mettl14 HET mice compared to WT mice. The expressions of hepatocyte growth factor (HGF) and tumor necrosis factor (TNF)-α, mitogens derived from non-parenchymal liver cells that stimulate the cell cycle, as well as the expressions of cyclin B1 and D1, which regulate the cell cycle, and the number of MKI67-positive cells, which indicate proliferative hepatocyte in the late G1-M phase, were significantly reduced in Mettl14 HET mice 72 h after PH. Our findings demonstrate that global Mettl14 mutation may interrupt the homeostasis of liver regeneration after an acute injury like PH by restraining certain mitogens, such as HGF and TNF-α, derived from sinusoidal endothelial cells, stellate cells, and Kupffer cells. These results provide new insights into the role of METTL14 in the clinical treatment strategies of liver disease. [BMB Reports 2022; 55(12): 633-638].
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Affiliation(s)
- Insook Yang
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Seung Yeon Oh
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea
| | - Suin Jang
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea
| | - Il Yong Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea
| | - You Me Sung
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul 08826, Korea
- Interdisciplinary Program for Bioinformatics and BIO-MAX Institute, Seoul National University, Seoul 08826, Korea
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23
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Ma W, Wu T. RNA m6A modification in liver biology and its implication in hepatic diseases and carcinogenesis. Am J Physiol Cell Physiol 2022; 323:C1190-C1205. [PMID: 36036444 PMCID: PMC9576175 DOI: 10.1152/ajpcell.00214.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/22/2022]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification in eukaryotic RNAs. This modification is regulated by three different factors (writers, erasers, and readers) and affects multiple aspects of RNA metabolism, including RNA splicing, nuclear export, translation, stability and decay. The m6A-mediated modification plays important roles in posttranscriptional regulation of gene expression and mediates a variety of cellular and biological processes. Accordingly, deregulation in m6A modification is closely related to the occurrence and development of human diseases. The liver is the largest digestive and metabolic organ in human and recent studies have shown that m6A modification is importantly implicated in liver cellular and physiological functions and in the pathogenesis of hepatic diseases and cancers. In the current review, we summarize the functions of m6A in RNA metabolism and its roles in liver cell biology and discuss its implication in hepatic diseases and carcinogenesis.
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Affiliation(s)
- Wenbo Ma
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
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24
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METTL3 mediates osteoblast apoptosis by regulating endoplasmic reticulum stress during LPS-induced inflammation. Cell Signal 2022; 95:110335. [DOI: 10.1016/j.cellsig.2022.110335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/21/2022] [Accepted: 04/14/2022] [Indexed: 11/17/2022]
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25
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Li N, Guo Q, Zhang Q, Chen BJ, Li XA, Zhou Y. Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer. Front Cell Dev Biol 2022; 9:760912. [PMID: 35087827 PMCID: PMC8787460 DOI: 10.3389/fcell.2021.760912] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/08/2021] [Indexed: 11/13/2022] Open
Abstract
Aim: To comprehensively profile the landscape of the mRNA N6-methyladenosine (m6A) modification in human colorectal cancer (CRC). Methods: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was explored to compare the difference in mRNA N6-methyladenosine (m6A) methylation between CRC tissues and adjacent normal control (NC) tissue. RNA-sequencing (RNA-seq) was performed to transcribe differentially expressed mRNAs. Conjoint analysis of MeRIP-seq and RNA-seq data was conducted to predict RNA-binding proteins (RBPs). Results: MeRIP-seq identified 1110 differentially m6A methylated sites (DMMSs) and 980 differentially m6A methylated genes (DMMGs) in CRC, with 50.13% of all modified genes showing unique m6A-modified peaks in CRC. RNA-seq showed 915 upregulated genes and 1463 downregulated genes in CRC. QRT-PCR verified the RNA-seq results by detecting the expression of some mRNAs. Conjoint analysis of MeRIP-seq and RNA-seq identified 400 differentially m6A methylated and expressed genes (DEGs), and pathway analysis detected that DMMGs and DEGs were closely related to cancer. After analyzing these DMMGs and DEGs through the GEPIA database, we found that the expression of B3GNT6, DKC1, SRPK1, and RIMKLB were associated with prognosis, and the expression of B3GNT6 and RIMKLB were associated with clinical stage. 17 RBPs were identified based on the DMMGs and DEGs, among which FXR1, FXR2, FMR1, IGF2BP2, IGF2BP3, and SRSF1 were obviously highly expressed in CRC, and FMR1, IGF2BP2, and IGF2BP3 were closely related to methylation, and might be involved in the development of CRC. Conclusion: This study comprehensively profiled m6A modification of mRNAs in CRC, which revealed possible mechanisms of m6A-mediated gene expression regulation.
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Affiliation(s)
- Na Li
- Department Of Gastroenterology, The First People's Hospital of Aksu District, Aksu, China
| | - Qin Guo
- The First Affiliated Hospital of Chengdu Medical College, School of clinical medicine, Chengdu Medical College, Chengdu, China
| | - Qiao Zhang
- The First Affiliated Hospital of Chengdu Medical College, School of clinical medicine, Chengdu Medical College, Chengdu, China
| | - Bai-Jun Chen
- The First Affiliated Hospital of Chengdu Medical College, School of clinical medicine, Chengdu Medical College, Chengdu, China
| | - Xiao-An Li
- Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Yan Zhou
- Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
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26
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Ma W, Wu T. METTL3-Mediated m6A Modification Links Liver Homeostasis and Pathology. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:18-20. [PMID: 34774849 PMCID: PMC8747002 DOI: 10.1016/j.ajpath.2021.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 10/26/2021] [Indexed: 01/03/2023]
Affiliation(s)
- Wenbo Ma
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana.
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27
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Fan C, Ma Y, Chen S, Zhou Q, Jiang H, Zhang J, Wu F. Comprehensive Analysis of the Transcriptome-Wide m6A Methylation Modification Difference in Liver Fibrosis Mice by High-Throughput m6A Sequencing. Front Cell Dev Biol 2021; 9:767051. [PMID: 34869362 PMCID: PMC8635166 DOI: 10.3389/fcell.2021.767051] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/01/2021] [Indexed: 01/01/2023] Open
Abstract
N6-Methyladenosine (m6A), a unique and common mRNA modification method in eukaryotes, is involved in the occurrence and development of many diseases. Liver fibrosis (LF) is a common response to chronic liver injury and may lead to cirrhosis and even liver cancer. However, the involvement of m6A methylation in the development of LF is still unknown. In this study, we performed a systematic evaluation of hepatic genome-wide m6A modification and mRNA expression by m6A-seq and RNA-seq using LF mice. There were 3,315 genes with significant differential m6A levels, of which 2,498 were hypermethylated and 817 hypomethylated. GO and KEGG analyses illustrated that differentially expressed m6A genes were closely correlated with processes such as the endoplasmic reticulum stress response, PPAR signaling pathway and TGF-β signaling pathway. Moreover, a total of 90 genes had both a significant change in the m6A level and mRNA expression shown by joint analysis of m6A-seq and RNA-seq. Hence, the critical elements of m6A modification, including methyltransferase WTAP, demethylases ALKBH5 and binding proteins YTHDF1 were confirmed by RT-qPCR and Western blot. In an additional cell experiment, we also observed that the decreased expression of WTAP induced the development of LF as a result of promoting hepatic stellate cell (HSC) activation. Therefore, this study revealed unique differential m6A methylation patterns in LF mice and suggested that m6A methylation was associated with the occurrence and course of LF to some extent.
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Affiliation(s)
- Chang Fan
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yanzhen Ma
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Sen Chen
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Qiumei Zhou
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Jiafu Zhang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Furong Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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