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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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2
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Su X, Lu R, Qu Y, Mu D. Diagnostic and therapeutic potentials of methyltransferase-like 3 in liver diseases. Biomed Pharmacother 2024; 172:116157. [PMID: 38301420 DOI: 10.1016/j.biopha.2024.116157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Methyltransferase-like 3 (METTL3), a component of the RNA N6-methyladenosine (m6A) modification with a specific catalytic capacity, controls gene expression by actively regulating RNA splicing, nuclear export, stability, and translation, determines the fate of RNAs and assists in regulating biological processes. Studies conducted in recent decades have demonstrated the pivotal regulatory role of METTL3 in liver disorders, including hepatic lipid metabolism disorders, liver fibrosis, nonalcoholic steatohepatitis, and liver cancer. Although METTL3's roles in these diseases have been extensively investigated, the regulatory network of METTL3 and its potential applications remain unexplored. In this review, we provide a comprehensive overview of the roles and mechanisms of METTL3 implicated in these diseases, establish a regulatory network of METTL3, evaluate the potential for targeting METTL3 for diagnosis and treatment, and discuss avenues for future development and research. We found relatively upregulated expressions of METTL3 in these liver diseases, demonstrating its potential as a diagnostic biomarker and therapeutic target.
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Affiliation(s)
- Xiaojuan Su
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu 610041, China; NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu 610041, China
| | - Ruifeng Lu
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu 610041, China; NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu 610041, China.
| | - Yi Qu
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu 610041, China; NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu 610041, China
| | - Dezhi Mu
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu 610041, China; NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu 610041, China.
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3
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Mao-Mao, Zhang JJ, Xu YP, Shao MM, Wang MC. Regulatory effects of natural products on N6-methyladenosine modification: A novel therapeutic strategy for cancer. Drug Discov Today 2024; 29:103875. [PMID: 38176674 DOI: 10.1016/j.drudis.2023.103875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/17/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
Abstract
N6-methyladenosine (m6A) is considered to be the most common and abundant epigenetics modification in messenger RNA (mRNA) and noncoding RNA. Abnormal modification of m6A is closely related to the occurrence, development, progression, and prognosis of cancer. m6A regulators have been identified as novel targets for anticancer drugs. Natural products, a rich source of traditional anticancer drugs, have been utilized for the development of m6A-targeting drugs. Here, we review the key role of m6A modification in cancer progression and explore the prospects and structural modification mechanisms of natural products as potential drugs targeting m6A modification for cancer treatment.
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Affiliation(s)
- Mao-Mao
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, China
| | - Jin-Jing Zhang
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, China
| | - Yue-Ping Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, China
| | - Min-Min Shao
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, China
| | - Meng-Chuan Wang
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, China.
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4
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Zhen X, Sun Y, Lin H, Huang Y, Liu T, Li Y, Peng H. Elucidating the role of nicotinamide N-methyltransferase-p53 axis in the progression of chronic kidney disease. PeerJ 2023; 11:e16301. [PMID: 37953778 PMCID: PMC10638915 DOI: 10.7717/peerj.16301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/25/2023] [Indexed: 11/14/2023] Open
Abstract
Background Chronic kidney disease (CKD) is a significant global health issue characterized by progressive loss of kidney function. Renal interstitial fibrosis (TIF) is a common feature of CKD, but current treatments are seldom effective in reversing TIF. Nicotinamide N-methyltransferase (NNMT) has been found to increase in kidneys with TIF, but its role in renal fibrosis is unclear. Methods Using mice with unilateral ureteral obstruction (UUO) and cultured renal interstitial fibroblast cells (NRK-49F) stimulated with transforming growth factor-β1 (TGF-β1), we investigated the function of NNMT in vivo and in vitro. Results We performed single-cell transcriptome sequencing (scRNA-seq) on the kidneys of mice and found that NNMT increased mainly in fibroblasts of UUO mice compared to sham mice. Additionally, NNMT was positively correlated with the expression of renal fibrosis-related genes after UUO injury. Knocking down NNMT expression reduced fibroblast activation and was accompanied by an increase in DNA methylation of p53 and a decrease in its phosphorylation. Conclusions Our findings suggest that chronic kidney injury leads to an accumulation of NNMT, which might decrease p53 methylation, and increase the expression and activity of p53. We propose that NNMT promotes fibroblast activation and renal fibrosis, making NNMT a novel target for preventing and treating renal fibrosis.
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Affiliation(s)
- Xin Zhen
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuxiang Sun
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongchun Lin
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuebo Huang
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tianwei Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuanqing Li
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Peng
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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5
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Wu L, Tang H. The role of N6-methyladenosine modification in rodent models of neuropathic pain: from the mechanism to therapeutic potential. Biomed Pharmacother 2023; 166:115398. [PMID: 37647691 DOI: 10.1016/j.biopha.2023.115398] [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: 05/21/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/01/2023] Open
Abstract
Neuropathic pain (NP) is a common chronic pain condition resulted from lesions or diseases of somatosensory nervous system, but the pathogenesis remains unclear. A growing body of evidence supports the relationship between pathogenesis and N6-methyladenosine (m6A) modifications of RNA. However, studies on the role of m6A modifications in NP are still at an early stage. Elucidating different etiologies is important for understanding the specific pathogenesis of NP. This article provides a comprehensive review on the role of m6A methylation modifications including methyltransferases ("writers"), demethylases ("erasers"), and m6A binding proteins ("readers") in NP models. Further analysis of the pathogenic mechanism relationship between m6A and NP provided novel theoretical and practical significance for clinical treatment of NP.
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Affiliation(s)
- Liping Wu
- Guangxi University of Traditional Chinese Medicine, Nanning, China; The First Clinical Medical College of Guangxi University of Traditional Chinese Medicine, Nanning, China
| | - Hongliang Tang
- Guangxi Traditional Chinese Medicine University Affiliated Fangchenggang Hospital.
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Hu J, Lin H, Wang C, Su Q, Cao B. METTL14‑mediated RNA methylation in digestive system tumors. Int J Mol Med 2023; 52:86. [PMID: 37539726 PMCID: PMC10555478 DOI: 10.3892/ijmm.2023.5289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
N6‑methyladenosine (m6A) RNA methylation is one of the most common post‑transcriptional modification mechanism in eukaryotes. m6A is involved in almost all stages of the mRNA life cycle, specifically regulating its stability, splicing, export and translation. Methyltransferase‑like 14 (METTL14) is a particularly important m6A methylation 'writer' that can recognize RNA substrates. METTL14 has been documented to improve the activity and catalytic efficiency of METTL3. However, as individual proteins they can also regulate different biological processes. Malignancies in the digestive system are some of the most common malignancies found in humans, which are typically associated with poor prognoses with limited clinical solutions. METTL14‑mediated methylation has been implicated in both the potentiation and inhibition of digestive system tumor growth, cell invasion and metastasis, in addition to drug resistance. In the present review, the research progress and regulatory mechanisms of METTL14‑mediated methylation in digestive system malignancies were summarized. In addition, future research directions and the potential for its clinical application were examined.
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Affiliation(s)
- Jiexuan Hu
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Haishan Lin
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Cong Wang
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Qiang Su
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Bangwei Cao
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
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7
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Seçme M, Urgancı ABE, Üzen R, Aslan A, Tıraş F. Determination of the effects of fusaric acid, a mycotoxin, on cytotoxicity, gamma-H2AX, 8-hydroxy-2 deoxyguanosine and DNA repair gene expressions in pancreatic cancer cells. Toxicon 2023; 231:107179. [PMID: 37321408 DOI: 10.1016/j.toxicon.2023.107179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/20/2023] [Accepted: 06/04/2023] [Indexed: 06/17/2023]
Abstract
Pancreatic cancer has a poor prognosis and is an important public health problem for developing countries. Oxidative stress plays an important role in cancer initiation, progression, proliferation, invasion, angiogenesis and metastasis. For this reason, one of the important strategic targets of new cancer therapeutics is to drive cancer cells into apoptosis through oxidative stress. In nuclear and mitochondrial DNA, 8-hydroxy-2'-deoxyguanosine and gamma-H2AX (γ-H2AX) are used as important oxidative stress biomarkers. Fusaric acid (FA) is a mycotoxin that mediates toxicity produced by Fusarium species and exhibits anticancer effects in various cancers via inducing apoptosis, cell cycle arrest, or other cellular mechanisms. The aim of this study was to determine the effects of fusaric acid on cytotoxic and oxidative damage in MIA PaCa-2 and PANC-1 cell lines. In this context, dose and time dependent cytotoxic effect of fusaric acid was determined by XTT method, mRNA expression levels of genes related to DNA repair were determined by RT-PCR, and its effect on 8-hydroxy-2'-deoxyguanosine and γ-H2AX levels was revealed by ELISA assay. According to XTT results, fusaric acid inhibits cell proliferation in MIA PaCa-2 and Panc-1 cells in a dose- and time-dependent manner. IC50 doses were determined as 187.74 μM at 48 h in MIA PaCa-2 cells and 134.83 μM at 48 h in PANC-1 cells, respectively. γ-H2AX and 8-OHdG changes were not found significant in pancreatic cancer cells. The mRNA expression levels of DNA repair-related genes NEIL1, OGG1, XRCC and Apex-1 change with exposure to fusaric acid. This study contributes to the therapeutic approaches to be developed for pancreatic cancer and demonstrates the potential of fusaric acid as an anticancer agent.
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Affiliation(s)
- Mücahit Seçme
- Department of Medical Biology, Faculty of Medicine, Ordu University, Ordu, Turkey.
| | - Ayşen Buket Er Urgancı
- Department of Medical Biology, Faculty of Medicine, Pamukkale University, Denizli, Turkey
| | - Ramazan Üzen
- Department of Medical Biology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Ali Aslan
- Department of Physiology, Faculty of Medicine, Ordu University, Ordu, Turkey
| | - Fatih Tıraş
- Leverhulme Research Centre for Forensic Science, Dundee University, Dundee, Scotland, UK
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Yang C, Sun J, Wu Z, Jiang M, Li D, Wang X, Zhou C, Liu X, Ren Z, Wang J, Sun M, Sun W, Gao J. FoRSR1 Is Important for Conidiation, Fusaric Acid Production, and Pathogenicity in Fusarium oxysporum f. sp. ginseng. PHYTOPATHOLOGY 2023; 113:1244-1253. [PMID: 36706002 DOI: 10.1094/phyto-10-22-0372-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The root rot disease caused by Fusarium oxysporum f. sp. ginseng is one of the most destructive diseases of ginseng, an economically important herb. However, little is known about the pathogen's toxin biosynthesis or the molecular mechanisms regulating infection of ginseng. In this study we identified and functionally characterized the FoRSR1 gene that encodes a Ras-related (RSR) small GTPase homologous to yeast Rsr1 in F. oxysporum f. sp. ginseng. Disruption of FoRSR1 resulted in a significant reduction in mycelial dry weight in liquid cultures, although vegetative growth rate was not affected on culture plates. Notably, the Forsr1 mutant exhibited blunted and swollen hyphae with multi-nucleated compartments. It produced fewer and morphologically abnormal conidia and was defective in chlamydospore formation. In infection assays with ginseng roots, the Forsr1 mutant was significantly less virulent and caused only limited necrosis at the wounding sites. Deletion of FoRSR1 also affected pigmentation, autophagy, and production of fusaric acid. Furthermore, the expression of many candidate genes involved in secondary metabolism was significantly downregulated in the mutant, suggesting that FoRSR1 is also important for secondary metabolism. Overall, our results indicated that FoRSR1 plays important roles in conidiation, vacuolar morphology, secondary metabolism, and pathogenesis in F. oxysporum f. sp. ginseng.
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Affiliation(s)
- Cui Yang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Jing Sun
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Zhaoqun Wu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Maozhu Jiang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Dayong Li
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Xinjie Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Chunxiang Zhou
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Xuecheng Liu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Zhiguo Ren
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Jun Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Manli Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Wenxian Sun
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Jie Gao
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China
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9
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Li L, He Z, Shi Y, Sun H, Yuan B, Cai J, Chen J, Long M. Role of epigenetics in mycotoxin toxicity: a review. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 100:104154. [PMID: 37209890 DOI: 10.1016/j.etap.2023.104154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/25/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023]
Abstract
Mycotoxins can induce cell cycle disorders, cell proliferation, oxidative stress, and apoptosis through pathways such as those associated with MAPK, JAK2/STAT3, and Bcl-w/caspase-3, and cause reproductive toxicity, immunotoxicity, and genotoxicity. Previous studies have explored the toxicity mechanism of mycotoxins from the levels of DNA, RNA, and proteins, and proved that mycotoxins have epigenetic toxicity. To explore the toxic effects and mechanisms of these changes in mycotoxins, this paper summarizes the changes in DNA methylation, non-coding RNA, RNA and histone modification induced by several common mycotoxins (zearalenone, aflatoxin B1, ochratoxin A, deoxynivalenol, T-2 toxin, etc.) based on epigenetic studies. In addition, the roles of mycotoxin-induced epigenetic toxicity in germ cell maturation, embryonic development, and carcinogenesis are highlighted. In summary, this review provides theoretical support for a better understanding of the regulatory mechanism of mycotoxin epigenotoxicity and the diagnosis and treatment of diseases.
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Affiliation(s)
- Liuliu Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China; Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, P.R. China.
| | - Ziqi He
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China; Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, P.R. China.
| | - Yang Shi
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China; Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, P.R. China.
| | - Huiying Sun
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China; Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, P.R. China.
| | - Bowei Yuan
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China; Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, P.R. China.
| | - Jing Cai
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China; Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, P.R. China.
| | - Jia Chen
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China; Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, P.R. China.
| | - Miao Long
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China; Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, P.R. China.
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10
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Zhu X, Fu H, Sun J, Xu Q. Interaction between N6-methyladenosine (m6A) modification and environmental chemical-induced diseases in various organ systems. Chem Biol Interact 2023; 373:110376. [PMID: 36736874 DOI: 10.1016/j.cbi.2023.110376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
A wide variety of chemicals are ubiquitous in the environment and thus exposure to these environmental chemicals poses a serious threat to public health. Particularly, environmental factors such as air pollution, heavy metals, and endocrine-disrupting chemicals (EDCs) can lead to diseases in various organ systems. Recent research in environmental epigenetics has demonstrated that N6-methyladenosine (m6A) modification is a key mechanism of environment-related diseases. m6A modification is the most abundant chemical modification in mRNAs, which can specifically regulate gene expression by affecting RNA translation, stability, processing, and nuclear export. In this review, we discussed how environmental chemicals affected m6A modification and mediated environment-related disease occurrence by classifying the diseases of various systems. Here, we conclude that environmental chemicals alter the levels of m6A and its modulators, which then participate in the occurrence of diseases in various systems by regulating gene expression and downstream signaling pathways such as METTL3/m6A ZBTB4/YTHDF2/EZH2, Foxo3a/FTO/m6A ephrin-B2/YTHDF2, and HIF1A/METTL3/m6A BIRC5/IGF2BP3/VEGFA. Considering the significant role of m6A and its modulators in response to environmental chemicals, they are expected to be used as biomarkers of environment-related diseases. Additionally, targeting m6A modulators using small molecule inhibitors and activators is expected to be a new method for the treatment of environment-related diseases. This review systematically and comprehensively clarifies the important role of m6A in diseases caused by environmental chemicals, thus establishing a scientific basis for the treatment of diseases in various organ systems.
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Affiliation(s)
- Xiaofang Zhu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, No. 87 Ding jia qiao Road, Gulou District, Nanjing, 210009, China
| | - Haowei Fu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, No. 87 Ding jia qiao Road, Gulou District, Nanjing, 210009, China
| | - Jiahui Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, No. 87 Ding jia qiao Road, Gulou District, Nanjing, 210009, China
| | - Qian Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, No. 87 Ding jia qiao Road, Gulou District, Nanjing, 210009, China.
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11
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Sarraf G, Chhabra R. Emerging role of mRNA methylation in regulating the hallmarks of cancer. Biochimie 2023; 206:61-72. [PMID: 36244577 DOI: 10.1016/j.biochi.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/29/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
Abstract
The dynamic chemical modifications of DNA, RNA, and proteins can transform normal cells into malignant ones. While the DNA and protein modifications in cancer have been described extensively in the literature, there are fewer reports about the role of RNA modifications in cancer. There are over 100 forms of RNA modifications and one of these, mRNA methylation, plays a critical role in the malignant properties of the cells. mRNA methylation is a reversible modification responsible for regulating protein expression at the post-transcriptional level. Despite being discovered in the 1970s, a complete understanding of the different proteins involved and the mechanism behind mRNA methylation remains largely unknown. However, these mRNA methylations have been shown to foster cancer hallmarks via specific cellular targets inside the cell. In this review, we provide a brief overview of mRNA methylation and its emerging role in regulating the various hallmarks of cancer.
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Affiliation(s)
- Gargi Sarraf
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India.
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12
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Kisan A, Chhabra R. Modulation of gene expression by YTH domain family (YTHDF) proteins in human physiology and pathology. J Cell Physiol 2023; 238:5-31. [PMID: 36326110 DOI: 10.1002/jcp.30907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
The advent of high throughput techniques in the past decade has significantly advanced the field of epitranscriptomics. The internal chemical modification of the target RNA at a specific site is a basic feature of epitranscriptomics and is critical for its structural stability and functional property. More than 170 modifications at the transcriptomic level have been reported so far, among which m6A methylation is one of the more conserved internal RNA modifications, abundantly found in eukaryotic mRNAs and frequently involved in enhancing the target messenger RNA's (mRNA) stability and translation. m6A modification of mRNAs is essential for multiple physiological processes including stem cell differentiation, nervous system development and gametogenesis. Any aberration in the m6A modification can often result in a pathological condition. The deregulation of m6A methylation has already been described in inflammation, viral infection, cardiovascular diseases and cancer. The m6A modification is reversible in nature and is carried out by specialized m6A proteins including writers (m6A methyltransferases) that add methyl groups and erasers (m6A demethylases) that remove methyl groups selectively. The fate of m6A-modified mRNA is heavily reliant on the various m6A-binding proteins ("readers") which recognize and generate a functional signal from m6A-modified mRNA. In this review, we discuss the role of a family of reader proteins, "YT521-B homology domain containing family" (YTHDF) proteins, in human physiology and pathology. In addition, we critically evaluate the potential of YTHDF proteins as therapeutic targets in human diseases.
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Affiliation(s)
- Aju Kisan
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
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Wu J, Wang X, Li X. N6-methyladenosine methylation regulator FTO promotes oxidative stress and induces cell apoptosis in ovarian cancer. Epigenomics 2022; 14:1509-1522. [PMID: 36815224 DOI: 10.2217/epi-2022-0403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Aims: This study aimed to reveal the possible molecular mechanism of n6-methyladenosine (m6A) methylation regulator FTO in the biological activities of ovarian cancer (OC) based on The Cancer Genome Atlas, Genotype-Tissue Expression and Gene Expression Omnibus databases. Materials & methods: A risk score model was constructed to predict the prognosis of patients with OC. The key m6A methylation regulator was screened out based on OC-related microarray datasets. Results: 22 m6A methylation regulators were differentially expressed and interacted with each other in OC. FTO, a key m6A methylation regulator, was singled out. In vivo experiments verified that FTO promoted oxidative stress and apoptosis of OC cells to inhibit tumor growth in nude mice. Conclusion: This study highlighted the tumor-suppressive mechanism of m6A methylation regulator FTO in OC.
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Affiliation(s)
- Jun Wu
- The Fifth Department of Gynecology, Ningbo Women's & Children's Hospital, Ningbo, 315012, P.R. China
| | - Xiaoqin Wang
- The Fifth Department of Gynecology, Ningbo Women's & Children's Hospital, Ningbo, 315012, P.R. China
| | - Xin Li
- The Fifth Department of Gynecology, Ningbo Women's & Children's Hospital, Ningbo, 315012, P.R. China
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Wang Z, Zhou J, Zhang H, Ge L, Li J, Wang H. RNA m 6 A methylation in cancer. Mol Oncol 2022; 17:195-229. [PMID: 36260366 PMCID: PMC9892831 DOI: 10.1002/1878-0261.13326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/28/2022] [Accepted: 10/18/2022] [Indexed: 02/04/2023] Open
Abstract
N6 -methyladenosine (m6 A) is one of the most abundant internal modifications in eukaryotic messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). It is a reversible and dynamic RNA modification that has been observed in both internal coding segments and untranslated regions. Studies indicate that m6 A modifications play important roles in translation, RNA splicing, export, degradation and ncRNA processing control. In this review, we focus on the profiles and biological functions of RNA m6 A methylation on both mRNAs and ncRNAs. The dynamic modification of m6 A and its potential roles in cancer development are discussed. Moreover, we discuss the possibility of m6 A modifications serving as potential biomarkers for cancer diagnosis and targets for therapy.
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Affiliation(s)
- Zhaotong Wang
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Jiawang Zhou
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Haisheng Zhang
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Lichen Ge
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Jiexin Li
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Hongsheng Wang
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
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15
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Feng Y, Liu T, Xu S, Ren Y, Ge Y, Yin L, Pu Y, Liang G. The role of N6-methyladenosine methylation in environmental exposure-induced health damage. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:69153-69175. [PMID: 35951238 DOI: 10.1007/s11356-022-22093-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
The health risks caused by environmental pollution have long been of substantial concern. With the development of epigenetics, a large number of studies have demonstrated that N6-methyladenosine (m6A) modification is involved in the regulation of various important life activities associated with various diseases. Recent studies have revealed that m6A plays a key role in health damage caused by environmental exposure by regulating post-transcriptional gene expression. Therefore, our study outlined the effects of environmental pollutant exposure on m6A methylation and its regulator levels. Moreover, we found that m6A methylation modifications were involved in the development of various health damages by regulating important life activities in vivo, such as reactive oxygen species imbalance, apoptosis, epithelial-mesenchymal transition (EMT), and inflammatory processes. More importantly, we delved into the regulatory mechanisms of m6A methylation dysregulation in environmental pollution-induced diseases. Finally, by examining the published literature, we found that methyltransferase-like protein 3 (METTL3) and fat mass- and obesity-associated protein (FTO) were potentially used as biomarkers of health damage induced by particulate matter exposure and heavy metal exposure, respectively. The current studies on regulators of METTL3 and FTO were more promising to bring new perspectives for the treatment of environmental health-related diseases.
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Affiliation(s)
- Yanlu Feng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Tong Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Siyi Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Yiyi Ren
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Yiling Ge
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Geyu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China.
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16
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Multilevel regulation of N6-methyladenosine RNA modifications: Implications in tumorigenesis and therapeutic opportunities. Genes Dis 2022. [PMID: 37492716 PMCID: PMC10363589 DOI: 10.1016/j.gendis.2022.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
N6-methyladenosine (m6A) RNA modification is widely perceived as the most abundant and common modification in transcripts. This modification is dynamically regulated by specific m6A "writers", "erasers" and "readers" and is reportedly involved in the occurrence and development of many diseases. Since m6A RNA modification was discovered in the 1970s, with the progress of relevant research technologies, an increasing number of functions of m6A have been reported, and a preliminary understanding of m6A has been obtained. In this review, we summarize the mechanisms through which m6A RNA modification is regulated from the perspectives of expression, posttranslational modification and protein interaction. In addition, we also summarize how external and internal environmental factors affect m6A RNA modification and its functions in tumors. The mechanisms through which m6A methylases, m6A demethylases and m6A-binding proteins are regulated are complicated and have not been fully elucidated. Therefore, we hope to promote further research in this field by summarizing these mechanisms and look forward to the future application of m6A in tumors.
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Xia Z, Kong F, Wang K, Zhang X. Role of N6-Methyladenosine Methylation Regulators in the Drug Therapy of Digestive System Tumours. Front Pharmacol 2022; 13:908079. [PMID: 35754499 PMCID: PMC9218687 DOI: 10.3389/fphar.2022.908079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/17/2022] [Indexed: 12/12/2022] Open
Abstract
Digestive system tumours, including stomach, colon, esophagus, liver and pancreatic tumours, are serious diseases affecting human health. Although surgical treatment and postoperative chemoradiotherapy effectively improve patient survival, current diagnostic and therapeutic strategies for digestive system tumours lack sensitivity and specificity. Moreover, the tumour's tolerance to drug therapy is enhanced owing to tumour cell heterogeneity. Thus, primary or acquired treatment resistance is currently the main hindrance to chemotherapy efficiency. N6-methyladenosine (m6A) has various biological functions in RNA modification. m6A modification, a key regulator of transcription expression, regulates RNA metabolism and biological processes through the interaction of m6A methyltransferase ("writers") and demethylase ("erasers") with the binding protein decoding m6A methylation ("readers"). Additionally, m6A modification regulates the occurrence and development of tumours and is a potential driving factor of tumour drug resistance. This review systematically summarises the regulatory mechanisms of m6A modification in the drug therapy of digestive system malignancies. Furthermore, it clarifies the related mechanisms and therapeutic prospects of m6A modification in the resistence of digestive system malignancies to drug therapy.
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Affiliation(s)
- Zhelin Xia
- Department of Pharmacy, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Fanhua Kong
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Hubei Clinical Research Center for Natural Polymer Biological Liver, Hubei Engineering Center of Natural Polymer-based Medical Materials, Wuhan, China
| | - Kunpeng Wang
- Department of General Surgery Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, China
| | - Xin Zhang
- Department of Pharmacy, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
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Jin H, Wu Z, Tan B, Liu Z, Zu Z, Wu X, Bi Y, Hu X. Ibuprofen promotes p75 neurotrophin receptor expression through modifying promoter methylation and N6-methyladenosine-RNA-methylation in human gastric cancer cells. Bioengineered 2022; 13:14595-14604. [PMID: 35758042 PMCID: PMC9342148 DOI: 10.1080/21655979.2022.2092674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
It is acknowledged that nonsteroidal anti-inflammatory drugs (NSAIDs) can participate in various signaling pathways, while information about their epigenetic effects are limited. p75NTR (p75 neurotrophin receptor) can inhibit tumor growth by inducing cell cycle arrest and regulating cell cycle arrest and apoptotic cell death. The expression of p75NTR is influenced by epigenetic roles. We explored the effects of ibuprofen on p75NTR expression and investigated whether promoter methylation and N6-methyladenosine (m6A) RNA methylation regulates this process in human gastric cancer cells (SGC7901 and MKN45). Cell lines were treated with ibuprofen 0, 2.5, 5, 10, 20 µM, and then DNA, RNA, and protein were isolated 24 h later. Expression and promoter methylation of p75NTR were detected by RT-qPCR and Western blot. The levels of m6A-p75NTR were measured by RNA immunoprecipitation. We also used RT-qPCR to determine the levels of m6A-related regulators, METTL3, METTL14, ALKBH5, FTO, YTHDC2, and YTHDF1-3. Ibuprofen attenuated p75NTR promoter methylation (p < 0.01) and increased p75NTR level (p < 0.001). Ibuprofen increased m6A-p53 expression (p < 0.01) by promoting the expression of METTL3 (p < 0.01) and METTL14 (p < 0.05); and increased levels of YTHDF1 (p < 0.001), YTHDF3 (p < 0.001), and YTHDC2 (p < 0.01) that finally reinforced p53 translation (p < 0.01). Therefore, our results present that ibuprofen epigenetically increased p75NTR expression by downregulating promoter methylation and upregulating m6A-RNA-methylation in SGC7901 and MKN45 cells. Our study unveils a novel mechanism for p75NTR regulation by NSAIDs and helps the design of treatment targets.
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Affiliation(s)
- Haifeng Jin
- Department of Gastroenterology, The 980th Hospital of the PLA Joint Logistics Support Force (Primary Bethune International Peace Hospital of PLA), Shijiazhuang, Hebei, China
| | - Zheng Wu
- Department of Tumor Immunology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Bibo Tan
- Department of General Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhen Liu
- Department of Gastroenterology, The 980th Hospital of the PLA Joint Logistics Support Force (Primary Bethune International Peace Hospital of PLA), Shijiazhuang, Hebei, China
| | - Zhanfei Zu
- Department of Gastroenterology, The 980th Hospital of the PLA Joint Logistics Support Force (Primary Bethune International Peace Hospital of PLA), Shijiazhuang, Hebei, China
| | - Xiaoyun Wu
- Department of Gastroenterology, The 980th Hospital of the PLA Joint Logistics Support Force (Primary Bethune International Peace Hospital of PLA), Shijiazhuang, Hebei, China
| | - Yuwang Bi
- Information Section, The 980th Hospital of the PLA Joint Logistics Support Force (Primary Bethune International Peace Hospital of PLA)
| | - Xingmao Hu
- Medical Management Office of the Medical Service Bureau of the Joint Logistics Support Force
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19
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Liu X, Wang Z, Yang Q, Hu X, Fu Q, Zhang X, Li W. RNA Demethylase ALKBH5 Prevents Lung Cancer Progression by Regulating EMT and Stemness via Regulating p53. Front Oncol 2022; 12:858694. [PMID: 35530319 PMCID: PMC9076132 DOI: 10.3389/fonc.2022.858694] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/22/2022] [Indexed: 01/08/2023] Open
Abstract
BackgroundAlthough N6-methyladenosine (m6A) RNA methylation is the most abundant reversible methylation of mRNA, which plays a critical role in regulating cancer processing, few studies have examined the role of m6A in nonsmall-cell lung cancer-derived cancer stem-like cells (CSCs).MethodsCSCs were enriched by culturing NSCLC cells in a serum-free medium, and stem factors, including CD24, CD44, ALDH1, Nanog, Oct4, and Sox2 were detected by Western blot. ALKBH5 expression was measured by employing a tissue array. Global m6A methylation was measured after ALKBH5 knockdown. Malignances of CSCs were detected by performing CCK-8 assay, invasion assay, cell cycle analysis, and tumor formation in vitro and in vivo.Resultsm6A demethylase ALKBH5 is highly expressed in CSCs derived from NSCLC. Knockdown of ALKBH5 increased global m6A level, and also increased E-cadherin, decreased stem hallmarkers, Nanog and Oct4, and inhibited stemness of CSCs. In lung carcinoma, ALKBH5 is found to be positively correlated with p53 by using Gene Expression Profiling Interactive Analysis (GEPIA) online tool. P53 transcriptionally regulates ALKBH5 and subsequently regulates the global m6A methylation level. Knockdown of p53 or inhibition of p53’s transcriptional activity by addition of its specific inhibitor PFT-α decreased expression of ALKBH5 and CSCs’ malignancies, including proliferation, invasion, and tumor formation ability, indicating that p53 may partially regulate CSC’s malignancies via ALKBH5. Furthermore, we also found p53 transcriptionally regulates PRRX1, which is consistent with our previous report.ConclusionCollectively, our findings indicate the pivotal role of ALKBH5 in CSCs derived from NSCLC and highlight the regulatory function of the p53/ALKBH5 axis in modulating CSC progression, which could be a promising therapeutic target for NSCLC.
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Deng LJ, Deng WQ, Fan SR, Chen MF, Qi M, Lyu WY, Qi Q, Tiwari AK, Chen JX, Zhang DM, Chen ZS. m6A modification: recent advances, anticancer targeted drug discovery and beyond. Mol Cancer 2022; 21:52. [PMID: 35164788 PMCID: PMC8842557 DOI: 10.1186/s12943-022-01510-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/15/2022] [Indexed: 12/12/2022] Open
Abstract
AbstractAbnormal N6-methyladenosine (m6A) modification is closely associated with the occurrence, development, progression and prognosis of cancer, and aberrant m6A regulators have been identified as novel anticancer drug targets. Both traditional medicine-related approaches and modern drug discovery platforms have been used in an attempt to develop m6A-targeted drugs. Here, we provide an update of the latest findings on m6A modification and the critical roles of m6A modification in cancer progression, and we summarize rational sources for the discovery of m6A-targeted anticancer agents from traditional medicines and computer-based chemosynthetic compounds. This review highlights the potential agents targeting m6A modification for cancer treatment and proposes the advantage of artificial intelligence (AI) in the discovery of m6A-targeting anticancer drugs.
Graphical abstract
Three stages of m6A-targeting anticancer drug discovery: traditional medicine-based natural products, modern chemical modification or synthesis, and artificial intelligence (AI)-assisted approaches for the future.
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21
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Ma C, Chen K, Wang Y, Cen C, Zhai Q, Zhang J. Establishing a novel colorectal cancer predictive model based on unique gut microbial single nucleotide variant markers. Gut Microbes 2022; 13:1-6. [PMID: 33430705 PMCID: PMC7808391 DOI: 10.1080/19490976.2020.1869505] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Current metagenomic species-based colorectal cancer (CRC) microbial biomarkers may confuse diagnosis because the genetic content of different microbial strains, even those belonging to the same species, may differ from 5% to 30%. Here, a total of 7549 non-redundant single nucleotide variants (SNVs) were annotated in 25 species from 3 CRC cohorts (n = 249). Then, 22 microbial SNV markers that contributed to distinguishing subjects with CRC from healthy subjects were identified by the random forest algorithm to construct a novel CRC predictive model. Excitingly, the predictive model showed high accuracy both in the training (AUC = 75.35%) and validation cohorts (AUC = 73.08%-88.02%). We further explored the specificity of these SNV markers in a broader background by performing a meta-analysis across 4 metabolic disease cohorts. Among these SNV markers, 3 SNVs that were enriched in CRC patients and located in the genomes of Eubacterium rectale and Faecalibacterium prausnitzii were CRC specific (AUC = 72.51%-94.07%).
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Affiliation(s)
- Chenchen Ma
- College of Food Science and Engineering, Hainan University, Haikou, Hainan, P. R. China,Key Laboratory of Food Nutrition and Functional Food of HainanProvince, Hainan University, Haikou, Hainan, China
| | - Kaining Chen
- Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, P. R. China
| | - Yuanyuan Wang
- College of Food Science and Engineering, Hainan University, Haikou, Hainan, P. R. China,Key Laboratory of Food Nutrition and Functional Food of HainanProvince, Hainan University, Haikou, Hainan, China
| | - Chaoping Cen
- Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, P. R. China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, P. R China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,Qixiao Zhai State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, P. R China
| | - Jiachao Zhang
- College of Food Science and Engineering, Hainan University, Haikou, Hainan, P. R. China,Key Laboratory of Food Nutrition and Functional Food of HainanProvince, Hainan University, Haikou, Hainan, China,CONTACT Jiachao Zhang College of Food Science and Engineering, Hainan University, Haikou, Hainan570228, P. R. China
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22
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Li Z, Xu Q, Huangfu N, Chen X, Zhu J. Mettl3 promotes oxLDL-mediated inflammation through activating STAT1 signaling. J Clin Lab Anal 2021; 36:e24019. [PMID: 34825733 PMCID: PMC8761454 DOI: 10.1002/jcla.24019] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/10/2021] [Accepted: 09/07/2021] [Indexed: 12/16/2022] Open
Abstract
Background Atherosclerosis (AS) is the main cause of cerebrovascular diseases, and macrophages act important roles during the AS pathological process through regulating inflammation. Modification of the novel N(6)‐methyladenine (m6A) RNA is reported to be associated with AS, but its role in AS is largely unknown. The aim of this study was to investigate the role and mechanism of m6A modification in inflammation triggered by oxidized low‐density lipoprotein (oxLDL) in macrophages during AS. Methods RAW264.7 macrophage cells were stimulated with 40 μg/ml ox‐LDL, Dot blot, Immunoprecipitation, western blot, Rip and chip experiments were used in our study. Results We found oxLDL stimulation significantly promoted m6A modification level of mRNA in macrophages and knockdown of Methyltransferase‐Like Protein 3 (Mettl3) inhibited oxLDL‐induced m6A modification and inflammatory response. Mettl3 promoted oxLDL‐induced inflammatory response in macrophages through regulating m6A modification of Signal transducer and activator of transcription 1 (STAT1) mRNA, thereby affecting STAT1 expression and activation. Moreover, oxLDL stimulation enhanced the interaction between Mettl3 and STAT1 protein, promoting STAT1 transcriptional regulation of inflammatory factor expression in macrophages eventually. Conclusions These results indicate that Mettl3 promotes oxLDL‐triggered inflammation through interacting with STAT1 protein and mRNA in RAW264.7 macrophages, suggesting that Mettl3 may be as a potential target for the clinical treatment of AS.
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Affiliation(s)
- Zhenwei Li
- Department of Cardiology, The first Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Cardiology, Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Qingqing Xu
- Department of Nephrology, Ningbo First Hospital, Ningbo, China
| | - Ning Huangfu
- Department of Cardiology, Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Xiaomin Chen
- Department of Cardiology, Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Jianhua Zhu
- Department of Cardiology, The first Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Ghazi T, Chuturgoon AA. Mycotoxins exacerbate HIV infection: the potential of N 6-methyladenosine RNA methylation. Epigenomics 2021; 13:1905-1908. [PMID: 34657481 DOI: 10.2217/epi-2021-0363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Terisha Ghazi
- Discipline of Medical Biochemistry, School of Laboratory Medicine & Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine & Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
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Ghazi T, Nagiah S, Chuturgoon AA. Fusaric acid induces hepatic global m6A RNA methylation and differential expression of m6A regulatory genes in vivo - a pilot study. Epigenetics 2021; 17:695-703. [PMID: 34517792 DOI: 10.1080/15592294.2021.1975937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) is an abundant epitranscriptomic mark that regulates gene expression to execute cellular developmental programmes and environmental adaptation. Fusaric acid (FA) is a mycotoxin that contaminates agricultural foods and exerts toxicity in humans and animals; however, its epitranscriptomic effects are unclear. We investigated the effect of FA on global m6A RNA methylation and mRNA expression levels of key m6A regulatory genes in C57BL/6 mouse livers. C57BL/6 mice (n = 6/group) were orally administered 0.1 M phosphate-buffered saline (PBS) or 50 mg/kg FA. Mice were euthanized 24 h after oral administration, livers were harvested, and RNA was isolated. RNA samples were assayed for global m6A levels using an m6A RNA Methylation Quantification Kit. The mRNA expression of m6A regulators i.e. writers, erasers, and readers were measured by qRT-PCR. FA increased global m6A RNA methylation (p < 0.0001) in mouse livers. FA increased the expression of METTL3 (p = 0.0143) and METTL14 (p = 0.0281), and decreased the expression of FTO (p = 0.0036) and ALKBH5 (p = 0.0035). The expression of YTHDF2 (p = 0.0007), YTHDF3 (p = 0.0061), and YTHDC2 (p = 0.0258) were increased by FA in mouse livers. This study shows that the liver m6A epitranscriptome can be modified by FA exposure in an in vivo model and can be useful for identifying the molecular mechanisms whereby m6A RNA modifications influence the toxicological outcomes of FA exposure.
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Affiliation(s)
- Terisha Ghazi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Savania Nagiah
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban, South Africa
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Huang J, Shao Y, Gu W. Function and clinical significance of N6-methyladenosine in digestive system tumours. Exp Hematol Oncol 2021; 10:40. [PMID: 34246319 PMCID: PMC8272376 DOI: 10.1186/s40164-021-00234-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/03/2021] [Indexed: 12/21/2022] Open
Abstract
RNA modification, like DNA methylation, histone modification, non-coding RNA modification and chromatin rearrangement, plays an important role in tumours. N6-methyladenosine (m6A) is the most abundant RNA modification in cells, and it regulates RNA transcription, processing, splicing, degradation, and translation. m6A-associated proteins have been used as new biomarkers and therapeutic targets for tumour prediction and monitoring. There are three main types of proteins involved in m6A methylation: methyltransferases (METTL3, METTL14, WTAP, RBM15, ZC3H13 and KIAA1429), demethylases (FTO, ALKBH5 and ALKBH3) and RNA-binding proteins (YTHDF1-3, YTHDC1-2, IGF2BPs and HNRNPs). This article reviews the origins, characteristics and functions of m6A and its relationship with digestive system tumours based on recent research. The expression of m6A regulators can be used as an evaluation indicator of tumour growth and progression and as a prognostic indicator. In-depth research on m6A methylation in digestive system tumours may provide new directions for clinical prediction and further treatment.
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Affiliation(s)
- Junchao Huang
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
| | - Yingjie Shao
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
| | - Wendong Gu
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
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Du Y, Ma Y, Zhu Q, Liu T, Jiao Y, Yuan P, Wang X. An m6A-Related Prognostic Biomarker Associated With the Hepatocellular Carcinoma Immune Microenvironment. Front Pharmacol 2021; 12:707930. [PMID: 34248650 PMCID: PMC8263919 DOI: 10.3389/fphar.2021.707930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022] Open
Abstract
Background: N6-methyladenosine (m6A) is related to the progression of multiple cancers. However, the underlying influences of m6A-associated genes on the tumor immune microenvironment in hepatocellular carcinoma (HCC) remain poorly understood. Therefore, we sought to construct a survival prediction model using m6A-associated genes to clarify the molecular and immune characteristics of HCC. Methods: HCC case data were downloaded from The Cancer Genome Atlas (TCGA). Then, by applying consensus clustering, we identified two distinct HCC clusters. Next, four m6A-related genes were identified to construct a prognostic model, which we validated with Gene Expression Omnibus (GEO) and International Cancer Genome Consortium (ICGC) datasets. Additionally, the molecular and immune characteristics in different subgroups were analyzed. Results: m6A RNA methylation regulators were differentially expressed between HCC and normal samples and linked with immune checkpoint expression. Using consensus clustering, we divided HCC samples into two subtypes with distinct clinical features. Cluster 2 was associated with unfavorable prognosis, higher immune checkpoint expression and immune cell infiltration levels. In addition, the immune and carcinogenic signaling pathways were enriched in cluster 2. Furthermore, we constructed a risk model using four m6A-associated genes. Patients with different risk scores had distinct survival times, expression levels of immunotherapy biomarkers, TP53 mutation rates, and sensitivities to chemotherapy and targeted therapy. Similarly, the model exhibited an identical impact on overall survival in the validation cohorts. Conclusion: The constructed m6A-based signature may be promising as a biomarker for prognostics and to distinguish immune characteristics in HCC.
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Affiliation(s)
- Yingxi Du
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yarui Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qing Zhu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tongzheng Liu
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Yuan
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Jing JJ, Zhao X, Li H, Sun LP, Yuan Y. Expression profiles and prognostic roles of m6A writers, erasers and readers in gastric cancer. FUTURE ONCOLOGY (LONDON, ENGLAND) 2021; 17:2605-2620. [PMID: 33878934 DOI: 10.2217/fon-2020-0630] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aim: To explore the expression profiles of N6-methyladenosine (m6A) enzymes (writers, erasers and readers) and their associations with gastric cancer (GC) prognosis. Methods: Gene expression was analyzed using the UALCAN and Oncomine web resources. The prognostic roles of these genes in GC were analyzed using data from The Cancer Genome Atlas. Results: Thirteen m6A enzymes were found to be upregulated in GC tissues. The expression of m6A writers METTL3, RBM15 and WTAP was associated with pathological stage. The m6A eraser FTO was related to tumor stage and ALKBH5 expression was related to GC prognosis. The m6A reader YTHDF3 expression was associated with tumor stage. YTHDC2 was associated with survival of GC patients. Conclusion: Abnormal changes of key genes involved in m6A RNA methylation may have an important impact on GC development and prognosis.
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Affiliation(s)
- Jing-Jing Jing
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Xu Zhao
- Mathematical Computer Teaching & Research Office, Liaoning Vocational College of Medicine, Shenyang, 110101, China
| | - Hao Li
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Li-Ping Sun
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Yuan Yuan
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
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Fumonisin B 1 alters global m6A RNA methylation and epigenetically regulates Keap1-Nrf2 signaling in human hepatoma (HepG2) cells. Arch Toxicol 2021; 95:1367-1378. [PMID: 33496827 DOI: 10.1007/s00204-021-02986-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/14/2021] [Indexed: 12/29/2022]
Abstract
FB1 is a common contaminant of cereal grains that affects human and animal health. It has become increasingly evident that epigenetic changes are implicated in FB1 toxicity. N6-methyladenosine (m6A), the most abundant post-transcriptional RNA modification, is influenced by fluctuations in redox status. Since oxidative stress is a characteristic of FB1 exposure, we determined if there is cross-talk between oxidative stress and m6A in FB1-exposed HepG2 cells. Briefly, HepG2 cells were treated with FB1 (0, 5, 50, 100, 200 µM; 24 h) and ROS, LDH and m6A levels were quantified. qPCR was used to determine the expression of m6A modulators, Nrf2, Keap1 and miR-27b, while western blotting was used to quantify Keap1 and Nrf2 protein expression. Methylation status of Keap1 and Nrf2 promoters was assessed and RNA immunoprecipitation quantified m6A-Keap1 and m6A-Nrf2 levels. FB1 induced accumulation of intracellular ROS (p ≤ 0.001) and LDH leakage (p ≤ 0.001). Elevated m6A levels (p ≤ 0.05) were accompanied by an increase in m6A "writers" [METLL3 (p ≤ 0.01) and METLL14 (p ≤ 0.01)], and "readers" [YTHDF1 (p ≤ 0.01), YTHDF2 (p ≤ 0.01), YTHDF3 (p ≤ 0.001) and YTHDC2 (p ≤ 0.01)] and a decrease in m6A "erasers" [ALKBH5 (p ≤ 0.001) and FTO (p ≤ 0.001)]. Hypermethylation and hypomethylation occurred at Keap1 (p ≤ 0.001) and Nrf2 (p ≤ 0.001) promoters, respectively. MiR-27b was reduced (p ≤ 0.001); however, m6A-Keap1 (p ≤ 0.05) and m6A-Nrf2 (p ≤ 0.01) levels were upregulated. This resulted in the ultimate decrease in Keap1 (p ≤ 0.001) and increase in Nrf2 (p ≤ 0.001) expression. Our findings reveal that m6A RNA methylation can be modified by exposure to FB1, and a cross-talk between m6A and redox regulators does occur.
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