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Guan J, Chen X, Li Z, Deng S, Wumaier A, Ma Y, Xie L, Huang S, Zhu Y, Zhuo Y. Role of N6-methyladenosine-related lncRnas in pseudoexfoliation glaucoma. Epigenetics 2024; 19:2348840. [PMID: 38716769 PMCID: PMC11086004 DOI: 10.1080/15592294.2024.2348840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
To explore the role of lncRNA m6A methylation modification in aqueous humour (AH) of patients with pseudoexfoliation glaucoma (PXG). Patients with open-angle PXG under surgery from June 2021 to December 2021 were selected. Age- and gender-matched patients with age-related cataract (ARC) were chosen as control. Patients underwent detailed ophthalmic examinations. 0.05-0.1 ml AH were extracted during surgery for MeRIP-Seq and RNA-Seq. Joint analysis was used to screen lncRNAs with differential m6A methylation modification and expression. Online software tools were used to draw lncRNA-miRNA-mRNA network (ceRNA). Expression of lncRNAs and mRNAs was confirmed using quantitative real-time PCR. A total of 4151 lncRNAs and 4386 associated m6A methylation modified peaks were identified in the PXG group. Similarly, 2490 lncRNAs and 2595 associated m6A methylation modified peaks were detected in the control. Compared to the ARC group, the PXG group had 234 hypermethylated and 402 hypomethylated m6A peaks, with statistically significant differences (| Fold Change (FC) |≥2, p < 0.05). Bioinformatic analysis revealed that these differentially methylated lncRNA enriched in extracellular matrix formation, tight adhesion, TGF- β signalling pathway, AMPK signalling pathway, and MAPK signalling pathway. Joint analysis identified 10 lncRNAs with differential m6A methylation and expression simultaneously. Among them, the expression of ENST000000485383 and ROCK1 were confirmed downregulated in the PXG group by RT-qPCR. m6A methylation modification may affect the expression of lncRNA and participate in the pathogenesis of PXG through the ceRNA network. ENST000000485383-hsa miR592-ROCK1 May be a potential target pathway for further investigation in PXG m6A methylation.
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Affiliation(s)
- Jieying Guan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaohong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Zhidong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Shuifeng Deng
- The Department of Ophthalmology, Huizhou Hospital Affiliated to Guangzhou Medical University (Huizhou Third People’s Hospital), Huizhou, China
| | - Aizezi Wumaier
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Yuncheng Ma
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Lingling Xie
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Shengsong Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
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Huang T, Zhang C, Ren J, Shuai Q, Li X, Li X, Xie J, Xu J. FTO-mediated m 6A demethylation of ULK1 mRNA promotes autophagy and activation of hepatic stellate cells in liver fibrosis. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39175431 DOI: 10.3724/abbs.2024098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024] Open
Abstract
The activation of hepatic stellate cells (HSCs) is central to the occurrence and development of liver fibrosis. Our previous studies showed that autophagy promotes HSC activation and ultimately accelerates liver fibrosis. Unc-51-like autophagy activating kinase 1 (ULK1) is an autophagic initiator in mammals, and N 6-methyladenosine (m 6A) modification is closely related to autophagy. In this study, we find that the m 6A demethylase fat mass and obesity-associated protein (FTO), which is the m 6A methylase with the most significant difference in expression, is upregulated during HSC activation and bile duct ligation (BDL)-induced hepatic fibrosis. Importantly, we identify that FTO overexpression aggravates HSC activation and hepatic fibrosis via autophagy. Mechanistically, compared with other autophagy-related genes, ULK1 is a target of FTO because FTO mainly mediates the m 6A demethylation of ULK1 and upregulates its expression, thereby enhancing autophagy and the activation of HSCs. Notably, the m 6A reader YTH domain-containing protein 2 (YTHDC2) decreases ULK1 mRNA level by recognizing the m 6A binding site and ultimately inhibiting autophagy and HSC activation. Taken together, our findings highlight m6A-dependent ULK1 as an essential regulator of HSC autophagy and reveal that ULK1 is a novel potential therapeutic target for hepatic fibrosis treatment.
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Affiliation(s)
- Tingjuan Huang
- Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan 030001, China
| | - Chunhong Zhang
- Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan 030001, China
| | - Junjie Ren
- Department of Gastroenterology and Hepatology, the First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Qizhi Shuai
- Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan 030001, China
| | - Xiaonan Li
- Department of Cancer Radiotherapy Department, Shanxi Provincial People's Hospital, Taiyuan 030001, China
| | - Xuewei Li
- Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan 030001, China
| | - Jun Xie
- Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan 030001, China
| | - Jun Xu
- Department of Hepatopancreatobiliary Surgery, the First Hospital of Shanxi Medical University, Taiyuan 030001, China
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Ogbe SE, Wang J, Shi Y, Wang Y, Xu Z, Abankwa JK, Dal Pozzo L, Zhao S, Zhou H, Peng Y, Chu X, Wang X, Bian Y. Insights into the epitranscriptomic role of N 6-methyladenosine on aging skeletal muscle. Biomed Pharmacother 2024; 177:117041. [PMID: 38964182 DOI: 10.1016/j.biopha.2024.117041] [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: 04/21/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
The modification of RNA through the N6-methyladenosine (m6A) has emerged as a growing area of research due to its regulatory role in gene expression and various biological processes regulating the expression of genes. m6A RNA methylation is a post-transcriptional modification that is dynamic and reversible and found in mRNA, tRNA, rRNA, and other non-coding RNA of most eukaryotic cells. It is executed by special proteins known as "writers," which initiate methylation; "erasers," which remove methylation; and "readers," which recognize it and regulate the expression of the gene. Modification by m6A regulates gene expression by affecting the splicing, translation, stability, and localization of mRNA. Aging causes molecular and cellular damage, which forms the basis of most age-related diseases. The decline in skeletal muscle mass and functionality because of aging leads to metabolic disorders and morbidities. The inability of aged muscles to regenerate and repair after injury poses a great challenge to the geriatric populace. This review seeks to explore the m6A epigenetic regulation in the myogenesis and regeneration processes in skeletal muscle as well as the progress made on the m6A epigenetic regulation of aging skeletal muscles.
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Affiliation(s)
- Susan Enechojo Ogbe
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Department of Physiology, Federal University, Wukari, Taraba 670101, Nigeria
| | - JiDa Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - YueXuan Shi
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ying Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhe Xu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Joseph Kofi Abankwa
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lisa Dal Pozzo
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - ShuWu Zhao
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - HuiFang Zhou
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - YanFei Peng
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - XiaoQian Chu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - XiangLing Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - YuHong Bian
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Zhao L, Wei X, Chen F, Yuan L, Chen B, Li R. N6-methyladenosine RNA methyltransferase CpMTA1 mediates CpAphA mRNA stability through a YTHDF1-dependent m6A modification in the chestnut blight fungus. PLoS Pathog 2024; 20:e1012476. [PMID: 39159278 PMCID: PMC11361730 DOI: 10.1371/journal.ppat.1012476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 08/29/2024] [Accepted: 08/04/2024] [Indexed: 08/21/2024] Open
Abstract
In eukaryotic cells, N6-methyladenosine (m6A) is the most prevalent RNA epigenetic modification that plays crucial roles in multiple biological processes. Nevertheless, the functions and regulatory mechanisms of m6A in phytopathogenic fungi are poorly understood. Here, we showed that CpMTA1, an m6A methyltransferase in Cryphonectria parasitica, plays a crucial role in fungal phenotypic traits, virulence, and stress tolerance. Furthermore, the acid phosphatase gene CpAphA was implicated to be a target of CpMTA1 by integrated analysis of m6A-seq and RNA-seq, as in vivo RIP assay data confirmed that CpMTA1 directly interacts with CpAphA mRNA. Deletion of CpMTA1 drastically lowered the m6A level of CpAphA and reduced its mRNA expression. Moreover, we found that an m6A reader protein CpYTHDF1 recognizes CpAphA mRNA and increases its stability. Typically, the levels of CpAphA mRNA and protein exhibited a positive correlation with CpMTA1 and CpYTHDF1. Importantly, site-specific mutagenesis demonstrated that the m6A sites, A1306 and A1341, of CpAphA mRNA are important for fungal phenotypic traits and virulence in C. parasitica. Together, our findings demonstrate the essential role of the m6A methyltransferase CpMTA1 in C. parasitica, thereby advancing our understanding of fungal gene regulation through m6A modification.
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Affiliation(s)
- Lijiu Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xiangyu Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Fengyue Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Luying Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
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5
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Gunage R, Zon LI. Role of RNA modifications in blood development and regeneration. Exp Hematol 2024; 138:104279. [PMID: 39009277 DOI: 10.1016/j.exphem.2024.104279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024]
Abstract
Blood development and regeneration require rapid turnover of cells, and ribonucleic acid (RNA) modifications play a key role in it via regulating stemness and cell fate regulation. RNA modifications affect gene activity via posttranscriptional and translation-mediated mechanisms. Diverse molecular players involved in RNA-modification processes are abundantly expressed by hematopoietic stem cells and lineages. Close to 150 RNA chemical modifications have been reported, but only N6-methyl adenosine (m6A), inosine (I), pseudouridine (Ψ), and m1A-a handful-have been studied in-cell fate regulation. The role of RNA modification in blood diseases and disorders is an emerging field and offers potential for therapeutic interventions. Knowledge of RNA-modification and enzymatic activities could be used to design therapies in the future. Here, we summarized the recent advances in RNA modification and the epitranscriptome field and discussed their regulation of blood development and regeneration.
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Affiliation(s)
- Rajesh Gunage
- Stem Cell Program and Division of Hematology/Oncology, Department of Medicine, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Department of Medicine, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA.
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6
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Liu S, Cao Y, Zhang Y. Regulatory roles of RNA methylation in vascular lesions in ocular and cardiopulmonary diseases. Crit Rev Clin Lab Sci 2024:1-15. [PMID: 38957015 DOI: 10.1080/10408363.2024.2370267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
RNA methylation is a widespread regulatory mechanism that controls gene expression in physiological processes. In recent years, the mechanisms and functions of RNA methylation under diseased conditions have been increasingly unveiled by RNA sequencing technologies with large scale and high resolution. In this review, the fundamental concept of RNA methylation is introduced, and the common types of transcript methylation and their machineries are described. Then, the regulatory roles of RNA methylation, particularly N6-methyladenosine and 5-methylcytosine, in the vascular lesions of ocular and cardiopulmonary diseases are discussed and compared. The ocular diseases include corneal neovascularization, retinopathy of prematurity, diabetic retinopathy, and pathologic myopia; whereas the cardiopulmonary ailments involve atherosclerosis and pulmonary hypertension. This review hopes to shed light on the common regulatory mechanisms underlying the vascular lesions in these ocular and cardiopulmonary diseases, which may be conducive to developing therapeutic strategies in clinical practice.
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Affiliation(s)
- Siyi Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Yunshan Cao
- Department of Cardiology, Gansu Provincial Hospital, Lanzhou, China
| | - Yan Zhang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
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Fu M, Chen Y, Shi X. ZC3H13 Accelerates Keloid Formation by Mediating N 6-methyladenosine Modification of HIPK2. Biochem Genet 2024; 62:1857-1871. [PMID: 37752292 DOI: 10.1007/s10528-023-10514-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
Keloids are fibroproliferative skin disorders caused by the improper healing of wounded skin. A growing body of evidence suggests the involvement of N6-Methyladenosine (m6A) modification in various bioprocesses; however, its role in keloid formation has not yet been investigated. The aim of this study was to determine the effect of the m6A regulator zinc finger CCCH domain containing protein 13 (ZC3H13) on the pathogenesis of keloid formation. ZC3H13 and homeodomain-interacting protein kinase 2 (HIPK2) expression was evaluated in healthy skin and keloid tissues, as well as in human dermal fibroblasts and human keloid fibroblasts (HKF), using qRT-PCR and western blotting. The effects of ZC3H13 overexpression and knockdown on the cell function of HKFs were assessed using CCK8, transwell, and flow cytometry. Furthermore, the influence of ZC3H13 on HIPK2 m6A modification was assessed using MeRIP-qPCR and mRNA stability assays. Both ZC3H13 expression and m6A RNA methylation were upregulated in keloid tissues and HKFs. Silencing of ZC3H13 inhibited proliferation and migration, while enhancing apoptosis in HKFs, whereas overexpression had the opposite effect. Furthermore, HIPK2 levels were high in keloid tissues and HKFs, and a positive correlation was observed between ZC3H13 and HIPK2. In HKFs, ZC3H13 overexpression elevated the m6A levels of HIPK2 mRNA and reduced the rate of HIPK2 mRNA degradation. Mechanically, ZC3H13-induced m6A modifications significantly improved HIPK2 mRNA stability. Collectively, ZC3H13 accelerated keloid formation by mediating the m6A modification of HIPK2 mRNA and maintaining its stability.
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Affiliation(s)
- Manni Fu
- Department of dermatology, Huangshi Central Hospital, No.293, Hospital Street, Xisai District, Huangshi, 435000, Hubei, China
| | - Yongjun Chen
- Department of dermatology, Huangshi Central Hospital, No.293, Hospital Street, Xisai District, Huangshi, 435000, Hubei, China
| | - Xian Shi
- Department of dermatology, Huangshi Central Hospital, No.293, Hospital Street, Xisai District, Huangshi, 435000, Hubei, China.
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Zhu Y, Zhang Y, Jiang Y, Cai H, Liang J, Li H, Wang C, Hou J. Retinoic Acid Upregulates METTL14 Expression and the m 6A Modification Level to Inhibit the Proliferation of Embryonic Palate Mesenchymal Cells in Cleft Palate Mice. Int J Mol Sci 2024; 25:4538. [PMID: 38674123 PMCID: PMC11050043 DOI: 10.3390/ijms25084538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Cleft palate only (CPO) is one of the most common craniofacial birth defects. Environmental factors can induce cleft palate by affecting epigenetic modifications such as DNA methylation, histone acetylation, and non-coding RNA. However, there are few reports focusing on the RNA modifications. In this study, all-trans retinoic acid (atRA) was used to simulate environmental factors to induce a C57BL/6J fetal mouse cleft palate model. Techniques such as dot blotting and immunofluorescence were used to find the changes in m6A modification when cleft palate occurs. RNA-seq and KEGG analysis were used to screen for significantly differentially expressed pathways downstream. Primary mouse embryonic palate mesenchymal (MEPM) cells were successfully isolated and used for in vitro experimental verification. We found that an increased m6A methylation level was correlated with suppressed cell proliferation in the palatine process mesenchyme of cleft palate mice. This change is due to the abnormally high expression of m6A methyltransferase METTL14. When using siRNAs and the m6A methyltransferase complex inhibitor SAH to interfere with the expression or function of METTL14, the teratogenic effect of atRA on primary cells was partially alleviated. In conclusion, METTL14 regulates palatal mesenchymal cell proliferation and cycle-related protein expression relies on m6A methylation modification, affecting the occurrence of cleft palate.
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Affiliation(s)
- Yue Zhu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; (Y.Z.); (Y.Z.); (Y.J.); (H.C.); (J.L.); (H.L.)
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yadong Zhang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; (Y.Z.); (Y.Z.); (Y.J.); (H.C.); (J.L.); (H.L.)
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yaoqi Jiang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; (Y.Z.); (Y.Z.); (Y.J.); (H.C.); (J.L.); (H.L.)
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Hongshi Cai
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; (Y.Z.); (Y.Z.); (Y.J.); (H.C.); (J.L.); (H.L.)
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Jianfeng Liang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; (Y.Z.); (Y.Z.); (Y.J.); (H.C.); (J.L.); (H.L.)
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Hongyu Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; (Y.Z.); (Y.Z.); (Y.J.); (H.C.); (J.L.); (H.L.)
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Cheng Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; (Y.Z.); (Y.Z.); (Y.J.); (H.C.); (J.L.); (H.L.)
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Jinsong Hou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; (Y.Z.); (Y.Z.); (Y.J.); (H.C.); (J.L.); (H.L.)
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
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9
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Chen S, Duan X, He Y, Chen W. METTL3 promotes osteogenic differentiation of human umbilical cord mesenchymal stem cells by up-regulating m6A modification of circCTTN. Biosci Rep 2024; 44:BSR20231186. [PMID: 38358895 PMCID: PMC10932744 DOI: 10.1042/bsr20231186] [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: 07/28/2023] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Human umbilical cord mesenchymal stem cells (hUCMSCs) are promising seed cells in bone tissue engineering. circRNA and N6-methyladenosine (m6A) RNA methylation play important roles in osteogenic differentiation. Here, we investigated the potential relevance of a critical circRNA, hsa_circ_0003376 (circCTTN), and methyltransferase-like 3 (METTL3) in osteogenic differentiation of hUCMSCs. METHODS Expression of circCTTN after hUCMSC osteogenic induction was detected by qRT-PCR. Three databases (RMBase v2.0, BERMP, and SRAMP) were used to predict m6A sites of circCTTN. RNA was enriched by methylated RNA immunoprecipitation (MeRIP), followed by quantitative real-time polymerase chain reaction to detect m6A level of circCTTN after METTL3 overexpression and osteogenic induction. RNA pull-down, Western blotting, and protein mass spectrometry were performed to investigate the potential mechanisms by which METTL3 promoted m6A modification of circCTTN. Bioinformatic analyses based on database (STRING) search and co-immunoprecipitation were used to analyze the proteins that interacted with METTL3. RESULTS Overexpression of METTL3 promoted osteogenic differentiation of hUCMSCs and increased m6A level of circCTTN. Two potential m6A modification sites of circCTTN were predicted. No direct interaction between METTL3 and circCTTN was observed. Thirty-one proteins were pulled down by probes specific for circCTTN, including NOP2, and two m6A reading proteins, EIF3A and SND1. Bioinformatics analysis and co-immunoprecipitation showed that METTL3 interacted with EIF3A indirectly through NOP2. CONCLUSIONS METTL3 promotes the osteogenic differentiation of hUCMSCs by increasing the m6A level of circCTTN. However, METTL3 does not bind directly to circCTTN. METTL3 interacts with circCTTN indirectly through NOP2 and EIF3A.
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Affiliation(s)
- Shujiang Chen
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China school of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoqiong Duan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Yanjin He
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China school of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Wenchuan Chen
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China school of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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10
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Jin J, Liu M, Yu F, Sun MA, Wu Z. METTL3 enhances E. coli F18 resistance by targeting IKBKG/NF-κB signaling via an m 6A-YTHDF1-dependent manner in IPEC-J2 cells. Int J Biol Macromol 2024; 262:130101. [PMID: 38346619 DOI: 10.1016/j.ijbiomac.2024.130101] [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: 11/29/2023] [Revised: 01/24/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Post-weaning diarrhea caused by enterotoxigenic E. coli F18 introduces enormous losses to the porcine industry. N6-methyladenosine (m6A) is a ubiquitous epitranscriptomic biomarker that modulates host cell resistance to pathogen infection, however, its significance in E. coli F18-treated IPEC-J2 cells remains unexplored. Herein, we revealed that m6A and associated modulators strongly controlled E. coli F18 susceptibility. The data indicated an enhancement of METTL3 contents in E. coli F18-treated IPEC-J2 cells. METTL3 is known to be a major modulator of E. coli F18 adhesion within IPEC-J2 cells. As expected, METTL3 deficiency was observed to reduce m6A content at the IKBKG 5'-UTR, leading to critical suppression of YTHDF1-dependent IKBKG translation. Therefore, the activation of the NF-κB axis was observed, which enhanced IPEC-J2 resistance to E. coli F18 infection. Taken together, these findings uncover a potential mechanism underlying the m6A-mediated control of E. coli F18 susceptibility. This information may contribute to the establishment of new approaches for combating bacteria-induced diarrhea in piglets.
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Affiliation(s)
- Jian Jin
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Mengyuan Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Fuying Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ming-An Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Zhengchang Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China.
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11
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Chen H, Gong S, Zhang H, Chen Y, Liu Y, Hao J, Liu H, Li X. From the regulatory mechanism of TFEB to its therapeutic implications. Cell Death Discov 2024; 10:84. [PMID: 38365838 PMCID: PMC10873368 DOI: 10.1038/s41420-024-01850-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
Transcription factor EB (TFEB), known as a major transcriptional regulator of the autophagy-lysosomal pathway, regulates target gene expression by binding to coordinated lysosomal expression and regulation (CLEAR) elements. TFEB are regulated by multiple links, such as transcriptional regulation, post-transcriptional regulation, translational-level regulation, post-translational modification (PTM), and nuclear competitive regulation. Targeted regulation of TFEB has been victoriously used as a treatment strategy in several disease models such as ischemic injury, lysosomal storage disorders (LSDs), cancer, metabolic disorders, neurodegenerative diseases, and inflammation. In this review, we aimed to elucidate the regulatory mechanism of TFEB and its applications in several disease models by targeting the regulation of TFEB as a treatment strategy.
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Affiliation(s)
- Huixia Chen
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Siqiao Gong
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Hongyong Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhan-jiang Central Hospital, Zhanjiang, 524001, China
| | - Yongming Chen
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Yonghan Liu
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Junfeng Hao
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China.
| | - Huafeng Liu
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China.
| | - Xiaoyu Li
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China.
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12
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Yang C, Wu D, Lin H, Ma D, Fu W, Yao Y, Pan X, Wang S, Zhuang Z. Role of RNA Modifications, Especially m6A, in Aflatoxin Biosynthesis of Aspergillus flavus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:726-741. [PMID: 38112282 DOI: 10.1021/acs.jafc.3c05926] [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: 12/21/2023]
Abstract
RNA modifications play key roles in eukaryotes, but the functions in Aspergillus flavus are still unknown. Temperature has been reported previously to be a critical environmental factor that regulates the aflatoxin production of A. flavus, but much remains to be learned about the molecular networks. Here, we demonstrated that 12 kinds of RNA modifications in A. flavus were significantly changed under 29 °C compared to 37 °C incubation; among them, m6A was further verified by a colorimetric method. Then, the transcriptome-wide m6A methylome and m6A-altered genes were comprehensively illuminated through methylated RNA immunoprecipitation sequencing and RNA sequencing, from which 22 differentially methylated and expressed transcripts under 29 °C were screened out. It is especially notable that AFCA_009549, an aflatoxin biosynthetic pathway gene (aflQ), and the m6A methylation of its 332nd adenine in the mRNA significantly affect aflatoxin biosynthesis in A. flavus both on media and crop kernels. The content of sterigmatocystin in both ΔaflQ and aflQA332C strains was significantly higher than that in the WT strain. Together, these findings reveal that RNA modifications are associated with secondary metabolite biosynthesis of A. flavus.
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Affiliation(s)
- Chi Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Dandan Wu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Lin
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Ma
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wangzhuo Fu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanfang Yao
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaohua Pan
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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13
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Lin L, Zhao Y, Zheng Q, Zhang J, Li H, Wu W. Epigenetic targeting of autophagy for cancer: DNA and RNA methylation. Front Oncol 2023; 13:1290330. [PMID: 38148841 PMCID: PMC10749975 DOI: 10.3389/fonc.2023.1290330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/28/2023] [Indexed: 12/28/2023] Open
Abstract
Autophagy, a crucial cellular mechanism responsible for degradation and recycling of intracellular components, is modulated by an intricate network of molecular signals. Its paradoxical involvement in oncogenesis, acting as both a tumor suppressor and promoter, has been underscored in recent studies. Central to this regulatory network are the epigenetic modifications of DNA and RNA methylation, notably the presence of N6-methyldeoxyadenosine (6mA) in genomic DNA and N6-methyladenosine (m6A) in eukaryotic mRNA. The 6mA modification in genomic DNA adds an extra dimension of epigenetic regulation, potentially impacting the transcriptional dynamics of genes linked to autophagy and, especially, cancer. Conversely, m6A modification, governed by methyltransferases and demethylases, influences mRNA stability, processing, and translation, affecting genes central to autophagic pathways. As we delve deeper into the complexities of autophagy regulation, the importance of these methylation modifications grows more evident. The interplay of 6mA, m6A, and autophagy points to a layered regulatory mechanism, illuminating cellular reactions to a range of conditions. This review delves into the nexus between DNA 6mA and RNA m6A methylation and their influence on autophagy in cancer contexts. By closely examining these epigenetic markers, we underscore their promise as therapeutic avenues, suggesting novel approaches for cancer intervention through autophagy modulation.
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Affiliation(s)
- Luobin Lin
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Yuntao Zhao
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Qinzhou Zheng
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Jiayang Zhang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Huaqin Li
- School of Health Sciences, Guangzhou Xinhua University, Guangzhou, Guangdong, China
| | - Wenmei Wu
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
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14
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Li C, Wu X, Yang Y, Shi J, Wang S, Li J, Tian Y, Liu C, Han H, Xu S, Han X, Ma Y, Zheng L, Li J. METTL14 and FTO mediated m 6A modification regulate PCV2 replication by affecting miR-30a-5p maturity. Virulence 2023; 14:2232910. [PMID: 37418592 PMCID: PMC10332184 DOI: 10.1080/21505594.2023.2232910] [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: 02/15/2023] [Revised: 05/16/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023] Open
Abstract
The epigenetic modification of the N6-methyladenosine (m6A) methylation plays an important role in virus infection and replication. However, its role in Porcine circovirus type 2 (PCV2) replication has not been well studied. Here, we demonstrated that m6A modifications are increased in PK-15 cells after PCV2 infection. In particular, PCV2 infection could increase the expression of methyltransferase METTL14 and demethylase FTO. Moreover, interfering with METTL14 accumulation reduced the m6A methylation level and virus reproduction, whereas depleting the FTO demethylase enhanced the m6A methylation level and stimulated virus reproduction. Besides, we showed that METTL14 and FTO regulate PCV2 replication by affecting the process of miRNA maturity, especially the miRNA-30a-5p. Taken together, our results demonstrated that the m6A modification positively affects PCV2 replication and the role of m6A modification in the replication mechanism of the PCV2 virus provides a new idea for the prevention and control of the PCV2.
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Affiliation(s)
- Chen Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Xiaoyan Wu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Ying Yang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jianli Shi
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Shuo Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, China
| | - Jiaxin Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yao Tian
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Chang Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Hong Han
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Shaojian Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Xianjie Han
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yingru Ma
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Limei Zheng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jun Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, China
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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15
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Guo S, Pei J, Wang X, Cao M, Xiong L, Kang Y, Ding Z, La Y, Chu M, Bao P, Guo X. Transcriptome Studies Reveal the N6-Methyladenosine Differences in Testis of Yaks at Juvenile and Sexual Maturity Stages. Animals (Basel) 2023; 13:2815. [PMID: 37760215 PMCID: PMC10525320 DOI: 10.3390/ani13182815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Studying the mechanism of spermatogenesis is key to exploring the reproductive characteristics of male yaks. Although N6-methyladenosine (m6A) RNA modification has been reported to regulate spermatogenesis and reproductive function in mammals, the molecular mechanism of m6A in yak testis development and spermatogenesis remains largely unknown. Therefore, we collected testicular tissue from juvenile and adult yaks and found that the m6A level significantly increased after sexual maturity in yaks. In MeRIP-seq, 1702 hypermethylated peaks and 724 hypomethylated peaks were identified. The hypermethylated differentially methylated RNAs (DMRs) (CIB2, AK1, FOXJ2, PKDREJ, SLC9A3, and TOPAZ1) mainly regulated spermatogenesis. Functional enrichment analysis showed that DMRs were significantly enriched in the adherens junction, gap junction, and Wnt, PI3K, and mTOR signaling pathways, regulating cell development, spermatogenesis, and testicular endocrine function. The functional analysis of differentially expressed genes showed that they were involved in the biological processes of mitosis, meiosis, and flagellated sperm motility during the sexual maturity of yak testis. We also screened the key regulatory factors of testis development and spermatogenesis by combined analysis, which included BRCA1, CREBBP, STAT3, and SMAD4. This study indexed the m6A characteristics of yak testicles at different developmental stages, providing basic data for further research of m6A modification regulating yak testicular development.
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Affiliation(s)
- Shaoke Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xingdong Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Mengli Cao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yandong Kang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ziqiang Ding
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yongfu La
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.G.); (J.P.); (X.W.); (M.C.); (L.X.); (Y.K.); (Z.D.); (Y.L.); (M.C.); (P.B.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
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Guan J, Li Z, Wumaier A, Ma Y, Xie L, Wu H, Chen R, Zhu Y, Zhuo Y. Critical role of transcriptome-wide m6A methylation in the aqueous humor of patients with pseudoexfoliation glaucoma. Exp Eye Res 2023; 231:109473. [PMID: 37061115 DOI: 10.1016/j.exer.2023.109473] [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: 01/22/2023] [Revised: 03/13/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023]
Abstract
N6-methyladenosine (m6A) modification is one of the most common types of methylation modifications in eukaryotic mRNA. However, its role in the pathogenesis of pseudoexfoliation glaucoma (PXG) has not yet been reported. To enhance understanding in this regard, we assessed the m6A methylome in the aqueous humor of patients with PXG. MeRIP-Seq and RNA-Seq analyses were performed to compare the m6A methylomes and gene expression profiles of the aqueous humor of patients with PXG with those of patients with age-related cataract (ARC). Colorimetric m6A quantification was performed to detect global m6A levels. Quantitative reverse transcription PCR confirmed the expression of m6A-related enzymes and mRNAs in both groups. Results showed significantly higher aqueous humor m6A levels in the PXG group than in the ARC group. Five m6A-related enzymes, including METTL3, YTHDC2, HNRNPA2B1, HNRNPC, and LRPPRC, were significantly up-regulated in PXG specimens. We also observed 9728 m6A-modified peaks related to 6126 gene transcripts in the PXG group, with more than 250 genes containing one m6A peak (hypomethylated or hypermethylated). The distribution of the m6A peaks was enriched in coding sequences and 3'-untranslated regions for both groups. GGAC motif structures were also significantly enriched. Bioinformatics analysis further revealed that m6A plays a critical role in extracellular matrix formation and histone deacetylation. Additionally, MMP14, ADAMTSL1, FN1, and HDAC1 showed significant changes in m6A methylation and mRNA expression in the PXG group. Therefore, m6A methylation may regulate extracellular matrix composition in PXG and METTL3 may be a pivotal regulator of this process. In the future, it would be necessary to investigate MMP14, ADAMTSL1, FN1, and HDAC1, which are potential target genes.
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Affiliation(s)
- Jieying Guan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China; Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China; The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, 844000, China; The First Department of Ophthalmology, The First People's Hospital of Kashi Prefecture, Kashi, Xinjiang, 844000, China.
| | - Zhidong 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; Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Aizezi Wumaier
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, 844000, China; The First Department of Ophthalmology, The First People's Hospital of Kashi Prefecture, Kashi, Xinjiang, 844000, China.
| | - Yuncheng Ma
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, 844000, China; The First Department of Ophthalmology, The First People's Hospital of Kashi Prefecture, Kashi, Xinjiang, 844000, China.
| | - Lingling Xie
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, 844000, China; The First Department of Ophthalmology, The First People's Hospital of Kashi Prefecture, Kashi, Xinjiang, 844000, China.
| | - Heping Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China; Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Rongxin Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China; Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China; Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China; Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
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17
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Zhen J, Pan J, Zhou X, Yu Z, Jiang Y, Gong Y, Ding Y, Liu Y, Guo L. FARSB serves as a novel hypomethylated and immune cell infiltration related prognostic biomarker in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:2937-2969. [PMID: 37074800 DOI: 10.18632/aging.204619] [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: 12/28/2022] [Accepted: 03/09/2023] [Indexed: 04/20/2023]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is a prevalent tumor with high morbidity, and an unfavourable prognosis. FARSB is an aminoacyl tRNA synthase, and plays a key role in protein synthesis in cells. Furthermore, previous reports have indicated that FARSB is overexpressed in gastric tumor tissues and is associated with a poor prognosis and tumorigenesis. However, the function of FARSB in HCC has not been studied. RESULTS The results showed that FARSB mRNA and protein levels were upregulated in HCC and were closely related to many clinicopathological characteristics. Besides, according to multivariate Cox analysis, high FARSB expression was linked with a shorter survival time in HCC and may be an independent prognostic factor. In addition, the FARSB promoter methylation level was negatively associated with the expression of FARSB. Furthermore, enrichment analysis showed that FARSB was related to the cell cycle. And TIMER analysis revealed that the FARSB expression was closely linked to tumor purity and immune cell infiltration. The TCGA and ICGC data analysis suggested that FARSB expression is greatly related to m6A modifier related genes. Potential FARSB-related ceRNA regulatory networks were also constructed. What's more, based on the FARSB-protein interaction network, molecular docking models of FARSB and RPLP1 were constructed. Finally, drug susceptibility testing revealed that FARSB was susceptible to 38 different drugs or small molecules. CONCLUSIONS FARSB can serve as a prognostic biomarker for HCC and provide clues about immune infiltration, and m6A modification.
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Affiliation(s)
- Jing Zhen
- Second Affiliated Hospital of Nanchang University, Nanchang, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yongqi Ding
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yue Liu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Liangyun Guo
- Department of Ultrasonography, Second Affiliated Hospital of Nanchang University, Nanchang, China
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Transcriptome-Wide Study Revealed That N6-Methyladenosine Participates in Regulation Meat Production in Goats. Foods 2023; 12:foods12061159. [PMID: 36981086 PMCID: PMC10048064 DOI: 10.3390/foods12061159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
In mammals, skeletal muscle development is a complex biological process regulated by many factors. N6-methyladenosine (m6A) RNA modification plays an important role in many biological processes. However, the regulation of m6A on skeletal muscle growth and development in adult goats remains unclear. In this study, Duan goats (DA) and Nubia goats (NBY), both female and 12 months old, were selected as the research objects, and m6A-Seq and RNA-Seq were mainly used to detect the difference of m6A modification and gene expression during the development of the longissimus dorsi (LD) muscle in the two breeds. The results showed that compared with DA, the meat production performance of NBY was better than that of DA, and the modification level of m6A was higher than that of DA in LD. The m6A-Seq of LD indicated m6A peaks were mainly enriched in the coding sequence (CDS) and stop codon. A total of 161 differentially methylated genes (DMGs) and 1294 differentially expressed genes (DEGs) were identified in two breeds. GO and KEGG analysis showed that DMGs were closely related to cellular metabolism, and most of DMGs were enriched in pathways related to energy metabolism, muscle growth and development, mainly MAPK signaling pathway, Wnt signaling pathway and CGMP-PKG signaling pathway. The DEGs were significantly enriched in actin binding, calcium ion binding, angiogenesis, and other biological processes, and most of them were enriched in PI3K-Akt and CGMP-PKG signaling pathways. Combined analysis of m6A-Seq and RNA-Seq data revealed a negative correlation between differentially methylated m6A levels and mRNA abundance, and mRNA expression of the gene with m6A peak near 3′UTR will decrease. In addition, 11 DMGs regulating cell differentiation, muscle growth and development were identified. This study displayed the m6A profiles and distribution patterns in the goat transcriptome, determined the potential role of m6A modification in muscle growth and provided a new reference for the further study of goat skeletal muscle development.
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Hu Y, Chen J, Wang Y, Sun J, Huang P, Feng J, Liu T, Sun X. Fat mass and obesity-associated protein alleviates Aβ 1-40 induced retinal pigment epithelial cells degeneration via PKA/CREB signaling pathway. Cell Biol Int 2023; 47:584-597. [PMID: 36378581 DOI: 10.1002/cbin.11959] [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: 05/07/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022]
Abstract
Amyloid-β (Aβ) is thought to be a critical pathologic factor of retinal pigment epithelium (RPE) degeneration in age-related macular degeneration (AMD). Aβ induces inflammatory responses in RPE cells and recent studies demonstrate the N6-methyladenosine (m6A) regulatory role in RPE cell inflammation. m6A is a reversible epigenetic posttranslational modification, but its relationship with Aβ-induced RPE degeneration is yet to be thoroughly investigated. The present study explored the role and mechanism of m6A in Aβ-induced RPE degeneration model. This model was induced via intravitreally injecting oligomeric Aβ and the morphology of its retina was analyzed. One of m6A demethylases, the fat mass and obesity-associated (FTO) gene expression, was assessed. An m6A-messenger RNA (mRNA) epitranscriptomic microarray was employed for further bioinformatic analyses. It was confirmed that Aβ induced FTO upregulation within the RPE. Hypopigmentation alterations and structural disorganization were observed in Aβ-treated eyes, and inhibition of FTO exacerbated retinal degeneration and RPE impairment. Moreover, the m6A-mRNA epitranscriptomic microarray suggested that protein kinase A (PKA) was a target of FTO, and the PKA/cyclic AMP-responsive element binding (CREB) signaling pathway was involved in Aβ-induced RPE degeneration. m6A-RNA binding protein immunoprecipitation confirmed that FTO demethylated PKA within the RPE cells of Aβ-treated eyes. Altered expression of PKA and its downstream targets (CREB and brain-derived neurotrophic factor) was confirmed by quantitative reverse-transcription polymerase chain reaction and Western blot analyses. Hence, this study's findings shed light on FTO-mediated m6A modification in Aβ-induced RPE degeneration and indicate potential therapeutic targets for AMD.
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Affiliation(s)
- Yifan Hu
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), National Clinical Research Center for Ophthalmic Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.,Department of Ophthalmology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, and Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Jieqiong Chen
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), National Clinical Research Center for Ophthalmic Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yuwei Wang
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), National Clinical Research Center for Ophthalmic Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.,Department of Ophthalmology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junran Sun
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), National Clinical Research Center for Ophthalmic Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Peirong Huang
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), National Clinical Research Center for Ophthalmic Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Jingyang Feng
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), National Clinical Research Center for Ophthalmic Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Te Liu
- Central Laboratory, Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaodong Sun
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), National Clinical Research Center for Ophthalmic Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.,Department of Ophthalmology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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20
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Xu T, Zhang W, Chai L, Liu C, Zhang S, Xu T. Methyltransferase-like 3-induced N6-methyladenosine upregulation promotes oral squamous cell carcinoma by through p38. Oral Dis 2023; 29:639-648. [PMID: 34479400 DOI: 10.1111/odi.14016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/07/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC), a main type of squamous cell cancer, is associated with considerable morbidity and mortality. Recent reports suggested methyltransferase-like 3 (METTL3)-mediated N6-methyladenosine (m6A) modification to be an essential regulator in the fate determination of stem cells. However, the functional significance of METTL3 in OSCC remains largely unknown. METHODS METTL3 expression was examined in OSCC patient samples, followed by correlation analysis against clinical tumor features. Functional assays, such as assessment of surface marker expression, colony forming, BrdU incorporation, tumor xenograft assay, and m6A dot blot, were conducted to study the impact of METTL3 knockdown (KD) in OSCC cells. RESULTS High METTL3 expression was positively correlated with more severe clinical features of OSCC tumors. METTL3 KD caused impairment of stem-like capacities in OSCC cells, such as tumorigenicity in vivo and colony-forming ability in vitro. Furthermore, METTL3-KD and cycloleucine, a methylation inhibitor, decreased m6A levels and down-regulated p38 expression in OSCC cells. On the contrary, the impaired cell proliferation capacity of OSCC cells after METTL3-KD was restored by exogenous expression of p38. CONCLUSION Our findings identified m6A methyltransferase METTL3 as a key element in the regulation of tumorigenesis in OSCC.
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Affiliation(s)
- Ting Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenbo Zhang
- Department of Stomatology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Li Chai
- Hospital of JIER Machine-Tool Group Co., Ltd, Jinan, China
| | - Chao Liu
- Department of Stomatology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Shizhou Zhang
- Department of Stomatology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Tong Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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21
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The Comprehensive Analysis of N6-Methyadenosine Writer METTL3 and METTL14 in Gastric Cancer. JOURNAL OF ONCOLOGY 2023; 2023:9822995. [PMID: 36866236 PMCID: PMC9974280 DOI: 10.1155/2023/9822995] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/13/2022] [Accepted: 11/24/2022] [Indexed: 02/23/2023]
Abstract
Methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14) were two core components of the N6-methyadenosine (m6A) methyltransferase complex (MTC) and played a basic role in maintaining an appropriate m6A level of target genes. In gastric cancer (GC), previous researches on the expression and role of METTL3 and METTL14 were not consistent, and their specific function and mechanism have remained elusive. In this study, the expression of METTL3 and METTL14 was evaluated based on the TCGA database, 9 paired GEO datasets, and our 33 GC patient samples, and METTL3 was highly expressed and acted as a poor prognostic factor, whereas METTL14 showed no significant difference. Moreover, GO and GSEA analyses were performed, and the results pointed out that METTL3 and METTL14 were jointly involved in multiple biological processes, while they could also take part in different oncogenic pathways independently. And BCLAF1 was predicted and identified as a novel shared target of METTL3 and METTL14 in GC. In total, we conducted a comprehensive analysis of METTL3 and METTL14 in GC including their expression, function, and role, which could provide a novel insight into the research of m6A modification in GC.
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22
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Hu B, Zou X, Yu Y, Jiang Y, Xu H. METTL3 promotes SMSCs chondrogenic differentiation by targeting the MMP3, MMP13, and GATA3. Regen Ther 2023; 22:148-159. [PMID: 36793308 PMCID: PMC9923043 DOI: 10.1016/j.reth.2023.01.005] [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: 12/13/2022] [Revised: 01/09/2023] [Accepted: 01/14/2023] [Indexed: 01/30/2023] Open
Abstract
Objective Synovium-derived mesenchymal stem cells (SMSCs) are multipotential non-hematopoietic progenitor cells that can differentiate into various mesenchymal lineages in adipose and bone tissue, especially in chondrogenesis. Post-transcriptional methylation modifications are relative to the various biological development procedures. N6-methyladenosine (m6A) methylation has been identified as one of the abundant widespread post-transcriptional modifications. However, the connection between the SMSCs differentiation and m6A methylation remains unknown and needs further exploration. Methods SMSCs were derived from synovial tissues of the knee joint of male Sprague-Dawley (SD) rats. In the chondrogenesis of SMSCs, m6A regulators were detected by quantitative real-time PCR (RT-PCR) and Western blot (WB). We observed the situation that the knockdown of m6A "writer" protein methyltransferase-like (METTL)3 in the chondrogenesis of SMSCs. We also mapped the transcript-wide m6A landscape in chondrogenic differentiation of SMSCs and combined RNA-seq and MeRIP-seq in SMSCs by the interference of METTL3. Results The expression of m6A regulators were regulated in the chondrogenesis of SMSCs, only METTL3 is the most significant factor. In addition, after the knockdown of METTL3, MeRIP-seq and RNA-seq technology were applied to analyze the transcriptome level in SMSCs. 832 DEGs displayed significant changes, consisting of 438 upregulated genes and 394 downregulated genes. DEGs were enriched in signaling pathways regulating the glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate and ECM-receptor interaction via Kyoto Encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. The findings of this study indicate a difference in transcripts of MMP3, MMP13, and GATA3 containing consensus m6A motifs required for methylation by METTL3. Further, the reduction of METTL3 decreased the expression of MMP3, MMP13, and GATA3. Conclusion These findings confirm the molecular mechanisms of METTL3-mediated m6A post-transcriptional change in the modulation of SMSCs differentiating into chondrocytes, thus highlighting the potential therapeutic effect of SMSCs for cartilage regeneration.
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Affiliation(s)
- Bin Hu
- Department of Sports Medicine and Joint Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiangjie Zou
- Department of Orthopedics, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaohui Yu
- Department of Sports Medicine and Joint Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yiqiu Jiang
- Department of Sports Medicine and Joint Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China,Corresponding authors. Department of Sports Medicine and Joint Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hongyao Xu
- Department of Sports Medicine and Joint Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China,Corresponding authors. Department of Sports Medicine and Joint Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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23
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Integrated Profiles of Transcriptome and mRNA m6A Modification Reveal the Intestinal Cytotoxicity of Aflatoxin B1 on HCT116 Cells. Genes (Basel) 2022; 14:genes14010079. [PMID: 36672820 PMCID: PMC9858580 DOI: 10.3390/genes14010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Aflatoxin B1 (AFB1) is widely prevalent in foods and animal feeds and is one of the most toxic and carcinogenic aflatoxin subtypes. Existing studies have proved that the intestine is targeted by AFB1, and adverse organic effects have been observed. This study aimed to investigate the relationship between AFB1-induced intestinal toxicity and N6-methyladenosine (m6A) RNA methylation, which involves the post-transcriptional regulation of mRNA expression. The transcriptome-wide m6A methylome and transcriptome profiles in human intestinal cells treated with AFB1 are presented. Methylated RNA immunoprecipitation sequencing and mRNA sequencing were carried out to determine the distinctions in m6A methylation and different genes expressed in AFB1-induced intestinal toxicity. The results showed that there were 2289 overlapping genes of the differentially expressed mRNAs and differentially m6A-methylation-modified mRNAs. After enrichment of the signaling pathways and biological processes, these genes participated in the terms of the cell cycle, endoplasmic reticulum, tight junction, and mitophagy. In conclusion, the study demonstrated that AFB1-induced HCT116 injury was related to the disruptions to the levels of m6A methylation modifications of target genes and the abnormal expression of m6A regulators.
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24
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Comprehensive Analysis Revealed the Potential Roles of N6-Methyladenosine (m6A) Mediating E. coli F18 Susceptibility in IPEC-J2 Cells. Int J Mol Sci 2022; 23:ijms232113602. [DOI: 10.3390/ijms232113602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/20/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Post-weaning diarrhea caused by enterotoxigenic Escherichia coli F18 (E. coli F18) causes significant economic losses for pig producers. N6-methyladenosine (m6A) is a highly abundant epitranscriptomic marker that has been found to be involved in regulating the resistance of host cells to pathogenic infection, but its potential role in E. coli F18-exposed intestinal porcine epithelial cells (IPEC-J2) remains undetermined. Here, we demonstrated that m6A and its regulators modulate E. coli F18 susceptibility. Briefly, we revealed that the Wilms’ tumor 1-associating protein (WTAP) expressions were markedly elevated in IPEC-J2 cells upon E. coli F18 exposure. WTAP are required for the regulation of E. coli F18 adhesion in IPEC-J2 cells. Additionally, WTAP knockdown significantly suppressed m6A level at N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase (GCNT2) 3′UTR, resulting in the enhancement of TH N6-methyladenosine RNA binding protein 2 (YTHDF2)-mediated GCNT2 mRNA stability. Subsequently, the altered GCNT2 expressions could inhibit the glycosphingolipid biosynthesis, thus improving resistance to E. coli F18 infection in IPEC-J2. Collectively, our analyses highlighted the mechanism behind the m6A-mediated management of E. coli F18 susceptibility, which will aid in the development of novel approaches that protect against bacterial diarrhea in piglets.
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25
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The RNA m 6A writer WTAP in diseases: structure, roles, and mechanisms. Cell Death Dis 2022; 13:852. [PMID: 36207306 PMCID: PMC9546849 DOI: 10.1038/s41419-022-05268-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/11/2022] [Accepted: 09/14/2022] [Indexed: 11/05/2022]
Abstract
N6-methyladenosine (m6A) is a widely investigated RNA modification in studies on the "epigenetic regulation" of mRNAs that is ubiquitously present in eukaryotes. Abnormal changes in m6A levels are closely related to the regulation of RNA metabolism, heat shock stress, tumor occurrence, and development. m6A modifications are catalyzed by the m6A writer complex, which contains RNA methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14), Wilms tumor 1-associated protein (WTAP), and other proteins with methyltransferase (MTase) capability, such as RNA-binding motif protein 15 (RBM15), KIAA1429 and zinc finger CCCH-type containing 13 (ZC3H13). Although METTL3 is the main catalytic subunit, WTAP is a regulatory subunit whose function is to recruit the m6A methyltransferase complex to the target mRNA. Specifically, WTAP is required for the accumulation of METTL3 and METTL14 in nuclear speckles. In this paper, we briefly introduce the molecular mechanism of m6A modification. Then, we focus on WTAP, a component of the m6A methyltransferase complex, and introduce its structure, localization, and physiological functions. Finally, we describe its roles and mechanisms in cancer.
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26
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Li S, Yang Q, Jiao R, Xu P, Sun Y, Li X. m6A Topological Transition Coupled to Developmental Regulation of Gene Expression During Mammalian Tissue Development. Front Cell Dev Biol 2022; 10:916423. [PMID: 35865625 PMCID: PMC9294180 DOI: 10.3389/fcell.2022.916423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification and reversible epitranscriptomic mark in messenger RNAs (mRNAs) and plays essential roles in a variety of biological processes. However, the dynamic distribution patterns of m6A and their significance during mammalian tissue development are poorly understood. Here, we found that based on m6A distribution patterns, protein-coding genes were classified into five groups with significantly distinct biological features and functions. Strikingly, comparison of the m6A methylomes of multiple mammalian tissues between fetal and adult stages revealed dynamic m6A topological transition during mammalian tissue development, and identified large numbers of genes with significant m6A loss in 5′UTRs or m6A gain around stop codons. The genes with m6A loss in 5′UTRs were highly enriched in developmental stage-specific genes, and their m6A topological transitions were strongly associated with gene expression regulation during tissue development. The genes with m6A gain around the stop codons were associated with tissue-specific functions. Our findings revealed the existence of different m6A topologies among protein-coding genes that were associated with distinct characteristics. More importantly, these genes with m6A topological transitions were crucial for tissue development via regulation of gene expression, suggesting the importance of dynamic m6A topological transitions during mammalian tissue development.
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Affiliation(s)
- Shanshan Li
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Qing Yang
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Rui Jiao
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Pengfei Xu
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yazhou Sun
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- *Correspondence: Yazhou Sun, ; Xin Li,
| | - Xin Li
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- *Correspondence: Yazhou Sun, ; Xin Li,
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Zhai G, Xiao L, Jiang C, Yue S, Zhang M, zheng J, Liu Z, Dong Y. Regulatory Role of N6-Methyladenosine (m6A) Modification in Osteoarthritis. Front Cell Dev Biol 2022; 10:946219. [PMID: 35846376 PMCID: PMC9282717 DOI: 10.3389/fcell.2022.946219] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Osteoarthritis (OA) is the most common joint disease, usually occurring in middle-aged and elderly people. However, current treatment for OA in its early stages is ineffective, and drug therapy is often ineffective in slowing the progression of the disease. In fact, a deeper understanding of the underlying molecular mechanisms of OA could help us to better develop effective therapeutic measures. N6-methyladenosine (m6A) is a methylation that occurs at the adenosine N6-position, which is the most common internal modification on eukaryotic mRNAs. The role and mechanisms of m6A in mammalian gene regulation have been extensively studied. The “Writer”, “eraser”, and “reader” proteins are key proteins involved in the dynamic regulation of m6A modifications. Recent studies on post-transcriptional regulation alone have shown that m6a modification has an important role in the development of OA. This paper summarizes the specific regulatory processes of M6A in disease and reviews the role of m6A in OA, describing its pathophysiological role and molecular mechanisms, as well as its future research trends and potential clinical applications in OA.
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Affiliation(s)
- Ganggang Zhai
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Likang Xiao
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Chenyang Jiang
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Songkai Yue
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Meng Zhang
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Jia zheng
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Zeming Liu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yonghui Dong, ; Zeming Liu,
| | - Yonghui Dong
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
- Microbiome Laboratory, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yonghui Dong, ; Zeming Liu,
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Liu J, Zhu J, Wang X, Zhou Z, Liu H, Zhu D. A Novel YTHDF3-Based Model to Predict Prognosis and Therapeutic Response in Breast Cancer. Front Mol Biosci 2022; 9:874532. [PMID: 35755811 PMCID: PMC9218665 DOI: 10.3389/fmolb.2022.874532] [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: 02/12/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Due to high tumor heterogeneity, breast cancer (BC) patients still suffer poor survival outcomes. YTHDF3 plays a critical role in the prognosis of BC patients. Hence, we aimed to construct a YTHDF3-based model for the prediction of the overall survival (OS) and the sensitivity of therapeutic agents in BC patients. Methods: Based on The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/) database, we obtained BC patients’ data (n = 999) with YTHDF3 expression profiles. The association between YTHDF3 expression and 5-year OS was determined via Cox proportional hazards regression (CPHR) analysis. By integrating the variables, we established a prognostic nomogram. The model was estimated via discrimination, calibration ability, and decision curve analysis (DCA). The performance of the model was compared with the TNM stage system through receiver operating characteristic (ROC) curves and DCA. By means of the Genomics of Drug Sensitivity in Cancer (GDSC) database (https://www.cancerrxgene.org/), the therapeutic agents’ response was estimated. Gene set enrichment analysis (GSEA) demonstrated possible biological mechanisms related to YTHDF3. TIMER and CIBERSORTx were employed to analyze the association between YTHDF3 and tumor-infiltrating immune cells. Results: The high YTHDF3 expression was significantly correlated with poor 5-year OS in BC patients. Through multivariate CPHR, four independent prognostic variables (age, TNM stage, YTHDF3 expression, and molecular subtype) were determined. On the basis of the four factors, a YTHDF3-based nomogram was built. The area under the curve (AUC) of the ROC curve for the model surpassed that of the TNM stage system (0.72 vs. 0.63, p = 0.00028). The model predictions showed close consistency with the actual observations via the calibration plot. Therapeutic response prediction was conducted in high- and low-risk groups and compared with each other. The BC patients with higher risk scores showed more therapeutic resistance than those with a lower risk score. Conclusion: YTHDF3 was verified as a prognostic biomarker of BC, and a novel YTHDF3-based model was constructed to predict the 5-year OS of BC patients. Our model could be applied to effectively predict the therapeutic response of commonly used agents for BC patients.
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Affiliation(s)
- Jie Liu
- Department of Breast Cancer, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Jing Zhu
- Department of Breast Cancer, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Xin Wang
- Group of Ultrasonography in Obstetrics, Department of Obstetrics, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Zhisheng Zhou
- Department of Breast Cancer, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Haiyan Liu
- Department of Breast Cancer, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Dajiang Zhu
- Department of Breast Cancer, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, China
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HIF-1 α Regulated WTAP Overexpression Promoting the Warburg Effect of Ovarian Cancer by m6A-Dependent Manner. J Immunol Res 2022; 2022:6130806. [PMID: 35733918 PMCID: PMC9207020 DOI: 10.1155/2022/6130806] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 12/21/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation has been determined to execute crucial functions in tumorigenesis and cancer development. WT1-associated protein (WTAP) has an important “writer” role in m6A modification, and it is also a nuclear protein that colocalizes with splicing factors and plays a critical role in cell function and cancer progression. However, little is known about the role of WTAP in ovarian cancer (OC) and its mechanisms. In this study, we found for the first time that hypoxia-inducible factor (HIF)-1α could positively regulate increased expression of WTAP under hypoxia. And further results revealed that WTAP expression was closely associated with the clinicopathological features of OC, and high expression of WTAP predicted low survival rate in patients with OC. In addition, cell proliferation and invasive capacity were significantly reduced after knockdown of WTAP expression in OC cells. However, cell proliferation and invasive ability were significantly enhanced after overexpression of WTAP. Additionally, we find that WTAP interacts with DGCR8 (a crucial chip protein) to regulate the expression of microRNA-200 (miR-200) in an m6A-dependent way. Further experiments showed that the key glycolysis enzyme HK2 could be positively regulated by miR-200, which significantly affected the intracellular Warburg effect. In conclusion, this is considered uncovered that upregulation of WTAP expression by HIF-1α intercedes with miRNA processing, accelerates the Warburg impact, and advances the event and advancement of tumor, thus giving a novel viewpoint on m6A adjustment in OC movement.
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Luo G, Wang S, Ai Y, Li J, Ren Z. N6-Methyladenosine Methylome Profiling of Muscle and Adipose Tissues Reveals Methylase-mRNA Metabolic Regulatory Networks in Fat Deposition of Rex Rabbits. BIOLOGY 2022; 11:biology11070944. [PMID: 36101325 PMCID: PMC9312354 DOI: 10.3390/biology11070944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and plays an important role in cancer, immunity, reproduction, development, and fat deposition. Intramuscular fat is the main factor used to measure the meat quality of an animal. The deposition of intramuscular fat and perirenal fat increases with age. However, there is no data on m6A modification of Rex rabbits and its potential biological roles in adipose deposition and muscle growth. Here, we performed two high-throughput sequencing methods, m6A-modified RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq), to identify key genes with m6A modification on fat deposition in the muscle and adipose tissues of Rex rabbits. Then, qRT-PCR was used to identify the differently methylated genes related to fat deposition. Our findings showed that there were 12,876 and 10,973 m6A peaks in the rabbit muscle and adipose tissue transcriptomes, respectively. Stop codons, 3′-untranslated regions, and coding regions were found to be mainly enriched for m6A peaks. In addition, we found 5 differential methylases and 12 key genes of methylation modification related to fat deposition between muscle and adipose tissues samples. The expression levels of six random key genes were significantly higher in the fat than that in the muscle of Rex rabbits at different stages (p < 0.01). Finally, five differential methylases were found to regulate adipogenesis by affecting the expression of screened genes in different ways. These findings provided a theoretical basis for our future research on the function of m6A modification during the growth of fat deposits.
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Chen J, Lai K, Yong X, Yin H, Chen Z, Wang H, Chen K, Zheng J. Silencing METTL3 Stabilizes Atherosclerotic Plaques by Regulating the Phenotypic Transformation of Vascular Smooth Muscle Cells via the miR-375-3p/PDK1 Axis. Cardiovasc Drugs Ther 2022; 37:471-486. [PMID: 35704246 DOI: 10.1007/s10557-022-07348-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/27/2022]
Abstract
PURPOSE Atherosclerosis (AS) is a primary cause of cardiovascular diseases. This study investigated the mechanism of methyltransferase-like 3 (METTL3) in AS plaques via modulating the phenotypic transformation of vascular smooth muscle cells (VSMCs). METHODS AS mouse models and MOVAS cell models were established through high-fat diet and the treatment of ox-LDL, respectively. METTL3 expression in AS models was detected via RT-qPCR and Western blot. The AS plaques, lipid deposition, and collagen fibers were examined via histological staining. The levels of Ly-6c, α-SMA, and OPN were examined via Western blot. The blood lipid indexes in mouse aortic tissues were determined using kits. The proliferation and migration of MOVAS cells were detected via CCK-8 and Transwell assays. The m6A modification level of mRNA was quantified. The binding relationship between pri-miR-375 and DGCR8, and the enrichment of m6A on pri-miR-375 were detected via RIP. The binding relationship between miR-375-3p and 3-phosphoinositide-dependent protein kinase-1 (PDK1) was verified via dual-luciferase assay. Joint experiments were designed to investigate the role of miR-375-3P/PDK1 in the phenotypic transformation of VSMCs. RESULTS METTL3 was highly expressed in AS. Silencing METTL3 alleviated AS progression and stabilized AS plaques in mice, and limited the phenotypic transformation of VSMCs induced by ox-LDL. Silencing METTL3 inhibited m6A level and decreased the binding of DGCR8 to pri-miR-375 and further limited miR-375-3p expression. miR-375-3p targeted PDK1 transcription. miR-375-3p upregulation or PDK1 downregulation facilitated the phenotypic transformation of VSMCs. CONCLUSION METTL3-mediated m6A modification promoted VSMC phenotype transformation and made AS plaques more vulnerable via the miR-375-3p/PDK1 axis.
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Affiliation(s)
- Jingquan Chen
- Department of Vascular Surgery, Affiliated Hospital of North Sichuan Medical College, No.1 Maoyuan south road, Shunqing district, Nanchong, 637000, Sichuan, China
| | - Kun Lai
- Department of Vascular Surgery, Affiliated Hospital of North Sichuan Medical College, No.1 Maoyuan south road, Shunqing district, Nanchong, 637000, Sichuan, China
| | - Xi Yong
- Department of Vascular Surgery, Affiliated Hospital of North Sichuan Medical College, No.1 Maoyuan south road, Shunqing district, Nanchong, 637000, Sichuan, China
| | - Hongshun Yin
- Department of Vascular Surgery, Affiliated Hospital of North Sichuan Medical College, No.1 Maoyuan south road, Shunqing district, Nanchong, 637000, Sichuan, China
| | - Zhilong Chen
- Department of Vascular Surgery, Affiliated Hospital of North Sichuan Medical College, No.1 Maoyuan south road, Shunqing district, Nanchong, 637000, Sichuan, China
| | - Haifei Wang
- Department of Vascular Surgery, Affiliated Hospital of North Sichuan Medical College, No.1 Maoyuan south road, Shunqing district, Nanchong, 637000, Sichuan, China
| | - Kai Chen
- Department of Vascular Surgery, Affiliated Hospital of North Sichuan Medical College, No.1 Maoyuan south road, Shunqing district, Nanchong, 637000, Sichuan, China
| | - Jianghua Zheng
- Department of Vascular Surgery, Affiliated Hospital of North Sichuan Medical College, No.1 Maoyuan south road, Shunqing district, Nanchong, 637000, Sichuan, China.
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Luo G, Zhu T, Ren Z. METTL3 Regulated the Meat Quality of Rex Rabbits by Controlling PCK2 Expression via a YTHDF2–N6-Methyladenosine Axis. Foods 2022; 11:foods11111549. [PMID: 35681299 PMCID: PMC9180525 DOI: 10.3390/foods11111549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/10/2022] [Accepted: 05/15/2022] [Indexed: 01/27/2023] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent internal mRNA modification in eukaryotes. The M6A modification plays an important role in transcription and cell function. The mechanism by which m6A modification regulates meat quality remains elusive. In this study, gene knockout and overexpression were used to explore m6A-modified regulation of meat quality. The content of PCK2 in blood increased significantly with the increase of Rex rabbits’ age. PCK2 expression levels in the longissimus lumborum and liver also increased significantly with the increase of Rex rabbits’ age. However, the expression level of PCK2 showed no significant difference in adipose tissue. In cell experiments, we found that METTL3 inhibited adipocyte differentiation by targeting the PCK2 gene via the recognition function of YTHDF2. Finally, the results of correlation analysis showed that PCK2 expression was positively correlated with intramuscular fat, whereas PCK2 expression was negatively correlated with total water loss rate at three different stages. In addition, PCK2 expression was also negatively correlated with reduced pH value at 75 and 165 days. Intramuscular fat content, pH and muscle water holding capacity are the main factors affecting the taste and flavor of muscle. Therefore, N6-methyladenosine regulated muscle quality by targeting the PCK2 gene.
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Zhuo R, Xu M, Wang X, Zhou B, Wu X, Leone V, Chang EB, Zhong X. The regulatory role of N 6 -methyladenosine modification in the interaction between host and microbes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1725. [PMID: 35301791 DOI: 10.1002/wrna.1725] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/21/2022] [Accepted: 02/21/2022] [Indexed: 01/02/2023]
Abstract
N6 -methyladenosine (m6 A) is the most prevalent posttranscriptional modification in eukaryotic mRNAs. Dynamic and reversible m6 A modification regulates gene expression to control cellular processes and diverse biological functions. Growing evidence indicated that m6 A modification is involved in the homeostasis of host and microbes (mostly viruses and bacteria). Disturbance of m6 A modification affects the life cycles of viruses and bacteria, however, these microbes could in turn change host m6 A modification leading to human disease including autoimmune diseases and cancer. Thus, we raise the concept that m6 A could be a "messenger" molecule to participate in the interactions between host and microbes. In this review, we summarize the regulatory mechanisms of m6 A modification on viruses and commensal microbiota, highlight the roles of m6 A methylation in the interaction of host and microbes, and finally discuss drugs development targeting m6 A modification. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Ruhao Zhuo
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Menghui Xu
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyun Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Bin Zhou
- Joint International Research Laboratory of Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xin Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Vanessa Leone
- Department of Animal Biologics and Metabolism, University of Wisconsin, Madison, Wisconsin, USA.,Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Eugene B Chang
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Xiang Zhong
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Tang J, Su Q, Guo Z, Zhou J, Zheng F, Yu G, Shao W, Hu H, Wu S, Li H. N6-methyladenosine(m 6A) demethylase FTO regulates cellular apoptosis following cobalt-induced oxidative stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 297:118749. [PMID: 34968619 DOI: 10.1016/j.envpol.2021.118749] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Cobalt is an environmental toxicant that is known to damage human health. However, the molecular mechanisms underlying cobalt-induced neurotoxicity have not been elucidated in detail. In the present research, we used human neuroglioma H4 cells as an in vitro model. Cells were exposed to CoCl2 (0, 100, 200, 400 μM) for 24 h. We performed m6A sequencing techniques and constructed FTO-knockdown/FTO-overexpressing cells to investigate the role of FTO-mediated m6A modification in regulating apoptosis following CoCl2 induced oxidative stress. Our study has shown CoCl2 exposure led to the decrease of demethylase FTO as well as elevated oxidative stress. However, NAC treatment could partly reverse the reduction of FTO expression as well as the degree of ROS via eliminating oxidative stress. Meanwhile, MeRIP-seq and RNA-seq further revealed the potential function m6A modification in regulating apoptosis. More importantly, KEGG pathway and Gene ontology (GO) analyses further elucidated that the differentially m6A-modified genes were aggregated in apoptosis-related pathways. Mechanistic analysis indicated that knockdown of FTO facilitated CoCl2-induced apoptosis via caspase activation and G1/S cell cycle arrest. Nevertheless, overexpression of FTO partly attenuated the increased apoptosis following CoCl2 exposure. More notably, we observed that FTO regulated apoptosis in an m6A-dependent manner. Therefore, our findings reveal that CoCl2 induced ROS affected the m6A modification of apoptosis-related genes by decreasing the expression of FTO, thereby resulting in the activation of apoptosis. These findings provide important insights into CoCl2-induced apoptosis and m6A modification and propose a novel strategy for studying environmental toxicant-related neurodegeneration.
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Affiliation(s)
- Jianping Tang
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Qianqian Su
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Zhenkun Guo
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Jinfu Zhou
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Fuli Zheng
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Guangxia Yu
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Wenya Shao
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Hong Hu
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Siying Wu
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Huangyuan Li
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China.
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Zhang N, Ding C, Zuo Y, Peng Y, Zuo L. N6-methyladenosine and Neurological Diseases. Mol Neurobiol 2022; 59:1925-1937. [PMID: 35032318 DOI: 10.1007/s12035-022-02739-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/08/2022] [Indexed: 12/14/2022]
Abstract
N6-methyladenosine (m6A) is a dynamic reversible methylation modification of the adenosine N6 position and is the most common chemical epigenetic modification among mRNA post-transcriptional modifications, including methylation, demethylation, and recognition. Post-transcriptional modification involves multiple protein molecules, including METTL3, METTL14, WTAP, KIAA1429, ALKBH5, YTHDF1/2/3, and YTHDC1/2. m6A-related proteins are expressed in almost all cells. However, the abnormal expression of m6A-related proteins may occur in the nervous system, thereby affecting neuritogenesis, brain volume, learning and memory, memory formation and consolidation, etc., and is implicated in the development of diseases, such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, depression, epilepsy, and brain tumors. This review focuses on the functions of m6A in the development of central nervous system diseases, thus contributing to a deeper understanding of disease pathogenesis and providing potential clinical therapeutic targets for neurological diseases.
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Affiliation(s)
- Nan Zhang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Chunhong Ding
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Yuxin Zuo
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Yu Peng
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Lielian Zuo
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China.
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Dong G, Yu J, Shan G, Su L, Yu N, Yang S. N6-Methyladenosine Methyltransferase METTL3 Promotes Angiogenesis and Atherosclerosis by Upregulating the JAK2/STAT3 Pathway via m6A Reader IGF2BP1. Front Cell Dev Biol 2021; 9:731810. [PMID: 34950654 PMCID: PMC8689138 DOI: 10.3389/fcell.2021.731810] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/19/2021] [Indexed: 01/15/2023] Open
Abstract
Atherosclerosis (AS) is a life-threatening vascular disease. RNA N6-methyladenosine (m6A) modification level is dysregulated in multiple pathophysiologic processes including AS. In this text, the roles and molecular mechanisms of m6A writer METTL3 in AS progression were explored in vitro and in vivo. In the present study, cell proliferative, migratory, and tube formation capacities were assessed through CCK-8, Transwell migration, and tube formation assays, respectively. RNA m6A level was examined through a commercial kit. RNA and protein levels of genes were measured through RT-qPCR and western blot assays, respectively. VEGF secretion level was tested through ELISA assay. JAK2 mRNA stability was detected through actinomycin D assay. The relationship of METTL3, IGF2BP1, and JAK2 was investigated through bioinformatics analysis, MeRIP, RIP, RNA pull-down, and luciferase reporter assays. An AS mouse model was established to examine the effect of METTL3 knockdown on AS development in vivo. The angiogenetic activity was examined through chick chorioallantoic membrane assay in vivo. The results showed that METTL3 was highly expressed in ox-LDL-induced dysregulated HUVECs. METTL3 knockdown inhibited cell proliferation, migration, tube formation, and VEGF expression/secretion in ox-LDL-treated HUVECs, hampered AS process in vivo, and prevented in vivo angiogenesis of developing embryos. METTL3 positively regulated JAK2 expression and JAK2/STAT3 pathway in an m6A dependent manner in HUVECs. IGF2BP1 positively regulated JAK2 expression through directly binding to an m6A site within JAK2 mRNA in HUVECs. METTL3 knockdown weakened the interaction of JAK2 and IGF2BP1. METTL3 exerted its functions through JAK2/STAT3 pathway. In conclusion, METTL3 knockdown prevented AS progression by inhibiting JAK2/STAT3 pathway via IGF2BP1.
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Affiliation(s)
- Guo Dong
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiangbo Yu
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Gaojun Shan
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lide Su
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Nannan Yu
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shusen Yang
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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Tomé-Carneiro J, de Las Hazas MCL, Boughanem H, Böttcher Y, Cayir A, Macias González M, Dávalos A. Up-to-date on the evidence linking miRNA-related epitranscriptomic modifications and disease settings. Can these modifications affect cross-kingdom regulation? RNA Biol 2021; 18:586-599. [PMID: 34843412 DOI: 10.1080/15476286.2021.2002003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The field of epitranscriptomics is rapidly developing. Several modifications (e.g. methylations) have been identified for different RNA types. Current evidence shows that chemical RNA modifications can influence the whole molecule's secondary structure, translatability, functionality, stability, and degradation, and some are dynamically and reversibly modulated. miRNAs, in particular, are not only post-transcriptional modulators of gene expression but are themselves submitted to regulatory mechanisms. Understanding how these modifications are regulated and the resulting pathological consequences when dysregulation occurs is essential for the development of new therapeutic targets. In humans and other mammals, dietary components have been shown to affect miRNA expression and may also induce chemical modifications in miRNAs. The identification of chemical modifications in miRNAs (endogenous and exogenous) that can impact host gene expression opens up an alternative way to select new specific therapeutic targets.Hence, the aim of this review is to briefly address how RNA epitranscriptomic modifications can affect miRNA biogenesis and to summarize the existing evidence showing the connection between the (de)regulation of these processes and disease settings. In addition, we hypothesize on the potential effect certain chemical modifications could have on the potential cross-kingdom journey of dietary plant miRNAs.
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Affiliation(s)
- João Tomé-Carneiro
- Laboratory of Functional Foods, Madrid Institute for Advanced Studies (IMDEA)-food, CEI UAM + CSIM, Spain
| | | | - Hatim Boughanem
- Instituto de Investigación Biomédica de Málaga (Ibima), Unidad de Gestión Clínica de Endocrinología Y Nutrición Del Hospital Virgen de La Victoria, Málaga, Spain.,Instituto de Salud Carlos Iii (Isciii), Consorcio Ciber, M.p. Fisiopatología de La Obesidad Y Nutrición (Ciberobn), Madrid, Spain.,Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Yvonne Böttcher
- Institute of Clinical Medicine, Department of Clinical Molecular Biology (EpiGen), University of Oslo, Oslo, Norway.,Department of Medical Services and Techniques (EpiGen), Akershus Universitetssykehus, Lørenskog, Norway
| | - Akin Cayir
- Institute of Clinical Medicine, Department of Clinical Molecular Biology (EpiGen), University of Oslo, Oslo, Norway.,Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Manuel Macias González
- Instituto de Investigación Biomédica de Málaga (Ibima), Unidad de Gestión Clínica de Endocrinología Y Nutrición Del Hospital Virgen de La Victoria, Málaga, Spain.,Instituto de Salud Carlos Iii (Isciii), Consorcio Ciber, M.p. Fisiopatología de La Obesidad Y Nutrición (Ciberobn), Madrid, Spain
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-food, CEI UAM + CSIC, Spain
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38
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Wu R, Chen Y, Liu Y, Zhuang L, Chen W, Zeng B, Liao X, Guo G, Wang Y, Wang X. m6A methylation promotes white-to-beige fat transition by facilitating Hif1a translation. EMBO Rep 2021; 22:e52348. [PMID: 34569703 DOI: 10.15252/embr.202052348] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 08/02/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
Obesity mainly results from a chronic energy imbalance. Promoting browning of white adipocytes is a promising strategy to enhance energy expenditure and combat obesity. N6-methyladenosine (m6A), the most abundant mRNA modification in eukaryotes, plays an important role in regulating adipogenesis. However, whether m6A regulates white adipocyte browning was unknown. Here, we report that adipose tissue-specific deletion of Fto, an m6A demethylase, predisposes mice to prevent high-fat diet (HFD)-induced obesity by enhancing energy expenditure. Additionally, deletion of FTO in vitro promotes thermogenesis and white-to-beige adipocyte transition. Mechanistically, FTO deficiency increases the m6A level of Hif1a mRNA, which is recognized by m6A-binding protein YTHDC2, facilitating mRNA translation and increasing HIF1A protein abundance. HIF1A activates the transcription of thermogenic genes, including Ppaggc1a, Prdm16, and Pparg, thereby promoting Ucp1 expression and the browning process. Collectively, these results unveil an epigenetic mechanism by which m6A-facilitated HIF1A expression controls browning of white adipocytes and thermogenesis, providing a potential target to counteract obesity and metabolic disease.
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Affiliation(s)
- Ruifan Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yushi Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
| | - Youhua Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
| | - Lenan Zhuang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
| | - Wei Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
| | - Botao Zeng
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
| | - Xing Liao
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
| | - Guanqun Guo
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
| | - Xinxia Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, China
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39
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Kugelberg U, Nätt D, Skog S, Kutter C, Öst A. 5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA. RNA Biol 2021; 18:1588-1599. [PMID: 33382953 PMCID: PMC8594926 DOI: 10.1080/15476286.2020.1861770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 12/21/2022] Open
Abstract
Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5´ nucleotide modifications, make many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that captures a more complete picture of sRNA. By tagging 5´P sRNA during library preparation, 5XP-seq combines an open approach that includes all types of 5'-terminal modifications (5´X), with a selective approach for 5-phosphorylated sRNA (5´P). We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to insect translation of several tRNA (tRFs) and rRNA (rRFs) fragments. By combining 5´ insensitive library strategies with 5´ sensitive tagging, we have successfully tackled an intrinsic bias in modern sRNA sequencing that will help us reveal the true complexity and the evolutionary significance of the sRNA world.
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Affiliation(s)
- Unn Kugelberg
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Daniel Nätt
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Signe Skog
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm
| | - Anita Öst
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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40
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Sun J, Ping Y, Huang J, Zeng B, Ji P, Li D. N6-Methyladenosine-Regulated mRNAs: Potential Prognostic Biomarkers for Patients With Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:705962. [PMID: 34422827 PMCID: PMC8377381 DOI: 10.3389/fcell.2021.705962] [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: 05/06/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Aberrant regulation of m6A mRNA modification can lead to changes in gene expression, thus contributing to tumorigenesis in several types of solid tumors. In this study, by integrating analyses of m6A methylation and mRNA expression, we identified 84 m6A-regulated mRNAs in lung adenocarcinoma (LUAD). Although the m6A methylation levels of total RNA in LUAD patient tumor tissue were reduced, the majority (75.2%) of m6A-regulated mRNAs were hypermethylated. The m6A-hypermethylated mRNAs were mainly enriched in terms related to transcription factor activity. We established a 10-m6A-regulated-mRNA signature score system through least absolute shrinkage and selection operator Cox regression analysis, with its predictive value validated by Kaplan–Meier curve and time-dependent receiver operating characteristic curves. RFXAP and KHDRBS2 from the signature also exhibited an independent prognostic value. The co-expression and interaction network analyses demonstrated the strong correlation between m6A regulators and the genes in the signature, further supporting the results of the m6A methylation modification patterns. These findings highlight the potential utility of integrating multi-omics data (m6A methylation level and mRNA expression) to accurately obtain potential prognostic biomarkers, which may provide important insights into developing novel and effective therapies for LUAD.
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Affiliation(s)
- Junjun Sun
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yili Ping
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jingjuan Huang
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bingjie Zeng
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ping Ji
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Dong Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
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41
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Dynamic Patterns of N6-Methyladenosine Profiles of Messenger RNA Correlated with the Cardiomyocyte Regenerability during the Early Heart Development in Mice. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5537804. [PMID: 34413927 PMCID: PMC8369182 DOI: 10.1155/2021/5537804] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/13/2021] [Indexed: 12/16/2022]
Abstract
N6-Methyladenosine (m6A) plays important roles in regulating mRNA processing. Despite rapid progress in this field, little is known about the role and mechanism of m6A modification in myocardial development and cardiomyocyte regeneration. Existing studies have shown that the heart tissues of newborn mice have the capability of proliferation and regeneration, but its mechanism, particularly its relation to m6A methylation, remains unknown. Methods. To systematically profile the mRNA m6A modification pattern in the heart tissues of mice at different developmental stages, we jointly performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) of heart tissues of mice, respectively, aged 1 day old, 7 days old, and 28 days old. Results. We identified the linkages and association between differentially expressed mRNA transcripts and hyper or hypomethylated m6A peaks in C57BL/6J mice at different heart developmental stages. Results showed that the amount of m6A peaks and the level of m6A modification were the lowest in the heart of mice at 1 day old. By contrast, heart tissues from 7-day-old mice tended to possess the most m6A peaks and the highest global m6A level. However, the m6A characteristics of myocardial tissue changed little after 7 days old as compared to that of 1 day old. Specifically, we found 1269 downmethylated genes of 1434 methylated genes in 7-day-old mouse heart tissues as compared to those in 1-day-old mice. Hypermethylation of some specific genes may correlate with the heart's strong proliferative and regenerative capability at the first day after birth. In terms of m6A density, the tendency shifted from coding sequences (CDS) to 3′-untranslated regions (3′UTR) and stop codon with the progression of heart development. In addition, some genes demonstrated remarkable changes both in methylation and expression, like kiss1, plekha6, and megf6, which may play important roles in proliferation. Furthermore, signaling pathways highly related to proliferation such as “Wnt signaling pathway,” “ECM-receptor interaction,” and “cardiac chamber formation” were significantly enriched in 1-day-old methylated genes. Conclusions. Our results reveal a pattern that different m6A modifications are distributed in C57BL/6J heart tissue at different developmental stages, which provides new insights into a novel function of m6A methylation of mRNA in myocardial development and regeneration.
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42
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Purslow JA, Nguyen TT, Khatiwada B, Singh A, Venditti V. N 6-methyladenosine binding induces a metal-centered rearrangement that activates the human RNA demethylase Alkbh5. SCIENCE ADVANCES 2021; 7:7/34/eabi8215. [PMID: 34407931 PMCID: PMC8373141 DOI: 10.1126/sciadv.abi8215] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/29/2021] [Indexed: 05/13/2023]
Abstract
Alkbh5 catalyzes demethylation of the N 6-methyladenosine (m6A), an epigenetic mark that controls several physiological processes including carcinogenesis and stem cell differentiation. The activity of Alkbh5 comprises two coupled reactions. The first reaction involves decarboxylation of α-ketoglutarate (αKG) and formation of a Fe4+═O species. This oxyferryl intermediate oxidizes the m6A to reestablish the canonical base. Despite coupling between the two reactions being required for the correct Alkbh5 functioning, the mechanisms linking dioxygen activation to m6A binding are not fully understood. Here, we use solution NMR to investigate the structure and dynamics of apo and holo Alkbh5. We show that binding of m6A to Alkbh5 induces a metal-centered rearrangement of αKG that increases the exposed area of the metal, making it available for binding O2 Our study reveals the molecular mechanisms underlying activation of Alkbh5, therefore opening new perspectives for the design of novel strategies to control gene expression and cancer progression.
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Affiliation(s)
| | - Trang T Nguyen
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | | | - Aayushi Singh
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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43
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Chen X, Wang J, Tahir M, Zhang F, Ran Y, Liu Z, Wang J. Current insights into the implications of m6A RNA methylation and autophagy interaction in human diseases. Cell Biosci 2021; 11:147. [PMID: 34315538 PMCID: PMC8314498 DOI: 10.1186/s13578-021-00661-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
Autophagy is a conserved degradation process crucial to maintaining the primary function of cellular and organismal metabolism. Impaired autophagy could develop numerous diseases, including cancer, cardiomyopathy, neurodegenerative disorders, and aging. N6-methyladenosine (m6A) is the most common RNA modification in eukaryotic cells, and the fate of m6A modified transcripts is controlled by m6A RNA binding proteins. m6A modification influences mRNA alternative splicing, stability, translation, and subcellular localization. Intriguingly, recent studies show that m6A RNA methylation could alter the expression of essential autophagy-related (ATG) genes and influence the autophagy function. Thus, both m6A modification and autophagy could play a crucial role in the onset and progression of various human diseases. In this review, we summarize the latest studies describing the impact of m6A modification in autophagy regulation and discuss the role of m6A modification-autophagy axis in different human diseases, including obesity, heart disease, azoospermatism or oligospermatism, intervertebral disc degeneration, and cancer. The comprehensive understanding of the m6A modification and autophagy interplay may help in interpreting their impact on human diseases and may aid in devising future therapeutic strategies.
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Affiliation(s)
- Xuechai Chen
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing, 100124, People's Republic of China
| | - Jianan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing, 100124, People's Republic of China
| | - Muhammad Tahir
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing, 100124, People's Republic of China
| | - Fangfang Zhang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing, 100124, People's Republic of China
| | - Yuanyuan Ran
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Xixiazhuang, Badachu, Beijing, 100144, People's Republic of China
| | - Zongjian Liu
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Xixiazhuang, Badachu, Beijing, 100144, People's Republic of China.
| | - Juan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing, 100124, People's Republic of China.
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44
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Feng Q, Zhao H, Xu L, Xie Z. N6-Methyladenosine Modification and Its Regulation of Respiratory Viruses. Front Cell Dev Biol 2021; 9:699997. [PMID: 34368152 PMCID: PMC8342946 DOI: 10.3389/fcell.2021.699997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/28/2021] [Indexed: 11/23/2022] Open
Abstract
N6-methyladenosine (m6A) is a ubiquitous RNA modification in eukaryotes. It plays important roles in the translocation, stabilization and translation of mRNA. Many recent studies have shown that the dysregulation of m6A modification is connected with diseases caused by pathogenic viruses, and studies on the role of m6A in virus-host interactions have shown that m6A plays a wide range of regulatory roles in the life cycle of viruses. Respiratory viruses are common pathogens that can impose a large disease burden on young children and elderly people. Here, we review the effects of m6A modification on respiratory virus replication and life cycle and host immunity against viruses.
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Affiliation(s)
- Qianyu Feng
- Beijing Key Laboratory of Paediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, National Key Discipline of Paediatrics (Capital Medical University), Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Paediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.,Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongwei Zhao
- Beijing Key Laboratory of Paediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, National Key Discipline of Paediatrics (Capital Medical University), Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Paediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.,Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Xu
- Beijing Key Laboratory of Paediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, National Key Discipline of Paediatrics (Capital Medical University), Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Paediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.,Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Paediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, National Key Discipline of Paediatrics (Capital Medical University), Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Paediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.,Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
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45
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Maternal effects in mammals: Broadening our understanding of offspring programming. Front Neuroendocrinol 2021; 62:100924. [PMID: 33992652 DOI: 10.1016/j.yfrne.2021.100924] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/18/2021] [Accepted: 05/11/2021] [Indexed: 12/17/2022]
Abstract
The perinatal period is a sensitive time in mammalian development that can have long-lasting consequences on offspring phenotype via maternal effects. Maternal effects have been most intensively studied with respect to two major conditions: maternal diet and maternal stress. In this review, we shift the focus by discussing five major additional maternal cues and their influence on offspring phenotype: maternal androgen levels, photoperiod (melatonin), microbiome, immune regulation, and milk composition. We present the key findings for each of these topics in mammals, their mechanisms of action, and how they interact with each other and with the maternal influences of diet and stress. We explore their impacts in the contexts of both predictive adaptive responses and the developmental origins of disease, identify knowledge gaps and research opportunities in the field, and place a particular emphasis on the application and consideration of these effects in non-model species and natural ecological systems.
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46
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Wang M, Xie J, Xu S. M6A-BiNP: predicting N 6-methyladenosine sites based on bidirectional position-specific propensities of polynucleotides and pointwise joint mutual information. RNA Biol 2021; 18:2498-2512. [PMID: 34161188 PMCID: PMC8632114 DOI: 10.1080/15476286.2021.1930729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) plays an important role in various biological processes. Identifying m6A site is a key step in exploring its biological functions. One of the biggest challenges in identifying m6A sites is how to extract features comprising rich categorical information to distinguish m6A and non-m6A sites. To address this challenge, we propose bidirectional dinucleotide and trinucleotide position-specific propensities, respectively, in this paper. Based on this, we propose two feature-encoding algorithms: Position-Specific Propensities and Pointwise Mutual Information (PSP-PMI) and Position-Specific Propensities and Pointwise Joint Mutual Information (PSP-PJMI). PSP-PMI is based on the bidirectional dinucleotide propensity and the pointwise mutual information, while PSP-PJMI is based on the bidirectional trinucleotide position-specific propensity and the proposed pointwise joint mutual information in this paper. We introduce parameters α and β in PSP-PMI and PSP-PJMI, respectively, to represent the distance from the nucleotide to its forward or backward adjacent nucleotide or dinucleotide, so as to extract features containing local and global classification information. Finally, we propose the M6A-BiNP predictor based on PSP-PMI or PSP-PJMI and SVM classifier. The 10-fold cross-validation experimental results on the benchmark datasets of non-single-base resolution and single-base resolution demonstrate that PSP-PMI and PSP-PJMI can extract features with strong capabilities to identify m6A and non-m6A sites. The M6A-BiNP predictor based on our proposed feature encoding algorithm PSP-PJMI is better than the state-of-the-art predictors, and it is so far the best model to identify m6A and non-m6A sites.
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Affiliation(s)
- Mingzhao Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Juanying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Shengquan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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47
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Loss of WTAP Impairs Early Parthenogenetic Embryo Development. Animals (Basel) 2021; 11:ani11061675. [PMID: 34199793 PMCID: PMC8229322 DOI: 10.3390/ani11061675] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/29/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
m6A is one of the most common and abundant modifications of RNA molecules present in eukaryotes. The methyltransferase complex, consisting of methyltransferase-like 3 (METTL3), METTL14, and WTAP, is responsible for the m6A modification of RNA. WTAP was identified as an mRNA splicing regulator. Its role as a regulatory subunit of the m6A methyltransferase complex in embryonic development remains largely unknown. To investigate the role of WTAP in porcine early embryonic development, si-WTAP was microinjected into porcine parthenogenetic zygotes. WTAP knockdown significantly reduced the blastocyst rate and global m6A levels, but did not affect the cleavage rate. Betaine was supplemented into the in vitro culture (IVC) to increase the m6A levels. Betaine significantly increased the global m6A levels but did not affect the blastocyst rate. Furthermore, the pluripotency genes, including OCT4, SOX2, and NANOG, were downregulated following WTAP knockdown. The apoptotic genes BAX and CASPASE 3 were upregulated, while the anti-apoptotic gene BCL2 was downregulated in WTAP knockdown blastocysts. TUNEL staining revealed that the number of apoptotic cells was significantly increased following WTAP knockdown. Our study indicated that WTAP has an indispensable role in porcine early embryonic development.
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48
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Sun M, Zhang X. Epigenetic regulation of N6-methyladenosine modifications in obesity. J Diabetes Investig 2021; 12:1306-1315. [PMID: 33979018 PMCID: PMC8354493 DOI: 10.1111/jdi.13571] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/28/2021] [Accepted: 05/06/2021] [Indexed: 01/21/2023] Open
Abstract
Obesity is a serious health issue in the world and is related to a higher risk of suffering metabolic diseases. Understanding the molecular basis of obesity is critical to identify new targets to treat obesity and obesity-associated metabolic diseases. N6-methyladenosine (m6A) modification is the most common form of ribonucleic acid modification, which has attracted increasing interest of researchers in recent years, as it is reported that m6A has vital functions in diseases and everyday life activities. Recent studies showed that m6A modification was decreased in obese adipose tissue, and appeared to play a regulatory role in many obesity-associated biological processes, including adipogenesis, lipid metabolism and insulin resistance. In this review, we discussed the emerging advances in m6A modification in obesity to provide a novel therapeutic strategy for fighting against obesity.
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Affiliation(s)
- Mingli Sun
- School of Kinesiology, Shenyang Sport University, Shenyang, China
| | - Xinan Zhang
- School of Kinesiology, Shenyang Sport University, Shenyang, China
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49
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Pan ZP, Wang B, Hou DY, You RL, Wang XT, Xie WH, Huang HF. METTL3 mediates bone marrow mesenchymal stem cell adipogenesis to promote chemoresistance in acute myeloid leukaemia. FEBS Open Bio 2021; 11:1659-1672. [PMID: 33932138 PMCID: PMC8167861 DOI: 10.1002/2211-5463.13165] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/13/2021] [Accepted: 04/12/2021] [Indexed: 02/02/2023] Open
Abstract
Adipogenesis of bone marrow mesenchymal stem cells (MSCs) promotes chemoresistance of acute myeloid leukaemia (AML) cells. MSCs from AML patients (AML‐MSCs) display enhanced adipogenesis compared with bone marrow MSCs from healthy donors. However, the precise molecular mechanism by which adipogenesis of MSCs from AML marrow differs from normal counterparts remains obscure. We found that METTL3 significantly inhibits MSC adipogenesis. Here, we aimed to identify the molecular mechanism linking METTL3 and MSC adipogenesis. Analysis of m6A epigenetic changes in MSCs determined via RIP‐qPCR and MeRIP‐qPCR indicated that METTL3 affects AKT protein expression in MSCs by mediating m6A modification of AKT1‐mRNA. Downregulated METTL3 expression in AML‐MSCs induced an increase in AKT protein, resulting in enhanced MSC adipogenesis, thereby contributing to chemoresistance in AML cells. Therefore, targeting AKT regulation by mRNA modification in MSC adipogenesis might provide a novel therapeutic strategy to overcome AML chemoresistance.
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Affiliation(s)
- Zhi-Peng Pan
- Central Laboratory, Fujian Medical University Union Hospital, China
| | - Bin Wang
- Central Laboratory, Fujian Medical University Union Hospital, China.,Clinical Laboratory, Fujian Maternal and Child Health Hospital, Fujian Children's Hospital, China
| | - Di-Yu Hou
- Central Laboratory, Fujian Medical University Union Hospital, China
| | - Ruo-Lan You
- Central Laboratory, Fujian Medical University Union Hospital, China
| | - Xiao-Ting Wang
- Central Laboratory, Fujian Medical University Union Hospital, China
| | - Wen-Hui Xie
- Graduate School, Fujian Medical University, Fujian Medical University Union Hospital, China
| | - Hui-Fang Huang
- Central Laboratory, Fujian Medical University Union Hospital, China
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Zhang Y, Wang Y, Ying L, Tao S, Shi M, Lin P, Wang Y, Han B. Regulatory Role of N6-methyladenosine (m 6A) Modification in Osteosarcoma. Front Oncol 2021; 11:683768. [PMID: 34094986 PMCID: PMC8170137 DOI: 10.3389/fonc.2021.683768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022] Open
Abstract
Osteosarcoma is the most common primary bone malignancy, typically occurring in childhood or adolescence. Unfortunately, the clinical outcomes of patients with osteosarcoma are usually poor because of the aggressive nature of this disease and few treatment advances in the past four decades. N6-methyladenosine (m6A) is one of the most extensive forms of RNA modification in eukaryotes found both in coding and non-coding RNAs. Accumulating evidence suggests that m6A-related factors are dysregulated in multiple osteosarcoma processes. In this review, we highlight m6A modification implicated in osteosarcoma, describing its pathophysiological role and molecular mechanism, as well as future research trends and potential clinical application in osteosarcoma.
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Affiliation(s)
- Yujie Zhang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanyan Wang
- Department of Oncology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liwei Ying
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sifeng Tao
- Department of Oncology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mingmin Shi
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peng Lin
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yangxin Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Han
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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