1
|
Ahi EP, Singh P. Emerging Orchestrator of Ecological Adaptation: m 6A Regulation of Post-Transcriptional Mechanisms. Mol Ecol 2024:e17545. [PMID: 39367666 DOI: 10.1111/mec.17545] [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: 02/09/2024] [Revised: 09/01/2024] [Accepted: 09/19/2024] [Indexed: 10/06/2024]
Abstract
Genetic mechanisms have been at the forefront of our exploration into the substrate of adaptive evolution and phenotypic diversification. However, genetic variation only accounts for a fraction of phenotypic variation. In the last decade, the significance of RNA modification mechanisms has become more apparent in the context of organismal adaptation to rapidly changing environments. RNA m6A methylation, the most abundant form of RNA modification, is emerging as a potentially significant player in various biological processes. Despite its fundamental function to regulate other major post-transcriptional mechanisms such as microRNA and alternative splicing, its role in ecology and evolution has been understudied. This review highlights the potential importance of m6A RNA methylation in ecological adaptation, emphasising the need for further research, especially in natural systems. We focus on how m6A not only affects mRNA fate but also influences miRNA-mediated gene regulation and alternative splicing, potentially contributing to organismal adaptation. The aim of this review is to synthesise key background information to enhance our understanding of m6A mechanisms driving species survival in dynamic environments and motivate future research into the dynamics of adaptive RNA methylation.
Collapse
Affiliation(s)
- Ehsan Pashay Ahi
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Pooja Singh
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| |
Collapse
|
2
|
Zhang Y, Chen XN, Zhang H, Wen JK, Gao HT, Shi B, Wang DD, Han ZW, Gu JF, Zhao CM, Xue WY, Zhang YP, Qu CB, Yang Z. CDK13 promotes lipid deposition and prostate cancer progression by stimulating NSUN5-mediated m5C modification of ACC1 mRNA. Cell Death Differ 2023; 30:2462-2476. [PMID: 37845385 PMCID: PMC10733287 DOI: 10.1038/s41418-023-01223-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) regulate cell cycle progression and the transcription of a number of genes, including lipid metabolism-related genes, and aberrant lipid metabolism is involved in prostate carcinogenesis. Previous studies have shown that CDK13 expression is upregulated and fatty acid synthesis is increased in prostate cancer (PCa). However, the molecular mechanisms linking CDK13 upregulation and aberrant lipid metabolism in PCa cells remain largely unknown. Here, we showed that upregulation of CDK13 in PCa cells increases the fatty acyl chains and lipid classes, leading to lipid deposition in the cells, which is positively correlated with the expression of acetyl-CoA carboxylase (ACC1), the first rate-limiting enzyme in fatty acid synthesis. Gain- and loss-of-function studies showed that ACC1 mediates CDK13-induced lipid accumulation and PCa progression by enhancing lipid synthesis. Mechanistically, CDK13 interacts with RNA-methyltransferase NSUN5 to promote its phosphorylation at Ser327. In turn, phosphorylated NSUN5 catalyzes the m5C modification of ACC1 mRNA, and then the m5C-modified ACC1 mRNA binds to ALYREF to enhance its stability and nuclear export, thereby contributing to an increase in ACC1 expression and lipid deposition in PCa cells. Overall, our results disclose a novel function of CDK13 in regulating the ACC1 expression and identify a previously unrecognized CDK13/NSUN5/ACC1 pathway that mediates fatty acid synthesis and lipid accumulation in PCa cells, and targeting this newly identified pathway may be a novel therapeutic option for the treatment of PCa.
Collapse
Affiliation(s)
- Yong Zhang
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
| | - Xiao-Nan Chen
- Department of Urology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, 110004, P R China
| | - Hong Zhang
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Jin-Kun Wen
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Hai-Tao Gao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Bei Shi
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Dan-Dan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Zhen-Wei Han
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Jun-Fei Gu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chen-Ming Zhao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Wen-Yong Xue
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Yan-Ping Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chang-Bao Qu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
| | - Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
| |
Collapse
|
3
|
Integrated Analysis of N1-Methyladenosine Methylation Regulators-Related lncRNAs in Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:cancers15061800. [PMID: 36980686 PMCID: PMC10046959 DOI: 10.3390/cancers15061800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
N1-methyladenosine (m1A) and long non-coding RNAs (lncRNAs) play significant roles in tumor progression in hepatocellular carcinoma (HCC). However, their association with HCC is still unclear. In this study, lncRNAs related to m1A were extracted from the mRNA expression matrix in The Cancer Genome Atlas (TCGA) database. Five m1A-related lncRNAs (AL031985.3, NRAV, WAC-AS1, AC026412.3, and AC099850.4) were identified based on lasso Cox regression and they generated a prognostic signature of HCC. The prognostic signature was identified as an independent prognosis factor in HCC patients. Moreover, the prognostic signature achieved better performance than TP53 mutation status or tumor mutational burden (TMB) scores in the stratification of patient survival. The immune landscape indicated that most immune checkpoint genes and immune cells were distributed differently between both risk groups. A higher IC50 of chemotherapeutics (sorafenib, nilotinib, sunitinib, and gefitinib) was observed in the high-risk group, and a lower IC50 of gemcitabine in the low-risk group, suggesting the potential of the prognostic signature in chemosensitivity. In addition, fifty-five potential small molecular drugs were found based on drug sensitivity and NRAV expression. Together, five m1A-related lncRNAs generated a prognostic signature that could be a promising prognostic prediction approach and therapeutic response assessment tool for HCC patients.
Collapse
|
4
|
Zhang C, Yi X, Hou M, Li Q, Li X, Lu L, Qi E, Wu M, Qi L, Jian H, Qi Z, Lv Y, Kong X, Bi M, Feng S, Zhou H. The landscape of m 1A modification and its posttranscriptional regulatory functions in primary neurons. eLife 2023; 12:85324. [PMID: 36880874 PMCID: PMC9991057 DOI: 10.7554/elife.85324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Cerebral ischaemia‒reperfusion injury (IRI), during which neurons undergo oxygen-glucose deprivation/reoxygenation (OGD/R), is a notable pathological process in many neurological diseases. N1-methyladenosine (m1A) is an RNA modification that can affect gene expression and RNA stability. The m1A landscape and potential functions of m1A modification in neurons remain poorly understood. We explored RNA (mRNA, lncRNA, and circRNA) m1A modification in normal and OGD/R-treated mouse neurons and the effect of m1A on diverse RNAs. We investigated the m1A landscape in primary neurons, identified m1A-modified RNAs, and found that OGD/R increased the number of m1A RNAs. m1A modification might also affect the regulatory mechanisms of noncoding RNAs, e.g., lncRNA-RNA binding proteins (RBPs) interactions and circRNA translation. We showed that m1A modification mediates the circRNA/lncRNA‒miRNA-mRNA competing endogenous RNA (ceRNA) mechanism and that 3' untranslated region (3'UTR) modification of mRNAs can hinder miRNA-mRNA binding. Three modification patterns were identified, and genes with different patterns had intrinsic mechanisms with potential m1A-regulatory specificity. Systematic analysis of the m1A landscape in normal and OGD/R neurons lays a critical foundation for understanding RNA modification and provides new perspectives and a theoretical basis for treating and developing drugs for OGD/R pathology-related diseases.
Collapse
Affiliation(s)
- Chi Zhang
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Xianfu Yi
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical UniversityTianjinChina
| | - Mengfan Hou
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Qingyang Li
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Xueying Li
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Lu Lu
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Enlin Qi
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Mingxin Wu
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Lin Qi
- Department of Orthopedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South UniversityChangshaChina
| | - Huan Jian
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Zhangyang Qi
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Yigang Lv
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Xiaohong Kong
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Mingjun Bi
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Shiqing Feng
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Hengxing Zhou
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| |
Collapse
|
5
|
Sarraf G, Chhabra R. Emerging role of mRNA methylation in regulating the hallmarks of cancer. Biochimie 2023; 206:61-72. [PMID: 36244577 DOI: 10.1016/j.biochi.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/29/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
Abstract
The dynamic chemical modifications of DNA, RNA, and proteins can transform normal cells into malignant ones. While the DNA and protein modifications in cancer have been described extensively in the literature, there are fewer reports about the role of RNA modifications in cancer. There are over 100 forms of RNA modifications and one of these, mRNA methylation, plays a critical role in the malignant properties of the cells. mRNA methylation is a reversible modification responsible for regulating protein expression at the post-transcriptional level. Despite being discovered in the 1970s, a complete understanding of the different proteins involved and the mechanism behind mRNA methylation remains largely unknown. However, these mRNA methylations have been shown to foster cancer hallmarks via specific cellular targets inside the cell. In this review, we provide a brief overview of mRNA methylation and its emerging role in regulating the various hallmarks of cancer.
Collapse
Affiliation(s)
- Gargi Sarraf
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India.
| |
Collapse
|
6
|
Knockdown of METTL16 disrupts learning and memory by reducing the stability of MAT2A mRNA. Cell Death Dis 2022; 8:432. [PMID: 36307396 PMCID: PMC9616879 DOI: 10.1038/s41420-022-01220-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/18/2022]
Abstract
N6-methyladenosine (m6A) is abundant in the mammalian brain and is considered to have a wide range of effects on learning and memory. Here, we found that the upregulated methyltransferase-like protein 16 (METTL16) in the hippocampal tissues of Morris water maze (MWM)-trained mice contributed to improved memory formation and hippocampal synaptic plasticity. Mechanismly, METTL16 promoted the expression of methionine adenosyltransferase 2A (MAT2A) by the m6A methylation of the MAT2A mRNA-3′UTR-end to increase its stability, and this involved in improving hippocampal global m6A levels, plasticity of dendritic spine, learning and memory. This study provides a new perspective to explore the regulatory mechanisms of m6A for learning and memory. ![]()
Collapse
|
7
|
Peng J, Ghosh D, Zhang F, Yang L, Wu J, Pang J, Zhang L, Yin S, Jiang Y. Advancement of epigenetics in stroke. Front Neurosci 2022; 16:981726. [PMID: 36312038 PMCID: PMC9610114 DOI: 10.3389/fnins.2022.981726] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/27/2022] [Indexed: 10/14/2023] Open
Abstract
A wide plethora of intervention procedures, tissue plasminogen activators, mechanical thrombectomy, and several neuroprotective drugs were reported in stroke research over the last decennium. However, against this vivid background of newly emerging pieces of evidence, there is little to no advancement in the overall functional outcomes. With the advancement of epigenetic tools and technologies associated with intervention medicine, stroke research has entered a new fertile. The stroke involves an overabundance of inflammatory responses arising in part due to the body's immune response to brain injury. Neuroinflammation contributes to significant neuronal cell death and the development of functional impairment and even death in stroke patients. Recent studies have demonstrated that epigenetics plays a key role in post-stroke conditions, leading to inflammatory responses and alteration of the microenvironment within the injured tissue. In this review, we summarize the progress of epigenetics which provides an overview of recent advancements on the emerging key role of secondary brain injury in stroke. We also discuss potential epigenetic therapies related to clinical practice.
Collapse
Affiliation(s)
- Jianhua Peng
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China
- Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Dipritu Ghosh
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Fan Zhang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lei Yang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinpeng Wu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinwei Pang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lifang Zhang
- Sichuan Clinical Research Center for Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shigang Yin
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China
| | - Yong Jiang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China
- Sichuan Clinical Research Center for Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| |
Collapse
|
8
|
Roy B, Ochi S, Dwivedi Y. M6A RNA Methylation-Based Epitranscriptomic Modifications in Plasticity-Related Genes via miR-124-C/EBPα-FTO-Transcriptional Axis in the Hippocampus of Learned Helplessness Rats. Int J Neuropsychopharmacol 2022; 25:1037-1049. [PMID: 36161325 PMCID: PMC9743968 DOI: 10.1093/ijnp/pyac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Impaired synaptic plasticity has been linked to dynamic gene regulatory network changes. Recently, gene regulation has been introduced with the emerging concept of unique N6-methyladenosine (m6A)-based reversible transcript methylation. In this study, we tested whether m6A RNA methylation may potentially serve as a link between the stressful insults and altered expression of plasticity-related genes. METHODS Expression of plasticity genes Nr3c1, Creb1, Ntrk2; m6A-modifying enzymes Fto, methyltransferase like (Mettl)-3 and 14; DNA methylation enzymes Dnmt1, Dnmt3a; transcription factor C/ebp-α; and miRNA-124-3p were determined by quantitative polymerase chain reaction (qPCR) in the hippocampus of rats that showed susceptibility to develop stress-induced depression (learned helplessness). M6A methylation of plasticity-related genes was determined following m6A mRNA immunoprecipitation. Chromatin immunoprecipitation was used to examine the endogenous binding of C/EBP-α to the Fto promoter. MiR-124-mediated post-transcriptional inhibition of Fto via C/EBPα was determined using an in vitro model. RESULTS Hippocampus of learned helplessness rats showed downregulation of Nr3c1, Creb1, and Ntrk2 along with enrichment in their m6A methylation. A downregulation in demethylating enzyme Fto and upregulation in methylating enzyme Mettl3 were also noted. The Fto promoter was hypomethylated due to the lower expression of Dnmt1 and Dnmt3a. At the same time, there was a lower occupancy of transcription factor C/EBPα on the Fto promoter. Conversely, C/ebp-α transcript was downregulated via induced miR-124-3p expression. CONCLUSIONS Our study mechanistically linked defective C/EBP-α-FTO-axis, epigenetically influenced by induced expression of miR-124-3p, in modifying m6A enrichment in plasticity-related genes. This could potentially be linked with abnormal neuronal plasticity in depression.
Collapse
Affiliation(s)
- Bhaskar Roy
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama atBirmingham, Birmingham, Alabama, USA
| | - Shinichiro Ochi
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama atBirmingham, Birmingham, Alabama, USA,Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yogesh Dwivedi
- Correspondence: Yogesh Dwivedi, PhD, Elesabeth Ridgely Shook Professor, Director of Translational Research, UAB Mood Disorder Program, Codirector, Depression and Suicide Center, Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, SC711 Sparks Center, 1720 2nd Avenue South, Birmingham, AL, USA ()
| |
Collapse
|
9
|
Bao G, Li T, Guan X, Yao Y, Liang J, Xiang Y, Zhong X. Comprehensive Analysis of the Function, Immune Profiles, and Clinical Implication of m1A Regulators in Lung Adenocarcinoma. Front Oncol 2022; 12:882292. [PMID: 35712502 PMCID: PMC9197195 DOI: 10.3389/fonc.2022.882292] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Background Previous studies have demonstrated that transcriptional RNA methyladenosine modification significantly affects tumor initiation and progression. However, clinical implications of N1-methyladenosine (m1A) regulators and their effect on tumor immunity in lung adenocarcinoma (LUAD) are still poorly elucidated. Methods Herein, the characteristics of somatic mutation, copy number variation (CNV), DNA methylation, and expression levels of m1A regulators were thoroughly analyzed. We classified 955 lung adenocarcinoma patients into different m1A modification patterns based on an unsupervised consensus clustering algorithm. We then calculated the differences in gene expression, prognosis outcomes, and immune profiles among different m1A clusters. Subsequently, we screened differently expressed genes (DEGs) related to prognosis among different m1A clusters. We identified m1A related gene clusters according to the prognosis-related different expressed genes. We further constructed a scoring standard named the m1A score and comprehensively analyzed the survival outcomes, clinical-pathological features, immune microenvironment, treatment responses of immunotherapy, and drug susceptibility in different m1A score groups. Results In total, three different m1A modification patterns were identified, which contained cluster A, B, and C. Among them, cluster A processed the poorest clinical outcomes, the lowest immune cell infiltration rate, and the highest tumor purity score. Then, three m1A gene clusters (gene cluster A, B, C) were speculated. Subsequently, we combined m1A modification patterns and m1A gene cluster to classify lung adenocarcinoma patients into high and low m1A score groups. The low m1A score group was accompanied by higher mortality, higher tumor mutation burden (TMB) and genome mutation frequency, and lower programmed cell death-Ligand 1 (PD-L1) expression and tumor immune dysfunction and exclusion (TIDE) expression. Moreover, the m1A score exhibited positive correlation with almost all immune cells. Finally, common chemotherapeutic and targeted therapy agents exhibited obvious differences in drug susceptibility in different m1A score groups. Conclusions Collectively, we explored the potential value of m1A regulators in the prognosis and treatment of lung adenocarcinoma in multiple dimensions and provided some preliminary basis for the follow-up study of m1A regulators in lung adenocarcinoma.
Collapse
Affiliation(s)
- Guangyao Bao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi’an, China
- *Correspondence: Xinwen Zhong, ; Tian Li,
| | - Xiaojiao Guan
- Department of Pathology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Yao Yao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Jie Liang
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yifang Xiang
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Xinwen Zhong
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
- *Correspondence: Xinwen Zhong, ; Tian Li,
| |
Collapse
|
10
|
The Effects of Moxibustion on Learning and Memory and m6A RNA Methylation in APP/PS1 Mice. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2998301. [PMID: 35356237 PMCID: PMC8959951 DOI: 10.1155/2022/2998301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/18/2022] [Accepted: 02/18/2022] [Indexed: 12/30/2022]
Abstract
Objectives To study whether moxibustion can improve the learning and memory ability of APP/PS1 mice by reducing the pathological products Aβ and Tau protein via decreasing N6-methyladenosine (m6A). Methods APP/PS1 mice were randomly divided into model group (APP/PS1) and moxibustion group (APP/PS1+Mox). C57BL/6J mice were used as a control group (Control). Learning and memory abilities were assessed by the Morris water maze. Aβ, Tau, phosphorylated Tau (p-Tau), and YTHDF1 proteins were detected in the mouse cortex and hippocampus by immunofluorescence and western blot. Altered m6A expression levels in hippocampal and cortical tissues were measured with the m6A RNA methylation quantification assay kit. RNA transcript levels of YTHDF1, METTL3, and FTO in the hippocampus and cortex were measured by q-PCR. Results Moxibustion shortened the escape latency, increased the number of platform crossings, and increased the percentage of swimming time in the target quadrant of APP/PS1 mice. Meanwhile, moxibustion reduced the levels of Aβ, Tau, and p-Tau proteins both in the hippocampal and cortical regions of APP/PS1 mice. In addition, the total amount of m6A in the hippocampal and cortical regions of APP/PS1 mice was significantly reduced after moxibustion. The expression of YTHDF1 in the hippocampal region of APP/PS1 mice increased and that in the cortical region decreased after moxibustion treatment. Conclusion Moxibustion improves the learning and memory abilities and reduces the deposition of Aβ and Tau protein pathological products in APP/PS1 mice. This may be related to the fact that moxibustion reduces the total amount of m6A and inhibits its binding enzyme YTHDF1 in the hippocampus and cortex of APP/PS1 mice.
Collapse
|
11
|
Zhang R, Zhang Y, Guo F, Li S, Cui H. RNA N6-Methyladenosine Modifications and Its Roles in Alzheimer's Disease. Front Cell Neurosci 2022; 16:820378. [PMID: 35401117 PMCID: PMC8989074 DOI: 10.3389/fncel.2022.820378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of epitranscriptomics in regulating gene expression has received widespread attention. Recently, RNA methylation modifications, particularly N6-methyladenosine (m6A), have received marked attention. m6A, the most common and abundant type of eukaryotic methylation modification in RNAs, is a dynamic reversible modification that regulates nuclear splicing, stability, translation, and subcellular localization of RNAs. These processes are involved in the occurrence and development of many diseases. An increasing number of studies have focused on the role of m6A modification in Alzheimer's disease, which is the most common neurodegenerative disease. This review focuses on the general features, mechanisms, and functions of m6A methylation modification and its role in Alzheimer's disease.
Collapse
Affiliation(s)
- Runjiao Zhang
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
| | - Yizhou Zhang
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China
| | - Fangzhen Guo
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
| | - Sha Li
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China
| | - Huixian Cui
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China
| |
Collapse
|
12
|
Moura FH, Fonseca MA, Macias-Franco A, Archilia EC, Batalha IM, Pena-Bello CA, Silva AEM, Moreira GM, Schütz LF, Norris AB. Characterization of body composition and liver epigenetic markers during periods of negative energy balance and subsequent compensatory growth in postpubertal beef bulls. J Anim Sci 2022; 100:6532621. [PMID: 35184171 PMCID: PMC9036401 DOI: 10.1093/jas/skac047] [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: 12/23/2021] [Accepted: 02/16/2022] [Indexed: 11/14/2022] Open
Abstract
This study aimed to characterize the effects of dietary restriction and subsequent re-alimentation on body composition and hepatic gene expression of epigenetic markers of DNA methylation, RNA m6A methylation, and histone acetylation in the liver of postpubertal beef bulls. Twelve Angus × Hereford crossbred bulls (n = 6, 23 ± 0.55 mo [young bulls], 558 ± 6.1 kg; and n = 6, 47 ± 1.2 mo [mature bulls], 740 ± 30.5 kg) were submitted to two dietary regimes per offering of the same hay: low plane of nutrition (90 d) and compensatory growth (90 d). Each animal acted as its own control and were fed Beardless wheat (Triticum aestivum) hay and mineral mix during the trial. Statistical analyses were performed using SAS 9.4 following a pre-post repeated measures design. Bulls in negative energy balance (NEB) decreased (P < 0.001) empty body weight (EBW; 23.1% [-139.1 kg]), empty body fat (EBF; 39.8% [-85.4 kg]), and empty body protein (EBP; 14.9% [-13.5 kg]) and fully recovered at the end of the trial. Body fat accounted for 77.1% of daily changes in body energy status, whereas body protein accounted for only 22.9% (P < 0.001). Relative abundance of epigenetic markers transcripts was analyzed via qPCR. Bulls at NEB tended (P ≤ 0.097) to increase gene expression of epigenetic markers of RNA m6A methylation (METTL14, VIRMA, and WTAP) and increased (P ≤ 0.050) the gene expression of epigenetic markers of DNA methylation (DNMT3A) and histone-acetylation (SIRT3 and SIRT7). Young bulls had a tendency (P ≤ 0.072) of higher RNA m6A methylation, VIRMA, and WTAP than mature bulls. Effect of diet × age interaction was not detected (P ≥ 0.137) for METTL14, VIRMA, WTAP, DNMT3A, SIRT3, or SIRT7. Younger bulls tended to have greater RNA m6A methylation levels than mature bulls, indicating that, while contemporaneously fed the same diet during periods of undernourishment followed by compensatory growth, age has an impact on this epigenetic mechanism. In conclusion, metabolic status seems to carry a greater impact on regulating bovine hepatic epigenetic mechanisms that modulate gene transcription, such as DNA methylation and histone acetylation, than on epigenetic mechanisms that regulate gene translation, such as RNA m6A methylation. During periods of undernourishment followed by compensatory growth, body fat pools appear to change more dynamically and are easily detected having a greater impact on epigenetic markers that modulate hepatic gene transcription rather than translation.
Collapse
Affiliation(s)
- Felipe H Moura
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Reno, NV 89557, USA
| | - Mozart A Fonseca
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Reno, NV 89557, USA,Corresponding author:
| | - Arturo Macias-Franco
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Reno, NV 89557, USA
| | - Evandro C Archilia
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Reno, NV 89557, USA
| | - Isadora M Batalha
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Reno, NV 89557, USA
| | - Camilo A Pena-Bello
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Reno, NV 89557, USA
| | - Aghata E M Silva
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Reno, NV 89557, USA
| | - Gabriel M Moreira
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Reno, NV 89557, USA
| | - Luis F Schütz
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Reno, NV 89557, USA
| | - Aaron B Norris
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX 79430, USA
| |
Collapse
|
13
|
Li K, Gao S, Ma L, Sun Y, Peng ZY, Wu J, Du N, Ren H, Tang SC, Sun X. Stimulation of Let-7 Maturation by Metformin Improved the Response to Tyrosine Kinase Inhibitor Therapy in an m6A Dependent Manner. Front Oncol 2022; 11:731561. [PMID: 35070958 PMCID: PMC8770959 DOI: 10.3389/fonc.2021.731561] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 12/09/2021] [Indexed: 12/29/2022] Open
Abstract
The molecular mechanism of the tyrosine kinase inhibitor (TKI) resistant lung adenocarcinoma is currently unclear, and the role of methylated adenosine at the N6 position in the resistance of cancer stem cells (CSCs) therapy is unknown. This study identified a novel and effective strategy to enhance TKIs therapy response. We first confirmed the sensitization of Metformin enforcing on Osimertinib treatment and revealed the mature miRNAs signatures of the Osimertinib resistant H1975 and HCC827 cells. Let-7b expression was stimulated when adding Metformin and then increasing the therapy sensitivity by decreasing the stem cell groups expanding. Methyltransferase-like 3 (METTL3) increased the pri-Let-7b, decreased both the pre-Let-7b and mature Let-7b, attenuating the Let-7b controlling of stem cell renewal. The addition of Metformin increased the bindings of DNA methyltransferase-3a/b (DNMT3a/b) to the METTL3 promoter. With the help of the readers of NKAP and HNRNPA2B1, the cluster mediated m6A formation on pri-Let-7b processing increased the mature Let-7b, the key player in suppressing Notch signaling and re-captivating Osimertinib treatment. We revealed that the maturation processing signaling stimulated the methylation regulation of the miRNAs, and may determine the stemness control of the therapy resistance. Our findings may open up future drug development, targeting this pathway for lung cancer patients.
Collapse
Affiliation(s)
- Kai Li
- Department of Thoracic Surgery, Department of Thoracic Surgery and Oncology, Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China
| | - Shan Gao
- Department of Thoracic Surgery, Department of Thoracic Surgery and Oncology, Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China
| | - Lei Ma
- Department of Anesthesiology and Perioperative Medicine, Operating Centre, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China
| | - Ye Sun
- Department of Anesthesiology and Operation, Operating Centre, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China
| | - Zi-Yang Peng
- Department of Thoracic Surgery, Department of Thoracic Surgery and Oncology, Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China
| | - Jie Wu
- Department of Thoracic Surgery, Department of Thoracic Surgery and Oncology, Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China
| | - Ning Du
- Department of Thoracic Surgery, Department of Thoracic Surgery and Oncology, Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China
| | - Hong Ren
- Department of Thoracic Surgery, Department of Thoracic Surgery and Oncology, Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China
| | - Shou-Ching Tang
- University of Mississippi Medical Center, Cancer Center and Research Institute, University of Mississippi, Jackson, MS, United States
| | - Xin Sun
- Department of Thoracic Surgery, Department of Thoracic Surgery and Oncology, Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China
| |
Collapse
|
14
|
Li M, Zhong X, Zhao Z, Zeng Z, Yuan Q, Xiao X, Zu X, Liu J. The expression of m6A enzymes in the hippocampus of diabetic cognitive impairment mice and the possible improvement of YTHDF1. Brain Res 2021; 1777:147766. [PMID: 34953798 DOI: 10.1016/j.brainres.2021.147766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022]
Abstract
Cognitive impairment is a severe diabetes-related complication and seriously challenges the demand for future health resources. However, the potential therapeutic targets and mechanisms are not fully understood. Herein, we investigated the expression of the m6A enzyme in the hippocampus of mice with diabetes-induced cognitive impairment and possible improvement with overexpression of YTHDF1. A type 1 diabetes (T1D) mouse model was established by streptozotocin (STZ) intraperitoneal injection. Diabetic mice showed significant cognitive dysfunction, which was detected by novel object recognition tests and novel place recognition tests. Western blot analysis showed that compared with the control group, the protein levels of YTHDC2 and ALKBH5 were significantly upregulated in the hippocampus in the STZ group, while the expression of YTHDF1, YTHDF3 and WTAP was significantly downregulated. Furthermore, overexpression of YTHDF1 by AAV-YTHDF1 injection in the hippocampus significantly improved STZ-induced diabetic cognitive dysfunction. These results indicate that the m6A enzyme may play a key role in the cognitive dysfunction induced by diabetes, and YTHDF1 may be a promising therapeutic target.
Collapse
Affiliation(s)
- Menglin Li
- The First Affiliated Hospital, Department of Endocrinology and Metabolism, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Xiaolin Zhong
- The First Affiliated Hospital, Department of Endocrinology and Metabolism, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Zhibo Zhao
- The First Affiliated Hospital, Department of Endocrinology and Metabolism, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Zhaolin Zeng
- The First Affiliated Hospital, Department of Endocrinology and Metabolism, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Qing Yuan
- The First Affiliated Hospital, Department of Endocrinology and Metabolism, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Xinhua Xiao
- The First Affiliated Hospital, Department of Endocrinology and Metabolism, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Xuyu Zu
- The First Affiliated Hospital, Department of Endocrinology and Metabolism, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China; The First Affiliated Hospital, Institute of Clinical Medicine Center, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.
| | - Jinghua Liu
- The First Affiliated Hospital, Department of Endocrinology and Metabolism, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.
| |
Collapse
|
15
|
Liu J, Chen C, Wang Y, Qian C, Wei J, Xing Y, Bai J. Comprehensive of N1-Methyladenosine Modifications Patterns and Immunological Characteristics in Ovarian Cancer. Front Immunol 2021; 12:746647. [PMID: 34777359 PMCID: PMC8588846 DOI: 10.3389/fimmu.2021.746647] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/14/2021] [Indexed: 12/20/2022] Open
Abstract
Background recently, many researches have concentrated on the relevance between N1-methyladenosine (m1A) methylation modifications and tumor progression and prognosis. However, it remains unknown whether m1A modification has an effect in the prognosis of ovarian cancer (OC) and its immune infiltration. Methods Based on 10 m1A modulators, we comprehensively assessed m1A modification patterns in 474 OC patients and linked them to TME immune infiltration characteristics. m1Ascore computed with principal component analysis algorithm was applied to quantify m1A modification pattern in OC patients. m1A regulators protein and mRNA expression were respectively obtained by HPA website and RT-PCR in clinical OC and normal samples. Results We finally identified three different m1A modification patterns. The immune infiltration features of these m1A modification patterns correspond to three tumor immune phenotypes, including immune-desert, immune-inflamed and immune-excluded phenotypes. The results demonstrate individual tumor m1A modification patterns can predict patient survival, stage and grade. The m1Ascore was calculated to quantify individual OC patient's m1A modification pattern. A high m1Ascore is usually accompanied by a better survival advantage and a lower mutational load. Research on m1Ascore in the treatment of OC patients showed that patients with high m1Ascore showed marked therapeutic benefits and clinical outcomes in terms of chemotherapy and immunotherapy. Lastly, we obtained four small molecule drugs that may potentially ameliorate prognosis. Conclusion This research demonstrates that m1A methylation modification makes an essential function in the prognosis of OC and in shaping the immune microenvironment. Comprehensive evaluation of m1A modifications improves our knowledge of immune infiltration profile and provides a more efficient individualized immunotherapy strategy for OC patients.
Collapse
Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Can Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Yichun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cheng Qian
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Junting Wei
- The Second Clinical School of Nanjing Medical University, Nanjing, China
| | - Yan Xing
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianling Bai
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, Nanjing, China
| |
Collapse
|
16
|
Deng Y, Zhu H, Xiao L, Liu C, Liu YL, Gao W. Identification of the function and mechanism of m6A reader IGF2BP2 in Alzheimer's disease. Aging (Albany NY) 2021; 13:24086-24100. [PMID: 34705667 PMCID: PMC8610118 DOI: 10.18632/aging.203652] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/03/2021] [Indexed: 01/06/2023]
Abstract
Alzheimer’s disease, the most common form of dementia in the elderly, is a kind of neurodegenerative disease. However, its pathogenesis and diagnosis remain unclear. M6A is related to nervous system development and neurodegenerative diseases. Here in this study, using multiple RNA-seq datasets of Alzheimer’s brain tissues, along with bioinformatic analysis, we innovatively found that m6A reader protein IGF2BP2 was abnormally highly expressed in Alzheimer’s patients. After compared between Alzheimer’s and normal brain samples, and between IGF2BP2- high and IGF2BP2- low subgroups of Alzheimer’s patients, we took the shared differentially expressed genes as the relevant gene sets of IGF2PB2 affecting Alzheimer’s disease occurrence for subsequent analysis. Then, weight gene correlation analysis was conducted and 17 functional modules were identified. The module that most positively correlated with Alzheimer’s disease and IGF2PB2-high subgroups were mainly participated in ECM receptor interaction, focal adhesion, cytokine-cytokine receptor interaction, and TGF-beta signaling pathway. Afterwards, a hub gene-based model including 20 genes was constructed by LASSO regression and validated by ROC curve for Alzheimer diagnosis. Finally, we preliminarily elucidated that IGF2BP2 could bind with mRNAs in a m6A-dependent manner. This study first elucidates the pathogenic role of IGF2BP2 in Alzheimer’s disease. IGF2BP2 and its relevant m6A modifications are potential to be new diagnostic and therapeutic targets for Alzheimer’s patients.
Collapse
Affiliation(s)
- Yanyao Deng
- Department of Neurology, The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Hongwei Zhu
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Le Xiao
- Department of Neurology, The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Chao Liu
- Department of Neurology, The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Ya-Lin Liu
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China.,Xiangya School of Medicine, Central South University, Changsha, Hunan Province, China
| | - Wenzhe Gao
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| |
Collapse
|
17
|
Wang B, Niu L, Wang Z, Zhao Z. RNA m1A Methyltransferase TRMT6 Predicts Poorer Prognosis and Promotes Malignant Behavior in Glioma. Front Mol Biosci 2021; 8:692130. [PMID: 34631793 PMCID: PMC8493077 DOI: 10.3389/fmolb.2021.692130] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/11/2021] [Indexed: 12/26/2022] Open
Abstract
Background: Glioma is the most prevalent central nervous system tumor in humans, and its prognosis remains unsatisfactory due to a lack of effective therapeutic targets. The ectopic expression of N1-methyladenosine (m1A) regulators is a key participant in tumorigenesis and progression. However, the m1A regulator expression status, prognostic value, and relationship with tumor clinical features in glioma remain unclear. Methods: Public datasets were used to analyze the mRNA and protein expression levels of m1A regulators. Kaplan-Meier and Cox regression analyses were performed to confirm the prognostic value of m1A regulators in glioma. Cellular experiments were conducted to verify the effect of TRMT6 on cell function. A comprehensive bioinformatics analysis was conducted to identify the potential molecular mechanisms regulated by TEMT6 in glioma. Results: We found that the dysregulation of m1A regulators was closely associated with tumorigenesis and progression in glioma. Furthermore, TRMT6 might be a powerful and independent biomarker for prognosis in glioma. Our study showed that inhibition of TRMT6 suppressed the proliferation, migration, and invasion of glioma cells. Mechanistically, TRMT6 may be involved in glioma progression by regulating cell cycle, PI3K-AKT, TGF-beta, MTORC1, NOTCH, and MYC pathways. Conclusions: Variation in m1A regulators was closely associated with malignant progression in glioma. Silencing TRMT6 suppressed the cell proliferation, migration, and invasion in glioma. m1A regulators, especially TRMT6, might play an essential role in the malignant progression of glioma.
Collapse
Affiliation(s)
- Beibei Wang
- Pathology Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lihua Niu
- Pathology Department, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhengyang Wang
- Pathology Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhihua Zhao
- Pathology Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
18
|
Emerging Roles of N6-Methyladenosine Modification in Neurodevelopment and Neurodegeneration. Cells 2021; 10:cells10102694. [PMID: 34685675 PMCID: PMC8534826 DOI: 10.3390/cells10102694] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
N6-methyladenosine (m6A), the most abundant modification in messenger RNAs (mRNAs), is deposited by methyltransferases ("writers") Mettl3 and Mettl14 and erased by demethylases ("erasers") Fto and Alkbh5. m6A can be recognized by m6A-binding proteins ("readers"), such as Yth domain family proteins (Ythdfs) and Yth domain-containing protein 1 (Ythdc1). Previous studies have indicated that m6A plays an essential function in various fundamental biological processes, including neurogenesis and neuronal development. Dysregulated m6A modification contributes to neurological disorders, including neurodegenerative diseases. In this review, we summarize the current knowledge about the roles of m6A machinery, including writers, erasers, and readers, in regulating gene expression and the function of m6A in neurodevelopment and neurodegeneration. We also discuss the perspectives for studying m6A methylation.
Collapse
|
19
|
Abstract
Cancer is an unpleasant, painful disease. It is one of the most devastating diseases worldwide diminishing many lives. Many genetic and epigenetic changes occur before cancer develops. Mutation in SETD2 gene is one such example. RNA splicing, DNA damage repair, DNA methylation and histone methylation are some of the biological processes mediated by SETD2. SETD2 (histone H3 lysine 36 methyltransferase) is a frequently mutated gene in different types of cancer. Loss of SETD2 is associated with worse prognosis and aggressive phenotypes. Histone modification is one of the epigenetic regulation having a significant effect on gene regulation. N6-methyladenosine (m6A) mRNA modification is a well-known posttranscriptional modification playing a pivotal role in many normal and pathological processes affecting RNA metabolism. SETD2 catalyses H3K36 trimethylation and in turn H3K36me3 guides the deposition of m6A on nascent RNA transcripts. Finally, this review summarizes the deep understanding of the role of SETD2 in RNA methylation/modification and how SETD2 mutation contributes to tumour development.
Collapse
|
20
|
Qi Z, Li J, Li M, Du X, Zhang L, Wang S, Xu B, Liu W, Xu Z, Deng Y. The Essential Role of Epigenetic Modifications in Neurodegenerative Diseases with Dyskinesia. Cell Mol Neurobiol 2021; 42:2459-2472. [PMID: 34383231 DOI: 10.1007/s10571-021-01133-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/18/2021] [Indexed: 12/20/2022]
Abstract
Epigenetics play an essential role in the occurrence and improvement of many diseases. Evidence shows that epigenetic modifications are crucial to the regulation of gene expression. DNA methylation is closely linked to embryonic development in mammalian. In recent years, epigenetic drugs have shown unexpected therapeutic effects on neurological diseases, leading to the study of the epigenetic mechanism in neurodegenerative diseases. Unlike genetics, epigenetics modify the genome without changing the DNA sequence. Research shows that epigenetics is involved in all aspects of neurodegenerative diseases. The study of epigenetic will provide valuable insights into the molecular mechanism of neurodegenerative diseases, which may lead to new treatments and diagnoses. This article reviews the role of epigenetic modifications neurodegenerative diseases with dyskinesia, and discusses the therapeutic potential of epigenetic drugs in neurodegenerative diseases.
Collapse
Affiliation(s)
- Zhipeng Qi
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Jiashuo Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Minghui Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Xianchao Du
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Lei Zhang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Shuang Wang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Bin Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Wei Liu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Zhaofa Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China.
| |
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
Pan T, Wu F, Li L, Wu S, Zhou F, Zhang P, Sun C, Xia L. The role m 6A RNA methylation is CNS development and glioma pathogenesis. Mol Brain 2021; 14:119. [PMID: 34281602 PMCID: PMC8290532 DOI: 10.1186/s13041-021-00831-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
Epigenetic abnormalities play a crucial role in many tumors, including glioma. RNA methylation occurs as an epigenetic modification similar to DNA methylation and histone modification. m6A methylation is the most common and most intensively studied RNA methylation, which can be found throughout the RNA life cycle and exert biological functions by affecting RNA metabolism. The m6A modification is primarily associated with three types of protease, which are encoded by the writer, eraser and reader genes, respectively. It has been shown that the m6A methylation has close connections with the occurrence and development of many tumors, including glioma. In this study, the concept and the research progress of m6A methylation are reviewed, especially the role of m6A methylation in glioma. Moreover, we will discuss how glioma is paving the way to the development of new therapeutic options based on the inhibition of m6A deposition.
Collapse
Affiliation(s)
- Ting Pan
- School of the Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Department of Gynecological Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China
| | - Fan Wu
- School of the Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Liwen Li
- Department of Neurosurgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China.,Key Laboratory of Head & Neck Cancer, Translational Research of Zhejiang Province, Hangzhou, 310022, People's Republic of China
| | - Shiyan Wu
- School of the Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Department of Gynecological Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China
| | - Fang Zhou
- School of the Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Department of Gynecological Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China
| | - Ping Zhang
- Department of Gynecological Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China.
| | - Caixing Sun
- Department of Neurosurgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China. .,Key Laboratory of Head & Neck Cancer, Translational Research of Zhejiang Province, Hangzhou, 310022, People's Republic of China.
| | - Liang Xia
- Department of Neurosurgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China. .,Key Laboratory of Head & Neck Cancer, Translational Research of Zhejiang Province, Hangzhou, 310022, People's Republic of China.
| |
Collapse
|
23
|
Liu C, Yang Z, Li R, Wu Y, Chi M, Gao S, Sun X, Meng X, Wang B. Potential roles of N6-methyladenosine (m6A) in immune cells. J Transl Med 2021; 19:251. [PMID: 34103054 PMCID: PMC8186046 DOI: 10.1186/s12967-021-02918-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/29/2021] [Indexed: 12/20/2022] Open
Abstract
N6-methyl-adenosine (m6A) is one of the most common internal modifications on RNA molecules present in mammalian cells. Deregulation of m6A modification has been recently implicated in many types of human diseases. Therefore, m6A modification has become a research hotspot for its potential therapeutic applications in the treatment of various diseases. The immune system mostly involves different types of immune cells to provide the first line of defense against infections. The immunoregulatory network that orchestrate the immune responses to new pathogens plays a pivotal role in the development of the disease. And m6A modification has been demonstrated to be a major post-transcriptional regulator of immune responses in cells. In this review, we summarize the participants involved in m6A regulation and try to reveal how m6A modification affects the immune responses via changing the immunoregulatory networks.
Collapse
Affiliation(s)
- Chang Liu
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, No. 155 NanJing North Road, Shenyang, China
| | - Zhe Yang
- College of Life Science, Liaoning University, 66 Chongshan Road, Shenyang, 110036, People's Republic of China
| | - Rong Li
- College of Life Science, Liaoning University, 66 Chongshan Road, Shenyang, 110036, People's Republic of China
| | - Yanju Wu
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Ming Chi
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Shuting Gao
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Xun Sun
- Department of Immunology, College of Basic Medical Sciences of China Medical University, , No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Xin Meng
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Biao Wang
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China.
| |
Collapse
|
24
|
Sokpor G, Xie Y, Nguyen HP, Tuoc T. Emerging Role of m 6 A Methylome in Brain Development: Implications for Neurological Disorders and Potential Treatment. Front Cell Dev Biol 2021; 9:656849. [PMID: 34095121 PMCID: PMC8170044 DOI: 10.3389/fcell.2021.656849] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/07/2021] [Indexed: 12/22/2022] Open
Abstract
Dynamic modification of RNA affords proximal regulation of gene expression triggered by non-genomic or environmental changes. One such epitranscriptomic alteration in RNA metabolism is the installation of a methyl group on adenosine [N6-methyladenosine (m6A)] known to be the most prevalent modified state of messenger RNA (mRNA) in the mammalian cell. The methylation machinery responsible for the dynamic deposition and recognition of m6A on mRNA is composed of subunits that play specific roles, including reading, writing, and erasing of m6A marks on mRNA to influence gene expression. As a result, peculiar cellular perturbations have been linked to dysregulation of components of the mRNA methylation machinery or its cofactors. It is increasingly clear that neural tissues/cells, especially in the brain, make the most of m6A modification in maintaining normal morphology and function. Neurons in particular display dynamic distribution of m6A marks during development and in adulthood. Interestingly, such dynamic m6A patterns are responsive to external cues and experience. Specific disturbances in the neural m6A landscape lead to anomalous phenotypes, including aberrant stem/progenitor cell proliferation and differentiation, defective cell fate choices, and abnormal synaptogenesis. Such m6A-linked neural perturbations may singularly or together have implications for syndromic or non-syndromic neurological diseases, given that most RNAs in the brain are enriched with m6A tags. Here, we review the current perspectives on the m6A machinery and function, its role in brain development and possible association with brain disorders, and the prospects of applying the clustered regularly interspaced short palindromic repeats (CRISPR)–dCas13b system to obviate m6A-related neurological anomalies.
Collapse
Affiliation(s)
- Godwin Sokpor
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
| | - Yuanbin Xie
- Department of Biochemistry and Molecular Biology, Gannan Medical University, Ganzhou, China
| | - Huu P Nguyen
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
| | - Tran Tuoc
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
| |
Collapse
|
25
|
Wang Y, Jiang T, Xu J, Gu Y, Zhou Y, Lin Y, Wu Y, Li W, Wang C, Shen B, Mo X, Wang X, Zhou B, Ding C, Hu Z. Mutations in RNA Methyltransferase Gene NSUN5 Confer High Risk of Outflow Tract Malformation. Front Cell Dev Biol 2021; 9:623394. [PMID: 33968922 PMCID: PMC8097101 DOI: 10.3389/fcell.2021.623394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
NSUN5, encoding a cytosine-5 RNA methyltransferase and located in the 7q11.23 locus, is a candidate gene for tetralogy of Fallot (TOF). Deletion of the 7q11.23 locus in humans is linked to cardiac outflow tract (OFT) disorders including TOF. We identified four potential pathogenic mutations in the coding region of NSUN5 and which were enriched in TOF patients by an association study of 132 TOF patients and 2,000 in-house controls (P = 1.44 × 10-5). We then generated a Nsun5 null (Nsun5 -/-) mouse model to validate the human findings by defining the functions of Nsun5 in OFT morphogenesis. The OFT did not develop properly in the Nsun5 deletion embryonic heart. We found a misalignment of the aorta and septum defects caused by the delayed fusion of the membraneous ventricular spetum as an OFT development delay. This caused OFT development delay in 27 of 64 (42.2%) Nsun5 -/- mice. Moreover, we also found OFT development delay in 8 of 51 (15.7%) Nsun5 +/- mice. Further functional experiments showed that the loss of Nsun5 function impaired the 5-methylcytosine (m5C) modification and translation efficiency of essential cardiac genes. Nsun5 is required for normal OFT morphogenesis and it regulates the m5C modification of essential cardiac genes. Our findings suggest the involvement of NSUN5 in the pathogenesis of TOF.
Collapse
Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Jiani Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Yayun Gu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Yan Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Yuan Lin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Yifei Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Wei Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xuming Mo
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaowei Wang
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bin Zhou
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, United States
| | - Chenyue Ding
- Center of Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing, China
| |
Collapse
|
26
|
Wilkinson E, Cui YH, He YY. Context-Dependent Roles of RNA Modifications in Stress Responses and Diseases. Int J Mol Sci 2021; 22:ijms22041949. [PMID: 33669361 PMCID: PMC7920320 DOI: 10.3390/ijms22041949] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
RNA modifications are diverse post-transcriptional modifications that regulate RNA metabolism and gene expression. RNA modifications, and the writers, erasers, and readers that catalyze these modifications, serve as important signaling machineries in cellular stress responses and disease pathogenesis. In response to stress, RNA modifications are mobilized to activate or inhibit the signaling pathways that combat stresses, including oxidative stress, hypoxia, therapeutic stress, metabolic stress, heat shock, DNA damage, and ER stress. The role of RNA modifications in response to these cellular stressors is context- and cell-type-dependent. Due to their pervasive roles in cell biology, RNA modifications have been implicated in the pathogenesis of different diseases, including cancer, neurologic and developmental disorders and diseases, and metabolic diseases. In this review, we aim to summarize the roles of RNA modifications in molecular and cellular stress responses and diseases.
Collapse
|
27
|
Li J, Zhang C, Yuan X, Cao Y. Molecular Characteristics of N1-Methyladenosine Regulators and Their Correlation with Overall Cancer Survival. DNA Cell Biol 2021; 40:513-522. [PMID: 33416433 DOI: 10.1089/dna.2020.6214] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
N1-methyladenosine (m1A) is a prevalent RNA modification widely affecting RNA structural stability, folding, and interactions with proteins. Recently, there have been increasing reports on the roles of m1A regulators in tumors. However, their mechanisms and clinical relevance remain unclear. This study systematically evaluates the epigenetic characteristics and clinical relevance of m1A regulators using bioinformatic methods. Our results show widespread gene expression changes for m1A regulators, which are related to the activation and inhibition of carcinogenic pathways and overall patient survival. Collectively, this investigation provides new insights into assessing tumor prognosis and targeted therapy.
Collapse
Affiliation(s)
- Juan Li
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China.,Department of Infectious Diseases and The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Chunting Zhang
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China.,Department of Infectious Diseases and The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Xin Yuan
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China.,Department of Infectious Diseases and The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Yuan Cao
- Department of Gynaecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| |
Collapse
|
28
|
Guo W, Zhang C, Feng P, Li M, Wang X, Xia Y, Chen D, Li J. M6A methylation of DEGS2, a key ceramide-synthesizing enzyme, is involved in colorectal cancer progression through ceramide synthesis. Oncogene 2021; 40:5913-5924. [PMID: 34363020 PMCID: PMC8497269 DOI: 10.1038/s41388-021-01987-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent RNA epigenetic regulator in cancer. However, the understanding of m6A modification on lipid metabolism regulation in colorectal cancer (CRC) is very limited. Here, we observed that human CRCs exhibited increased m6A mRNA methylation mediated by dysregulation of m6A erasers and readers. By performing methylated RNA-immunoprecipitation sequencing (MeRIP-seq) and transcriptomic sequencing (RNA-seq), we identified DEGS2 as a downstream target of m6A dysregulation. Overexpression or knockdown of DEGS2 confirmed the role of DEGS2 in proliferation, invasion and metastasis of CRC both in vitro and in vivo. Mechanistic studies identified the specific m6A modification site within DEGS2 mRNA, and mutation of this target site was found to drastically enhance the proliferative and invasive ability of CRC cells in vitro and promote tumorigenicity in vivo. Lipidome analysis showed that lipid metabolism was dysregulated in CRC. Moreover, ceramide synthesis was suppressed due to DEGS2 upregulation mediated by m6A modification in CRC tissues. Our findings highlight that the function of DEGS2 m6A methylation in CRC and extend the understanding of the importance of RNA epigenetics in cancer biology.
Collapse
Affiliation(s)
- Wei Guo
- grid.27255.370000 0004 1761 1174Department of Colorectal Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Cuiyu Zhang
- grid.27255.370000 0004 1761 1174Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Panpan Feng
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Mingying Li
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Xia Wang
- grid.27255.370000 0004 1761 1174Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Yuan Xia
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Dawei Chen
- grid.411374.40000 0000 8607 6858Laboratory of Medical Chemistry, Interdisciplinary Cluster for Applied Genoproteomics (GIGA) Stem Cells, Faculty of Medicine, University of Liège, CHU, Sart-Tilman, Liège, Belgium
| | - Jingxin Li
- grid.27255.370000 0004 1761 1174Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| |
Collapse
|
29
|
Wang YN, Jin HZ. Transcriptome-Wide m 6A Methylation in Skin Lesions From Patients With Psoriasis Vulgaris. Front Cell Dev Biol 2020; 8:591629. [PMID: 33251217 PMCID: PMC7674922 DOI: 10.3389/fcell.2020.591629] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/14/2020] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) methylation, as the most prevalent internal RNA modification, has been revealed to play critical roles in various biological functions. In this study, we performed m6A transcriptome-wide profiling in three kinds of skin tissue: involved psoriatic skin (PP), uninvolved psoriatic skin (PN), and healthy control skin samples (NN). The findings revealed that transcripts of PP contained the fewest m6A peaks and lowest m6A peak density. The greatest differences of m6A methylation were observed in the PP vs. NN and PP vs. PN comparisons. Intriguingly, in these comparisons, hypermethylated m6A was mainly enriched within the CDSs and 3′UTRs, while hypomethylated m6A was not only enriched within CDSs and 3′UTRs, but also within 5′UTRs. GO and KEGG pathway analyses indicated that hypermethylated transcripts in PP were particularly associated with response-associated terms, cytokine production, and olfactory transduction. Meanwhile, hypomethylated transcripts in PP were mainly associated with development-related processes and the Wnt signaling pathway. In addition, we discovered that 19.3–48.4% of the differentially expressed transcripts in psoriasis vulgaris were modified by m6A, and that transcripts with lower expression were more preferentially modified by m6A. Moreover, upregulation of gene expression was often accompanied by upregulation of m6A methylation, suggesting a regulatory role of m6A in psoriasis vulgaris gene expression.
Collapse
Affiliation(s)
- Ya-Nan Wang
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hong-Zhong Jin
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
30
|
Song N, Du J, Gao Y, Yang S. Epitranscriptome of the ventral tegmental area in a deep brain-stimulated chronic unpredictable mild stress mouse model. Transl Neurosci 2020; 11:402-418. [PMID: 33343932 PMCID: PMC7724003 DOI: 10.1515/tnsci-2020-0146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/08/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022] Open
Abstract
Deep brain stimulation (DBS) applied to the nucleus accumbens (NAc) alleviates the depressive symptoms of major depressive disorders. We investigated the mechanism of this effect by assessing gene expression and RNA methylation changes in the ventral tegmental area (VTA) following NAc-DBS in a chronic unpredictable mild stress (CUMS) mouse model of depression. Gene expression and N 6-methyladenosine (m6A) levels in the VTA were measured in mice subjected to CUMS and then DBS, and transcriptome-wide m6A changes were profiled using immunoprecipitated methylated RNAs with microarrays, prior to gene ontology analysis. The expression levels of genes linked to neurotransmitter receptors, transporters, transcription factors, neuronal activities, synaptic functions, and mitogen-activated protein kinase and dopamine signaling were upregulated in the VTA upon NAc-DBS. Furthermore, m6A modifications included both hypermethylation and hypomethylation, and changes were positively correlated with the upregulation of some genes. Moreover, the effects of CUMS on gene expression and m6A-mRNA modification were reversed by DBS for some genes. Interestingly, while the expression of certain genes was not changed by DBS, long-term stimulation did alter their m6A modifications. NAc-DBS-induced modifications are correlated largely with upregulation but sometimes downregulation of genes in CUMS mice. Our findings improve the current understanding of the molecular mechanisms underlying DBS effects on depression.
Collapse
Affiliation(s)
- Nan Song
- Center of Military Brain Science, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences (AMMS), The Academy of Military Sciences, No. 27 Taiping Road, Haidian District, Beijing, China, 100850
| | - Jun Du
- Center of Military Brain Science, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences (AMMS), The Academy of Military Sciences, No. 27 Taiping Road, Haidian District, Beijing, China, 100850
| | - Yan Gao
- Center of Military Brain Science, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences (AMMS), The Academy of Military Sciences, No. 27 Taiping Road, Haidian District, Beijing, China, 100850
| | - Shenglian Yang
- Center of Military Brain Science, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences (AMMS), The Academy of Military Sciences, No. 27 Taiping Road, Haidian District, Beijing, China, 100850
| |
Collapse
|
31
|
An Emerging Role of m6A in Memory: A Case for Translational Priming. Int J Mol Sci 2020; 21:ijms21207447. [PMID: 33050279 PMCID: PMC7589748 DOI: 10.3390/ijms21207447] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/30/2022] Open
Abstract
Investigation into the role of methylation of the adenosine base (m6A) of RNA has only recently begun, but it quickly became apparent that m6A is able to control and fine-tune many aspects of mRNA, from splicing to translation. The ability of m6A to regulate translation distally, away from traditional sites near the nucleus, quickly caught the eye of neuroscientists because of implications for selective protein translation at synapses. Work in the brain has demonstrated how m6A is functionally required for many neuronal functions, but two in particular are covered at length here: The role of m6A in 1) neuron development; and 2) memory formation. The purpose of this review is not to cover all data about m6A in the brain. Instead, this review will focus on connecting mechanisms of m6A function in neuron development, with m6A’s known function in memory formation. We will introduce the concept of “translational priming” and discuss how current data fit into this model, then speculate how m6A-mediated translational priming during memory consolidation can regulate learning and memory locally at the synapse.
Collapse
|
32
|
Lu Z, Liu J, Yuan C, Jin M, Quan K, Chu M, Wei C. m 6A mRNA methylation analysis provides novel insights into heat stress responses in the liver tissue of sheep. Genomics 2020; 113:484-492. [PMID: 32976974 DOI: 10.1016/j.ygeno.2020.09.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/31/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
N6-methyladenosine (m6A) mRNA methylation varies in response to stress. However, no map of m6A mRNA methylation has been obtained for sheep, nor is it known what effect this has on regulating heat stress in sheep. Here, we obtained m6A methylation maps of sheep liver tissues with and without heat stress by MeRIP-seq. In total, 8306 m6A peaks associated with 2697 genes were detected in the heat stress group, and 12,958 m6A peaks associated with 5494 genes were detected in the control group. Peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. Methylation levels of heat stress and control sheep were higher near stop codons, although methylation was significantly lower in heat stress sheep. GO and KEGG revealed that differential m6A-containing genes were significantly enriched in the stress response and fat metabolism. Our results showed that m6A mRNA methylation modifications regulate heat stress in sheep.
Collapse
Affiliation(s)
- Zengkui Lu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Meilin Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China..
| | - Caihong Wei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China..
| |
Collapse
|
33
|
Zhang Y, Geng X, Li Q, Xu J, Tan Y, Xiao M, Song J, Liu F, Fang C, Wang H. m6A modification in RNA: biogenesis, functions and roles in gliomas. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020. [PMID: 32943100 DOI: 10.1186/s13046-020-01706-8.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The chemical modification of RNA is a newly discovered epigenetic regulation mechanism in cells and plays a crucial role in a variety of biological processes. N6-methyladenine (m6A) mRNA modification is the most abundant form of posttranscriptional RNA modification in eukaryotes. Through the development of m6A RNA sequencing, the relevant molecular mechanism of m6A modification has gradually been revealed. It has been found that the effect of m6A modification on RNA metabolism involves processing, nuclear export, translation and even decay. As the most common malignant tumour of the central nervous system, gliomas (especially glioblastoma) have a very poor prognosis, and treatment efficacy is not ideal even with the application of high-intensity treatment measures of surgery combined with chemoradiotherapy. Exploring the origin and development mechanisms of tumour cells from the perspective of tumour biogenesis has always been a hotspot in the field of glioma research. Emerging evidence suggests that m6A modification can play a key role in gliomas through a variety of mechanisms, providing more possibilities for early diagnosis and targeted therapy of gliomas. The aim of the present review is to focus on the research progress regarding the association between m6A modification and gliomas. And to provide a theoretical basis according to the currently available literature for further exploring this association. This review may provide new insights for the molecular mechanism, early diagnosis, histologic grading, targeted therapy and prognostic evaluation of gliomas.
Collapse
Affiliation(s)
- Yuhao Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Xiuchao Geng
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China
| | - Qiang Li
- Faculty of Acupuncture-Moxibustion and Tuina, Hebei University of Chinese Medicine, 050200, Shijiazhuang, China
| | - Jianglong Xu
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Yanli Tan
- Department of Pathology, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Menglin Xiao
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Jia Song
- School of Basic Medicine, Hebei University, 071000, Baoding, China
| | - Fulin Liu
- Office of Academic Research, Affiliated Hospital of Hebei University, 071000, Baoding, China.
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China.
| | - Hong Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China. .,Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China. .,Hebei Key Laboratory of Chinese Medicine Research on Cardio-Cerebrovascular Disease, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China.
| |
Collapse
|
34
|
Zhang Y, Geng X, Li Q, Xu J, Tan Y, Xiao M, Song J, Liu F, Fang C, Wang H. m6A modification in RNA: biogenesis, functions and roles in gliomas. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:192. [PMID: 32943100 PMCID: PMC7500025 DOI: 10.1186/s13046-020-01706-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/10/2020] [Indexed: 12/30/2022]
Abstract
The chemical modification of RNA is a newly discovered epigenetic regulation mechanism in cells and plays a crucial role in a variety of biological processes. N6-methyladenine (m6A) mRNA modification is the most abundant form of posttranscriptional RNA modification in eukaryotes. Through the development of m6A RNA sequencing, the relevant molecular mechanism of m6A modification has gradually been revealed. It has been found that the effect of m6A modification on RNA metabolism involves processing, nuclear export, translation and even decay. As the most common malignant tumour of the central nervous system, gliomas (especially glioblastoma) have a very poor prognosis, and treatment efficacy is not ideal even with the application of high-intensity treatment measures of surgery combined with chemoradiotherapy. Exploring the origin and development mechanisms of tumour cells from the perspective of tumour biogenesis has always been a hotspot in the field of glioma research. Emerging evidence suggests that m6A modification can play a key role in gliomas through a variety of mechanisms, providing more possibilities for early diagnosis and targeted therapy of gliomas. The aim of the present review is to focus on the research progress regarding the association between m6A modification and gliomas. And to provide a theoretical basis according to the currently available literature for further exploring this association. This review may provide new insights for the molecular mechanism, early diagnosis, histologic grading, targeted therapy and prognostic evaluation of gliomas.
Collapse
Affiliation(s)
- Yuhao Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Xiuchao Geng
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China
| | - Qiang Li
- Faculty of Acupuncture-Moxibustion and Tuina, Hebei University of Chinese Medicine, 050200, Shijiazhuang, China
| | - Jianglong Xu
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Yanli Tan
- Department of Pathology, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Menglin Xiao
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Jia Song
- School of Basic Medicine, Hebei University, 071000, Baoding, China
| | - Fulin Liu
- Office of Academic Research, Affiliated Hospital of Hebei University, 071000, Baoding, China.
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China.
| | - Hong Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China. .,Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China. .,Hebei Key Laboratory of Chinese Medicine Research on Cardio-Cerebrovascular Disease, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China.
| |
Collapse
|
35
|
Altered Expression of the m6A Methyltransferase METTL3 in Alzheimer's Disease. eNeuro 2020; 7:ENEURO.0125-20.2020. [PMID: 32847866 PMCID: PMC7540926 DOI: 10.1523/eneuro.0125-20.2020] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/27/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Cognitive impairment in Alzheimer’s disease (AD) is associated with dysregulation of the RNA and protein expression profiles in the brain. Recent studies have highlighted the importance of RNA post-transcriptional regulation (epitranscriptomics) in higher order brain functions. Specifically, N6-methyladenosine (m6A), which controls RNA stability, splicing, translation and trafficking, plays an important role in learning and memory. This raises the question of whether m6A signaling is perturbed in AD. To address this, we investigated the expression profile of known m6A-regulatory genes using a public RNA-seq dataset and identified a subset of genes which were significantly dysregulated in the human AD brain. Among these, genes encoding the m6A methyltransferase, METTL3, and a member of the m6A methyltransferase complex (MACOM), RBM15B, were downregulated and upregulated in the hippocampus, respectively. These findings were validated at the protein level using an independent cohort of postmortem human brain samples. Unexpectedly, we observed an accumulation of methyltransferase-like 3 (METTL3), but not RBM15B, in the insoluble fractions, which positively correlated with the levels of insoluble Tau protein in the postmortem human AD samples. Aberrant expression and distribution of METTL3 in the hippocampus of the AD brain may therefore represent an epitranscriptomic mechanism underlying the altered gene expression patterns associated with disease pathogenesis.
Collapse
|
36
|
Dermentzaki G, Lotti F. New Insights on the Role of N 6-Methyladenosine RNA Methylation in the Physiology and Pathology of the Nervous System. Front Mol Biosci 2020; 7:555372. [PMID: 32984403 PMCID: PMC7492240 DOI: 10.3389/fmolb.2020.555372] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022] Open
Abstract
RNA modifications termed epitranscriptomics represent an additional layer of gene regulation similar to epigenetic mechanisms operating on DNA. The dynamic nature and the increasing number of RNA modifications offer new opportunities for a rapid fine-tuning of gene expression in response to specific environmental cues. In cooperation with a diverse and versatile set of effector proteins that "recognize" them, these RNA modifications have the ability to mediate and control diverse fundamental cellular functions, such as pre-mRNA splicing, nuclear export, stability, and translation. N 6-methyladenosine (m6A) is the most abundant of these RNA modifications, particularly in the nervous system, where recent studies have highlighted it as an important post-transcriptional regulator of physiological functions from development to synaptic plasticity, learning and memory. Here we review recent findings surrounding the role of m6A modification in regulating physiological responses of the mammalian nervous system and we discuss its emerging role in pathological conditions such as neuropsychiatric and neurodegenerative disorders.
Collapse
Affiliation(s)
- Georgia Dermentzaki
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York City, NY, United States
- Department of Neurology, Columbia University, New York City, NY, United States
| | - Francesco Lotti
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York City, NY, United States
- Department of Neurology, Columbia University, New York City, NY, United States
| |
Collapse
|
37
|
Wang Q, Chen C, Ding Q, Zhao Y, Wang Z, Chen J, Jiang Z, Zhang Y, Xu G, Zhang J, Zhou J, Sun B, Zou X, Wang S. METTL3-mediated m 6A modification of HDGF mRNA promotes gastric cancer progression and has prognostic significance. Gut 2020; 69:1193-1205. [PMID: 31582403 DOI: 10.1136/gutjnl-2019-319639] [Citation(s) in RCA: 515] [Impact Index Per Article: 128.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE N6-methyladenosine (m6A) RNA methylation and its associated methyltransferase METTL3 are involved in tumour initiation and progression via the regulation of RNA function. This study explored the biological function and clinical significance of METTL3 in gastric cancer (GC). DESIGN The prognostic value of METTL3 expression was evaluated using tissue microarray and immunohistochemical staining analyses in a human GC cohort. The biological role and mechanism of METTL3 in GC tumour growth and liver metastasis were determined in vitro and in vivo. RESULTS The level of m6A RNA was significantly increased in GC, and METTL3 was the main regulator involved in the abundant m6A RNA modification. METTL3 expression was significantly elevated in GC tissues and associated with poor prognosis. Multivariate Cox regression analysis revealed that METTL3 expression was an independent prognostic factor and effective predictor in human patients with GC. Moreover, METTL3 overexpression promoted GC proliferation and liver metastasis in vitro and in vivo. Mechanistically, P300-mediated H3K27 acetylation activation in the promoter of METTL3 induced METTL3 transcription, which stimulated m6A modification of HDGF mRNA, and the m6A reader IGF2BP3 then directly recognised and bound to the m6A site on HDGF mRNA and enhanced HDGF mRNA stability. Secreted HDGF promoted tumour angiogenesis, while nuclear HDGF activated GLUT4 and ENO2 expression, followed by an increase in glycolysis in GC cells, which was correlated with subsequent tumour growth and liver metastasis. CONCLUSIONS Elevated METTL3 expression promotes tumour angiogenesis and glycolysis in GC, indicating that METTL3 expression is a potential prognostic biomarker and therapeutic target for human GC.
Collapse
Affiliation(s)
- Qiang Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Chen Chen
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Qingqing Ding
- Department of Geriatric Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yan Zhao
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Zhangding Wang
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Junjie Chen
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Zerun Jiang
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yan Zhang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Guifang Xu
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Jingjing Zhang
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Beicheng Sun
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaoping Zou
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Shouyu Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China .,Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China.,Center for Public Health Research, Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China
| |
Collapse
|
38
|
Programmable m 6A modification of cellular RNAs with a Cas13-directed methyltransferase. Nat Biotechnol 2020; 38:1431-1440. [PMID: 32601430 PMCID: PMC7718427 DOI: 10.1038/s41587-020-0572-6] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/20/2020] [Indexed: 12/19/2022]
Abstract
N6-Methyladenosine (m6A) is the most widespread internal messenger RNA modification in humans. Despite recent progress in understanding the biological roles of m6A, the inability to install m6A site specifically in individual transcripts has hampered efforts to elucidate causal relationships between the presence of a specific m6A and phenotypic outcomes. In the present study, we demonstrate that nucleus-localized dCas13 fusions with a truncated METTL3 methyltransferase domain and cytoplasm-localized fusions with a modified METTL3:METTL14 methyltransferase complex can direct site-specific m6A incorporation in distinct cellular compartments, with the former fusion protein having particularly low off-target activity. Independent cellular assays across multiple sites confirm that this targeted RNA methylation (TRM) system mediates efficient m6A installation in endogenous RNA transcripts with high specificity. Finally, we show that TRM can induce m6A-mediated changes to transcript abundance and alternative splicing. These findings establish TRM as a tool for targeted epitranscriptome engineering that can reveal the effect of individual m6A modifications and dissect their functional roles.
Collapse
|
39
|
Xiang M, Liu W, Tian W, You A, Deng D. RNA N-6-methyladenosine enzymes and resistance of cancer cells to chemotherapy and radiotherapy. Epigenomics 2020; 12:801-809. [PMID: 32515221 DOI: 10.2217/epi-2019-0358] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: As one of the early adaptive mechanisms by which cells respond to environmental changes, RNA modification appears to be a very promising target for cancer treatment. Results: RNA modifications are currently a hot topic in epigenetic research. Emerging experimental studies show that expression alterations of multiple m6A enzymes, including demethylase FTO, methyltransferase METTL3 and WTAP, mediate the development of resistance of cancer cells to various treatments. A set of small molecular chemical drugs targeted to these m6A enzymes are under development. Intervention of RNA m6A methylation is a possible therapeutic strategy to overcome drug resistance. Conclusions: RNA m6A methylation may play a crucial role in drug resistance development and intervention in cancer cells.
Collapse
Affiliation(s)
- Meiyi Xiang
- Key Laboratory of Carcinogenesis & Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Fu-Cheng-Lu #52, Haidian District, Beijing 100142, PR China
| | - Wensu Liu
- Key Laboratory of Carcinogenesis & Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Fu-Cheng-Lu #52, Haidian District, Beijing 100142, PR China
| | - Wei Tian
- Key Laboratory of Carcinogenesis & Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Fu-Cheng-Lu #52, Haidian District, Beijing 100142, PR China
| | - Abin You
- Key Laboratory of Carcinogenesis & Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Fu-Cheng-Lu #52, Haidian District, Beijing 100142, PR China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis & Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital & Institute, Fu-Cheng-Lu #52, Haidian District, Beijing 100142, PR China
| |
Collapse
|
40
|
Si W, Li Y, Ye S, Li Z, Liu Y, Kuang W, Chen D, Zhu M. Methyltransferase 3 Mediated miRNA m6A Methylation Promotes Stress Granule Formation in the Early Stage of Acute Ischemic Stroke. Front Mol Neurosci 2020; 13:103. [PMID: 32581712 PMCID: PMC7289951 DOI: 10.3389/fnmol.2020.00103] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/13/2020] [Indexed: 12/21/2022] Open
Abstract
The modification of methyltransferase-like (METTL) enzymes plays important roles in various cellular responses by regulating microRNA expression. However, how m6A modification is involved in stress granule (SG) formation in the early stage of acute ischemic stroke by affecting the biogenesis processing of microRNAs remains unclear. Here, we established a middle cerebral artery occlusion (MCAO) model in rats and an oxygen-glucose deprivation/reperfusion (OGD/R) model in primary cortical neurons and PC12 cells to explore the potential mechanism between m6A modification and SG formation. The in vivo results showed that the level of infarction and apoptosis increased while SG formation decreased significantly within the ischemic cortex with improved reperfusion time after 2 h of ischemia. Consistent with the in vivo data, an inverse association between the apoptosis level and SG formation was observed in PC12 cells during the reperfusion period after 6 h of OGD stimulation. Both in vivo and in vitro results showed that the expression of METTL3 protein, m6A and miR-335 was significantly decreased with the reperfusion period. Overexpression of the METTL3 and METTL3 gene-knockdown in PC12 cells were achieved via plasmid transfection and CRISPR-Cas9 technology, respectively. Overexpression or knockdown of METTL3 in oxygen-glucose deprivation of PC12 cells resulted in functional maturation of miR-335, SG formation and apoptosis levels. In addition, we found that miR-335 enhanced SG formation through degradation of the mRNA of the eukaryotic translation termination factor (Erf1). In conclusion, we found that METTL3-mediated m6A methylation increases the maturation of miR-335, which promotes SG formation and reduces the apoptosis level of injury neurons and cells, and provides a potential therapeutic strategy for AIS.
Collapse
Affiliation(s)
- Wenwen Si
- Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yi Li
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shanyu Ye
- Department of Anatomy, The Research Center of Basic Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Zhen Li
- Department of Anatomy, The Research Center of Basic Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Yangping Liu
- Department of Anatomy, The Research Center of Basic Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Weihong Kuang
- The Second Clinical Medical College, Guangdong Medical University, Dongguan, China
| | - Dongfeng Chen
- Department of Anatomy, The Research Center of Basic Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Meiling Zhu
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| |
Collapse
|
41
|
Wang K, Jiang L, Zhang Y, Chen C. Progression of Thyroid Carcinoma Is Promoted by the m6A Methyltransferase METTL3 Through Regulating m 6A Methylation on TCF1. Onco Targets Ther 2020; 13:1605-1612. [PMID: 32158230 PMCID: PMC7044742 DOI: 10.2147/ott.s234751] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/04/2020] [Indexed: 12/17/2022] Open
Abstract
Objective This study aims to uncover the progression of thyroid carcinoma influenced by the m6A methyltransferase METTL3 through regulating m6A methylation on TCF1 mRNA and the activated Wnt pathway. Methods Thyroid carcinoma tissues and paracancerous ones were collected for detecting levels of METTL3 and TCF1. Potential correlation between levels of METTL3 and TCF1 was analyzed by Pearson analysis. Survival of thyroid carcinoma patients influenced by METTL3 level was assessed by Kaplan–Meier method. Regulatory effect of METTL3 on migratory ability in TPC-1 cells was examined by wound healing assay. The interaction between METTL3 with TCF1 and IGF2BP2 was verified by RNA-Binding Protein Immunoprecipitation (RIP) assay. Meanwhile, the activity of the Wnt pathway was reflected by TOP/FOP-Flash. At last, rescue experiments were conducted to clarify the involvement of TCF1 in phenotype changes of thyroid carcinoma cells that were regulated by METTL3. Results METTL3 and TCF1 were upregulated in thyroid carcinoma. Similarly, METTL3 was highly expressed in thyroid carcinoma cells as well. Kaplan–Meier method uncovered poor prognosis in thyroid carcinoma patients expressing a high level of METTL3. Silence of METTL3 inhibited migratory ability and Wnt activity in TPC-1 cells. RIP assay confirmed the interaction between TCF1 and METTL3 or IGF2BP2. Moreover, METTL3 positively regulated the enrichment abundance of TCF1 in anti-IGF2BP2. Rescue experiments demonstrated that TCF1 was responsible for METTL3-regulated thyroid carcinoma progression via the m6A methylation. Conclusion Upregulated m6A methyltransferase METTL3 promotes the progression of thyroid carcinoma through m6A methylation on TCF1.
Collapse
Affiliation(s)
- Kejin Wang
- Department of Head and Neck Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Lin Jiang
- Department of Head and Neck Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Yan Zhang
- Department of Head and Neck Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Chao Chen
- Department of Head and Neck Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| |
Collapse
|
42
|
RNA N 6-Methyladenosine Modifications and the Immune Response. J Immunol Res 2020; 2020:6327614. [PMID: 32411802 PMCID: PMC7204177 DOI: 10.1155/2020/6327614] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/13/2019] [Accepted: 12/24/2019] [Indexed: 01/09/2023] Open
Abstract
N6-methyladenosine (m6A) is the most important modification of messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) in higher eukaryotes. Modulation of m6A modifications relies on methyltransferases and demethylases. The discovery of binding proteins confirms that the m6A modification has a wide range of biological effects and significance at the molecular, cellular, and physiological levels. In recent years, techniques for investigating m6A modifications of RNA have developed rapidly. This article reviews the biological significance of RNA m6A modifications in the innate immune response, adaptive immune response, and viral infection.
Collapse
|
43
|
The m 6A epitranscriptome: transcriptome plasticity in brain development and function. Nat Rev Neurosci 2019; 21:36-51. [PMID: 31804615 DOI: 10.1038/s41583-019-0244-z] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2019] [Indexed: 02/08/2023]
Abstract
The field of epitranscriptomics examines the recently deciphered form of gene expression regulation that is mediated by type- and site-specific RNA modifications. Similarly to the role played by epigenetic mechanisms - which operate via DNA and histone modifications - epitranscriptomic modifications are involved in the control of the delicate gene expression patterns that are needed for the development and activity of the nervous system and are essential for basic and higher brain functions. Here we describe the mechanisms that are involved in the writing, erasing and reading of N6-methyladenosine, the most prevalent internal mRNA modification, and the emerging roles played by N6-methyladenosine in the nervous system.
Collapse
|
44
|
Abstract
Discovered in 1987 as a potent endothelial cell-derived vasoconstrictor peptide, endothelin-1 (ET-1), the predominant member of the endothelin peptide family, is now recognized as a multifunctional peptide with cytokine-like activity contributing to almost all aspects of physiology and cell function. More than 30 000 scientific articles on endothelin were published over the past 3 decades, leading to the development and subsequent regulatory approval of a new class of therapeutics-the endothelin receptor antagonists (ERAs). This article reviews the history of the discovery of endothelin and its role in genetics, physiology, and disease. Here, we summarize the main clinical trials using ERAs and discuss the role of endothelin in cardiovascular diseases such as arterial hypertension, preecclampsia, coronary atherosclerosis, myocardial infarction in the absence of obstructive coronary artery disease (MINOCA) caused by spontaneous coronary artery dissection (SCAD), Takotsubo syndrome, and heart failure. We also discuss how endothelins contributes to diabetic kidney disease and focal segmental glomerulosclerosis, pulmonary arterial hypertension, as well as cancer, immune disorders, and allograft rejection (which all involve ETA autoantibodies), and neurological diseases. The application of ERAs, dual endothelin receptor/angiotensin receptor antagonists (DARAs), selective ETB agonists, novel biologics such as receptor-targeting antibodies, or immunization against ETA receptors holds the potential to slow the progression or even reverse chronic noncommunicable diseases. Future clinical studies will show whether targeting endothelin receptors can prevent or reduce disability from disease and improve clinical outcome, quality of life, and survival in patients.
Collapse
Affiliation(s)
- Matthias Barton
- From Molecular Internal Medicine, University of Zürich, Switzerland (M.B.)
- Andreas Grüntzig Foundation, Zürich, Switzerland (M.B.)
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS) and Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Japan (M.Y.)
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX (M.Y.)
| |
Collapse
|
45
|
Li J, Yang X, Qi Z, Sang Y, Liu Y, Xu B, Liu W, Xu Z, Deng Y. The role of mRNA m 6A methylation in the nervous system. Cell Biosci 2019; 9:66. [PMID: 31452869 PMCID: PMC6701067 DOI: 10.1186/s13578-019-0330-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/14/2019] [Indexed: 11/21/2022] Open
Abstract
Epitranscriptomics, also known as “RNA epigenetics”, is a chemical modification for RNA regulation. Ribonucleic acid (RNA) methylation is considered to be a major discovery following the deoxyribonucleic acid (DNA) and histone methylation. Messenger RNA (mRNA) methylation modification accounts for more than 60% of all RNA modifications and N6-methyladenosine (m6A) is known as one of the most common type of eukaryotic mRNA methylation modifications in current. The m6A modification is a dynamic reversible modification, which can directly or indirectly affect biological processes, such as RNA degradation, translation and splicing, and can play important biological roles in vivo. This article introduces the mRNA m6A methylation modification enzymes and binding proteins, and reviews the research progress and related mechanisms of the role of mRNA m6A methylation in the nervous system from the aspects of neural stem cells, learning and memory, brain development, axon growth and glioblastoma.
Collapse
Affiliation(s)
- Jiashuo Li
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Xinxin Yang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhipeng Qi
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanqi Sang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanan Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Bin Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Wei Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhaofa Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yu Deng
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| |
Collapse
|
46
|
Engel M, Eggert C, Kaplick PM, Eder M, Röh S, Tietze L, Namendorf C, Arloth J, Weber P, Rex-Haffner M, Geula S, Jakovcevski M, Hanna JH, Leshkowitz D, Uhr M, Wotjak CT, Schmidt MV, Deussing JM, Binder EB, Chen A. The Role of m 6A/m-RNA Methylation in Stress Response Regulation. Neuron 2019; 99:389-403.e9. [PMID: 30048615 PMCID: PMC6069762 DOI: 10.1016/j.neuron.2018.07.009] [Citation(s) in RCA: 263] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 05/04/2018] [Accepted: 07/05/2018] [Indexed: 12/04/2022]
Abstract
N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m6A/m, in the stress response in the adult brain in vivo is currently unknown. Here, we provide a detailed analysis of the stress epitranscriptome using m6A/m-seq, global and gene-specific m6A/m measurements. We show that stress exposure and glucocorticoids region and time specifically alter m6A/m and its regulatory network. We demonstrate that deletion of the methyltransferase Mettl3 or the demethylase Fto in adult neurons alters the m6A/m epitranscriptome, increases fear memory, and changes the transcriptome response to fear and synaptic plasticity. Moreover, we report that regulation of m6A/m is impaired in major depressive disorder patients following glucocorticoid stimulation. Our findings indicate that brain m6A/m represents a novel layer of complexity in gene expression regulation after stress and that dysregulation of the m6A/m response may contribute to the pathophysiology of stress-related psychiatric disorders. m6A/m mRNA methylation in the adult mouse brain is regulated by stress m6A/m mRNA regulation is brain region, time, and gene specific Mettl3 and Fto cKO alter m6A/m, fear memory, expression, and synaptic plasticity The m6A/m glucocorticoid response is impaired in major depressive disorder patients
Collapse
Affiliation(s)
- Mareen Engel
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Carola Eggert
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Paul M Kaplick
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Matthias Eder
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Lisa Tietze
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Christian Namendorf
- Clinical Laboratory, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Janine Arloth
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Peter Weber
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Monika Rex-Haffner
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Shay Geula
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Manfred Uhr
- Clinical Laboratory, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Carsten T Wotjak
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Mathias V Schmidt
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Jan M Deussing
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
47
|
Gomes‐Filho JV, Randau L. RNA stabilization in hyperthermophilic archaea. Ann N Y Acad Sci 2019; 1447:88-96. [DOI: 10.1111/nyas.14060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/26/2019] [Accepted: 03/10/2019] [Indexed: 12/23/2022]
Affiliation(s)
| | - Lennart Randau
- Prokaryotic Small RNA BiologyMax Planck Institute for Terrestrial Microbiology Marburg Germany
| |
Collapse
|
48
|
Lence T, Paolantoni C, Worpenberg L, Roignant JY. Mechanistic insights into m6A RNA enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:222-229. [DOI: 10.1016/j.bbagrm.2018.10.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/27/2018] [Indexed: 12/09/2022]
|
49
|
Yang J, Wang H, Zhang W. Regulation of Virus Replication and T Cell Homeostasis by N 6-Methyladenosine. Virol Sin 2019; 34:22-29. [PMID: 30671921 DOI: 10.1007/s12250-018-0075-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/26/2018] [Indexed: 01/04/2023] Open
Abstract
RNA modifications are abundant in eukaryotes, bacteria, and archaea. N6-methyladenosine (m6A), a type of RNA modification mainly found in messenger RNA (mRNA), has significant effects on the metabolism and function of mRNAs. This modification is governed by three types of proteins, namely methyltransferases as "writers", demethylases as "erasers", and specific m6A-binding proteins (YTHDF1-3) as "readers". Further, it is important for the regulation of cell fate and has a critical function in many biological processes including virus replication, stem cell differentiation, and cancer development, and exerts its effect by controlling gene expression. Herein, we summarize recent advances in research on m6A in virus replication and T cell regulation, which is a rapidly emerging field that will facilitate the development of antiviral therapies and the study of innate immunity.
Collapse
Affiliation(s)
- Jing Yang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, China
| | - Hong Wang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, China.
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, China.
| |
Collapse
|
50
|
The Emerging Role of Epitranscriptomics in Cancer: Focus on Urological Tumors. Genes (Basel) 2018; 9:genes9110552. [PMID: 30428628 PMCID: PMC6265908 DOI: 10.3390/genes9110552] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/27/2018] [Accepted: 11/08/2018] [Indexed: 12/11/2022] Open
Abstract
Epitranscriptomics has gained ground in recent years, especially after the advent of techniques for accurately studying these mechanisms. Among all modifications occurring in RNA molecules, N6-methyladenosine (m6A) is the most frequent, especially among mRNAs. m6A has been demonstrated to play important roles in many physiological processes and several disease states, including various cancer models (from solid to liquid tumors). Tumor cells’ epitranscriptome is indeed disrupted in a way to promote cancer-prone features, by means of up/downregulating m6A-related players: the so-called writers, readers and erasers. These proteins modulate m6A establishment, removal and determine mRNAs fate, acting in a context-dependent manner, so that a single player may act as an oncogenic signal in one tumor model (methyltransferase like 3 (METTL3) in lung cancer) and as a tumor suppressor in another context (METTL3 in glioblastoma). Despite recent advances, however, little attention has been directed towards urological cancer. By means of a thorough analysis of the publicly available TCGA (The Cancer Genome Atlas) database, we disclosed the most relevant players in four major urogenital neoplasms—kidney, bladder, prostate and testicular cancer—for prognostic, subtype discrimination and survival purposes. In all tumor models assessed, the most promising player was shown to be Vir like m6A methyltransferase associated (VIRMA), which could constitute a potential target for personalized therapies.
Collapse
|