101
|
Luo L, Cao H, Zhou L, Zhang G, Wu L. Anti-resorption role of low-intensity pulsed ultrasound (LIPUS) during large-scale bone reconstruction using porous titanium alloy scaffolds through inhibiting osteoclast differentiation. BIOMATERIALS ADVANCES 2023; 154:213634. [PMID: 37783002 DOI: 10.1016/j.bioadv.2023.213634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
BACKGROUND Ti6Al4V biomaterials combine with low-intensity pulsed ultrasound (LIPUS) has been reported with great bone regeneration capacity. It is important to better understand how LIPUS benefits bone microenvironment to seek for target of therapeutic medicine. Osteoclast differentiation plays a crucial role in bone resorption. Recent advances in molecular biology have revealed that N6-methyladenosine (m6A) RNA modifications can modulate biological processes, but their role in bone biology, particularly in osteoclast differentiation, remains unclear. We aim to understand how LIPUS regulates bone microenvironment especially osteoclast formation during bone regeneration to provide new therapeutic options for preventing and delaying bone resorption, thus with better bone regeneration efficiency. RESULTS 1. LIPUS promoted bone ingrowth and bone maturity while inhibiting osteoclast formation within Ti6Al4V scaffolds in large-scale bone defect model. 2. LIPUS was found to inhibit osteoclast differentiation by decreasing the overall expression of osteoclast markers in vitro. 3. LIPUS decreases RNA m6A-modification level through upregulating FTO expression during osteoclast differentiation during. 4. Inhibiting FTO expression and function leads to less inhibition during osteoclast differentiation. CONCLUSION LIPUS suppresses osteoclast differentiation during bone regeneration through reducing m6A modification of osteoclastic RNAs by up regulating FTO expression.
Collapse
Affiliation(s)
- Lin Luo
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang 110001, China
| | - Hongjuan Cao
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang 110001, China
| | - Liang Zhou
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang 110001, China
| | - Guangdao Zhang
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang 110001, China.
| | - Lin Wu
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang 110001, China.
| |
Collapse
|
102
|
Jiang N, Li W, Jiang S, Xie M, Liu R. Acetylation in pathogenesis: Revealing emerging mechanisms and therapeutic prospects. Biomed Pharmacother 2023; 167:115519. [PMID: 37729729 DOI: 10.1016/j.biopha.2023.115519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023] Open
Abstract
Protein acetylation modifications play a central and pivotal role in a myriad of biological processes, spanning cellular metabolism, proliferation, differentiation, apoptosis, and beyond, by effectively reshaping protein structure and function. The metabolic state of cells is intricately connected to epigenetic modifications, which in turn influence chromatin status and gene expression patterns. Notably, pathological alterations in protein acetylation modifications are frequently observed in diseases such as metabolic syndrome, cardiovascular disorders, and cancer. Such abnormalities can result in altered protein properties and loss of function, which are closely associated with developing and progressing related diseases. In recent years, the advancement of precision medicine has highlighted the potential value of protein acetylation in disease diagnosis, treatment, and prevention. This review includes provocative and thought-provoking papers outlining recent breakthroughs in acetylation modifications as they relate to cardiovascular disease, mitochondrial metabolic regulation, liver health, neurological health, obesity, diabetes, and cancer. Additionally, it covers the molecular mechanisms and research challenges in understanding the role of acetylation in disease regulation. By summarizing novel targets and prognostic markers for the treatment of related diseases, we aim to contribute to the field. Furthermore, we discuss current hot topics in acetylation research related to health regulation, including N4-acetylcytidine and liquid-liquid phase separation. The primary objective of this review is to provide insights into the functional diversity and underlying mechanisms by which acetylation regulates proteins in disease contexts.
Collapse
Affiliation(s)
- Nan Jiang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Wenyong Li
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, Anhui 236037, China
| | - Shuanglin Jiang
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, Anhui 236037, China
| | - Ming Xie
- North China Petroleum Bureau General Hospital, Renqiu 062550, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| |
Collapse
|
103
|
Zhang J, Liu T, Wang Y, Yan X, Li Y, Xu F, Zhang R. Dynamic alterations of the transcriptome-wide m 6A methylome in cytogenetically normal acute myeloid leukaemia during initial diagnosis and relapse. Genomics 2023; 115:110725. [PMID: 37820824 DOI: 10.1016/j.ygeno.2023.110725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/08/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023]
Abstract
Accumulating studies have indicated that N6-methyladenosine (m6A) plays an important role in acute myeloid leukaemia (AML). However, little is known about the m6A methylome at a transcriptome-wide scale in AML patients. We obtained three pairs of bone marrow (BM) samples from cytogenetically normal AML patients at the timepoints of diagnosis (AML) and relapse (R_AML) and three BM samples from healthy donors used as normal controls (NCs). Methylated RNA immunoprecipitation next-generation sequencing (MeRIP-Seq) was conducted to identify differences in the m6A methylomes between AML and NC and between R_AML and AML. We identified a total of 11,076 and 11,962 differential m6A peaks in AML and R_AML group, respectively. These dysregulated m6A peaks were detected on all chromosomes, especially chr1, chr19 and chr17, and were mainly enriched in 3' untranslated regions, stop codon and coding sequence regions. Moreover, GO and KEGG analyses indicated that m6A -modified genes were significantly enriched in cancer-related biological functions and pathways. Additionally, we identified a link between the m6A methylome and RNA transcriptome via combined analyses of MeRIP-seq and RNA-seq data. In addition, 5 genes, HSPG2, HOMER3, TSPO2, CXCL12 and FUT1 regulated by m6A modification potentially, were shown to be related to the prognosis of AML patients. Additionally, we detected the mRNA expression of major m6A regulators and potential target mRNA on the leukemogenesis and found that the expression of IGF2BP2, HSPG2 and HOMER3 were upregulated in AML at the time of diagnosis. Moreover, their expression became downregulated after remission and then elevated again at relapse. Our study provides the first data on the differential m6A methylome in AML patients during initial diagnosis and relapse. This study demonstrates a novel relationship between m6A modification and AML relapse and paves the way for further studies aimed at elucidating the epigenic mechanisms involved in the relapse of AML.
Collapse
Affiliation(s)
- Jinjing Zhang
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Tong Liu
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yue Wang
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Xiaojing Yan
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yan Li
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Feng Xu
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Rui Zhang
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China.
| |
Collapse
|
104
|
Peng Q, Qiao J, Li W, You Q, Hu S, Liu Y, Liu W, Hu K, Sun B. Global m6A methylation and gene expression patterns in human microglial HMC3 cells infected with HIV-1. Heliyon 2023; 9:e21307. [PMID: 38027859 PMCID: PMC10643106 DOI: 10.1016/j.heliyon.2023.e21307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
N6-methyladenosine (m6A) methylation of human immunodeficiency virus type 1 (HIV-1) RNA regulates viral replication, and the m6A of host RNA is affected by HIV-1 infection, but its global pattern and function are still unclear. In this study, we report that the number and position of m6A peaks in huge genes of human microglial HMC3 cells were modulated by a single cycle HIV-1 pseudotyped with VSV-G envelope glycoprotein infection using methylated RNA immunoprecipitation sequencing (MeRIP-seq). A conjoint analysis of MeRIP-seq and high-throughput sequencing for mRNA (RNA-seq) explored four groups of clearly classified genes, including 45 hyper-up (m6A-mRNA), 45 hyper-down, 120 hypo-up, and 54 hypo-down genes, in HIV-1 infected cells compared to uninfected ones. KEGG pathway analysis showed that these genes were mainly enriched in the Wnt and TNF signaling pathway, and cytokine-cytokine receptor interaction, which might be related to the immune response in HMC3 cells. And some of these genes might be associated with the pathway of axon guidance and neuroactive ligan-receptor interaction, which affect the neuronal state. However, the cognitive disorders caused by HIV-1 is associated with inflammatory changes that have not yet been well clarified. Furthermore, we confirmed the expression and m6A levels of four genes using RT-PCR and MeRIP-qPCR. Similar to the sequencing results, the expressions of these genes were significantly upregulated by HIV-1 infection. And the m6A level of IL-6 was downregulated, and those of HLA-B, CFB, and OLR1 were upregulated. These results suggest that HIV-1-induced changes in gene expression may be achieved through the regulation of methylation. Our study revealed the global m6A methylation and gene expression patterns under HIV-1 infection in human microglia, which might provide clues for understanding the interaction between HIV-1 and host cells and the cognitive disorders caused by HIV-1.
Collapse
Affiliation(s)
- Qian Peng
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and MolecularPharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education &Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), HubeiUniversity of Technology, Wuhan, China
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jialu Qiao
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei, 430056, China
| | - Weiling Li
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Qiang You
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Song Hu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Yuchen Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Wei Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Kanghong Hu
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and MolecularPharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education &Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), HubeiUniversity of Technology, Wuhan, China
| | - Binlian Sun
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei, 430056, China
| |
Collapse
|
105
|
Wallace L, Obeng EA. Noncoding rules of survival: epigenetic regulation of normal and malignant hematopoiesis. Front Mol Biosci 2023; 10:1273046. [PMID: 38028538 PMCID: PMC10644717 DOI: 10.3389/fmolb.2023.1273046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Hematopoiesis is an essential process for organismal development and homeostasis. Epigenetic regulation of gene expression is critical for stem cell self-renewal and differentiation in normal hematopoiesis. Increasing evidence shows that disrupting the balance between self-renewal and cell fate decisions can give rise to hematological diseases such as bone marrow failure and leukemia. Consequently, next-generation sequencing studies have identified various aberrations in histone modifications, DNA methylation, RNA splicing, and RNA modifications in hematologic diseases. Favorable outcomes after targeting epigenetic regulators during disease states have further emphasized their importance in hematological malignancy. However, these targeted therapies are only effective in some patients, suggesting that further research is needed to decipher the complexity of epigenetic regulation during hematopoiesis. In this review, an update on the impact of the epigenome on normal hematopoiesis, disease initiation and progression, and current therapeutic advancements will be discussed.
Collapse
Affiliation(s)
| | - Esther A. Obeng
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, United States
| |
Collapse
|
106
|
Li Z, Liu X, Wang L, Zhao H, Wang S, Yu G, Wu D, Chu J, Han J. Integrated analysis of single-cell RNA-seq and bulk RNA-seq reveals RNA N6-methyladenosine modification associated with prognosis and drug resistance in acute myeloid leukemia. Front Immunol 2023; 14:1281687. [PMID: 38022588 PMCID: PMC10644381 DOI: 10.3389/fimmu.2023.1281687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Acute myeloid leukemia (AML) is a type of blood cancer that is identified by the unrestricted growth of immature myeloid cells within the bone marrow. Despite therapeutic advances, AML prognosis remains highly variable, and there is a lack of biomarkers for customizing treatment. RNA N6-methyladenosine (m6A) modification is a reversible and dynamic process that plays a critical role in cancer progression and drug resistance. Methods To investigate the m6A modification patterns in AML and their potential clinical significance, we used the AUCell method to describe the m6A modification activity of cells in AML patients based on 23 m6A modification enzymes and further integrated with bulk RNA-seq data. Results We found that m6A modification was more effective in leukemic cells than in immune cells and induced significant changes in gene expression in leukemic cells rather than immune cells. Furthermore, network analysis revealed a correlation between transcription factor activation and the m6A modification status in leukemia cells, while active m6A-modified immune cells exhibited a higher interaction density in their gene regulatory networks. Hierarchical clustering based on m6A-related genes identified three distinct AML subtypes. The immune dysregulation subtype, characterized by RUNX1 mutation and KMT2A copy number variation, was associated with a worse prognosis and exhibited a specific gene expression pattern with high expression level of IGF2BP3 and FMR1, and low expression level of ELAVL1 and YTHDF2. Notably, patients with the immune dysregulation subtype were sensitive to immunotherapy and chemotherapy. Discussion Collectively, our findings suggest that m6A modification could be a potential therapeutic target for AML, and the identified subtypes could guide personalized therapy.
Collapse
Affiliation(s)
- Zhongzheng Li
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, China
| | - Xin Liu
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Lan Wang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, China
| | - Huabin Zhao
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, China
| | - Shenghui Wang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, China
| | - Depei Wu
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jianhong Chu
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jingjing Han
- The First Affiliated Hospital of Soochow University, National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| |
Collapse
|
107
|
Yu S, Wang S, Xiong B, Peng C. Gut microbiota: key facilitator in metastasis of colorectal cancer. Front Oncol 2023; 13:1270991. [PMID: 38023192 PMCID: PMC10643165 DOI: 10.3389/fonc.2023.1270991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Colorectal cancer (CRC) ranks third in terms of incidence among all kinds of cancer. The main cause of death is metastasis. Recent studies have shown that the gut microbiota could facilitate cancer metastasis by promoting cancer cells proliferation, invasion, dissemination, and survival. Multiple mechanisms have been implicated, such as RNA-mediated targeting effects, activation of tumor signaling cascades, secretion of microbiota-derived functional substances, regulation of mRNA methylation, facilitated immune evasion, increased intravasation of cancer cells, and remodeling of tumor microenvironment (TME). The understanding of CRC metastasis was further deepened by the mechanisms mentioned above. In this review, the mechanisms by which the gut microbiota participates in the process of CRC metastasis were reviewed as followed based on recent studies.
Collapse
Affiliation(s)
- Siyi Yu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Shuyi Wang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Bin Xiong
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Chunwei Peng
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| |
Collapse
|
108
|
Wang M, Liu Z, Fang X, Cong X, Hu Y. The emerging role of m 6A modification of non-coding RNA in gastrointestinal cancers: a comprehensive review. Front Cell Dev Biol 2023; 11:1264552. [PMID: 37965577 PMCID: PMC10642577 DOI: 10.3389/fcell.2023.1264552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Gastrointestinal (GI) cancer is a series of malignant tumors with a high incidence globally. Although approaches for tumor diagnosis and therapy have advanced substantially, the mechanisms underlying the occurrence and progression of GI cancer are still unclear. Increasing evidence supports an important role for N6-methyladenosine (m6A) modification in many biological processes, including cancer-related processes via splicing, export, degradation, and translation of mRNAs. Under distinct cancer contexts, m6A regulators have different expression patterns and can regulate or be regulated by mRNAs and non-coding RNAs, especially long non-coding RNAs. The roles of m6A in cancer development have attracted increasing attention in epigenetics research. In this review, we synthesize progress in our understanding of m6A and its roles in GI cancer, especially esophageal, gastric, and colorectal cancers. Furthermore, we clarify the mechanism by which m6A contributes to GI cancer, providing a basis for the development of diagnostic, prognostic, and therapeutic targets.
Collapse
Affiliation(s)
- Meiqi Wang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhuo Liu
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xuedong Fang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xianling Cong
- Department of Biobank, the China-Japan Union Hospital of Jilin University, Changchun, China
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yue Hu
- Department of Biobank, the China-Japan Union Hospital of Jilin University, Changchun, China
| |
Collapse
|
109
|
He M, Li Z, Xie X. The Roles of N6-Methyladenosine Modification in Plant-RNA Virus Interactions. Int J Mol Sci 2023; 24:15608. [PMID: 37958594 PMCID: PMC10649972 DOI: 10.3390/ijms242115608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification. Recently, its role in viruses has led to the study of viral epitranscriptomics. m6A has been observed in viral genomes and alters the transcriptomes of both the host cell and virus during infection. The effects of m6A modifications on host plant mRNA can either increase the likelihood of viral infection or enhance the resistance of the host to the virus. However, to date, the regulatory mechanisms of m6A in viral infection and host immune responses have not been fully elucidated. With the development of sequencing-based biotechnologies, the study of m6A in plant viruses has received increasing attention. In this mini review, we summarize the positive and negative consequences of m6A modification in different RNA viral infections. Given its increasingly important roles in multiple viruses, m6A represents a new potential target for antiviral defense.
Collapse
Affiliation(s)
- Min He
- Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China;
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Xin Xie
- Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China;
| |
Collapse
|
110
|
Tan L, Li W, Su Q. The comprehensive analysis of the prognostic and functional role of N-terminal methyltransferases 1 in pan-cancer. PeerJ 2023; 11:e16263. [PMID: 37901469 PMCID: PMC10607204 DOI: 10.7717/peerj.16263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Background NTMT1, a transfer methylase that adds methyl groups to the N-terminus of proteins, has been identified as a critical player in tumor development and progression. However, its precise function in pan-cancer is still unclear. To gain a more comprehensive understanding of its role in cancer, we performed a thorough bioinformatics analysis. Methods To conduct our analysis, we gathered data from multiple sources, including RNA sequencing and clinical data from the TCGA database, protein expression data from the UALCAN and HPA databases, and single-cell expression data from the CancerSEA database. Additionally, we utilized TISIDB to investigate the interaction between the tumor and the immune system. To assess the impact of NTMT1 on the proliferation of SNU1076 cells, we performed a CCK8 assay. We also employed cellular immunofluorescence to detect DNA damage and used flow cytometry to measure tumor cell apoptosis. Results Our analysis revealed that NTMT1 was significantly overexpressed in various types of tumors and that high levels of NTMT1 were associated with poor survival outcomes. Functional enrichment analysis indicated that NTMT1 may contribute to tumor development and progression by regulating pathways involved in cell proliferation and immune response. In addition, we found that knockdown of NTMT1 expression led to reduced cell proliferation, increased DNA damage, and enhanced apoptosis in HNSCC cells. Conclusion High expression of NTMT1 in tumors is associated with poor prognosis. The underlying regulatory mechanism of NTMT1 in cancer is complex, and it may be involved in both the promotion of tumor development and the inhibition of the tumor immune microenvironment.
Collapse
Affiliation(s)
- Lifan Tan
- Department of Otolaryngology, West China-Guang’an Hospital, Sichuan University, Guang’an, Sichuan, China
| | - Wensong Li
- Department of Otolaryngology, West China-Guang’an Hospital, Sichuan University, Guang’an, Sichuan, China
| | - Qin Su
- Department of Otolaryngology, The People’s Hospital of Dujiangyan, Dujiangyan, Sichuan, China
| |
Collapse
|
111
|
Yi J, Peng F, Zhao J, Gong X. METTL3/IGF2BP2 axis affects the progression of colorectal cancer by regulating m6A modification of STAG3. Sci Rep 2023; 13:17292. [PMID: 37828232 PMCID: PMC10570365 DOI: 10.1038/s41598-023-44379-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/07/2023] [Indexed: 10/14/2023] Open
Abstract
Colorectal cancer (CRC) is among the commonest malignant tumors of humans. Existing evidence has linked the poor prognosis of CRC with high expression of stromal antigen 3 (STAG3), but, the exact biological effect of STAG3 in CRC is still unclear. The aim of this research is to reveal the biological function and molecular mechanism of STAG3 in CRC. To investigate the differential expression of STAG3 in CRC tissues and cell lines compared to normal colon tissues and cell lines, Western blot (WB) and quantitative real-time PCR (qRT-PCR) techniques were utilized. STAG3 N6-methyladenosine (m6A) modification level were identified using m6A RNA immunoprecipitation (MeRIP). Additionally, the functional roles of methyltransferase-like protein 3 (METTL3) and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) in CRC were explored by manipulating their levels via knockdown or overexpression. Cell proliferation was evaluated through Cell Counting Kit 8 (CCK-8) and clone formation experiments, while cell migration was assessed through wound healing experiments. Furthermore, cell apoptosis was detected using flow cytometry, and the protein expressions associated with proliferation and apoptosis were detected using WB. To identify the specific binding of target genes, RIP and pull-down assays were employed. Finally, the biological function of STAG3 in vivo was investigated through a xenotransplantation mouse tumor model. In CRC tissues and cell lines, STAG3 was up-regulated and accompanied by m6A methylation. Additionally, the expression of METTL3 was found to be upregulated in CRC tissues. Knocking down METTL3 resulted in a decrease in both the m6A level and protein expression of STAG3, inhibited cell proliferation and migration while promoting apoptosis, which were restored through STAG3 overexpression. Furthermore, online prediction indicated the interaction between STAG3 mRNA and IGF2BP2 protein, which was further verified by RIP experiments. IGF2BP2 downregulation led to decreased STAG3 protein expression, cell proliferation, and migration, but increased apoptosis. However, these impacts were reversed by STAG3 overexpression. Finally, subcutaneous tumor experiments conducted in nude mice also confirmed that METTL3 regulated CRC progression through STAG3 in vivo. The METTL3/IGF2BP2/STAG3 axis affects CRC progression in an m6A modification-dependent manner. This may guide targeted therapy in CRC patients.
Collapse
Affiliation(s)
- Jianmei Yi
- The Department of General Surgery 2, Zhuzhou Central Hospital (Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University), 116 Changjiang South Road, Tianyuan District, Zhuzhou, 412007, Hunan, China
| | - Feng Peng
- The Department of General Surgery 2, Zhuzhou Central Hospital (Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University), 116 Changjiang South Road, Tianyuan District, Zhuzhou, 412007, Hunan, China
| | - Jingli Zhao
- The Department of Operating Room, Zhuzhou Central Hospital (Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University), Zhuzhou, 412007, China
| | - Xiaosong Gong
- The Department of General Surgery 2, Zhuzhou Central Hospital (Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University), 116 Changjiang South Road, Tianyuan District, Zhuzhou, 412007, Hunan, China.
| |
Collapse
|
112
|
Guirguis AA, Ofir-Rosenfeld Y, Knezevic K, Blackaby W, Hardick D, Chan YC, Motazedian A, Gillespie A, Vassiliadis D, Lam EYN, Tran K, Andrews B, Harbour ME, Vasiliauskaite L, Saunders CJ, Tsagkogeorga G, Azevedo A, Obacz J, Pilka ES, Carkill M, MacPherson L, Wainwright EN, Liddicoat B, Blyth BJ, Albertella MR, Rausch O, Dawson MA. Inhibition of METTL3 Results in a Cell-Intrinsic Interferon Response That Enhances Antitumor Immunity. Cancer Discov 2023; 13:2228-2247. [PMID: 37548590 DOI: 10.1158/2159-8290.cd-23-0007] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/06/2023] [Accepted: 08/02/2023] [Indexed: 08/08/2023]
Abstract
Therapies that enhance antitumor immunity have altered the natural history of many cancers. Consequently, leveraging nonoverlapping mechanisms to increase immunogenicity of cancer cells remains a priority. Using a novel enzymatic inhibitor of the RNA methyl-transferase METTL3, we demonstrate a global decrease in N6-methyladenosine (m6A) results in double-stranded RNA (dsRNA) formation and a profound cell-intrinsic interferon response. Through unbiased CRISPR screens, we establish dsRNA-sensing and interferon signaling are primary mediators that potentiate T-cell killing of cancer cells following METTL3 inhibition. We show in a range of immunocompetent mouse models that although METTL3 inhibition is equally efficacious to anti-PD-1 therapy, the combination has far greater preclinical activity. Using SPLINTR barcoding, we demonstrate that anti-PD-1 therapy and METTL3 inhibition target distinct malignant clones, and the combination of these therapies overcomes clones insensitive to the single agents. These data provide the mole-cular and preclinical rationale for employing METTL3 inhibitors to promote antitumor immunity in the clinic. SIGNIFICANCE This work demonstrates that METTL3 inhibition stimulates a cell-intrinsic interferon response through dsRNA formation. This immunomodulatory mechanism is distinct from current immunotherapeutic agents and provides the molecular rationale for combination with anti-PD-1 immune-checkpoint blockade to augment antitumor immunity. This article is featured in Selected Articles from This Issue, p. 2109.
Collapse
Affiliation(s)
- Andrew A Guirguis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | - Kathy Knezevic
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | | | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Ali Motazedian
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Andrea Gillespie
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dane Vassiliadis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Kevin Tran
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | | | | | | | | | - Georgia Tsagkogeorga
- Storm Therapeutics Ltd, Cambridge, United Kingdom
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Joanna Obacz
- Storm Therapeutics Ltd, Cambridge, United Kingdom
| | | | - Marie Carkill
- Charles River Laboratories, Portishead, United -Kingdom
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Elanor N Wainwright
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Brian Liddicoat
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Benjamin J Blyth
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | | | | | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, -Victoria, Australia
| |
Collapse
|
113
|
Lin Y, Luo G, Liu Q, Yang R, Sol Reinach P, Yan D. METTL3-Mediated RNA m6A Modification Regulates the Angiogenic Behaviors of Retinal Endothelial Cells by Methylating MMP2 and TIE2. Invest Ophthalmol Vis Sci 2023; 64:18. [PMID: 37819742 PMCID: PMC10573643 DOI: 10.1167/iovs.64.13.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/17/2023] [Indexed: 10/13/2023] Open
Abstract
Purpose N6-methyladenosine (m6A) is a commonly occurring modification of mRNAs, catalyzed by a complex containing methyltransferase like 3 (METTL3). Our research aims to explore how METTL3-dependent m6A modification affects the functions of retinal endothelial cells (RECs). Methods An oxygen-induced retinopathy (OIR) mouse model was established, and RECs were isolated using magnetic beads method. Human retinal microvascular endothelial cells (HRMECs) were treated with normoxia (21% O2) or hypoxia (1% O2). Dot blot assay determined m6A modification levels. Quantitative RT-PCR and Western blot detected the mRNA and protein expression levels of the target candidates, respectively. Genes were knocked down by small interfering RNA transfection. Matrigel-based angiogenesis and transwell assays evaluated the abilities of endothelial tube formation and migration, respectively. Methylated RNA immunoprecipitation-qPCR determined the levels of m6A modification in the target genes. Results The m6A modification levels were significantly upregulated in the retinas and RECs of OIR mice. Exposure to hypoxia significantly elevated both METTL3 expression and m6A modification levels in HRMECs. METTL3 knockdown curtailed endothelial tube formation and migration in vitro under both normoxic and hypoxic conditions. Concurrently, this knockdown in HRMECs resulted in reduced m6A modification levels of MMP2 and TIE2 transcripts, subsequently leading to a decrease in their respective protein expressions. Notably, knockdown of MMP2 and TIE2 also markedly inhibited the angiogenic activities of HRMECs. Conclusions METTL3-mediated m6A modification promotes the angiogenic behaviors of RECs by targeting MMP2 and TIE2, suggesting its significance in retinal angiogenesis and METTL3 as a potential therapeutic target.
Collapse
Affiliation(s)
- Yong Lin
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Guangying Luo
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Qi Liu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Rusen Yang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Peter Sol Reinach
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Dongsheng Yan
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
114
|
García-Vílchez R, Añazco-Guenkova AM, López J, Dietmann S, Tomé M, Jimeno S, Azkargorta M, Elortza F, Bárcena L, Gonzalez-Lopez M, Aransay AM, Sánchez-Martín MA, Huertas P, Durán RV, Blanco S. N7-methylguanosine methylation of tRNAs regulates survival to stress in cancer. Oncogene 2023; 42:3169-3181. [PMID: 37660182 PMCID: PMC10589097 DOI: 10.1038/s41388-023-02825-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 07/27/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Tumour progression and therapy tolerance are highly regulated and complex processes largely dependent on the plasticity of cancer cells and their capacity to respond to stress. The higher plasticity of cancer cells highlights the need for identifying targetable molecular pathways that challenge cancer cell survival. Here, we show that N7-guanosine methylation (m7G) of tRNAs, mediated by METTL1, regulates survival to stress conditions in cancer cells. Mechanistically, we find that m7G in tRNAs protects them from stress-induced cleavage and processing into 5' tRNA fragments. Our analyses reveal that the loss of tRNA m7G methylation activates stress response pathways, sensitising cancer cells to stress. Furthermore, we find that the loss of METTL1 reduces tumour growth and increases cytotoxic stress in vivo. Our study uncovers the role of m7G methylation of tRNAs in stress responses and highlights the potential of targeting METTL1 to sensitise cancer cells to chemotherapy.
Collapse
Affiliation(s)
- Raquel García-Vílchez
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Ana M Añazco-Guenkova
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Judith López
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Sabine Dietmann
- Washington University School of Medicine in St. Louis, 660S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Mercedes Tomé
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
| | - Sonia Jimeno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Mikel Azkargorta
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
| | - Félix Elortza
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Laura Bárcena
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Ana M Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Manuel A Sánchez-Martín
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, 37007, Salamanca, Spain
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Raúl V Durán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
| | - Sandra Blanco
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
| |
Collapse
|
115
|
Kotekar A, Singh AK, Devaiah BN. BRD4 and MYC: power couple in transcription and disease. FEBS J 2023; 290:4820-4842. [PMID: 35866356 PMCID: PMC9867786 DOI: 10.1111/febs.16580] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 01/26/2023]
Abstract
The MYC proto-oncogene and BRD4, a BET family protein, are two cardinal proteins that have a broad influence in cell biology and disease. Both proteins are expressed ubiquitously in mammalian cells and play central roles in controlling growth, development, stress responses and metabolic function. As chromatin and transcriptional regulators, they play a critical role in regulating the expression of a burgeoning array of genes, maintaining chromatin architecture and genome stability. Consequently, impairment of their function or regulation leads to many diseases, with cancer being the most predominant. Interestingly, accumulating evidence indicates that regulation of the expression and functions of MYC are tightly intertwined with BRD4 at both transcriptional and post-transcriptional levels. Here, we review the mechanisms by which MYC and BRD4 are regulated, their functions in governing various molecular mechanisms and the consequences of their dysregulation that lead to disease. We present a perspective of how the regulatory mechanisms for the two proteins could be entwined at multiple points in a BRD4-MYC nexus that leads to the modulation of their functions and disease upon dysregulation.
Collapse
Affiliation(s)
- Aparna Kotekar
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Amit Kumar Singh
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | | |
Collapse
|
116
|
Yang J, Li L, Cheng J, Lu J, Zhang S, Wang S, Zhao L, Zhou L. The m6A modulator-mediated cytarabine sensitivity and immune cell infiltration signature in acute myeloid leukemia. J Cancer Res Clin Oncol 2023; 149:11457-11469. [PMID: 37391640 DOI: 10.1007/s00432-023-05029-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
PURPOSE The study aims to investigate the impact of m6A modulators on drug resistance and the immune microenvironment in acute myeloid leukemia (AML). The emergence of drug resistance is a significant factor that contributes to relapse and refractory AML, leading to a poor prognosis. METHODS The AML transcriptome data were retrieved from the TCGA database. The "oncoPredict" R package was utilized to assess the sensitivity of each sample to cytarabine (Ara-C) and classify them into distinct groups. Differential expression analysis was performed to identify m6A modulators differentially expressed between the two groups. Select Random Forest (RF) to build a predictive model. Model performance was evaluated using calibration curve, clinical decision curve, and clinical impact curve. The impacts of METTL3 on Ara-C sensitivity and immune microenvironment in AML were examined using GO, KEGG, CIBERSORT, and GSEA analyses. RESULTS Seventeen out of 26 m6A modulators exhibited differential expression between the Ara-C-sensitive and resistant groups, with a high degree of correlation. We selected the 5 genes with the highest scores in the RF model to build a reliable and accurate prediction model. METTL3 plays a vital role in m6A modification, and further analysis shows its impact on the sensitivity of AML cells to Ara-C through its interaction with 7 types of immune-infiltrating cells and autophagy. CONCLUSION This study utilizes m6A modulators to develop a prediction model for the sensitivity of AML patients to Ara-C, which can assist in treating AML drug resistance by targeting mRNA methylation.
Collapse
Affiliation(s)
- Jincai Yang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Liangliang Li
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, Gansu, China
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou, 730000, Gansu, China
| | - Juan Cheng
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Jianle Lu
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Shuling Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Shan Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Li Zhao
- Central Laboratory, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu, China.
- Gansu Key Laboratory of Genetic Study of Hematopathy, Lanzhou, 730000, Gansu, China.
| | - Lanxia Zhou
- Central Laboratory, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu, China.
- Gansu Key Laboratory of Genetic Study of Hematopathy, Lanzhou, 730000, Gansu, China.
| |
Collapse
|
117
|
Zhou X, Jin L, Li Y, Wang Y, Li W, Shen X. Comprehensive analysis of N6-methyladenosine-related RNA methylation in the mouse hippocampus after acquired hearing loss. BMC Genomics 2023; 24:577. [PMID: 37759187 PMCID: PMC10537436 DOI: 10.1186/s12864-023-09697-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The mechanism underlying cognitive impairment after hearing loss (HL) remains unclear. N6-methyladenosine (m6A) is involved in many neurodegenerative diseases; however, its role in cognitive impairment after HL has not yet been investigated. Therefore, we aimed to analyze the m6A modification profile of the mouse hippocampus after HL exposure. A mouse model of neomycin-induced HL was established. An auditory brainstem-response test was utilized for detecting hearing threshold. The passive avoidance test was served as the mean for evaluating cognitive function. The m6A-regulated enzyme expression levels were analyzed by using reverse transcription quantitative real-time polymerase chain reaction and western blot analyses. RNA sequencing (RNA-Seq) and methylated RNA immunoprecipitation sequencing (MeRIP-Seq) were performed with the aim of investigating gene expression differences and m6A modification in the mouse hippocampus. RESULTS Neomycin administration induced severe HL in mice. At four months of age, the mice in the HL group showed poorer cognitive performance than the mice in the control group. METTL14, WTAP, and YTHDF2 mRNA levels were downregulated in the hippocampi of HL mice, whereas ALKBH5 and FTO mRNA levels were significantly upregulated. At the protein level, METTL3 and FTO were significantly upregulated. Methylated RNA immunoprecipitation sequencing analysis revealed 387 and 361 m6A hypermethylation and hypomethylation peaks, respectively. Moreover, combined analysis of mRNA expression levels and m6A peaks revealed eight mRNAs with significantly changed expression levels and methylation. CONCLUSIONS Our findings revealed the m6A transcriptome-wide profile in the hippocampus of HL mice, which may provide a basis for understanding the association between HL and cognitive impairment from the perspective of epigenetic modifications.
Collapse
Affiliation(s)
- Xuehua Zhou
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, 200031, Shanghai, China
| | - Lin Jin
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, 200031, Shanghai, China
| | - Yufeng Li
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, 200031, Shanghai, China
| | - Yiru Wang
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, 200031, Shanghai, China
| | - Wen Li
- ENT Institute, Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, 200031, Shanghai, China
| | - Xia Shen
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, 200031, Shanghai, China.
| |
Collapse
|
118
|
Wang F, Sun Z, Zhang Q, Yang H, Yang G, Yang Q, Zhu Y, Wu W, Xu W, Wu X. Curdione induces ferroptosis mediated by m6A methylation via METTL14 and YTHDF2 in colorectal cancer. Chin Med 2023; 18:122. [PMID: 37735401 PMCID: PMC10512537 DOI: 10.1186/s13020-023-00820-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/11/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Curdione is a sesquiterpene isolated from Curcumae Rhizoma that possesses high biological activity and extensive pharmacological effects. As a traditional Chinese medicine, Curcumae Rhizoma can inhibit the development of many types of cancer, especially colorectal cancer. However, the anti-colorectal mechanism of its monomer curdione remains unclear. METHODS Colorectal cancer (CRC) cells were treated with curdione at doses of 12.5 μM, 25 μM, and 50 μM, and then the cells' activity was measured with methyl thiazolyl tetrazolium (MTT). Nude mice were administered different doses of curdione subcutaneously and oxaliplatin by tail vein injection, and then hematoxylin-eosin (HE) staining was adopted to examine tumor histology. Moreover, flow cytometry was applied to detect reactive oxygen species in cells and tissues. Kits were employed to detect the levels of iron ions, malondialdehyde, lipid hydroperoxide, and glutathione. Polymerase chain reaction (PCR) and Western blotting were adopted to detect ferroptosis and m6A modification-related factors. A methylation spot hybridization assay was performed to measure changes in overall methylation. SLC7A11 and HOXA13 were measured by MeRIP-qPCR. The shRNA-METTL14 plasmid was constructed to verify the inhibitory effect of curdione on CRC. RESULTS A dose-dependent decrease in activity was observed in curdione-treated cells. Curdione increased the accumulation of reactive oxygen species in CRC cells and tumor tissues, greatly enhanced the levels of malondialdehyde, lipid hydroperoxide and Fe2+, and lowered the activity of glutathione. According to the qPCR and Western blot results, curdione promoted the expression of METTL14 and YTHDF2 in CRC cells and tissues, respectively, and decreased the expression of SLC7A11, SLC3A2, HOXA13, and glutathione peroxidase 4. Additionally, in animal experiments, the curdione-treated group showed severe necrosis of tumor cells, as displayed by HE staining. Furthermore, compared with the control group, levels of m6A modifying factors (namely, SLC7A11 and HOXA13) were increased in the tissues after drug intervention. METTL14 knockdown was followed by an increase in CRC cell activity and glutathione levels. However, the levels of reactive oxygen species, malondialdehyde, and iron ions decreased. The expression levels of SLC7A11, SLC3A2, HOXA13, and GPX4 were all increased after METTL14 knockdown. CONCLUSION The results suggest that curdione induces ferroptosis in CRC by virtue of m6A methylation.
Collapse
Affiliation(s)
- Fang Wang
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210046, Jiangsu, China
| | - Zheng Sun
- Department of Surgical Oncology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Qunyao Zhang
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210046, Jiangsu, China
| | - Hao Yang
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210046, Jiangsu, China
| | - Gang Yang
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210046, Jiangsu, China
| | - Qi Yang
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210046, Jiangsu, China
| | - Yimiao Zhu
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210046, Jiangsu, China
| | - Wenya Wu
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210046, Jiangsu, China
| | - Wenwen Xu
- Department of Gynecology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.
| | - Xiaoyu Wu
- Department of Surgical Oncology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.
| |
Collapse
|
119
|
Zhao SS, Liu J, Wu QC, Zhou XL. Role of histone lactylation interference RNA m 6A modification and immune microenvironment homeostasis in pulmonary arterial hypertension. Front Cell Dev Biol 2023; 11:1268646. [PMID: 37771377 PMCID: PMC10522917 DOI: 10.3389/fcell.2023.1268646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a severe disease resulting from progressive increases in pulmonary vascular resistance and pulmonary vascular remodeling, ultimately leading to right ventricular failure and even death. Hypoxia, inflammation, immune reactions, and epigenetic modifications all play significant contributory roles in the mechanism of PAH. Increasingly, epigenetic changes and their modifying factors involved in reprogramming through regulation of methylation or the immune microenvironment have been identified. Among them, histone lactylation is a new post-translational modification (PTM), which provides a novel visual angle on the functional mechanism of lactate and provides a promising diagnosis and treatment method for PAH. This review detailed introduces the function of lactate as an important molecule in PAH, and the effects of lactylation on N6-methyladenosine (m6A) and immune cells. It provides a new perspective to further explore the development of lactate regulation of pulmonary hypertension through histone lactylation modification.
Collapse
Affiliation(s)
- Shuai-shuai Zhao
- Department of Cardiac Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Jinlong Liu
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Qi-cai Wu
- Department of Cardiac Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Xue-liang Zhou
- Department of Cardiac Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| |
Collapse
|
120
|
Breger K, Kunkler CN, O'Leary NJ, Hulewicz JP, Brown JA. Ghost authors revealed: The structure and function of human N 6 -methyladenosine RNA methyltransferases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1810. [PMID: 37674370 PMCID: PMC10915109 DOI: 10.1002/wrna.1810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 09/08/2023]
Abstract
Despite the discovery of modified nucleic acids nearly 75 years ago, their biological functions are still being elucidated. N6 -methyladenosine (m6 A) is the most abundant modification in eukaryotic messenger RNA (mRNA) and has also been detected in non-coding RNAs, including long non-coding RNA, ribosomal RNA, and small nuclear RNA. In general, m6 A marks can alter RNA secondary structure and initiate unique RNA-protein interactions that can alter splicing, mRNA turnover, and translation, just to name a few. Although m6 A marks in human RNAs have been known to exist since 1974, the structures and functions of methyltransferases responsible for writing m6 A marks have been established only recently. Thus far, there are four confirmed human methyltransferases that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the N6 position of adenosine, producing m6 A: methyltransferase-like protein (METTL) 3/METTL14 complex, METTL16, METTL5, and zinc-finger CCHC-domain-containing protein 4. Though the methyltransferases have unique RNA targets, all human m6 A RNA methyltransferases contain a Rossmann fold with a conserved SAM-binding pocket, suggesting that they utilize a similar catalytic mechanism for methyl transfer. For each of the human m6 A RNA methyltransferases, we present the biological functions and links to human disease, RNA targets, catalytic and kinetic mechanisms, and macromolecular structures. We also discuss m6 A marks in human viruses and parasites, assigning m6 A marks in the transcriptome to specific methyltransferases, small molecules targeting m6 A methyltransferases, and the enzymes responsible for hypermodified m6 A marks and their biological functions in humans. Understanding m6 A methyltransferases is a critical steppingstone toward establishing the m6 A epitranscriptome and more broadly the RNome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| |
Collapse
|
121
|
Hui Y, Ma Q, Zhou XR, Wang H, Dong JH, Gao LN, Zhang T, Li YY, Gong T. Immunological characterization and diagnostic models of RNA N6-methyladenosine regulators in Alzheimer's disease. Sci Rep 2023; 13:14588. [PMID: 37666846 PMCID: PMC10477294 DOI: 10.1038/s41598-023-41129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/22/2023] [Indexed: 09/06/2023] Open
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia, and it displays both clinical and molecular variability. RNA N6-methyladenosine (m6A) regulators are involved in a wide range of essential cellular processes. In this study, we aimed to identify molecular signatures associated with m6A in Alzheimer's disease and use those signatures to develop a predictive model. We examined the expression patterns of m6A regulators and immune features in Alzheimer's disease using the GSE33000 dataset. We examined the immune cell infiltration and molecular groups based on m6A-related genes in 310 Alzheimer's disease samples. The WGCNA algorithm was utilized to determine differently expressed genes within each cluster. After evaluating the strengths and weaknesses of the random forest model, the support vector machine model, the generalized linear model, and eXtreme Gradient Boosting, the best machine model was selected. Methods such as nomograms, calibration curves, judgment curve analysis, and the use of independent data sets were used to verify the accuracy of the predictions made. Alzheimer's disease and non-disease Alzheimer's groups were compared to identify dysregulated m6A-related genes and activated immune responses. In Alzheimer's disease, two molecular clusters linked to m6A were identified. Immune infiltration analysis indicated substantial variation in protection between groups. Cluster 1 included processes like the Toll-like receptor signaling cascade, positive regulation of chromatin binding, and numerous malignancies; cluster 2 included processes like the cell cycle, mRNA transport, and ubiquitin-mediated proteolysis. With a lower residual and root mean square error and a larger area under the curve (AUC = 0.951), the Random forest machine model showed the greatest discriminative performance. The resulting random forest model was based on five genes, and it performed well (AUC = 0.894) on external validation datasets. Accuracy in predicting Alzheimer's disease subgroups was also shown by analyses of nomograms, calibration curves, and decision curves. In this research, we methodically outlined the tangled web of connections between m6A and AD and created a promising prediction model for gauging the correlation between m6A subtype risk and AD pathology.
Collapse
Affiliation(s)
- Yuan Hui
- School of Integrative Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Qi Ma
- School of Integrative Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Xue-Rui Zhou
- School of Integrative Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Huan Wang
- School of Integrative Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Jian-Hua Dong
- School of Integrative Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Li-Na Gao
- School of Integrative Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Tian Zhang
- School of Integrative Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Yan-Yi Li
- Department of Encephalopathy II, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China
| | - Ting Gong
- Department of Encephalopathy II, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China.
| |
Collapse
|
122
|
Dong S, Sun Y, Liu C, Li Y, Yu S, Zhang Q, Xu Y. Stage-specific requirement for m 6A RNA methylation during cardiac differentiation of pluripotent stem cells. Differentiation 2023; 133:77-87. [PMID: 37506593 DOI: 10.1016/j.diff.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/16/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
Precise spatiotemporal control of gene expression patterns is critical for normal development. Pluripotent stem cells, including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), with the ability of unlimited self-renewal and differentiation into any cell type, provide a unique tool for understanding the underlying mechanism of development and disease in a dish. N6-methyl-adenosine (m6A) modification is the most extensive internal mRNA modification, which regulates almost all aspects of mRNA metabolism and thus extensively participates in gene expression regulation. However, the role of m6A during cardiogenesis still needs to be fully elucidated. Here, we found that core components of m6A methyltransferase decreased during cardiomyocyte differentiation. Impeding m6A deposition, by either deleting the m6A methyltransferase Mettl3 or overexpressing m6A demethylase alkB homolog 5 (Alkbh5), at early stages of cardiac differentiation of mouse pluripotent stem cells, led to inhibition of cardiac gene activation and retardation of the outgrowth of embryoid bodies, whereas interfering m6A modification at later stages of differentiation had minimal effects. Consistently, stage-specific inhibition of METTL3 with METTL3 inhibitor STM2457 during human ESCs (hESCs) cardiac differentiation demonstrated a similarly pivotal role of METTL3 for the induction of mesodermal cells while dispensable function for later stages. In summary, our study reveals a stage-specific requirement of m6A on the cardiac differentiation of pluripotent stem cells and demonstrates that precise tuning of m6A level is critical for cardiac differentiation.
Collapse
Affiliation(s)
- Shuai Dong
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuetong Sun
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chang Liu
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanli Li
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shanshan Yu
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qi Zhang
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Cell-gene Therapy Translational Medicine Research Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Xu
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
123
|
Kim J, Chun Y, Ramirez CB, Hoffner LA, Jung S, Jang KH, Rubtsova VI, Jang C, Lee G. MAPK13 stabilization via m 6A mRNA modification limits anticancer efficacy of rapamycin. J Biol Chem 2023; 299:105175. [PMID: 37599001 PMCID: PMC10511813 DOI: 10.1016/j.jbc.2023.105175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/22/2023] Open
Abstract
N6-adenosine methylation (m6A) is the most abundant mRNA modification that controls gene expression through diverse mechanisms. Accordingly, m6A-dependent regulation of oncogenes and tumor suppressors contributes to tumor development. However, the role of m6A-mediated gene regulation upon drug treatment or resistance is poorly understood. Here, we report that m6A modification of mitogen-activated protein kinase 13 (MAPK13) mRNA determines the sensitivity of cancer cells to the mechanistic target of rapamycin complex 1 (mTORC1)-targeting agent rapamycin. mTORC1 induces m6A modification of MAPK13 mRNA at its 3' untranslated region through the methyltransferase-like 3 (METTL3)-METTL14-Wilms' tumor 1-associating protein(WTAP) methyltransferase complex, facilitating its mRNA degradation via an m6A reader protein YTH domain family protein 2. Rapamycin blunts this process and stabilizes MAPK13. On the other hand, genetic or pharmacological inhibition of MAPK13 enhances rapamycin's anticancer effects, which suggests that MAPK13 confers a progrowth signal upon rapamycin treatment, thereby limiting rapamycin efficacy. Together, our data indicate that rapamycin-mediated MAPK13 mRNA stabilization underlies drug resistance, and it should be considered as a promising therapeutic target to sensitize cancer cells to rapamycin.
Collapse
Affiliation(s)
- Joohwan Kim
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Yujin Chun
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Cuauhtemoc B Ramirez
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA; Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Lauren A Hoffner
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Sunhee Jung
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Ki-Hong Jang
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Varvara I Rubtsova
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA; School of Biological Sciences, University of California Irvine, Irvine, California, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Gina Lee
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA.
| |
Collapse
|
124
|
Russell J, Tzelepis K. A non-coding m 6A reader promotes leukaemia. Nat Cell Biol 2023; 25:1247-1249. [PMID: 37640840 DOI: 10.1038/s41556-023-01205-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Affiliation(s)
- James Russell
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Konstantinos Tzelepis
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
| |
Collapse
|
125
|
Fan J, Zhuang M, Fan W, Hou M. RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA. PeerJ 2023; 11:e15706. [PMID: 37663284 PMCID: PMC10474828 DOI: 10.7717/peerj.15706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/15/2023] [Indexed: 09/05/2023] Open
Abstract
Background N6-methyladenosine (m6A) methylation epigenetically regulates normal hematopoiesis and plays a role in the pathogenesis of acute myeloid leukemia (AML). However, its potential value for prognosis remains elusive. Methods Analysis of the datasets downloaded from The Cancer Genome Atlas and Genotype Tissue Expression databases revealed that the expression level of 20 regulators related to m6A RNA methylation differ between patients with AML and normal individuals. A prognostic risk model with three genes (YTHDF3, IGF2BP3, and HNRNPA2B1) was developed using univariate Cox regression and the least absolute shrinkage and selection operator Cox regression methods. Results This established signature demonstrated good predictive efficacy with an area under the curve of 0.892 and 0.731 in the training cohort and the validation cohort, respectively. Patients with AML and an increased level of Insulin growth factor 2 mRNA binding protein 3 (IGF2BP3) expression exhibited a poor prognosis. IGF2BP3 knockdown significantly induced G0/G1 phase arrest and inhibited cell proliferation, apoptosis, and/or differentiation. Further, the JAK/STAT pathway may be involved in the regulation of EPOR expression by IGF2BP3-mediated m6A RNA methylation. Conclusion These findings indicate that IGF2BP3 plays a carcinogenic role in AML, implying that it can predict patient survival and could be an effective strategy for AML therapy.
Collapse
Affiliation(s)
- Jin Fan
- Qilu Hospital of Shandong University, Jinan, China
| | | | - Wei Fan
- Department of Pharmacy and Medical Laboratory, Heze Medical College, Heze, China
| | - Ming Hou
- Qilu Hospital of Shandong University, Jinan, China
| |
Collapse
|
126
|
Liu R, Zhao E, Yu H, Yuan C, Abbas MN, Cui H. Methylation across the central dogma in health and diseases: new therapeutic strategies. Signal Transduct Target Ther 2023; 8:310. [PMID: 37620312 PMCID: PMC10449936 DOI: 10.1038/s41392-023-01528-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 08/26/2023] Open
Abstract
The proper transfer of genetic information from DNA to RNA to protein is essential for cell-fate control, development, and health. Methylation of DNA, RNAs, histones, and non-histone proteins is a reversible post-synthesis modification that finetunes gene expression and function in diverse physiological processes. Aberrant methylation caused by genetic mutations or environmental stimuli promotes various diseases and accelerates aging, necessitating the development of therapies to correct the disease-driver methylation imbalance. In this Review, we summarize the operating system of methylation across the central dogma, which includes writers, erasers, readers, and reader-independent outputs. We then discuss how dysregulation of the system contributes to neurological disorders, cancer, and aging. Current small-molecule compounds that target the modifiers show modest success in certain cancers. The methylome-wide action and lack of specificity lead to undesirable biological effects and cytotoxicity, limiting their therapeutic application, especially for diseases with a monogenic cause or different directions of methylation changes. Emerging tools capable of site-specific methylation manipulation hold great promise to solve this dilemma. With the refinement of delivery vehicles, these new tools are well positioned to advance the basic research and clinical translation of the methylation field.
Collapse
Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Erhu Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Huijuan Yu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Chaoyu Yuan
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
127
|
Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:25. [PMID: 37612540 PMCID: PMC10447785 DOI: 10.1186/s43556-023-00139-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.
Collapse
Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Qian Jing
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yanbo Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
| |
Collapse
|
128
|
Qi S, Gupta YK. A cryptic pocket in METTL3-METTL14 regulates m 6A conversion and sensing. RESEARCH SQUARE 2023:rs.3.rs-3150186. [PMID: 37609305 PMCID: PMC10441475 DOI: 10.21203/rs.3.rs-3150186/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The nuclear METTL3-METTL14 enzyme complex transfers a methyl group from S-adenosyl-L-methionine (SAM) to the N6 amino group of an adenosine (A) base in RNA to convert it to m6A and in ssDNA to 6mA. m6A marks are prevalent in eukaryotic mRNAs and lncRNAs and modulate their stability and fate in a context-dependent manner. The cytoplasmic METTL3 can act as a m6A reader to regulate mRNA translation. However, the precise mechanism that actuates the switch from m6A writer to reader/sensor is unclear. Here, we present a ~2.5Å crystal structure of the methyltransferase core of human METTL3-METTL14 in complex with the reaction product, N6-methyladenosine monophosphate (m6A), representing a state post-catalysis but before the release of m6A. m6A occupies a novel evolutionarily conserved cryptic pocket in METTL3-METTL14 located ~16Å away from the SAM pocket that frequently mutates in cancer. We propose a two-step model of swiveling of target A upon conversion to m6A and sensing its methylation status by the cryptic pocket, enabling it to actuate enzymes' switch from writer to an m6A-sensor. Cancer-associated mutations cannot distinguish methylated from unmethylated adenine and show impaired RNA binding, de-stacking, and defective m6A writing and sensing.
Collapse
Affiliation(s)
- Shan Qi
- Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Yogesh K. Gupta
- Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| |
Collapse
|
129
|
Kahraman S, De Jesus DF, Wei J, Brown NK, Zou Z, Hu J, He C, Kulkarni RN. m 6 A mRNA Methylation Regulates Early Pancreatic β-Cell Differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551675. [PMID: 37577492 PMCID: PMC10418275 DOI: 10.1101/2023.08.03.551675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
N 6 -methyladenosine (m 6 A) is the most abundant chemical modification in mRNA, and plays important roles in human and mouse embryonic stem cell pluripotency, maintenance, and differentiation. We have recently reported, for the first time, the role of m 6 A in the postnatal control of β-cell function in physiological states and in Type 1 and 2 Diabetes. However, the precise mechanisms by which m 6 A acts to regulate the development of human and mouse β-cells are unexplored. Here, we show that the m 6 A landscape is dynamic during human pancreas development, and that METTL14, one of the m 6 A writer complex proteins, is essential for the early differentiation of both human and mouse β-cells.
Collapse
|
130
|
Gao J, Fang Y, Chen J, Tang Z, Tian M, Jiang X, Tao C, Huang R, Zhu G, Qu W, Wu X, Zhou J, Fan J, Liu W, Shi Y. Methyltransferase like 3 inhibition limits intrahepatic cholangiocarcinoma metabolic reprogramming and potentiates the efficacy of chemotherapy. Oncogene 2023; 42:2507-2520. [PMID: 37420030 DOI: 10.1038/s41388-023-02760-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 07/09/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation and its associated methyltransferase like 3 (METTL3) are involved in the development and maintenance of various tumors. The present study aimed to evaluate the cross-talk of METTL3 with glucose metabolism and reveal a novel mechanism for intrahepatic cholangiocarcinoma (ICC) progression. Real-time quantitative PCR, western blotting, and immunohistochemistry analyses suggested that METTL3 was highly expressed in ICC, which was correlated with poor patient prognosis. Immunoprecipitation sequencing of m6A-RNA showed that METTL3 upregulated m6A modification of NFAT5, which recruited IGF2BP1 for NFAT5 mRNA stabilization. Elevated expression of NFAT5 increased the expression of the gluconeogenesis-related genes GLUT1 and PGK1, resulting in enhanced aerobic glycolysis, proliferation, and tumor metastasis of ICC. Moreover, higher METTL3 expression was observed in tumor tissues of ICC patients with activated ICC glucose metabolism. Importantly, STM2457, a highly potent METTL3 inhibitor, which inhibited METTL3 activity and acted synergistically with gemcitabine, suggests that reprogramming RNA epigenetic modifications may serve as a potential therapeutic strategy. Overall, our findings highlighted the role of METTL3-mediated m6A modification of NFAT5 in activating glycolytic reprogramming in ICC and proposed that the METTL3/NFAT5 axis was a clinical target for the management of ICC chemoresistance by targeting cancer glycolysis.
Collapse
Affiliation(s)
- Jun Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuan Fang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiafeng Chen
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
| | - Zheng Tang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
| | - Mengxin Tian
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xifei Jiang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
| | - Chenyang Tao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
| | - Run Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guiqi Zhu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
| | - Weifeng Qu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoling Wu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Weiren Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China.
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yinghong Shi
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China.
- Research Unit of Liver Cancer Recurrence and Metastasis, Chinese Academy of Medical Sciences, Beijing, China.
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, China.
| |
Collapse
|
131
|
Wang P, Wang J, Yao S, Cui M, Cheng Y, Liu W, Gao Z, Hu J, Zhang J, Zhang H. Deubiquitinase USP9X stabilizes RNA m 6A demethylase ALKBH5 and promotes acute myeloid leukemia cell survival. J Biol Chem 2023; 299:105055. [PMID: 37454738 PMCID: PMC10424212 DOI: 10.1016/j.jbc.2023.105055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Post-translational modifications including protein ubiquitination regulate a plethora of cellular processes in distinct manners. RNA N6-methyladenosine is the most abundant post-transcriptional modification on mammalian mRNAs and plays important roles in various physiological and pathological conditions including hematologic malignancies. We previously determined that the RNA N6-methyladenosine eraser ALKBH5 is necessary for the maintenance of acute myeloid leukemia (AML) stem cell function, but the post-translational modifications involved in ALKBH5 regulation remain elusive. Here, we show that deubiquitinase ubiquitin-specific peptidase 9X (USP9X) stabilizes ALKBH5 and promotes AML cell survival. Through the use of mass spectrometry as an unbiased approach, we identify USP9X and confirm that it directly binds to ALKBH5. USP9X stabilizes ALKBH5 by removing the K48-linked polyubiquitin chain at K57. Using human myeloid leukemia cells and a murine AML model, we find that genetic knockdown or pharmaceutical inhibition of USP9X inhibits leukemia cell proliferation, induces apoptosis, and delays AML development. Ectopic expression of ALKBH5 partially mediates the function of USP9X in AML. Overall, this study uncovers deubiquitinase USP9X as a key for stabilizing ALKBH5 expression and reveals the important role of USP9X in AML, which provides a promising therapeutic strategy for AML treatment in the clinic.
Collapse
Affiliation(s)
- Peipei Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jing Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Shuxin Yao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Manman Cui
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Ying Cheng
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Weidong Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Zhuying Gao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jin Hu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jinfang Zhang
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Haojian Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
| |
Collapse
|
132
|
Deng X, Qing Y, Horne D, Huang H, Chen J. The roles and implications of RNA m 6A modification in cancer. Nat Rev Clin Oncol 2023; 20:507-526. [PMID: 37221357 DOI: 10.1038/s41571-023-00774-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
N6-Methyladenosine (m6A), the most prevalent internal modification in eukaryotic mRNA, has been extensively and increasingly studied over the past decade. Dysregulation of RNA m6A modification and its associated machinery, including writers, erasers and readers, is frequently observed in various cancer types, and the dysregulation profiles might serve as diagnostic, prognostic and/or predictive biomarkers. Dysregulated m6A modifiers have been shown to function as oncoproteins or tumour suppressors with essential roles in cancer initiation, progression, metastasis, metabolism, therapy resistance and immune evasion as well as in cancer stem cell self-renewal and the tumour microenvironment, highlighting the therapeutic potential of targeting the dysregulated m6A machinery for cancer treatment. In this Review, we discuss the mechanisms by which m6A modifiers determine the fate of target RNAs and thereby influence protein expression, molecular pathways and cell phenotypes. We also describe the state-of-the-art methodologies for mapping global m6A epitranscriptomes in cancer. We further summarize discoveries regarding the dysregulation of m6A modifiers and modifications in cancer, their pathological roles, and the underlying molecular mechanisms. Finally, we discuss m6A-related prognostic and predictive molecular biomarkers in cancer as well as the development of small-molecule inhibitors targeting oncogenic m6A modifiers and their activity in preclinical models.
Collapse
Affiliation(s)
- Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - David Horne
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
- Gehr Family Center for Leukemia Research & City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
| |
Collapse
|
133
|
Cao S, Zhu H, Cui J, Liu S, Li Y, Shi J, Mo J, Wang Z, Wang H, Hu J, Chen L, Li Y, Xia L, Xiao S. Allele-specific RNA N 6-methyladenosine modifications reveal functional genetic variants in human tissues. Genome Res 2023; 33:1369-1380. [PMID: 37714712 PMCID: PMC10547253 DOI: 10.1101/gr.277704.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 06/13/2023] [Indexed: 09/17/2023]
Abstract
An intricate network of cis- and trans-elements acts on RNA N 6-methyladenosine (m6A), which in turn may affect gene expression and, ultimately, human health. A complete understanding of this network requires new approaches to accurately measure the subtle m6A differences arising from genetic variants, many of which have been associated with common diseases. To address this gap, we developed a method to accurately and sensitively detect transcriptome-wide allele-specific m6A (ASm6A) from MeRIP-seq data and applied it to uncover 12,056 high-confidence ASm6A modifications from 25 human tissues. We also identified 1184 putative functional variants for ASm6A regulation, a subset of which we experimentally validated. Importantly, we found that many of these ASm6A-associated genetic variants were enriched for common disease-associated and complex trait-associated risk loci, and verified that two disease risk variants can change m6A modification status. Together, this work provides a tool to detangle the dynamic network of RNA modifications at the allelic level and highlights the interplay of m6A and genetics in human health and disease.
Collapse
Affiliation(s)
- Shuo Cao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Haoran Zhu
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jinru Cui
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Sun Liu
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuhe Li
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junfang Shi
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junyuan Mo
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zihan Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hailan Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Hu
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lizhi Chen
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuan Li
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Laixin Xia
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China;
| | - Shan Xiao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China;
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou 510515, China
| |
Collapse
|
134
|
Zhu WH, Chen J, Huang RK, Zhang Y, Huang ZX, Pang XQ, Hu B, Yang Y, Li X. Erythroid-transdifferentiated myeloid cells promote portal vein tumor thrombus in hepatocellular carcinoma. Theranostics 2023; 13:4316-4332. [PMID: 37649603 PMCID: PMC10465220 DOI: 10.7150/thno.82907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023] Open
Abstract
Rationale: Hepatocellular carcinoma (HCC) is primarily characterized by a high incidence of vascular invasion. However, the specific mechanism underlying portal vein tumor thrombus (PVTT) in HCC remains unclear. As a consequence of myeloid cell developmental arrest, CD71+ erythroid progenitor cells (EPCs) and myeloid-derived suppressor cells play important roles in HCC; however, their roles in PVTT remain unclear. Methods: The role of CD71+ EPCs in the HCC tumor microenvironment (TME) was evaluated via morphological, RNA-sequencing, enzyme-linked immunosorbent assay, and flow cytometric analyses. Co-culture techniques were employed to assess the CD45+ EPCs and their vascular compromising effect. Additionally, the PVTT-promoting function of CD45+ EPCs was explored in vivo in a murine model. Results: The CD45+EPCs in HCC tissues exhibited increased myeloid cell features, including morphology, surface markers, transforming growth factor (TGF)-β generation, and gene expression, compared with those in circulation. Hence, a large proportion of CD45+EPCs, particularly those in TMEs, comprise erythroid-transdifferentiated myeloid cells (EDMCs). Additionally, the expression of C-C chemokine receptor type 2 (CCR2) mRNA was upregulated in CD45+EPCs within the TME. Tumor macrophages from HCC tissues induced substantial migration of CD45+EPCs in a dose-dependent manner. Meanwhile, results from immunofluorescence analyses revealed that these two cell types are positively associated in the TME and circulation. That is, EDMCs are chemoattracted by HCC macrophages mainly via CCR2 from CD45+ EPCs in the circulation. Additionally, the expressions of FX, FVII, FGB, C4b, CFB, and CFH were elevated in CD45+EPCs within the TME compared with those in the spleen. The CD45+EPCs from the HCC TME promoted vessel endothelial cell migration and compromised tube formation through TGF-β and FGB, respectively. Additionally, CD45+EPCs from the TME induced HCC cell migration. HCC macrophage-induced CD45+EPCs to exhibit higher levels of FX, FVII, FGB, and TGF-β. Meanwhile, upregulation of CCAAT/enhancer binding protein beta expression induced FGB and TGF-β generation in CD45+EPCs in the TME. WTAP, a major RNA m6A writer, stabilized FX and FVII mRNA and enhanced their nuclear export in CD45+EPCs from the TME. CD45+EPCs from the TME were positively associated with PVTT and poor prognosis. Splenectomy reduced the level of CD45+EPCs in the circulation and TME, as well as the incidence of microvascular invasion. The incidence of microvascular invasion increased following the transfer of HCC tissue CD45+EPCs to splenectomized HCC-bearing mice. Conclusions: The CD45+EPCs enriched in the HCC microenvironment are EDMCs, which are induced by HCC macrophages to migrate from the circulation to the TME. Subsequently, EDMCs promote PVTT by compromising the blood vessel endothelium, aggravating coagulation, and promoting HCC cell migration.
Collapse
Affiliation(s)
- Wei-Hang Zhu
- Department of Medical Oncology, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
- Guangdong Key laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
| | - Jie Chen
- Department of Medical Oncology, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
- Guangdong Key laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
| | - Run-Kai Huang
- Department of Medical Oncology, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
- Guangdong Key laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
| | - Yuan Zhang
- Department of Obstetrics, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
| | - Ze-Xuan Huang
- Guangdong Key laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
| | - Xiu-Qing Pang
- Guangdong Key laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
| | - Bo Hu
- Department of Laboratory Medicine, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou, 510630, China
| | - Yang Yang
- Department of Hepatic Surgery and Liver Transplantation Center & Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, 600 Tianhe Road, Guangzhou, 510630, China
| | - Xing Li
- Department of Medical Oncology, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
- Guangdong Key laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China
| |
Collapse
|
135
|
Yuan XN, Liu Q, Shao YC, Guan XQ, Yang ZL, Chu MF, Zhang JW, Tian YH, Wei L. Mettl3 synergistically regulates TGF-β/SMAD2/3 to promote proliferation and metastasis of gastric cancer. Am J Cancer Res 2023; 13:3185-3202. [PMID: 37560008 PMCID: PMC10408465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/06/2023] [Indexed: 08/11/2023] Open
Abstract
Transforming Growth factor-β (TGF-β)/Smad signaling is a complex regulatory network that both inhibits and promotes tumorigenesis. However, the mechanisms underlying the function of TGF-β/Smad signaling pathway remain to be fully elucidated. As a methyltransferase, METTL3 is closely related to tumor development, but the role of METTL3 in the proliferation and metastasis of TGF-β/Smad-activated gastric cancer (GC) is unclear. In this study, we identified TGF-β/Smad2/3 axis as an important carcinogenic pathway in GC, which significantly promoted the proliferation and metastasis of GC. Furthermore, we found that Smad3 mRNA could be modified by m6A, which was subsequently recognized and stabilized by IGF2BP2, thereby enhancing Smad3 protein expression and promoting the activation of TGF-β/Smad pathway. Importantly, we also found that METTL3 could combine with p-Smad3 to regulate the transcription of downstream target genes. Therefore, this study revealed a novel mechanism by which METTL3 synergistically regulates TGF-β/Smad2/3 signaling and provide a new potential therapeutic target for the treatment of GC.
Collapse
Affiliation(s)
- Xiao-Ning Yuan
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan UniversityWuhan 430071, Hubei, P. R. China
| | - Qin Liu
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan UniversityWuhan 430071, Hubei, P. R. China
| | - You-Cheng Shao
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan UniversityWuhan 430071, Hubei, P. R. China
| | - Xiao-Qing Guan
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan UniversityWuhan 430071, Hubei, P. R. China
| | - Ze-Lin Yang
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan UniversityWuhan 430071, Hubei, P. R. China
| | - Meng-Fei Chu
- Department of Human Anatomy, TaiKang Medical School (School of Basic Medical Sciences), Wuhan UniversityWuhan 430071, Hubei, P. R. China
| | - Jing-Wei Zhang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study CenterWuhan 430071, Hubei, P. R. China
| | - Yi-Hao Tian
- Department of Human Anatomy, TaiKang Medical School (School of Basic Medical Sciences), Wuhan UniversityWuhan 430071, Hubei, P. R. China
| | - Lei Wei
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan UniversityWuhan 430071, Hubei, P. R. China
| |
Collapse
|
136
|
Luo Z, Ma Q, Sun S, Li N, Wang H, Ying Z, Ke S. Exon-intron boundary inhibits m 6A deposition, enabling m 6A distribution hallmark, longer mRNA half-life and flexible protein coding. Nat Commun 2023; 14:4172. [PMID: 37443320 PMCID: PMC10345190 DOI: 10.1038/s41467-023-39897-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Regional bias of N6-methyladenosine (m6A) mRNA modification avoiding splice site region, calls for an open hypothesis whether exon-intron boundary could affect m6A deposition. By deep learning modeling, we find that exon-intron boundary represses a proportion (12% to 34%) of m6A deposition at adjacent exons (~100 nt to splice site). Experiments validate that m6A signal increases once the host gene does not undergo pre-mRNA splicing to produce the same mRNA. Inhibited m6A sites have higher m6A enhancers and lower m6A silencers locally and show high heterogeneity at different exons genome-widely, with only a small proportion (12% to 15%) of exons showing strong inhibition, enabling more stable mRNAs and flexible protein coding. m6A is majorly responsible for why mRNAs with more exons be more stable. Exon junction complex (EJC) only partially contributes to this exon-intron boundary m6A inhibition in some short internal exons, highlighting additional factors yet to be identified.
Collapse
Affiliation(s)
- Zhiyuan Luo
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Qilian Ma
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Shan Sun
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ningning Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Hongfeng Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zheng Ying
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Shengdong Ke
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
| |
Collapse
|
137
|
Meng Q, Schatten H, Zhou Q, Chen J. Crosstalk between m6A and coding/non-coding RNA in cancer and detection methods of m6A modification residues. Aging (Albany NY) 2023; 15:6577-6619. [PMID: 37437245 PMCID: PMC10373953 DOI: 10.18632/aging.204836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
N6-methyladenosine (m6A) is one of the most common and well-known internal RNA modifications that occur on mRNAs or ncRNAs. It affects various aspects of RNA metabolism, including splicing, stability, translocation, and translation. An abundance of evidence demonstrates that m6A plays a crucial role in various pathological and biological processes, especially in tumorigenesis and tumor progression. In this article, we introduce the potential functions of m6A regulators, including "writers" that install m6A marks, "erasers" that demethylate m6A, and "readers" that determine the fate of m6A-modified targets. We have conducted a review on the molecular functions of m6A, focusing on both coding and noncoding RNAs. Additionally, we have compiled an overview of the effects noncoding RNAs have on m6A regulators and explored the dual roles of m6A in the development and advancement of cancer. Our review also includes a detailed summary of the most advanced databases for m6A, state-of-the-art experimental and sequencing detection methods, and machine learning-based computational predictors for identifying m6A sites.
Collapse
Affiliation(s)
- Qingren Meng
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, The Second Hospital Affiliated with the Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Qian Zhou
- International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong Province, China
| | - Jun Chen
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, The Second Hospital Affiliated with the Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| |
Collapse
|
138
|
Li Y, Yi Y, Lv J, Gao X, Yu Y, Babu S, Bruno I, Zhao D, Xia B, Peng W, Zhu J, Chen H, Zhang L, Cao Q, Chen K. Low RNA stability signifies increased post-transcriptional regulation of cell identity genes. Nucleic Acids Res 2023; 51:6020-6038. [PMID: 37125636 PMCID: PMC10325912 DOI: 10.1093/nar/gkad300] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023] Open
Abstract
Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g. by super-enhancers and broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, probably due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-sequencing showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run-and-brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.
Collapse
Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yi
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jie Lv
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yu
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sahana Suresh Babu
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Ivone Bruno
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Bo Xia
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Jun Zhu
- Systems Biology Center, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Hong Chen
- Vascular Biology Program, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
- Broad Institute of MIT and Harvard, Boston, MA 02115, USA
- Dana-Farber/Harvard Cancer Center, Boston, MA 02115, USA
| |
Collapse
|
139
|
Zhang ZW, Zhao XS, Guo H, Huang XJ. The role of m 6A demethylase FTO in chemotherapy resistance mediating acute myeloid leukemia relapse. Cell Death Discov 2023; 9:225. [PMID: 37402730 DOI: 10.1038/s41420-023-01505-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/05/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common hematopoietic malignancies, and chemotherapy resistance is one of the main causes of relapse. Because of lower survival rate for patients with relapse, it is pivotal to identify etiological factors responsible for chemo-resistance. In this work, direct MeRIP-seq analysis of sequential samples at stage of complete remission (CR) and relapse identifies that dysregulated N6-methyladenosine (m6A) methylation is involved in this progression, and hypomethylated RNAs are related to cell differentiation. m6A demethylase FTO is overexpressed in relapse samples, which enhances the drug resistance of AML cells in vivo and in vitro. In addition, FTO knockdown cells exhibit stronger capacity of differentiation towards granules and myeloid lineages after cytosine arabinoside (Ara-C) treatment. Mechanistically, FOXO3 is identified as a downstream target of FTO, the hypomethylation of FOXO3 mRNA affects its RNA degradation and further reduces its own expression, which ultimately result in attenuated cell differentiation. Collectively, these results demonstrate that FTO-m6A-FOXO3 is the main regulatory axis to affect the chemotherapy resistance of AML cells and FTO is a potential therapeutic target of chemotherapy resistance in AML.
Collapse
Affiliation(s)
- Zhi-Wei Zhang
- Peking University People's Hospital & Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University, 100044, Beijing, China
| | - Xiao-Su Zhao
- Peking University People's Hospital & Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University, 100044, Beijing, China
| | - Huidong Guo
- Peking University People's Hospital & Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University, 100044, Beijing, China
| | - Xiao-Jun Huang
- Peking University People's Hospital & Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University, 100044, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, 100044, Beijing, China.
| |
Collapse
|
140
|
Pomaville MM, He C. Advances in targeting RNA modifications for anticancer therapy. Trends Cancer 2023; 9:528-542. [PMID: 37147166 PMCID: PMC10330282 DOI: 10.1016/j.trecan.2023.04.003] [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: 02/28/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
Numerous strategies are employed by cancer cells to control gene expression and facilitate tumorigenesis. In the study of epitranscriptomics, a diverse set of modifications to RNA represent a new player of gene regulation in disease and in development. N6-methyladenosine (m6A) is the most common modification on mammalian messenger RNA and tends to be aberrantly placed in cancer. Recognized by a series of reader proteins that dictate the fate of the RNA, m6A-modified RNA could promote tumorigenesis by driving protumor gene expression signatures and altering the immunologic response to tumors. Preclinical evidence suggests m6A writer, reader, and eraser proteins are attractive therapeutic targets. First-in-human studies are currently testing small molecule inhibition against the methyltransferase-like 3 (METTL3)/methyltransferase-like 14 (METTL14) methyltransferase complex. Additional modifications to RNA are adopted by cancers to drive tumor development and are under investigation.
Collapse
Affiliation(s)
- Monica M Pomaville
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA; Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| | - Chuan He
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA; Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| |
Collapse
|
141
|
Miyake K, Costa Cruz PH, Nagatomo I, Kato Y, Motooka D, Satoh S, Adachi Y, Takeda Y, Kawahara Y, Kumanogoh A. A cancer-associated METTL14 mutation induces aberrant m6A modification, affecting tumor growth. Cell Rep 2023; 42:112688. [PMID: 37355987 DOI: 10.1016/j.celrep.2023.112688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/25/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023] Open
Abstract
The methyltransferase-like 3 (METTL3)-/METTL14-containing complex predominantly catalyzes N6-methyladenosine (m6A) modification, which affects mRNA stability. Although the METTL14 R298P mutation is found in multiple cancer types, its biological effects are not completely understood. Here, we show that the heterozygous R298P mutation promotes cancer cell proliferation, whereas the homozygous mutation reduces proliferation. Methylated RNA immunoprecipitation sequencing analysis indicates that the R298P mutation reduces m6A modification at canonical motifs. Furthermore, this mutation induces m6A modification at aberrant motifs, which is evident only in cell lines harboring the homozygous mutation. The aberrant recognition of m6A modification sites alters the methylation efficiency at surrounding canonical motifs. One example is c-MET mRNA, which is highly methylated at canonical motifs close to the aberrantly methylated sites. Consequently, c-MET mRNA is severely destabilized, reducing c-Myc expression and suppressing cell proliferation. These data suggest that the METTL14 R298P mutation affects target recognition for m6A modification, perturbing gene expression patterns and cell growth.
Collapse
Affiliation(s)
- Kotaro Miyake
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shingo Satoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuichi Adachi
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Department of Immunopathology, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
142
|
Rivera M, Zhang H, Pham J, Isquith J, Zhou QJ, Sasik R, Mark A, Ma W, Holm F, Fisch KM, Kuo DJ, Jamieson C, Jiang Q. Malignant A-to-I RNA editing by ADAR1 drives T-cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensing. RESEARCH SQUARE 2023:rs.3.rs-2444524. [PMID: 37398458 PMCID: PMC10312963 DOI: 10.21203/rs.3.rs-2444524/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Leukemia initiating cells (LICs) are regarded as the origin of leukemia relapse and therapeutic resistance. Identifying direct stemness determinants that fuel LIC self-renewal is critical for developing targeted approaches to eliminate LICs and prevent relapse. Here, we show that the RNA editing enzyme ADAR1 is a crucial stemness factor that promotes LIC self-renewal by attenuating aberrant double-stranded RNA (dsRNA) sensing. Elevated adenosine-to-inosine (A-to-I) editing is a common attribute of relapsed T-ALL regardless of molecular subtypes. Consequently, knockdown of ADAR1 severely inhibits LIC self-renewal capacity and prolongs survival in T-ALL PDX models. Mechanistically, ADAR1 directs hyper-editing of immunogenic dsRNA and retains unedited nuclear dsRNA to avoid detection by the innate immune sensor MDA5. Moreover, we uncovered that the cell intrinsic level of MDA5 dictates the dependency on ADAR1-MDA5 axis in T-ALL. Collectively, our results show that ADAR1 functions as a self-renewal factor that limits the sensing of endogenous dsRNA. Thus, targeting ADAR1 presents a safe and effective therapeutic strategy for eliminating T-ALL LICs.
Collapse
Affiliation(s)
- Maria Rivera
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Haoran Zhang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Jessica Pham
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jane Isquith
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qingchen Jenny Zhou
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, 92093-0681
| | - Adam Mark
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, 92093-0681
| | - Wenxue Ma
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frida Holm
- Department of Women’s and Children’s Health, Division of Pediatric Oncology and Surgery, Karolinska Institutet, Sweden
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, 92093-0681
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, La Jolla, CA
| | - Dennis John Kuo
- Moores Cancer Center, La Jolla, CA 92037, USA
- Division of Pediatric Hematology-Oncology, Rady Children’s Hospital San Diego, University of California, San Diego, CA
| | - Catriona Jamieson
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| |
Collapse
|
143
|
Piperi C, Markouli M, Gargalionis AN, Papavassiliou KA, Papavassiliou AG. Deciphering glioma epitranscriptome: focus on RNA modifications. Oncogene 2023:10.1038/s41388-023-02746-y. [PMID: 37322070 DOI: 10.1038/s41388-023-02746-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Abstract
Gliomas are highly malignant tumors accounting for the majority of brain neoplasms. They are characterized by nuclear atypia, high mitotic rate and cellular polymorphism that often contributes to aggressiveness and resistance to standard therapy. They often associate with challenging treatment approaches and poor outcomes. New treatment strategies or regimens to improve the efficacy of glioma treatment require a deeper understanding of glioma occurrence and development as well as elucidation of their molecular biological characteristics. Recent studies have revealed RNA modifications as a key regulatory mechanism involved in tumorigenesis, tumor progression, immune regulation, and response to therapy. The present review discusses research advances on several RNA modifications involved in glioma progression and tumor microenvironment (TME) immunoregulation as well as in the development of adaptive drug resistance, summarizing current progress on major RNA modification targeting strategies.
Collapse
Affiliation(s)
- Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Antonios N Gargalionis
- Department of Biopathology, 'Eginition' Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Kostas A Papavassiliou
- First University Department of Respiratory Medicine, 'Sotiria' Hospital, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| |
Collapse
|
144
|
Yang X, Han F, Hu X, Li G, Wu H, Can C, Wei Y, Liu J, Wang R, Jia W, Ji C, Ma D. EIF4A3-induced Circ_0001187 facilitates AML suppression through promoting ubiquitin-proteasomal degradation of METTL3 and decreasing m6A modification level mediated by miR-499a-5p/RNF113A pathway. Biomark Res 2023; 11:59. [PMID: 37280654 DOI: 10.1186/s40364-023-00495-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Aberrant expression of circRNAs has been proven to play a crucial role in the progression of acute myeloid leukemia (AML); however, its regulatory mechanism remains unclear. Herein, we identified a novel circRNA, Circ_0001187, which is downregulated in AML patients, and its low level contributes to a poor prognosis. We further validated their expression in large-scale samples and found that only the expression of Circ_0001187 was significantly decreased in newly diagnosed (ND) AML patients and increased in patients with hematological complete remission (HCR) compared with controls. Knockdown of Circ_0001187 significantly promoted proliferation and inhibited apoptosis of AML cells in vitro and in vivo, whereas overexpression of Circ _0001187 exerted the opposite effects. Interestingly, we found that Circ_0001187 decreases mRNA m6A modification in AML cells by enhancing METTL3 protein degradation. Mechanistically, Circ_0001187 sponges miR-499a-5p to enhance the expression of E3 ubiquitin ligase RNF113A, which mediates METTL3 ubiquitin/proteasome-dependent degradation via K48-linked polyubiquitin chains. Moreover, we found that the low expression of Circ _0001187 is regulated by promoter DNA methylation and histone acetylation. Collectively, our findings highlight the potential clinical implications of Circ _0001187 as a key tumor suppressor in AML via the miR-499a-5p/RNF113A/METTL3 pathway.
Collapse
Affiliation(s)
- Xinyu Yang
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Fengjiao Han
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Xiang Hu
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Guosheng Li
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Hanyang Wu
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Can Can
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Yihong Wei
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Jinting Liu
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Ruiqing Wang
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Wenbo Jia
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China.
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.
| |
Collapse
|
145
|
Sun S, Han Y, Lei Y, Yu Y, Dong Y, Chen J. Hematopoietic Stem Cell: Regulation and Nutritional Intervention. Nutrients 2023; 15:nu15112605. [PMID: 37299568 DOI: 10.3390/nu15112605] [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: 05/08/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are crucial for the life maintenance of bio-organisms. However, the mechanism of HSC regulation is intricate. Studies have shown that there are various factors, either intrinsically or extrinsically, that shape the profile of HSCs. This review systematically summarizes the intrinsic factors (i.e., RNA-binding protein, modulators in epigenetics and enhancer-promotor-mediated transcription) that are reported to play a pivotal role in the function of HSCs, therapies for bone marrow transplantation, and the relationship between HSCs and autoimmune diseases. It also demonstrates the current studies on the effects of high-fat diets and nutrients (i.e., vitamins, amino acids, probiotics and prebiotics) on regulating HSCs, providing a deep insight into the future HSC research.
Collapse
Affiliation(s)
- Siyuan Sun
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100190, China
| | - Yingxue Han
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yumei Lei
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100190, China
| | - Yifei Yu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100190, China
| | - Yanbin Dong
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100045, China
| | - Juan Chen
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100190, China
| |
Collapse
|
146
|
Zhang L, Xu X, Su X. Modifications of noncoding RNAs in cancer and their therapeutic implications. Cell Signal 2023:110726. [PMID: 37230201 DOI: 10.1016/j.cellsig.2023.110726] [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: 03/10/2023] [Revised: 05/06/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
In the last 50 years, over 150 various chemical modifications on RNA molecules, including mRNAs, rRNAs, tRNAs, and other noncoding RNAs (ncRNAs), have been identified and characterized. These RNA modifications regulate RNA biogenesis and biological functions and are widely involved in various physiological processes and diseases, including cancer. In recent decades, broad interest has arisen in the epigenetic modification of ncRNAs due to the increased knowledge of the critical roles of ncRNAs in cancer. In this review, we summarize the various modifications of ncRNAs and highlight their roles in cancer initiation and progression. In particular, we discuss the potential of RNA modifications as novel biomarkers and therapeutic targets in cancer.
Collapse
Affiliation(s)
- Le Zhang
- Center for Reproductive Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China
| | - Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612-9497, USA
| | - Xiulan Su
- Clinical Medical Research Center, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China.
| |
Collapse
|
147
|
Bukhari SIA, Truesdell SS, Datta C, Choudhury P, Wu KQ, Shrestha J, Maharjan R, Plotsker E, Elased R, Laisa S, Bhambhani V, Lin Y, Kreuzer J, Morris R, Koh SB, Ellisen LW, Haas W, Ly A, Vasudevan S. Regulation of RNA methylation by therapy treatment, promotes tumor survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.540602. [PMID: 37292633 PMCID: PMC10245743 DOI: 10.1101/2023.05.19.540602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Our data previously revealed that chemosurviving cancer cells translate specific genes. Here, we find that the m6A-RNA-methyltransferase, METTL3, increases transiently in chemotherapy-treated breast cancer and leukemic cells in vitro and in vivo. Consistently, m6A increases on RNA from chemo-treated cells, and is needed for chemosurvival. This is regulated by eIF2α phosphorylation and mTOR inhibition upon therapy treatment. METTL3 mRNA purification reveals that eIF3 promotes METTL3 translation that is reduced by mutating a 5'UTR m6A-motif or depleting METTL3. METTL3 increase is transient after therapy treatment, as metabolic enzymes that control methylation and thus m6A levels on METTL3 RNA, are altered over time after therapy. Increased METTL3 reduces proliferation and anti-viral immune response genes, and enhances invasion genes, which promote tumor survival. Consistently, overriding phospho-eIF2α prevents METTL3 elevation, and reduces chemosurvival and immune-cell migration. These data reveal that therapy-induced stress signals transiently upregulate METTL3 translation, to alter gene expression for tumor survival.
Collapse
Affiliation(s)
- Syed IA Bukhari
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Samuel S Truesdell
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Chandreyee Datta
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Pritha Choudhury
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Keith Q Wu
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Jitendra Shrestha
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Ruby Maharjan
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Ethan Plotsker
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Ramzi Elased
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Sadia Laisa
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Vijeta Bhambhani
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Yue Lin
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Johannes Kreuzer
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Siang-Boon Koh
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Leif W. Ellisen
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| | - Shobha Vasudevan
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Brigham and Harvard Medical School, Boston, MA 02114
| |
Collapse
|
148
|
Zhao NN, Zhang X, Zou X, Zhang Y, Zhang CY. Controllable assembly of dendritic DNA nanostructures for ultrasensitive detection of METTL3-METTL14 m 6A methyltransferase activity in cancer cells and human breast tissues. Biosens Bioelectron 2023; 228:115217. [PMID: 36924687 DOI: 10.1016/j.bios.2023.115217] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/12/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
N6-Methyladenosine (m6A) is a reversible chemical modification in eukaryotic messenger RNAs and long noncoding RNAs. The aberrant expression of RNA methyltransferase METTL3-METTL14 complex may change the m6A methylation level and cause multiple diseases including cancers. The conventional METTL3-METTL14 assays commonly suffer from time-consuming procedures and poor sensitivity. Herein, we develop a controllable amplification machinery based on MazF-activated terminal deoxynucleotidyl transferase (TdT)-assisted dendritic DNA structure assembly for ultrasensitive detection of METTL3-METTL14 complex activity in cancer cells and breast tissues. The presence of METTL3-METTL14 complex catalyzes the formation of m6A in detection probe, effectively preventing the cleavage of methylated detection probes by MazF. The methylated detection probes with 3'-OH termini can function as the primers for template-free polymerization catalyzed by TdT on magnetic beads (MBs), producing long chains of poly-thymidine (poly-T) sequences. Then poly-T sequences hybridize with signal probes that contain poly-adenine (poly-A) sequence, inducing TdT-mediated polymerization and the subsequent hybridization with more poly-A signal probes for generating dendritic DNA nanostructures assembled on MBs. After magnetic separation and elevated temperature treatment, the signal probes are disassembled from MBs to generate a high fluorescence signal. This method possesses excellent specificity and high sensitivity with a limit of detection (LOD) of 2.61 × 10-15 M, and it can accurately quantify cellular METTL3-METTL14 complex at single-cell level. Furthermore, it can screen inhibitors, evaluate kinetic parameters, and discriminate breast cancer tissues from normal tissues.
Collapse
Affiliation(s)
- Ning-Ning Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Xinyi Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, 528458, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Yan Zhang
- College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
| |
Collapse
|
149
|
Vujovic A, de Rooij L, Chahi AK, Chen HT, Yee BA, Loganathan SK, Liu L, Chan DC, Tajik A, Tsao E, Moreira S, Joshi P, Xu J, Wong N, Balde Z, Jahangiri S, Zandi S, Aigner S, Dick JE, Minden MD, Schramek D, Yeo GW, Hope KJ. In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target. Blood Cancer Discov 2023; 4:180-207. [PMID: 36763002 PMCID: PMC10150294 DOI: 10.1158/2643-3230.bcd-22-0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/30/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Acute myeloid leukemia (AML) is fueled by leukemic stem cells (LSC) whose determinants are challenging to discern from hematopoietic stem cells (HSC) or uncover by approaches focused on general cell properties. We have identified a set of RNA-binding proteins (RBP) selectively enriched in human AML LSCs. Using an in vivo two-step CRISPR-Cas9 screen to assay stem cell functionality, we found 32 RBPs essential for LSCs in MLL-AF9;NrasG12D AML. Loss-of-function approaches targeting key hit RBP ELAVL1 compromised LSC-driven in vivo leukemic reconstitution, and selectively depleted primitive malignant versus healthy cells. Integrative multiomics revealed differentiation, splicing, and mitochondrial metabolism as key features defining the leukemic ELAVL1-mRNA interactome with mitochondrial import protein, TOMM34, being a direct ELAVL1-stabilized target whose repression impairs AML propagation. Altogether, using a stem cell-adapted in vivo CRISPR screen, this work demonstrates pervasive reliance on RBPs as regulators of LSCs and highlights their potential as therapeutic targets in AML. SIGNIFICANCE LSC-targeted therapies remain a significant unmet need in AML. We developed a stem-cell-adapted in vivo CRISPR screen to identify key LSC drivers. We uncover widespread RNA-binding protein dependencies in LSCs, including ELAVL1, which we identify as a novel therapeutic vulnerability through its regulation of mitochondrial metabolism. This article is highlighted in the In This Issue feature, p. 171.
Collapse
Affiliation(s)
- Ana Vujovic
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Laura de Rooij
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ava Keyvani Chahi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - He Tian Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Sampath K. Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Lina Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Derek C.H. Chan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Amanda Tajik
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Emily Tsao
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Steven Moreira
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Pratik Joshi
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Joshua Xu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Nicholas Wong
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Zaldy Balde
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Soheil Jahangiri
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Sasan Zandi
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - John E. Dick
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Mark D. Minden
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Kristin J. Hope
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| |
Collapse
|
150
|
Wu Y, Jin M, Fernandez M, Hart KL, Liao A, Ge X, Fernandes SM, McDonald T, Chen Z, Röth D, Ghoda LY, Marcucci G, Kalkum M, Pillai RK, Danilov AV, Li JJ, Chen J, Brown JR, Rosen ST, Siddiqi T, Wang L. METTL3-Mediated m6A Modification Controls Splicing Factor Abundance and Contributes to Aggressive CLL. Blood Cancer Discov 2023; 4:228-245. [PMID: 37067905 PMCID: PMC10150290 DOI: 10.1158/2643-3230.bcd-22-0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 04/18/2023] Open
Abstract
RNA splicing dysregulation underlies the onset and progression of cancers. In chronic lymphocytic leukemia (CLL), spliceosome mutations leading to aberrant splicing occur in ∼20% of patients. However, the mechanism for splicing defects in spliceosome-unmutated CLL cases remains elusive. Through an integrative transcriptomic and proteomic analysis, we discover that proteins involved in RNA splicing are posttranscriptionally upregulated in CLL cells, resulting in splicing dysregulation. The abundance of splicing complexes is an independent risk factor for poor prognosis. Moreover, increased splicing factor expression is highly correlated with the abundance of METTL3, an RNA methyltransferase that deposits N6-methyladenosine (m6A) on mRNA. METTL3 is essential for cell growth in vitro and in vivo and controls splicing factor protein expression in a methyltransferase-dependent manner through m6A modification-mediated ribosome recycling and decoding. Our results uncover METTL3-mediated m6A modification as a novel regulatory axis in driving splicing dysregulation and contributing to aggressive CLL. SIGNIFICANCE METTL3 controls widespread splicing factor abundance via translational control of m6A-modified mRNA, contributes to RNA splicing dysregulation and disease progression in CLL, and serves as a potential therapeutic target in aggressive CLL. See related commentary by Janin and Esteller, p. 176. This article is highlighted in the In This Issue feature, p. 171.
Collapse
Affiliation(s)
- Yiming Wu
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Meiling Jin
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Mike Fernandez
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Kevyn L. Hart
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Aijun Liao
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Xinzhou Ge
- Department of Statistics, University of California, Los Angeles, California
- Department of Computational Medicine, University of California, Los Angeles, California
| | - Stacey M. Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tinisha McDonald
- The Hematopoietic Tissue Biorepository, City of Hope National Comprehensive Cancer Center, Duarte, California
- Department of Hematological Malignancies Translational Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Daniel Röth
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, California
| | - Lucy Y. Ghoda
- The Hematopoietic Tissue Biorepository, City of Hope National Comprehensive Cancer Center, Duarte, California
- Department of Hematological Malignancies Translational Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Guido Marcucci
- The Hematopoietic Tissue Biorepository, City of Hope National Comprehensive Cancer Center, Duarte, California
- Department of Hematological Malignancies Translational Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, California
| | - Raju K. Pillai
- Department of Pathology, City of Hope National Comprehensive Cancer Center, Duarte, California
| | - Alexey V. Danilov
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope Comprehensive Cancer Center, Duarte, California
- Toni Stephenson Lymphoma Center, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, California
- Department of Computational Medicine, University of California, Los Angeles, California
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Steven T. Rosen
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope Comprehensive Cancer Center, Duarte, California
- Toni Stephenson Lymphoma Center, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Tanya Siddiqi
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope Comprehensive Cancer Center, Duarte, California
- Toni Stephenson Lymphoma Center, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
- Toni Stephenson Lymphoma Center, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| |
Collapse
|