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Rana P, Ujjainiya R, Bharti V, Maiti S, Ekka MK. IGF2BP1-Mediated Regulation of CCN1 Expression by Specific Binding to G-Quadruplex Structure in Its 3'UTR. Biochemistry 2024; 63:2166-2182. [PMID: 39133064 DOI: 10.1021/acs.biochem.4c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The intricate regulation of gene expression is fundamental to the biological complexity of higher organisms, and is primarily governed by transcriptional and post-transcriptional mechanisms. The 3'-untranslated region (3'UTR) of mRNA is rich in cis-regulatory elements like G-quadruplexes (G4s), and plays a crucial role in post-transcriptional regulation. G4s have emerged as significant gene regulators, impacting mRNA stability, translation, and localization. In this study, we investigate the role of a robust parallel G4 structure situated within the 3'UTR of CCN1 mRNA in post-transcriptional regulation. This G4 structure is proximal to the stop codon of human CCN1, and evolutionarily conserved. We elucidated its interaction with the insulin-like growth factor 2 binding protein 1 (IGF2BP1), a noncanonical RNA N6-methyladenosine (m6A) modification reader, revealing a novel interplay between RNA modifications and G-quadruplex structures. Knockdown experiments and mutagenesis studies demonstrate that IGF2BP1 binds specifically to the G4 structure, modulating CCN1 mRNA stability. Additionally, we unveil the role of IGF2BP1's RNA recognition motifs in G4 recognition, highlighting this enthalpically driven interaction. Our findings offer fresh perspectives on the complex mechanisms of post-transcriptional gene regulation mediated by G4 RNA secondary structures.
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Affiliation(s)
- Priya Rana
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishal Bharti
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Souvik Maiti
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mary K Ekka
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Su Y, Hu Y, Qu B, Lei R, Guo G. METTL3 Promotes OSCC Progression by Down-Regulating WEE1 in a m6A-YTHDF2-Dependent Manner. Mol Biotechnol 2024:10.1007/s12033-024-01165-y. [PMID: 38744787 DOI: 10.1007/s12033-024-01165-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
Oral squamous cell carcinoma (OSCC) is a common and highly lethal epithelial cancer. This study aimed to confirm the role of METTL3 in promoting OSCC and investigate its specific underlying mechanisms. Expression of the METTL3, YTH domain-containing family 2 (YTHDF2), and WEE1 were examined in normal oral epithelial cells and OSCC cells. Cell functions were examined after overexpressing WEE1 in OSCC cells. MeRIP-qPCR analysis was used to detect WEE1 m6A levels in HOK, SCC25, and CAL27 cells. WEE1 and its m6A levels were evaluated in OSCC cells by knocking down METTL3/YTHDF2, assessing the interaction between METTL3/YTHDF2 and WEE1. The impact of METTL3 and YTHDF2 downregulation on WEE1 mRNA stability was also investigated. The tumor weight and volume in a nude mouse model of OSCC after overexpression of WEE1 and YTHDF2 were measured. Expression of Ki-67 and WEE1 in OSCC tissue was detected using immunohistochemistry. Compared to normal oral epithelial cells, METTL3 and YTHDF2 were upregulated in OSCC cells, while WEE1 was downregulated, and there was a negative correlation between WEE1 and METTL3/YTHDF2 expression. WEE1 overexpression inhibited proliferation, invasion, and migration while promoting apoptosis in OSCC cells. METTL3 and YTHDF2 bound to WEE1 mRNA. METTL3/YTHDF2 knockdown increased WEE1 levels and WEE1 mRNA stability. METTL3 inhibition reduced WEE1 m6A levels. Inhibition of METTL3 weakened the interaction between YTHDF2 and WEE1 mRNA. In vivo, overexpression of WEE1 suppressed OSCC development, which was reversed by overexpression of YTHDF2. METTL3 facilitates the progression of OSCC through m6A-YTHDF2-dependent downregulation of WEE1.
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Affiliation(s)
- Yongxu Su
- Department of Oral and Maxilofacial Sugery, Changsha Stomatological Hospital, Changsha, 410004, Hunan, China.
| | - Yanjia Hu
- Department of Oral and Maxilofacial Sugery, Xiangya Stomatological Hospital Central South University, Changsha, 410000, Hunan, China
| | - Binbin Qu
- Department of Oral and Maxilofacial Sugery, Changsha Stomatological Hospital, Changsha, 410004, Hunan, China
| | - Rongchang Lei
- Department of Oral and Maxilofacial Sugery, Changsha Stomatological Hospital, Changsha, 410004, Hunan, China
| | - Ge Guo
- Department of Oral and Maxilofacial Sugery, Changsha Stomatological Hospital, Changsha, 410004, Hunan, China
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Gu J, Cao H, Chen X, Zhang XD, Thorne RF, Liu X. RNA m6A modifications regulate crosstalk between tumor metabolism and immunity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1829. [PMID: 38114887 DOI: 10.1002/wrna.1829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
In recent years, m6A modifications in RNA transcripts have arisen as a hot topic in cancer research. Indeed, a number of independent studies have elaborated that the m6A modification impacts the behavior of tumor cells and tumor-infiltrating immune cells, altering tumor cell metabolism along with the differentiation and functional activity of immune cells. This review elaborates on the links between RNA m6A modifications, tumor cell metabolism, and immune cell behavior, discussing this topic from the viewpoint of reciprocal regulation through "RNA m6A-tumor cell metabolism-immune cell behavior" and "RNA m6A-immune cell behavior-tumor cell metabolism" axes. In addition, we discuss the various factors affecting RNA m6A modifications in the tumor microenvironment, particularly the effects of hypoxia associated with cancer cell metabolism along with immune cell-secreted cytokines. Our analysis proposes the conclusion that RNA m6A modifications support widespread interactions between tumor metabolism and tumor immunity. With the current viewpoint that long-term cancer control must tackle cancer cell malignant behavior while strengthening anti-tumor immunity, the recognition of RNA m6A modifications as a key factor provides a new direction for the targeted therapy of tumors. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Jinghua Gu
- School of Life Sciences, Anhui Medical University, Hefei, China
- The First Clinical Medical College of Anhui Medical University, Hefei, China
| | - Huake Cao
- School of Life Sciences, Anhui Medical University, Hefei, China
- The First Clinical Medical College of Anhui Medical University, Hefei, China
| | - Xiaoli Chen
- Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial Key Laboratory of Long Non-coding RNA and Cancer Metabolism, Translational Research Institute of Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Henan, China
| | - Xu Dong Zhang
- Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial Key Laboratory of Long Non-coding RNA and Cancer Metabolism, Translational Research Institute of Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Henan, China
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Rick F Thorne
- Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial Key Laboratory of Long Non-coding RNA and Cancer Metabolism, Translational Research Institute of Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Henan, China
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Xiaoying Liu
- School of Life Sciences, Anhui Medical University, Hefei, China
- Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial Key Laboratory of Long Non-coding RNA and Cancer Metabolism, Translational Research Institute of Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Henan, China
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Liang J, Cai H, Hou C, Song F, Jiang Y, Wang Z, Qiu D, Zhu Y, Wang F, Yu D, Hou J. METTL14 inhibits malignant progression of oral squamous cell carcinoma by targeting the autophagy-related gene RB1CC1 in an m6A-IGF2BP2-dependent manner. Clin Sci (Lond) 2023; 137:1373-1389. [PMID: 37615536 PMCID: PMC10500204 DOI: 10.1042/cs20230219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 08/25/2023]
Abstract
N6-methyladenosine (m6A) plays crucial roles in tumorigenesis and autophagy. However, the underlying mechanisms mediated by m6A and autophagy in the malignant progression of oral squamous cell carcinoma (OSCC) remain unclear. In the present study, we revealed that down-regulated expression of METTL14 was correlated with advanced clinicopathological characteristics and poor prognosis in OSCC. METTL14 knockdown significantly inhibited autophagy and facilitated malignant progression in vitro, and promoted tumor growth and metastasis in vivo. A cell model of rapamycin-induced autophagy was established to identify RB1CC1 as a potential target gene involved in m6A-regulated autophagy in OSCC, through RNA sequencing and methylated RNA immunoprecipitation sequencing (meRIP-seq) analysis. Mechanistically, we confirmed that METTL14 posttranscriptionally enhanced RB1CC1 expression in an m6A-IGF2BP2-dependent manner, thereby affecting autophagy and progression in OSCC, through methylated RNA immunoprecipitation qRT-PCR (meRIP-qPCR), RNA stability assays, mutagenesis assays and dual-luciferase reporter. Collectively, our findings demonstrated that METTL14 serves as an OSCC suppressor by regulating the autophagy-related gene RB1CC1 through m6A modification, which may provide a new insight for the diagnosis and therapy of OSCC.
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Affiliation(s)
- Jianfeng Liang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Hongshi Cai
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Chen Hou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Fan Song
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yaoqi Jiang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Ziyi Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Danqi Qiu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yue Zhu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Fang Wang
- Department of Oral Surgery, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Dongsheng Yu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Jinsong Hou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
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Ye L, Yao X, Xu B, Chen W, Lou H, Tong X, Fang S, Zou R, Hu Y, Wang Z, Xiang D, Lin Q, Feng S, Xue X, Guo G. RNA epigenetic modifications in ovarian cancer: The changes, chances, and challenges. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1784. [PMID: 36811232 DOI: 10.1002/wrna.1784] [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: 11/01/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/23/2023]
Abstract
Ovarian cancer (OC) is the most common female cancer worldwide. Patients with OC have high mortality because of its complex and poorly understood pathogenesis. RNA epigenetic modifications, such as m6 A, m1 A, and m5 C, are closely associated with the occurrence and development of OC. RNA modifications can affect the stability of mRNA transcripts, nuclear export of RNAs, translation efficiency, and decoding accuracy. However, there are few overviews that summarize the link between m6 A RNA modification and OC. Here, we discuss the molecular and cellular functions of different RNA modifications and how their regulation contributes to the pathogenesis of OC. By improving our understanding of the role of RNA modifications in the etiology of OC, we provide new perspectives for their use in OC diagnosis and treatment. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Lele Ye
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xuyang Yao
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Binbing Xu
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Wenwen Chen
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Han Lou
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ruanmin Zou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yingying Hu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhibin Wang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dan Xiang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoai Lin
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shiyu Feng
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
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Yang F, Ma Q, Huang B, Wang X, Pan X, Yu T, Ran L, Jiang S, Li H, Chen Y, Liu Y, Liang C, Ren J, Zhang Y, Wang S, Li W, Xiao B. CircNFATC3 promotes the proliferation of gastric cancer through binding to IGF2BP3 and restricting its ubiquitination to enhance CCND1 mRNA stability. J Transl Med 2023; 21:402. [PMID: 37340423 DOI: 10.1186/s12967-023-04235-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/28/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Insulin like growth factor II mRNA binding protein 3 (IGF2BP3) is an RNA binding protein with multiple roles in regulation of gene expression at the post-transcriptional level and is implicated in tumorigenesis and progression of numerous cancers including gastric cancer (GC). Circular RNAs (circRNAs) are a diverse endogenous noncoding RNA population that have important regulatory roles in cancer. However, circRNAs that regulate the expression of IGF2BP3 in GC is largely unknown. METHODS CircRNAs that bound to IGF2BP3 were screened in GC cells using RNA immunoprecipitation and sequencing (RIP-seq). The identification and localization of circular nuclear factor of activated T cells 3 (circNFATC3) were identified using Sanger sequencing, RNase R assays, qRT-PCR, nuclear-cytoplasmic fractionation and RNA-FISH assays. CircNFATC3 expression in human GC tissues and adjacent normal tissues were measured by qRT-PCR and ISH. The biological role of circNFATC3 in GC was confirmed by in vivo and in vitro experiments. Furthermore, RIP, RNA-FISH/IF, IP and rescue experiments were performed to uncover interactions between circNFATC3, IGF2BP3 and cyclin D1 (CCND1). RESULTS We identified a GC-associated circRNA, circNFATC3, that interacted with IGF2BP3. CircNFATC3 was significantly overexpressed in GC tissues and was positively associated with tumor volume. Functionally, the proliferation of GC cells decreased significantly after circNFATC3 knockdown in vivo and in vitro. Mechanistically, circNFATC3 bound to IGF2BP3 in the cytoplasm, which enhanced the stability of IGF2BP3 by preventing ubiquitin E3 ligase TRIM25-mediated ubiquitination, thereby enhancing the regulatory axis of IGF2BP3-CCND1 and promoting CCND1 mRNA stability. CONCLUSIONS Our findings demonstrate that circNFATC3 promotes GC proliferation by stabilizing IGF2BP3 protein to enhance CCND1 mRNA stability. Therefore, circNFATC3 is a potential novel target for the treatment of GC.
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Affiliation(s)
- Feifei Yang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Qiang Ma
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Bo Huang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Xiaolin Wang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Xiaojuan Pan
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Ting Yu
- Department of Clinical Laboratory, The 89th Hospital of The People's Liberation Army, Weifang, 261000, People's Republic of China
| | - Lingyu Ran
- Department of Kidney, Southwest Hospital, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Shan Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518055, People's Republic of China
| | - Haiping Li
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Ye Chen
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Yuying Liu
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Ce Liang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Junwu Ren
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Yuying Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Shimin Wang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Wei Li
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, 400030, People's Republic of China.
| | - Bin Xiao
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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Xiang M, Liu L, Wu T, Wei B, Liu H. RNA-binding proteins in degenerative joint diseases: A systematic review. Ageing Res Rev 2023; 86:101870. [PMID: 36746279 DOI: 10.1016/j.arr.2023.101870] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/12/2023] [Accepted: 01/27/2023] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs), which are conserved proteins comprising multiple intermediate sequences, can interact with proteins, messenger RNA (mRNA) of coding genes, and non-coding RNAs to perform different biological functions, such as the regulation of mRNA stability, selective polyadenylation, and the management of non-coding microRNA (miRNA) synthesis to affect downstream targets. This article will highlight the functions of RBPs, in degenerative joint diseases (intervertebral disc degeneration [IVDD] and osteoarthritis [OA]). It will reviews the latest advancements on the regulatory mechanism of RBPs in degenerative joint diseases, in order to understand the pathophysiology, early diagnosis and treatment of OA and IVDD from a new perspective.
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Affiliation(s)
- Min Xiang
- Department of Orthopedics, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Ling Liu
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Tingrui Wu
- Department of Orthopedics, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Bo Wei
- Department of Orthopedics, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China.
| | - Huan Liu
- Department of Orthopedics, Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China.
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Issahaku AR, Mncube SM, Agoni C, Kwofie SK, Alahmdi MI, Abo-Dya NE, Sidhom PA, Tawfeek AM, Ibrahim MAA, Mukelabai N, Soremekun O, Soliman MES. Multi-dimensional structural footprint identification for the design of potential scaffolds targeting METTL3 in cancer treatment from natural compounds. J Mol Model 2023; 29:122. [PMID: 36995499 DOI: 10.1007/s00894-023-05516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
CONTEXT [Formula: see text]-adenosine-methyltransferase (METTL3) is the catalytic domain of the 'writer' proteins which is involved in the post modifications of [Formula: see text]-methyladinosine ([Formula: see text]). Though its activities are essential in many biological processes, it has been implicated in several types of cancer. Thus, drug developers and researchers are relentlessly in search of small molecule inhibitors that can ameliorate the oncogenic activities of METTL3. Currently, STM2457 is a potent, highly selective inhibitor of METTL3 but is yet to be approved. METHODS In this study, we employed structure-based virtual screening through consensus docking by using AutoDock Vina in PyRx interface and Glide virtual screening workflow of Schrodinger Glide. Thermodynamics via MM-PBSA calculations was further used to rank the compounds based on their total free binding energies. All atom molecular dynamics simulations were performed using AMBER 18 package. FF14SB force fields and Antechamber were used to parameterize the protein and compounds respectively. Post analysis of generated trajectories was analyzed with CPPTRAJ and PTRAJ modules incorporated in the AMBER package while Discovery studio and UCSF Chimera were used for visualization, and origin data tool used to plot all graphs. RESULTS Three compounds with total free binding energies higher than STM2457 were selected for extended molecular dynamics simulations. The compounds, SANCDB0370, SANCDB0867, and SANCDB1033, exhibited stability and deeper penetration into the hydrophobic core of the protein. They engaged in relatively stronger intermolecular interactions involving hydrogen bonds with resultant increase in stability, reduced flexibility, and decrease in the surface area of the protein available for solvent interactions suggesting an induced folding of the catalytic domain. Furthermore, in silico pharmacokinetics and physicochemical analysis of the compounds revealed good properties suggesting these compounds could serve as promising MEETL3 entry inhibitors upon modifications and optimizations as presented by natural compounds. Further biochemical testing and experimentations would aid in the discovery of effective inhibitors against the berserk activities of METTL3.
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Liu WW, Zhang ZY, Wang F, Wang H. Emerging roles of m6A RNA modification in cancer therapeutic resistance. Exp Hematol Oncol 2023; 12:21. [PMID: 36810281 PMCID: PMC9942381 DOI: 10.1186/s40164-023-00386-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/11/2023] [Indexed: 02/23/2023] Open
Abstract
Marvelous advancements have been made in cancer therapies to improve clinical outcomes over the years. However, therapeutic resistance has always been a major difficulty in cancer therapy, with extremely complicated mechanisms remain elusive. N6-methyladenosine (m6A) RNA modification, a hotspot in epigenetics, has gained growing attention as a potential determinant of therapeutic resistance. As the most prevalent RNA modification, m6A is involved in every links of RNA metabolism, including RNA splicing, nuclear export, translation and stability. Three kinds of regulators, "writer" (methyltransferase), "eraser" (demethylase) and "reader" (m6A binding proteins), together orchestrate the dynamic and reversible process of m6A modification. Herein, we primarily reviewed the regulatory mechanisms of m6A in therapeutic resistance, including chemotherapy, targeted therapy, radiotherapy and immunotherapy. Then we discussed the clinical potential of m6A modification to overcome resistance and optimize cancer therapy. Additionally, we proposed existing problems in current research and prospects for future research.
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Affiliation(s)
- Wei-Wei Liu
- grid.59053.3a0000000121679639Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China ,grid.27255.370000 0004 1761 1174School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Zhong-Yuan Zhang
- grid.59053.3a0000000121679639Department of Radiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fei Wang
- Neurosurgical Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Hao Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. .,Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China.
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10
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Gao Y, Cao H, Huang D, Zheng L, Nie Z, Zhang S. RNA-Binding Proteins in Bladder Cancer. Cancers (Basel) 2023; 15:cancers15041150. [PMID: 36831493 PMCID: PMC9953953 DOI: 10.3390/cancers15041150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
RNA-binding proteins (RBPs) are key regulators of transcription and translation, with highly dynamic spatio-temporal regulation. They are usually involved in the regulation of RNA splicing, polyadenylation, and mRNA stability and mediate processes such as mRNA localization and translation, thereby affecting the RNA life cycle and causing the production of abnormal protein phenotypes that lead to tumorigenesis and development. Accumulating evidence supports that RBPs play critical roles in vital life processes, such as bladder cancer initiation, progression, metastasis, and drug resistance. Uncovering the regulatory mechanisms of RBPs in bladder cancer is aimed at addressing the occurrence and progression of bladder cancer and finding new therapies for cancer treatment. This article reviews the effects and mechanisms of several RBPs on bladder cancer and summarizes the different types of RBPs involved in the progression of bladder cancer and the potential molecular mechanisms by which they are regulated, with a view to providing information for basic and clinical researchers.
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11
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Roles of RNA-binding proteins in neurological disorders, COVID-19, and cancer. Hum Cell 2023; 36:493-514. [PMID: 36528839 PMCID: PMC9760055 DOI: 10.1007/s13577-022-00843-w] [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: 08/30/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
RNA-binding proteins (RBPs) have emerged as important players in multiple biological processes including transcription regulation, splicing, R-loop homeostasis, DNA rearrangement, miRNA function, biogenesis, and ribosome biogenesis. A large number of RBPs had already been identified by different approaches in various organisms and exhibited regulatory functions on RNAs' fate. RBPs can either directly or indirectly interact with their target RNAs or mRNAs to assume a key biological function whose outcome may trigger disease or normal biological events. They also exert distinct functions related to their canonical and non-canonical forms. This review summarizes the current understanding of a wide range of RBPs' functions and highlights their emerging roles in the regulation of diverse pathways, different physiological processes, and their molecular links with diseases. Various types of diseases, encompassing colorectal carcinoma, non-small cell lung carcinoma, amyotrophic lateral sclerosis, and Severe acute respiratory syndrome coronavirus 2, aberrantly express RBPs. We also highlight some recent advances in the field that could prompt the development of RBPs-based therapeutic interventions.
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12
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Yin XH, Wang XY, Liu SC, Yan L, He BR, Hao DJ, Yang M, Liu ZK. lncRNA HHIP-AS1/HHIP modulates osteogenic differentiation of BM-MSCs by regulating Hedgehog signaling pathway. Aging (Albany NY) 2022; 14:8839-8855. [DOI: 10.18632/aging.204381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Xin-Hua Yin
- Department of Spine Surgery, Hong Hui Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, China
| | - Xiao-Yuan Wang
- Physical Examination Center, Xi'an International Medical Center Hospital, Xi’an, China
| | - Shi-Chang Liu
- Department of Spine Surgery, Hong Hui Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, China
| | - Liang Yan
- Department of Spine Surgery, Hong Hui Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, China
| | - Bao-Rong He
- Department of Spine Surgery, Hong Hui Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, China
| | - Ding-Jun Hao
- Department of Spine Surgery, Hong Hui Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, China
| | - Ming Yang
- Department of Spine Surgery, Hong Hui Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, China
| | - Zhong-Kai Liu
- Department of Spine Surgery, Hong Hui Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, China
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13
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Huang J, Jiang B, Li GW, Zheng D, Li M, Xie X, Pan Y, Wei M, Liu X, Jiang X, Zhang X, Yang L, Bao L, Wang B. m6A-modified lincRNA Dubr is required for neuronal development by stabilizing YTHDF1/3 and facilitating mRNA translation. Cell Rep 2022; 41:111693. [DOI: 10.1016/j.celrep.2022.111693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 09/16/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
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14
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Downregulation of METTL14 improves postmenopausal osteoporosis via IGF2BP1 dependent posttranscriptional silencing of SMAD1. Cell Death Dis 2022; 13:919. [PMID: 36319624 PMCID: PMC9626483 DOI: 10.1038/s41419-022-05362-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/19/2022] [Accepted: 10/20/2022] [Indexed: 11/21/2022]
Abstract
Osteoporosis (OP) tends to occur in postmenopausal women, making them prone to fractures. N6-methyladenosine (m6A) methylation plays a crucial role in OP. Herein, we aimed to explore the effects of METTL14 on osteogenesis and the underlying mechanism. Osteogenic differentiation was assessed through osteoblast markers expression, cell proliferation, ALP activity, and mineralization, which were detected by qRT-PCR, CCK-8, EdU assay, ALP staining assay, and ARS staining assay, respectively. Osteoporosis was evaluated in OVX mice using qRT-PCR, microcomputed tomography, and H&E staining assay. The levels of METTL14 and SMAD1 were measured using qRT-PCR and western blot, and their interaction was assessed using RIP and luciferase reporter assay. M6A methylation was analyzed using the Me-RIP assay. The results indicated that m6A, METTL14, and SMAD1 levels were downregulated in patients with OP and OVX mice, and upregulated in osteogenic BMSCs. Knockdown of METTL14 suppressed osteogenesis of BMSCs and reduced bone mass of OVX mice. Moreover, silencing of METTL14 positively related to SMAD1 and inhibited m6A modification of SMAD1 by suppressing its stability. IGF2BP1 was identified as the methylation reader, and which knockdown reversed the upregulation induced by SMAD1. Overexpression of SMAD1 reversed the suppression of osteogenic differentiation induced by METTL14 knockdown. In conclusion, interference with METTL14 inhibited osteogenic differentiation of BSMCs by m6A modification of SMAD1 in an IGFBP1 manner, suggesting that METTL14 might be a novel approach for improving osteoporosis.
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15
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The Potential Role of m6A in the Regulation of TBI-Induced BGA Dysfunction. Antioxidants (Basel) 2022; 11:antiox11081521. [PMID: 36009239 PMCID: PMC9405408 DOI: 10.3390/antiox11081521] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023] Open
Abstract
The brain–gut axis (BGA) is an important bidirectional communication pathway for the development, progress and interaction of many diseases between the brain and gut, but the mechanisms remain unclear, especially the post-transcriptional regulation of BGA after traumatic brain injury (TBI). RNA methylation is one of the most important modifications in post-transcriptional regulation. N6-methyladenosine (m6A), as the most abundant post-transcriptional modification of mRNA in eukaryotes, has recently been identified and characterized in both the brain and gut. The purpose of this review is to describe the pathophysiological changes in BGA after TBI, and then investigate the post-transcriptional bidirectional regulation mechanisms of TBI-induced BGA dysfunction. Here, we mainly focus on the characteristics of m6A RNA methylation in the post-TBI BGA, highlight the possible regulatory mechanisms of m6A modification in TBI-induced BGA dysfunction, and finally discuss the outcome of considering m6A as a therapeutic target to improve the recovery of the brain and gut dysfunction caused by TBI.
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16
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She J, Tan K, Liu J, Cao S, Li Z, Peng Y, Xiao Z, Diao R, Wang L. The Alteration of m 6A Modification at the Transcriptome-Wide Level in Human Villi During Spontaneous Abortion in the First Trimester. Front Genet 2022; 13:861853. [PMID: 35754822 PMCID: PMC9215105 DOI: 10.3389/fgene.2022.861853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
A growing number of studies have demonstrated that N6 methyladenine (m6A) acts as an important role in the pathogenesis of reproductive diseases. Therefore, it is essential to profile the genome-wide m6A modifications such as in spontaneous abortion. In this study, due to the trace of human villi during early pregnancy, we performed high-throughput sequencing in villous tissues from spontaneous abortion (SA group) and controls with induced abortion (normal group) in the first trimester. Based on meRIP-seq data, 18,568 m6A peaks were identified. These m6A peaks were mainly located in the coding region near the stop codon and were mainly characterized by AUGGAC and UGGACG motif. Compared with normal group, the SA group had 2,159 significantly upregulated m6A peaks and 281 downregulated m6A peaks. Biological function analyses revealed that differential m6A-modified genes were mainly involved in the Hippo and Wnt signaling pathways. Based on the conjoint analysis of meRIP-seq and RNA-seq data, we identified thirty-five genes with differentially methylated m6A peaks and synchronously differential expression. And these genes were mainly involved in the Wnt signaling pathway, phosphatase activity regulation, protein phosphatase inhibitor activity, and transcription inhibitor activity. This study is the first to profile the transcriptome-wide m6A methylome in spontaneous abortion during early pregnancy, which provide novel insights into the pathogenesis and treatment of spontaneous abortion in the first trimester.
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Affiliation(s)
- Jiajie She
- The First Affiliated Hospital of Shenzhen University, Reproductive Medicine Centre, Shenzhen Second People's Hospital, Shenzhen, China.,Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Kaifen Tan
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jie Liu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shuo Cao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zengguang Li
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - You Peng
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhuoyu Xiao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ruiying Diao
- The First Affiliated Hospital of Shenzhen University, Reproductive Medicine Centre, Shenzhen Second People's Hospital, Shenzhen, China
| | - Liping Wang
- The First Affiliated Hospital of Shenzhen University, Reproductive Medicine Centre, Shenzhen Second People's Hospital, Shenzhen, China
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17
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Comprehensive characterization of posttranscriptional impairment-related 3'-UTR mutations in 2413 whole genomes of cancer patients. NPJ Genom Med 2022; 7:34. [PMID: 35654793 PMCID: PMC9163142 DOI: 10.1038/s41525-022-00305-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
The 3' untranslated region (3'-UTR) is the vital element regulating gene expression, but most studies have focused on variations in RNA-binding proteins (RBPs), miRNAs, alternative polyadenylation (APA) and RNA modifications. To explore the posttranscriptional function of 3'-UTR somatic mutations in tumorigenesis, we collected whole-genome data from 2413 patients across 18 cancer types. Our updated algorithm, PIVar, revealed 25,216 3'-UTR posttranscriptional impairment-related SNVs (3'-UTR piSNVs) spanning 2930 genes; 24 related RBPs were significantly enriched. The somatic 3'-UTR piSNV ratio was markedly increased across all 18 cancer types, which was associated with worse survival for four cancer types. Several cancer-related genes appeared to facilitate tumorigenesis at the protein and posttranscriptional regulation levels, whereas some 3'-UTR piSNV-affected genes functioned mainly via posttranscriptional mechanisms. Moreover, we assessed immune cell and checkpoint characteristics between the high/low 3'-UTR piSNV ratio groups and predicted 80 compounds associated with the 3'-UTR piSNV-affected gene expression signature. In summary, our study revealed the prevalence and clinical relevance of 3'-UTR piSNVs in cancers, and also demonstrates that in addition to affecting miRNAs, 3'-UTR piSNVs perturb RBPs binding, APA and m6A RNA modification, which emphasized the importance of considering 3'-UTR piSNVs in cancer biology.
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18
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Ma L, Xue X, Zhang X, Yu K, Xu X, Tian X, Miao Y, Meng F, Liu X, Guo S, Qiu S, Wang Y, Cui J, Guo W, Li Y, Xia J, Yu Y, Wang J. The essential roles of m 6A RNA modification to stimulate ENO1-dependent glycolysis and tumorigenesis in lung adenocarcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:36. [PMID: 35078505 PMCID: PMC8788079 DOI: 10.1186/s13046-021-02200-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/26/2021] [Indexed: 12/31/2022]
Abstract
Background Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer. Patient prognosis is poor, and the existing therapeutic strategies for LUAD are far from satisfactory. Recently, targeting N6-methyladenosine (m6A) modification of RNA has been suggested as a potential strategy to impede tumor progression. However, the roles of m6A modification in LUAD tumorigenesis is unknown. Methods Global m6A levels and expressions of m6A writers, erasers and readers were evaluated by RNA methylation assay, dot blot, immunoblotting, immunohistochemistry and ELISA in human LUAD, mouse models and cell lines. Cell viability, 3D-spheroid generation, in vivo LUAD formation, experiments in cell- and patient-derived xenograft mice and survival analysis were conducted to explore the impact of m6A on LUAD. The RNA-protein interactions, translation, putative m6A sites and glycolysis were explored in the investigation of the mechanism underlying how m6A stimulates tumorigenesis. Results The elevation of global m6A level in most human LUAD specimens resulted from the combined upregulation of m6A writer methyltransferase 3 (METTL3) and downregulation of eraser alkB homolog 5 (ALKBH5). Elevated global m6A level was associated with a poor overall survival in LUAD patients. Reducing m6A levels by knocking out METTL3 and overexpressing ALKBH5 suppressed 3D-spheroid generation in LUAD cells and intra-pulmonary tumor formation in mice. Mechanistically, m6A-dependent stimulation of glycolysis and tumorigenesis occurred via enolase 1 (ENO1). ENO1 mRNA was m6A methylated at 359 A, which facilitated it’s binding with the m6A reader YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) and resulted in enhanced translation of ENO1. ENO1 positively correlated with METTL3 and global m6A levels, and negatively correlated with ALKBH5 in human LUAD. In addition, m6A-dependent elevation of ENO1 was associated with LUAD progression. In preclinical models, tumors with a higher global m6A level showed a more sensitive response to the inhibition of pan-methylation, glycolysis and ENO activity in LUAD. Conclusions The m6A-dependent stimulation of glycolysis and tumorigenesis in LUAD is at least partially orchestrated by the upregulation of METTL3, downregulation of ALKBH5, and stimulation of YTHDF1-mediated ENO1 translation. Blocking this mechanism may represent a potential treatment strategy for m6A-dependent LUAD. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02200-5.
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Affiliation(s)
- Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China.,Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Xiangfei Xue
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, 200072, Shanghai, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Keke Yu
- Department of Bio-bank, Shanghai Chest Hospital, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Xin Xu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Xiaoting Tian
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Yayou Miao
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Fanyu Meng
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Xiaoxin Liu
- Nursing Department, Shanghai Chest Hospital, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Susu Guo
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, 200072, Shanghai, China
| | - Shiyu Qiu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Yikun Wang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Jiangtao Cui
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Wanxin Guo
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - You Li
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China
| | - Jinjing Xia
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China.
| | - Yongchun Yu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China.
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China. .,Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, 200030, Shanghai, China. .,Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, 200072, Shanghai, China.
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19
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Pan Z, Zhao R, Li B, Qi Y, Qiu W, Guo Q, Zhang S, Zhao S, Xu H, Li M, Gao Z, Fan Y, Xu J, Wang H, Wang S, Qiu J, Wang Q, Guo X, Deng L, Zhang P, Xue H, Li G. EWSR1-induced circNEIL3 promotes glioma progression and exosome-mediated macrophage immunosuppressive polarization via stabilizing IGF2BP3. Mol Cancer 2022; 21:16. [PMID: 35031058 PMCID: PMC8759291 DOI: 10.1186/s12943-021-01485-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
Background Gliomas are the most common malignant primary brain tumours with a highly immunosuppressive tumour microenvironment (TME) and poor prognosis. Circular RNAs (circRNA), a newly found type of endogenous noncoding RNA, characterized by high stability, abundance, conservation, have been shown to play an important role in the pathophysiological processes and TME remodelling of various tumours. Methods CircRNA sequencing analysis was performed to explore circRNA expression profiles in normal and glioma tissues. The biological function of a novel circRNA, namely, circNEIL3, in glioma development was confirmed both in vitro and in vivo. Mechanistically, RNA pull-down, mass spectrum, RNA immunoprecipitation (RIP), luciferase reporter, and co-immunoprecipitation assays were conducted. Results We identified circNEIL3, which could be cyclized by EWS RNA-binding protein 1(EWSR1), to be upregulated in glioma tissues and to correlate positively with glioma malignant progression. Functionally, we confirmed that circNEIL3 promotes tumorigenesis and carcinogenic progression of glioma in vitro and in vivo. Mechanistically, circNEIL3 stabilizes IGF2BP3 (insulin-like growth factor 2 mRNA binding protein 3) protein, a known oncogenic protein, by preventing HECTD4-mediated ubiquitination. Moreover, circNEIL3 overexpression glioma cells drives macrophage infiltration into the tumour microenvironment (TME). Finally, circNEIL3 is packaged into exosomes by hnRNPA2B1 and transmitted to infiltrated tumour associated macrophages (TAMs), enabling them to acquire immunosuppressive properties by stabilizing IGF2BP3 and in turn promoting glioma progression. Conclusions This work reveals that circNEIL3 plays a nonnegligible multifaceted role in promoting gliomagenesis, malignant progression and macrophage tumour-promoting phenotypes polarization, highlighting that circNEIL3 is a potential prognostic biomarker and therapeutic target in glioma. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01485-6.
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Affiliation(s)
- Ziwen Pan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Boyan Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Yanhua Qi
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Wei Qiu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Qindong Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Shouji Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Shulin Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Hao Xu
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China.,Department of Neurosurgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Ming Li
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China.,Department of Neurosurgery, Taian Central Hospital, Taian, Shandong, China
| | - Zijie Gao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Yang Fan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Jianye Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Huizhi Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Shaobo Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Jiawei Qiu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Qingtong Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Xing Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Lin Deng
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Ping Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Hao Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China. .,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China.
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Western Road; Jinan, Shandong 250012, China, Jinan, 250012, Shandong, China. .,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China.
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20
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Xu P, Hu K, Zhang P, Sun ZG, Zhang N. Hypoxia-mediated YTHDF2 overexpression promotes lung squamous cell carcinoma progression by activation of the mTOR/AKT axis. Cancer Cell Int 2022; 22:13. [PMID: 34996459 PMCID: PMC8742419 DOI: 10.1186/s12935-021-02368-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is a dynamic and reversible internal RNA structure of eukaryotic mRNA. YTH domain family 2 (YTHDF2), an m6A-specific reader YTH domain family, plays fundamental roles in several types of cancer. However, the function of YTHDF2 in lung squamous cell carcinoma (LUSC) remains elusive. METHODS The knockdown and overexpression of YTHDF2 in LUSC cells were conducted to detect the biological characteristics of YTHDF2. In vivo assays, the role of YTHDF2 in tumor growth was further uncovered. In vitro assays, YTHDF2 was confirmed to be involved in activating the mTOR/AKT signaling and YTHDF2 overexpression induced the EMT process in LUSC. Clinically, immunohistochemical staining revealed the relationship between YTHDF2 expression levels and the clinicopathological characteristics of lung squamous cell carcinoma patients. Moreover, quantitative PCR (qPCR), western blot, CCK8 assay, transwell assay, and wound-healing assay were used to detect the expression level and function of YTHDF2 under hypoxia exposure in LUSC cells. RESULTS The results showed that hypoxia-mediated YTHDF2 overexpression promotes cell proliferation and invasion by activating the mTOR/AKT axis, and YTHDF2 overexpression induces the EMT process in LUSC. Moreover, YTHDF2 is closely associated with pN (pN- 37.0%, pN + 73.9%; P = 0.002) and pTNM stage (pI 50.0%, PII 43.3%, pIIIa 80.6%; P = 0.007), ultimately resulting in poor survival for LUSC patients. CONCLUSION In brief, the results highlight high-YTHDF2 expression predicted a worse prognosis of LUSC, while hypoxia-mediated YTHDF2 overexpression promotes lung squamous cell carcinoma progression by activation of the mTOR/AKT signaling pathway.
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Affiliation(s)
- Peng Xu
- Cheeloo College of Medicine, Shandong University, Jinan, 250013, Shangdong, China
| | - Kang Hu
- School of Clinical Medicine, Weifang Medical University, Weifang, 261053, Shangdong, China
| | - Ping Zhang
- Cheeloo College of Medicine, Shandong University, Jinan, 250013, Shangdong, China
| | - Zhi-Gang Sun
- Department of Thoracic Surgery, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250013, Shangdong, China.
| | - Nan Zhang
- Department of Oncology, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250013, Shangdong, China.
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21
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Qu N, Bo X, Li B, Ma L, Wang F, Zheng Q, Xiao X, Huang F, Shi Y, Zhang X. Role of N6-Methyladenosine (m 6A) Methylation Regulators in Hepatocellular Carcinoma. Front Oncol 2021; 11:755206. [PMID: 34692544 PMCID: PMC8529104 DOI: 10.3389/fonc.2021.755206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/22/2021] [Indexed: 12/21/2022] Open
Abstract
Liver cancer is the fifth most common malignant tumor in terms of incidence and the third leading cause of cancer-related mortality globally. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. Although great progress has been made in surgical techniques, hepatic artery chemoembolization, molecular targeting and immunotherapy, the prognosis of liver cancer patients remains very poor. N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic cells and regulates various stages of the RNA life cycle. Many studies have reported that the abnormal expression of m6A-related regulators in HCC represent diagnostic and prognostic markers and potential therapeutic targets. In this review, firstly, we introduce the latest research on m6A-related regulators in detail. Next, we summarize the mechanism of each regulator in the pathogenesis and progression of HCC. Finally, we summarize the potential diagnostic, prognostic and therapeutic value of the regulators currently reported in HCC.
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Affiliation(s)
- Nanfang Qu
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xiaotong Bo
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Bin Li
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Lei Ma
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Feng Wang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qinghua Zheng
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xuhua Xiao
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Fengmei Huang
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Yuanyuan Shi
- Department of Oncology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xuemei Zhang
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, China
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22
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m6A modification promotes miR-133a repression during cardiac development and hypertrophy via IGF2BP2. Cell Death Discov 2021; 7:157. [PMID: 34226535 PMCID: PMC8257704 DOI: 10.1038/s41420-021-00552-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/09/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
Both N6-methyladenosine (m6A) RNA modification and microRNAs (miRNAs) are common regulatory mechanisms for gene post-transcription by modulating mRNA stability and translation. They also share the same 3′-untranslated regions (UTRs) regions for their target gene. However, little is known about their potential interaction in cell development and biology. Here, we aimed to investigate how m6A regulates the specific miRNA repression during cardiac development and hypertrophy. Our multiple lines of bioinformatic and molecular biological evidence have shown that m6A modification on cardiac miR-133a target sequence promotes miR-133a repressive effect via AGO2-IGF2BP2 (Argonaute 2—Insulin-like growth factor 2 mRNA binding protein 2) complex. Among 139 cardiac miRNAs, only the seed sequence of miR-133a was inversely complement to m6A consensus motif “GGACH” by sequence alignment analysis. Immunofluorescence staining, luciferase reporter, and m6A-RIP (RNA immunoprecipitation) assays revealed that m6A modification facilitated miR-133a binding to and repressing their targets. The inhibition of the miR-133a on cardiac proliferation and hypertrophy could be prevented by silencing of Fto (FTO alpha-ketoglutarate dependent dioxygenase) which induced m6A modification. IGF2BP2, an m6A binding protein, physically interacted with AGO2 and increased more miR-133a accumulation on its target site, which was modified by m6A. In conclusion, our study revealed a novel and precise regulatory mechanism that the m6A modification promoted the repression of specific miRNA during heart development and hypertrophy. Targeting m6A modification might provide a strategy to repair hypertrophic gene expression induced by miR-133a.
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23
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Zhang H, Zhang SH, Hu JL, Wu YT, Ma XY, Chen Y, Yu B, Liao S, Huang H, Gao S. Structural and functional characterization of multiple myeloma associated cytoplasmic poly(A) polymerase FAM46C. Cancer Commun (Lond) 2021; 41:615-630. [PMID: 34048638 PMCID: PMC8286142 DOI: 10.1002/cac2.12163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/28/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Multiple myeloma (MM) is a hematologic malignancy characterized by the accumulation of aberrant plasma cells within the bone marrow. The high frequent mutation of family with sequence similarity 46, member C (FAM46C) is closely related with the occurrence and progression of MM. Recently, FAM46C has been identified as a non‐canonical poly(A) polymerase (PAP) that functions as a tumor suppressor in MM. This study aimed to elucidate the structural features of this novel non‐canonical PAP and how MM‐related mutations affect the structural and biochemical properties of FAM46C, eventually advancing our understandings towards FAM46C mutation‐related MM occurrence. Methods We purified and crystallized a mammalian FAM46C construct, and solved its structure. Next, we characterized the property of FAM46C as a PAP through a combination of structural analysis, site‐directed mutagenesis and biochemical assays, and by comparison with its homolog FAM46B. Finally, we structurally analyzed MM‐related FAM46C mutations and tested the enzymatic activity of corresponding mutants. Results We determined the crystal structure of a mammalian FAM46C protein at 2.35 Å, and confirmed that FAM46C preferentially consumed adenosine triphosphate (ATP) and extended A‐rich RNA substrates. FAM46C showed a weaker PAP activity than its homolog FAM46B, and this difference was largely dependent on the residue variance at particular sites. Of them, residues at positions 77, 290, and 298 of mouse FAM46C were most important for the divergence in enzymatic activity. Among the MM‐associated FAM46C mutants, those residing at the catalytic site (D90G and D90H) or putative RNA‐binding site (I155L, S156F, D182Y, F184L, Y247V, and M270V) showed abolished or compromised PAP activity of FAM46C, while N72A and S248A did not severely affect the PAP activity. FAM46C mutants D90G, D90H, I155L, S156F, F184L, Y247V, and M270V had significantly lower inhibitory effect on apoptosis of RPMI‐8226 cells as compared to wild‐type FAM46C. Conclusions FAM46C is a prokaryotic‐like PAP with preference for A‐rich RNA substrates, and showed distinct enzymatic efficiency with its homolog FAM46B. The MM‐related missense mutations of FAM46C lead to various structural and biochemical outcomes to the protein.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shi-Hui Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Jia-Li Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Yu-Tong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Xiao-Yan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Yang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Bing Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shuang Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong, 510530, P. R. China
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24
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Zhang SY, Zhang SW, Zhang T, Fan XN, Meng J. Recent advances in functional annotation and prediction of the epitranscriptome. Comput Struct Biotechnol J 2021; 19:3015-3026. [PMID: 34136099 PMCID: PMC8175281 DOI: 10.1016/j.csbj.2021.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
RNA modifications, in particular N6-methyladenosine (m6A), participate in every stages of RNA metabolism and play diverse roles in essential biological processes and disease pathogenesis. Thanks to the advances in sequencing technology, tens of thousands of RNA modification sites can be identified in a typical high-throughput experiment; however, it remains a major challenge to decipher the functional relevance of these sites, such as, affecting alternative splicing, regulation circuit in essential biological processes or association to diseases. As the focus of RNA epigenetics gradually shifts from site discovery to functional studies, we review here recent progress in functional annotation and prediction of RNA modification sites from a bioinformatics perspective. The review covers naïve annotation with associated biological events, e.g., single nucleotide polymorphism (SNP), RNA binding protein (RBP) and alternative splicing, prediction of key sites and their regulatory functions, inference of disease association, and mining the diagnosis and prognosis value of RNA modification regulators. We further discussed the limitations of existing approaches and some future perspectives.
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Affiliation(s)
- Song-Yao Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Teng Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xiao-Nan Fan
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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25
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Zhang SY, Zhang SW, Tang Y, Fan XN, Meng J. Funm6AViewer: a web server and R package for functional analysis of context-specific m6A RNA methylation. Bioinformatics 2021; 37:4277-4279. [PMID: 33974000 DOI: 10.1093/bioinformatics/btab362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/20/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION N6-methyladenosine (m6A) is the most abundant mammalian mRNA methylation with versatile functions. To date, although a number of bioinformatics tools have been developed for location discovery of m6A modification, functional understanding is still quite limited. As the focus of RNA epigenetics gradually shifts from site discovery to functional studies, there is an urgent need for user-friendly tools to identify and explore the functional relevance of context-specific m6A methylation to gain insights into the epitranscriptome layer of gene expression regulation. RESULTS We introduced here Funm6AViewer, a novel platform to identify, prioritize, and visualize the functional gene interaction networks mediated by dynamic m6A RNA methylation unveiled from a case control study. By taking the differential RNA methylation (DM) data and differential gene expression (DE) data, both of which can be inferred from the widely used MeRIP-seq data, as the inputs, Funm6AViewer enables a series of analysis, including: (1) examining the distribution of differential m6A sites, (2) prioritizing the genes mediated by dynamic m6A methylation, and (3) characterizing functionally the gene regulatory networks mediated by condition-specific m6A RNA methylation. Funm6AViewer should effectively facilitate the understanding of the epitranscriptome circuitry mediated by this reversible RNA modification. Funm6AViewer is available both as a convenient web server (https://www.xjtlu.edu.cn/biologicalsciences/funm6aviewer) with graphical interface and as an independent R package (https://github.com/NWPU-903PR/Funm6AViewer) for local usage. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Song-Yao Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xı´an 710072, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xı´an 710072, China
| | - Yujiao Tang
- Department of Biological Sciences.,Institute of Integrative Biology, University of Liverpool, Liverpool, L7 8TX, UK
| | - Xiao-Nan Fan
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xı´an 710072, China
| | - Jia Meng
- Department of Biological Sciences.,AI University Center, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China.,Institute of Integrative Biology, University of Liverpool, Liverpool, L7 8TX, UK
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26
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Zhang Y, Xu S, Xu G, Gao Y, Li S, Zhang K, Tian Z, Guo J, Li X, Xu J, Li Y. Dynamic Expression of m 6A Regulators During Multiple Human Tissue Development and Cancers. Front Cell Dev Biol 2021; 8:629030. [PMID: 33575259 PMCID: PMC7870680 DOI: 10.3389/fcell.2020.629030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/21/2020] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) plays critical roles in human development and cancer progression. However, our knowledge regarding the dynamic expression of m6A regulators during human tissue development is still lacking. Here, we comprehensively analyzed the dynamic expression alterations of m6A regulators during seven tissue development and eight cancer types. We found that m6A regulators globally exhibited decreased expression during development. In addition, IGF2BP1/2/3 (insulinlike growth factor 2 MRNA-binding protein 1/2/3) exhibited reverse expression pattern in cancer progression, suggesting an oncofetal reprogramming in cancer. The expressions of IGF2BP1/2/3 were regulated by genome alterations, particularly copy number amplification in cancer. Clinical association analysis revealed that higher expressions of IGF2BP1/2/3 were associated with worse survival of cancer patients. Finally, we found that genes significantly correlated with IGF2BP1/2/3 were significantly enriched in cancer hallmark-related pathways. In summary, dynamic expression analysis will guide both mechanistic and therapeutic roles of m6A regulators during tissue development and cancer progression.
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Affiliation(s)
- Ya Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Sicong Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Gang Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Yueying Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Si Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Ke Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Zhanyu Tian
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Jing Guo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Xia Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Juan Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
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