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Xu WQ, Cheah JS, Xu C, Messing J, Freibaum BD, Boeynaems S, Taylor JP, Udeshi ND, Carr SA, Ting AY. Dynamic mapping of proteome trafficking within and between living cells by TransitID. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527548. [PMID: 36798302 PMCID: PMC9934598 DOI: 10.1101/2023.02.07.527548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The ability to map trafficking for thousands of endogenous proteins at once in living cells would reveal biology currently invisible to both microscopy and mass spectrometry. Here we report TransitID, a method for unbiased mapping of endogenous proteome trafficking with nanometer spatial resolution in living cells. Two proximity labeling (PL) enzymes, TurboID and APEX, are targeted to source and destination compartments, and PL with each enzyme is performed in tandem via sequential addition of their small-molecule substrates. Mass spectrometry identifies the proteins tagged by both enzymes. Using TransitID, we mapped proteome trafficking between cytosol and mitochondria, cytosol and nucleus, and nucleolus and stress granules, uncovering a role for stress granules in protecting the transcription factor JUN from oxidative stress. TransitID also identifies proteins that signal intercellularly between macrophages and cancer cells. TransitID introduces a powerful approach for distinguishing protein populations based on compartment or cell type of origin.
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Pro-Viral and Anti-Viral Roles of the RNA-Binding Protein G3BP1. Viruses 2023; 15:v15020449. [PMID: 36851663 PMCID: PMC9959972 DOI: 10.3390/v15020449] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Viruses depend on host cellular resources to replicate. Interaction between viral and host proteins is essential for the pathogens to ward off immune responses as well as for virus propagation within the infected cells. While different viruses employ unique strategies to interact with diverse sets of host proteins, the multifunctional RNA-binding protein G3BP1 is one of the common targets for many viruses. G3BP1 controls several key cellular processes, including mRNA stability, translation, and immune responses. G3BP1 also serves as the central hub for the protein-protein and protein-RNA interactions within a class of biomolecular condensates called stress granules (SGs) during stress conditions, including viral infection. Increasing evidence suggests that viruses utilize distinct strategies to modulate G3BP1 function-either by degradation, sequestration, or redistribution-and control the viral life cycle positively and negatively. In this review, we summarize the pro-viral and anti-viral roles of G3BP1 during infection among different viral families.
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53
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Wang K, Gao XQ, Wang T, Zhou LY. The Function and Therapeutic Potential of Circular RNA in Cardiovascular Diseases. Cardiovasc Drugs Ther 2023; 37:181-198. [PMID: 34269929 DOI: 10.1007/s10557-021-07228-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/06/2021] [Indexed: 01/14/2023]
Abstract
Circular RNA (circRNA) has a closed-loop structure, and its 3' and 5' ends are directly covalently connected by reverse splicing, which is more stable than linear RNA. CircRNAs usually possess microRNA (miRNA) binding sites, which can bind miRNAs and inhibit miRNA function. Many studies have shown that circRNAs are involved in the processes of cell senescence, proliferation and apoptosis and a series of signalling pathways, playing an important role in the prevention and treatment of diseases. CircRNAs are potential biological diagnostic markers and therapeutic targets for cardiovascular diseases (CVDs). To identify biomarkers and potential effective therapeutic targets without toxicity for heart disease, we summarize the biogenesis, biology, characterization and functions of circRNAs in CVDs, hoping that this information will shed new light on the prevention and treatment of CVDs.
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Affiliation(s)
- Kai Wang
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, Shandong, China
| | - Xiang-Qian Gao
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, Shandong, China
| | - Tao Wang
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, Shandong, China
| | - Lu-Yu Zhou
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, Shandong, China.
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Ju M, Kim D, Son G, Han J. Circular RNAs in and out of Cells: Therapeutic Usages of Circular RNAs. Mol Cells 2023; 46:33-40. [PMID: 36697235 PMCID: PMC9880607 DOI: 10.14348/molcells.2023.2170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 01/27/2023] Open
Abstract
RNAs are versatile molecules that are primarily involved in gene regulation and can thus be widely used to advance the fields of therapeutics and diagnostics. In particular, circular RNAs which are highly stable, have emerged as strong candidates for use on next-generation therapeutic platforms. Endogenous circular RNAs control gene regulatory networks by interacting with other biomolecules or through translation into polypeptides. Circular RNAs exhibit cell-type specific expression patterns, which can be altered in tissues and body fluids depending on pathophysiological conditions. Circular RNAs that are aberrantly expressed in diseases can function as biomarkers or therapeutic targets. Moreover, exogenous circular RNAs synthesized in vitro can be introduced into cells as therapeutic molecules to modulate gene expression networks in vivo. Depending on the purpose, synthetic circular RNA sequences can either be identical to endogenous circular RNA sequences or artificially designed. In this review, we introduce the life cycle and known functions of intracellular circular RNAs. The current stage of endogenous circular RNAs as biomarkers and therapeutic targets is also described. Finally, approaches and considerations that are important for applying the available knowledge on endogenous circular RNAs to design exogenous circular RNAs for therapeutic purposes are presented.
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Affiliation(s)
- Mingyu Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Dayeon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Geurim Son
- Graduate School of Medical Science and Engineering, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jinju Han
- Graduate School of Medical Science and Engineering, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
- BioMedical Research Center, KAIST, Daejeon 34141, Korea
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Staszewski J, Lazarewicz N, Konczak J, Migdal I, Maciaszczyk-Dziubinska E. UPF1-From mRNA Degradation to Human Disorders. Cells 2023; 12:cells12030419. [PMID: 36766761 PMCID: PMC9914065 DOI: 10.3390/cells12030419] [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: 12/20/2022] [Revised: 01/07/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Up-frameshift protein 1 (UPF1) plays the role of a vital controller for transcripts, ready to react in the event of an incorrect translation mechanism. It is well known as one of the key elements involved in mRNA decay pathways and participates in transcript and protein quality control in several different aspects. Firstly, UPF1 specifically degrades premature termination codon (PTC)-containing products in a nonsense-mediated mRNA decay (NMD)-coupled manner. Additionally, UPF1 can potentially act as an E3 ligase and degrade target proteins independently from mRNA decay pathways. Thus, UPF1 protects cells against the accumulation of misfolded polypeptides. However, this multitasking protein may still hide many of its functions and abilities. In this article, we summarize important discoveries in the context of UPF1, its involvement in various cellular pathways, as well as its structural importance and mutational changes related to the emergence of various pathologies and disease states. Even though the state of knowledge about this protein has significantly increased over the years, there are still many intriguing aspects that remain unresolved.
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Affiliation(s)
- Jacek Staszewski
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
| | - Natalia Lazarewicz
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Institute of Genetics and Development of Rennes, CNRS UMR 6290, University of Rennes 1, 35000 Rennes, France
| | - Julia Konczak
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Iwona Migdal
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
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CircAMOTL1 RNA and AMOTL1 Protein: Complex Functions of AMOTL1 Gene Products. Int J Mol Sci 2023; 24:ijms24032103. [PMID: 36768425 PMCID: PMC9916871 DOI: 10.3390/ijms24032103] [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: 11/09/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
The complexity of the cellular proteome facilitates the control of a wide range of cellular processes. Non-coding RNAs, including microRNAs and long non-coding RNAs, greatly contribute to the repertoire of tools used by cells to orchestrate various functions. Circular RNAs (circRNAs) constitute a specific class of non-coding RNAs that have recently emerged as a widely generated class of molecules produced from many eukaryotic genes that play essential roles in regulating cellular processes in health and disease. This review summarizes current knowledge about circRNAs and focuses on the functions of AMOTL1 circRNAs and AMOTL1 protein. Both products from the AMOTL1 gene have well-known functions in physiology, cancer, and other disorders. Using AMOTL1 as an example, we illustrate how focusing on both circRNAs and proteins produced from the same gene contributes to a better understanding of gene functions.
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Nokkeaw A, Thamjamrassri P, Tangkijvanich P, Ariyachet C. Regulatory Functions and Mechanisms of Circular RNAs in Hepatic Stellate Cell Activation and Liver Fibrosis. Cells 2023; 12:cells12030378. [PMID: 36766720 PMCID: PMC9913196 DOI: 10.3390/cells12030378] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Chronic liver injury induces the activation of hepatic stellate cells (HSCs) into myofibroblasts, which produce excessive amounts of extracellular matrix (ECM), resulting in tissue fibrosis. If the injury persists, these fibrous scars could be permanent and disrupt liver architecture and function. Currently, effective anti-fibrotic therapies are lacking; hence, understanding molecular mechanisms that control HSC activation could hold a key to the development of new treatments. Recently, emerging studies have revealed roles of circular RNAs (circRNAs), a class of non-coding RNAs that was initially assumed to be the result of splicing errors, as new regulators in HSC activation. These circRNAs can modulate the activity of microRNAs (miRNAs) and their interacting protein partners involved in regulating fibrogenic signaling cascades. In this review, we will summarize the current knowledge of this class of non-coding RNAs for their molecular function in HSC activation and liver fibrosis progression.
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Affiliation(s)
- Archittapon Nokkeaw
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Medical Biochemistry Program, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pannathon Thamjamrassri
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Medical Biochemistry Program, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pisit Tangkijvanich
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (P.T.); (C.A.)
| | - Chaiyaboot Ariyachet
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (P.T.); (C.A.)
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Kharel P, Fay M, Manasova EV, Anderson PJ, Kurkin AV, Guo JU, Ivanov P. Stress promotes RNA G-quadruplex folding in human cells. Nat Commun 2023; 14:205. [PMID: 36639366 PMCID: PMC9839774 DOI: 10.1038/s41467-023-35811-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. In this report, we showed that the folding of putative rG4s in human cells into rG4 structures is dynamically regulated under stress. By using high-throughput dimethylsulfate (DMS) probing, we identified hundreds of endogenous stress-induced rG4s, and validated them by using an rG4 pull-down approach. Our results demonstrate that stress-induced rG4s are enriched in mRNA 3'-untranslated regions and enhance mRNA stability. Furthermore, stress-induced rG4 folding is readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in human cells and suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.
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Affiliation(s)
- Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marta Fay
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ekaterina V Manasova
- Chemistry Department of Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Paul J Anderson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Alexander V Kurkin
- Chemistry Department of Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Junjie U Guo
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06520, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, 02115, USA.
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RNA therapeutics: updates and future potential. SCIENCE CHINA. LIFE SCIENCES 2023; 66:12-30. [PMID: 36100838 PMCID: PMC9470505 DOI: 10.1007/s11427-022-2171-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/17/2022] [Indexed: 02/04/2023]
Abstract
Recent advancements in the production, modification, and cellular delivery of RNA molecules facilitated the expansion of RNA-based therapeutics. The increasing understanding of RNA biology initiated a corresponding growth in RNA therapeutics. In this review, the general concepts of five classes of RNA-based therapeutics, including RNA interference-based therapies, antisense oligonucleotides, small activating RNA therapies, circular RNA therapies, and messenger RNA-based therapeutics, will be discussed. Moreover, we also provide an overview of RNA-based therapeutics that have already received regulatory approval or are currently being evaluated in clinical trials, along with challenges faced by these technologies. RNA-based drugs demonstrated positive clinical trial results and have the ability to address previously "undruggable" targets, which delivers great promise as a disruptive therapeutic technology to fulfill its full clinical potentiality.
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Viegas JO, Azad GK, Lv Y, Fishman L, Paltiel T, Pattabiraman S, Park JE, Kaganovich D, Sze SK, Rabani M, Esteban MA, Meshorer E. RNA degradation eliminates developmental transcripts during murine embryonic stem cell differentiation via CAPRIN1-XRN2. Dev Cell 2022; 57:2731-2744.e5. [PMID: 36495875 PMCID: PMC9796812 DOI: 10.1016/j.devcel.2022.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 08/20/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Embryonic stem cells (ESCs) are self-renewing and pluripotent. In recent years, factors that control pluripotency, mostly nuclear, have been identified. To identify non-nuclear regulators of ESCs, we screened an endogenously labeled fluorescent fusion-protein library in mouse ESCs. One of the more compelling hits was the cell-cycle-associated protein 1 (CAPRIN1). CAPRIN1 knockout had little effect in ESCs, but it significantly altered differentiation and gene expression programs. Using RIP-seq and SLAM-seq, we found that CAPRIN1 associates with, and promotes the degradation of, thousands of RNA transcripts. CAPRIN1 interactome identified XRN2 as the likely ribonuclease. Upon early ESC differentiation, XRN2 is located in the nucleus and colocalizes with CAPRIN1 in small RNA granules in a CAPRIN1-dependent manner. We propose that CAPRIN1 regulates an RNA degradation pathway operating during early ESC differentiation, thus eliminating undesired spuriously transcribed transcripts in ESCs.
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Affiliation(s)
- Juliane O. Viegas
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Gajendra Kumar Azad
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel,Department of Zoology, Patna University, Patna, Bihar 800005, India
| | - Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lior Fishman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Tal Paltiel
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | | | - Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Daniel Kaganovich
- School of Biological Sciences, University of Southampton, Southampton SO171BJ, UK,Wren Therapeutics, Cambridge CB21EW, UK
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore,Faculty of Applied Health Sciences, Brock University, St. Catharines, ON, Canada
| | - Michal Rabani
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Miguel A. Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Eran Meshorer
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel,Corresponding author
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ADAM12 promotes gemcitabine resistance by activating EGFR signaling pathway and induces EMT in bladder cancer. Clin Transl Oncol 2022; 25:1425-1435. [PMID: 36512304 DOI: 10.1007/s12094-022-03044-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Gemcitabine (GEM)-based chemotherapy regimens is widely used in bladder cancer (BC) patients. However, GEM resistance may occur and result in treatment failure and disease progression. A disintegrin and metalloprotease 12 (ADAM12) plays a critical role in many cancers. However, the role of ADAM12 in GEM resistance of BC remains unclear. METHODS We analyzed the relationship between ADAM12 expression and tumor characteristics using the data downloaded from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database. Then, we established GEM resistant BC cell lines and used quantitative real-time PCR, western blot, cell counting kit-8, immunohistochemistry, and xenograft mouse model to investigate the role of ADAM12 in GEM resistance. RESULTS In general, ADAM12 was found to be upregulated in GEM resistant BC cells. ADAM12 knockdown increased the chemosensitivity of BC cells. We further proved that ADAM12 could promote GEM resistance by activating the epidermal growth factor receptor (EGFR) signaling pathway in BC. Furthermore, the epithelial-mesenchymal transition (EMT) phenotype was observed in GEM resistant BC cells. ADAM12 induced EMT process and promotes tumor progression in BC. CONCLUSION Our findings suggested that ADAM12 was a key gene for GEM resistance and positively correlated with malignancy of BC. It might serve as a novel and valuable therapeutic target for BC.
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Ren L, Jiang Q, Mo L, Tan L, Dong Q, Meng L, Yang N, Li G. Mechanisms of circular RNA degradation. Commun Biol 2022; 5:1355. [PMID: 36494488 PMCID: PMC9734648 DOI: 10.1038/s42003-022-04262-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (CircRNAs) are a class of noncoding RNAs formed by backsplicing during cotranscriptional and posttranscriptional processes, and they widely exist in various organisms. CircRNAs have multiple biological functions and are associated with the occurrence and development of many diseases. While the biogenesis and biological function of circRNAs have been extensively studied, there are few studies on circRNA degradation and only a few pathways for specific circRNA degradation have been identified. Here we outline basic information about circRNAs, summarize the research on the circRNA degradation mechanisms and discusses where this field might head, hoping to provide some inspiration and guidance for scholars who aim to study the degradation of circRNAs.
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Affiliation(s)
- Longxin Ren
- grid.412017.10000 0001 0266 8918The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan China
| | - Qingshan Jiang
- grid.412017.10000 0001 0266 8918Department of Otolaryngology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001 China
| | - Liyi Mo
- grid.412017.10000 0001 0266 8918The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan China
| | - Lijie Tan
- grid.412017.10000 0001 0266 8918The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan China
| | - Qifei Dong
- grid.412017.10000 0001 0266 8918The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan China
| | - Lijuan Meng
- grid.412017.10000 0001 0266 8918Department of Ultrasonography, Second Affiliated Hospital, University of South China, Hengyang Hunan, 421001 China
| | - Nanyang Yang
- grid.412017.10000 0001 0266 8918The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan China
| | - Guoqing Li
- grid.412017.10000 0001 0266 8918The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan China
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Liu Z, Zhou Y, Xia J. CircRNAs: Key molecules in the prevention and treatment of ischemic stroke. Biomed Pharmacother 2022; 156:113845. [DOI: 10.1016/j.biopha.2022.113845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/25/2022] Open
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Kurosaki T, Mitsutomi S, Hewko A, Akimitsu N, Maquat LE. Integrative omics indicate FMRP sequesters mRNA from translation and deadenylation in human neuronal cells. Mol Cell 2022; 82:4564-4581.e11. [PMID: 36356584 PMCID: PMC9753132 DOI: 10.1016/j.molcel.2022.10.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/17/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
How fragile X syndrome protein (FMRP) binds mRNAs and regulates mRNA metabolism remains unclear. Our previous work using human neuronal cells focused on mRNAs targeted for nonsense-mediated mRNA decay (NMD), which we showed are generally bound by FMRP and destabilized upon FMRP loss. Here, we identify >400 high-confidence FMRP-bound mRNAs, only ∼35% of which are NMD targets. Integrative transcriptomics together with SILAC-LC-MS/MS reveal that FMRP loss generally results in mRNA destabilization and more protein produced per FMRP target. We use our established RIP-seq technology to show that FMRP footprints are independent of protein-coding potential, target GC-rich and structured sequences, and are densest in 5' UTRs. Regardless of where within an mRNA FMRP binds, we find that FMRP protects mRNAs from deadenylation and directly binds the cytoplasmic poly(A)-binding protein. Our results reveal how FMRP sequesters polyadenylated mRNAs into stabilized and translationally repressed complexes, whose regulation is critical for neurogenesis and synaptic plasticity.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
| | - Shuhei Mitsutomi
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA; Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Alexander Hewko
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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Li W, Maekiniemi A, Sato H, Osman C, Singer RH. An improved imaging system that corrects MS2-induced RNA destabilization. Nat Methods 2022; 19:1558-1562. [PMID: 36357695 PMCID: PMC7613886 DOI: 10.1038/s41592-022-01658-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/21/2022] [Indexed: 11/12/2022]
Abstract
The MS2 and MS2-coat protein (MS2-MCP) imaging system is widely used to study messenger RNA (mRNA) spatial distribution in living cells. Here, we report that the MS2-MCP system destabilizes some tagged mRNAs by activating the nonsense-mediated mRNA decay pathway. We introduce an improved version, which counteracts this effect by increasing the efficiency of translation termination of the tagged mRNAs. Improved versions were developed for both yeast and mammalian systems.
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Affiliation(s)
- Weihan Li
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Correspondence: Weihan Li (); Anna Maekiniemi (); Robert H. Singer ()
| | - Anna Maekiniemi
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Correspondence: Weihan Li (); Anna Maekiniemi (); Robert H. Singer ()
| | - Hanae Sato
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Robert H. Singer
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Correspondence: Weihan Li (); Anna Maekiniemi (); Robert H. Singer ()
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66
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Xu R, Qi L, Ren X, Zhang W, Li C, Liu Z, Tu C, Li Z. Integrated Analysis of TME and Hypoxia Identifies a Classifier to Predict Prognosis and Therapeutic Biomarkers in Soft Tissue Sarcomas. Cancers (Basel) 2022; 14:cancers14225675. [PMID: 36428766 PMCID: PMC9688460 DOI: 10.3390/cancers14225675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Soft tissue sarcoma (STS) is one of the rarest but most aggressive cancer. It is important to note that intratumoral hypoxia and tumor microenvironment (TME) infiltration play a significant role in the growth and therapeutic resistance of STS. The goal of this study was therefore to determine whether linking hypoxia-related parameters to TME cells could provide a more accurate prediction of prognosis and therapeutic response. An analysis of 109 hypoxia-related genes and 64 TME cells was conducted in STS. Hypoxia-TME classifier was constructed based on 6 hypoxia prognostic genes and 8 TME cells. As a result, we evaluated the prognosis, tumor, and immune characteristics, as well as the effectiveness of therapies in Hypoxia-TME-defined subgroups. The Lowplus group showed a better prognosis and therapeutic response than any other subgroup. It is possible to unravel these differences based on immune-related molecules and somatic mutations in tumors. Further validation of Hypoxia-TME was done in an additional cohort of 225 STS patients. Additionally, we identified five key genes through differential analysis and RT-qPCR, namely, ACSM5, WNT7B, CA9, MMP13, and RAC3, which could be targeted for therapy. As a whole, the Hypoxia-TME classifier demonstrated a pretreatment predictive value for prognosis and therapeutic outcome, providing new approaches to therapy strategizing for patients.
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Affiliation(s)
- Ruiling Xu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha 410010, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha 410010, China
| | - Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha 410010, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha 410010, China
| | - Xiaolei Ren
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha 410010, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha 410010, China
| | - Wenchao Zhang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha 410010, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha 410010, China
| | - Chenbei Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha 410010, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha 410010, China
| | - Zhongyue Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha 410010, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha 410010, China
| | - Chao Tu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha 410010, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha 410010, China
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha 410010, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha 410010, China
- Correspondence:
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Wang Y, Li Q, Wang S, Wang BJ, Jin Y, Hu H, Fu QS, Wang JW, Wu Q, Qian L, Cao TT, Xia YB, Huang XX, Xu L. The role of noncoding RNAs in cancer lipid metabolism. Front Oncol 2022; 12:1026257. [PMID: 36452489 PMCID: PMC9704363 DOI: 10.3389/fonc.2022.1026257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/20/2022] [Indexed: 12/03/2023] Open
Abstract
Research on noncoding ribonucleic acids (ncRNAs) is mostly and broadly focused on microRNAs (miRNAs), cyclic RNAs (circRNAs), and long ncRNAs (lncRNAs), which have been confirmed to play important roles in tumor cell proliferation, invasion, and migration. Specifically, recent studies have shown that ncRNAs contribute to tumorigenesis and tumor development by mediating changes in enzymes related to lipid metabolism. The purpose of this review is to discuss the characterized ncRNAs involved in the lipid metabolism of tumors to highlight ncRNA-mediated lipid metabolism-related enzyme expression in malignant tumors and its importance to tumor development. In this review, we describe the types of ncRNA and the mechanism of tumor lipid metabolism and analyze the important role of ncRNA in tumor lipid metabolism and its future prospects from the perspectives of ncRNA biological function and lipid metabolic enzyme classification. However, several critical issues still need to be resolved. Because ncRNAs can affect tumor processes by regulating lipid metabolism enzymes, in the future, we can study the unique role of ncRNAs from four aspects: disease prevention, detection, diagnosis, and treatment. Therefore, in the future, the development of ncRNA-targeted therapy will become a hot direction and shoulder a major task in the medical field.
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Affiliation(s)
- Ye Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Qian Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Song Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Bi-jun Wang
- Department of Clinical Medicine, Clinical College of Anhui Medical University, Hefei, Anhui, China
| | - Yan Jin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Hao Hu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Qing-sheng Fu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Jia-wei Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Qing Wu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Long Qian
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Ting-ting Cao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Ya-bin Xia
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Xiao-xu Huang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
| | - Li Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wuhu, Anhui, China
- Non-coding RNA Research Center of Wannan Medical College, Yijishan Hospital, Wuhu, Anhui, China
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Analyses of circRNA Expression throughout the Light-Dark Cycle Reveal a Strong Regulation of Cdr1as, Associated with Light Entrainment in the SCN. Int J Mol Sci 2022; 23:ijms232012347. [PMID: 36293208 PMCID: PMC9604060 DOI: 10.3390/ijms232012347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
Circular RNAs (circRNAs) are a large class of relatively stable RNA molecules that are highly expressed in animal brains. Many circRNAs have been associated with CNS disorders accompanied by an aberrant wake-sleep cycle. However, the regulation of circRNAs in brain homeostasis over daily light-dark (LD) cycles has not been characterized. Here, we aim to quantify the daily expression changes of circRNAs in physiological conditions in healthy adult animals. Using newly generated and public RNA-Seq data, we monitored circRNA expression throughout the 12:12 h LD cycle in various mouse brain regions. We identified that Cdr1as, a conserved circRNA that regulates synaptic transmission, is highly expressed in the suprachiasmatic nucleus (SCN), the master circadian pacemaker. Despite its high stability, Cdr1as has a very dynamic expression in the SCN throughout the LD cycle, as well as a significant regulation in the hippocampus following the entry into the dark phase. Computational integration of different public datasets predicted that Cdr1as is important for regulating light entrainment in the SCN. We hypothesize that the expression changes of Cdr1as in the SCN, particularly during the dark phase, are associated with light-induced phase shifts. Importantly, our work revises the current beliefs about natural circRNA stability and suggests that the time component must be considered when studying circRNA regulation.
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69
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Abstract
Covalently closed, single-stranded circular RNAs can be produced from viral RNA genomes as well as from the processing of cellular housekeeping noncoding RNAs and precursor messenger RNAs. Recent transcriptomic studies have surprisingly uncovered that many protein-coding genes can be subjected to backsplicing, leading to widespread expression of a specific type of circular RNAs (circRNAs) in eukaryotic cells. Here, we discuss experimental strategies used to discover and characterize diverse circRNAs at both the genome and individual gene scales. We further highlight the current understanding of how circRNAs are generated and how the mature transcripts function. Some circRNAs act as noncoding RNAs to impact gene regulation by serving as decoys or competitors for microRNAs and proteins. Others form extensive networks of ribonucleoprotein complexes or encode functional peptides that are translated in response to certain cellular stresses. Overall, circRNAs have emerged as an important class of RNAmolecules in gene expression regulation that impact many physiological processes, including early development, immune responses, neurogenesis, and tumorigenesis.
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Affiliation(s)
- Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China;
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas, USA;
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China;
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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Seeler S, Moldovan LI, Bertelsen T, Hager H, Iversen L, Johansen C, Kjems J, Sommer Kristensen L. Global circRNA expression changes predate clinical and histological improvements of psoriasis patients upon secukinumab treatment. PLoS One 2022; 17:e0275219. [PMID: 36174034 PMCID: PMC9522259 DOI: 10.1371/journal.pone.0275219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022] Open
Abstract
Psoriasis is a common chronic inflammatory skin disease accompanied by heterogenous clinical and histological features, including a characteristic keratinocyte hyperproliferation and dermal immunogenic profile. In addition, psoriasis is associated with widespread transcriptomic alterations including changes in microRNA (miRNA) and circular RNA (circRNA) abundance, which constitute non-coding RNA (ncRNA) classes with specific regulatory capacities in diverse physiological and pathological processes. However, the knowledge about the expression dynamics of ncRNA during psoriasis treatment is sparse. To elucidate the dynamics of miRNA and circRNA abundance during secukinumab (anti-IL-17A) treatment, we studied their expression patterns in skin biopsies from 14 patients with severe plaque-type psoriasis before and during an 84-day secukinumab therapy at day 0, 4, 14, 42, and 84 using NanoString nCounter technology. We found a comprehensive downregulation of the majority of investigated circRNAs and specific alterations in the miRNA profile, including an upregulation of miR-203a-3p, miR-93-5p, and miR-378i in lesional compared to non-lesional skin before treatment. During treatment, the circRNAs progressively returned to the expression levels observed in non-lesional skin and already four days after treatment initiation most circRNAs were significantly upregulated. In comparison, for miRNAs, the normalization to baseline during treatment was delayed and limited to a subset of miRNAs. Moreover, we observed a strong correlation between multiple circRNAs, including ciRS-7 and circPTPRA, and the psoriasis area and severity index (PASI). Similar pronounced correlations could, however, not be found for miRNAs. Finally, we did not observe any significant changes in circRNA expression in peripheral blood mononuclear cells during treatment. In conclusion, we uncovered a rapid shift in global circRNA abundance upon anti-IL-17A treatment, which predated clinical and histological improvements, and a strong correlation with PASI, indicating a biomarker potential of individual circRNAs.
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Affiliation(s)
- Sabine Seeler
- Faculty of Health, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Liviu-Ionut Moldovan
- Faculty of Health, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Trine Bertelsen
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Hager
- Department of Clinical Pathology, Vejle Hospital, Vejle, Denmark
| | - Lars Iversen
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - Claus Johansen
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
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Yang E, Huang S, Jami-Alahmadi Y, McInerney GM, Wohlschlegel JA, Li MMH. Elucidation of TRIM25 ubiquitination targets involved in diverse cellular and antiviral processes. PLoS Pathog 2022; 18:e1010743. [PMID: 36067236 PMCID: PMC9481182 DOI: 10.1371/journal.ppat.1010743] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/16/2022] [Accepted: 07/15/2022] [Indexed: 11/19/2022] Open
Abstract
The tripartite motif (TRIM) family of E3 ubiquitin ligases is well known for its roles in antiviral restriction and innate immunity regulation, in addition to many other cellular pathways. In particular, TRIM25-mediated ubiquitination affects both carcinogenesis and antiviral response. While individual substrates have been identified for TRIM25, it remains unclear how it regulates diverse processes. Here we characterized a mutation, R54P, critical for TRIM25 catalytic activity, which we successfully utilized to "trap" substrates. We demonstrated that TRIM25 targets proteins implicated in stress granule formation (G3BP1/2), nonsense-mediated mRNA decay (UPF1), nucleoside synthesis (NME1), and mRNA translation and stability (PABPC4). The R54P mutation abolishes TRIM25 inhibition of alphaviruses independently of the host interferon response, suggesting that this antiviral effect is a direct consequence of ubiquitination. Consistent with that, we observed diminished antiviral activity upon knockdown of several TRIM25-R54P specific interactors including NME1 and PABPC4. Our findings highlight that multiple substrates mediate the cellular and antiviral activities of TRIM25, illustrating the multi-faceted role of this ubiquitination network in modulating diverse biological processes.
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Affiliation(s)
- Emily Yang
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Serina Huang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Gerald M. McInerney
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Melody M. H. Li
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
- AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail:
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Neyret A, Bernard E, Aïqui-Reboul-Paviet O, Bakhache W, Eldin P, Chaloin L, Briant L. Identification of a non-canonical G3BP-binding sequence in a Mayaro virus nsP3 hypervariable domain. Front Cell Infect Microbiol 2022; 12:958176. [PMID: 36034716 PMCID: PMC9403187 DOI: 10.3389/fcimb.2022.958176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022] Open
Abstract
Ras-GTPase-activating SH3 domain-binding-proteins 1 (G3BP1) and 2 (G3BP2) are multifunctional RNA-binding proteins involved in stress granule nucleation, previously identified as essential cofactors of Old World alphaviruses. They are recruited to viral replication complexes formed by the Chikungunya virus (CHIKV), Semliki Forest virus (SFV), and Sindbis virus (SINV) via an interaction with a duplicated FGxF motif conserved in the hypervariable domain (HVD) of virus-encoded nsP3. According to mutagenesis studies, this FGxF duplication is strictly required for G3BP binding and optimal viral growth. Contrasting with this scenario, nsP3 encoded by Mayaro virus (MAYV), an arthritogenic virus grouped with Old World alphaviruses, contains a single canonical FGxF sequence. In light of this unusual feature, we questioned MAYV nsP3/G3BPs relationships. We report that G3BP1 and G3BP2 are both required for MAYV growth in human cells and bind nsP3 protein. In infected cells, they are recruited to nsP3-containing cytosolic foci and active replication complexes. Unexpectedly, deletion of the single FGxF sequence in MAYV nsP3 did not abolish these phenotypes. Using mutagenesis and in silico modeling, we identify an upstream FGAP amino acid sequence as an additional MAYV nsP3/G3BP interaction motif required for optimal viral infectivity. These results, therefore, highlight a non-conventional G3BP binding sequence in MAYV nsP3.
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73
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Hu X, Zou Q, Yao L, Yang X. Survey of the binding preferences of RNA-binding proteins to RNA editing events. Genome Biol 2022; 23:169. [PMID: 35927743 PMCID: PMC9351184 DOI: 10.1186/s13059-022-02741-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/27/2022] [Indexed: 11/20/2022] Open
Abstract
Background Adenosine-to-inosine (A-to-I) editing is an important RNA posttranscriptional process related to a multitude of cellular and molecular activities. However, systematic characterizations of whether and how the events of RNA editing are associated with the binding preferences of RNA sequences to RNA-binding proteins (RBPs) are still lacking. Results With the RNA-seq and RBP eCLIP-seq datasets from the ENCODE project, we quantitatively survey the binding preferences of 150 RBPs to RNA editing events, followed by experimental validations. Such analyses of the RBP-associated RNA editing at nucleotide resolution and genome-wide scale shed light on the involvement of RBPs specifically in RNA editing-related processes, such as RNA splicing, RNA secondary structures, RNA decay, and other posttranscriptional processes. Conclusions These results highlight the relevance of RNA editing in the functions of many RBPs and therefore serve as a resource for further characterization of the functional associations between various RNA editing events and RBPs. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02741-8.
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Affiliation(s)
- Xiaolin Hu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Qin Zou
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Li Yao
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.
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74
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Yao X, Zhang Q. Function and Clinical Significance of Circular RNAs in Thyroid Cancer. Front Mol Biosci 2022; 9:925389. [PMID: 35936780 PMCID: PMC9353217 DOI: 10.3389/fmolb.2022.925389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/22/2022] [Indexed: 12/28/2022] Open
Abstract
Thyroid cancer (TC) is the leading cause and mortality of endocrine malignancies worldwide. Tumourigenesis involves multiple molecules including circular RNAs (circRNAs). circRNAs with covalently closed single-stranded structures have been identified as a type of regulatory RNA because of their high stability, abundance, and tissue/developmental stage-specific expression. Accumulating evidence has demonstrated that various circRNAs are aberrantly expressed in thyroid tissues, cells, exosomes, and body fluids in patients with TC. CircRNAs have been identified as either oncogenic or tumour suppressor roles in regulating tumourigenesis, tumour metabolism, metastasis, ferroptosis, and chemoradiation resistance in TC. Importantly, circRNAs exert pivotal effects on TC through various mechanisms, including acting as miRNA sponges or decoys, interacting with RNA-binding proteins, and translating functional peptides. Recent studies have suggested that many different circRNAs are associated with certain clinicopathological features, implying that the altered expression of circRNAs may be characteristic of TC. The purpose of this review is to provide an overview of recent advances on the dysregulation, functions, molecular mechanisms and potential clinical applications of circRNAs in TC. This review also aimes to improve our understanding of the functions of circRNAs in the initiation and progression of cancer, and to discuss the future perspectives on strategies targeting circRNAs in TC.
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75
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The G3BP1-UPF1-Associated Long Non-Coding RNA CALA Regulates RNA Turnover in the Cytoplasm. Noncoding RNA 2022; 8:ncrna8040049. [PMID: 35893232 PMCID: PMC9326601 DOI: 10.3390/ncrna8040049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/10/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022] Open
Abstract
Besides transcription, RNA decay accounts for a large proportion of regulated gene expression and is paramount for cellular functions. Classical RNA surveillance pathways, like nonsense-mediated decay (NMD), are also implicated in the turnover of non-mutant transcripts. Whereas numerous protein factors have been assigned to distinct RNA decay pathways, the contribution of long non-coding RNAs (lncRNAs) to RNA turnover remains unknown. Here we identify the lncRNA CALA as a potent regulator of RNA turnover in endothelial cells. We demonstrate that CALA forms cytoplasmic ribonucleoprotein complexes with G3BP1 and regulates endothelial cell functions. A detailed characterization of these G3BP1-positive complexes by mass spectrometry identifies UPF1 and numerous other NMD factors having cytoplasmic G3BP1-association that is CALA-dependent. Importantly, CALA silencing impairs degradation of NMD target transcripts, establishing CALA as a non-coding regulator of RNA steady-state levels in the endothelium.
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76
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Comparison of Selenium-Enriched Lactobacillusparacasei, Selenium-Enriched Yeast, and Selenite for the Alleviation of DSS-Induced Colitis in Mice. Nutrients 2022; 14:nu14122433. [PMID: 35745163 PMCID: PMC9231187 DOI: 10.3390/nu14122433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023] Open
Abstract
Patients with inflammatory bowel disease (IBD) have been found to have decreased immune function. Selenium (Se) is an essential trace element that is beneficial for human health, which has a significant stimulating effect on immune function. We compared the effects of different Se forms on the alleviation of colitis in DSS-induced mice. Moreover, we also aimed to determine whether Se-enriched Lactobacillus paracasei CCFM 1089 could be used as a new organic Se supplement. Different Se supplements (Se-enriched L. paracasei CCFM 1089, Se-enriched yeast and sodium selenite) were given to Se-deficient mice suffering from colitis. Se-enriched L. paracasei CCFM 1089, which is based on selenocysteine (SeCys), had similar effects in terms of reducing oxidative stress and inhibiting pro-inflammatory factors to Se-enriched yeast; however, selenase activity in the Se-enriched L. paracasei CCFM 1089-treated mice was higher than that in other treatment groups. In addition, Se-enriched L. paracasei CCFM 1089 could better protect the intestinal mucosa, which increased the expression of tight junction proteins (ZO-1 and occludin) in mice. Thus Se-enriched L. paracasei CCFM 1089 was shown to alleviate IBD, suggesting that it has potential as a good organic Se supplement.
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77
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Qi L, Xu R, Ren X, Zhang W, Yang Z, Tu C, Li Z. Comprehensive Profiling Reveals Prognostic and Immunogenic Characteristics of Necroptosis in Soft Tissue Sarcomas. Front Immunol 2022; 13:877815. [PMID: 35663937 PMCID: PMC9159500 DOI: 10.3389/fimmu.2022.877815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/14/2022] [Indexed: 12/31/2022] Open
Abstract
Soft tissue sarcomas (STSs) are heterogeneous malignancies derived from mesenchymal cells. Due to its rarity, heterogeneity, and limited overall response to chemotherapy, STSs represent a therapeutic challenge. Necroptosis is a novel therapeutic strategy for enhancing immunotherapy of cancer. Nevertheless, no research has explored the relationship between necroptosis-related genes (NRGs) and STSs. In this study, differentially expressed NRGs were identified using The Cancer Genome Atlas (TCGA) and The Cancer Genotype-Tissue Expression (GTEx) project. The expression levels of 34 NRGs were significantly different. Several key NRGs were validated using RT-qPCR and our own sequencing data. Patients with STSs were divided into two clusters using consensus cluster analysis, and significant differences were observed in their survival (p=0.002). We found the differentially expressed genes (DEGs) between the two clusters and carried out subsequent analysis. The necroptosis-related gene signatures with 10 key DEGs were identified with a risk score constructed. The prognosis of TCGA-SARC cohort with low necroptosis-related risk score was better (p<0.001). Meanwhile, the low-risk group had a significantly increased immune infiltration. Using the data of GSE17118 and another immunotherapy cohort as external validations, we observed significant survival differences between the two risk groups (p=0.019). The necroptosis-related risk score proved to be an independent prognostic factor, and a nomogram was further established and integrated with other clinical features. Notably, the necroptosis-related gene signature could also act as the prognostic indicator in other malignancies based on pan-cancer analysis. In summary, the study outlines NRGs in STSs and their potential role in prognosis and will be one of the important directions for future research.
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Affiliation(s)
- Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Ruiling Xu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Xiaolei Ren
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Wenchao Zhang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Zhimin Yang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China.,Department of Microbiology, Immunology & Molecular Genetics, UT Health Science Center, University of Texas Long School of Medicine, San Antonio, TX, United States
| | - Chao Tu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
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78
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Peinado JR, Chaplot K, Jarvela TS, Barbieri EM, Shorter J, Lindberg I. Sequestration of TDP-43 216-414 Aggregates by Cytoplasmic Expression of the proSAAS Chaperone. ACS Chem Neurosci 2022; 13:1651-1665. [PMID: 35549000 PMCID: PMC9731516 DOI: 10.1021/acschemneuro.2c00156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
As neurons age, protein homeostasis becomes less efficient, resulting in misfolding and aggregation. Chaperone proteins perform vital functions in the maintenance of cellular proteostasis, and chaperone-based therapies that promote sequestration of toxic aggregates may prove useful in blocking the development of neurodegenerative disease. We previously demonstrated that proSAAS, a small secreted neuronal protein, exhibits potent chaperone activity against protein aggregation in vitro and blocks the cytotoxic effects of amyloid and synuclein oligomers in cell culture systems. We now examine whether cytoplasmic expression of proSAAS results in interactions with protein aggregates in this cellular compartment. We report that expression of proSAAS within the cytoplasm generates dense, membraneless 2 μm proSAAS spheres which progressively fuse to form larger spheres, suggesting liquid droplet-like properties. ProSAAS spheres selectively accumulate a C-terminally truncated fluorescently tagged form of TDP-43, initiating its cellular redistribution; these TDP-43-containing spheres also exhibit dynamic fusion. Efficient encapsulation of TDP-43 into proSAAS spheres is driven by its C-terminal prion-like domain; spheres must be formed for sequestration to occur. Three proSAAS sequences, a predicted coiled-coil, a conserved region (residues 158-169), and the positively charged sequence 181-185, are all required for proSAAS to form spheres able to encapsulate TDP-43 aggregates. Substitution of lysines for arginines in the 181-185 sequence results in nuclear translocation of proSAAS and encapsulation of nuclear-localized TDP-43216-414. As a functional output, we demonstrate that proSAAS expression results in cytoprotection against full-length TDP-43 toxicity in yeast. We conclude that proSAAS can act as a functional holdase for TDP-43 via this phase-separation property, representing a cytoprotectant whose unusual biochemical properties can potentially be exploited in the design of therapeutic molecules.
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Affiliation(s)
- Juan R. Peinado
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201 USA
| | - Kriti Chaplot
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201 USA
| | - Timothy S. Jarvela
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201 USA
| | - Edward M. Barbieri
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201 USA
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79
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Guvenek A, Shin J, De Filippis L, Zheng D, Wang W, Pang ZP, Tian B. Neuronal Cells Display Distinct Stability Controls of Alternative Polyadenylation mRNA Isoforms, Long Non-Coding RNAs, and Mitochondrial RNAs. Front Genet 2022; 13:840369. [PMID: 35664307 PMCID: PMC9159357 DOI: 10.3389/fgene.2022.840369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/28/2022] [Indexed: 11/25/2022] Open
Abstract
RNA stability plays an important role in gene expression. Here, using 3' end sequencing of newly made and pre-existing poly(A)+ RNAs, we compare transcript stability in multiple human cell lines, including HEK293T, HepG2, and SH-SY5Y. We show that while mRNA stability is generally conserved across the cell lines, specific transcripts having a high GC content and possibly more stable secondary RNA structures are relatively more stable in SH-SY5Y cells compared to the other 2 cell lines. These features also differentiate stability levels of alternative polyadenylation (APA) 3'UTR isoforms in a cell type-specific manner. Using differentiation of a neural stem cell line as a model, we show that mRNA stability difference could contribute to gene expression changes in neurogenesis and confirm the neuronal identity of SH-SY5Y cells at both gene expression and APA levels. In addition, compared to transcripts using 3'-most exon cleavage/polyadenylation sites (PASs), those using intronic PASs are generally less stable, especially when the PAS-containing intron is large and has a strong 5' splice site, suggesting that intronic polyadenylation mostly plays a negative role in gene expression. Interestingly, the differential mRNA stability among APA isoforms appears to buffer PAS choice in these cell lines. Moreover, we found that several other poly(A)+ RNA species, including promoter-associated long noncoding RNAs and transcripts encoded by the mitochondrial genome, are more stable in SH-SY5Y cells than the other 2 cell lines, further highlighting distinct RNA metabolism in neuronal cells. Together, our results indicate that distinct RNA stability control in neuronal cells may contribute to the gene expression and APA programs that define their cell identity.
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Affiliation(s)
- Aysegul Guvenek
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, United States
- Rutgers School of Graduate Studies, Newark, NJ, United States
| | - Jihae Shin
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Lidia De Filippis
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Wei Wang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Zhiping P. Pang
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, United States
- Program in Gene Expression and Regulation, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, United States
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80
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Leeder WM, Geyer FK, Göringer HU. Fuzzy RNA recognition by the Trypanosoma brucei editosome. Nucleic Acids Res 2022; 50:5818-5833. [PMID: 35580050 PMCID: PMC9178004 DOI: 10.1093/nar/gkac357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
The assembly of high molecular mass ribonucleoprotein complexes typically relies on the binary interaction of defined RNA sequences or precisely folded RNA motifs with dedicated RNA-binding domains on the protein side. Here we describe a new molecular recognition principle of RNA molecules by a high molecular mass protein complex. By chemically probing the solvent accessibility of mitochondrial pre-mRNAs when bound to the Trypanosoma brucei editosome, we identified multiple similar but non-identical RNA motifs as editosome contact sites. However, by treating the different motifs as mathematical graph objects we demonstrate that they fit a consensus 2D-graph consisting of 4 vertices (V) and 3 edges (E) with a Laplacian eigenvalue of 0.5477 (λ2). We establish that synthetic 4V(3E)-RNAs are sufficient to compete for the editosomal pre-mRNA binding site and that they inhibit RNA editing in vitro. Furthermore, we demonstrate that only two topological indices are necessary to predict the binding of any RNA motif to the editosome with a high level of confidence. Our analysis corroborates that the editosome has adapted to the structural multiplicity of the mitochondrial mRNA folding space by recognizing a fuzzy continuum of RNA folds that fit a consensus graph descriptor.
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Affiliation(s)
| | - Felix Klaus Geyer
- Molecular Genetics, Technical University Darmstadt, 64287 Darmstadt, Germany
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81
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Ge Y, Jin J, Li J, Ye M, Jin X. The roles of G3BP1 in human diseases (review). Gene X 2022; 821:146294. [PMID: 35176431 DOI: 10.1016/j.gene.2022.146294] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/24/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022] Open
Abstract
Ras-GTPase-activating protein binding protein 1 (G3BP1) is a multifunctional binding protein involved in a variety of biological functions, including cell proliferation, metastasis, apoptosis, differentiation and RNA metabolism. It has been revealed that G3BP1, as an antiviral factor, can interact with viral proteins and regulate the assembly of stress granules (SGs), which can inhibit viral replication. Furthermore, several viruses have the ability to hijack G3BP1 as a cofactor, recruiting translation initiation factors to promote viral proliferation. However, many functions of G3BP1 are associated with other diseases. In various cancers, G3BP1 is a cancer-promoting factor, which can promote the proliferation, invasion and metastasis of cancer cells. Moreover, compared with normal tissues, G3BP1 expression is higher in tumor tissues, indicating that it can be used as an indicator for cancer diagnosis. In this review, the structure of G3BP1 and the regulation of G3BP1 in multiple dimensions are described. In addition, the effects and potential mechanisms of G3BP1 on various carcinomas, viral infections, nervous system diseases and cardiovascular diseases are elucidated, which may provide a direction for clinical applications of G3BP1 in the future.
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Affiliation(s)
- Yidong Ge
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Jiabei Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Jinyun Li
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
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82
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Kristensen LS, Jakobsen T, Hager H, Kjems J. The emerging roles of circRNAs in cancer and oncology. Nat Rev Clin Oncol 2022; 19:188-206. [PMID: 34912049 DOI: 10.1038/s41571-021-00585-y] [Citation(s) in RCA: 395] [Impact Index Per Article: 197.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
Over the past decade, circular RNAs (circRNAs) have emerged as a large class of primarily non-coding RNA molecules, many of which have key roles in cancer development and progression through diverse mechanisms of action. CircRNAs often have tissue-restricted and cancer-specific expression patterns, and accumulating data suggest that these molecules are of potential clinical relevance and utility. In particular, circRNAs have strong potential as diagnostic, prognostic and predictive biomarkers, which is underscored by their detectability in liquid biopsy samples such as in plasma, saliva and urine. However, technical issues in the detection and assessment of circRNAs as well as biological knowledge gaps need to be addressed to move this relatively young field of research forward and bring circRNAs to the forefront of clinical practice. Herein, we review the current knowledge regarding circRNA biogenesis, regulation and functions in cancer as well as their clinical potential as biomarkers, therapeutic agents and drug targets.
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Affiliation(s)
| | | | - Henrik Hager
- Department of Clinical Pathology, Vejle Hospital, Vejle, Denmark.,Danish Colorectal Cancer Center South, Vejle Hospital, Vejle, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus C, Denmark. .,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark.
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83
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Chen X, Zhou M, Yant L, Huang C. Circular RNA in disease: Basic properties and biomedical relevance. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1723. [PMID: 35194939 DOI: 10.1002/wrna.1723] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 12/26/2022]
Abstract
Circular RNAs (circRNAs) represent a class of covalently closed RNA molecules with great diversity in molecular features, functions, and regulatory mechanisms. Emerging advances in our understanding of circRNA biogenesis, nuclear export, and stability control have been made very recently. In particular, novel roles of circRNAs in diverse human diseases are increasingly recognized. Various circRNAs have been found to affect many disease-relevant pathways through a diverse array of mechanisms, including forming R-loops, sponging miRNAs or proteins, and translating functional proteins, resulting in different pathological phenotypes. This recent progress calls for a revised view of circRNAs in diseases threatening the lives and health of humans. In this review, we focus on the recently described functional relevance of disease-associated circRNAs as well as the potential of circRNAs in diverse clinical applications. This article is categorized under: RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Xiaolan Chen
- School of Life Sciences, Chongqing University, Chongqing, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Min Zhou
- School of Life Sciences, Chongqing University, Chongqing, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Levi Yant
- Future Food Beacon of Excellence and School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
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Yarmishyn AA, Ishola AA, Chen CY, Verusingam ND, Rengganaten V, Mustapha HA, Chuang HK, Teng YC, Phung VL, Hsu PK, Lin WC, Ma HI, Chiou SH, Wang ML. Circular RNAs Modulate Cancer Hallmark and Molecular Pathways to Support Cancer Progression and Metastasis. Cancers (Basel) 2022; 14:cancers14040862. [PMID: 35205610 PMCID: PMC8869994 DOI: 10.3390/cancers14040862] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/22/2022] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Circular RNAs (circRNA) are a type of RNA molecule of circular shape that are now being extensively studied due to the important roles they play in different biological processes. In addition, they were also shown to be implicated in disease such as cancer. Cancer is a complex process which is often defined by a combination of specific processes called cancer hallmarks. In this review, we summarize the literature on circRNAs in cancer and classify them as being implicated in specific cancer hallmarks. Abstract Circular RNAs (circRNAs) are noncoding products of backsplicing of pre-mRNAs which have been established to possess potent biological functions. Dysregulated circRNA expression has been linked to diseases including different types of cancer. Cancer progression is known to result from the dysregulation of several molecular mechanisms responsible for the maintenance of cellular and tissue homeostasis. The dysregulation of these processes is defined as cancer hallmarks, and the molecular pathways implicated in them are regarded as the targets of therapeutic interference. In this review, we summarize the literature on the investigation of circRNAs implicated in cancer hallmark molecular signaling. First, we present general information on the properties of circRNAs, such as their biogenesis and degradation mechanisms, as well as their basic molecular functions. Subsequently, we summarize the roles of circRNAs in the framework of each cancer hallmark and finally discuss the potential as therapeutic targets.
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Affiliation(s)
- Aliaksandr A. Yarmishyn
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
| | - Afeez Adekunle Ishola
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan
| | - Chieh-Yu Chen
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan
| | - Nalini Devi Verusingam
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Centre for Stem Cell Research, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
| | - Vimalan Rengganaten
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Postgraduate Programme, Department of Preclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
| | - Habeebat Aderonke Mustapha
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Hao-Kai Chuang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
| | - Yuan-Chi Teng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
| | - Van Long Phung
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Po-Kuei Hsu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan;
| | - Hsin-I Ma
- Department of Neurological Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan;
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Genomic Research Center, Academia Sinica, Taipei 112, Taiwan
| | - Mong-Lien Wang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Institute of Food Safety and Health Risk Assessment, School of Pharmaceutical Sciences, National Yang-Ming Chiao Tung University, Taipei 112, Taiwan
- Correspondence: ; Tel.: +886-2-5568-1156; Fax: +886-2-2875-7435
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Zhao X, Dong R, Zhang L, Guo J, Shi Y, Ge L, Wang J, Song Z, Ni B, You Y. N6-methyladenosine-dependent modification of circGARS acts as a new player that promotes SLE progression through the NF-κB/A20 axis. Arthritis Res Ther 2022; 24:37. [PMID: 35120571 PMCID: PMC8815128 DOI: 10.1186/s13075-022-02732-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
Background Certain circRNAs could be used as biomarkers to determine the risk of development and/or severity of systemic lupus erythematosus, and their new function in the regulation of gene expression has motivated us to investigate their role in SLE Methods Experimental methods including qRT-PCR, RNA immunoprecipitation (RIP), pulldown, dual luciferase reporter assay, RNA interference and cell transfection, RNA fluorescence in situ hybridization, western blotting, and mass spectrometry were used to assessed circGARS (hsa_circRNA_0009000) for immune functions and defined mechanisms by which circGARS promotes the progression in SLE. Results Our results demonstrated that the levels of circGARS was remarkably upregulated in SLE and correlated with clinicopathological features. CircGARS directly combined with microRNA-19a (miR-19a). Functionally, circGARS downregulated the expression of TNFAIP3 (A20, tumor necrosis factor alpha-induced protein 3) to mediate the activation of immune responses that were regulated by the nuclear factor-κB (NF-κB) pathway as a negative feedback mechanism. In addition, miR-19a regulated A20 (TNFAIP3) degradation by downregulating the expression of YTH N6-methyladenosine RNA-binding protein 2 (YTHDF2). Conclusions The circGARS sponges miR-19a to regulate YTHDF2 expression to promote SLE progression through the A20/NF-κB axis and may act as an independent biomarker to help the treatment of SLE patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-022-02732-x.
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Affiliation(s)
- Xingwang Zhao
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Rui Dong
- Chongqing International Institute for Immunology, Chongqing, China
| | - Longlong Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Science, Yunnan University, Kunming, China
| | - Junkai Guo
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Ying Shi
- Department of Traditional Chinese Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lan Ge
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Juan Wang
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhiqiang Song
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Bing Ni
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University (Third Military Medical University), Chongqing, China.
| | - Yi You
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China.
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86
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Nicolet BP, Jansen SBG, Heideveld E, Ouwehand WH, van den Akker E, von Lindern M, Wolkers MC. Circular RNAs exhibit limited evidence for translation, or translation regulation of the mRNA counterpart in terminal hematopoiesis. RNA (NEW YORK, N.Y.) 2022; 28:194-209. [PMID: 34732567 PMCID: PMC8906552 DOI: 10.1261/rna.078754.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Each day, about 1012 erythrocytes and platelets are released into the bloodstream. This substantial output from hematopoietic stem cells is tightly regulated by transcriptional and epigenetic factors. Whether and how circular RNAs (circRNAs) contribute to the differentiation and/or identity of hematopoietic cells is to date not known. We recently reported that erythrocytes and platelets contain the highest levels and numbers of circRNAs among hematopoietic cells. Here, we provide the first detailed analysis of circRNA expression during erythroid and megakaryoid differentiation. CircRNA expression not only significantly increased upon enucleation, but also had limited overlap between progenitor cells and mature cells, suggesting that circRNA expression stems from regulated processes rather than resulting from mere accumulation. To study circRNA function in hematopoiesis, we first compared the expression levels of circRNAs with the translation efficiency of their mRNA counterpart. We found that only one out of 2531 (0.04%) circRNAs associated with mRNA-translation regulation. Furthermore, irrespective of thousands of identified putative open reading frames, deep ribosome-footprinting sequencing, and mass spectrometry analysis provided little evidence for translation of endogenously expressed circRNAs. In conclusion, circRNAs alter their expression profile during terminal hematopoietic differentiation, yet their contribution to regulate cellular processes remains enigmatic.
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Affiliation(s)
- Benoit P Nicolet
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066CX Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Sjoert B G Jansen
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge CB2 0AW, United Kingdom
| | - Esther Heideveld
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066CX Amsterdam, The Netherlands
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge CB2 0AW, United Kingdom
| | - Emile van den Akker
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066CX Amsterdam, The Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066CX Amsterdam, The Netherlands
| | - Monika C Wolkers
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066CX Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
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87
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Della Bella E, Koch J, Baerenfaller K. Translation and emerging functions of non-coding RNAs in inflammation and immunity. Allergy 2022; 77:2025-2037. [PMID: 35094406 PMCID: PMC9302665 DOI: 10.1111/all.15234] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Regulatory non‐coding RNAs (ncRNAs) including small non‐coding RNAs (sRNAs), long non‐coding RNAs (lncRNAs), and circular RNAs (circRNAs) have gained considerable attention in the last few years. This is mainly due to their condition‐ and tissue‐specific expression and their various modes of action, which suggests them as promising biomarkers and therapeutic targets. One important mechanism of ncRNAs to regulate gene expression is through translation of short open reading frames (sORFs). These sORFs can be located in lncRNAs, in non‐translated regions of mRNAs where upstream ORFs (uORFs) represent the majority, or in circRNAs. Regulation of their translation can function as a quick way to adapt protein production to changing cellular or environmental cues, and can either depend solely on the initiation and elongation of translation, or on the roles of the produced functional peptides. Due to the experimental challenges to pinpoint translation events and to detect the produced peptides, translational regulation through regulatory RNAs is not well studied yet. In the case of circRNAs, they have only recently started to be recognized as regulatory molecules instead of mere artifacts of RNA biosynthesis. Of the many roles described for regulatory ncRNAs, we will focus here on their regulation during inflammation and in immunity.
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Affiliation(s)
| | - Jana Koch
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Swiss Institute of Bioinformatics (SIB) Davos Switzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Swiss Institute of Bioinformatics (SIB) Davos Switzerland
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88
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Insights into the multifaceted role of circular RNAs: implications for Parkinson's disease pathogenesis and diagnosis. NPJ Parkinsons Dis 2022; 8:7. [PMID: 35013342 PMCID: PMC8748951 DOI: 10.1038/s41531-021-00265-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
Parkinson's disease (PD) is a complex, age-related, neurodegenerative disease whose etiology, pathology, and clinical manifestations remain incompletely understood. As a result, care focuses primarily on symptoms relief. Circular RNAs (circRNAs) are a large class of mostly noncoding RNAs that accumulate with aging in the brain and are increasingly shown to regulate all aspects of neuronal and glial development and function. They are generated by the spliceosome through the backsplicing of linear RNA. Although their biological role remains largely unknown, they have been shown to regulate transcription and splicing, act as decoys for microRNAs and RNA binding proteins, used as templates for translation, and serve as scaffolding platforms for signaling components. Considering that they are stable, diverse, and detectable in easily accessible biofluids, they are deemed promising biomarkers for diagnosing diseases. CircRNAs are differentially expressed in the brain of patients with PD, and growing evidence suggests that they regulate PD pathogenetic processes. Here, the biogenesis, expression, degradation, and detection of circRNAs, as well as their proposed functions, are reviewed. Thereafter, research linking circRNAs to PD-related processes, including aging, alpha-synuclein dysregulation, neuroinflammation, and oxidative stress is highlighted, followed by recent evidence for their use as prognostic and diagnostic biomarkers for PD.
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89
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Li M, Tang Y, Zuo X, Meng S, Yi P. Loss of Ras GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) inhibits the progression of ovarian cancer in coordination with ubiquitin-specific protease 10 (USP10). Bioengineered 2022; 13:721-734. [PMID: 34967276 PMCID: PMC8805976 DOI: 10.1080/21655979.2021.2012624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022] Open
Abstract
Ovarian cancer (OC) is one of the most lethal gynecological malignancies. However, the molecular mechanisms underlying the development of OC remain unclear. Here, we report that loss of Ras GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) inhibits the progression of OC cells. Analysis of databases and clinical specimens showed that G3BP1 is upregulated in OC. The Kaplan-Meier plot results showed that G3BP1 is highly expressed in OC with a poor clinical outcome. Moreover, loss-of-G3BP1 suppresses the proliferation, migration, and invasion of OC cells. Protein-protein interaction network analysis and immunoprecipitation assay showed that ubiquitin-specific protease 10 (USP10) interacts with G3BP1. We next found that USP10 coordinately promotes tumor progression with G3BP1. Moreover, loss of USP10could restore the G3BP1-induced proliferation, migration, and invasion of OC cells. These data indicate that G3BP1 coordinated with USP10 to facilitate the progression of OC cells, and that G3BP1 may become a treatment target for OC.
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Affiliation(s)
- Mengyuan Li
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Tang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinzhao Zuo
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Silin Meng
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
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90
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Iselin L, Palmalux N, Kamel W, Simmonds P, Mohammed S, Castello A. Uncovering viral RNA-host cell interactions on a proteome-wide scale. Trends Biochem Sci 2022; 47:23-38. [PMID: 34509361 PMCID: PMC9187521 DOI: 10.1016/j.tibs.2021.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/12/2021] [Accepted: 08/06/2021] [Indexed: 01/14/2023]
Abstract
RNA viruses interact with a wide range of cellular RNA-binding proteins (RBPs) during their life cycle. The prevalence of these host-virus interactions has been highlighted by new methods that elucidate the composition of viral ribonucleoproteins (vRNPs). Applied to 11 viruses so far, these approaches have revealed hundreds of cellular RBPs that interact with viral (v)RNA in infected cells. However, consistency across methods is limited, raising questions about methodological considerations when designing and interpreting these studies. Here, we discuss these caveats and, through comparing available vRNA interactomes, describe RBPs that are consistently identified as vRNP components and outline their potential roles in infection. In summary, these novel approaches have uncovered a new universe of host-virus interactions holding great therapeutic potential.
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Affiliation(s)
- Louisa Iselin
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK,Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Wael Kamel
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK,The Rosalind Franklin Institute, Oxfordshire, OX11 0FA, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK),Correspondence:
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91
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D'Ambra E, Santini T, Vitiello E, D'Uva S, Silenzi V, Morlando M, Bozzoni I. Circ-Hdgfrp3 shuttles along neurites and is trapped in aggregates formed by ALS-associated mutant FUS. iScience 2021; 24:103504. [PMID: 34934923 DOI: 10.1016/j.isci.2021.103504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/12/2021] [Accepted: 11/21/2021] [Indexed: 12/17/2022] Open
Abstract
CircRNAs belong to a family of RNA molecules which are conserved in evolution, have tissue-specific expression, and are abundant in neuronal cells. Here, we define several features of circ-Hdgfrp3 and describe interesting alterations occurring in motor neurons (MNs) carrying ALS-associated FUS mutations. Through a highly sensitive in situ approach we describe that circ-Hdgfrp3 traffics along neurites, while upon oxidative stress it is retained in the perinuclear region. While in wild-type stressed MNs, circ-Hdgfrp3 localizes in stress granules (SGs), in MNs carrying mutant FUS, a higher proportion of circ-Hdgfrp3 was trapped into cytoplasmic aggregates. Upon stress removal, circ-Hdgfrp3 was easily freed from SGs whereas it was less efficiently released from FUS-aggregates. We found that the human circ-Hdgfrp3 counterpart was also similarly associated to mutant FUS-aggregates in stressed neuronal cells. Overall, the alteration of circ-Hdgfrp3 trafficking adds a further layer of complexity to the role of FUS-aggregates in ALS disease.
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Affiliation(s)
- Eleonora D'Ambra
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Rome, Italy
| | - Erika Vitiello
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Human Technology@ Istituto Italiano di Tecnologia, Genova, Italy
| | - Sara D'Uva
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Valentina Silenzi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Perugia, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Rome, Italy
- Center for Human Technology@ Istituto Italiano di Tecnologia, Genova, Italy
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92
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Schneider-Lunitz V, Ruiz-Orera J, Hubner N, van Heesch S. Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes. PLoS Comput Biol 2021; 17:e1009658. [PMID: 34879078 PMCID: PMC8687540 DOI: 10.1371/journal.pcbi.1009658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/20/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) can regulate more than a single aspect of RNA metabolism. We searched for such previously undiscovered multifunctionality within a set of 143 RBPs, by defining the predictive value of RBP abundance for the transcription and translation levels of known RBP target genes across 80 human hearts. This led us to newly associate 27 RBPs with cardiac translational regulation in vivo. Of these, 21 impacted both RNA expression and translation, albeit for virtually independent sets of target genes. We highlight a subset of these, including G3BP1, PUM1, UCHL5, and DDX3X, where dual regulation is achieved through differential affinity for target length, by which separate biological processes are controlled. Like the RNA helicase DDX3X, the known splicing factors EFTUD2 and PRPF8—all identified as multifunctional RBPs by our analysis—selectively influence target translation rates depending on 5’ UTR structure. Our analyses identify dozens of RBPs as being multifunctional and pinpoint potential novel regulators of translation, postulating unanticipated complexity of protein-RNA interactions at consecutive stages of gene expression. The lifecycle of an RNA molecule is controlled by hundreds of proteins that can bind RNA, also known as RNA-binding proteins (RBPs). These proteins recognize landing sites within the RNA and guide the RNA’s transcription from DNA, its processing into a mature messenger RNA, its translation into protein, or its degradation once the RNA is no longer needed. Although we now mechanistically understand how certain RBPs regulate these processes, for many RBP-target interactions the consequences imposed by RNA binding are not well understood. For 143 RBPs with known RNA binding positions, the authors of the current study investigated how RNA molecules responded to fluctuations in the expression levels of these RBPs, across each of 80 human hearts. Using statistical approaches, they could show that many RBPs influenced stages of the RNA lifecycle that they were not known to be involved in. Some RBPs turned out to be true "all-rounders" of RNA metabolism: they controlled the RNA transcript levels of some genes, whereas they influenced the translation rates of others. This unexpected multifunctionality unveiled previously hidden aspects of the everyday RNA-binding protein working life.
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Affiliation(s)
- Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- * E-mail: (NH); (SvH)
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- * E-mail: (NH); (SvH)
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93
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Liu CX, Guo SK, Nan F, Xu YF, Yang L, Chen LL. RNA circles with minimized immunogenicity as potent PKR inhibitors. Mol Cell 2021; 82:420-434.e6. [PMID: 34951963 DOI: 10.1016/j.molcel.2021.11.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/31/2021] [Accepted: 11/17/2021] [Indexed: 12/16/2022]
Abstract
Exon back-splicing-generated circular RNAs, as a group, can suppress double-stranded RNA (dsRNA)-activated protein kinase R (PKR) in cells. We have sought to synthesize immunogenicity-free, short dsRNA-containing RNA circles as PKR inhibitors. Here, we report that RNA circles synthesized by permuted self-splicing thymidylate synthase (td) introns from T4 bacteriophage or by Anabaena pre-tRNA group I intron could induce an immune response. Autocatalytic splicing introduces ∼74 nt td or ∼186 nt Anabaena extraneous fragments that can distort the folding status of original circular RNAs or form structures themselves to provoke innate immune responses. In contrast, synthesized RNA circles produced by T4 RNA ligase without extraneous fragments exhibit minimized immunogenicity. Importantly, directly ligated circular RNAs that form short dsRNA regions efficiently suppress PKR activation 103- to 106-fold higher than reported chemical compounds C16 and 2-AP, highlighting the future use of circular RNAs as potent inhibitors for diseases related to PKR overreaction.
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Affiliation(s)
- Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Si-Kun Guo
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Fang Nan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yi-Feng Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Li Yang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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94
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Iparraguirre L, Alberro A, Hansen TB, Castillo-Triviño T, Muñoz-Culla M, Otaegui D. Profiling of Plasma Extracellular Vesicle Transcriptome Reveals That circRNAs Are Prevalent and Differ between Multiple Sclerosis Patients and Healthy Controls. Biomedicines 2021; 9:biomedicines9121850. [PMID: 34944665 PMCID: PMC8698468 DOI: 10.3390/biomedicines9121850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 01/08/2023] Open
Abstract
(1) Background: Extracellular vesicles (EVs) are released by most cell types and are implicated in several biological and pathological processes, including multiple sclerosis (MS). Differences in the number and cargo of plasma-derived EVs have been described in MS. In this work, we have characterised the EV RNA cargo of MS patients, with particular attention to circular RNAs (circRNAs), which have attracted increasing attention for their roles in physiology and disease and their biomarker potential. (2) Methods: Plasma-derived EVs were isolated by differential centrifugation (20 patients, 8 controls), and RNA-Sequencing was used to identify differentially expressed linear and circRNAs. (3) Results: We found differences in the RNA type distribution, circRNAs being enriched in EVs vs. leucocytes. We found a number of (corrected p-value < 0.05) circRNA significantly DE between the groups. Nevertheless, highly structured circRNAs are preferentially retained in leukocytes. Differential expression analysis reports significant differences in circRNA and linear RNA expression between MS patients and controls, as well as between different MS types. (4) Conclusions: Plasma derived EV RNA cargo is not a representation of leukocytes’ cytoplasm but a message worth studying. Moreover, our results reveal the interest of circRNAs as part of this message, highlighting the importance of further understanding RNA regulation in MS.
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Affiliation(s)
- Leire Iparraguirre
- Multiple Sclerosis Unit, Biodonostia Health Research Institute, 20014 San Sebastián, Spain; (L.I.); (A.A.); (T.C.-T.)
| | - Ainhoa Alberro
- Multiple Sclerosis Unit, Biodonostia Health Research Institute, 20014 San Sebastián, Spain; (L.I.); (A.A.); (T.C.-T.)
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Thomas B. Hansen
- Molecular Biology and Genetics Department, Aarhus University, 8000 Aarhus C, Denmark;
| | - Tamara Castillo-Triviño
- Multiple Sclerosis Unit, Biodonostia Health Research Institute, 20014 San Sebastián, Spain; (L.I.); (A.A.); (T.C.-T.)
- Spanish Network of Multiple Sclerosis, 08028 Barcelona, Spain
- Neurology Department, Donostia University Hospital, 20014 San Sebastián, Spain
| | - Maider Muñoz-Culla
- Multiple Sclerosis Unit, Biodonostia Health Research Institute, 20014 San Sebastián, Spain; (L.I.); (A.A.); (T.C.-T.)
- Spanish Network of Multiple Sclerosis, 08028 Barcelona, Spain
- Department of Basic Psychological Processes and Their Development, University of the Basque Country, 20018 San Sebastián, Spain
- Correspondence: (M.M.-C.); (D.O.); Tel.: +34-943-01-52-18 (M.M.-C.); +34-943-00-62-93 (D.O.)
| | - David Otaegui
- Multiple Sclerosis Unit, Biodonostia Health Research Institute, 20014 San Sebastián, Spain; (L.I.); (A.A.); (T.C.-T.)
- Spanish Network of Multiple Sclerosis, 08028 Barcelona, Spain
- Correspondence: (M.M.-C.); (D.O.); Tel.: +34-943-01-52-18 (M.M.-C.); +34-943-00-62-93 (D.O.)
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95
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Chen L, Huang C, Shan G. Circular RNAs in physiology and non-immunological diseases. Trends Biochem Sci 2021; 47:250-264. [PMID: 34865956 DOI: 10.1016/j.tibs.2021.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/27/2022]
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs. Four subclasses of circRNAs have been identified in animal cells, and they have unique features in their biogenesis, degradation, and transport. CircRNAs have diverse molecular functions in sponging miRNAs, regulating transcription, modulating RNA-binding proteins, and even encoding proteins. Some circRNAs are important regulators of various physiological processes to maintain homeostasis. Dysregulation of circRNAs is associated with human disorders, and individual circRNAs are crucial factors that contribute to major diseases including non-immunological diseases such as cancers, neurological disorders, cardiovascular disease, and metabolic disease. Debates on circRNAs have also been raised in recent years, and further studies would help to resolve these disputes and potentially lead to biomedical applications of circRNAs.
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Affiliation(s)
- Liang Chen
- Department of Clinical Laboratory, First Affiliated Hospital of the USTC, Hefei National Laboratory for Physical Sciences at Microscale, Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China.
| | - Ge Shan
- Department of Clinical Laboratory, First Affiliated Hospital of the USTC, Hefei National Laboratory for Physical Sciences at Microscale, Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, China; Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
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96
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Wen G, Zhou T, Gu W. The potential of using blood circular RNA as liquid biopsy biomarker for human diseases. Protein Cell 2021; 12:911-946. [PMID: 33131025 PMCID: PMC8674396 DOI: 10.1007/s13238-020-00799-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a novel class of single-stranded RNAs with a closed loop structure. The majority of circRNAs are formed by a back-splicing process in pre-mRNA splicing. Their expression is dynamically regulated and shows spatiotemporal patterns among cell types, tissues and developmental stages. CircRNAs have important biological functions in many physiological processes, and their aberrant expression is implicated in many human diseases. Due to their high stability, circRNAs are becoming promising biomarkers in many human diseases, such as cardiovascular diseases, autoimmune diseases and human cancers. In this review, we focus on the translational potential of using human blood circRNAs as liquid biopsy biomarkers for human diseases. We highlight their abundant expression, essential biological functions and significant correlations to human diseases in various components of peripheral blood, including whole blood, blood cells and extracellular vesicles. In addition, we summarize the current knowledge of blood circRNA biomarkers for disease diagnosis or prognosis.
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Affiliation(s)
- Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, 89557, USA.
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China.
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97
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van Zonneveld AJ, Kölling M, Bijkerk R, Lorenzen JM. Circular RNAs in kidney disease and cancer. Nat Rev Nephrol 2021; 17:814-826. [PMID: 34381199 DOI: 10.1038/s41581-021-00465-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are a class of endogenously expressed regulatory RNAs with a single-stranded circular structure. They are generated by back splicing and their expression can be tightly regulated by RNA binding proteins. Cytoplasmic circRNAs can function as molecular sponges that inhibit microRNA-target interactions and protein function or as templates for the efficient generation of peptides via rolling circle amplification. They can also act as molecular scaffolds that enhance the reaction kinetics of enzyme-substrate interactions. In the nucleus, circRNAs might facilitate chromatin modifications and promote gene expression. CircRNAs are resistant to degradation and can be packaged in extracellular vesicles and transported in the circulation. Initial studies suggest that circRNAs have roles in kidney disease and associated cardiovascular complications. They have been implicated in hypertensive nephropathy, diabetic kidney disease, glomerular disease, acute kidney injury and kidney allograft rejection, as well as in microvascular and macrovascular complications of chronic kidney disease, including atherosclerotic vascular disease. In addition, several circRNAs have been reported to have oncogenic or tumour suppressor roles or to regulate drug resistance in kidney cancer. The available data suggest that circRNAs could be promising diagnostic and/or prognostic biomarkers and potential therapeutic targets for kidney disease, cardiovascular disease and kidney cancer.
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Affiliation(s)
- Anton Jan van Zonneveld
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Malte Kölling
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Roel Bijkerk
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Johan M Lorenzen
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland.
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98
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He X, Yuan J, Wang Y. G3BP1 binds to guanine quadruplexes in mRNAs to modulate their stabilities. Nucleic Acids Res 2021; 49:11323-11336. [PMID: 34614161 PMCID: PMC8565330 DOI: 10.1093/nar/gkab873] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 09/12/2021] [Accepted: 10/04/2021] [Indexed: 12/21/2022] Open
Abstract
RNA guanine quadruplexes (rG4) assume important roles in post-transcriptional regulations of gene expression, which are often modulated by rG4-binding proteins. Hence, understanding the biological functions of rG4s requires the identification and functional characterizations of rG4-recognition proteins. By employing a bioinformatic approach based on the analysis of overlap between peaks obtained from rG4-seq analysis and those detected in >230 eCLIP-seq datasets for RNA-binding proteins generated from the ENCODE project, we identified a large number of candidate rG4-binding proteins. We showed that one of these proteins, G3BP1, is able to bind directly to rG4 structures with high affinity and selectivity, where the binding entails its C-terminal RGG domain and is further enhanced by its RRM domain. Additionally, our seCLIP-Seq data revealed that pyridostatin, a small-molecule rG4 ligand, could displace G3BP1 from mRNA in cells, with the most pronounced effects being observed for the 3′-untranslated regions (3′-UTR) of mRNAs. Moreover, luciferase reporter assay results showed that G3BP1 positively regulates mRNA stability through its binding with rG4 structures. Together, we identified a number of candidate rG4-binding proteins and validated that G3BP1 can bind directly with rG4 structures and regulate the stabilities of mRNAs.
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Affiliation(s)
- Xiaomei He
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Jun Yuan
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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99
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Lakiotaki E, Kanakoglou DS, Pampalou A, Karatrasoglou EA, Piperi C, Korkolopoulou P. Dissecting the Role of Circular RNAs in Sarcomas with Emphasis on Osteosarcomas. Biomedicines 2021; 9:1642. [PMID: 34829872 PMCID: PMC8615931 DOI: 10.3390/biomedicines9111642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs (circRNAs) are single-stranded RNAs generated from exons back-splicing from a single pre-mRNA, forming covalently closed loop structures which lack 5'-3'-polarity or polyadenylated tail. Ongoing research depicts that circRNAs play a pivotal role in tumorigenesis, tumor progression, metastatic potential and chemoresistance by regulating transcription, microRNA (miRNA) sponging, RNA-binding protein interactions, alternative splicing and to a lesser degree, protein coding. Sarcomas are rare malignant tumors stemming from mesenchymal cells. Due to their clinically insidious onset, they often present at advanced stage and their treatment may require aggressive chemotherapeutic or surgical options. This review is mainly focused on the regulatory functions of circRNAs on osteosarcoma progression and their potential role as biomarkers, an area which has prompted lately extensive research. The attributed oncogenic role of circRNAs on other mesenchymal tumors such as Kaposi Sarcoma (KS), Rhabdomyosarcoma (RMS) or Gastrointestinal Stromal Tumors (GISTs) is also described. The involvement of circRNAs on sarcoma oncogenesis and relevant emerging diagnostic, prognostic and therapeutic applications are expected to gain more research interest in the future.
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Affiliation(s)
- Eleftheria Lakiotaki
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; (D.S.K.); (A.P.); (E.A.K.); (P.K.)
| | - Dimitrios S. Kanakoglou
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; (D.S.K.); (A.P.); (E.A.K.); (P.K.)
| | - Andromachi Pampalou
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; (D.S.K.); (A.P.); (E.A.K.); (P.K.)
| | - Eleni A. Karatrasoglou
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; (D.S.K.); (A.P.); (E.A.K.); (P.K.)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece;
| | - Penelope Korkolopoulou
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; (D.S.K.); (A.P.); (E.A.K.); (P.K.)
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100
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Xiao W, Li J, Hu J, Wang L, Huang JR, Sethi G, Ma Z. Circular RNAs in cell cycle regulation: Mechanisms to clinical significance. Cell Prolif 2021; 54:e13143. [PMID: 34672397 PMCID: PMC8666285 DOI: 10.1111/cpr.13143] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/20/2021] [Accepted: 10/03/2021] [Indexed: 12/27/2022] Open
Abstract
Circular RNAs (circRNAs), a type of non‐coding RNA, are single‐stranded circularized molecules characterized by high abundance, evolutionary conservation and cell development‐ and tissue‐specific expression. A large body of studies has found that circRNAs exert a wide variety of functions in diverse biological processes, including cell cycle. The cell cycle is controlled by the coordinated activation and deactivation of cell cycle regulators. CircRNAs exert mutifunctional roles by regulating gene expression via various mechanisms. However, the functional relevance of circRNAs and cell cycle regulation largely remains to be elucidated. Herein, we briefly describe the biogenesis and mechanistic models of circRNAs and summarize their functions and mechanisms in the regulation of critical cell cycle modulators, including cyclins, cyclin‐dependent kinases and cyclin‐dependent kinase inhibitors. Moreover, we highlight the participation of circRNAs in cell cycle‐related signalling pathways and the clinical value of circRNAs as promising biomarkers or therapeutic targets in diseases related to cell cycle disorder.
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Affiliation(s)
- Wei Xiao
- Health Science Center, Yangtze University, Jingzhou, China
| | - Juan Li
- Key Laboratory of Environmental Health, Ministry of Education, Department of Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - June Hu
- The Second School of Clinical Medicine, Yangtze University, Jingzhou, China
| | - Lingzhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhaowu Ma
- Health Science Center, Yangtze University, Jingzhou, China
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