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Conn VM, Chinnaiyan AM, Conn SJ. Circular RNA in cancer. Nat Rev Cancer 2024:10.1038/s41568-024-00721-7. [PMID: 39075222 DOI: 10.1038/s41568-024-00721-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/13/2024] [Indexed: 07/31/2024]
Abstract
Over the past decade, circular RNA (circRNA) research has evolved into a bona fide research field shedding light on the functional consequence of this unique family of RNA molecules in cancer. Although the method of formation and the abundance of circRNAs can differ from their cognate linear mRNA, the spectrum of interacting partners and their resultant cellular functions in oncogenesis are analogous. However, with 10 times more diversity in circRNA variants compared with linear RNA variants, combined with their hyperstability in the cell, circRNAs are equipped to influence every stage of oncogenesis. This is an opportune time to address the breadth of circRNA in cancer focused on their spatiotemporal expression, mutations in biogenesis factors and contemporary functions through each stage of cancer. In this Review, we highlight examples of functional circRNAs in specific cancers, which satisfy critical criteria, including their physical co-association with the target and circRNA abundance at stoichiometrically valid quantities. These considerations are essential to develop strategies for the therapeutic exploitation of circRNAs as biomarkers and targeted anticancer agents.
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Affiliation(s)
- Vanessa M Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Simon J Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia.
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Yellamaty R, Sharma S. Critical Cellular Functions and Mechanisms of Action of the RNA Helicase UAP56. J Mol Biol 2024; 436:168604. [PMID: 38729260 PMCID: PMC11168752 DOI: 10.1016/j.jmb.2024.168604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
Posttranscriptional maturation and export from the nucleus to the cytoplasm are essential steps in the normal processing of many cellular RNAs. The RNA helicase UAP56 (U2AF associated protein 56; also known as DDX39B) has emerged as a critical player in facilitating and co-transcriptionally linking these steps. Originally identified as a helicase involved in pre-mRNA splicing, UAP56 has been shown to facilitate formation of the A complex during spliceosome assembly. Additionally, it has been found to be critical for interactions between components of the exon junction and transcription and export complexes to promote the loading of export receptors. Although it appears to be structurally similar to other helicase superfamily 2 members, UAP56's ability to interact with multiple different protein partners allows it to perform its various cellular functions. Herein, we describe the structure-activity relationship studies that identified protein interactions of UAP56 and its human paralog URH49 (UAP56-related helicase 49; also known as DDX39A) and are beginning to reveal molecular mechanisms by which interacting proteins and substrate RNAs may regulate these helicases. We also provide an overview of reports that have demonstrated less well-characterized roles for UAP56, including R-loop resolution and telomere maintenance. Finally, we discuss studies that indicate a potential pathogenic effect of UAP56 in the development of autoimmune diseases and cancer, and identify the association of somatic and genetic mutations in UAP56 with neurodevelopmental disorders.
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Affiliation(s)
- Ryan Yellamaty
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA.
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Xie Y, Gao S, Zhang K, Bhat P, Clarke BP, Batten K, Mei M, Gazzara M, Shay JW, Lynch KW, Angelos AE, Hill PS, Ivey AL, Fontoura BMA, Ren Y. Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly. Cell Rep 2023; 42:112988. [PMID: 37578863 PMCID: PMC10508174 DOI: 10.1016/j.celrep.2023.112988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/10/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
mRNA in eukaryotic cells is packaged into highly compacted ribonucleoprotein particles (mRNPs) in the nucleus and exported to the cytoplasm for translation. mRNP packaging and export require the evolutionarily conserved transcription-export (TREX) complex. TREX facilitates loading of various RNA-binding proteins on mRNA through the action of its DDX39B subunit. SARNP (Tho1 [transcriptional defect of Hpr1 by overexpression 1] in yeast) is shown to interact with DDX39B and affect mRNA export. The molecular mechanism of how SARNP recognizes DDX39B and functions in mRNP assembly is unclear. Here, we determine the crystal structure of a Tho1/DDX39B/RNA complex, revealing a multivalent interaction mediated by tandem DDX39B interacting motifs in SARNP/Tho1. The high-order complex of SARNP and DDX39B is evolutionarily conserved, and human SARNP can engage with five DDX39B molecules. RNA sequencing (RNA-seq) from SARNP knockdown cells shows the most affected RNAs in export are GC rich. Our work suggests the role of the high-order SARNP/DDX39B/RNA complex in mRNP assembly and export.
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Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Prasanna Bhat
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Bradley P Clarke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Menghan Mei
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Matthew Gazzara
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexia E Angelos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Pate S Hill
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Austin L Ivey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA.
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
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Low-Dose Albendazole Inhibits Epithelial-Mesenchymal Transition of Melanoma Cells by Enhancing Phosphorylated GSK-3 β/Tyr216 Accumulation. JOURNAL OF ONCOLOGY 2021; 2021:4475192. [PMID: 34966427 PMCID: PMC8712124 DOI: 10.1155/2021/4475192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/16/2021] [Indexed: 11/18/2022]
Abstract
Albendazole (ABZ) is an effective broad-spectrum anthelmintic agent that has been widely used for humans and animals. Previous studies have reported that ABZ exhibits antitumor effects against melanoma and other different cancer types; however, it is unknown whether ABZ exerts the inhibitory effect against melanoma metastasis. In this study, we aimed to investigate the inhibitory effect of ABZ on melanoma cells. Through in vitro studies, we discovered that low-dose ABZ treatment significantly inhibited the migration and invasion, but not the proliferation, of A375 and B16-F10 cells in a dose-dependent manner. Further analysis revealed that ABZ treatment reduced the expression level of snail family transcriptional repressor 1 (Snail) in the cytoplasm and nucleus by decreasing the levels of phosphorylated AKT (pAKT) Ser473/GSK-3β (pGSK-3β) Ser9 and increasing pGSK-3β/Tyr216, resulting in a significant upregulation of E-cadherin and downregulation of N-cadherin and ultimately reversing the epithelial-mesenchymal transition (EMT) process of melanoma cells. In contrast, the continuous activation of AKT via transfected plasmids elevated the protein levels of pAKT Ser473/pGSK-3β Ser9 and Snail and antagonized the inhibitory action of ABZ. We also confirmed that ABZ treatment effectively inhibited the lung metastasis of melanoma in nude mice in vivo. Subsequent immunohistochemical analysis verified the decreased pAKT Ser473/pGSK-3β Ser9 and increased pGSK-3β/Tyr216 levels in ABZ-treated subcutaneous tumors. Therefore, our findings demonstrate that ABZ treatment can suppress the EMT progress of melanoma by increasing the pGSK-3β/Tyr216-mediated degradation of Snail, which may be used as a potential treatment strategy for metastatic melanoma.
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Gan L, Shi H, Zhang Y, Sun J, Chen H. Proteomic Screening and Verification of Biomarkers in Different Stages of Mycosis Fungoides: A pilot Study. Front Cell Dev Biol 2021; 9:747017. [PMID: 34966737 PMCID: PMC8711087 DOI: 10.3389/fcell.2021.747017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma; in advanced stages, it can involve multiple organs and has a poor prognosis. Early detection of the disease is still urgent, but there is no optimal therapy for advanced MF. In the present study, quantitative proteomic analyses (label-free quantitation, LFQ) were applied to tissue samples of different stages of MF and tissue samples from controls (eczema patients and healthy donors) to conduct preliminary molecular analysis to clarify the pathogenesis of the disease. Differential protein expression analysis demonstrated that 113 and 305 proteins were associated with the early and advanced stages of MF, respectively. Gene ontology (GO) enrichment analysis was conducted to determine the potential functions of the proteins, which could be classified into three categories: biological process, cellular component, and molecular function. The results revealed that a series of biological processes, including “initiation of DNA replication” and “nucleosome assembly,” were involved in the disease. Moreover, cellular components, including the “desmosome” and “integrin complex,” may affect the invasion and metastasis of MF via molecular functions, including “integrin binding” and “cadherin binding”. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that “focal adhesion DNA replication,” “Toll-like receptor signalling pathway” and other pathways were also involved. A parallel reaction monitoring (PRM) assay was applied to validate the identified differentially expressed proteins. In conclusion, the above proteomic findings may have great diagnostic and prognostic value in diverse malignancies, especially MF. Nevertheless, further studies are still needed to explore the precise mechanisms of MF.
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Affiliation(s)
- Lu Gan
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Haoze Shi
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Ying Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Jianfang Sun
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Hao Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
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Zhu L, Wang Z, Sun Y, Giamas G, Stebbing J, Yu Z, Peng L. A Prediction Model Using Alternative Splicing Events and the Immune Microenvironment Signature in Lung Adenocarcinoma. Front Oncol 2021; 11:778637. [PMID: 35004299 PMCID: PMC8728792 DOI: 10.3389/fonc.2021.778637] [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: 09/17/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
BackgroundAlternative splicing (AS) is a gene regulatory mechanism that drives protein diversity. Dysregulation of AS is thought to play an essential role in cancer initiation and development. This study aimed to construct a prognostic signature based on AS and explore the role in the tumor immune microenvironment (TIME) in lung adenocarcinoma.MethodsWe analyzed transcriptome profiling and clinical lung adenocarcinoma data from The Cancer Genome Atlas (TCGA) database and lists of AS-related and immune-related signatures from the SpliceSeq. Prognosis-related AS events were analyzed by univariate Cox regression analysis. Gene set enrichment analyses (GSEA) were performed for functional annotation. Prognostic signatures were identified and validated using univariate and multivariate Cox regression, LASSO regression, Kaplan–Meier survival analyses, and proportional hazards model. The context of TIME in lung adenocarcinoma was also analyzed. Gene and protein expression data of Cyclin-Dependent Kinase Inhibitor 2A (CDKN2A) were obtained from ONCOMINE and Human Protein Atlas. Splicing factor (SF) regulatory networks were visualized.ResultsA total of 19,054 survival-related AS events in lung adenocarcinoma were screened in 1,323 genes. Exon skip (ES) and mutually exclusive exons (ME) exhibited the most and fewest AS events, respectively. Based on AS subtypes, eight AS prognostic signatures were constructed. Patients with high-risk scores were associated with poor overall survival. A nomogram with good validity in prognostic prediction was generated. AUCs of risk scores at 1, 2, and 3 years were 0.775, 0.736, and 0.759, respectively. Furthermore, the prognostic signatures were significantly correlated with TIME diversity and immune checkpoint inhibitor (ICI)-related genes. Low-risk patients had a higher StromalScore, ImmuneScore, and ESTIMATEScore. AS-based risk score signature was positively associated with CD8+ T cells. CDKN2A was also found to be a prognostic factor in lung adenocarcinoma. Finally, potential functions of SFs were determined by regulatory networks.ConclusionTaken together, our findings show a clear association between AS and immune cell infiltration events and patient outcome, which could provide a basis for the identification of novel markers and therapeutic targets for lung adenocarcinoma. SF networks provide information of regulatory mechanisms.
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Affiliation(s)
- Liping Zhu
- Department of Medical Oncology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Zhiqiang Wang
- Department of Urology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Yilan Sun
- Department of Respiratory Disease, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Justin Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Zhentao Yu
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Center, National Cancer Center, Shenzhen, China
- *Correspondence: Ling Peng, ; Zhentao Yu,
| | - Ling Peng
- Department of Respiratory Disease, Zhejiang Provincial People’s Hospital, Hangzhou, China
- *Correspondence: Ling Peng, ; Zhentao Yu,
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Wang Q, Qian L, Tao M, Liu J, Qi FZ. Knockdown of DEAD-box RNA helicase 52 (DDX52) suppresses the proliferation of melanoma cells in vitro and of nude mouse xenografts by targeting c-Myc. Bioengineered 2021; 12:3539-3549. [PMID: 34233596 PMCID: PMC8806535 DOI: 10.1080/21655979.2021.1950283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The ATP-dependent protein DEAD-box RNA helicase 52 (DDX52) is an important regulator in RNA biology and has been implicated in the development of prostate and lung cancer. However, its biological functions and clinical importance in malignant melanoma (MM) are still unclear. Understanding the potential mechanism underlying the regulation of MM progression by DDX52 might lead to novel therapeutic strategies. The aim of the present study was to investigate the role of DDX52 in the regulation of MM progression and its clinical relevance. DDX52 expression in normal and MM tissues was evaluated by GEO analysis and immunohistochemistry. The effects of DDX52 on cell growth were evaluated in MM cells with downregulated DDX52 expression. In this study, we found that DDX52 was markedly overexpressed in MM tissues compared with nontumor tissues and was associated with shorter overall survival in patients; therefore, DDX52 might be a prognostic marker in MM. Downregulation of DDX52 expression in the MM cell lines A2058 and MV3 markedly inhibited cell proliferation and colony formation. Additionally, knockdown of DDX52 in MM cells caused significant regression of established tumors in nude mice and delayed the onset time. Moreover, downregulation of DDX52 markedly suppressed c-Myc mRNA and protein expression, and an RNA immunoprecipitation assay confirmed the association between DDX52 and c-Myc. Restoration of c-Myc expression partly rescued the effects of DDX52 deficiency in MM cells. In conclusion, our study found that DDX52 mediated oncogenesis by promoting the transcriptional activity of c-Myc and could be a therapeutic target in MM.
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Affiliation(s)
- Qiang Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Leqi Qian
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengyuan Tao
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiaqi Liu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fa-Zhi Qi
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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