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Pabis M, Popowicz GM, Stehle R, Fernández-Ramos D, Asami S, Warner L, García-Mauriño SM, Schlundt A, Martínez-Chantar ML, Díaz-Moreno I, Sattler M. HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs. Nucleic Acids Res 2019; 47:1011-1029. [PMID: 30418581 PMCID: PMC6344896 DOI: 10.1093/nar/gky1138] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/28/2018] [Indexed: 12/22/2022] Open
Abstract
HuR/ELAVL1 is an RNA-binding protein involved in differentiation and stress response that acts primarily by stabilizing messenger RNA (mRNA) targets. HuR comprises three RNA recognition motifs (RRMs) where the structure and RNA binding of RRM3 and of full-length HuR remain poorly understood. Here, we report crystal structures of RRM3 free and bound to cognate RNAs. Our structural, NMR and biochemical data show that RRM3 mediates canonical RNA interactions and reveal molecular details of a dimerization interface localized on the α-helical face of RRM3. NMR and SAXS analyses indicate that the three RRMs in full-length HuR are flexibly connected in the absence of RNA, while they adopt a more compact arrangement when bound to RNA. Based on these data and crystal structures of tandem RRM1,2-RNA and our RRM3-RNA complexes, we present a structural model of RNA recognition involving all three RRM domains of full-length HuR. Mutational analysis demonstrates that RRM3 dimerization and RNA binding is required for functional activity of full-length HuR in vitro and to regulate target mRNAs levels in human cells, thus providing a fine-tuning for HuR activity in vivo.
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Affiliation(s)
- Marta Pabis
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.,Max Planck Research Group hosted by the Malopolska Centre of Biotechnology of the Jagiellonian University, Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - David Fernández-Ramos
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias. Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Sam Asami
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Lisa Warner
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Andreas Schlundt
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - María L Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias. Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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52
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Terasaka T, Kim T, Dave H, Gangapurkar B, Nicholas DA, Muñoz O, Terasaka E, Li D, Lawson MA. The RNA-Binding Protein ELAVL1 Regulates GnRH Receptor Expression and the Response to GnRH. Endocrinology 2019; 160:1999-2014. [PMID: 31188427 PMCID: PMC6660905 DOI: 10.1210/en.2019-00203] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/04/2019] [Indexed: 01/11/2023]
Abstract
Gonadotropin secretion, which is elicited by GnRH stimulation of the anterior pituitary gonadotropes, is a critical feature of reproductive control and the maintenance of fertility. In addition, activation of the GnRH receptor (GnRHR) regulates transcription and translation of multiple factors that regulate the signaling response and synthesis of gonadotropins. GnRH stimulation results in a broad redistribution of mRNA between active and inactive polyribosomes within the cell, but the mechanism of redistribution is not known. The RNA-binding protein embryonic lethal, abnormal vision, Drosophila-like 1 (ELAVL1) binds to AU-rich elements in mRNA and is one of the most abundant mRNA-binding proteins in eukaryotic cells. It is known to serve as a core component of RNA-binding complexes that direct the fate of mRNA. In LβT2 gonadotropes, we showed that ELAVL1 binds to multiple mRNAs encoding factors that are crucial for gonadotropin synthesis and release. Association with some mRNAs is GnRH sensitive but does not correlate with abundance of binding. We also showed MAPK-dependent changes in intracellular localization of ELAVL1 in response to GnRH stimulation. Knockdown of ELAVL1 gene expression resulted in reduced Lhb and Gnrhr mRNA levels, reduced cell surface expression of GnRHR, and reduced LH secretion in response to GnRH stimulation. Overall, these observations not only support the role of ELAVL1 in GnRHR-mediated regulation of gene expression and LH secretion but also indicate that other factors may contribute to the precise fate of mRNA in response to GnRH stimulation of gonadotropes.
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Affiliation(s)
- Tomohiro Terasaka
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, California
| | - Taeshin Kim
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, California
| | - Hiral Dave
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, California
| | - Bhakti Gangapurkar
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, California
| | - Dequina A Nicholas
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, California
| | - Oscar Muñoz
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, California
| | - Eri Terasaka
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, California
| | - Danmei Li
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, California
| | - Mark A Lawson
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, California
- Correspondence: Mark A. Lawson, PhD, University of California, San Diego, Department of Obstetrics, Gynecology, and Reproductive Sciences, Mail Code 0674, 9500 Gilman Drive, La Jolla, California 92093. E-mail:
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53
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Inhibition of Caspase-2 Translation by the mRNA Binding Protein HuR: A Novel Path of Therapy Resistance in Colon Carcinoma Cells? Cells 2019; 8:cells8080797. [PMID: 31366165 PMCID: PMC6721497 DOI: 10.3390/cells8080797] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/28/2022] Open
Abstract
An increased expression and cytoplasmic abundance of the ubiquitous RNA binding protein human antigen R (HuR) is critically implicated in the dysregulated control of post- transcriptional gene expression during colorectal cancer development and is frequently associated with a high grade of malignancy and therapy resistance. Regardless of the fact that HuR elicits a broad cell survival program by increasing the stability of mRNAs coding for prominent anti-apoptotic factors, recent data suggest that HuR is critically involved in the regulation of translation, particularly, in the internal ribosome entry site (IRES) controlled translation of cell death regulatory proteins. Accordingly, data from human colon carcinoma cells revealed that HuR maintains constitutively reduced protein and activity levels of caspase-2 through negative interference with IRES-mediated translation. This review covers recent advances in the understanding of mechanisms underlying HuR's modulatory activity on IRES-triggered translation. With respect to the unique regulatory features of caspase-2 and its multiple roles (e.g., in DNA-damage-induced apoptosis, cell cycle regulation and maintenance of genomic stability), the pathophysiological consequences of negative caspase-2 regulation by HuR and its impact on therapy resistance of colorectal cancers will be discussed in detail. The negative HuR-caspase-2 axis may offer a novel target for tumor sensitizing therapies.
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54
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Liu L, Xiao L, Chung HK, Kwon MS, Li XX, Wu N, Rao JN, Wang JY. RNA-Binding Protein HuR Regulates Rac1 Nucleocytoplasmic Shuttling Through Nucleophosmin in the Intestinal Epithelium. Cell Mol Gastroenterol Hepatol 2019; 8:475-486. [PMID: 31195150 PMCID: PMC6718926 DOI: 10.1016/j.jcmgh.2019.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The mammalian intestinal epithelium is a rapidly self-renewing tissue in the body, and its homeostasis is tightly regulated via well-controlled mechanisms. The RNA-binding protein HuR is essential for maintaining gut epithelial integrity, and targeted deletion of HuR in intestinal epithelial cells (IECs) disrupts mucosal regeneration and delays repair after injury. Here, we defined the role of HuR in regulating subcellular distribution of small guanosine triphosphatase Rac1 and investigated the implication of nucleophosmin (NPM) as a molecular chaperone in this process. METHODS Studies were conducted in intestinal epithelial tissue-specific HuR knockout (IE-HuR-/-) mice and cultured IEC-6 cells, derived from rat small intestinal crypts. Functions of HuR and NPM in vitro were investigated via their gene silencing and overexpression. RESULTS The abundance of cytoplasmic Rac1 in the small intestinal mucosa increased significantly in IE-HuR-/- mice, although HuR deletion did not alter total Rac1 levels. HuR silencing in cultured IECs also increased the cytoplasmic Rac1 levels, without an effect on whole-cell Rac1 content. In addition, HuR deficiency in the intestinal epithelium decreased the levels of NPM in IE-HuR-/- mice and cultured IECs. NPM physically interacted with Rac1 and formed the NPM/Rac1 complex. NPM silencing decreased the NPM/Rac1 association and inhibited nuclear accumulation of Rac1, along with an increase in cytoplasmic abundances of Rac1. In contrast, ectopically expressed NPM enhanced Rac1 nuclear translocation and restored Rac1 subcellular localization to near normal in HuR-deficient cells. CONCLUSIONS These results indicate that HuR regulates Rac1 nucleocytoplasmic shuttling in the intestinal epithelium by altering NPM expression.
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Affiliation(s)
- Lan Liu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland,Research Service, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland,Research Service, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Hee K. Chung
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland,Research Service, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Min S. Kwon
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland,Research Service, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Xiao-Xue Li
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland,Research Service, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Na Wu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland,Research Service, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Jaladanki N. Rao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland,Research Service, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland,Research Service, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland,Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland,Correspondence Address correspondence to: Jian-Ying Wang, MD, PhD, Baltimore Veterans Affairs Medical Center (112), 10 North Greene Street, Baltimore, Maryland 21201. fax: (410) 706-1049.
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55
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Adipose HuR protects against diet-induced obesity and insulin resistance. Nat Commun 2019; 10:2375. [PMID: 31147543 PMCID: PMC6542850 DOI: 10.1038/s41467-019-10348-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/06/2019] [Indexed: 02/07/2023] Open
Abstract
Human antigen R (HuR) is a member of the Hu family of RNA-binding proteins and is involved in many physiological processes. Obesity, as a worldwide healthcare problem, has attracted more and more attention. To investigate the role of adipose HuR, we generate adipose-specific HuR knockout (HuRAKO) mice. As compared with control mice, HuRAKO mice show obesity when induced with a high-fat diet, along with insulin resistance, glucose intolerance, hypercholesterolemia and increased inflammation in adipose tissue. The obesity of HuRAKO mice is attributed to adipocyte hypertrophy in white adipose tissue due to decreased expression of adipose triglyceride lipase (ATGL). HuR positively regulates ATGL expression by promoting the mRNA stability and translation of ATGL. Consistently, the expression of HuR in adipose tissue is reduced in obese humans. This study suggests that adipose HuR may be a critical regulator of ATGL expression and lipolysis and thereby controls obesity and metabolic syndrome. Human antigen R (HuR) is a RNA-binding protein. Here the authors investigate its role in adipose tissue and find that it protects mice from diet-induced obesity, prevents adipocyte hypertrophy, and promotes lipolysis, which may at least in part be due to HuR-dependent ATGL mRNA stability regulation demonstrated in-vitro.
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56
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Karginov FV. HuR controls apoptosis and activation response without effects on cytokine 3' UTRs. RNA Biol 2019; 16:686-695. [PMID: 30777501 DOI: 10.1080/15476286.2019.1582954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
RNA binding proteins regulate gene expression through several post-transcriptional mechanisms. The broadly expressed HuR/ELAVL1 is important for proper function of multiple immune cell types, and has been proposed to regulate cytokine and other mRNA 3' UTRs upon activation. However, this mechanism has not been previously dissected in stable cellular settings. In this study, HuR demonstrated strong anti-apoptotic and activation roles in Jurkat T cells. Detailed transcriptomic analysis of HuR knockout cells revealed a substantial negative impact on the activation program, coordinately preventing the expression of immune response gene categories, including all cytokines. Knockout cells showed a significant defect in IL-2 production, which was rescued upon reintroduction of HuR. Interestingly, the mechanism of HuR regulation did not involve control of the cytokine 3' UTRs: HuR knockout did not affect the activity of 3' UTR reporters in 293 cells, and had no effect on IL-2 and TNF 3' UTRs in resting or activated Jurkats. Instead, impaired cytokine production corresponded with defective induction of the IL-2 promoter upon activation. Accordingly, upregulation of NFATC1 was also impaired, without 3' UTR effects. Together, these results indicate that HuR controls cytokine production through coordinated upstream pathways, and that additional mechanisms must be considered in investigating its function.
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Affiliation(s)
- Fedor V Karginov
- a Department of Molecular, Cell, and Systems Biology , Institute for Integrative Genome Biology, University of California , Riverside , CA , USA
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57
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Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM. Proc Natl Acad Sci U S A 2019; 116:2935-2944. [PMID: 30718402 PMCID: PMC6386705 DOI: 10.1073/pnas.1808696116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
HuR is a pivotal player in binding mRNAs containing AU-rich elements and regulating their stability and decay. HuR embeds three RNA recognition motifs (RRMs). The function of RRM3 is not completely understood, and the structure of the entire Hu protein family is so far unknown. Here, we provide structural and mechanistic insights into how HuR RRM3 discriminates between U-rich and AU-rich targets. RRM3 uses additional mechanisms, like multiple-register binding and homodimerization, to fine-tune its affinity for RNA. These results highlight the multifunctional role of HuR RRM3 but also the subtle adaptability of RRMs, the most abundant RNA-binding domain in eukaryotes. Since elevated HuR levels are associated with disease, our structure may help develop new therapeutic strategies. Human antigen R (HuR) is a key regulator of cellular mRNAs containing adenylate/uridylate–rich elements (AU-rich elements; AREs). These are a major class of cis elements within 3′ untranslated regions, targeting these mRNAs for rapid degradation. HuR contains three RNA recognition motifs (RRMs): a tandem RRM1 and 2, followed by a flexible linker and a C-terminal RRM3. While RRM1 and 2 are structurally characterized, little is known about RRM3. Here we present a 1.9-Å-resolution crystal structure of RRM3 bound to different ARE motifs. This structure together with biophysical methods and cell-culture assays revealed the mechanism of RRM3 ARE recognition and dimerization. While multiple RNA motifs can be bound, recognition of the canonical AUUUA pentameric motif is possible by binding to two registers. Additionally, RRM3 forms homodimers to increase its RNA binding affinity. Finally, although HuR stabilizes ARE-containing RNAs, we found that RRM3 counteracts this effect, as shown in a cell-based ARE reporter assay and by qPCR with native HuR mRNA targets containing multiple AUUUA motifs, possibly by competing with RRM12.
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58
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D'Agostino VG, Sighel D, Zucal C, Bonomo I, Micaelli M, Lolli G, Provenzani A, Quattrone A, Adami V. Screening Approaches for Targeting Ribonucleoprotein Complexes: A New Dimension for Drug Discovery. SLAS DISCOVERY 2019; 24:314-331. [PMID: 30616427 DOI: 10.1177/2472555218818065] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA-binding proteins (RBPs) are pleiotropic factors that control the processing and functional compartmentalization of transcripts by binding primarily to mRNA untranslated regions (UTRs). The competitive and/or cooperative interplay between RBPs and an array of coding and noncoding RNAs (ncRNAs) determines the posttranscriptional control of gene expression, influencing protein production. Recently, a variety of well-recognized and noncanonical RBP domains have been revealed by modern system-wide analyses, underlying an evolving classification of ribonucleoproteins (RNPs) and their importance in governing physiological RNA metabolism. The possibility of targeting selected RNA-protein interactions with small molecules is now expanding the concept of protein "druggability," with new implications for medicinal chemistry and for a deeper characterization of the mechanism of action of bioactive compounds. Here, taking SF3B1, HuR, LIN28, and Musashi proteins as paradigmatic case studies, we review the strategies applied for targeting RBPs, with emphasis on the technological advancements to study protein-RNA interactions and on the requirements of appropriate validation strategies to parallel high-throughput screening (HTS) efforts.
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Affiliation(s)
- Vito Giuseppe D'Agostino
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Denise Sighel
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Chiara Zucal
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Isabelle Bonomo
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Mariachiara Micaelli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Graziano Lolli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Provenzani
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Quattrone
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Valentina Adami
- 2 University of Trento, HTS Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
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Carrascoso I, Alcalde J, Tabas-Madrid D, Oliveros JC, Izquierdo JM. Transcriptome-wide analysis links the short-term expression of the b isoforms of TIA proteins to protective proteostasis-mediated cell quiescence response. PLoS One 2018; 13:e0208526. [PMID: 30533021 PMCID: PMC6289441 DOI: 10.1371/journal.pone.0208526] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/19/2018] [Indexed: 12/20/2022] Open
Abstract
Control of gene expression depends on genetics and environmental factors. The T-cell intracellular antigens T-cell intracellular antigen 1 (TIA1), TIA1-like/related protein (TIAL1/TIAR) and human antigen R (HuR/ELAVL1) are RNA-binding proteins that play crucial roles in regulating gene expression in both situations. This study used massive sequencing analysis to uncover molecular and functional mechanisms resulting from the short-time expression of the b isoforms of TIA1 and TIAR, and of HuR in HEK293 cells. Our gene profiling analysis identified several hundred differentially expressed genes (DEGs) and tens of alternative splicing events associated with TIA1b, TIARb and HuR overexpression. Gene ontology analysis revealed that the controlled expression of these proteins strongly influences the patterns of DEGs and RNA variants preferentially associated with development, reproduction, cell cycle, metabolism, autophagy and apoptosis. Mechanistically, TIA1b and TIARb isoforms display both common and differential effects on the regulation of gene expression, involving systematic perturbations of cell biosynthetic machineries (splicing and translation). The transcriptome outputs were validated using functional assays of the targeted cellular processes as well as expression analysis for selected genes. Collectively, our observations suggest that early TIA1b and TIARb expression operates to connect the regulatory crossroads to protective proteostasis responses associated with a survival quiescence phenotype.
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Affiliation(s)
- Isabel Carrascoso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
| | - José Alcalde
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
| | - Daniel Tabas-Madrid
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, C/ Darwin, Madrid, Spain
| | - Juan Carlos Oliveros
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, C/ Darwin, Madrid, Spain
| | - José M. Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
- * E-mail:
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60
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Zhaolin Z, Guohua L, Shiyuan W, Zuo W. Role of pyroptosis in cardiovascular disease. Cell Prolif 2018; 52:e12563. [PMID: 30525268 PMCID: PMC6496801 DOI: 10.1111/cpr.12563] [Citation(s) in RCA: 278] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022] Open
Abstract
Cardiac function is determined by the dynamic equilibrium of various cell types and the extracellular matrix that composes the heart. Cardiovascular diseases (CVDs), especially atherosclerosis and myocardial infarction, are often accompanied by cell death and acute/chronic inflammatory reactions. Caspase‐dependent pyroptosis is characterized by the activation of pathways leading to the activation of NOD‐like receptors, especially the NLRP3 inflammasome and its downstream effector inflammatory factors interleukin (IL)‐1β and IL‐18. Many studies in the past decade have investigated the role of pyroptosis in CVDs. The findings of these studies have led to the development of therapeutic approaches based on the regulation of pyroptosis, and some of these approaches are in clinical trials. This review summarizes the molecular mechanisms, regulation and cellular effects of pyroptosis briefly and then discusses the current pyroptosis studies in CVD research.
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Affiliation(s)
- Zeng Zhaolin
- Yueyang Maternal and Child Health Hospital, Yueyang, China.,Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang, China
| | - Li Guohua
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang, China
| | - Wu Shiyuan
- Yueyang Maternal and Child Health Hospital, Yueyang, China
| | - Wang Zuo
- Yueyang Maternal and Child Health Hospital, Yueyang, China.,Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang, China
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61
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Christodoulou-Vafeiadou E, Ioakeimidis F, Andreadou M, Giagkas G, Stamatakis G, Reczko M, Samiotaki M, Papanastasiou AD, Karakasiliotis I, Kontoyiannis DL. Divergent Innate and Epithelial Functions of the RNA-Binding Protein HuR in Intestinal Inflammation. Front Immunol 2018; 9:2732. [PMID: 30532756 PMCID: PMC6265365 DOI: 10.3389/fimmu.2018.02732] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/06/2018] [Indexed: 12/17/2022] Open
Abstract
HuR is an abundant RNA-binding protein acting as a post-transcriptional regulator of many RNAs including mRNAs encoding inflammatory mediators, cytokines, death signalers and cell cycle regulators. In the context of intestinal pathologies, elevated HuR is considered to enhance the stability and the translation of pro-tumorigenic mRNAs providing the rationale for its pharmacological targeting. However, HuR also possesses specific regulatory functions for innate immunity and cytokine mRNA control which can oppose intestinal inflammation and tumor promotion. Here, we aim to identify contexts of intestinal inflammation where the innate immune and the epithelial functions of HuR converge or diverge. To address this, we use a disease-oriented phenotypic approach using mice lacking HuR either in intestinal epithelia or myeloid-derived immune compartments. These mice were compared for their responses to (a) Chemically induced Colitis; (b) Colitis- associated Cancer (CAC); (c) T-cell mediated enterotoxicity; (d) Citrobacter rodentium-induced colitis; and (e) TNF-driven inflammatory bowel disease. Convergent functions of epithelial and myeloid HuR included their requirement for suppressing inflammation in chemically induced colitis and their redundancies in chronic TNF-driven IBD and microbiota control. In the other contexts however, their functions diversified. Epithelial HuR was required to protect the epithelial barrier from acute inflammatory or infectious degeneration but also to promote tumor growth. In contrast, myeloid HuR was required to suppress the beneficial inflammation for pathogen clearance and tumor suppression. This cellular dichotomy in HuR's functions was validated further in mice engineered to express ubiquitously higher levels of HuR which displayed diminished pathologic and beneficial inflammatory responses, resistance to epithelial damage yet a heightened susceptibility to CAC. Our study demonstrates that epithelial and myeloid HuR affect different cellular dynamics in the intestine that need to be carefully considered for its pharmacological exploitation and points toward potential windows for harnessing HuR functions in intestinal inflammation.
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Affiliation(s)
| | - Fotis Ioakeimidis
- Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - Margarita Andreadou
- Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - Giorgos Giagkas
- Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - George Stamatakis
- Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - Martin Reczko
- Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - Martina Samiotaki
- Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | | | - Ioannis Karakasiliotis
- Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - Dimitris L Kontoyiannis
- Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Vari, Greece.,Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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62
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Lei W, Wang ZL, Feng HJ, Lin XD, Li CZ, Fan D. Long non-coding RNA SNHG12promotes the proliferation and migration of glioma cells by binding to HuR. Int J Oncol 2018; 53:1374-1384. [PMID: 30015836 DOI: 10.3892/ijo.2018.4478] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/20/2018] [Indexed: 11/06/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in biological processes and provide a novel approach with which to understand the molecular mechanisms responsible for glioma. Previous studies have demonstrated that lncRNA small nucleolar RNA host gene 12 (SNHG12) is involved in cell growth and migration. However, the accurate expression pattern of SNHG12 in glioma and the possible associations between this pattern and the clinicopathological characteristics of glioma cohorts are not yet known. The present study investigated the role of lncRNA SNHG12 in the development and progression of glioma, as well as the potential diagnostic value of SNHG12 in patients with glioma. The levels of SNHG12 were detected in resected specimens from patients and in glioma cell lines using reverse transcription-quantitative polymerase chain reaction. The potential effects of SNHG12 on the viability, mobility and apoptosis of glioma cells were evaluated using in vitro assays. The association between SNHG12 and Hu antigen R (HuR) was also determined using RNA immunoprecipitation (RIP) and RNA pull-down assays. The results revealed that SNHG12 was significantly upregulated in glioma tissues and cell lines. High levels of SNHG12 were associated with the deterioration of patients with glioma. Patients with high levels of SNHG12 exhibited a reduced 5-year overall survival rate (compared to those with lower levels), particularly in cohorts with high-grade carcinoma (III-IV). The silencing of SNHG12 expression by RNA interference led to a reduced viability and mobility, and in an increased apoptosis of human glioma cells. Furthermore, RIP and RNA pull-down assays demonstrated that SNHG12 was associated with and was stabilized by HuR. The findings of the present study thus identify a novel therapeutic target in glioma.
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Affiliation(s)
- Wei Lei
- Institute of Neurology, General Hospital of Shenyang Military Command, Shengyang, Liaoning 110000, P.R. China
| | - Zhi-Long Wang
- Graduate School of Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - He-Jun Feng
- Graduate School of Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
| | - Xiang-Dan Lin
- Graduate School of Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
| | - Chuang-Zhong Li
- Institute of Neurology, General Hospital of Shenyang Military Command, Shengyang, Liaoning 110000, P.R. China
| | - Di Fan
- Institute of Neurology, General Hospital of Shenyang Military Command, Shengyang, Liaoning 110000, P.R. China
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63
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Lee KJ, Clegg PD, Comerford EJ, Canty-Laird EG. A comparison of the stem cell characteristics of murine tenocytes and tendon-derived stem cells. BMC Musculoskelet Disord 2018; 19:116. [PMID: 29650048 PMCID: PMC5897930 DOI: 10.1186/s12891-018-2038-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/04/2018] [Indexed: 12/11/2022] Open
Abstract
Tendon is a commonly injured soft musculoskeletal tissue, however, poor healing potential and ineffective treatment strategies result in persistent injuries and tissue that is unable to perform its normal physiological function. The identification of a stem cell population within tendon tissue holds therapeutic potential for treatment of tendon injuries. This study aimed, for the first time, to characterise and compare tenocyte and tendon-derived stem cell (TDSC) populations in murine tendon. Tenocytes and TDSCs were isolated from murine tail tendon. The cells were characterised for morphology, clonogenicity, proliferation, stem cell and tenogenic marker expression and multipotency. TDSCs demonstrated a rounded morphology, compared with a more fibroblastic morphology for tenocytes. Tenocytes had greater clonogenic potential and a smaller population doubling time compared with TDSCs. Stem cell and early tenogenic markers were more highly expressed in TDSCs, whereas late tenogenic markers were more highly expressed in tenocytes. Multipotency was increased in TDSCs with the presence of adipogenic differentiation which was absent in tenocytes. The differences in morphology, clonogenicity, stem cell marker expression and multipotency observed between tenocytes and TDSCs indicate that at least two cell populations are present in murine tail tendon. Determination of the most effective cell population for tendon repair is required in future studies, which in turn may aid in tendon repair strategies.
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Affiliation(s)
- Katie Joanna Lee
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Peter David Clegg
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.,School of Veterinary Science, Leahurst Campus, University of Liverpoo, Chester High Road, Neston, CH64 7TE, UK.,The MRC-Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool, UK
| | - Eithne Josephine Comerford
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.,School of Veterinary Science, Leahurst Campus, University of Liverpoo, Chester High Road, Neston, CH64 7TE, UK
| | - Elizabeth Gail Canty-Laird
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.,The MRC-Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool, UK
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64
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Janakiraman H, House RP, Gangaraju VK, Diehl JA, Howe PH, Palanisamy V. The Long (lncRNA) and Short (miRNA) of It: TGFβ-Mediated Control of RNA-Binding Proteins and Noncoding RNAs. Mol Cancer Res 2018; 16:567-579. [PMID: 29555893 DOI: 10.1158/1541-7786.mcr-17-0547] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/31/2017] [Accepted: 12/18/2017] [Indexed: 12/12/2022]
Abstract
RNA-binding proteins (RBP) and noncoding RNAs (ncRNA), such as long noncoding RNAs (lncRNA) and microRNAs (miRNA), control co- and posttranscriptional gene regulation (PTR). At the PTR level, RBPs and ncRNAs contribute to pre-mRNA processing, mRNA maturation, transport, localization, turnover, and translation. Deregulation of RBPs and ncRNAs promotes the onset of cancer progression and metastasis. Both RBPs and ncRNAs are altered by signaling cascades to cooperate or compete with each other to bind their nucleic acid targets. Most importantly, transforming growth factor-beta (TGFβ) signaling plays a significant role in controlling gene expression patterns by targeting RBPs and ncRNAs. Because of TGFβ signaling in cancer, RBP-RNA or RNA-RNA interactions are altered and cause enhanced cell growth and tumor cell dissemination. This review focuses on the emerging concepts of TGFβ signaling on posttranscriptional gene regulation and highlights the implications of RBPs and ncRNAs in cancer progression and metastasis. Mol Cancer Res; 16(4); 567-79. ©2018 AACR.
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Affiliation(s)
- Harinarayanan Janakiraman
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Reniqua P House
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Vamsi K Gangaraju
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Viswanathan Palanisamy
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, South Carolina.
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65
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de Bruin RG, Rabelink TJ, van Zonneveld AJ, van der Veer EP. Emerging roles for RNA-binding proteins as effectors and regulators of cardiovascular disease. Eur Heart J 2018; 38:1380-1388. [PMID: 28064149 DOI: 10.1093/eurheartj/ehw567] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/02/2016] [Indexed: 12/18/2022] Open
Abstract
The cardiovascular system comprises multiple cell types that possess the capacity to modulate their phenotype in response to acute or chronic injury. Transcriptional and post-transcriptional mechanisms play a key role in the regulation of remodelling and regenerative responses to damaged cardiovascular tissues. Simultaneously, insufficient regulation of cellular phenotype is tightly coupled with the persistence and exacerbation of cardiovascular disease. Recently, RNA-binding proteins such as Quaking, HuR, Muscleblind, and SRSF1 have emerged as pivotal regulators of these functional adaptations in the cardiovascular system by guiding a wide-ranging number of post-transcriptional events that dramatically impact RNA fate, including alternative splicing, stability, localization and translation. Moreover, homozygous disruption of RNA-binding protein genes is commonly associated with cardiac- and/or vascular complications. Here, we summarize the current knowledge on the versatile role of RNA-binding proteins in regulating the transcriptome during phenotype switching in cardiovascular health and disease. We also detail existing and potential DNA- and RNA-based therapeutic approaches that could impact the treatment of cardiovascular disease in the future.
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Affiliation(s)
- Ruben G de Bruin
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Ton J Rabelink
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Anton Jan van Zonneveld
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Eric P van der Veer
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
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66
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RNA binding protein, tristetraprolin in a murine model of recurrent pregnancy loss. Oncotarget 2018; 7:72486-72502. [PMID: 27732963 PMCID: PMC5341924 DOI: 10.18632/oncotarget.12539] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 09/26/2016] [Indexed: 01/23/2023] Open
Abstract
Recurrent pregnancy loss is a major reproductive pathology affecting 1-5% of pregnant women worldwide. A distinct feature of this reproductive pathology is involvement of key inflammatory cytokines and transcription factors such as tumor necrosis factor alpha (TNF-α), interleukin 6 (IL-6) and nuclear factor kappa beta (NF-κB). Special classes of RNA-binding proteins regulate the transcripts of many of these important cytokines and regulatory factors via binding to the 3' untranslated regions (UTRs) and/or poly(A) tail and destabilizing/stabilizing the transcript. The tristetraprolin (TTP/ZFP36) family have been found to be potent destabilizers of the aforementioned inflammatory and cellular response cytokines. The aim of this study was to evaluate whether tristetraprolin is expressed in the placenta and involved in modulating inflammation in mouse model of lipopolysaccharide (LPS)-induced fetal loss. In this study, Swiss-albino mice were injected with LPS at gestational day 15.5 and placental tissues were harvested 6 hours post-LPS injection. Histopathology and immunohistochemistry analyses clearly revealed cellular stress and death in LPS treated placentas compared to controls. TTP protein was downregulated, while targets TNF-α and IL-6 were upregulated in LPS group compared to controls. We observed increased TTP nuclear immunolocalization corresponding with higher NF-κB nuclear localization in trophoblasts from LPS treated placentas. Our results suggest that RNA-binding proteins such as TTP are expressed and perhaps involved in the modulation of inflammation-induced pregnancy pathologies.
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67
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Blagden S, Abdel Mouti M, Chettle J. Ancient and modern: hints of a core post-transcriptional network driving chemotherapy resistance in ovarian cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1432. [PMID: 28762650 PMCID: PMC5763387 DOI: 10.1002/wrna.1432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/12/2017] [Accepted: 06/12/2017] [Indexed: 01/04/2023]
Abstract
RNA-binding proteins (RBPs) and noncoding (nc)RNAs (such as microRNAs, long ncRNAs, and others) cooperate within a post-transcriptional network to regulate the expression of genes required for many aspects of cancer behavior including its sensitivity to chemotherapy. Here, using an RBP-centric approach, we explore the current knowledge surrounding contributers to post-transcriptional gene regulation (PTGR) in ovarian cancer and identify commonalities that hint at the existence of an evolutionarily conserved core PTGR network. This network regulates survival and chemotherapy resistance in the contemporary context of the cancer cell. There is emerging evidence that cancers become dependent on PTGR factors for their survival. Further understanding of this network may identify innovative therapeutic targets as well as yield crucial insights into the hard-wiring of many malignancies, including ovarian cancer. WIREs RNA 2018, 9:e1432. doi: 10.1002/wrna.1432 This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Mechanisms RNA in Disease and Development > RNA in Disease.
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68
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Lema I, Amazit L, Lamribet K, Fagart J, Blanchard A, Lombès M, Cherradi N, Viengchareun S. RNA-binding protein HuR enhances mineralocorticoid signaling in renal KC3AC1 cells under hypotonicity. Cell Mol Life Sci 2017; 74:4587-4597. [PMID: 28744670 PMCID: PMC11107542 DOI: 10.1007/s00018-017-2594-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 02/03/2023]
Abstract
Mineralocorticoid receptor (MR) mediates the sodium-retaining action of aldosterone in the distal nephron. Herein, we decipher mechanisms by which hypotonicity increases MR expression in renal principal cells. We identify HuR (human antigen R), an mRNA-stabilizing protein, as an important posttranscriptional regulator of MR expression. Hypotonicity triggers a rapid and reversible nuclear export of HuR in renal KC3AC1 cells, as quantified by high-throughput microscopy. We also identify a key hairpin motif in the 3'-untranslated region of MR transcript, pivotal for the interaction with HuR and its stabilizing function. Next, we show that hypotonicity increases MR recruitment onto Sgk1 promoter, a well-known MR target gene, thereby enhancing aldosterone responsiveness. Our data shed new light on the crucial role of HuR as a stabilizing factor for the MR transcript and provide evidence for a short autoregulatory loop in which expression of a nuclear receptor transcriptionally regulating water and sodium balance is controlled by osmotic tone.
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Affiliation(s)
- Ingrid Lema
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France
| | - Larbi Amazit
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France
- UMS 32, 94276, Le Kremlin-Bicêtre, France
| | - Khadija Lamribet
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France
| | - Jérôme Fagart
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France
| | - Anne Blanchard
- Inserm, Centre d'Investigations Cliniques 9201, 75015, Paris, France
| | - Marc Lombès
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France.
- Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Service d'Endocrinologie et des Maladies de la Reproduction, 94275, Le Kremlin-Bicêtre, France.
| | - Nadia Cherradi
- Institut National de la Santé et de la Recherche Médicale, Inserm U1036, 38000, Grenoble, France.
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biosciences et Biotechnologies de Grenoble, Laboratoire Biologie du Cancer et de l'Infection, 38000, Grenoble, France.
- Université Grenoble Alpes, Unité Mixte de Recherche-S1036, 38000, Grenoble, France.
| | - Say Viengchareun
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France.
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69
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T-Cell Intracellular Antigens and Hu Antigen R Antagonistically Modulate Mitochondrial Activity and Dynamics by Regulating Optic Atrophy 1 Gene Expression. Mol Cell Biol 2017. [PMID: 28630277 DOI: 10.1128/mcb.00174-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitochondria undergo frequent morphological changes to control their function. We show here that T-cell intracellular antigens (TIA1b/TIARb) and Hu antigen R (HuR) have antagonistic roles in mitochondrial function by modulating the expression of mitochondrial shaping proteins. Expression of TIA1b/TIARb alters the mitochondrial dynamic network by enhancing fission and clustering, which is accompanied by a decrease in respiration. In contrast, HuR expression promotes fusion and cristae remodeling and increases respiratory activity. Mechanistically, TIA proteins downregulate the expression of optic atrophy 1 (OPA1) protein via switching of the splicing patterns of OPA1 to facilitate the production of OPA1 variant 5 (OPA1v5). Conversely, HuR enhances the expression of OPA1 mRNA isoforms through increasing steady-state levels and targeting translational efficiency at the 3' untranslated region. Knockdown of TIA1/TIAR or HuR partially reversed the expression profile of OPA1, whereas knockdown of OPA1 or overexpression of OPA1v5 provoked mitochondrial clustering. Middle-term expression of TIA1b/TIARb triggers reactive oxygen species production and mitochondrial DNA damage, which is accompanied by mitophagy, autophagy, and apoptosis. In contrast, HuR expression promotes mitochondrion-dependent cell proliferation. Collectively, these results provide molecular insights into the antagonistic functions of TIA1b/TIARb and HuR in mitochondrial activity dynamics and suggest that their balance might contribute to mitochondrial physiopathology.
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70
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Khalaj K, Ahn SH, Bidarimath M, Nasirzadeh Y, Singh SS, Fazleabas AT, Young SL, Lessey BA, Koti M, Tayade C. A balancing act: RNA binding protein HuR/TTP axis in endometriosis patients. Sci Rep 2017; 7:5883. [PMID: 28724967 PMCID: PMC5517625 DOI: 10.1038/s41598-017-06081-7] [Citation(s) in RCA: 12] [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: 12/22/2016] [Accepted: 06/07/2017] [Indexed: 12/12/2022] Open
Abstract
Endometriosis, a major reproductive pathology affecting 8-10% of women is characterized by chronic inflammation and immune dysfunction. Human antigen R (HuR) and Tristetraprolin (TTP) are RNA binding proteins that competitively bind to cytokines involved in inflammation including: tumor necrosis factor alpha (TNF-α), granulocyte macrophage colony stimulating factor (GM-CSF), interleukin 6 (IL-6) among others, and stabilize and destabilize them, respectively. The aim of this study was to examine RNA binding protein (RNABP) HuR/TTP axis in endometriosis patients compared to menstrual stage matched healthy fertile controls in hopes of better understanding their contribution to the pathogenesis of endometriosis. Additionally, using a targeted in vitro siRNA approach, we examined whether knock-down of TTP can play a functional role on other RNABPs that competitively bind to inflammatory targets of TTP in both endometriotic and endometrial epithelial cell lines. Our results suggest that RNABPs TTP and HuR are dysregulated in endometriotic lesions compared to matched eutopic patient samples as well endometrium from healthy controls. Silencing of TTP in endometriotic and endometrial epithelial cells revealed differential response to inflammatory cytokines and other RNABPs. Our results suggest potential involvement of HuR/TTP RNA binding protein axis in regulation of inflammation in endometriosis.
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Affiliation(s)
- Kasra Khalaj
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Soo Hyun Ahn
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Mallikarjun Bidarimath
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Yasmin Nasirzadeh
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Sukhbir S Singh
- Department of Obstetrics and Gynecology, University of Ottawa, Ottawa, Ontario, K1H 7W9, Canada
| | - Asgerally T Fazleabas
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University College of Human Medicine, Grand Rapids, MI, 49503, USA
| | - Steven L Young
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, North Carolina, NC, 27514, USA
| | - Bruce A Lessey
- Department of Obstetrics and Gynecology, Greenville Health Systems, Greenville, South Carolina, SC, 29605, USA
| | - Madhuri Koti
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
| | - Chandrakant Tayade
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
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71
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Lang M, Berry D, Passecker K, Mesteri I, Bhuju S, Ebner F, Sedlyarov V, Evstatiev R, Dammann K, Loy A, Kuzyk O, Kovarik P, Khare V, Beibel M, Roma G, Meisner-Kober N, Gasche C. HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis. Cancer Res 2017; 77:2424-2438. [PMID: 28428272 PMCID: PMC5826591 DOI: 10.1158/0008-5472.can-15-1726] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 07/30/2015] [Accepted: 02/02/2017] [Indexed: 12/19/2022]
Abstract
HuR is an RNA-binding protein implicated in immune homeostasis and various cancers, including colorectal cancer. HuR binding to AU-rich elements within the 3' untranslated region of mRNAs encoding oncogenes, growth factors, and various cytokines leads message stability and translation. In this study, we evaluated HuR as a small-molecule target for preventing colorectal cancer in high-risk groups such as those with familial adenomatosis polyposis (FAP) or inflammatory bowel disease (IBD). In human specimens, levels of cytoplasmic HuR were increased in colonic epithelial cells from patients with IBD, IBD-cancer, FAP-adenoma, and colorectal cancer, but not in patients with IBD-dysplasia. Intraperitoneal injection of the HuR small-molecule inhibitor MS-444 in AOM/DSS mice, a model of IBD and inflammatory colon cancer, augmented DSS-induced weight loss and increased tumor multiplicity, size, and invasiveness. MS-444 treatment also abrogated tumor cell apoptosis and depleted tumor-associated eosinophils, accompanied by a decrease in IL18 and eotaxin-1. In contrast, HuR inhibition in APCMin mice, a model of FAP and colon cancer, diminished the number of small intestinal tumors generated. In this setting, fecal microbiota, evaluated by 16S rRNA gene amplicon sequencing, shifted to a state of reduced bacterial diversity, with an increased representation of Prevotella, Akkermansia, and Lachnospiraceae Taken together, our results indicate that HuR activation is an early event in FAP-adenoma but is not present in IBD-dysplasia. Furthermore, our results offer a preclinical proof of concept for HuR inhibition as an effective means of FAP chemoprevention, with caution advised in the setting of IBD. Cancer Res; 77(9); 2424-38. ©2017 AACR.
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Affiliation(s)
- Michaela Lang
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - David Berry
- Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Katharina Passecker
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Ildiko Mesteri
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Sabin Bhuju
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Florian Ebner
- Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Vitaly Sedlyarov
- Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Rayko Evstatiev
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Kyle Dammann
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Alexander Loy
- Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Orest Kuzyk
- Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Pavel Kovarik
- Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Vineeta Khare
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Martin Beibel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Basel, Switzerland
- Department of Biology, University of Naples Federico II, Complesso Universitario MSA, Naples, Italy
| | | | - Christoph Gasche
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria.
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72
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Khalaj K, Miller JE, Fenn CR, Ahn S, Luna RL, Symons L, Monsanto SP, Koti M, Tayade C. RNA-Binding Proteins in Female Reproductive Pathologies. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:1200-1210. [PMID: 28408123 DOI: 10.1016/j.ajpath.2017.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 01/26/2017] [Indexed: 12/14/2022]
Abstract
RNA-binding proteins are key regulatory molecules involved primarily in post-transcriptional gene regulation of RNAs. Post-transcriptional gene regulation is critical for adequate cellular growth and survival. Recent reports have shown key interactions between these RNA-binding proteins and other regulatory elements, such as miRNAs and long noncoding RNAs, either enhancing or diminishing their response to RNA stabilization. Many RNA-binding proteins have been reported to play a functional role in mediation of cytokines involved in inflammation and immune dysfunction, and some have been classified as global post-transcriptional regulators of inflammation. The ubiquitous expression of RNA-binding proteins in a wide variety of cell types and their unique mechanisms of degradative action provide evidence that they are involved in reproductive tract pathologies. Aberrant inflammation and immune dysfunction are major contributors to the pathogenesis and disease pathophysiology of many reproductive pathologies, including ovarian and endometrial cancers in the female reproductive tract. Herein, we discuss various RNA-binding proteins and their unique contributions to female reproductive pathologies with a focus on those mediated by aberrant inflammation and immune dysfunction.
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Affiliation(s)
- Kasra Khalaj
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Jessica E Miller
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Christian R Fenn
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - SooHyun Ahn
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Rayana L Luna
- Ultrastructure Laboratory, Aggeu Magalhães Research Center of the Oswaldo Cruz Foundation, Recife, Brazil
| | - Lindsey Symons
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Stephany P Monsanto
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Madhuri Koti
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Chandrakant Tayade
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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73
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Saltel F, Giese A, Azzi L, Elatmani H, Costet P, Ezzoukhry Z, Dugot-Senant N, Miquerol L, Boussadia O, Wodrich H, Dubus P, Jacquemin-Sablon H. Unr defines a novel class of nucleoplasmic reticulum involved in mRNA translation. J Cell Sci 2017; 130:1796-1808. [PMID: 28386023 DOI: 10.1242/jcs.198697] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/31/2017] [Indexed: 12/23/2022] Open
Abstract
Unr (officially known as CSDE1) is a cytoplasmic RNA-binding protein with roles in the regulation of mRNA stability and translation. In this study, we identified a novel function for Unr, which acts as a positive regulator of placental development. Unr expression studies in the developing placenta revealed the presence of Unr-rich foci that are apparently located in the nuclei of trophoblast giant cells (TGCs). We determined that what we initially thought to be foci, were actually cross sections of a network of double-wall nuclear membrane invaginations that contain a cytoplasmic core related to the nucleoplasmic reticulum (NR). We named them, accordingly, Unr-NRs. Unr-NRs constitute a novel type of NR because they contain high levels of poly(A) RNA and translation factors, and are sites of active translation. In murine tissues, Unr-NRs are only found in two polyploid cell types, in TGCs and hepatocytes. In vitro, their formation is linked to stress and polyploidy because, in three cancer cell lines, cytotoxic drugs that are known to promote polyploidization induce their formation. Finally, we show that Unr is required in vivo for the formation of Unr-containing NRs because these structures are absent in Unr-null TGCs.
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Affiliation(s)
- Frédéric Saltel
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France .,University of Bordeaux, F-33000 Bordeaux, France
| | - Alban Giese
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France
| | - Lamia Azzi
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France.,Department of Tumor Biology, CHU, F-33000 Bordeaux, France
| | - Habiba Elatmani
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France
| | - Pierre Costet
- Laboratoire de Transgenèse, Université Bordeaux, F-33000 Bordeaux, France
| | - Zakaria Ezzoukhry
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France
| | | | - Lucile Miquerol
- Aix-Marseille University, CNRS, IBDM UMR 7288, Marseille, France
| | | | - Harald Wodrich
- University of Bordeaux, F-33000 Bordeaux, France.,MFP CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, F-33000 Bordeaux, France
| | - Pierre Dubus
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France.,Department of Tumor Biology, CHU, F-33000 Bordeaux, France
| | - Hélène Jacquemin-Sablon
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France .,University of Bordeaux, F-33000 Bordeaux, France
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74
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HuR Enhances Early Restitution of the Intestinal Epithelium by Increasing Cdc42 Translation. Mol Cell Biol 2017; 37:MCB.00574-16. [PMID: 28031329 DOI: 10.1128/mcb.00574-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/21/2016] [Indexed: 12/27/2022] Open
Abstract
The mammalian intestinal mucosa exhibits a spectrum of responses after acute injury and repairs itself rapidly to restore the epithelial integrity. The RNA-binding protein HuR regulates the stability and translation of target mRNAs and is involved in many aspects of gut epithelium homeostasis, but its exact role in the regulation of mucosal repair after injury remains unknown. We show here that HuR is essential for early intestinal epithelial restitution by increasing the expression of cell division control protein 42 (Cdc42) at the posttranscriptional level. HuR bound to the Cdc42 mRNA via its 3' untranslated region, and this association specifically enhanced Cdc42 translation without an effect on the Cdc42 mRNA level. Intestinal epithelium-specific HuR knockout not only decreased Cdc42 levels in mucosal tissues, but it also inhibited repair of damaged mucosa induced by mesenteric ischemia/reperfusion in the small intestine and by dextran sulfate sodium in the colon. Furthermore, Cdc42 silencing prevented HuR-mediated stimulation of cell migration over the wounded area by altering the subcellular distribution of F-actin. These results indicate that HuR promotes early intestinal mucosal repair after injury by increasing Cdc42 translation and demonstrate the importance of HuR deficiency in the pathogenesis of delayed mucosal healing in certain pathological conditions.
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75
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Bersani C, Huss M, Giacomello S, Xu LD, Bianchi J, Eriksson S, Jerhammar F, Alexeyenko A, Vilborg A, Lundeberg J, Lui WO, Wiman KG. Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis. Oncotarget 2016; 7:1895-911. [PMID: 26672765 PMCID: PMC4811505 DOI: 10.18632/oncotarget.6557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/15/2015] [Indexed: 02/06/2023] Open
Abstract
RNA-binding proteins (RBPs) play important roles in the regulation of gene expression through a variety of post-transcriptional mechanisms. The p53-induced RBP Wig-1 (Zmat3) binds RNA through its zinc finger domains and enhances stability of p53 and N-Myc mRNAs and decreases stability of FAS mRNA. To identify novel Wig-1-bound RNAs, we performed RNA-immunoprecipitation followed by high-throughput sequencing (RIP-Seq) in HCT116 and Saos-2 cells. We identified 286 Wig-1-bound mRNAs common between the two cell lines. Sequence analysis revealed that AU-rich elements (AREs) are highly enriched in the 3′UTR of these Wig-1-bound mRNAs. Network enrichment analysis showed that Wig-1 preferentially binds mRNAs involved in cell cycle regulation. Moreover, we identified a 2D Wig-1 binding motif in HIF1A mRNA. Our findings confirm that Wig-1 is an ARE-BP that regulates cell cycle-related processes and provide a novel view of how Wig-1 may bind mRNA through a putative structural motif. We also significantly extend the repertoire of Wig-1 target mRNAs. Since Wig-1 is a transcriptional target of the tumor suppressor p53, these results have implications for our understanding of p53-dependent stress responses and tumor suppression.
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Affiliation(s)
- Cinzia Bersani
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Mikael Huss
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Li-Di Xu
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Julie Bianchi
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Sofi Eriksson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Fredrik Jerhammar
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Andrey Alexeyenko
- Department of Microbiology, Tumour and Cell biology, Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Anna Vilborg
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Joakim Lundeberg
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Weng-Onn Lui
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Klas G Wiman
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
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76
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Janakiraman H, House RP, Talwar S, Courtney SM, Hazard ES, Hardiman G, Mehrotra S, Howe PH, Gangaraju V, Palanisamy V. Repression of caspase-3 and RNA-binding protein HuR cleavage by cyclooxygenase-2 promotes drug resistance in oral squamous cell carcinoma. Oncogene 2016; 36:3137-3148. [PMID: 27941877 PMCID: PMC5453834 DOI: 10.1038/onc.2016.451] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/17/2016] [Accepted: 10/31/2016] [Indexed: 12/22/2022]
Abstract
A well-studied RNA-binding protein Hu Antigen-R (HuR), controls post-transcriptional gene regulation and undergoes stress-activated caspase-3 dependent cleavage in cancer cells. The cleavage products of HuR are known to promote cell death however, the underlying molecular mechanisms facilitating caspase-3 activation and HuR cleavage remains unknown. Here, we show that HuR cleavage associated with active caspase-3 in oral cancer cells treated with ionizing radiation and chemotherapeutic drug, paclitaxel. We determined that oral cancer cells overexpressing cyclooxygenase-2 (COX-2) limited the cleavage of caspase-3 and HuR, which reduced the rate of cell death in paclitaxel resistant oral cancer cells. Specific inhibition of COX-2 by celecoxib, promoted apoptosis through activation of caspase-3 and cleavage of HuR in paclitaxel-resistant oral cancer cells, both in vitro and in vivo. In addition, oral cancer cells overexpressing cellular HuR increased the half-life of COX-2 mRNA, promoted COX-2 protein expression and exhibited enhanced tumor growth in vivo in comparison with cells expressing a cleavable form of HuR. Finally, our ribonucleoprotein immunoprecipitation and sequencing (RIP-seq) analyses of HuR in oral cancer cells treated with ionizing radiation (IR), determined that HuR cleavage product-1 (HuR-CP1) bound and promoted the expression of mRNAs encoding proteins involved in apoptosis. Our results indicated that, cellular non-cleavable HuR controls COX-2 mRNA expression and enzymatic activity. In addition, overexpressed COX-2 protein repressed the cleavage of caspase-3 and HuR to promote drug resistance and tumor growth. Altogether, our observations support the use of the COX-2 inhibitor celecoxib, in combination with paclitaxel, for the management of paclitaxel resistant oral cancer cells.
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Affiliation(s)
- H Janakiraman
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - R P House
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - S Talwar
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - S M Courtney
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, Charleston, SC, USA
| | - E S Hazard
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA.,Library Science and Informatics, Medical University of South Carolina, Charleston, SC, USA
| | - G Hardiman
- Center for Genomics Medicine, Medical University of South Carolina, Charleston, SC, USA.,Departments of Medicine and Public Health, Medical University of South Carolina, Charleston, SC, USA
| | - S Mehrotra
- Department of Surgery, Medical University of South Carolina, Charleston, SC, USA
| | - P H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - V Gangaraju
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - V Palanisamy
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA.,Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
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77
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Hou W, Sarikaya DP, Jerome-Majewska LA. Ex vivo culture of pre-placental tissues reveals that the allantois is required for maintained expression of Gcm1 and Tpbpα. Placenta 2016; 47:12-23. [DOI: 10.1016/j.placenta.2016.08.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 08/05/2016] [Accepted: 08/29/2016] [Indexed: 11/17/2022]
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78
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Valenciano AL, Knudsen GM, Mackey ZB. Extracellular-signal regulated kinase 8 of Trypanosoma brucei uniquely phosphorylates its proliferating cell nuclear antigen homolog and reveals exploitable properties. Cell Cycle 2016; 15:2827-41. [PMID: 27589575 PMCID: PMC5053586 DOI: 10.1080/15384101.2016.1222340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Trypanosoma brucei subspecies T. brucei gambiense and T. brucei rhodesiense are vector-borne pathogens that cause sleeping sickness also known as Human African Trypanosomiasis (HAT), which is fatal if left untreated. The drugs that treat HAT are ineffective and cause toxic side effects. One strategy for identifying safer and more effective HAT drugs is to therapeutically exploit essential gene targets in T. brucei. Genes that make up a basic mitogen-activated protein kinase (MAPK) network are present in T. brucei. Tb927.10.5140 encodes an essential MAPK that is homologous to the human extracellular-signal regulated kinase 8 (HsERK8) which forms a tight complex with the replication factor proliferating cell nuclear antigen (PCNA) to stabilize intracellular PCNA levels. Here we demonstrate that (TbPCNA) is uniquely phos-phorylated on serine (S) and threonine (T) residues in T. brucei and that TbERK8 phosphorylates TbPCNA at each of these residues. The ability of an ERK8 homolog to phosphorylate a PCNA homolog is a novel biochemical property that is first demonstrated here in T. brucei and may be unique to this pathogen. We demonstrate that the potent HsERK8 inhibitor Ro318220, has an IC50 for TbERK8 that is several hundred times higher than its reported IC50 for HsERK8. This indicated that the active sites of TbERK8 and HsERK8 can be selectively inhibited, which provides a rational basis for discovering inhibitors that specifically target this essential parasite MAPK to kill the parasite.
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Affiliation(s)
- Ana L Valenciano
- a Department of Biochemistry and Fralin Life Science Institute , Vector-Borne Disease Division, Virginia Polytechnic Institute and State University , Blacksburg , VA , USA
| | - Giselle M Knudsen
- b Department of Pharmaceutical Chemistry , University of California San Francisco , San Francisco , CA , USA
| | - Zachary B Mackey
- a Department of Biochemistry and Fralin Life Science Institute , Vector-Borne Disease Division, Virginia Polytechnic Institute and State University , Blacksburg , VA , USA
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79
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Hansraj NZ, Xiao L, Wu J, Chen G, Turner DJ, Wang JY, Rao JN. Posttranscriptional regulation of 14-3-3ζ by RNA-binding protein HuR modulating intestinal epithelial restitution after wounding. Physiol Rep 2016; 4:4/13/e12858. [PMID: 27401462 PMCID: PMC4945840 DOI: 10.14814/phy2.12858] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/18/2016] [Indexed: 12/14/2022] Open
Abstract
The 14‐3‐3ζ is a member of the family of 14‐3‐3 proteins and participates in many aspects of cellular processes, but its regulation and involvement in gut mucosal homeostasis remain unknown. Here, we report that 14‐3‐3ζ expression is tightly regulated at the posttranscription level by RNA‐binding protein HuR and plays an important role in early intestinal epithelial restitution after wounding. The 14‐3‐3ζ was highly expressed in the mucosa of gastrointestinal tract and in cultured intestinal epithelial cells (IECs). The 3′ untranslated region (UTR) of the 14‐3‐3ζ mRNA was bound to HuR, and this association enhanced 14‐3‐3ζ translation without effect on its mRNA content. Conditional target deletion of HuR in IECs decreased the level of 14‐3‐3ζ protein in the intestinal mucosa. Silencing 14‐3‐3ζ by transfection with specific siRNA targeting the 14‐3‐3ζ mRNA suppressed intestinal epithelial restitution as indicated by a decrease in IEC migration after wounding, whereas ectopic overexpression of the wild‐type 14‐3‐3ζ promoted cell migration. These results indicate that HuR induces 14‐3‐3ζ translation via interaction with its 3′ UTR and that 14‐3‐3ζ is necessary for stimulation of IEC migration after wounding.
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Affiliation(s)
- Natasha Z Hansraj
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Jing Wu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Gang Chen
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Douglas J Turner
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland Baltimore Veterans Affairs Medical Center, Baltimore, Maryland Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Jaladanki N Rao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
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80
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McDermott B, Ellis S, Bou-Gharios G, Clegg P, Tew S. RNA binding proteins regulate anabolic and catabolic gene expression in chondrocytes. Osteoarthritis Cartilage 2016; 24:1263-73. [PMID: 26853752 PMCID: PMC4917896 DOI: 10.1016/j.joca.2016.01.988] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 01/21/2016] [Accepted: 01/29/2016] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Regulation of anabolic and catabolic factors is considered essential in maintaining the homoeostasis of healthy articular cartilage. In this study we investigated the influence of RNA binding proteins (RNABPs) in this process. DESIGN Using small interfering RNA (siRNA), RNABP expression was knocked down in SW1353 chondrosarcoma cells and human articular chondrocytes. Gene expression and messenger RNA (mRNA) decay of anabolic (SOX9, Aggrecan) and catabolic (matrix metalloproteinase (MMP)13) factors were analysed using reverse transcription quantitative polymerase chain reaction (RT-qPCR). RNA-electromobility shift assays (EMSAs) were used to investigate RNABP interactions with the SOX9 mRNA 3' untranslated region (UTR). Immunohistochemical localisation of MMP13 and the RNABP human antigen R (HuR) was performed in E13.5 and E16.5 mouse embryo sections. RESULTS SOX9 mRNA, mRNA half-life and protein expression were increased with siRNA targeting the RNABP tristetraprolin (TTP) in both HACs and SW1353s. TTP knockdown also stimulated aggrecan mRNA expression but did not affect its stability. RNA-EMSAs demonstrated that adenine uracil (AU)-rich elements in the SOX9 mRNA 3'UTR interacted with chondrocyte proteins with three specific elements interacting with TTP. HuR knockdown significantly increased MMP13 expression and also regulated the expression of a number of known transcriptional repressors of MMP13. HuR was ubiquitously expressed within mouse embryos yet displayed regional down-regulation within developing skeletal structures. CONCLUSION This study demonstrates for the first time how RNABPs are able to affect the balance of anabolic and catabolic gene expression in human chondrocytes. The post-transcriptional mechanisms controlled by RNABPs present novel avenues of regulation and potential points of intervention for controlling the expression of SOX9 and MMP13 in chondrocytes.
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Affiliation(s)
| | | | | | | | - S.R. Tew
- Address correspondence and reprint requests to: S.R. Tew, Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst Campus, Neston, Cheshire CH64 7TE, UK. Tel: 44-(0)-151-7956235; Fax: 44-(0)-151-7946034.
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81
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Sedlyarov V, Fallmann J, Ebner F, Huemer J, Sneezum L, Ivin M, Kreiner K, Tanzer A, Vogl C, Hofacker I, Kovarik P. Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution. Mol Syst Biol 2016; 12:868. [PMID: 27178967 PMCID: PMC4988506 DOI: 10.15252/msb.20156628] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Precise regulation of mRNA decay is fundamental for robust yet not exaggerated inflammatory responses to pathogens. However, a global model integrating regulation and functional consequences of inflammation‐associated mRNA decay remains to be established. Using time‐resolved high‐resolution RNA binding analysis of the mRNA‐destabilizing protein tristetraprolin (TTP), an inflammation‐limiting factor, we qualitatively and quantitatively characterize TTP binding positions in the transcriptome of immunostimulated macrophages. We identify pervasive destabilizing and non‐destabilizing TTP binding, including a robust intronic binding, showing that TTP binding is not sufficient for mRNA destabilization. A low degree of flanking RNA structuredness distinguishes occupied from silent binding motifs. By functionally relating TTP binding sites to mRNA stability and levels, we identify a TTP‐controlled switch for the transition from inflammatory into the resolution phase of the macrophage immune response. Mapping of binding positions of the mRNA‐stabilizing protein HuR reveals little target and functional overlap with TTP, implying a limited co‐regulation of inflammatory mRNA decay by these proteins. Our study establishes a functionally annotated and navigable transcriptome‐wide atlas (http://ttp-atlas.univie.ac.at) of cis‐acting elements controlling mRNA decay in inflammation.
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Affiliation(s)
- Vitaly Sedlyarov
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Jörg Fallmann
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Florian Ebner
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Jakob Huemer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Lucy Sneezum
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Masa Ivin
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Kristina Kreiner
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Andrea Tanzer
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ivo Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark
| | - Pavel Kovarik
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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82
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Post-transcriptional regulation of Wnt co-receptor LRP6 and RNA-binding protein HuR by miR-29b in intestinal epithelial cells. Biochem J 2016; 473:1641-9. [PMID: 27089893 PMCID: PMC4888462 DOI: 10.1042/bcj20160057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/05/2016] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) control gene expression by binding to their target mRNAs for degradation and/or translation repression and are implicated in many aspects of cellular physiology. Our previous study shows that miR-29b acts as a biological repressor of intestinal mucosal growth, but its exact downstream targets remain largely unknown. In the present study, we found that mRNAs, encoding Wnt co-receptor LRP6 (low-density lipoprotein-receptor-related protein 6) and RNA-binding protein (RBP) HuR, are novel targets of miR-29b in intestinal epithelial cells (IECs) and that expression of LRP6 and HuR is tightly regulated by miR-29b at the post-transcriptional level. miR-29b interacted with both Lrp6 and HuR mRNAs via their 3′-UTRs and inhibited LRP6 and HuR expression by destabilizing Lrp6 and HuR mRNAs and repressing their translation. Studies using heterologous reporter constructs revealed a greater repressive effect of miR-29b through a single binding site in the Lrp6 or HuR 3′-UTR, whereas deletion mutation of this site prevented miR-29b-induced repression of LRP6 and HuR expression. Repression of HuR by miR-29b in turn also contributed to miR-29b-induced LRP6 inhibition, since ectopic overexpression of HuR in cells overexpressing miR-29b restored LRP6 expression to near normal levels. Taken together, our results suggest that miR-29b inhibits expression of LRP6 and HuR post-transcriptionally, thus playing a role in the regulation of IEC proliferation and intestinal epithelial homoeostasis.
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83
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Huang YH, Peng W, Furuuchi N, Gerhart J, Rhodes K, Mukherjee N, Jimbo M, Gonye GE, Brody JR, Getts RC, Sawicki JA. Delivery of Therapeutics Targeting the mRNA-Binding Protein HuR Using 3DNA Nanocarriers Suppresses Ovarian Tumor Growth. Cancer Res 2016; 76:1549-59. [PMID: 26921342 DOI: 10.1158/0008-5472.can-15-2073] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/08/2016] [Indexed: 11/16/2022]
Abstract
Growing evidence shows that cancer cells use mRNA-binding proteins and miRNAs to posttranscriptionally regulate signaling pathways to adapt to harsh tumor microenvironments. In ovarian cancer, cytoplasmic accumulation of mRNA-binding protein HuR (ELAVL1) is associated with poor prognosis. In this study, we observed high HuR expression in ovarian cancer cells compared with ovarian primary cells, providing a rationale for targeting HuR. RNAi-mediated silencing of HuR in ovarian cancer cells significantly decreased cell proliferation and anchorage-independent growth, and impaired migration and invasion. In addition, HuR-depleted human ovarian xenografts were smaller than control tumors. A biodistribution study showed effective tumor-targeting by a novel Cy3-labeled folic acid (FA)-derivatized DNA dendrimer nanocarrier (3DNA). We combined siRNAs against HuR with FA-3DNA and found that systemic administration of the resultant FA-3DNA-siHuR conjugates to ovarian tumor-bearing mice suppressed tumor growth and ascites development, significantly prolonging lifespan. NanoString gene expression analysis identified multiple HuR-regulated genes that function in many essential cellular and molecular pathways, an attractive feature of candidate therapeutic targets. Taken together, these results are the first to demonstrate the versatility of the 3DNA nanocarrier for in vivo-targeted delivery of a cancer therapeutic and support further preclinical investigation of this system adapted to siHuR-targeted therapy for ovarian cancer.
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Affiliation(s)
- Yu-Hung Huang
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania. Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Weidan Peng
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania
| | - Narumi Furuuchi
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania
| | | | | | - Neelanjan Mukherjee
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Masaya Jimbo
- Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Jonathan R Brody
- Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Janet A Sawicki
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
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84
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Latorre E, Carelli S, Caremoli F, Giallongo T, Colli M, Canazza A, Provenzani A, Di Giulio AM, Gorio A. Human Antigen R Binding and Regulation of SOX2 mRNA in Human Mesenchymal Stem Cells. Mol Pharmacol 2015; 89:243-52. [PMID: 26677051 DOI: 10.1124/mol.115.100701] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/11/2015] [Indexed: 02/02/2023] Open
Abstract
Since 2005, sex determining region y-box 2 (SOX2) has drawn the attention of the scientific community for being one of the key transcription factors responsible for pluripotency induction in somatic stem cells. Our research investigated the turnover regulation of SOX2 mRNA in human adipose-derived stem cells, considered one of the most valuable sources of somatic stem cells in regenerative medicine. Mitoxantrone is a drug that acts on nucleic acids primarily used to treat certain types of cancer and was recently shown to ameliorate the outcome of autoimmune diseases such as multiple sclerosis. In addition, mitoxantrone has been shown to inhibit the binding of human antigen R (HuR) RNA-binding protein to tumor necrosis factor-α mRNA. Our results show that HuR binds to the 3'-untranslated region of SOX2 mRNA together with the RNA-induced silencing complex miR145. The HuR binding works by stabilizing the interaction between the 3'-untranslated region and the RNA-induced silencing complex. Cell exposure to mitoxantrone leads to HuR detachment and the subsequent prolongation of the SOX2 mRNA half-life. The prolonged SOX2 half-life allows improvement of the spheroid-forming capability of the adipose-derived stem cells. The silencing of HuR confirmed the above observations and illustrates how the RNA-binding protein HuR may be a required molecule for regulation of SOX2 mRNA decay.
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Affiliation(s)
- Elisa Latorre
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy (E.L., S.C., F.C., T.G., M.C., A.M.D.G., A.G.); Laboratory of Cell Biology, Cerebrovascular Diseases Unit, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy (A.C.); and Laboratory of Genomic Screening Center for Integrative Biology, University of Trento, Trento, Italy (A.P.)
| | - Stephana Carelli
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy (E.L., S.C., F.C., T.G., M.C., A.M.D.G., A.G.); Laboratory of Cell Biology, Cerebrovascular Diseases Unit, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy (A.C.); and Laboratory of Genomic Screening Center for Integrative Biology, University of Trento, Trento, Italy (A.P.)
| | - Filippo Caremoli
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy (E.L., S.C., F.C., T.G., M.C., A.M.D.G., A.G.); Laboratory of Cell Biology, Cerebrovascular Diseases Unit, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy (A.C.); and Laboratory of Genomic Screening Center for Integrative Biology, University of Trento, Trento, Italy (A.P.)
| | - Toniella Giallongo
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy (E.L., S.C., F.C., T.G., M.C., A.M.D.G., A.G.); Laboratory of Cell Biology, Cerebrovascular Diseases Unit, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy (A.C.); and Laboratory of Genomic Screening Center for Integrative Biology, University of Trento, Trento, Italy (A.P.)
| | - Mattia Colli
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy (E.L., S.C., F.C., T.G., M.C., A.M.D.G., A.G.); Laboratory of Cell Biology, Cerebrovascular Diseases Unit, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy (A.C.); and Laboratory of Genomic Screening Center for Integrative Biology, University of Trento, Trento, Italy (A.P.)
| | - Alessandra Canazza
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy (E.L., S.C., F.C., T.G., M.C., A.M.D.G., A.G.); Laboratory of Cell Biology, Cerebrovascular Diseases Unit, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy (A.C.); and Laboratory of Genomic Screening Center for Integrative Biology, University of Trento, Trento, Italy (A.P.)
| | - Alessandro Provenzani
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy (E.L., S.C., F.C., T.G., M.C., A.M.D.G., A.G.); Laboratory of Cell Biology, Cerebrovascular Diseases Unit, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy (A.C.); and Laboratory of Genomic Screening Center for Integrative Biology, University of Trento, Trento, Italy (A.P.)
| | - Anna Maria Di Giulio
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy (E.L., S.C., F.C., T.G., M.C., A.M.D.G., A.G.); Laboratory of Cell Biology, Cerebrovascular Diseases Unit, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy (A.C.); and Laboratory of Genomic Screening Center for Integrative Biology, University of Trento, Trento, Italy (A.P.)
| | - Alfredo Gorio
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy (E.L., S.C., F.C., T.G., M.C., A.M.D.G., A.G.); Laboratory of Cell Biology, Cerebrovascular Diseases Unit, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy (A.C.); and Laboratory of Genomic Screening Center for Integrative Biology, University of Trento, Trento, Italy (A.P.)
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85
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Kovarik P, Ebner F, Sedlyarov V. Posttranscriptional regulation of cytokine expression. Cytokine 2015; 89:21-26. [PMID: 26586165 DOI: 10.1016/j.cyto.2015.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 01/20/2023]
Abstract
Expression of cytokines and chemokines is regulated at multiple steps during the transfer of the genetic information from DNA sequence to the functional protein. The multilayered control of cytokine expression reflects the need of the immune system to precisely and rapidly adjust the magnitude and duration of immune responses to external cues. Common features of the regulation of cytokine expression are temporal and highly dynamic changes in cytokine mRNA stability. Failures in the timing and extent of mRNA decay can result in disease. Recent advances in transcriptome-wide approaches began to shed light into the complex network of cis-acting sequence elements and trans-acting factors controlling mRNA stability. These approaches led to the discovery of novel unexpected paradigms but they also revealed new questions. This review will discuss the control of cytokine mRNA stability both in the context of high content approaches as well as focused mechanistic studies and animal models. The article highlights the need for systems biology approaches as important means to understand how cytokine mRNA decay helps maintain the immune and tissue homeostasis, and to explore options for therapeutical exploitation of mRNA stability regulation.
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Affiliation(s)
- Pavel Kovarik
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
| | - Florian Ebner
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Vitaly Sedlyarov
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
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86
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Thalamic WNT3 Secretion Spatiotemporally Regulates the Neocortical Ribosome Signature and mRNA Translation to Specify Neocortical Cell Subtypes. J Neurosci 2015; 35:10911-26. [PMID: 26245956 DOI: 10.1523/jneurosci.0601-15.2015] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED Neocortical development requires tightly controlled spatiotemporal gene expression. However, the mechanisms regulating ribosomal complexes and the timed specificity of neocortical mRNA translation are poorly understood. We show that active mRNA translation complexes (polysomes) contain ribosomal protein subsets that undergo dynamic spatiotemporal rearrangements during mouse neocortical development. Ribosomal protein specificity within polysome complexes is regulated by the arrival of in-growing thalamic axons, which secrete the morphogen Wingless-related MMTV (mouse mammary tumor virus) integration site 3 (WNT3). Thalamic WNT3 release during midneurogenesis promotes a change in the levels of Ribosomal protein L7 in polysomes, thereby regulating neocortical translation machinery specificity. Furthermore, we present an RNA sequencing dataset analyzing mRNAs that dynamically associate with polysome complexes as neocortical development progresses, and thus may be regulated spatiotemporally at the level of translation. Thalamic WNT3 regulates neocortical translation of two such mRNAs, Foxp2 and Apc, to promote FOXP2 expression while inhibiting APC expression, thereby driving neocortical neuronal differentiation and suppressing oligodendrocyte maturation, respectively. This mechanism may enable targeted and rapid spatiotemporal control of ribosome composition and selective mRNA translation in complex developing systems like the neocortex. SIGNIFICANCE STATEMENT The neocortex is a highly complex circuit generating the most evolutionarily advanced complex cognitive and sensorimotor functions. An intricate progression of molecular and cellular steps during neocortical development determines its structure and function. Our goal is to study the steps regulating spatiotemporal specificity of mRNA translation that govern neocortical development. In this work, we show that the timed secretion of Wingless-related MMTV (mouse mammary tumor virus) integration site 3 (WNT3) by ingrowing axons from the thalamus regulates the combinatorial composition of ribosomal proteins in developing neocortex, which we term the "neocortical ribosome signature." Thalamic WNT3 further regulates the specificity of mRNA translation and development of neurons and oligodendrocytes in the neocortex. This study advances our overall understanding of WNT signaling and the spatiotemporal regulation of mRNA translation in highly complex developing systems.
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87
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The Poly(C) Binding Protein Pcbp2 and Its Retrotransposed Derivative Pcbp1 Are Independently Essential to Mouse Development. Mol Cell Biol 2015; 36:304-19. [PMID: 26527618 DOI: 10.1128/mcb.00936-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 10/28/2015] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins participate in a complex array of posttranscriptional controls essential to cell type specification and somatic development. Despite their detailed biochemical characterizations, the degree to which each RNA-binding protein impacts mammalian embryonic development remains incompletely defined, and the level of functional redundancy among subsets of these proteins remains open to question. The poly(C) binding proteins, PCBPs (αCPs and hnRNP E proteins), are encoded by a highly conserved and broadly expressed gene family. The two major Pcbp isoforms, Pcbp2 and Pcbp1, are robustly expressed in a wide range of tissues and exert both nuclear and cytoplasmic controls over gene expression. Here, we report that Pcbp1-null embryos are rendered nonviable in the peri-implantation stage. In contrast, Pcbp2-null embryos undergo normal development until midgestation (12.5 to 13.5 days postcoitum), at which time they undergo a dramatic loss in viability associated with combined cardiovascular and hematopoietic abnormalities. Mice heterozygous for either Pcbp1 or Pcbp2 null alleles display a mild and nondisruptive defect in initial postpartum weight gain. These data reveal that Pcbp1 and Pcbp2 are individually essential for mouse embryonic development and have distinct impacts on embryonic viability and that Pcpb2 has a nonredundant in vivo role in hematopoiesis. These data further provide direct evidence that Pcbp1, a retrotransposed derivative of Pcpb2, has evolved an essential function(s) in the mammalian genome.
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88
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Li H, Hou S, Hao T, Azam S, Liu C, Shi L, Lei H. HuR antagonizes the effect of an intronic pyrimidine-rich sequence in regulating WT1 +/-KTS isoforms. RNA Biol 2015; 12:1364-71. [PMID: 26512748 DOI: 10.1080/15476286.2015.1102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
WT1 + KTS and -KTS isoforms only differ in 3 amino acids in protein sequence but show significant functional difference. The +/-KTS isoforms were generated by alternative usage of 2 adjacent 5' splice sites at RNA level, however, how these 2 isoforms are regulated is still elusive. Here we report the identification of an intronic pyrimidine-rich sequence that is critical for the ratio of +/-KTS isoforms, deletion or partial replacement of the sequence led to full/significant shift to -KTS isoform. To identify trans-factors that can regulate +/-KTS isoforms via the binding to the element, we performed RNP assembly using in vitro transcribed RNA with or without the pyrimidine-rich sequence. Mass spectrometry analysis of purified RNPs showed that the element associated with many splicing factors. Co-transfection of these factors with WT1 reporter revealed that HuR promoted the production of -KTS isoform at the reporter level. RNA immuno-precipitation experiment indicated that HuR interacted with the pyrimidine-rich element in WT1 intron 9. We further presented evidence that transient or stable over-expression of HuR led to enhanced expression of endogenous -KTS isoform. Moreover, knockdown of HuR resulted in decreased expression of endogenous -KTS isoform in 293T, SW620, SNU-387 and AGS cell lines. Together, these data indicate that HuR binds to the pyrimidine-rich sequence and antagonize its effect in regulating WT1 +/-KTS isoforms.
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Affiliation(s)
- Hui Li
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China.,c Equal contribution
| | - Shuai Hou
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China.,c Equal contribution
| | - Tian Hao
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China
| | - Sikandar Azam
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China
| | - Caigang Liu
- b Breast Disease and Reconstruction Center; Breast Cancer Key Lab of Dalian; the Second Hospital of Dalian Medical University ; Dalian , P.R. China
| | - Lei Shi
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China
| | - Haixin Lei
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China
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89
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Newman R, McHugh J, Turner M. RNA binding proteins as regulators of immune cell biology. Clin Exp Immunol 2015. [PMID: 26201441 DOI: 10.1111/cei.12684] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific RNA binding proteins (RBP) are important regulators of the immune response. RBP modulate gene expression by regulating splicing, polyadenylation, localization, translation and decay of target mRNAs. Increasing evidence suggests that RBP play critical roles in the development, activation and function of lymphocyte populations in the immune system. This review will discuss the post-transcriptional regulation of gene expression by RBP during lymphocyte development, with particular focus on the Tristetraprolin family of RBP.
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Affiliation(s)
- R Newman
- Babraham Institute, Cambridge, UK
| | - J McHugh
- Babraham Institute, Cambridge, UK
| | - M Turner
- Babraham Institute, Cambridge, UK
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90
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Splicing Regulation of Pro-Inflammatory Cytokines and Chemokines: At the Interface of the Neuroendocrine and Immune Systems. Biomolecules 2015; 5:2073-100. [PMID: 26371053 PMCID: PMC4598789 DOI: 10.3390/biom5032073] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/28/2015] [Indexed: 01/13/2023] Open
Abstract
Alternative splicing plays a key role in posttranscriptional regulation of gene expression, allowing a single gene to encode multiple protein isoforms. As such, alternative splicing amplifies the coding capacity of the genome enormously, generates protein diversity, and alters protein function. More than 90% of human genes undergo alternative splicing, and alternative splicing is especially prevalent in the nervous and immune systems, tissues where cells need to react swiftly and adapt to changes in the environment through carefully regulated mechanisms of cell differentiation, migration, targeting, and activation. Given its prevalence and complexity, this highly regulated mode of gene expression is prone to be affected by disease. In the following review, we look at how alternative splicing of signaling molecules—cytokines and their receptors—changes in different pathological conditions, from chronic inflammation to neurologic disorders, providing means of functional interaction between the immune and neuroendocrine systems. Switches in alternative splicing patterns can be very dynamic and can produce signaling molecules with distinct or antagonistic functions and localization to different subcellular compartments. This newly discovered link expands our understanding of the biology of immune and neuroendocrine cells, and has the potential to open new windows of opportunity for treatment of neurodegenerative disorders.
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91
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DeMicco A, Naradikian MS, Sindhava VJ, Yoon JH, Gorospe M, Wertheim GB, Cancro MP, Bassing CH. B Cell-Intrinsic Expression of the HuR RNA-Binding Protein Is Required for the T Cell-Dependent Immune Response In Vivo. THE JOURNAL OF IMMUNOLOGY 2015; 195:3449-62. [PMID: 26320247 DOI: 10.4049/jimmunol.1500512] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/03/2015] [Indexed: 11/19/2022]
Abstract
The HuR RNA-binding protein posttranscriptionally controls expression of genes involved in cellular survival, proliferation, and differentiation. To determine roles of HuR in B cell development and function, we analyzed mice with B lineage-specific deletion of the HuR gene. These HuRΔ/Δ mice have reduced numbers of immature bone marrow and mature splenic B cells, with only the former rescued by p53 inactivation, indicating that HuR supports B lineage cells through developmental stage-specific mechanisms. Upon in vitro activation, HuRΔ/Δ B cells have a mild proliferation defect and impaired ability to produce mRNAs that encode IgH chains of secreted Abs, but no deficiencies in survival, isotype switching, or expression of germinal center (GC) markers. In contrast, HuRΔ/Δ mice have minimal serum titers of all Ab isotypes, decreased numbers of GC and plasma B cells, and few peritoneal B-1 B cells. Moreover, HuRΔ/Δ mice have severely decreased GCs, T follicular helper cells, and high-affinity Abs after immunization with a T cell-dependent Ag. This failure of HuRΔ/Δ mice to mount a T cell-dependent Ab response contrasts with the ability of HuRΔ/Δ B cells to become GC-like in vitro, indicating that HuR is essential for aspects of B cell activation unique to the in vivo environment. Consistent with this notion, we find in vitro stimulated HuRΔ/Δ B cells exhibit modestly reduced surface expression of costimulatory molecules whose expression is similarly decreased in humans with common variable immunodeficiency. HuRΔ/Δ mice provide a model to identify B cell-intrinsic factors that promote T cell-dependent immune responses in vivo.
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Affiliation(s)
- Amy DeMicco
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Cell and Molecular Biology Graduate Group, Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Martin S Naradikian
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Vishal J Sindhava
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224; and
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224; and
| | - Gerald B Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Michael P Cancro
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Craig H Bassing
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Cell and Molecular Biology Graduate Group, Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
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Neelamraju Y, Hashemikhabir S, Janga SC. The human RBPome: from genes and proteins to human disease. J Proteomics 2015; 127:61-70. [PMID: 25982388 DOI: 10.1016/j.jprot.2015.04.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/07/2015] [Accepted: 04/28/2015] [Indexed: 12/29/2022]
Abstract
RNA binding proteins (RBPs) play a central role in mediating post transcriptional regulation of genes. However less is understood about them and their regulatory mechanisms. In this study, we construct a catalogue of 1344 experimentally confirmed RBPs. The domain architecture of RBPs enabled us to classify them into three groups - Classical (29%), Non-classical (19%) and unclassified (52%). A higher percentage of proteins with unclassified domains reveals the presence of various uncharacterised motifs that can potentially bind RNA. RBPs were found to be highly disordered compared to Non-RBPs (p<2.2e-16, Fisher's exact test), suggestive of a dynamic regulatory role of RBPs in cellular signalling and homeostasis. Evolutionary analysis in 62 different species showed that RBPs are highly conserved compared to Non-RBPs (p<2.2e-16, Wilcox-test), reflecting the conservation of various biological processes like mRNA splicing and ribosome biogenesis. The expression patterns of RBPs from human proteome map revealed that ~40% of them are ubiquitously expressed and ~60% are tissue-specific. RBPs were also seen to be highly associated with several neurological disorders, cancer and inflammatory diseases. Anatomical contexts like B cells, T-cells, foetal liver and foetal brain were found to be strongly enriched for RBPs, implying a prominent role of RBPs in immune responses and different developmental stages. The catalogue and meta-analysis presented here should form a foundation for furthering our understanding of RBPs and the cellular networks they control, in years to come. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Yaseswini Neelamraju
- Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Seyedsasan Hashemikhabir
- Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Sarath Chandra Janga
- Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, United States.
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93
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Wang C, Chen Y, Deng H, Gao S, Li L. Rbm46 Regulates Trophectoderm Differentiation by Stabilizing Cdx2 mRNA in Early Mouse Embryos. Stem Cells Dev 2015; 24:904-15. [DOI: 10.1089/scd.2014.0323] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chenchen Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing, China
- SARI Center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuanfan Chen
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing, China
- SARI Center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Shanghai, China
| | - Hongkui Deng
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing, China
| | - Shaorong Gao
- National Institute of Biological Sciences, Beijing, China
| | - Lingsong Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing, China
- SARI Center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Shanghai, China
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94
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Chaturvedi P, Neelamraju Y, Arif W, Kalsotra A, Janga SC. Uncovering RNA binding proteins associated with age and gender during liver maturation. Sci Rep 2015; 5:9512. [PMID: 25824884 PMCID: PMC4379467 DOI: 10.1038/srep09512] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/09/2015] [Indexed: 11/09/2022] Open
Abstract
In the present study, we perform an association analysis focusing on the expression changes of 1344 RNA Binding proteins (RBPs) as a function of age and gender in human liver. We identify 88 and 45 RBPs to be significantly associated with age and gender respectively. Experimental verification of several of the predicted associations in mice confirmed our findings. Our results suggest that a small fraction of the gender-associated RBPs (~40%) are expressed higher in males than females. Altogether, these observations show that several of these RBPs are important and conserved regulators in maintaining liver function. Further analysis of the protein interaction network of RBPs associated with age and gender based on the centrality measures like degree, betweenness and closeness revealed that several of these RBPs might be prominent players in aging liver and impart gender specific alterations in gene expression via the formation of protein complexes. Indeed, both age and gender-associated RBPs in liver were found to show significantly higher clustering coefficients and network centrality measures compared to non-associated RBPs. The compendium of RBPs and this study will help us gain insight into the role of post-transcriptional regulatory molecules in aging and gender specific expression of genes.
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Affiliation(s)
- Praneet Chaturvedi
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202
| | - Yaseswini Neelamraju
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202
| | - Waqar Arif
- Departments of Biochemistry and Medical Biochemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Auinash Kalsotra
- Departments of Biochemistry and Medical Biochemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Sarath Chandra Janga
- 1] Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202 [2] Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, Indiana, 46202 [3] Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, Indiana, 46202
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95
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Perspective: The RNA exosome, cytokine gene regulation and links to autoimmunity. Cytokine 2015; 74:175-80. [PMID: 25835609 DOI: 10.1016/j.cyto.2015.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/04/2015] [Indexed: 12/24/2022]
Abstract
The RNA exosome is a highly conserved exoribonuclease complex that is involved in RNA processing, quality control and turnover regulation. The exosome plays pleiotropic functions by recruiting different cofactors that regulate its target specificity. Recently, the exosome has been implicated in the regulation of immune processes including cytokine production and negative regulation of innate sensing of nucleic acids. Careful regulation of such mechanisms is critical to avoid a breakdown of self-tolerance and the pathogenesis of autoimmune disorders. This perspective briefly introduces the exosome, its its normal function in RNA biology and summarizes regulatory roles of the RNA exosome in immunity. Finally we discuss how dysregulation of exosome function can lead to autoimmune disease.
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96
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Diaz-Muñoz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, Curk T, Heggermont WA, Heymans S, Gibson GE, Kontoyiannis DL, Ule J, Turner M. The RNA-binding protein HuR is essential for the B cell antibody response. Nat Immunol 2015; 16:415-25. [PMID: 25706746 PMCID: PMC4479220 DOI: 10.1038/ni.3115] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/28/2015] [Indexed: 12/26/2022]
Abstract
Post-transcriptional regulation of mRNA by the RNA-binding protein HuR (encoded by Elavl1) is required in B cells for the germinal center reaction and for the production of class-switched antibodies in response to thymus-independent antigens. Transcriptome-wide examination of RNA isoforms and their abundance and translation in HuR-deficient B cells, together with direct measurements of HuR-RNA interactions, revealed that HuR-dependent splicing of mRNA affected hundreds of transcripts, including that encoding dihydrolipoamide S-succinyltransferase (Dlst), a subunit of the 2-oxoglutarate dehydrogenase (α-KGDH) complex. In the absence of HuR, defective mitochondrial metabolism resulted in large amounts of reactive oxygen species and B cell death. Our study shows how post-transcriptional processes control the balance of energy metabolism required for the proliferation and differentiation of B cells.
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Affiliation(s)
- Manuel D Diaz-Muñoz
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Sarah E Bell
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Kirsten Fairfax
- 1] Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK. [2] The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Elisa Monzon-Casanova
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Adam F Cunningham
- MRC Centre for Immune Regulation, Institute of Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham, UK
| | - Mar Gonzalez-Porta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Victoria I Bunik
- A. N. Belozersky Institute of PhysicoChemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
| | - Tomaž Curk
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, Slovenia
| | | | - Stephane Heymans
- 1] Center for Molecular and Vascular Biology, KU Leuven, Belgium. [2] Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Gary E Gibson
- Weill Cornell Medical College, Brain and Mind Research Institute, Burke Medical Research Institute, White Plains, New York, USA
| | - Dimitris L Kontoyiannis
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Jernej Ule
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, London, UK
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
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97
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Suresh Babu S, Joladarashi D, Jeyabal P, Thandavarayan RA, Krishnamurthy P. RNA-stabilizing proteins as molecular targets in cardiovascular pathologies. Trends Cardiovasc Med 2015; 25:676-83. [PMID: 25801788 DOI: 10.1016/j.tcm.2015.02.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/31/2015] [Accepted: 02/13/2015] [Indexed: 01/08/2023]
Abstract
The stability of mRNA has emerged as a key step in the regulation of eukaryotic gene expression and function. RNA stabilizing proteins (RSPs) contain several RNA recognition motifs, and selectively bind to adenylate-uridylate-rich elements in the 3' untranslated region of several mRNAs leading to altered processing, stability, and translation. These post-transcriptional gene regulations play a critical role in cellular homeostasis; therefore act as molecular switch between 'normal cell' and 'disease state.' Many mRNA binding proteins have been discovered to date, which either stabilize (HuR/HuA, HuB, HuC, HuD) or destabilize (AUF1, tristetraprolin, KSRP) the target transcripts. Although the function of RSPs has been widely studied in cancer biology, its role in cardiovascular pathologies is only beginning to evolve. The current review provides an overall understanding of the potential role of RSPs, specifically HuR-mediated mRNA stability in myocardial infarction, hypertension and hypertrophy. Also, the effect of RSPs on various cellular processes including inflammation, fibrosis, angiogenesis, cell-death, and proliferation and its relevance to cardiovascular pathophysiological processes is presented. We also discuss the potential clinical implications of RSPs as therapeutic targets in cardiovascular diseases.
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Affiliation(s)
- Sahana Suresh Babu
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Darukeshwara Joladarashi
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Prince Jeyabal
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Rajarajan A Thandavarayan
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Prasanna Krishnamurthy
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX.
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98
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Abstract
PURPOSE OF REVIEW This review summarizes recent findings in the area of post-transcriptional regulation of gene expression during angiogenesis, also known as new blood vessel formation. Specifically, we focus on gene regulation by HuR, an RNA-binding protein (RBP), and microRNAs (miRNAs) and their interplay, which ultimately influences cellular phenotypes of cells involved in angiogenesis. RECENT FINDINGS Recently, RBPs and miRNAs have emerged as key regulators of angiogenesis. We and others have demonstrated that the RBP HuR (a.k.a. Elavl1) stabilizes vascular endothelial growth factor-A mRNA, a potent angiogenic factor in the settings of tumor development and inflammation. However, several miRNAs were shown to modulate gene expression during developmental (miR-126), physiological (miR-126, miR-92a), and pathological angiogenesis (miR-200b, miR-132). Moreover, the interplay of HuR and miRNAs in the regulation of genes involved in angiogenesis was described. In addition, recent work suggests a new role of circulating miRNAs as paracrine mediators in angiogenesis. SUMMARY The elucidation of novel posttranscriptional gene regulatory mechanisms has expanded our understanding of angiogenesis in physiological and pathological conditions. We anticipate that this knowledge will ultimately lead to new insights for discovering novel therapeutic strategies to control pathological angiogenesis.
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99
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Puscheck EE, Awonuga AO, Yang Y, Jiang Z, Rappolee DA. Molecular biology of the stress response in the early embryo and its stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 843:77-128. [PMID: 25956296 DOI: 10.1007/978-1-4939-2480-6_4] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stress is normal during early embryogenesis and transient, elevated stress is commonplace. Stress in the milieu of the peri-implantation embryo is a summation of maternal hormones, and other elements of the maternal milieu, that signal preparedness for development and implantation. Examples discussed here are leptin, adrenaline, cortisol, and progesterone. These hormones signal maternal nutritional status and provide energy, but also signal stress that diverts maternal and embryonic energy from an optimal embryonic developmental trajectory. These hormones communicate endocrine maternal effects and local embryonic effects although signaling mechanisms are not well understood. Other in vivo stresses affect the embryo such as local infection and inflammation, hypoxia, environmental toxins such as benzopyrene, dioxin, or metals, heat shock, and hyperosmotic stress due to dehydration or diabetes. In vitro, stresses include shear during handling, improper culture media and oxygen levels, cryopreservation, and manipulations of the embryo to introduce sperm or mitochondria. We define stress as any stimulus that slows stem cell accumulation or diminishes the ability of cells to produce normal and sufficient parenchymal products upon differentiation. Thus stress deflects downwards the normal trajectories of development, growth and differentiation. Typically stress is inversely proportional to embryonic developmental and proliferative rates, but can be proportional to induction of differentiation of stem cells in the peri-implantation embryo. When modeling stress it is most interesting to produce a 'runting model' where stress exposures slow accumulation but do not create excessive apoptosis or morbidity. Windows of stress sensitivity may occur when major new embryonic developmental programs require large amounts of energy and are exacerbated if nutritional flow decreases and removes energy from the normal developmental programs and stress responses. These windows correspond to zygotic genome activation, the large mRNA program initiated at compaction, ion pumping required for cavitation, the differentiation of the first lineages, integration with the uterine environment at implantation, rapid proliferation of stem cells, and production of certain lineages which require the highest energy and are most sensitive to mitochondrial inhibition. Stress response mechanisms insure that stem cells for the early embryo and placenta survive at lower stress exposures, and that the organism survives through compensatory and prioritized stem cell differentiation, at higher stress exposures. These servomechanisms include a small set of stress enzymes from the 500 protein kinases in the kinome; the part of the genome coding for protein kinases that hierarchically regulate the activity of other proteins and enzymes. Important protein kinases that mediate the stress response of embryos and their stem cells are SAPK, p38MAPK, AMPK, PI3K, Akt, MEK1/2, MEKK4, PKA, IRE1 and PERK. These stress enzymes have cytosolic function in cell survival at low stress exposures and nuclear function in modifying transcription factor activity at higher stress exposures. Some of the transcription factors (TFs) that are most important in the stress response are JunC, JunB, MAPKAPs, ATF4, XBP1, Oct1, Oct4, HIFs, Nrf2/KEAP, NFKB, MT1, Nfat5, HSF1/2 and potency-maintaining factors Id2, Cdx2, Eomes, Sox2, Nanog, Rex1, and Oct4. Clearly the stress enzymes have a large number of cytosolic and nuclear substrates and the TFs regulate large numbers of genes. The interaction of stress enzymes and TFs in the early embryo and its stem cells are a continuing central focus of research. In vitro regulation of TFs by stress enzymes leads to reprogramming of the stem cell when stress diminishes stem cell accumulation. Since more differentiated product is produced by fewer cells, the process compensates for fewer cells. Coupled with stress-induced compensatory differentiation of stem cells is a tendency to prioritize differentiation by increasing the first essential lineage and decreasing later lineages. These mechanisms include stress enzymes that regulate TFs and provide stress-specific, shared homeostatic cellular and organismal responses of prioritized differentiation.
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Affiliation(s)
- Elizabeth E Puscheck
- Department of Ob/Gyn, REI Division, Wayne State University School of Medicine, Detroit, MI, USA
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100
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Lu YC, Chang SH, Hafner M, Li X, Tuschl T, Elemento O, Hla T. ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages. Cell Rep 2014; 9:2330-43. [PMID: 25533351 DOI: 10.1016/j.celrep.2014.11.030] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 09/17/2014] [Accepted: 11/19/2014] [Indexed: 12/19/2022] Open
Abstract
Posttranscriptional gene regulation by miRNAs and RNA binding proteins (RBP) is important in development, physiology, and disease. To examine the interplay between miRNAs and the RBP ELAVL1 (HuR), we mapped miRNA binding sites at the transcriptome-wide scale in wild-type and Elavl1 knockout murine bone-marrow-derived macrophages. Proximity of ELAVL1 binding sites attenuated miRNA binding to transcripts and promoted gene expression. Transcripts that regulate angiogenesis and macrophage/endothelial crosstalk were preferentially targeted by miRNAs, suggesting that ELAVL1 promotes angiogenesis, at least in part by antagonism of miRNA function. We found that ELAVL1 antagonized binding of miR-27 to the 3' UTR of Zfp36 mRNA and alleviated miR-27-mediated suppression of the RBP ZFP36 (Tristetraprolin). Thus, the miR-27-regulated mechanism synchronizes the expression of ELAVL1 and ZFP36. This study provides a resource for systems-level interrogation of posttranscriptional gene regulation in macrophages, a key cell type in inflammation, angiogenesis, and tissue homeostasis.
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Affiliation(s)
- Yi-Chien Lu
- Center for Vascular Biology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Sung-Hee Chang
- Center for Vascular Biology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Markus Hafner
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Xi Li
- Center for Vascular Biology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Timothy Hla
- Center for Vascular Biology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.
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