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Liu Y, Su Z, Tavana O, Gu W. Understanding the complexity of p53 in a new era of tumor suppression. Cancer Cell 2024; 42:946-967. [PMID: 38729160 DOI: 10.1016/j.ccell.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
p53 was discovered 45 years ago as an SV40 large T antigen binding protein, coded by the most frequently mutated TP53 gene in human cancers. As a transcription factor, p53 is tightly regulated by a rich network of post-translational modifications to execute its diverse functions in tumor suppression. Although early studies established p53-mediated cell-cycle arrest, apoptosis, and senescence as the classic barriers in cancer development, a growing number of new functions of p53 have been discovered and the scope of p53-mediated anti-tumor activity is largely expanded. Here, we review the complexity of different layers of p53 regulation, and the recent advance of the p53 pathway in metabolism, ferroptosis, immunity, and others that contribute to tumor suppression. We also discuss the challenge regarding how to activate p53 function specifically effective in inhibiting tumor growth without harming normal homeostasis for cancer therapy.
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Affiliation(s)
- Yanqing Liu
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhenyi Su
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Omid Tavana
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Wei Gu
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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2
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Tumenbayar BI, Tutino VM, Brazzo JA, Yao P, Bae Y. FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575789. [PMID: 38293187 PMCID: PMC10827115 DOI: 10.1101/2024.01.15.575789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Cellular metabolism is influenced by the stiffness of the extracellular matrix. Focal adhesion kinase (FAK) and its binding partner, p130Cas, transmit biomechanical signals about substrate stiffness to the cell to regulate a variety of cellular responses, but their roles in early transcriptional and metabolic responses remain largely unexplored. We cultured mouse embryonic fibroblasts with or without siRNA-mediated FAK or p130Cas knockdown and assessed the early transcriptional responses of these cells to placement on soft and stiff substrates by RNA sequencing and bioinformatics analyses. Exposure to the stiff ECM altered the expression of genes important for metabolic and biosynthetic processes, and these responses were influenced by knockdown of FAK and p130Cas. Our findings reveal that FAK-p130Cas signaling mechanotransduces ECM stiffness to early transcriptional changes that alter cellular metabolism and biosynthesis.
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Affiliation(s)
- Bat-Ider Tumenbayar
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Vincent M. Tutino
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biomedical Engineering, School of Engineering and Applied Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Joseph A. Brazzo
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Yongho Bae
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biomedical Engineering, School of Engineering and Applied Sciences, University at Buffalo, Buffalo, NY 14260, USA
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3
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Podszywalow-Bartnicka P, Neugebauer KM. Multiple roles for AU-rich RNA binding proteins in the development of haematologic malignancies and their resistance to chemotherapy. RNA Biol 2024; 21:1-17. [PMID: 38798162 PMCID: PMC11135835 DOI: 10.1080/15476286.2024.2346688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2024] [Indexed: 05/29/2024] Open
Abstract
Post-transcriptional regulation by RNA binding proteins can determine gene expression levels and drive changes in cancer cell proteomes. Identifying mechanisms of protein-RNA binding, including preferred sequence motifs bound in vivo, provides insights into protein-RNA networks and how they impact mRNA structure, function, and stability. In this review, we will focus on proteins that bind to AU-rich elements (AREs) in nascent or mature mRNA where they play roles in response to stresses encountered by cancer cells. ARE-binding proteins (ARE-BPs) specifically impact alternative splicing, stability, decay and translation, and formation of RNA-rich biomolecular condensates like cytoplasmic stress granules (SGs). For example, recent findings highlight the role of ARE-BPs - like TIAR and HUR - in chemotherapy resistance and in translational regulation of mRNAs encoding pro-inflammatory cytokines. We will discuss emerging evidence that different modes of ARE-BP activity impact leukaemia and lymphoma development, progression, adaptation to microenvironment and chemotherapy resistance.
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Affiliation(s)
- Paulina Podszywalow-Bartnicka
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karla M. Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
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4
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Osma-Garcia IC, Mouysset M, Capitan-Sobrino D, Aubert Y, Turner M, Diaz-Muñoz MD. The RNA binding proteins TIA1 and TIAL1 promote Mcl1 mRNA translation to protect germinal center responses from apoptosis. Cell Mol Immunol 2023; 20:1063-1076. [PMID: 37474714 PMCID: PMC10469172 DOI: 10.1038/s41423-023-01063-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/24/2023] [Indexed: 07/22/2023] Open
Abstract
Germinal centers (GCs) are essential for the establishment of long-lasting antibody responses. GC B cells rely on post-transcriptional RNA mechanisms to translate activation-associated transcriptional programs into functional changes in the cell proteome. However, the critical proteins driving these key mechanisms are still unknown. Here, we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses. TIA1- and TIAL1-deficient GC B cells fail to undergo antigen-mediated positive selection, expansion and differentiation into B-cell clones producing high-affinity antibodies. Mechanistically, TIA1 and TIAL1 control the transcriptional identity of dark- and light-zone GC B cells and enable timely expression of the prosurvival molecule MCL1. Thus, we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.
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Affiliation(s)
- Ines C Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Mailys Mouysset
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Dunja Capitan-Sobrino
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Yann Aubert
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Martin Turner
- Immunology Program, The Babraham Institute, Cambridge, UK
| | - Manuel D Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France.
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5
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Feng Y, Zhu S, Liu T, Zhi G, Shao B, Liu J, Li B, Jiang C, Feng Q, Wu P, Wang D. Surmounting Cancer Drug Resistance: New Perspective on RNA-Binding Proteins. Pharmaceuticals (Basel) 2023; 16:1114. [PMID: 37631029 PMCID: PMC10458901 DOI: 10.3390/ph16081114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
RNA-binding proteins (RBPs), being pivotal elements in both physiological and pathological processes, possess the ability to directly impact RNA, thereby exerting a profound influence on cellular life. Furthermore, the dysregulation of RBPs not only induces alterations in the expression levels of genes associated with cancer but also impairs the occurrence of post-transcriptional regulatory mechanisms. Consequently, these circumstances can give rise to aberrations in cellular processes, ultimately resulting in alterations within the proteome. An aberrant proteome can disrupt the equilibrium between oncogenes and tumor suppressor genes, promoting cancer progression. Given their significant role in modulating gene expression and post-transcriptional regulation, directing therapeutic interventions towards RBPs represents a viable strategy for combating drug resistance in cancer treatment. RBPs possess significant potential as diagnostic and prognostic markers for diverse cancer types. Gaining comprehensive insights into the structure and functionality of RBPs, along with delving deeper into the molecular mechanisms underlying RBPs in tumor drug resistance, can enhance cancer treatment strategies and augment the prognostic outcomes for individuals afflicted with cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peijie Wu
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
| | - Dong Wang
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
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6
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Silva JL, Foguel D, Ferreira VF, Vieira TCRG, Marques MA, Ferretti GDS, Outeiro TF, Cordeiro Y, de Oliveira GAP. Targeting Biomolecular Condensation and Protein Aggregation against Cancer. Chem Rev 2023. [PMID: 37379327 DOI: 10.1021/acs.chemrev.3c00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Biomolecular condensates, membrane-less entities arising from liquid-liquid phase separation, hold dichotomous roles in health and disease. Alongside their physiological functions, these condensates can transition to a solid phase, producing amyloid-like structures implicated in degenerative diseases and cancer. This review thoroughly examines the dual nature of biomolecular condensates, spotlighting their role in cancer, particularly concerning the p53 tumor suppressor. Given that over half of the malignant tumors possess mutations in the TP53 gene, this topic carries profound implications for future cancer treatment strategies. Notably, p53 not only misfolds but also forms biomolecular condensates and aggregates analogous to other protein-based amyloids, thus significantly influencing cancer progression through loss-of-function, negative dominance, and gain-of-function pathways. The exact molecular mechanisms underpinning the gain-of-function in mutant p53 remain elusive. However, cofactors like nucleic acids and glycosaminoglycans are known to be critical players in this intersection between diseases. Importantly, we reveal that molecules capable of inhibiting mutant p53 aggregation can curtail tumor proliferation and migration. Hence, targeting phase transitions to solid-like amorphous and amyloid-like states of mutant p53 offers a promising direction for innovative cancer diagnostics and therapeutics.
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Affiliation(s)
- Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Debora Foguel
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Vitor F Ferreira
- Faculty of Pharmacy, Fluminense Federal University (UFF), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tuane C R G Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Giulia D S Ferretti
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center, 37075 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, U.K
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37075 Göttingen, Germany
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
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7
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Xing F, Qin Y, Xu J, Wang W, Zhang B. Stress granules dynamics and promising functions in pancreatic cancer. Biochim Biophys Acta Rev Cancer 2023; 1878:188885. [PMID: 36990249 DOI: 10.1016/j.bbcan.2023.188885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
Stress granules (SGs), non-membrane subcellular organelles made up of non-translational messenger ribonucleoproteins (mRNPs), assemble in response to various environmental stimuli in cancer cells, including pancreatic cancer, particularly pancreatic ductal adenocarcinoma (PDAC) which has a low 5-year survival rate of 10%. The pertinent research on SGs and pancreatic cancer has not, however, been compiled. In this review, we talk about the dynamics of SGs and their positive effects on pancreatic cancer such as SGs promote PDAC viability and repress apoptosis, meanwhile emphasizing the connection between SGs in pancreatic cancer and signature mutations such KRAS, P53, and SMAD4 as well as the functions of SGs in antitumor drug resistance. This novel stress management technique may open the door to better treatment options in the future.
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8
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Nuclear α-Synuclein-Derived Cytotoxic Effect via Altered Ribosomal RNA Processing in Primary Mouse Embryonic Fibroblasts. Int J Mol Sci 2023; 24:ijms24032132. [PMID: 36768455 PMCID: PMC9917353 DOI: 10.3390/ijms24032132] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
α-Synuclein (αSyn) is an important player in Parkinson's disease (PD) pathogenesis. The aggregation of αSyn is mainly formed in the cytoplasm, whereas some αSyn accumulation has also been found in the nuclei of neurons. To assess the effect of nuclear αSyn, we generated αSyn conjugated with a nuclear export signal (NES) or a nuclear localization signal (NLS), and compared them with wild-type αSyn in primary mouse embryonic fibroblasts (MEF) using DNA transfection. Overexpression of NLS-αSyn increased cytotoxicity. The levels of apoptotic markers were increased by NLS-αSyn in MEF. Interestingly, an increase in the levels of 40S ribosomal protein 15 was observed in MEF expressing NLS-αSyn. These MEF also showed a higher 28S/18S rRNA ratio. Intriguingly, the expression of NLS-αSyn in MEF enhanced segmentation of nucleolin (NCL)-positive nucleolar structures. We also observed that the downregulation of NCL, using shRNA, promoted a relatively higher 28S/18S rRNA ratio. The reduction in NCL expression accelerated the accumulation of αSyn, and NCL transfection enhanced the degradation of αSyn. These results suggest that nuclear αSyn contributes to the alteration in ribosomal RNA processing via NCL malfunction-mediated nucleolar segmentation, and that NCL is a key factor for the degradation of αSyn.
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9
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Osma-Garcia IC, Capitan-Sobrino D, Mouysset M, Aubert Y, Maloudi O, Turner M, Diaz-Muñoz MD. The splicing regulators TIA1 and TIAL1 are required for the expression of the DNA damage repair machinery during B cell lymphopoiesis. Cell Rep 2022; 41:111869. [PMID: 36543128 PMCID: PMC9794549 DOI: 10.1016/j.celrep.2022.111869] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/01/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
B cell lymphopoiesis requires dynamic modulation of the B cell transcriptome for timely coordination of somatic mutagenesis and DNA repair in progenitor B (pro-B) cells. Here, we show that, in pro-B cells, the RNA-binding proteins T cell intracellular antigen 1 (TIA1) and TIA1-like protein (TIAL1) act redundantly to enable developmental progression. They are global splicing regulators that control the expression of hundreds of mRNAs, including those involved in DNA damage repair. Mechanistically, TIA1 and TIAL1 bind to 5' splice sites for exon definition, splicing, and expression of DNA damage sensors, such as Chek2 and Rif1. In their absence, pro-B cells show exacerbated DNA damage, altered P53 expression, and increased cell death. Our study uncovers the importance of tight regulation of RNA splicing by TIA1 and TIAL1 for the expression of integrative transcriptional programs that control DNA damage sensing and repair during B cell development.
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Affiliation(s)
- Ines C. Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Dunja Capitan-Sobrino
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Mailys Mouysset
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Yann Aubert
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Orlane Maloudi
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Martin Turner
- Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Manuel D. Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France,Corresponding author
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10
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Shiftless Restricts Viral Gene Expression and Influences RNA Granule Formation during Kaposi’s Sarcoma-Associated Herpesvirus Lytic Replication. J Virol 2022; 96:e0146922. [PMID: 36326276 PMCID: PMC9682979 DOI: 10.1128/jvi.01469-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the past 5 years, SHFL has emerged as a novel and integral piece of the innate immune response to viral infection. SHFL has been reported to restrict the replication of multiple viruses, including several flaviviruses and the retrovirus HIV-1.
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11
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Yi Q, Deng Z, Yue J, He J, Xiong J, Sun W, Sun W. RNA binding proteins in osteoarthritis. Front Cell Dev Biol 2022; 10:954376. [PMID: 36003144 PMCID: PMC9393224 DOI: 10.3389/fcell.2022.954376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Osteoarthritis (OA) is a common chronic degenerative joint disease worldwide. The pathological features of OA are the erosion of articular cartilage, subchondral bone sclerosis, synovitis, and metabolic disorder. Its progression is characterized by aberrant expression of genes involved in inflammation, proliferation, and metabolism of chondrocytes. Effective therapeutic strategies are limited, as mechanisms underlying OA pathophysiology remain unclear. Significant research efforts are ongoing to elucidate the complex molecular mechanisms underlying OA focused on gene transcription. However, posttranscriptional alterations also play significant function in inflammation and metabolic changes related diseases. RNA binding proteins (RBPs) have been recognized as important regulators in posttranscriptional regulation. RBPs regulate RNA subcellular localization, stability, and translational efficiency by binding to their target mRNAs, thereby controlling their protein expression. However, their role in OA is less clear. Identifying RBPs in OA is of great importance to better understand OA pathophysiology and to figure out potential targets for OA treatment. Hence, in this manuscript, we summarize the recent knowledge on the role of dysregulated RBPs in OA and hope it will provide new insight for OA study and targeted treatment.
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Affiliation(s)
- Qian Yi
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
- Department of Physiology, School of Basic Medical Science, Southwest Medical University, Luzhou, China
| | - Zhenhan Deng
- Department of Sports Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Jiaji Yue
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
| | - Jinglong He
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
| | - Jianyi Xiong
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
| | - Wei Sun
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
- *Correspondence: Wei Sun, ; Weichao Sun,
| | - Weichao Sun
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
- The Central Laboratory, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
- *Correspondence: Wei Sun, ; Weichao Sun,
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12
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Li L, Garg M, Wang Y, Wang W, Godbout R. DEAD Box 1 (DDX1) protein binds to and protects cytoplasmic stress response mRNAs in cells exposed to oxidative stress. J Biol Chem 2022; 298:102180. [PMID: 35752363 PMCID: PMC9293777 DOI: 10.1016/j.jbc.2022.102180] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022] Open
Abstract
The integrated stress response is a network of highly orchestrated pathways activated when cells are exposed to environmental stressors. While global repression of translation is a well-recognized hallmark of the integrated stress response, less is known about the regulation of mRNA stability during stress. DEAD box proteins are a family of RNA unwinding/remodeling enzymes involved in every aspect of RNA metabolism. We previously showed that DEAD box 1 (DDX1) protein accumulates at DNA double-strand breaks during genotoxic stress and promotes DNA double-strand break repair via homologous recombination. Here, we examine the role of DDX1 in response to environmental stress. We show that DDX1 is recruited to stress granules (SGs) in cells exposed to a variety of environmental stressors, including arsenite, hydrogen peroxide, and thapsigargin. We also show that DDX1 depletion delays resolution of arsenite-induced SGs. Using RNA immunoprecipitation sequencing, we identify RNA targets bound to endogenous DDX1, including RNAs transcribed from genes previously implicated in stress responses. We show the amount of target RNAs bound to DDX1 increases when cells are exposed to stress, and the overall levels of these RNAs are increased during stress in a DDX1-dependent manner. Even though DDX1’s RNA-binding property is critical for maintenance of its target mRNA levels, we found RNA binding is not required for localization of DDX1 to SGs. Furthermore, DDX1 knockdown does not appear to affect RNA localization to SGs. Taken together, our results reveal a novel role for DDX1 in maintaining cytoplasmic mRNA levels in cells exposed to oxidative stress.
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Affiliation(s)
- Lei Li
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Mansi Garg
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Yixiong Wang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Weiwei Wang
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Roseline Godbout
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada.
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13
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Dolicka D, Zahoran S, Correia de Sousa M, Gjorgjieva M, Sempoux C, Fournier M, Maeder C, Collart MA, Foti M, Sobolewski C. TIA1 Loss Exacerbates Fatty Liver Disease but Exerts a Dual Role in Hepatocarcinogenesis. Cancers (Basel) 2022; 14:cancers14071704. [PMID: 35406476 PMCID: PMC8997004 DOI: 10.3390/cancers14071704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alterations in specific RNA-binding protein expression/activity importantly contribute to the development of fatty liver disease (FLD) and hepatocellular carcinoma (HCC). In particular, adenylate–uridylate-rich element binding proteins (AUBPs) were reported to control the post-transcriptional regulation of genes involved in both metabolic and cancerous processes. Herein, we investigated the pathophysiological functions of the AUBP, T-cell-restricted intracellular antigen-1 (TIA1) in the development of FLD and HCC. Analysis of TIA1 expression in mouse and human models of FLD and HCC indicated that TIA1 is downregulated in human HCC. In vivo silencing of TIA1 using AAV8-delivered shRNAs in mice worsens hepatic steatosis and fibrosis induced by a methionine and choline-deficient diet and increases the hepatic tumor burden in liver-specific PTEN knockout (LPTENKO) mice. In contrast, our in vitro data indicated that TIA1 expression promoted proliferation and migration in HCC cell lines, thus suggesting a dual and context-dependent role for TIA1 in tumor initiation versus progression. Consistent with a dual function of TIA1 in tumorigenesis, translatome analysis revealed that TIA1 appears to control the expression of both pro- and anti-tumorigenic factors in hepatic cancer cells. This duality of TIA1′s function in hepatocarcinogenesis calls for cautiousness when considering TIA1 as a therapeutic target or biomarker in HCC.
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Affiliation(s)
- Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Szabolcs Zahoran
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (S.Z.); (M.A.C.)
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Christine Sempoux
- Service of Clinical Pathology, Institute of Pathology, Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland;
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Martine A. Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (S.Z.); (M.A.C.)
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
- Correspondence: or
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14
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RNA-binding proteins and cancer metastasis. Semin Cancer Biol 2022; 86:748-768. [PMID: 35339667 DOI: 10.1016/j.semcancer.2022.03.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins (RBPs) can regulate gene expression through post-transcriptionally influencing all manner of RNA biology, including alternative splicing (AS), polyadenylation, stability, and translation of mRNAs, as well as microRNAs (miRNAs) and circular RNAs (circRNAs) processing. There is accumulating evidence reinforcing the perception that dysregulation or dysfunction of RBPs can lead to various human diseases, including cancers. RBPs influence diverse cancer-associated cellular phenotypes, such as proliferation, apoptosis, senescence, migration, invasion, and angiogenesis, contributing to the initiation and development of tumors, as well as clinical prognosis. Metastasis is the leading cause of cancer-related recurrence and death. Therefore, it is necessary to elucidate the molecular mechanisms behind tumor metastasis. In fact, a growing body of published research has proved that RBPs play pivotal roles in cancer metastasis. In this review, we will summarize the recent advances for helping us understand the role of RBPs in tumor metastasis, and discuss dysfunctions and dysregulations of RBPs affecting metastasis-associated processes including epithelial-mesenchymal transition (EMT), migration, and invasion of cancer cells. Furthermore, we will discuss emerging RBP-based strategy for the treatment of cancer metastasis.
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15
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Enterobacteria impair host p53 tumor suppressor activity through mRNA destabilization. Oncogene 2022; 41:2173-2186. [PMID: 35197571 PMCID: PMC8993692 DOI: 10.1038/s41388-022-02238-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/25/2022]
Abstract
Increasing evidence highlights the role of bacteria in the physiopathology of cancer. However, the underlying molecular mechanisms remains poorly understood. Several cancer-associated bacteria have been shown to produce toxins which interfere with the host defense against tumorigenesis. Here, we show that lipopolysaccharides from Klebsiella pneumoniae and other Enterobacteria strongly inhibit the host tumor suppressor p53 pathway through a novel mechanism of p53 regulation. We found that lipopolysaccharides destabilize TP53 mRNA through a TLR4-NF-κB-mediated inhibition of the RNA-binding factor Wig-1. Importantly, we show that K. pneumoniae disables two major tumor barriers, oncogene-induced DNA damage signaling and senescence, by impairing p53 transcriptional activity upon DNA damage and oncogenic stress. Furthermore, we found an inverse correlation between the levels of TLR4 and p53 mutation in colorectal tumors. Hence, our data suggest that the repression of p53 by Enterobacteria via TLR4 alleviates the selection pressure for p53 oncogenic mutations and shapes the genomic evolution of cancer.
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Gourdomichali O, Zonke K, Kattan FG, Makridakis M, Kontostathi G, Vlahou A, Doxakis E. In Situ Peroxidase Labeling Followed by Mass-Spectrometry Reveals TIA1 Interactome. BIOLOGY 2022; 11:biology11020287. [PMID: 35205152 PMCID: PMC8869308 DOI: 10.3390/biology11020287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 01/15/2023]
Abstract
TIA1 is a broadly expressed DNA/RNA binding protein that regulates multiple aspects of RNA metabolism. It is best known for its role in stress granule assembly during the cellular stress response. Three RNA recognition motifs mediate TIA1 functions along with a prion-like domain that supports multivalent protein-protein interactions that are yet poorly characterized. Here, by fusing the enhanced ascorbate peroxidase 2 (APEX2) biotin-labeling enzyme to TIA1 combined with mass spectrometry, the proteins in the immediate vicinity of TIA1 were defined in situ. Eighty-six and 203 protein partners, mostly associated with ribonucleoprotein complexes, were identified in unstressed control and acute stress conditions, respectively. Remarkably, the repertoire of TIA1 protein partners was highly dissimilar between the two cellular states. Under unstressed control conditions, the biological processes associated with the TIA1 interactome were enriched for cytosolic ontologies related to mRNA metabolism, such as translation initiation, nucleocytoplasmic transport, and RNA catabolism, while the protein identities were primarily represented by RNA binding proteins, ribosomal subunits, and eicosanoid regulators. Under acute stress, TIA1-labeled partners displayed a broader subcellular distribution that included the chromosomes and mitochondria. The enriched biological processes included splicing, translation, and protein synthesis regulation, while the molecular function of the proteins was enriched for RNA binding activity, ribosomal subunits, DNA double-strand break repair, and amide metabolism. Altogether, these data highlight the TIA1 spatial environment with its different partners in diverse cellular states and pave the way to dissect TIA1 role in these processes.
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Affiliation(s)
- Olga Gourdomichali
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Katerina Zonke
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Fedon-Giasin Kattan
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
- Department of Biological Applications and Technology, Faculty of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Manousos Makridakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Georgia Kontostathi
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Antonia Vlahou
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
- Correspondence:
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The Multifunctional Faces of T-Cell Intracellular Antigen 1 in Health and Disease. Int J Mol Sci 2022; 23:ijms23031400. [PMID: 35163320 PMCID: PMC8836218 DOI: 10.3390/ijms23031400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 02/06/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is expressed in many tissues and in the vast majority of species, although it was first discovered as a component of human cytotoxic T lymphocytes. TIA1 has a dual localization in the nucleus and cytoplasm, where it plays an important role as a regulator of gene-expression flux. As a multifunctional master modulator, TIA1 controls biological processes relevant to the physiological functioning of the organism and the development and/or progression of several human pathologies. This review summarizes our current knowledge of the molecular aspects and cellular processes involving TIA1, with relevance for human pathophysiology.
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18
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AU-Rich Element RNA Binding Proteins: At the Crossroads of Post-Transcriptional Regulation and Genome Integrity. Int J Mol Sci 2021; 23:ijms23010096. [PMID: 35008519 PMCID: PMC8744917 DOI: 10.3390/ijms23010096] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 12/14/2022] Open
Abstract
Genome integrity must be tightly preserved to ensure cellular survival and to deter the genesis of disease. Endogenous and exogenous stressors that impose threats to genomic stability through DNA damage are counteracted by a tightly regulated DNA damage response (DDR). RNA binding proteins (RBPs) are emerging as regulators and mediators of diverse biological processes. Specifically, RBPs that bind to adenine uridine (AU)-rich elements (AREs) in the 3' untranslated region (UTR) of mRNAs (AU-RBPs) have emerged as key players in regulating the DDR and preserving genome integrity. Here we review eight established AU-RBPs (AUF1, HuR, KHSRP, TIA-1, TIAR, ZFP36, ZFP36L1, ZFP36L2) and their ability to maintain genome integrity through various interactions. We have reviewed canonical roles of AU-RBPs in regulating the fate of mRNA transcripts encoding DDR genes at multiple post-transcriptional levels. We have also attempted to shed light on non-canonical roles of AU-RBPs exploring their post-translational modifications (PTMs) and sub-cellular localization in response to genotoxic stresses by various factors involved in DDR and genome maintenance. Dysfunctional AU-RBPs have been increasingly found to be associated with many human cancers. Further understanding of the roles of AU-RBPS in maintaining genomic integrity may uncover novel therapeutic strategies for cancer.
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19
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Carrascoso I, Velasco BR, Izquierdo JM. Deficiency of T-Cell Intracellular Antigen 1 in Murine Embryonic Fibroblasts Is Associated with Changes in Mitochondrial Morphology and Respiration. Int J Mol Sci 2021; 22:ijms222312775. [PMID: 34884582 PMCID: PMC8657690 DOI: 10.3390/ijms222312775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 01/14/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is a multifunctional RNA-binding protein involved in regulating gene expression and splicing during development and in response to environmental stress, to maintain cell homeostasis and promote survival. Herein, we used TIA1-deficient murine embryonic fibroblasts (MEFs) to study their role in mitochondria homeostasis. We found that the loss of TIA1 was associated with changes in mitochondrial morphology, promoting the appearance of elongated mitochondria with heterogeneous cristae density and size. The proteomic patterns of TIA1-deficient MEFs were consistent with expression changes in molecular components related to mitochondrial dynamics/organization and respiration. Bioenergetics analysis illustrated that TIA1 deficiency enhances mitochondrial respiration. Overall, our findings shed light on the role of TIA1 in mitochondrial dynamics and highlight a point of crosstalk between potential pro-survival and pro-senescence pathways.
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20
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Nicolet BP, Zandhuis ND, Lattanzio VM, Wolkers MC. Sequence determinants as key regulators in gene expression of T cells. Immunol Rev 2021; 304:10-29. [PMID: 34486113 PMCID: PMC9292449 DOI: 10.1111/imr.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
T cell homeostasis, T cell differentiation, and T cell effector function rely on the constant fine-tuning of gene expression. To alter the T cell state, substantial remodeling of the proteome is required. This remodeling depends on the intricate interplay of regulatory mechanisms, including post-transcriptional gene regulation. In this review, we discuss how the sequence of a transcript influences these post-transcriptional events. In particular, we review how sequence determinants such as sequence conservation, GC content, and chemical modifications define the levels of the mRNA and the protein in a T cell. We describe the effect of different forms of alternative splicing on mRNA expression and protein production, and their effect on subcellular localization. In addition, we discuss the role of sequences and structures as binding hubs for miRNAs and RNA-binding proteins in T cells. The review thus highlights how the intimate interplay of post-transcriptional mechanisms dictate cellular fate decisions in T cells.
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Affiliation(s)
- Benoit P. Nicolet
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Nordin D. Zandhuis
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - V. Maria Lattanzio
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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21
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Vadivel Gnanasundram S, Bonczek O, Wang L, Chen S, Fahraeus R. p53 mRNA Metabolism Links with the DNA Damage Response. Genes (Basel) 2021; 12:genes12091446. [PMID: 34573428 PMCID: PMC8465283 DOI: 10.3390/genes12091446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/14/2022] Open
Abstract
Human cells are subjected to continuous challenges by different genotoxic stress attacks. DNA damage leads to erroneous mutations, which can alter the function of oncogenes or tumor suppressors, resulting in cancer development. To circumvent this, cells activate the DNA damage response (DDR), which mainly involves cell cycle regulation and DNA repair processes. The tumor suppressor p53 plays a pivotal role in the DDR by halting the cell cycle and facilitating the DNA repair processes. Various pathways and factors participating in the detection and repair of DNA have been described, including scores of RNA-binding proteins (RBPs) and RNAs. It has become increasingly clear that p53’s role is multitasking, and p53 mRNA regulation plays a prominent part in the DDR. This review is aimed at covering the p53 RNA metabolism linked to the DDR and highlights the recent findings.
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Affiliation(s)
- Sivakumar Vadivel Gnanasundram
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
- Correspondence: (S.V.G.); (R.F.)
| | - Ondrej Bonczek
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656-53 Brno, Czech Republic
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
| | - Sa Chen
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
| | - Robin Fahraeus
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656-53 Brno, Czech Republic
- Inserm UMRS1131, Institut de Genetique Moleculaire, Universite Paris 7, Hopital St Louis, F-75010 Paris, France
- International Centre for Cancer Vaccine Science, University of Gdansk, 80-822 Gdansk, Poland
- Correspondence: (S.V.G.); (R.F.)
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22
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Byres LP, Mufteev M, Yuki KE, Wei W, Piekna A, Wilson MD, Rodrigues DC, Ellis J. Identification of TIA1 mRNA targets during human neuronal development. Mol Biol Rep 2021; 48:6349-6361. [PMID: 34410578 PMCID: PMC8437838 DOI: 10.1007/s11033-021-06634-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022]
Abstract
Background Neuronal development is a tightly controlled process involving multi-layered regulatory mechanisms. While transcriptional pathways regulating neurodevelopment are well characterized, post-transcriptional programs are still poorly understood. TIA1 is an RNA-binding protein that can regulate splicing, stability, or translation of target mRNAs, and has been shown to play critical roles in stress response and neurodevelopment. However, the identity of mRNAs regulated by TIA1 during neurodevelopment under unstressed conditions is still unknown. Methods and Results To identify the mRNAs targeted by TIA1 during the first stages of human neurodevelopment, we performed RNA immunoprecipitation-sequencing (RIP-seq) on human embryonic stem cells (hESCs) and derived neural progenitor cells (NPCs), and cortical neurons under unstressed conditions. While there was no change in TIA1 protein levels, the number of TIA1 targeted mRNAs decreased from pluripotent cells to neurons. We identified 2400, 845, and 330 TIA1 mRNA targets in hESCs, NPC, and neurons, respectively. The vast majority of mRNA targets in hESC were genes associated with neurodevelopment and included autism spectrum disorder-risk genes that were not bound in neurons. Additionally, we found that most TIA1 mRNA targets have reduced ribosomal engagement levels. Conclusion Our results reveal TIA1 mRNA targets in hESCs and during human neurodevelopment, indicate that translation repression is a key process targeted by TIA1 binding and implicate TIA1 function in neuronal differentiation. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-021-06634-0.
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Affiliation(s)
- Loryn P Byres
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Marat Mufteev
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kyoko E Yuki
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wei Wei
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alina Piekna
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Deivid C Rodrigues
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
| | - James Ellis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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Diaz-Muñoz MD, Osma-Garcia IC. The RNA regulatory programs that govern lymphocyte development and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1683. [PMID: 34327847 DOI: 10.1002/wrna.1683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/25/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022]
Abstract
Lymphocytes require of constant and dynamic changes in their transcriptome for timely activation and production of effector molecules to combat external pathogens. Synthesis and translation of messenger (m)RNAs into these effector proteins is controlled both quantitatively and qualitatively by RNA binding proteins (RBPs). RBP-dependent regulation of RNA editing, subcellular location, stability, and translation shapes immune cell development and immunity. Extensive evidences have now been gathered from few model RBPs, HuR, PTBP1, ZFP36, and Roquin. However, recently developed methodologies for global characterization of protein:RNA interactions suggest the existence of complex RNA regulatory networks in which RBPs co-ordinately regulate the fate of sets of RNAs controlling cellular pathways and functions. In turn, RNA can also act as scaffolding of functionally related proteins modulating their activation and function. Here we review current knowledge about how RBP-dependent regulation of RNA shapes our immune system and discuss about the existence of a hidden immune cell epitranscriptome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Manuel D Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
| | - Ines C Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
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24
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The role of DNA damage response in amyotrophic lateral sclerosis. Essays Biochem 2021; 64:847-861. [PMID: 33078197 PMCID: PMC7588667 DOI: 10.1042/ebc20200002] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly disabling and fatal neurodegenerative disease. Due to insufficient disease-modifying treatments, there is an unmet and urgent need for elucidating disease mechanisms that occur early and represent common triggers in both familial and sporadic ALS. Emerging evidence suggests that impaired DNA damage response contributes to age-related somatic accumulation of genomic instability and can trigger or accelerate ALS pathological manifestations. In this review, we summarize and discuss recent studies indicating a direct link between DNA damage response and ALS. Further mechanistic understanding of the role genomic instability is playing in ALS disease pathophysiology will be critical for discovering new therapeutic avenues.
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25
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Krismer K, Bird MA, Varmeh S, Handly ED, Gattinger A, Bernwinkler T, Anderson DA, Heinzel A, Joughin BA, Kong YW, Cannell IG, Yaffe MB. Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression. Cell Rep 2021; 32:108064. [PMID: 32846122 PMCID: PMC8204639 DOI: 10.1016/j.celrep.2020.108064] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/28/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play critical roles in regulating gene expression by modulating splicing, RNA stability, and protein translation. Stimulus-induced alterations in RBP function contribute to global changes in gene expression, but identifying which RBPs are responsible for the observed changes remains an unmet need. Here, we present Transite, a computational approach that systematically infers RBPs influencing gene expression through changes in RNA stability and degradation. As a proof of principle, we apply Transite to RNA expression data from human patients with non-small-cell lung cancer whose tumors were sampled at diagnosis or after recurrence following treatment with platinum-based chemotherapy. Transite implicates known RBP regulators of the DNA damage response and identifies hnRNPC as a new modulator of chemotherapeutic resistance, which we subsequently validated experimentally. Transite serves as a framework for the identification of RBPs that drive cell-state transitions and adds additional value to the vast collection of publicly available gene expression datasets. Krismer et al. present a computational approach to identify RNA-binding proteins (RBPs) that modulate post-transcriptional control of gene expression using RNA expression data as inputs. By applying this approach to publicly available patient datasets, they identify and experimentally confirm that the RBP hnRNPC contributes to chemotherapy resistance in lung cancer.
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Affiliation(s)
- Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Molly A Bird
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Shohreh Varmeh
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA
| | - Erika D Handly
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Anna Gattinger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Thomas Bernwinkler
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Daniel A Anderson
- Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Andreas Heinzel
- Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Brian A Joughin
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yi Wen Kong
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA.
| | - Ian G Cannell
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
| | - Michael B Yaffe
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Divisions of Acute Care Surgery, Trauma and Surgical Critical Care, and Surgical Oncology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.
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26
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Freen-van Heeren JJ. Post-transcriptional control of T-cell cytokine production: Implications for cancer therapy. Immunology 2021; 164:57-72. [PMID: 33884612 DOI: 10.1111/imm.13339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/05/2023] Open
Abstract
As part of the adaptive immune system, T cells are vital for the eradication of infected and malignantly transformed cells. To perform their protective function, T cells produce effector molecules that are either directly cytotoxic, such as granzymes, perforin, interferon-γ and tumour necrosis factor α, or attract and stimulate (immune) cells, such as interleukin-2. As these molecules can also induce immunopathology, tight control of their production is required. Indeed, inflammatory cytokine production is regulated on multiple levels. Firstly, locus accessibility and transcription factor availability and activity determine the amount of mRNA produced. Secondly, post-transcriptional mechanisms, influencing mRNA splicing/codon usage, stability, decay, localization and translation rate subsequently determine the amount of protein that is produced. In the immune suppressive environments of tumours, T cells gradually lose the capacity to produce effector molecules, resulting in tumour immune escape. Recently, the role of post-transcriptional regulation in fine-tuning T-cell effector function has become more appreciated. Furthermore, several groups have shown that exhausted or dysfunctional T cells from cancer patients or murine models possess mRNA for inflammatory mediators, but fail to produce effector molecules, hinting that post-transcriptional events also play a role in hampering tumour-infiltrating lymphocyte effector function. Here, the post-transcriptional regulatory events governing T-cell cytokine production are reviewed, with a specific focus on the importance of post-transcriptional regulation in anti-tumour responses. Furthermore, potential approaches to circumvent tumour-mediated dampening of T-cell effector function through the (dis)engagement of post-transcriptional events are explored, such as CRISPR/Cas9-mediated genome editing or chimeric antigen receptors.
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27
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Loughlin FE, West DL, Gunzburg MJ, Waris S, Crawford SA, Wilce MCJ, Wilce JA. Tandem RNA binding sites induce self-association of the stress granule marker protein TIA-1. Nucleic Acids Res 2021; 49:2403-2417. [PMID: 33621982 PMCID: PMC7969032 DOI: 10.1093/nar/gkab080] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/01/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022] Open
Abstract
TIA-1 is an RNA-binding protein that sequesters target RNA into stress granules under conditions of cellular stress. Promotion of stress granule formation by TIA-1 depends upon self-association of its prion-like domain that facilitates liquid-liquid phase separation and is thought to be enhanced via RNA binding. However, the mechanisms underlying the influence of RNA on TIA-1 self-association have not been previously demonstrated. Here we have investigated the self-associating properties of full-length TIA-1 in the presence of designed and native TIA-1 nucleic acid binding sites in vitro, monitoring phase separation, fibril formation and shape. We show that single stranded RNA and DNA induce liquid-liquid phase separation of TIA-1 in a multisite, sequence-specific manner and also efficiently promote formation of amyloid-like fibrils. Although RNA binding to a single site induces a small conformational change in TIA-1, this alone does not enhance phase separation of TIA-1. Tandem binding sites are required to enhance phase separation of TIA-1 and this is finely tuned by the protein:binding site stoichiometry rather than nucleic acid length. Native tandem TIA-1 binding sites within the 3′ UTR of p53 mRNA also efficiently enhance phase separation of TIA-1 and thus may potentially act as potent nucleation sites for stress granule assembly.
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Affiliation(s)
- Fionna E Loughlin
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Danella L West
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Menachem J Gunzburg
- Monash Institute of Pharmaceutical Sciences, Monash University, Victoria 3052, Australia
| | - Saboora Waris
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Simon A Crawford
- Ramaciotti Centre For Cryo Electron Microscopy, Monash University, Victoria 3800, Australia
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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28
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Curdy N, Lanvin O, Cadot S, Laurent C, Fournié JJ, Franchini DM. Stress Granules in the Post-transcriptional Regulation of Immune Cells. Front Cell Dev Biol 2021; 8:611185. [PMID: 33520991 PMCID: PMC7841200 DOI: 10.3389/fcell.2020.611185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022] Open
Abstract
Immune cell activation triggers transcriptional and translational programs eliciting cellular processes, such as differentiation or proliferation, essential for an efficient immune response. These dynamic processes require an intricate orchestration of regulatory mechanisms to control the precise spatiotemporal expression of proteins. Post-transcriptional regulation ensures the control of messenger RNA metabolism and appropriate translation. Among these post-transcriptional regulatory mechanisms, stress granules participate in the control of protein synthesis. Stress granules are ribonucleoprotein complexes that form upon stress, typically under control of the integrated stress response. Such structures assemble upon stimulation of immune cells where they control selective translational programs ensuring the establishment of accurate effector functions. In this review, we summarize the current knowledge about post-transcriptional regulation in immune cells and highlight the role of stress sensors and stress granules in such regulation.
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Affiliation(s)
- Nicolas Curdy
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Olivia Lanvin
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Sarah Cadot
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Camille Laurent
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France.,Département de Pathologie, Centre Hospitalier Universitaire (CHU) de Toulouse, Toulouse, France
| | - Jean-Jacques Fournié
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Don-Marc Franchini
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
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29
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Qin H, Ni H, Liu Y, Yuan Y, Xi T, Li X, Zheng L. RNA-binding proteins in tumor progression. J Hematol Oncol 2020; 13:90. [PMID: 32653017 PMCID: PMC7353687 DOI: 10.1186/s13045-020-00927-w] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/25/2020] [Indexed: 02/08/2023] Open
Abstract
RNA-binding protein (RBP) has a highly dynamic spatiotemporal regulation process and important biological functions. They are critical to maintain the transcriptome through post-transcriptionally controlling the processing and transportation of RNA, including regulating RNA splicing, polyadenylation, mRNA stability, mRNA localization, and translation. Alteration of each process will affect the RNA life cycle, produce abnormal protein phenotypes, and thus lead to the occurrence and development of tumors. Here, we summarize RBPs involved in tumor progression and the underlying molecular mechanisms whereby they are regulated and exert their effects. This analysis is an important step towards the comprehensive characterization of post-transcriptional gene regulation involved in tumor progression.
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Affiliation(s)
- Hai Qin
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Haiwei Ni
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Yichen Liu
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Yaqin Yuan
- Guizhou Medical Device Testing Center, Guiyang, 550004, Guizhou, People's Republic of China
| | - Tao Xi
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China.
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
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30
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Ke L, Yang DC, Wang Y, Ding Y, Gao G. AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse. Nucleic Acids Res 2020; 48:W230-W238. [PMID: 32406920 PMCID: PMC7319567 DOI: 10.1093/nar/gkaa368] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/21/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
With the abundant mammalian lncRNAs identified recently, a comprehensive annotation resource for these novel lncRNAs is an urgent need. Since its first release in November 2016, AnnoLnc has been the only online server for comprehensively annotating novel human lncRNAs on-the-fly. Here, with significant updates to multiple annotation modules, backend datasets and the code base, AnnoLnc2 continues the effort to provide the scientific community with a one-stop online portal for systematically annotating novel human and mouse lncRNAs with a comprehensive functional spectrum covering sequences, structure, expression, regulation, genetic association and evolution. In response to numerous requests from multiple users, a standalone package is also provided for large-scale offline analysis. We believe that updated AnnoLnc2 (http://annolnc.gao-lab.org/) will help both computational and bench biologists identify lncRNA functions and investigate underlying mechanisms.
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Affiliation(s)
- Lan Ke
- School of Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - De-Chang Yang
- School of Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Yu Wang
- School of Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Yang Ding
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ge Gao
- School of Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
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31
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Franchini DM, Lanvin O, Tosolini M, Patras de Campaigno E, Cammas A, Péricart S, Scarlata CM, Lebras M, Rossi C, Ligat L, Pont F, Arimondo PB, Laurent C, Ayyoub M, Despas F, Lapeyre-Mestre M, Millevoi S, Fournié JJ. Microtubule-Driven Stress Granule Dynamics Regulate Inhibitory Immune Checkpoint Expression in T Cells. Cell Rep 2020; 26:94-107.e7. [PMID: 30605689 DOI: 10.1016/j.celrep.2018.12.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/02/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022] Open
Abstract
Despite the clinical success of blocking inhibitory immune checkpoint receptors such as programmed cell death-1 (PD-1) in cancer, the mechanisms controlling the expression of these receptors have not been fully elucidated. Here, we identify a post-transcriptional mechanism regulating PD-1 expression in T cells. Upon activation, the PDCD1 mRNA and ribonucleoprotein complexes coalesce into stress granules that require microtubules and the kinesin 1 molecular motor to proceed to translation. Hence, PD-1 expression is highly sensitive to microtubule or stress granule inhibitors targeting this pathway. Evidence from healthy donors and cancer patients reveals a common regulation for the translation of CTLA4, LAG3, TIM3, TIGIT, and BTLA but not of the stimulatory co-receptors OX40, GITR, and 4-1BB mRNAs. In patients, disproportionality analysis of immune-related adverse events for currently used microtubule drugs unveils a significantly higher risk of autoimmunity. Our findings reveal a fundamental mechanism of immunoregulation with great importance in cancer immunotherapy.
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Affiliation(s)
- Don-Marc Franchini
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France.
| | - Olivia Lanvin
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Marie Tosolini
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Emilie Patras de Campaigno
- Medical and Clinical Pharmacology Unit, CHU Toulouse University Hospital, 31000 Toulouse, France; Medical and Pharmacoepidemiology Research Unit, INSERM 1027, 31000 Toulouse, France; Centre d'Investigations Cliniques, CIC 1436, Toulouse University Hospital, 31000 Toulouse, France
| | - Anne Cammas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France
| | - Sarah Péricart
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Clara-Maria Scarlata
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Morgane Lebras
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France
| | - Cédric Rossi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Laetitia Ligat
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France
| | - Fréderic Pont
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France
| | - Paola B Arimondo
- Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Epigenetic Targeting of Cancer, FRE3600 CNRS, 31035 Toulouse, France
| | - Camille Laurent
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Maha Ayyoub
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Fabien Despas
- Medical and Clinical Pharmacology Unit, CHU Toulouse University Hospital, 31000 Toulouse, France; Medical and Pharmacoepidemiology Research Unit, INSERM 1027, 31000 Toulouse, France; Centre d'Investigations Cliniques, CIC 1436, Toulouse University Hospital, 31000 Toulouse, France
| | - Maryse Lapeyre-Mestre
- Medical and Clinical Pharmacology Unit, CHU Toulouse University Hospital, 31000 Toulouse, France; Medical and Pharmacoepidemiology Research Unit, INSERM 1027, 31000 Toulouse, France; Centre d'Investigations Cliniques, CIC 1436, Toulouse University Hospital, 31000 Toulouse, France
| | - Stefania Millevoi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France.
| | - Jean-Jacques Fournié
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France.
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32
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Salerno F, Turner M, Wolkers MC. Dynamic Post-Transcriptional Events Governing CD8+ T Cell Homeostasis and Effector Function. Trends Immunol 2020; 41:240-254. [DOI: 10.1016/j.it.2020.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 12/31/2022]
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33
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Yang F, Wang W, Cetinbas M, Sadreyev RI, Blower MD. Genome-wide analysis identifies cis-acting elements regulating mRNA polyadenylation and translation during vertebrate oocyte maturation. RNA (NEW YORK, N.Y.) 2020; 26:324-344. [PMID: 31896558 PMCID: PMC7025505 DOI: 10.1261/rna.073247.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/30/2019] [Indexed: 05/10/2023]
Abstract
Most cells change patterns of gene expression through transcriptional regulation. In contrast, oocytes are transcriptionally silent and regulate mRNA poly(A) tail length to control protein production. However, the genome-wide relationship of poly(A) tail changes to mRNA translation during vertebrate oocyte maturation is not known. We used Tail-seq and polyribosome analysis to measure poly(A) tail and translational changes during oocyte maturation in Xenopus laevis We identified large-scale poly(A) and translational changes during oocyte maturation, with poly(A) tail length changes preceding translational changes. Proteins important for completion of the meiotic divisions and early development exhibited increased polyadenylation and translation during oocyte maturation. A family of U-rich sequence elements was enriched near the polyadenylation signal of polyadenylated and translationally activated mRNAs. We propose that changes in mRNA polyadenylation are a conserved mechanism regulating protein expression during vertebrate oocyte maturation and that these changes are controlled by a spatial code of cis-acting sequence elements.
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Affiliation(s)
- Fei Yang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wei Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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34
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Apicco DJ, Zhang C, Maziuk B, Jiang L, Ballance HI, Boudeau S, Ung C, Li H, Wolozin B. Dysregulation of RNA Splicing in Tauopathies. Cell Rep 2019; 29:4377-4388.e4. [PMID: 31875547 PMCID: PMC6941411 DOI: 10.1016/j.celrep.2019.11.093] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/28/2019] [Accepted: 11/22/2019] [Indexed: 12/13/2022] Open
Abstract
Pathological aggregation of RNA binding proteins (RBPs) is associated with dysregulation of RNA splicing in PS19 P301S tau transgenic mice and in Alzheimer's disease brain tissues. The dysregulated splicing particularly affects genes involved in synaptic transmission. The effects of neuroprotective TIA1 reduction on PS19 mice are also examined. TIA1 reduction reduces disease-linked alternative splicing events for the major synaptic mRNA transcripts examined, suggesting that normalization of RBP functions is associated with the neuroprotection. Use of the NetDecoder informatics algorithm identifies key upstream biological targets, including MYC and EGFR, underlying the transcriptional and splicing changes in the protected compared to tauopathy mice. Pharmacological inhibition of MYC and EGFR activity in neuronal cultures tau recapitulates the neuroprotective effects of TIA1 reduction. These results demonstrate that dysfunction of RBPs and RNA splicing processes are major elements of the pathophysiology of tauopathies, as well as potential therapeutic targets for tauopathies.
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Affiliation(s)
- Daniel J Apicco
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | | | - Brandon Maziuk
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | - Lulu Jiang
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | - Heather I Ballance
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | - Samantha Boudeau
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | | | - Hu Li
- Mayo Clinic, Rochester, MN, USA.
| | - Benjamin Wolozin
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA; Boston University School of Medicine, Department of Neurology, Boston, MA, USA.
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35
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Haronikova L, Olivares-Illana V, Wang L, Karakostis K, Chen S, Fåhraeus R. The p53 mRNA: an integral part of the cellular stress response. Nucleic Acids Res 2019; 47:3257-3271. [PMID: 30828720 PMCID: PMC6468297 DOI: 10.1093/nar/gkz124] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/12/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulated via a hierarchical order of post-translational modifications and regulated protein-protein interactions. The mechanisms governing these processes provide a model for how cells optimize the genetic information for maximal diversity. The p53 mRNA also plays a role in this process and this review aims to illustrate how protein and RNA interactions throughout the p53 mRNA in response to different signalling pathways control RNA stability, translation efficiency or alternative initiation of translation. We also describe how a p53 mRNA platform shows riboswitch-like features and controls the rate of p53 synthesis, protein stability and modifications of the nascent p53 protein. A single cancer-derived synonymous mutation disrupts the folding of this platform and prevents p53 activation following DNA damage. The role of the p53 mRNA as a target for signalling pathways illustrates how mRNA sequences have co-evolved with the function of the encoded protein and sheds new light on the information hidden within mRNAs.
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Affiliation(s)
- Lucia Haronikova
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y cáncer. Instituto de Física Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona universitaria, 78290 SLP, México
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | - Robin Fåhraeus
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic.,Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden.,Inserm U1162, 27 rue Juliette Dodu, 75010 Paris, France.,ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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Franchini DM, Lanvin O, Curdy N, Fournié JJ. [Control of lymphocyte activity by stress granules. New targets for immunotherapy ?]. Med Sci (Paris) 2019; 35:507-509. [PMID: 31274077 DOI: 10.1051/medsci/2019109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Don-Marc Franchini
- Centre de Recherches en Cancérologie de Toulouse, Inserm UMR1037 ; Université Toulouse III Paul Sabatier ; CNRS ERL5294, 2, avenue Hubert Curien, 31037 Toulouse, France - Institut universitaire du cancer de Toulouse-oncopole, 1, avenue Irène Joliot-Curie, 31059 Toulouse, France
| | - Olivia Lanvin
- Centre de Recherches en Cancérologie de Toulouse, Inserm UMR1037 ; Université Toulouse III Paul Sabatier ; CNRS ERL5294, 2, avenue Hubert Curien, 31037 Toulouse, France - Institut universitaire du cancer de Toulouse-oncopole, 1, avenue Irène Joliot-Curie, 31059 Toulouse, France
| | - Nicolas Curdy
- Centre de Recherches en Cancérologie de Toulouse, Inserm UMR1037 ; Université Toulouse III Paul Sabatier ; CNRS ERL5294, 2, avenue Hubert Curien, 31037 Toulouse, France - Institut universitaire du cancer de Toulouse-oncopole, 1, avenue Irène Joliot-Curie, 31059 Toulouse, France
| | - Jean-Jacques Fournié
- Centre de Recherches en Cancérologie de Toulouse, Inserm UMR1037 ; Université Toulouse III Paul Sabatier ; CNRS ERL5294, 2, avenue Hubert Curien, 31037 Toulouse, France - Institut universitaire du cancer de Toulouse-oncopole, 1, avenue Irène Joliot-Curie, 31059 Toulouse, France
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37
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Ostareck DH, Ostareck-Lederer A. RNA-Binding Proteins in the Control of LPS-Induced Macrophage Response. Front Genet 2019; 10:31. [PMID: 30778370 PMCID: PMC6369361 DOI: 10.3389/fgene.2019.00031] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/17/2019] [Indexed: 12/18/2022] Open
Abstract
Innate immune response is triggered by pathogen components, like lipopolysaccharides (LPS) of gram-negative bacteria. LPS initiates Toll-like receptor 4 (TLR4) signaling, which involves mitogen activated protein kinases (MAPK) and nuclear factor kappa B (NFκB) in different pathway branches and ultimately induces inflammatory cytokine and chemokine expression, macrophage migration and phagocytosis. Timely gene transcription and post-transcriptional control of gene expression confer the adequate synthesis of signaling molecules. As trans-acting factors RNA binding proteins (RBPs) contribute significantly to the surveillance of gene expression. RBPs are involved in the regulation of mRNA processing, localization, stability and translation. Thereby they enable rapid cellular responses to inflammatory mediators and facilitate a coordinated systemic immune response. Specific RBP binding to conserved sequence motifs in their target mRNAs is mediated by RNA binding domains, like Zink-finger domains, RNA recognition motifs (RRM), and hnRNP K homology domains (KH), often arranged in modular arrays. In this review, we focus on RBPs Tristetraprolin (TTP), human antigen R (HUR), T-cell intracellular antigen 1 related protein (TIAR), and heterogeneous ribonuclear protein K (hnRNP K) in LPS induced macrophages as primary responding immune cells. We discuss recent experiments employing RNA immunoprecipitation and microarray analysis (RIP-Chip) and newly developed individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP), photoactivatable ribonucleoside-enhanced crosslinking (PAR-iCLIP) and RNA sequencing techniques (RNA-Seq). The global mRNA interaction profile analysis of TTP, HUR, TIAR, and hnRNP K exhibited valuable information about the post-transcriptional control of inflammation related gene expression with a broad impact on intracellular signaling and temporal cytokine expression.
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Affiliation(s)
- Dirk H Ostareck
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen, Germany
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Zheng D, Wang R, Ding Q, Wang T, Xie B, Wei L, Zhong Z, Tian B. Cellular stress alters 3'UTR landscape through alternative polyadenylation and isoform-specific degradation. Nat Commun 2018; 9:2268. [PMID: 29891946 PMCID: PMC5995920 DOI: 10.1038/s41467-018-04730-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 05/17/2018] [Indexed: 12/18/2022] Open
Abstract
Most eukaryotic genes express alternative polyadenylation (APA) isoforms with different 3'UTR lengths, production of which is influenced by cellular conditions. Here, we show that arsenic stress elicits global shortening of 3'UTRs through preferential usage of proximal polyadenylation sites during stress and enhanced degradation of long 3'UTR isoforms during recovery. We demonstrate that RNA-binding protein TIA1 preferentially interacts with alternative 3'UTR sequences through U-rich motifs, correlating with stress granule association and mRNA decay of long 3'UTR isoforms. By contrast, genes with shortened 3'UTRs due to stress-induced APA can evade mRNA clearance and maintain transcript abundance post stress. Furthermore, we show that stress causes distinct 3'UTR size changes in proliferating and differentiated cells, highlighting its context-specific impacts on the 3'UTR landscape. Together, our data reveal a global, 3'UTR-based mRNA stability control in stressed cells and indicate that APA can function as an adaptive mechanism to preserve mRNAs in response to stress.
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Affiliation(s)
- Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Ruijia Wang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Qingbao Ding
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Tianying Wang
- Department of Microbiology, Harbin Medical University, Harbin,, 150081, China
| | - Bingning Xie
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Lu Wei
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Zhaohua Zhong
- Department of Microbiology, Harbin Medical University, Harbin,, 150081, China
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA.
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Díaz-Muñoz MD, Turner M. Uncovering the Role of RNA-Binding Proteins in Gene Expression in the Immune System. Front Immunol 2018; 9:1094. [PMID: 29875770 PMCID: PMC5974052 DOI: 10.3389/fimmu.2018.01094] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/02/2018] [Indexed: 12/29/2022] Open
Abstract
Fighting external pathogens requires an ever-changing immune system that relies on tight regulation of gene expression. Transcriptional control is the first step to build efficient responses while preventing immunodeficiencies and autoimmunity. Post-transcriptional regulation of RNA editing, location, stability, and translation are the other key steps for final gene expression, and they are all controlled by RNA-binding proteins (RBPs). Nowadays we have a deep understanding of how transcription factors control the immune system but recent evidences suggest that post-transcriptional regulation by RBPs is equally important for both development and activation of immune responses. Here, we review current knowledge about how post-transcriptional control by RBPs shapes our immune system and discuss the perspective of RBPs being the key players of a hidden immune cell epitranscriptome.
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Affiliation(s)
- Manuel D Díaz-Muñoz
- Centre de Physiopathologie Toulouse-Purpan, INSERM UMR1043/CNRS U5282, Toulouse, France
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
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40
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RNA-binding proteins control gene expression and cell fate in the immune system. Nat Immunol 2018; 19:120-129. [PMID: 29348497 DOI: 10.1038/s41590-017-0028-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 12/19/2022]
Abstract
RNA-binding proteins (RBPs) are essential for the development and function of the immune system. They interact dynamically with RNA to control its biogenesis and turnover by transcription-dependent and transcription-independent mechanisms. In this Review, we discuss the molecular mechanisms by which RBPs allow gene expression changes to occur at different speeds and to varying degrees, and which RBPs regulate the diversity of the transcriptome and proteome. These proteins are nodes for integration of transcriptional and signaling networks and are intimately linked to intermediary metabolism. They are essential components of regulatory feedback mechanisms that maintain immune tolerance and limit inflammation. The role of RBPs in malignancy and autoimmunity has led to their emergence as targets for the development of new therapeutic modalities.
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41
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Lehmkuhl EM, Zarnescu DC. Lost in Translation: Evidence for Protein Synthesis Deficits in ALS/FTD and Related Neurodegenerative Diseases. ADVANCES IN NEUROBIOLOGY 2018; 20:283-301. [PMID: 29916024 DOI: 10.1007/978-3-319-89689-2_11] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Cells utilize a complex network of proteins to regulate translation, involving post-transcriptional processing of RNA and assembly of the ribosomal unit. Although the complexity provides robust regulation of proteostasis, it also offers several opportunities for translational dysregulation, as has been observed in many neurodegenerative disorders. Defective mRNA localization, mRNA sequatration, inhibited ribogenesis, mutant tRNA synthetases, and translation of hexanucleotide expansions have all been associated with neurodegenerative disease. Here, we review dysregulation of translation in the context of age-related neurodegeneration and discuss novel methods to interrogate translation. This review primarily focuses on amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), a spectrum disorder heavily associated with RNA metabolism, while also analyzing translational inhibition in the context of related neurodegenerative disorders such as Alzheimer's disease and Huntington's disease and the translation-related pathomechanisms common in neurodegenerative disease.
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Affiliation(s)
- Erik M Lehmkuhl
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Daniela C Zarnescu
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA. .,Department of Neuroscience, University of Arizona, Tucson, AZ, USA. .,Department of Neurology, University of Arizona, Tucson, AZ, USA.
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42
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Singh RN, Singh NN. Mechanism of Splicing Regulation of Spinal Muscular Atrophy Genes. ADVANCES IN NEUROBIOLOGY 2018; 20:31-61. [PMID: 29916015 DOI: 10.1007/978-3-319-89689-2_2] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Spinal muscular atrophy (SMA) is one of the major genetic disorders associated with infant mortality. More than 90% cases of SMA result from deletions or mutations of Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, does not compensate for the loss of SMN1 due to predominant skipping of exon 7. However, correction of SMN2 exon 7 splicing has proven to confer therapeutic benefits in SMA patients. The only approved drug for SMA is an antisense oligonucleotide (Spinraza™/Nusinersen), which corrects SMN2 exon 7 splicing by blocking intronic splicing silencer N1 (ISS-N1) located immediately downstream of exon 7. ISS-N1 is a complex regulatory element encompassing overlapping negative motifs and sequestering a cryptic splice site. More than 40 protein factors have been implicated in the regulation of SMN exon 7 splicing. There is evidence to support that multiple exons of SMN are alternatively spliced during oxidative stress, which is associated with a growing number of pathological conditions. Here, we provide the most up to date account of the mechanism of splicing regulation of the SMN genes.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA.
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
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