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Dery KJ, Wong Z, Wei M, Kupiec-Weglinski JW. Mechanistic Insights into Alternative Gene Splicing in Oxidative Stress and Tissue Injury. Antioxid Redox Signal 2023. [PMID: 37776178 DOI: 10.1089/ars.2023.0437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Significance: Oxidative stress (OS) and inflammation are inducers of tissue injury. Alternative splicing (AS) is an essential regulatory step for diversifying the eukaryotic proteome. Human diseases link AS to OS; however, the underlying mechanisms must be better understood. Recent Advances: Genome‑wide profiling studies identify new differentially expressed genes induced by OS-dependent ischemia/reperfusion injury. Overexpression of RNA-binding protein RBFOX1 protects against inflammation. Hypoxia-inducible factor-1α directs polypyrimidine tract binding protein 1 to regulate mouse carcinoembryonic antigen-related cell adhesion molecule 1 (Ceacam1) AS under OS conditions. Heterogeneous nuclear ribonucleoprotein L variant 1 contains an RGG/RG motif that coordinates with transcription factors to influence human CEACAM1 AS. Hypoxia intervention involving short interfering RNAs directed to long-noncoding RNA 260 polarizes M2 macrophages toward an anti-inflammatory phenotype and alleviates OS by inhibiting IL-28RA gene AS. Critical Issues: Protective mechanisms that eliminate reactive oxygen species (ROS) are important for resolving imbalances that lead to chronic inflammation. Defects in AS can cause ROS generation, cell death regulation, and the activation of innate and adaptive immune factors. We propose that AS pathways link redox regulation to the activation or suppression of the inflammatory response during cellular stress. Future Directions: Emergent studies using molecule-mediated RNA splicing are being conducted to exploit the immunogenicity of AS protein products. Deciphering the mechanisms that connect misspliced OS and pathologies should remain a priority. Controlled release of RNA directly into cells with clinical applications is needed as the demand for innovative nucleic acid delivery systems continues to be demonstrated.
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Affiliation(s)
- Kenneth J Dery
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Zeriel Wong
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Megan Wei
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jerzy W Kupiec-Weglinski
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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2
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Gillespie MS, Ward CM, Davies CC. DNA Repair and Therapeutic Strategies in Cancer Stem Cells. Cancers (Basel) 2023; 15:1897. [PMID: 36980782 PMCID: PMC10047301 DOI: 10.3390/cancers15061897] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
First-line cancer treatments successfully eradicate the differentiated tumour mass but are comparatively ineffective against cancer stem cells (CSCs), a self-renewing subpopulation thought to be responsible for tumour initiation, metastasis, heterogeneity, and recurrence. CSCs are thus presented as the principal target for elimination during cancer treatment. However, CSCs are challenging to drug target because of numerous intrinsic and extrinsic mechanisms of drug resistance. One such mechanism that remains relatively understudied is the DNA damage response (DDR). CSCs are presumed to possess properties that enable enhanced DNA repair efficiency relative to their highly proliferative bulk progeny, facilitating improved repair of double-strand breaks induced by radiotherapy and most chemotherapeutics. This can occur through multiple mechanisms, including increased expression and splicing fidelity of DNA repair genes, robust activation of cell cycle checkpoints, and elevated homologous recombination-mediated DNA repair. Herein, we summarise the current knowledge concerning improved genome integrity in non-transformed stem cells and CSCs, discuss therapeutic opportunities within the DDR for re-sensitising CSCs to genotoxic stressors, and consider the challenges posed regarding unbiased identification of novel DDR-directed strategies in CSCs. A better understanding of the DDR mediating chemo/radioresistance mechanisms in CSCs could lead to novel therapeutic approaches, thereby enhancing treatment efficacy in cancer patients.
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Affiliation(s)
- Matthew S. Gillespie
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (M.S.G.)
- School of Cancer Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Ciara M. Ward
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (M.S.G.)
| | - Clare C. Davies
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (M.S.G.)
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3
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Corcos L, Le Scanf E, Quéré G, Arzur D, Cueff G, Jossic-Corcos CL, Le Maréchal C. Microsatellite Instability and Aberrant Pre-mRNA Splicing: How Intimate Is It? Genes (Basel) 2023; 14:genes14020311. [PMID: 36833239 PMCID: PMC9957390 DOI: 10.3390/genes14020311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
Cancers that belong to the microsatellite instability (MSI) class can account for up to 15% of all cancers of the digestive tract. These cancers are characterized by inactivation, through the mutation or epigenetic silencing of one or several genes from the DNA MisMatch Repair (MMR) machinery, including MLH1, MLH3, MSH2, MSH3, MSH6, PMS1, PMS2 and Exo1. The unrepaired DNA replication errors turn into mutations at several thousand sites that contain repetitive sequences, mainly mono- or dinucleotides, and some of them are related to Lynch syndrome, a predisposition condition linked to a germline mutation in one of these genes. In addition, some mutations shortening the microsatellite (MS) stretch could occur in the 3'-intronic regions, i.e., in the ATM (ATM serine/threonine kinase), MRE11 (MRE11 homolog) or the HSP110 (Heat shock protein family H) genes. In these three cases, aberrant pre-mRNA splicing was observed, and it was characterized by the occurrence of selective exon skipping in mature mRNAs. Because both the ATM and MRE11 genes, which as act as players in the MNR (MRE11/NBS1 (Nibrin)/RAD50 (RAD50 double strand break repair protein) DNA damage repair system, participate in double strand breaks (DSB) repair, their frequent splicing alterations in MSI cancers lead to impaired activity. This reveals the existence of a functional link between the MMR/DSB repair systems and the pre-mRNA splicing machinery, the diverted function of which is the consequence of mutations in the MS sequences.
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Affiliation(s)
- Laurent Corcos
- Inserm U1078, Univ Brest, EFS, F-29200 Brest, France
- CHRU Brest, F-29200 Brest, France
- Correspondence:
| | | | - Gaël Quéré
- Inserm U1078, Univ Brest, EFS, F-29200 Brest, France
| | | | | | | | - Cédric Le Maréchal
- Inserm U1078, Univ Brest, EFS, F-29200 Brest, France
- CHRU Brest, F-29200 Brest, France
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4
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de Oliveira Freitas Machado C, Schafranek M, Brüggemann M, Hernández Cañás M, Keller M, Di Liddo A, Brezski A, Blümel N, Arnold B, Bremm A, Wittig I, Jaé N, McNicoll F, Dimmeler S, Zarnack K, Müller-McNicoll M. Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia. Nucleic Acids Res 2023; 51:870-890. [PMID: 36620874 PMCID: PMC9881134 DOI: 10.1093/nar/gkac1225] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 01/10/2023] Open
Abstract
Hypoxia induces massive changes in alternative splicing (AS) to adapt cells to the lack of oxygen. Here, we identify the splicing factor SRSF6 as a key factor in the AS response to hypoxia. The SRSF6 level is strongly reduced in acute hypoxia, which serves a dual purpose: it allows for exon skipping and triggers the dispersal of nuclear speckles. Our data suggest that cells use dispersal of nuclear speckles to reprogram their gene expression during hypoxic adaptation and that SRSF6 plays an important role in cohesion of nuclear speckles. Down-regulation of SRSF6 is achieved through inclusion of a poison cassette exon (PCE) promoted by SRSF4. Removing the PCE 3' splice site using CRISPR/Cas9 abolishes SRSF6 reduction in hypoxia. Aberrantly high SRSF6 levels in hypoxia attenuate hypoxia-mediated AS and impair dispersal of nuclear speckles. As a consequence, proliferation and genomic instability are increased, while the stress response is suppressed. The SRSF4-PCE-SRSF6 hypoxia axis is active in different cancer types, and high SRSF6 expression in hypoxic tumors correlates with a poor prognosis. We propose that the ultra-conserved PCE of SRSF6 acts as a tumor suppressor and that its inclusion in hypoxia is crucial to reduce SRSF6 levels. This may prevent tumor cells from entering the metastatic route of hypoxia adaptation.
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Affiliation(s)
- Camila de Oliveira Freitas Machado
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - Michal Schafranek
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Mirko Brüggemann
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | | | - Mario Keller
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Antonella Di Liddo
- Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Andre Brezski
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Nicole Blümel
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Benjamin Arnold
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Anja Bremm
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Nicolas Jaé
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - François McNicoll
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - Kathi Zarnack
- Correspondence may also be addressed to Kathi Zarnack.
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Ruta V, Pagliarini V, Sette C. Coordination of RNA Processing Regulation by Signal Transduction Pathways. Biomolecules 2021; 11:biom11101475. [PMID: 34680108 PMCID: PMC8533259 DOI: 10.3390/biom11101475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Signal transduction pathways transmit the information received from external and internal cues and generate a response that allows the cell to adapt to changes in the surrounding environment. Signaling pathways trigger rapid responses by changing the activity or localization of existing molecules, as well as long-term responses that require the activation of gene expression programs. All steps involved in the regulation of gene expression, from transcription to processing and utilization of new transcripts, are modulated by multiple signal transduction pathways. This review provides a broad overview of the post-translational regulation of factors involved in RNA processing events by signal transduction pathways, with particular focus on the regulation of pre-mRNA splicing, cleavage and polyadenylation. The effects of several post-translational modifications (i.e., sumoylation, ubiquitination, methylation, acetylation and phosphorylation) on the expression, subcellular localization, stability and affinity for RNA and protein partners of many RNA-binding proteins are highlighted. Moreover, examples of how some of the most common signal transduction pathways can modulate biological processes through changes in RNA processing regulation are illustrated. Lastly, we discuss challenges and opportunities of therapeutic approaches that correct RNA processing defects and target signaling molecules.
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Affiliation(s)
- Veronica Ruta
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Correspondence:
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6
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Goyal M, Singh BK, Simantov K, Kaufman Y, Eshar S, Dzikowski R. An SR protein is essential for activating DNA repair in malaria parasites. J Cell Sci 2021; 134:271848. [PMID: 34291805 PMCID: PMC8435287 DOI: 10.1242/jcs.258572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/14/2021] [Indexed: 11/24/2022] Open
Abstract
Plasmodium falciparum, the parasite responsible for the deadliest form of human malaria, replicates within the erythrocytes of its host, where it encounters numerous pressures that cause extensive DNA damage, which must be repaired efficiently to ensure parasite survival. Malaria parasites, which have lost the non-homologous end joining (NHEJ) pathway for repairing DNA double-strand breaks, have evolved unique mechanisms that enable them to robustly maintain genome integrity under such harsh conditions. However, the nature of these adaptations is unknown. We show that a highly conserved RNA splicing factor, P. falciparum (Pf)SR1, plays an unexpected and crucial role in DNA repair in malaria parasites. Using an inducible and reversible system to manipulate PfSR1 expression, we demonstrate that this protein is recruited to foci of DNA damage. Although loss of PfSR1 does not impair parasite viability, the protein is essential for their recovery from DNA-damaging agents or exposure to artemisinin, the first-line antimalarial drug, demonstrating its necessity for DNA repair. These findings provide key insights into the evolution of DNA repair pathways in malaria parasites as well as the ability of the parasite to recover from antimalarial treatment. Summary: There is an unexpected role for the alternative splicing factor PfSR1 in activating the DNA damage response in the human malaria parasite Plasmodium falciparum.
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Affiliation(s)
- Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Brajesh Kumar Singh
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yotam Kaufman
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Shiri Eshar
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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7
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Deletion of RBMX RGG/RG motif in Shashi-XLID syndrome leads to aberrant p53 activation and neuronal differentiation defects. Cell Rep 2021; 36:109337. [PMID: 34260915 DOI: 10.1016/j.celrep.2021.109337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/29/2021] [Accepted: 06/11/2021] [Indexed: 01/01/2023] Open
Abstract
RNA-binding proteins play important roles in X-linked intellectual disability (XLID). In this study, we investigate the contribution of the XLID-associated RBMX in neuronal differentiation. We show that RBMX-depleted cells exhibit aberrant activation of the p53 pathway. Moreover, we identify that the RBMX RGG/RG motif is methylated by protein arginine methyltransferase 5 (PRMT5), and this regulates assembly with the SRSF1 splicing factor into higher-order complexes. Depletion of RBMX or disruption of the RBMX/SRSF1 complex in PRMT5-depleted cells reduces SRSF1 binding to the MDM4 precursor (pre-)mRNA, leading to exon 6 exclusion and lower MDM4 protein levels. Transcriptomic analysis of isogenic Shashi-XLID human-induced pluripotent stem cells (hiPSCs) generated using CRISPR-Cas9 reveals a dysregulation of MDM4 splicing and aberrant p53 upregulation. Shashi-XLID neural progenitor cells (NPCs) display differentiation and morphological abnormalities accompanied with excessive apoptosis. Our findings identify RBMX as a regulator of SRSF1 and the p53 pathway, suggesting that the loss of function of the RBMX RGG/RG motif is the cause of Shashi-XLID syndrome.
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8
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Mollaei M, Hassan ZM, Khorshidi F, Langroudi L. Chemotherapeutic drugs: Cell death- and resistance-related signaling pathways. Are they really as smart as the tumor cells? Transl Oncol 2021; 14:101056. [PMID: 33684837 PMCID: PMC7938256 DOI: 10.1016/j.tranon.2021.101056] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
Chemotherapeutic drugs kill cancer cells or control their progression all over the patient's body, while radiation- and surgery-based treatments perform in a particular site. Based on their mechanisms of action, they are classified into different groups, including alkylating substrates, antimetabolite agents, anti-tumor antibiotics, inhibitors of topoisomerase I and II, mitotic inhibitors, and finally, corticosteroids. Although chemotherapeutic drugs have brought about more life expectancy, two major and severe complications during chemotherapy are chemoresistance and tumor relapse. Therefore, we aimed to review the underlying intracellular signaling pathways involved in cell death and resistance in different chemotherapeutic drug families to clarify the shortcomings in the conventional single chemotherapy applications. Moreover, we have summarized the current combination chemotherapy applications, including numerous combined-, and encapsulated-combined-chemotherapeutic drugs. We further discussed the possibilities and applications of precision medicine, machine learning, next-generation sequencing (NGS), and whole-exome sequencing (WES) in promoting cancer immunotherapies. Finally, some of the recent clinical trials concerning the application of immunotherapies and combination chemotherapies were included as well, in order to provide a practical perspective toward the future of therapies in cancer cases.
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Affiliation(s)
- Mojtaba Mollaei
- Department of Immunology, School of Medicine, Tarbiat Modares University, Tehran, Iran.
| | | | - Fatemeh Khorshidi
- Department of Immunology, School of Medicine, Tarbiat Modares University, Tehran, Iran; Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Langroudi
- Department of Immunology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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9
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021. [PMID: 33565261 DOI: 10.1002/wrna.1643.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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10
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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11
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Wagner RE, Frye M. Noncanonical functions of the serine-arginine-rich splicing factor (SR) family of proteins in development and disease. Bioessays 2021; 43:e2000242. [PMID: 33554347 DOI: 10.1002/bies.202000242] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/19/2022]
Abstract
Members of the serine/arginine (SR)-rich protein family of splicing factors play versatile roles in RNA processing steps and are often essential for normal development. Dynamic changes in RNA processing and turnover allow fast cellular adaptions to a changing microenvironment and thereby closely cooperate with transcription factor networks that establish cell identity within tissues. SR proteins play fundamental roles in the processing of pre-mRNAs by regulating constitutive and alternative splicing. More recently, SR proteins have also been implicated in other aspects of RNA metabolism such as mRNA stability, transport and translation. The- emerging noncanonical functions highlight the multifaceted functions of these SR proteins and identify them as important coordinators of gene expression programmes. Accordingly, most SR proteins are essential for normal cell function and their misregulation contributes to human diseases such as cancer.
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Affiliation(s)
- Rebecca E Wagner
- German Cancer Research Center - Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Michaela Frye
- German Cancer Research Center - Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
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12
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Zhao L, Zhang J, Liu Z, Wang Y, Xuan S, Zhao P. Comprehensive Characterization of Alternative mRNA Splicing Events in Glioblastoma: Implications for Prognosis, Molecular Subtypes, and Immune Microenvironment Remodeling. Front Oncol 2021; 10:555632. [PMID: 33575206 PMCID: PMC7870873 DOI: 10.3389/fonc.2020.555632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022] Open
Abstract
Alternative splicing (AS) of pre-mRNA has been widely reported to be associated with the progression of malignant tumors. However, a systematic investigation into the prognostic value of AS events in glioblastoma (GBM) is urgently required. The gene expression profile and matched AS events data of GBM patients were obtained from The Cancer Genome Atlas Project (TCGA) and TCGA SpliceSeq database, respectively. 775 AS events were identified as prognostic factors using univariate Cox regression analysis. The least absolute shrinkage and selection operator (LASSO) cox model was performed to narrow down candidate AS events, and a risk score model based on several AS events were developed subsequently. The risk score-based signature was proved as an efficient predictor of overall survival and was closely related to the tumor purity and immunosuppression in GBM. Combined similarity network fusion and consensus clustering (SNF-CC) analysis revealed two distinct GBM subtypes based on the prognostic AS events, and the associations between this novel molecular classification and clinicopathological factors, immune cell infiltration, as well as immunogenic features were further explored. We also constructed a regulatory network to depict the potential mechanisms that how prognostic splicing factors (SFs) regulate splicing patterns in GBM. Finally, a nomogram incorporating AS events signature and other clinical-relevant covariates was built for clinical application. This comprehensive analysis highlights the potential implications for predicting prognosis and clinical management in GBM.
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Affiliation(s)
- Liang Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiayue Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiyuan Liu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yu Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shurui Xuan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Peng Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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13
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Nimeth BA, Riegler S, Kalyna M. Alternative Splicing and DNA Damage Response in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:91. [PMID: 32140165 PMCID: PMC7042379 DOI: 10.3389/fpls.2020.00091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/21/2020] [Indexed: 05/06/2023]
Abstract
Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.
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14
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Anufrieva KS, Shender VO, Arapidi GP, Lagarkova MA, Govorun VM. The Diverse Roles of Spliceosomal Proteins in the Regulation of Cell Processes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Xu L, Zhang H, Mei M, Du C, Huang X, Li J, Wang Y, Bao S, Zheng H. Phosphorylation of serine/arginine-rich splicing factor 1 at tyrosine 19 promotes cell proliferation in pediatric acute lymphoblastic leukemia. Cancer Sci 2018; 109:3805-3815. [PMID: 30320932 PMCID: PMC6272096 DOI: 10.1111/cas.13834] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022] Open
Abstract
Serine/arginine‐rich splicing factor 1 (SRSF1) has been linked to various human cancers including pediatric acute lymphoblastic leukemia (ALL). Our previous study has shown that SRSF1 potentially contributes to leukemogenesis; however, its underlying mechanism remains unclear. In this study, leukemic cells were isolated from pediatric ALL bone marrow samples, followed by immunoprecipitation assays and mass spectrometry analysis specific to SRSF1. Subcellular localization of the SRSF1 protein and its mutants were analyzed by immunofluorescence staining. Cell growth, colony formation, cell apoptosis, and the cell cycle were investigated using stable leukemic cell lines generated with lentivirus‐mediated overexpressed WT or mutant plasmids. Cytotoxicity of the Tie2 kinase inhibitor was also evaluated. Our results showed the phosphorylation of SRSF1 at tyrosine 19 (Tyr‐19) was identified in newly diagnosed ALL samples, but not in complete remission or normal control samples. Compared to the SRSF1 WT cells, the missense mutants of the Tyr‐19 phosphorylation affected the subcellular localization of SRSF1. In addition, the Tyr‐19 phosphorylation of SRSF1 also led to increased cell proliferation and enhanced colony‐forming properties by promoting the cell cycle. Remarkably, we further identified the kinase Tie2 as a potential therapeutic target in leukemia cells. In conclusion, we identify for the first time that the phosphorylation state of SRSF1 is linked to different phases in pediatric ALL. The Tyr‐19 phosphorylation of SRSF1 disrupts its subcellular localization and promotes proliferation in leukemia cells by driving cell‐cycle progression. Inhibitors targeting Tie2 kinase that could catalyze Tyr‐19 phosphorylation of SRSF1 offer a promising therapeutic target for treatment of pediatric ALL.
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Affiliation(s)
- Liting Xu
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Han Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Mei Mei
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chaohao Du
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiahe Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yingchun Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shilai Bao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huyong Zheng
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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16
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Alternative Splicing as a Target for Cancer Treatment. Int J Mol Sci 2018; 19:ijms19020545. [PMID: 29439487 PMCID: PMC5855767 DOI: 10.3390/ijms19020545] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 02/06/2023] Open
Abstract
Alternative splicing is a key mechanism determinant for gene expression in metazoan. During alternative splicing, non-coding sequences are removed to generate different mature messenger RNAs due to a combination of sequence elements and cellular factors that contribute to splicing regulation. A different combination of splicing sites, exonic or intronic sequences, mutually exclusive exons or retained introns could be selected during alternative splicing to generate different mature mRNAs that could in turn produce distinct protein products. Alternative splicing is the main source of protein diversity responsible for 90% of human gene expression, and it has recently become a hallmark for cancer with a full potential as a prognostic and therapeutic tool. Currently, more than 15,000 alternative splicing events have been associated to different aspects of cancer biology, including cell proliferation and invasion, apoptosis resistance and susceptibility to different chemotherapeutic drugs. Here, we present well established and newly discovered splicing events that occur in different cancer-related genes, their modification by several approaches and the current status of key tools developed to target alternative splicing with diagnostic and therapeutic purposes.
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17
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Shkreta L, Toutant J, Durand M, Manley JL, Chabot B. SRSF10 Connects DNA Damage to the Alternative Splicing of Transcripts Encoding Apoptosis, Cell-Cycle Control, and DNA Repair Factors. Cell Rep 2017; 17:1990-2003. [PMID: 27851963 PMCID: PMC5483951 DOI: 10.1016/j.celrep.2016.10.071] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/19/2016] [Accepted: 10/20/2016] [Indexed: 11/12/2022] Open
Abstract
RNA binding proteins and signaling components control the production of pro-death and pro-survival splice variants of Bcl-x. DNA damage promoted by oxaliplatin increases the level of pro-apoptotic Bcl-xS in an ATM/CHK2-dependent manner, but how this shift is enforced is not known. Here, we show that in normally growing cells, when the 5′ splice site of Bcl-xS is largely repressed, SRSF10 partially relieves repression and interacts with repressor hnRNP K and stimulatory hnRNP F/H proteins. Oxaliplatin abrogates the interaction of SRSF10 with hnRNP F/H and decreases the association of SRSF10 and hnRNP K with the Bcl-x pre-mRNA. Dephosphorylation of SRSF10 is linked with these changes. A broader analysis reveals that DNA damage co-opts SRSF10 to control splicing decisions in transcripts encoding components involved in DNA repair, cell-cycle control, and apoptosis. DNA damage therefore alters the interactions between splicing regulators to elicit a splicing response that determines cell fate.
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Affiliation(s)
- Lulzim Shkreta
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Johanne Toutant
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Mathieu Durand
- Laboratory of Functional Genomics, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Benoit Chabot
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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18
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A missense MT-ND5 mutation in differentiated Parkinson Disease cytoplasmic hybrid induces ROS-dependent DNA Damage Response amplified by DROSHA. Sci Rep 2017; 7:9528. [PMID: 28842646 PMCID: PMC5573376 DOI: 10.1038/s41598-017-09910-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/31/2017] [Indexed: 12/14/2022] Open
Abstract
Genome integrity is continuously threatened by endogenous sources of DNA damage including reactive oxygen species (ROS) produced by cell metabolism. Factors of the RNA interference (RNAi) machinery have been recently involved in the cellular response to DNA damage (DDR) in proliferating cells. To investigate the impact of component of RNAi machinery on DDR activation in terminally differentiated cells, we exploited cytoplasmic hybrid (cybrid) cell lines in which mitochondria of sporadic Parkinson’s disease patients repopulate neuroblastoma SH-SY5Y-Rho(0) cells. Upon differentiation into dopaminergic neuron-like cells, PD63 cybrid showed increased intracellular level of ROS and chronic DDR activation, compared to other cybrids with the same nuclear background. Importantly, DDR activation in these cells can be prevented by ROS scavenging treatment suggesting that ROS production is indeed causative of nuclear DNA damage. Sequence analysis of the mitogenomes identified a rare and heteroplasmic missense mutation affecting a highly conserved residue of the ND5-subunit of respiratory complex I, which accounts for ROS increase. We demonstrated that the assembly of nuclear DDR foci elicited by oxidative stress in these cells relies on DROSHA, providing the first evidence that components of RNAi machinery play a crucial role also in the mounting of ROS-induced DDR in non-replicating neuronal cells.
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19
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Dominguez D, Tsai YH, Weatheritt R, Wang Y, Blencowe BJ, Wang Z. An extensive program of periodic alternative splicing linked to cell cycle progression. eLife 2016; 5. [PMID: 27015110 PMCID: PMC4884079 DOI: 10.7554/elife.10288] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 03/24/2016] [Indexed: 12/28/2022] Open
Abstract
Progression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1300 genes with cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose level undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control.
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Affiliation(s)
- Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Yi-Hsuan Tsai
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Robert Weatheritt
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Yang Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Zefeng Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Science, Shanghai, China
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20
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Giono LE, Nieto Moreno N, Cambindo Botto AE, Dujardin G, Muñoz MJ, Kornblihtt AR. The RNA Response to DNA Damage. J Mol Biol 2016; 428:2636-2651. [PMID: 26979557 DOI: 10.1016/j.jmb.2016.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/01/2016] [Accepted: 03/07/2016] [Indexed: 02/01/2023]
Abstract
Multicellular organisms must ensure genome integrity to prevent accumulation of mutations, cell death, and cancer. The DNA damage response (DDR) is a complex network that senses, signals, and executes multiple programs including DNA repair, cell cycle arrest, senescence, and apoptosis. This entails regulation of a variety of cellular processes: DNA replication and transcription, RNA processing, mRNA translation and turnover, and post-translational modification, degradation, and relocalization of proteins. Accumulated evidence over the past decades has shown that RNAs and RNA metabolism are both regulators and regulated actors of the DDR. This review aims to present a comprehensive overview of the current knowledge on the many interactions between the DNA damage and RNA fields.
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Affiliation(s)
- Luciana E Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Nicolás Nieto Moreno
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Adrián E Cambindo Botto
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Gwendal Dujardin
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Centre for Genomic Regulation, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Manuel J Muñoz
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
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21
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Shkreta L, Chabot B. The RNA Splicing Response to DNA Damage. Biomolecules 2015; 5:2935-77. [PMID: 26529031 PMCID: PMC4693264 DOI: 10.3390/biom5042935] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/20/2015] [Accepted: 10/16/2015] [Indexed: 12/29/2022] Open
Abstract
The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.
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Affiliation(s)
- Lulzim Shkreta
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| | - Benoit Chabot
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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22
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Posttranscriptional Regulation of Splicing Factor SRSF1 and Its Role in Cancer Cell Biology. BIOMED RESEARCH INTERNATIONAL 2015; 2015:287048. [PMID: 26273603 PMCID: PMC4529898 DOI: 10.1155/2015/287048] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/16/2014] [Indexed: 01/23/2023]
Abstract
Over the past decade, alternative splicing has been progressively recognized as a major mechanism regulating gene expression patterns in different tissues and disease states through the generation of multiple mRNAs from the same gene transcript. This process requires the joining of selected exons or usage of different pairs of splice sites and is regulated by gene-specific combinations of RNA-binding proteins. One archetypical splicing regulator is SRSF1, for which we review the molecular mechanisms and posttranscriptional modifications involved in its life cycle. These include alternative splicing of SRSF1 itself, regulatory protein phosphorylation events, and the role of nuclear versus cytoplasmic SRSF1 localization. In addition, we resume current knowledge on deregulated SRSF1 expression in tumors and describe SRSF1-regulated alternative transcripts with functional consequences for cancer cell biology at different stages of tumor development.
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23
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Cremaschi P, Oliverio M, Leva V, Bione S, Carriero R, Mazzucco G, Palamidessi A, Scita G, Biamonti G, Montecucco A. Chronic Replication Problems Impact Cell Morphology and Adhesion of DNA Ligase I Defective Cells. PLoS One 2015; 10:e0130561. [PMID: 26151554 PMCID: PMC4495043 DOI: 10.1371/journal.pone.0130561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022] Open
Abstract
Moderate DNA damage resulting from metabolic activities or sub-lethal doses of exogenous insults may eventually lead to cancer onset. Human 46BR.1G1 cells bear a mutation in replicative DNA ligase I (LigI) which results in low levels of replication-dependent DNA damage. This replication stress elicits a constitutive phosphorylation of the ataxia telangiectasia mutated (ATM) checkpoint kinase that fails to arrest cell cycle progression or to activate apoptosis or cell senescence. Stable transfection of wild type LigI, as in 7A3 cells, prevents DNA damage and ATM activation. Here we show that parental 46BR.1G1 and 7A3 cells differ in important features such as cell morphology, adhesion and migration. Comparison of gene expression profiles in the two cell lines detects Bio-Functional categories consistent with the morphological and migration properties of LigI deficient cells. Interestingly, ATM inhibition makes 46BR.1G1 more similar to 7A3 cells for what concerns morphology, adhesion and expression of cell-cell adhesion receptors. These observations extend the influence of the DNA damage response checkpoint pathways and unveil a role for ATM kinase activity in modulating cell biology parameters relevant to cancer progression.
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Affiliation(s)
- Paolo Cremaschi
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
| | - Matteo Oliverio
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Valentina Leva
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Silvia Bione
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Roberta Carriero
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- Istituto Universitario di Studi Superiori (IUSS), Pavia, Italy
| | - Giulia Mazzucco
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
| | | | - Giorgio Scita
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milano, Italy
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Alessandra Montecucco
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- * E-mail:
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24
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Boucas J, Fritz C, Schmitt A, Riabinska A, Thelen L, Peifer M, Leeser U, Nuernberg P, Altmueller J, Gaestel M, Dieterich C, Reinhardt HC. Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression. PLoS One 2015; 10:e0125745. [PMID: 25993413 PMCID: PMC4439058 DOI: 10.1371/journal.pone.0125745] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/26/2015] [Indexed: 12/11/2022] Open
Abstract
Growing evidence suggests a key role for RNA binding proteins (RBPs) in genome stability programs. Additionally, recent developments in RNA sequencing technologies, as well as mass-spectrometry techniques, have greatly expanded our knowledge on protein-RNA interactions. We here use full transcriptome sequencing and label-free LC/MS/MS to identify global changes in protein-RNA interactions in response to etoposide-induced genotoxic stress. We show that RBPs have distinct binding patterns in response to genotoxic stress and that inactivation of the RBP regulator module, p38/MK2, can affect the entire spectrum of protein-RNA interactions that take place in response to stress. In addition to validating the role of known RBPs like Srsf1, Srsf2, Elavl1 in the genotoxic stress response, we add a new collection of RBPs to the DNA damage response. We identify Khsrp as a highly regulated RBP in response to genotoxic stress and further validate its role as a driver of the G(1/)S transition through the suppression of Cdkn1a(P21) transcripts. Finally, we identify KHSRP as an indicator of overall survival, as well as disease free survival in glioblastoma multiforme.
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Affiliation(s)
- Jorge Boucas
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Christian Fritz
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Anna Schmitt
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Arina Riabinska
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Lisa Thelen
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Uschi Leeser
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Peter Nuernberg
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Janine Altmueller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Matthias Gaestel
- Institute of Biochemistry, Hannover Medical School, Hannover, Germany
| | - Christoph Dieterich
- Computational RNA Biology and Ageing, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Straße 9b, 50913, Cologne, Germany
| | - H. Christian Reinhardt
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
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25
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Xue F, Li X, Zhao X, Wang L, Liu M, Shi R, Zheng J. SRSF1 facilitates cytosolic DNA-induced production of type I interferons recognized by RIG-I. PLoS One 2015; 10:e0115354. [PMID: 25658361 PMCID: PMC4319963 DOI: 10.1371/journal.pone.0115354] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Evidence has shown that psoriasis is closely associated with infection; however, the mechanism of this association remains unclear. In mammalian cells, viral or bacterial infection is accompanied by the release of cytosolic DNA, which in turn triggers the production of type-I interferons (IFNs). Type I IFNs and their associated genes are significantly upregulated in psoriatic lesions. RIG-I is also highly upregulated in psoriatic lesions and is responsible for IFN production. However, RIG-I mediated regulatory signaling in psoriasis is poorly understood. METHODS We screened a cDNA library and identified potential RIG-I interacting partners that may play a role in psoriasis. RESULTS We found that serine/arginine-rich splicing factor 1 (SRSF1) could specifically interact with RIG-I to facilitate RIG-I mediated production of type-I IFN that is triggered by cytosolic DNA. We found SRSF1 associates with RNA polymerase III and RIG-I in a DNA-dependent manner. In addition, treatment with a TNFα inhibitor downregulated SRSF1 expression in peripheral blood mononuclear cells (PBMCs) from psoriasis vulgaris patients. DISCUSSION Based on the abundance of pathogenic cytosolic DNA that is detected in psoriatic lesions, our finding that RIG-I interacts with SRSF1 to regulate type-I IFN production reveals a critical link regarding how cytosolic DNA specifically activates aberrant IFN expression. These data may provide new therapeutic targets for the treatment of psoriasis.
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Affiliation(s)
- Feng Xue
- Laboratory of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Li
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqing Zhao
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanqi Wang
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Min Liu
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruofei Shi
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Zheng
- Laboratory of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Montecucco A, Zanetta F, Biamonti G. Molecular mechanisms of etoposide. EXCLI JOURNAL 2015; 14:95-108. [PMID: 26600742 PMCID: PMC4652635 DOI: 10.17179/excli2015-561] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/24/2014] [Indexed: 12/21/2022]
Abstract
Etoposide derives from podophyllotoxin, a toxin found in the American Mayapple. It was first synthesized in 1966 and approved for cancer therapy in 1983 by the U.S. Food and Drug Administration (Hande, 1998[25]). Starting from 1980s several studies demonstrated that etoposide targets DNA topoisomerase II activities thus leading to the production of DNA breaks and eliciting a response that affects several aspects of cell metabolisms. In this review we will focus on molecular mechanisms that account for the biological effect of etoposide.
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Affiliation(s)
| | - Francesca Zanetta
- Istituto di Genetica Molecolare, CNR, via Abbiategrasso 207, Pavia ; Dipartimento di Biologia e Biotecnologia, Università degli Studi di Pavia, via Ferrata 9, Pavia, Italy
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Biamonti G, Catillo M, Pignataro D, Montecucco A, Ghigna C. The alternative splicing side of cancer. Semin Cell Dev Biol 2014; 32:30-6. [PMID: 24657195 DOI: 10.1016/j.semcdb.2014.03.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/11/2014] [Indexed: 12/22/2022]
Abstract
Alternative splicing emerges as a potent and pervasive mechanism of gene expression regulation that expands the coding capacity of the genome and forms an intermediate layer of regulation between transcriptional and post-translational networks. Indeed, alternative splicing occupies a pivotal position in developmental programs and in the cell response to external and internal stimuli. Not surprisingly, therefore, its deregulation frequently leads to human disease. In this review we provide an updated overview of the impact of alternative splicing on tumorigenesis. Moreover, we discuss the intricacy of the reciprocal interactions between alternative splicing programs and signal transduction pathways, which appear to be crucially linked to cancer progression in response to the tumor microenvironment. Finally, we focus on the recently described interplay between splicing and chromatin organization which is expected to shed new lights into gene expression regulation in normal and cancer cells.
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Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy.
| | - Morena Catillo
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy
| | - Daniela Pignataro
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy
| | | | - Claudia Ghigna
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy
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RNA splicing: a new player in the DNA damage response. Int J Cell Biol 2013; 2013:153634. [PMID: 24159334 PMCID: PMC3789447 DOI: 10.1155/2013/153634] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 12/16/2022] Open
Abstract
It is widely accepted that tumorigenesis is a multistep process characterized by the sequential accumulation of genetic alterations. However, the molecular basis of genomic instability in cancer is still partially understood. The observation that hereditary cancers are often characterized by mutations in DNA repair and checkpoint genes suggests that accumulation of DNA damage is a major contributor to the oncogenic transformation. It is therefore of great interest to identify all the cellular pathways that contribute to the response to DNA damage. Recently, RNA processing has emerged as a novel pathway that may contribute to the maintenance of genome stability. In this review, we illustrate several different mechanisms through which pre-mRNA splicing and genomic stability can influence each other. We specifically focus on the role of splicing factors in the DNA damage response and describe how, in turn, activation of the DDR can influence the activity of splicing factors.
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Mórocz M, Gali H, Raskó I, Downes CS, Haracska L. Single cell analysis of human RAD18-dependent DNA post-replication repair by alkaline bromodeoxyuridine comet assay. PLoS One 2013; 8:e70391. [PMID: 23936422 PMCID: PMC3735594 DOI: 10.1371/journal.pone.0070391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/19/2013] [Indexed: 01/02/2023] Open
Abstract
Damage to DNA can block replication progression resulting in gaps in the newly synthesized DNA. Cells utilize a number of post-replication repair (PRR) mechanisms such as the RAD18 controlled translesion synthesis or template switching to overcome the discontinuities formed opposite the DNA lesions and to complete DNA replication. Gaining more insights into the role of PRR genes promotes better understanding of DNA damage tolerance and of how their malfunction can lead to increased genome instability and cancer. However, a simple and efficient method to characterise gene specific PRR deficiencies at a single cell level has not been developed. Here we describe the so named BrdU comet PRR assay to test the contribution of human RAD18 to PRR at a single cell level, by which we kinetically characterized the consequences of the deletion of human RAD18 on the replication of UV-damaged DNA. Moreover, we demonstrate the capability of our method to evaluate PRR at a single cell level in unsynchronized cell population.
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Affiliation(s)
- Mónika Mórocz
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
| | - Himabindu Gali
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
| | - István Raskó
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
| | - C. Stephen Downes
- Biomedical Sciences Research Institute, School of Biomedical Sciences, University of Ulster, Coleraine, Londonderry, Northern Ireland
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail:
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Montecucco A, Biamonti G. Pre-mRNA processing factors meet the DNA damage response. Front Genet 2013; 4:102. [PMID: 23761808 PMCID: PMC3674313 DOI: 10.3389/fgene.2013.00102] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 05/20/2013] [Indexed: 12/04/2022] Open
Abstract
It is well-known that DNA-damaging agents induce genome instability, but only recently have we begun to appreciate that chromosomes are fragile per se and frequently subject to DNA breakage. DNA replication further magnifies such fragility, because it leads to accumulation of single-stranded DNA. Recent findings suggest that chromosome fragility is similarly increased during transcription. Transcripts produced by RNA polymerase II (RNAPII) are subject to multiple processing steps, including maturation of 5′ and 3′ ends and splicing, followed by transport to the cytoplasm. RNA maturation starts on nascent transcripts and is mediated by a number of diverse proteins and ribonucleoprotein particles some of which are recruited cotranscriptionally through interactions with the carboxy-terminal domain of RNAPII. This coupling is thought to maximize efficiency of pre-mRNA maturation and directly impacts the choice of alternative splice sites. Mounting evidence suggests that lack of coordination among different RNA maturation steps, by perturbing the interaction of nascent transcripts with the DNA template, has deleterious effects on genome stability. Thus, in the absence of proper surveillance mechanisms, transcription could be a major source of DNA damage in cancer. Recent high-throughput screenings in human cells and budding yeast have identified several factors implicated in RNA metabolism that are targets of DNA damage checkpoint kinases: ATM (ataxia telangiectasia mutated) and ATR (ATM-Rad3 related) (Tel1 and Mec1 in budding yeast, respectively). Moreover, inactivation of various RNA processing factors induces accumulation of γH2AX foci, an early sign of DNA damage. Thus, a complex network is emerging that links DNA repair and RNA metabolism. In this review we provide a comprehensive overview of the role played by pre-mRNA processing factors in the cell response to DNA damage and in the maintenance of genome stability.
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