1
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Lopez-Pedrera C, Patiño-Trives AM, Cerdó T, Ortega-Castro R, Sanchez-Pareja I, Ibañez-Costa A, Muñoz-Barrera L, Ábalos-Aguilera MC, Ruiz-Vilchez D, Seguí Azpilcueta P, Espinosa M, Barbarroja N, Escudero-Contreras A, Castaño JP, Luque RM, Ortega R, Aguirre MA, Perez-Sanchez C. Splicing machinery is profoundly altered in systemic lupus erythematosus and antiphospholipid syndrome and directly linked to key clinical features. J Autoimmun 2023; 135:102990. [PMID: 36621176 DOI: 10.1016/j.jaut.2022.102990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
OBJECTIVES To characterize the splicing machinery (SM) of leukocytes from primary antiphospholipid syndrome (APS), systemic lupus erythematosus (SLE) and antiphospholipid syndrome with lupus (APS + SLE) patients, and to assess its clinical involvement. METHODS Monocytes, lymphocytes and neutrophils from 80 patients (22 APS, 35 SLE and 23 APS + SLE) and 50 HD were purified, and 45 selected SM components were evaluated by qPCR-microfluidic array. Relationship with clinical features and underlying regulatory mechanisms were assessed. RESULTS APS, SLE and APS + SLE leukocytes displayed significant and specific alterations in SM-components (SMC), associated with clinical features [autoimmune profiles, disease activity, lupus nephritis (LN), and CV-risk markers]. A remarkable relationship among dysregulated SMC in monocytes and the presence of LN in SLE was highlighted, revealing a novel pathological mechanism, which was further explored. Immunohistology analysis of renal biopsies highlighted the pathological role of the myeloid compartment in LN. Transcriptomic analysis of monocytes from SLE-LN(+) vs SLE-LN(-) identified 271 genes differentially expressed, mainly involved in inflammation and IFN-signaling. Levels of IFN-related genes correlated with those of SMC in SLE-LN(+). These results were validated in two external SLE-LN(+) datasets of whole-blood and kidney biopsies. In vitro, SLE-LN(+)-serum promoted a concomitant dysregulation of both, the IFN signature and several SMC, further reversed by JAKinibs treatment. Interestingly, IFNs, key inflammatory cytokines in SLE pathology, also altered SMC. Lastly, the over/down-expression of selected SMC in SLE-monocytes reduced the release of inflammatory cytokines and their adhesion capacity. CONCLUSION Overall, we have identified, for the first time, a specific alteration of SMC in leukocytes from APS, SLE and APS + SLE patients that would be responsible for the development of distinctive clinical profiles.
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Affiliation(s)
- Ch Lopez-Pedrera
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain.
| | - A M Patiño-Trives
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - T Cerdó
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - R Ortega-Castro
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - I Sanchez-Pareja
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - A Ibañez-Costa
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004, Córdoba, Spain; Department of Cell Biology, Physiology and Immunology, Universidad de Córdoba, 14004, Córdoba, Spain; Reina Sofia University Hospital, 14004, Córdoba, Spain; CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), 14004, Córdoba, Spain
| | - L Muñoz-Barrera
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - M C Ábalos-Aguilera
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - D Ruiz-Vilchez
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - P Seguí Azpilcueta
- Radiology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - M Espinosa
- Nephrology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - N Barbarroja
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - A Escudero-Contreras
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - J P Castaño
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004, Córdoba, Spain; Department of Cell Biology, Physiology and Immunology, Universidad de Córdoba, 14004, Córdoba, Spain; Reina Sofia University Hospital, 14004, Córdoba, Spain; CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), 14004, Córdoba, Spain
| | - R M Luque
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004, Córdoba, Spain; Department of Cell Biology, Physiology and Immunology, Universidad de Córdoba, 14004, Córdoba, Spain; Reina Sofia University Hospital, 14004, Córdoba, Spain; CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), 14004, Córdoba, Spain
| | - R Ortega
- Pathology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - M A Aguirre
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - C Perez-Sanchez
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
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2
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Fu Y, Bai C, Wang S, Chen D, Zhang P, Wei H, Rong F, Zhang C, Chen S, Wang Z. AKT1 phosphorylates RBM17 to promote Sox2 transcription by modulating alternative splicing of FOXM1 to enhance cancer stem cell properties in colorectal cancer cells. FASEB J 2023; 37:e22707. [PMID: 36520054 DOI: 10.1096/fj.202201255r] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. The existence of cancer stem cells (CSC) causes tumor relapses, metastasis, and resistance to conventional therapy. Alternative splicing has been shown to affect physiological and pathological processes. Accumulating evidence has confirmed that targeting alternative splicing could be an effective strategy to treat CRC. Currently, the role of alternative splicing in the regulation of CSC properties in CRC has not been elucidated. Here, we show that RBM17 displays oncogenic roles in CRC cells. RBM17 enhances cell proliferation and reduces chemotherapeutic-induced apoptosis in CRC cells. Besides, RBM17 increases CD133 positive and ALDEFLUOR positive populations and promotes sphere formation in CRC cells. In mechanism studies, we found that FOXM1 is critical for RBM17 enhanced CSC properties. Moreover, FOXM1 alternative splicing is essential for RBM17 enhanced CSC properties in CRC cells. Additionally, RBM17 enhances CSC characteristics by controlling FOXM1 expression to promote Sox2 expression. Furthermore, AKT1 works as an upstream kinase to control RBM17-mediated FOXM1 alternative splicing and enhancement of CSC properties in CRC cells. Our study reveals that AKT1-RBM17-FOXM1-Sox2 axis could be a potential target for modulating alternative splicing to reduce CSC properties in CRC cells.
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Affiliation(s)
- Yan Fu
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China.,Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Center for Evidence Based Medicine and Clinical Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chen Bai
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Shengsheng Wang
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Denggang Chen
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Peng Zhang
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Hailang Wei
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Fan Rong
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chao Zhang
- Center for Evidence Based Medicine and Clinical Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Shaojuan Chen
- Department of Stomatology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhenjun Wang
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
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3
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Characterization of the RAS/RAF/ERK Signal Cascade as a Novel Regulating Factor in Alpha-Amanitin-Induced Cytotoxicity in Huh-7 Cells. Int J Mol Sci 2022; 23:ijms232012294. [PMID: 36293151 PMCID: PMC9603094 DOI: 10.3390/ijms232012294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
The well-known hepatotoxicity mechanism resulting from alpha-amanitin (α-AMA) exposure arises from RNA polymerase II (RNAP II) inhibition. RNAP Ⅱ inhibition occurs through the dysregulation of mRNA synthesis. However, the signaling pathways in hepatocytes that arise from α-AMA have not yet been fully elucidated. Here, we identified that the RAS/RAF/ERK signaling pathway was activated through quantitative phosphoproteomic and molecular biological analyses in Huh-7 cells. Bioinformatics analysis showed that α-AMA exposure increased protein phosphorylation in a time-dependent α-AMA exposure. In addition, phosphorylation increased not only the components of the ERK signaling pathway but also U2AF65 and SPF45, known splicing factors. Therefore, we propose a novel mechanism of α-AMA as follows. The RAS/RAF/ERK signaling pathway involved in aberrant splicing events is activated by α-AMA exposure followed by aberrant splicing events leading to cell death in Huh-7 cells.
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4
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Liu L, Vujovic A, Deshpande NP, Sathe S, Anande G, Chen HTT, Xu J, Minden MD, Yeo GW, Unnikrishnan A, Hope KJ, Lu Y. The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors. Nat Commun 2022; 13:3833. [PMID: 35781533 PMCID: PMC9250932 DOI: 10.1038/s41467-022-31155-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 05/30/2022] [Indexed: 12/01/2022] Open
Abstract
Chemo-resistance in acute myeloid leukemia (AML) patients is driven by leukemic stem cells (LSCs) resulting in high rates of relapse and low overall survival. Here, we demonstrate that upregulation of the splicing factor, RBM17 preferentially marks and sustains LSCs and directly correlates with shorten patient survival. RBM17 knockdown in primary AML cells leads to myeloid differentiation and impaired colony formation and in vivo engraftment. Integrative multi-omics analyses show that RBM17 repression leads to inclusion of poison exons and production of nonsense-mediated decay (NMD)-sensitive transcripts for pro-leukemic factors and the translation initiation factor, EIF4A2. We show that EIF4A2 is enriched in LSCs and its inhibition impairs primary AML progenitor activity. Proteomic analysis of EIF4A2-depleted AML cells shows recapitulation of the RBM17 knockdown biological effects, including pronounced suppression of proteins involved in ribosome biogenesis. Overall, these results provide a rationale to target RBM17 and/or its downstream NMD-sensitive splicing substrates for AML treatment.
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Affiliation(s)
- Lina Liu
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ana Vujovic
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nandan P Deshpande
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, San Diego, CA, USA
| | - Govardhan Anande
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - He Tian Tony Chen
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Joshua Xu
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mark D Minden
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, San Diego, CA, USA
| | - Ashwin Unnikrishnan
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Kristin J Hope
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| | - Yu Lu
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
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5
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Zhang T, Fassl A, Vaites LP, Fu S, Sicinski P, Paulo JA, Gygi SP. Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment. J Proteome Res 2022; 21:494-506. [PMID: 35044772 PMCID: PMC9142857 DOI: 10.1021/acs.jproteome.1c00865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Kinases govern many cellular responses through the reversible transfer of a phosphate moiety to their substrates. However, pairing a substrate with a kinase is challenging. In proximity labeling experiments, proteins proximal to a target protein are marked by biotinylation, and mass spectrometry can be used for their identification. Here, we combine ascorbate peroxidase (APEX) proximity labeling and a phosphorylation enrichment-based workflow, Phospho-APEX (pAPEX), to rapidly identify phosphorylated and biotinylated neighbor proteins which can be considered for candidate substrates. The pAPEX strategy enriches and quantifies differences in proximity for proteins and phosphorylation sites proximal to an APEX2-tagged kinase under the kinase "ON" and kinase "OFF" conditions. As a proof of concept, we identified candidate substrates of MAPK1 in HEK293T and HCT116 cells and candidate substrates of PKA in HEK293T cells. In addition to many known substrates, C15orf39 was identified and confirmed as a novel MAPK1 substrate. In all, we adapted the proximity labeling-based platform to accommodate phosphorylation analysis for kinase substrate identification.
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Affiliation(s)
- Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura P. Vaites
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sipei Fu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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6
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Kip AM, Valverde JM, Altelaar M, Heeren RMA, Hundscheid IHR, Dejong CHC, Olde Damink SWM, Balluff B, Lenaerts K. Combined Quantitative (Phospho)proteomics and Mass Spectrometry Imaging Reveal Temporal and Spatial Protein Changes in Human Intestinal Ischemia-Reperfusion. J Proteome Res 2021; 21:49-66. [PMID: 34874173 PMCID: PMC8750167 DOI: 10.1021/acs.jproteome.1c00447] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Intestinal ischemia–reperfusion
(IR) injury is a severe
clinical condition, and unraveling its pathophysiology is crucial
to improve therapeutic strategies and reduce the high morbidity and
mortality rates. Here, we studied the dynamic proteome and phosphoproteome
in the human intestine during ischemia and reperfusion, using liquid
chromatography-tandem mass spectrometry (LC-MS/MS) analysis to gain
quantitative information of thousands of proteins and phosphorylation
sites, as well as mass spectrometry imaging (MSI) to obtain spatial
information. We identified a significant decrease in abundance of
proteins related to intestinal absorption, microvillus, and cell junction,
whereas proteins involved in innate immunity, in particular the complement
cascade, and extracellular matrix organization increased in abundance
after IR. Differentially phosphorylated proteins were involved in
RNA splicing events and cytoskeletal and cell junction organization.
In addition, our analysis points to mitogen-activated protein kinase
(MAPK) and cyclin-dependent kinase (CDK) families to be active kinases
during IR. Finally, matrix-assisted laser desorption ionization time-of-flight
(MALDI-TOF) MSI presented peptide alterations in abundance and distribution,
which resulted, in combination with Fourier-transform ion cyclotron
resonance (FTICR) MSI and LC-MS/MS, in the annotation of proteins
related to RNA splicing, the complement cascade, and extracellular
matrix organization. This study expanded our understanding of the
molecular changes that occur during IR in the human intestine and
highlights the value of the complementary use of different MS-based
methodologies.
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Affiliation(s)
- Anna M Kip
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Inca H R Hundscheid
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Cornelis H C Dejong
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.,Department of General, Visceral- and Transplantation Surgery, RWTH Aachen University Hospital, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Steven W M Olde Damink
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.,Department of General, Visceral- and Transplantation Surgery, RWTH Aachen University Hospital, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Benjamin Balluff
- Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Kaatje Lenaerts
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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7
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Martín E, Vivori C, Rogalska M, Herrero-Vicente J, Valcárcel J. Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation. RNA (NEW YORK, N.Y.) 2021; 27:1557-1576. [PMID: 34544891 PMCID: PMC8594467 DOI: 10.1261/rna.078935.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/11/2021] [Indexed: 06/10/2023]
Abstract
The regulation of pre-mRNA processing has important consequences for cell division and the control of cancer cell proliferation, but the underlying molecular mechanisms remain poorly understood. We report that three splicing factors, SPF45, SR140, and CHERP, form a tight physical and functionally coherent complex that regulates a variety of alternative splicing events, frequently by repressing short exons flanked by suboptimal 3' splice sites. These comprise alternative exons embedded in genes with important functions in cell-cycle progression, including the G2/M key regulator FOXM1 and the spindle regulator SPDL1. Knockdown of either of the three factors leads to G2/M arrest and to enhanced apoptosis in HeLa cells. Promoting the changes in FOXM1 or SPDL1 splicing induced by SPF45/SR140/CHERP knockdown partially recapitulates the effects on cell growth, arguing that the complex orchestrates a program of alternative splicing necessary for efficient cell proliferation.
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Affiliation(s)
- Elena Martín
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Claudia Vivori
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Malgorzata Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Jorge Herrero-Vicente
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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8
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Naro C, Bielli P, Sette C. Oncogenic dysregulation of pre-mRNA processing by protein kinases: challenges and therapeutic opportunities. FEBS J 2021; 288:6250-6272. [PMID: 34092037 PMCID: PMC8596628 DOI: 10.1111/febs.16057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/13/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022]
Abstract
Alternative splicing and polyadenylation represent two major steps in pre-mRNA-processing, which ensure proper gene expression and diversification of human transcriptomes. Deregulation of these processes contributes to oncogenic programmes involved in the onset, progression and evolution of human cancers, which often result in the acquisition of resistance to existing therapies. On the other hand, cancer cells frequently increase their transcriptional rate and develop a transcriptional addiction, which imposes a high stress on the pre-mRNA-processing machinery and establishes a therapeutically exploitable vulnerability. A prominent role in fine-tuning pre-mRNA-processing mechanisms is played by three main families of protein kinases: serine arginine protein kinase (SRPK), CDC-like kinase (CLK) and cyclin-dependent kinase (CDK). These kinases phosphorylate the RNA polymerase, splicing factors and regulatory proteins involved in cleavage and polyadenylation of the nascent transcripts. The activity of SRPKs, CLKs and CDKs can be altered in cancer cells, and their inhibition was shown to exert anticancer effects. In this review, we describe key findings that have been reported on these topics and discuss challenges and opportunities of developing therapeutic approaches targeting splicing factor kinases.
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Affiliation(s)
- Chiara Naro
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Policlinico Universitario A. GemelliIRCCSRomeItaly
| | - Pamela Bielli
- Department of Biomedicine and PreventionUniversity of Rome Tor VergataItaly
- Fondazione Santa LuciaIRCCSRomeItaly
| | - Claudio Sette
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Santa LuciaIRCCSRomeItaly
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9
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Ibáñez-Costa A, Perez-Sanchez C, Patiño-Trives AM, Luque-Tevar M, Font P, Arias de la Rosa I, Roman-Rodriguez C, Abalos-Aguilera MC, Conde C, Gonzalez A, Pedraza-Arevalo S, Del Rio-Moreno M, Blazquez-Encinas R, Segui P, Calvo J, Ortega Castro R, Escudero-Contreras A, Barbarroja N, Aguirre MA, Castaño JP, Luque RM, Collantes-Estevez E, Lopez-Pedrera C. Splicing machinery is impaired in rheumatoid arthritis, associated with disease activity and modulated by anti-TNF therapy. Ann Rheum Dis 2021; 81:56-67. [PMID: 34625402 PMCID: PMC8762032 DOI: 10.1136/annrheumdis-2021-220308] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/18/2021] [Indexed: 12/29/2022]
Abstract
OBJECTIVES To characterise splicing machinery (SM) alterations in leucocytes of patients with rheumatoid arthritis (RA), and to assess its influence on their clinical profile and therapeutic response. METHODS Leucocyte subtypes from 129 patients with RA and 29 healthy donors (HD) were purified, and 45 selected SM elements (SME) were evaluated by quantitative PCR-array based on microfluidic technology (Fluidigm). Modulation by anti-tumour necrosis factor (TNF) therapy and underlying regulatory mechanisms were assessed. RESULTS An altered expression of several SME was found in RA leucocytes. Eight elements (SNRNP70, SNRNP200, U2AF2, RNU4ATAC, RBM3, RBM17, KHDRBS1 and SRSF10) were equally altered in all leucocytes subtypes. Logistic regressions revealed that this signature might: discriminate RA and HD, and anti-citrullinated protein antibodies (ACPAs) positivity; classify high-disease activity (disease activity score-28 (DAS28) >5.1); recognise radiological involvement; and identify patients showing atheroma plaques. Furthermore, this signature was altered in RA synovial fluid and ankle joints of K/BxN-arthritic mice. An available RNA-seq data set enabled to validate data and identified distinctive splicing events and splicing variants among patients with RA expressing high and low SME levels. 3 and 6 months anti-TNF therapy reversed their expression in parallel to the reduction of the inflammatory profile. In vitro, ACPAs modulated SME, at least partially, by Fc Receptor (FcR)-dependent mechanisms. Key inflammatory cytokines further altered SME. Lastly, induced SNRNP70-overexpression and KHDRBS1-overexpression reversed inflammation in lymphocytes, NETosis in neutrophils and adhesion in RA monocytes and influenced activity of RA synovial fibroblasts. CONCLUSIONS Overall, we have characterised for the first time a signature comprising eight dysregulated SME in RA leucocytes from both peripheral blood and synovial fluid, linked to disease pathophysiology, modulated by ACPAs and reversed by anti-TNF therapy.
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Affiliation(s)
- Alejandro Ibáñez-Costa
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Carlos Perez-Sanchez
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Alejandra María Patiño-Trives
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Maria Luque-Tevar
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Pilar Font
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Ivan Arias de la Rosa
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Cristobal Roman-Rodriguez
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Mª Carmen Abalos-Aguilera
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Carmen Conde
- Laboratorio de Investigación 8, Instituto de Investigación Sanitaria (IDIS), Hospital Clinico de Santiago (CHUS), Santiago de Compostela, Spain
| | - Antonio Gonzalez
- Experimental and Observational Rheumatology, Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Sergio Pedraza-Arevalo
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Mercedes Del Rio-Moreno
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Ricardo Blazquez-Encinas
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Pedro Segui
- Radiology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Jerusalem Calvo
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Rafaela Ortega Castro
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Alejandro Escudero-Contreras
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Nuria Barbarroja
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Mª Angeles Aguirre
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Justo P Castaño
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Raul M Luque
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Eduardo Collantes-Estevez
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Chary Lopez-Pedrera
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
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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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11
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Vilys L, Peciuliene I, Jakubauskiene E, Zinkeviciute R, Makino Y, Kanopka A. U2AF - Hypoxia-induced fas alternative splicing regulator. Exp Cell Res 2020; 399:112444. [PMID: 33347855 DOI: 10.1016/j.yexcr.2020.112444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 01/21/2023]
Abstract
The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many disease states. Recent studies have revealed that tumorigenesis and hypoxia are involved in large-scale alterations in alternative pre-mRNA splicing. Fas pre-mRNA is alternatively spliced by excluding exon 6 to produce soluble Fas (sFas) protein that lacks a transmembrane domain and acts by inhibiting Fas mediated apoptosis. In the present study we show that U2AF is involved in hypoxia dependent anti-apoptotic Fas mRNA isoform formation. Our performed studies show that U2AF-RNA interaction is reduced in hypoxic cells, leading to reduction of Fas and increased sFas mRNAs formation. Efficient U2AF-RNA interactions of both subunits are important for Fas exon 6 inclusion into forming mRNA in normoxic and hypoxic cells.
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Affiliation(s)
- Laurynas Vilys
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Inga Peciuliene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egle Jakubauskiene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ruta Zinkeviciute
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Yuichi Makino
- Division of Metabolism and Biosystemic Science, Department of Medicine, Asahikawa Medical College, Asahikawa, Hokkaido, Japan
| | - Arvydas Kanopka
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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12
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Nuclear P38: Roles in Physiological and Pathological Processes and Regulation of Nuclear Translocation. Int J Mol Sci 2020; 21:ijms21176102. [PMID: 32847129 PMCID: PMC7504396 DOI: 10.3390/ijms21176102] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023] Open
Abstract
The p38 mitogen-activated protein kinase (p38MAPK, termed here p38) cascade is a central signaling pathway that transmits stress and other signals to various intracellular targets in the cytoplasm and nucleus. More than 150 substrates of p38α/β have been identified, and this number is likely to increase. The phosphorylation of these substrates initiates or regulates a large number of cellular processes including transcription, translation, RNA processing and cell cycle progression, as well as degradation and the nuclear translocation of various proteins. Being such a central signaling cascade, its dysregulation is associated with many pathologies, particularly inflammation and cancer. One of the hallmarks of p38α/β signaling is its stimulated nuclear translocation, which occurs shortly after extracellular stimulation. Although p38α/β do not contain nuclear localization or nuclear export signals, they rapidly and robustly translocate to the nucleus, and they are exported back to the cytoplasm within minutes to hours. Here, we describe the physiological and pathological roles of p38α/β phosphorylation, concentrating mainly on the ill-reviewed regulation of p38α/β substrate degradation and nuclear translocation. In addition, we provide information on the p38α/β ’s substrates, concentrating mainly on the nuclear targets and their role in p38α/β functions. Finally, we also provide information on the mechanisms of nuclear p38α/β translocation and its use as a therapeutic target for p38α/β-dependent diseases.
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Han J, Wu J, Silke J. An overview of mammalian p38 mitogen-activated protein kinases, central regulators of cell stress and receptor signaling. F1000Res 2020; 9. [PMID: 32612808 PMCID: PMC7324945 DOI: 10.12688/f1000research.22092.1] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
The p38 family is a highly evolutionarily conserved group of mitogen-activated protein kinases (MAPKs) that is involved in and helps co-ordinate cellular responses to nearly all stressful stimuli. This review provides a succinct summary of multiple aspects of the biology, role, and substrates of the mammalian family of p38 kinases. Since p38 activity is implicated in inflammatory and other diseases, we also discuss the clinical implications and pharmaceutical approaches to inhibit p38.
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Affiliation(s)
- Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jianfeng Wu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - John Silke
- The Walter and Eliza Hall Institute, IG Royal Parade, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3050, Australia
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14
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Dumont AA, Dumont L, Berthiaume J, Auger-Messier M. p38α MAPK proximity assay reveals a regulatory mechanism of alternative splicing in cardiomyocytes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118557. [PMID: 31505169 DOI: 10.1016/j.bbamcr.2019.118557] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 11/26/2022]
Abstract
The p38 mitogen-activated protein kinase (MAPK) signaling pathway is essential for normal heart function. However, p38 also contributes to heart failure pathogenesis by affecting cardiomyocytes contractility and survival. To unravel part of the complex role of p38 in cardiac function, we performed an APEX2-based proximity assay in cultured neonatal rat ventricular myocytes and identified the protein interaction networks (interactomes) of two highly expressed p38 isoforms in the heart. We found that p38α and p38γ have distinct interactomes in cardiomyocytes under both basal and osmotic stress-activated states. Interestingly, the activated p38α interactome contains many RNA-binding proteins implicated in splicing, including the serine/arginine-rich splicing factor 3 (SRSF3). Its interaction with the activated p38α was validated by co-immunoprecipitation. The cytoplasmic abundance and alternative splicing function of SRSF3 are also both modulated by the p38 signaling pathway. Our findings reveal a new function for p38 as a specific regulator of SRSF3 in cardiomyocytes.
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Affiliation(s)
- Audrey-Ann Dumont
- Département de Médecine, Service de Cardiologie, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Lauralyne Dumont
- Département de Médecine, Service de Cardiologie, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jonathan Berthiaume
- Département de Médecine, Service de Cardiologie, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mannix Auger-Messier
- Département de Médecine, Service de Cardiologie, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.
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Tari M, Manceau V, de Matha Salone J, Kobayashi A, Pastré D, Maucuer A. U2AF 65 assemblies drive sequence-specific splice site recognition. EMBO Rep 2019; 20:e47604. [PMID: 31271494 PMCID: PMC6681011 DOI: 10.15252/embr.201847604] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023] Open
Abstract
The essential splicing factor U2AF65 is known to help anchoring U2 snRNP at the branch site. Its C-terminal UHM domain interacts with ULM motifs of SF3b155, an U2 snRNP protein. Here, we report a cooperative binding of U2AF65 and the related protein CAPERα to the multi-ULM domain of SF3b155. In addition, we show that the RS domain of U2AF65 drives a liquid-liquid phase separation that is amplified by intronic RNA with repeated pyrimidine tracts. In cells, knockdown of either U2AF65 or CAPERα improves the inclusion of cassette exons that are preceded by such repeated pyrimidine-rich motifs. These results support a model in which liquid-like assemblies of U2AF65 and CAPERα on repetitive pyrimidine-rich RNA sequences are driven by their RS domains, and facilitate the recruitment of the multi-ULM domain of SF3b155. We anticipate that posttranslational modifications and proteins recruited in dynamical U2AF65 and CAPERα condensates may further contribute to the complex mechanisms leading to specific splice site choice that occurs in cells.
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Affiliation(s)
- Manel Tari
- SABNPUniv EvryINSERM U1204Université Paris‐SaclayEvryFrance
| | - Valérie Manceau
- Institut Necker Enfants Malades (INEM)Inserm U1151 – CNRS UMR 8253Université Paris DescartesParisFrance
- Present address:
Faculty of MedicineInstitut Necker Enfants Malades (INEM)Inserm U1151–CNRS UMR 8253University Paris DescartesSorbonne Paris CitéParisFrance
| | | | | | - David Pastré
- SABNPUniv EvryINSERM U1204Université Paris‐SaclayEvryFrance
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More than a messenger: Alternative splicing as a therapeutic target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194395. [PMID: 31271898 DOI: 10.1016/j.bbagrm.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
Alternative splicing of pre-mRNA is an essential post- and co-transcriptional mechanism of gene expression regulation that produces multiple mature mRNA transcripts from a single gene. Genetic mutations that affect splicing underlie numerous devastating diseases. The complexity of splicing regulation allows for multiple therapeutic approaches to correct disease-associated mis-splicing events. In this review, we first highlight recent findings from therapeutic strategies that have used splice switching antisense oligonucleotides and small molecules that bind directly to RNA. Second, we summarize different genetic and chemical approaches to target components of the spliceosome to correct splicing defects in pathological conditions. Finally, we present an overview of compounds that target kinases and accessory pathways that intersect with the splicing machinery. Advancements in the understanding of disease-specific defects caused by mis-regulation of alternative splicing will certainly increase the development of therapeutic options for the clinic. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Peciuliene I, Vilys L, Jakubauskiene E, Zaliauskiene L, Kanopka A. Hypoxia alters splicing of the cancer associated Fas gene. Exp Cell Res 2019; 380:29-35. [PMID: 31002816 DOI: 10.1016/j.yexcr.2019.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/08/2019] [Accepted: 04/14/2019] [Indexed: 02/02/2023]
Abstract
The removal of introns from mRNA precursors (pre-mRNAs) is an essential step in eukaryotic gene expression. The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many disease states. Recent studies have revealed that tumorigenesis and hypoxia involve large-scale alterations in alternative pre-mRNA splicing. Cancer associated Fas protein plays a central role in the physiological regulation of programmed cell death and has been implicated in the pathogenesis of various malignancies and diseases of the immune system. Fas pre-mRNA is alternatively spliced by excluding exon 6 to produce soluble Fas (sFas) protein that lacks a transmembrane domain and acts by inhibiting Fas mediated apoptosis. Another cancer related protein Rac1 plays an important regulatory role specifically in cells' motility, growth and survival. Rac pre-mRNA is alternatively spliced to produce Rac1b protein, which is upregulated in metastatic diseases. In the present study we, for the first time, show that anti-apoptotic Fas mRNA isoform formation is regulated by cellular microenvironment - hypoxia. Hypoxic microenvironment, however, does not influence Rac1 pre-mRNAs alternative splicing. Also our presented results indicate that splicing factors hnRNP A1 and SPF45, previously shown to regulate Fas alternative splicing in normoxic cells, are not involved in hypoxia dependent alternative Fas pre-mRNA splicing regulation in an amount dependent manner. Our observations on hypoxia dependent alternative Fas pre-mRNA splicing regulation indicate a probable involvement of other, yet unidentified splicing factors. Presented data also shows the contribution of pre-mRNA splicing to cell survival under unfavorable conditions.
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Affiliation(s)
- Inga Peciuliene
- Department of Immunology and Cell Biology, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania
| | - Laurynas Vilys
- Department of Immunology and Cell Biology, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania
| | - Egle Jakubauskiene
- Department of Immunology and Cell Biology, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania
| | | | - Arvydas Kanopka
- Department of Immunology and Cell Biology, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania.
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Carbonell C, Ulsamer A, Vivori C, Papasaikas P, Böttcher R, Joaquin M, Miñana B, Tejedor JR, de Nadal E, Valcárcel J, Posas F. Functional Network Analysis Reveals the Relevance of SKIIP in the Regulation of Alternative Splicing by p38 SAPK. Cell Rep 2019; 27:847-859.e6. [PMID: 30995481 PMCID: PMC6484779 DOI: 10.1016/j.celrep.2019.03.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023] Open
Abstract
Alternative splicing is a prevalent mechanism of gene regulation that is modulated in response to a wide range of extracellular stimuli. Stress-activated protein kinases (SAPKs) play a key role in controlling several steps of mRNA biogenesis. Here, we show that osmostress has an impact on the regulation of alternative splicing (AS), which is partly mediated through the action of p38 SAPK. Splicing network analysis revealed a functional connection between p38 and the spliceosome component SKIIP, whose depletion abolished a significant fraction of p38-mediated AS changes. Importantly, p38 interacted with and directly phosphorylated SKIIP, thereby altering its activity. SKIIP phosphorylation regulated AS of GADD45α, the upstream activator of the p38 pathway, uncovering a negative feedback loop involving AS regulation. Our data reveal mechanisms and targets of SAPK function in stress adaptation through the regulation of AS.
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Affiliation(s)
- Caterina Carbonell
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Arnau Ulsamer
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Claudia Vivori
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Panagiotis Papasaikas
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - René Böttcher
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Manel Joaquin
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Belén Miñana
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juan Ramón Tejedor
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain.
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
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Li Z, Liu T, Gilmore A, Gómez NM, Mitchell CH, Li YP, Oursler MJ, Yang S. Regulator of G Protein Signaling Protein 12 (Rgs12) Controls Mouse Osteoblast Differentiation via Calcium Channel/Oscillation and Gαi-ERK Signaling. J Bone Miner Res 2019; 34:752-764. [PMID: 30489658 PMCID: PMC7675783 DOI: 10.1002/jbmr.3645] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 11/13/2018] [Accepted: 11/17/2018] [Indexed: 12/11/2022]
Abstract
Bone homeostasis intimately relies on the balance between osteoblasts (OBs) and osteoclasts (OCs). Our previous studies have revealed that regulator of G protein signaling protein 12 (Rgs12), the largest protein in the Rgs super family, is essential for osteoclastogenesis from hematopoietic cells and OC precursors. However, how Rgs12 regulates OB differentiation and function is still unknown. To understand that, we generated an OB-targeted Rgs12 conditional knockout (CKO) mice model by crossing Rgs12fl/fl mice with Osterix (Osx)-Cre transgenic mice. We found that Rgs12 was highly expressed in both OB precursor cells (OPCs) and OBs of wild-type (WT) mice, and gradually increased during OB differentiation, whereas Rgs12-CKO mice (OsxCre/+ ; Rgs12fl/fl ) exhibited a dramatic decrease in both trabecular and cortical bone mass, with reduced numbers of OBs and increased apoptotic cell population. Loss of Rgs12 in OPCs in vitro significantly inhibited OB differentiation and the expression of OB marker genes, resulting in suppression of OB maturation and mineralization. Further mechanism study showed that deletion of Rgs12 in OPCs significantly inhibited guanosine triphosphatase (GTPase) activity and cyclic adenosine monophosphate (cAMP) level, and impaired Calcium (Ca2+ ) oscillations via restraints of major Ca2+ entry sources (extracellular Ca2+ influx and intracellular Ca2+ release from endoplasmic reticulum), partially contributed by the blockage of L-type Ca2+ channel mediated Ca2+ influx. Downstream mediator extracellular signal-related protein kinase (ERK) was found inactive in OBs of OsxCre/+ ; Rgs12fl/fl mice and in OPCs after Rgs12 deletion, whereas application of pertussis toxin (PTX) or overexpression of Rgs12 could rescue the defective OB differentiation via restoration of ERK phosphorylation. Our findings reveal that Rgs12 is an important regulator during osteogenesis and highlight Rgs12 as a potential therapeutic target for bone disorders. © 2018 American Society for Bone and Mineral Research.
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Affiliation(s)
- Ziqing Li
- Department of Anatomy and Cell Biology, School of Dental Medicine, University of Pennsylvania Philadelphia, PA 19104, USA
| | - Tongjun Liu
- Department of Oral Biology, School of Dental Medicine, University of Buffalo, State University of New York, Buffalo, NY 14215, USA
- Department of Implantology, Shandong Provincial Key Laboratory of Oral Biomedicine, School of Stomatology, Shandong University
- Department of Stomatology, the Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong province 250000, China
| | - Alyssa Gilmore
- Department of Oral Biology, School of Dental Medicine, University of Buffalo, State University of New York, Buffalo, NY 14215, USA
| | - Néstor Más Gómez
- Department of Anatomy and Cell Biology, School of Dental Medicine, University of Pennsylvania Philadelphia, PA 19104, USA
| | - Claire H Mitchell
- Department of Anatomy and Cell Biology, School of Dental Medicine, University of Pennsylvania Philadelphia, PA 19104, USA
- Department of Physiology, School of Medicine, University of Pennsylvania Philadelphia, PA 19104, USA
| | - Yi-ping Li
- Department of Pathology, University of Alabama in Birmingham, Birmingham, AL 35294, USA
| | - Merry J Oursler
- Department of Medicine, Endocrine Research Unit, Mayo Clinic, Rochester, MN 55905, USA
| | - Shuying Yang
- Department of Anatomy and Cell Biology, School of Dental Medicine, University of Pennsylvania Philadelphia, PA 19104, USA
- The Penn Center for Musculoskeletal Disorders, University of Pennsylvania Philadelphia, PA 19104, USA
- Department of Oral Biology, School of Dental Medicine, University of Buffalo, State University of New York, Buffalo, NY 14215, USA
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20
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Kawata K, Yugi K, Hatano A, Kokaji T, Tomizawa Y, Fujii M, Uda S, Kubota H, Matsumoto M, Nakayama KI, Kuroda S. Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data. Genes Cells 2018; 24:82-93. [PMID: 30417516 DOI: 10.1111/gtc.12655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022]
Abstract
Cellular signaling regulates various cellular functions via protein phosphorylation. Phosphoproteomic data potentially include information for a global regulatory network from signaling to cellular functions, but a procedure to reconstruct this network using such data has yet to be established. In this paper, we provide a procedure to reconstruct a global regulatory network from signaling to cellular functions from phosphoproteomic data by integrating prior knowledge of cellular functions and inference of the kinase-substrate relationships (KSRs). We used phosphoproteomic data from insulin-stimulated Fao hepatoma cells and identified protein phosphorylation regulated by insulin specifically over-represented in cellular functions in the KEGG database. We inferred kinases for protein phosphorylation by KSRs, and connected the kinases in the insulin signaling layer to the phosphorylated proteins in the cellular functions, revealing that the insulin signal is selectively transmitted via the Pi3k-Akt and Erk signaling pathways to cellular adhesions and RNA maturation, respectively. Thus, we provide a method to reconstruct global regulatory network from signaling to cellular functions based on phosphoproteomic data.
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Affiliation(s)
- Kentaro Kawata
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
| | - Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan.,YCI Laboratory for Trans-Omics, Young Chief Investigator Program, RIKEN Center for Integrative Medical Science, Yokohama, Japan.,Institute for Advanced Biosciences, Keio University, Fujisawa, Japan.,PRESTO, Japan Science and Technology Agency, Yokohama, Japan
| | - Atsushi Hatano
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
| | - Toshiya Kokaji
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Yoko Tomizawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
| | - Masashi Fujii
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan.,Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
| | - Shinsuke Uda
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Bunkyo-ku, Japan
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21
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Patel M, Sachidanandan M, Adnan M. Serine arginine protein kinase 1 (SRPK1): a moonlighting protein with theranostic ability in cancer prevention. Mol Biol Rep 2018; 46:1487-1497. [PMID: 30535769 DOI: 10.1007/s11033-018-4545-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/30/2018] [Indexed: 12/15/2022]
Abstract
Serine/arginine protein kinase 1 (SRPK1); a versatile functional moonlighting protein involved in varied cellular activities comprised of cell cycle progression, innate immune response, chromatin reorganization, negative and positive regulation of viral genome replication, protein amino acid phosphorylation, regulation of numerous mRNA-processing pathways, germ cell development as well as inflammation due to acquaintances with many transcription factors and signaling pathways. Several diseases including cancer have been associated with dysregulation of SRPK1. The function of SRPK1 in cancer is contradictory and inexplicable because it acts as both tumor suppressor and promoter based on the type of cell and locale. Over expression of SRPK1 including its role has been recently narrated and associated with several cancers, which includes, lung, glioma, prostate and breast via dysregulated signals from the Akt/eIF4E/HIF-1/VEGF, Erk or MAPK, PI3K/AKT/mTOR, TGF-β, and Wnt/β-catenin signaling pathways. Therefore, SRPK1 has occurred as a promising and possible curative target in cancer. In recent years, few natural and synthetic SRPK1 inhibitors have been discovered. This review emphasizes and highlights the complicated connections between SRPK1 and oncogenic signaling circuits together with the possibility of aiming SRPK1 in the treatment of cancer.
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Affiliation(s)
- Mitesh Patel
- Department of Biosciences, Bapalal Vaidya Botanical Research Centre, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Manojkumar Sachidanandan
- Department of Oral Radiology, College of Dentistry, University of Hail, P O Box 2440, Hail, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, Faculty of Science, University of Hail, P O Box 2440, Hail, Saudi Arabia.
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22
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PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in Arabidopsis thaliana. Genetics 2018; 210:1267-1285. [PMID: 30297453 PMCID: PMC6283158 DOI: 10.1534/genetics.118.301515] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 10/03/2018] [Indexed: 01/08/2023] Open
Abstract
Prp4 kinase (Prp4k) is the first spliceosome-associated kinase shown to regulate splicing in fungi and metazoans, but nothing is yet known about its functions in plants. Here, Kanno and Venhuizen et al. report... Splicing of precursor messenger RNAs (pre-mRNAs) is an essential step in the expression of most eukaryotic genes. Both constitutive splicing and alternative splicing, which produces multiple messenger RNA (mRNA) isoforms from a single primary transcript, are modulated by reversible protein phosphorylation. Although the plant splicing machinery is known to be a target for phosphorylation, the protein kinases involved remain to be fully defined. We report here the identification of pre-mRNA processing 4 (PRP4) KINASE A (PRP4KA) in a forward genetic screen based on an alternatively spliced GFP reporter gene in Arabidopsis thaliana (Arabidopsis). Prp4 kinase is the first spliceosome-associated kinase shown to regulate splicing in fungi and mammals but it has not yet been studied in plants. In the same screen we identified mutants defective in SAC3A, a putative mRNA export factor that is highly coexpressed with PRP4KA in Arabidopsis. Whereas the sac3a mutants appear normal, the prp4ka mutants display a pleiotropic phenotype featuring atypical rosettes, late flowering, tall final stature, reduced branching, and lowered seed set. Analysis of RNA-sequencing data from prp4ka and sac3a mutants identified widespread and partially overlapping perturbations in alternative splicing in the two mutants. Quantitative phosphoproteomic profiling of a prp4ka mutant detected phosphorylation changes in several serine/arginine-rich proteins, which regulate constitutive and alternative splicing, and other splicing-related factors. Tests of PRP4KB, the paralog of PRP4KA, indicated that the two genes are not functionally redundant. The results demonstrate the importance of PRP4KA for alternative splicing and plant phenotype, and suggest that PRP4KA may influence alternative splicing patterns by phosphorylating a subset of splicing regulators.
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23
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Lu J, Li Q, Cai L, Zhu Z, Guan J, Wang C, Xia J, Xia L, Wen M, Zheng W, Su Z, Wang C. RBM17 controls apoptosis and proliferation to promote Glioma progression. Biochem Biophys Res Commun 2018; 505:20-28. [PMID: 30227940 DOI: 10.1016/j.bbrc.2018.09.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/09/2018] [Indexed: 01/13/2023]
Abstract
The splicing factor SPF45 (RBM17) is a well-known component of the spliceosome that is involved in alternative splicing. RBM17 is frequently overexpressed in many tumors and plays a crucial role in cancer progression and drug resistance. However, the role of RBM17 in the development of glioma has not been thoroughly elucidated to date. In the present study, we found that RBM17 was overexpressed in glioma and that a high level of expression of RBM17 was closely associated with a poor prognosis in glioma patients. We investigated the effect of RBM17 on apoptosis, cell growth and cell cycle indexes and the activation of apoptosis signaling by shRNA in human U87 and U251 glioma cells. The downregulated expression of RBM17 mRNA was accompanied by the induction of cell cycle arrest, and apoptosis, reduced cell proliferation in the two cell lines, and reduced cell survival, as measured by the increased activation of caspase-3, caspase-9, and PARP (poly ADP-ribose polymerase). Furthermore, in subcutaneous U87 cell xenograft tumors in nude mice, intradermal administration of an shRNA targeting RBM17 significantly downregulated RBM17 expression in vivo and was accompanied by the suppressed growth of glioma. To the best of our knowledge, our results are the first to confirm that RBM17 functions in promoting cell proliferation, affecting the cell cycle, and inducing apoptosis in human glioma cells both in vitro and in vivo. These results indicate that RBM17 may be a therapeutic target in the clinical management of glioma.
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Affiliation(s)
- Jianglong Lu
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Qun Li
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Lin Cai
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhangzhang Zhu
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Jiaqing Guan
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Chunyong Wang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Jia Xia
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Lei Xia
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Min Wen
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Weiming Zheng
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhipeng Su
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Chengde Wang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
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24
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Eblen ST. Extracellular-Regulated Kinases: Signaling From Ras to ERK Substrates to Control Biological Outcomes. Adv Cancer Res 2018; 138:99-142. [PMID: 29551131 DOI: 10.1016/bs.acr.2018.02.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The extracellular-regulated kinases ERK1 and ERK2 are evolutionarily conserved, ubiquitous serine-threonine kinases that are involved in regulating cellular signaling in both normal and pathological conditions. Their expression is critical for development and their hyperactivation is a major factor in cancer development and progression. Since their discovery as one of the major signaling mediators activated by mitogens and Ras mutation, we have learned much about their regulation, including their activation, binding partners and substrates. In this review I will discuss some of what has been discovered about the members of the Ras to ERK pathway, including regulation of their activation by growth factors and cell adhesion pathways. Looking downstream of ERK activation I will also highlight some of the many ERK substrates that have been discovered, including those involved in feedback regulation, cell migration and cell cycle progression through the control of transcription, pre-mRNA splicing and protein synthesis.
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Affiliation(s)
- Scott T Eblen
- Medical University of South Carolina, Charleston, SC, United States.
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25
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Xu L, Dai W, Li J, He L, Wang F, Xia Y, Chen K, Li S, Liu T, Lu J, Zhou Y, Wang Y, Guo C. Methylation-regulated miR-124-1 suppresses tumorigenesis in hepatocellular carcinoma by targeting CASC3. Oncotarget 2018; 7:26027-41. [PMID: 27029030 PMCID: PMC5041962 DOI: 10.18632/oncotarget.8266] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 03/08/2016] [Indexed: 12/27/2022] Open
Abstract
This study was to investigate the roles and mechanisms of miR-124-1 in hepatocellular carcinoma (HCC). We analyzed the expression of miR-124-1 in human HCC tissues and cell lines. Luciferase reporter assays were used to analyze the target of miR-124-1. Human HCC cell lines were transduced with lentiviruses expressing miR-124-1, and proliferation and colony formation were analyzed. The growth of human HCC cells overexpressing miR-124-1 was assessed in nude mice. The expression of p38-MAPK, JNK, ERK and related signaling molecules was detected by western blotting and immunohistochemistry. Our results showed that miR-124-1 levels were reduced in HCC tissues and cell lines compared with those in adjacent non-cancer tissues and normal liver cell lines respectively. Downregulation of miR-124-1 in HCC cell lines were attributed to hypermethylation of its promoter region. Overexpression of miR-124-1 inhibited HCC cell proliferation in vitro, whereas miR-124-1 was correlated with clinicopathological parameters of HCC patients. HCC cell-mediated overexpression of miR-124-1 in nude mice suppressed tumor growth. Cancer susceptibility candidate 3 (CASC3) was identified as a direct target of miR-124-1 by computational analysis and experimental assays. MiR-124-1-mediated downregulation of CASC3 resulted in the inactivation of p38-MAPK, JNK and ERK. Our findings provide potential new targets for the prevention or treatment of HCC.
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Affiliation(s)
- Ling Xu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Department of Gastroenterology, Shanghai Tongren Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Weiqi Dai
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - JingJing Li
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Lei He
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Fan Wang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yujing Xia
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Kan Chen
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Sainan Li
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Tong Liu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jie Lu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yingqun Zhou
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yugang Wang
- Department of Gastroenterology, Shanghai Tongren Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Chuanyong Guo
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
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26
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Han Y, Zhang M, Chen D, Li H, Wang X, Ma S. Downregulation of RNA binding motif protein 17 expression inhibits proliferation of hypopharyngeal carcinoma FaDu cells. Oncol Lett 2018; 15:5680-5684. [PMID: 29552202 PMCID: PMC5840662 DOI: 10.3892/ol.2018.8012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/12/2017] [Indexed: 12/13/2022] Open
Abstract
RNA binding motif protein 17 (RBM17) is a protein-coding gene. The protein encoded by RBM17 is involved in the regulation of alternative splicing and is overexpressed in cancer. The present study aimed to determine the effect of RBM17-knockdown in hypopharyngeal carcinoma FaDu cells using the lentivirus-mediated shRNA method. Cell proliferation was detected by an MTT assay. Flow cytometry analysis was used to determine cell cycle distribution and apoptosis. The results of the present study demonstrated that RBM17 expression was significantly decreased in FaDu cells infected with lentivirus-shRNA. Knockdown of RBM17 expression by shRNA significantly reduced cell proliferation, augmented cell apoptosis and arrested cells at the G2/M phase in FaDu cells. The results of the present study indicate that RBM17 serves a notable role in cell proliferation, cell cycle progression and apoptosis of hypopharyngeal carcinoma cells.
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Affiliation(s)
- Yuefeng Han
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233000, P.R. China
| | - Mingjie Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233000, P.R. China
| | - Deshang Chen
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233000, P.R. China
| | - Hui Li
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233000, P.R. China
| | - Xiaomin Wang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233000, P.R. China
| | - Shiyin Ma
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233000, P.R. China
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27
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Signaling Pathways Driving Aberrant Splicing in Cancer Cells. Genes (Basel) 2017; 9:genes9010009. [PMID: 29286307 PMCID: PMC5793162 DOI: 10.3390/genes9010009] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/07/2017] [Accepted: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Aberrant profiles of pre-mRNA splicing are frequently observed in cancer. At the molecular level, an altered profile results from a complex interplay between chromatin modifications, the transcriptional elongation rate of RNA polymerase, and effective binding of the spliceosome to the generated transcripts. Key players in this interplay are regulatory splicing factors (SFs) that bind to gene-specific splice-regulatory sequence elements. Although mutations in genes of some SFs were described, a major driver of aberrant splicing profiles is oncogenic signal transduction pathways. Signaling can affect either the transcriptional expression levels of SFs or the post-translational modification of SF proteins, and both modulate the ratio of nuclear versus cytoplasmic SFs in a given cell. Here, we will review currently known mechanisms by which cancer cell signaling, including the mitogen-activated protein kinases (MAPK), phosphatidylinositol 3 (PI3)-kinase pathway (PI3K) and wingless (Wnt) pathways but also signals from the tumor microenvironment, modulate the activity or subcellular localization of the Ser/Arg rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) families of SFs.
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28
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Villamizar O, Chambers CB, Riberdy JM, Persons DA, Wilber A. Long noncoding RNA Saf and splicing factor 45 increase soluble Fas and resistance to apoptosis. Oncotarget 2017; 7:13810-26. [PMID: 26885613 PMCID: PMC4924680 DOI: 10.18632/oncotarget.7329] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/29/2016] [Indexed: 12/21/2022] Open
Abstract
In multicellular organisms, cell growth and differentiation is controlled in part by programmed cell death or apoptosis. One major apoptotic pathway is triggered by Fas receptor (Fas)-Fas ligand (FasL) interaction. Neoplastic cells are frequently resistant to Fas-mediated apoptosis, evade Fas signals through down regulation of Fas and produce soluble Fas proteins that bind FasL thereby blocking apoptosis. Soluble Fas (sFas) is an alternative splice product of Fas pre-mRNA, commonly created by exclusion of transmembrane spanning sequences encoded within exon 6 (FasΔEx6). Long non-coding RNAs (lncRNAs) interact with other RNAs, DNA, and proteins to regulate gene expression. One lncRNA, Fas-antisense or Saf, was shown to participate in alternative splicing of Fas pre-mRNA through unknown mechanisms. We show that Saf is localized in the nucleus where it interacts with Fas receptor pre-mRNA and human splicing factor 45 (SPF45) to facilitate alternative splicing and exclusion of exon 6. The product is a soluble Fas protein that protects cells against FasL-induced apoptosis. Collectively, these studies reveal a novel mechanism to modulate this critical cell death program by an lncRNA and its protein partner.
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Affiliation(s)
- Olga Villamizar
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, USA.,Department of Microbiology, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Christopher B Chambers
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Janice M Riberdy
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Derek A Persons
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Andrew Wilber
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, USA
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29
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Xin R, Zhu L, Salomé PA, Mancini E, Marshall CM, Harmon FG, Yanovsky MJ, Weigel D, Huq E. SPF45-related splicing factor for phytochrome signaling promotes photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:E7018-E7027. [PMID: 28760995 PMCID: PMC5565451 DOI: 10.1073/pnas.1706379114] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Light signals regulate plant growth and development by controlling a plethora of gene expression changes. Posttranscriptional regulation, especially pre-mRNA processing, is a key modulator of gene expression; however, the molecular mechanisms linking pre-mRNA processing and light signaling are not well understood. Here we report a protein related to the human splicing factor 45 (SPF45) named splicing factor for phytochrome signaling (SFPS), which directly interacts with the photoreceptor phytochrome B (phyB). In response to light, SFPS-RFP (red fluorescent protein) colocalizes with phyB-GFP in photobodies. sfps loss-of-function plants are hyposensitive to red, far-red, and blue light, and flower precociously. SFPS colocalizes with U2 small nuclear ribonucleoprotein-associated factors including U2AF65B, U2A', and U2AF35A in nuclear speckles, suggesting SFPS might be involved in the 3' splice site determination. SFPS regulates pre-mRNA splicing of a large number of genes, of which many are involved in regulating light signaling, photosynthesis, and the circadian clock under both dark and light conditions. In vivo RNA immunoprecipitation (RIP) assays revealed that SFPS associates with EARLY FLOWERING 3 (ELF3) mRNA, a critical link between light signaling and the circadian clock. Moreover, PHYTOCHROME INTERACTING FACTORS (PIFs) transcription factor genes act downstream of SFPS, as the quadruple pif mutant pifq suppresses defects of sfps mutants. Taken together, these data strongly suggest SFPS modulates light-regulated developmental processes by controlling pre-mRNA splicing of light signaling and circadian clock genes.
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Affiliation(s)
- Ruijiao Xin
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Ling Zhu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Patrice A Salomé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Estefania Mancini
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE Buenos Aires, Argentina
| | - Carine M Marshall
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research Service, Albany, CA 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720
| | - Frank G Harmon
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research Service, Albany, CA 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE Buenos Aires, Argentina
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712;
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
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30
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Cieslik KA, Trial J, Entman ML. Aicar treatment reduces interstitial fibrosis in aging mice: Suppression of the inflammatory fibroblast. J Mol Cell Cardiol 2017; 111:81-85. [PMID: 28826664 DOI: 10.1016/j.yjmcc.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 01/16/2023]
Abstract
In 2030, elderly people will represent 20% of the United States population. Even now, chronic cardiac diseases, especially heart failure with preserved systolic function (HFpEF), are the most expensive DRGs for Medicare. Progressive interstitial fibrosis in the aging heart is well recognized as an important component of HFpEF. Our recent studies suggested an important pathophysiologic role for reduced TGF-β receptor 1 (TGFβR1) signaling in mesenchymal stem cells (MSCs) and their mesenchymal fibroblast progeny in the development of interstitial fibrosis. This report arises from our previous studies, which suggest that an inflammatory phenotype exists in these mesenchymal fibroblasts as a result of a reduced TGF-β-Smad-dependent pathway but upregulated farnesyltransferase (FTase)-Ras-Erk signaling. In this report we provide evidence for a therapeutic approach that downregulates Erk activation through an adenosine monophosphate-activated kinase (AMPK) pathway. Aging C57BL/6J mice were treated with AICAR (an AMPK activator) for a 30-day period. This treatment suppressed excessive monocyte chemoattractant protein-1 (MCP-1) generation, which diminished leukocyte infiltration and in consequence suppressed the formation of macrophage-derived myeloid fibroblasts. Interestingly, the number of mesenchymal fibroblasts was also reduced. In addition, we observed changes in extracellular matrix (ECM) deposition, specifically that collagen type I and the alternatively spliced variant of fibronectin (EDA) expressions were reduced. These data suggest that the upregulation of AMPK activity is a potential therapeutic approach to fibrosis in the aging heart.
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Affiliation(s)
- Katarzyna A Cieslik
- Division of Cardiovascular Sciences, DeBakey Heart Center, Department of Medicine, Baylor College of Medicine, Houston, TX, United States; Houston Methodist Hospital, Houston, TX, United States
| | - JoAnn Trial
- Division of Cardiovascular Sciences, DeBakey Heart Center, Department of Medicine, Baylor College of Medicine, Houston, TX, United States; Houston Methodist Hospital, Houston, TX, United States
| | - Mark L Entman
- Division of Cardiovascular Sciences, DeBakey Heart Center, Department of Medicine, Baylor College of Medicine, Houston, TX, United States; Houston Methodist Hospital, Houston, TX, United States.
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31
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Tan Q, Yalamanchili HK, Park J, De Maio A, Lu HC, Wan YW, White JJ, Bondar VV, Sayegh LS, Liu X, Gao Y, Sillitoe RV, Orr HT, Liu Z, Zoghbi HY. Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models. Hum Mol Genet 2017; 25:5083-5093. [PMID: 28007900 DOI: 10.1093/hmg/ddw337] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/29/2016] [Indexed: 12/12/2022] Open
Abstract
Splicing regulation is an important step of post-transcriptional gene regulation. It is a highly dynamic process orchestrated by RNA-binding proteins (RBPs). RBP dysfunction and global splicing dysregulation have been implicated in many human diseases, but the in vivo functions of most RBPs and the splicing outcome upon their loss remain largely unexplored. Here we report that constitutive deletion of Rbm17, which encodes an RBP with a putative role in splicing, causes early embryonic lethality in mice and that its loss in Purkinje neurons leads to rapid degeneration. Transcriptome profiling of Rbm17-deficient and control neurons and subsequent splicing analyses using CrypSplice, a new computational method that we developed, revealed that more than half of RBM17-dependent splicing changes are cryptic. Importantly, RBM17 represses cryptic splicing of genes that likely contribute to motor coordination and cell survival. This finding prompted us to re-analyze published datasets from a recent report on TDP-43, an RBP implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), as it was demonstrated that TDP-43 represses cryptic exon splicing to promote cell survival. We uncovered a large number of TDP-43-dependent splicing defects that were not previously discovered, revealing that TDP-43 extensively regulates cryptic splicing. Moreover, we found a significant overlap in genes that undergo both RBM17- and TDP-43-dependent cryptic splicing repression, many of which are associated with survival. We propose that repression of cryptic splicing by RBPs is critical for neuronal health and survival. CrypSplice is available at www.liuzlab.org/CrypSplice.
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Affiliation(s)
- Qiumin Tan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Hari Krishna Yalamanchili
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Jeehye Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Antonia De Maio
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Program in Developmental Biology
| | - Hsiang-Chih Lu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Program in Developmental Biology
| | - Ying-Wooi Wan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Joshua J White
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Department of Neuroscience.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vitaliy V Bondar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Layal S Sayegh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Xiuyun Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Yan Gao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Roy V Sillitoe
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Program in Developmental Biology.,Department of Neuroscience.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Harry T Orr
- Institute for Translational Neuroscience.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Department of Pediatrics
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA.,Program in Developmental Biology.,Department of Neuroscience.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
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32
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Grañé-Boladeras N, Spring CM, Hanna WJB, Pastor-Anglada M, Coe IR. Novel nuclear hENT2 isoforms regulate cell cycle progression via controlling nucleoside transport and nuclear reservoir. Cell Mol Life Sci 2016; 73:4559-4575. [PMID: 27271752 PMCID: PMC11108336 DOI: 10.1007/s00018-016-2288-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 10/25/2022]
Abstract
Nucleosides participate in many cellular processes and are the fundamental building blocks of nucleic acids. Nucleoside transporters translocate nucleosides across plasma membranes although the mechanism by which nucleos(t)ides are translocated into the nucleus during DNA replication is unknown. Here, we identify two novel functional splice variants of equilibrative nucleoside transporter 2 (ENT2), which are present at the nuclear envelope. Under proliferative conditions, these splice variants are up-regulated and recruit wild-type ENT2 to the nuclear envelope to translocate nucleosides into the nucleus for incorporation into DNA during replication. Reduced presence of hENT2 splice variants resulted in a dramatic decrease in cell proliferation and dysregulation of cell cycle due to a lower incorporation of nucleotides into DNA. Our findings support a novel model of nucleoside compartmentalisation at the nuclear envelope and translocation into the nucleus through hENT2 and its variants, which are essential for effective DNA synthesis and cell proliferation.
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Affiliation(s)
- Natalia Grañé-Boladeras
- Department of Biochemistry and Molecular Biology, Institute of Biomedicine (IBUB), University of Barcelona, 08028, Barcelona, Spain.
- Oncology Program, CIBER EHD, Instituto de Salud Carlos III, 28029, Madrid, Spain.
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, M5B 2K3, Canada.
| | - Christopher M Spring
- Research Core Facilities, Keenan Research Centre, Li Ka Shing Knowledge Institute, Saint Michael's Hospital, Toronto, ON, M5B 1T8, Canada
| | - W J Brad Hanna
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Marçal Pastor-Anglada
- Department of Biochemistry and Molecular Biology, Institute of Biomedicine (IBUB), University of Barcelona, 08028, Barcelona, Spain
- Oncology Program, CIBER EHD, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Imogen R Coe
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, M5B 2K3, Canada
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33
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Mikula M, Skrzypczak M, Goryca K, Paczkowska K, Ledwon JK, Statkiewicz M, Kulecka M, Grzelak M, Dabrowska M, Kuklinska U, Karczmarski J, Rumienczyk I, Jastrzebski K, Miaczynska M, Ginalski K, Bomsztyk K, Ostrowski J. Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy. Nucleic Acids Res 2016; 44:10150-10164. [PMID: 27587583 PMCID: PMC5137434 DOI: 10.1093/nar/gkw763] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 01/20/2023] Open
Abstract
Genome-wide mechanisms that coordinate expression of subsets of functionally related genes are largely unknown. Recent studies show that receptor tyrosine kinases and components of signal transduction cascades including the extracellular signal-regulated protein kinase (ERK), once thought to act predominantly in the vicinity of plasma membrane and in the cytoplasm, can be recruited to chromatin encompassing transcribed genes. Genome-wide distribution of these transducers and their relationship to transcribing RNA polymerase II (Pol2) could provide new insights about co-regulation of functionally related gene subsets. Chromatin immunoprecipitations (ChIP) followed by deep sequencing, ChIP-Seq, revealed that genome-wide binding of epidermal growth factor receptor, EGFR and ERK pathway components at EGF-responsive genes was highly correlated with characteristic mitogen-induced Pol2-profile. Endosomes play a role in intracellular trafficking of proteins including their nuclear import. Immunofluorescence revealed that EGF-activated EGFR, MEK1/2 and ERK1/2 co-localize on endosomes. Perturbation of endosome internalization process, through the depletion of AP2M1 protein, resulted in decreased number of the EGFR containing endosomes and inhibition of Pol2, EGFR/ERK recruitment to EGR1 gene. Thus, mitogen-induced co-recruitment of EGFR/ERK components to subsets of genes, a kinase module possibly pre-assembled on endosome to synchronize their nuclear import, could coordinate genome-wide transcriptional events to ensure effective cell proliferation.
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Affiliation(s)
- M Mikula
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - M Skrzypczak
- University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089, Poland
| | - K Goryca
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - K Paczkowska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - J K Ledwon
- Medical Center for Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - M Statkiewicz
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - M Kulecka
- Medical Center for Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - M Grzelak
- University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089, Poland
| | - M Dabrowska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - U Kuklinska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - J Karczmarski
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - I Rumienczyk
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - K Jastrzebski
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - M Miaczynska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - K Ginalski
- University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089, Poland
| | - K Bomsztyk
- University of Washington, Department of Medicine, 850 Republican Street, Seattle, WA, USA
| | - J Ostrowski
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland.,Medical Center for Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Roentgena 5, 02-781 Warsaw, Poland
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34
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Li Y, Yuan Y. Alternative RNA splicing and gastric cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 773:263-273. [PMID: 28927534 DOI: 10.1016/j.mrrev.2016.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 07/06/2016] [Accepted: 07/28/2016] [Indexed: 02/07/2023]
Abstract
Alternative splicing (AS) linked to diseases, especially to tumors. Recently, more and more studies focused on the relationship between AS and gastric cancer (GC). This review surveyed the hot topic from four aspects: First, the common types of AS in cancer, including exon skipping, intron retention, mutually exclusive exon, alternative 5 ' or 3' splice site, alternative first or last exon and alternative 3' untranslated regions. Second, basic mechanisms of AS and its relationship with cancer. RNA splicing in eukaryotes follows the GT-AG rule by both cis-elements and trans-acting factors regulatory. Through RNA splicing, different proteins with different forms and functions can be produced and may be associated with carcinogenesis. Third, AS types of GC-related genes and their splicing variants. In this paper, we listed 10 common genes with AS and illustrated its possible molecular mechanisms owing to genetic variation (mutation and /or polymorphism). Fourth, the splicing variants of GC-associated genes and gastric carcinogenesis, invasion and metastasis. Many studies have found that the different splicing variants of the same gene are differentially expressed in GC and its precancerous diseases, suggesting AS has important implications in GC development. Taking together, this review highlighted the role of AS and splicing variants in the process of GC. We hope that this is not only beneficial to advances in the study field of GC, but also can provide valuable information to other similar tumor research.Although we already know some gene splicing and splicing variants play an important role in the development of GC, but many phenomena and mechanisms are still unknown. For example, how the tumor microenvironment and signal transduction pathway effect the forming and function of AS? Unfortunately, this review did not cover the contents because the current study is limited. It is no doubt that clarifying the phenomena and mechanisms of these unknown may help to reveal the relationship of AS with complex tumor genetic variation and the occurrence and development of tumors.
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Affiliation(s)
- Ying Li
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China.
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35
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JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships. Microbiol Mol Biol Rev 2016; 80:793-835. [PMID: 27466283 DOI: 10.1128/mmbr.00043-14] [Citation(s) in RCA: 321] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The c-Jun N-terminal kinases (JNKs), as members of the mitogen-activated protein kinase (MAPK) family, mediate eukaryotic cell responses to a wide range of abiotic and biotic stress insults. JNKs also regulate important physiological processes, including neuronal functions, immunological actions, and embryonic development, via their impact on gene expression, cytoskeletal protein dynamics, and cell death/survival pathways. Although the JNK pathway has been under study for >20 years, its complexity is still perplexing, with multiple protein partners of JNKs underlying the diversity of actions. Here we review the current knowledge of JNK structure and isoforms as well as the partnerships of JNKs with a range of intracellular proteins. Many of these proteins are direct substrates of the JNKs. We analyzed almost 100 of these target proteins in detail within a framework of their classification based on their regulation by JNKs. Examples of these JNK substrates include a diverse assortment of nuclear transcription factors (Jun, ATF2, Myc, Elk1), cytoplasmic proteins involved in cytoskeleton regulation (DCX, Tau, WDR62) or vesicular transport (JIP1, JIP3), cell membrane receptors (BMPR2), and mitochondrial proteins (Mcl1, Bim). In addition, because upstream signaling components impact JNK activity, we critically assessed the involvement of signaling scaffolds and the roles of feedback mechanisms in the JNK pathway. Despite a clarification of many regulatory events in JNK-dependent signaling during the past decade, many other structural and mechanistic insights are just beginning to be revealed. These advances open new opportunities to understand the role of JNK signaling in diverse physiological and pathophysiological states.
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36
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Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors. Oncotarget 2016; 6:6825-39. [PMID: 25749525 PMCID: PMC4466652 DOI: 10.18632/oncotarget.3145] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/12/2015] [Indexed: 11/25/2022] Open
Abstract
Dysregulation of alternative splicing (AS) is one of the molecular hallmarks of cancer, with splicing alteration of numerous genes in cancer patients. However, studying splicing mis-regulation in cancer is complicated by the large noise generated from tissue-specific splicing. To obtain a global picture of cancer-specific splicing, we analyzed transcriptome sequencing data from 1149 patients in The Cancer Genome Atlas project, producing a core set of AS events significantly altered across multiple cancer types. These cancer-specific AS events are highly conserved, are more likely to maintain protein reading frame, and mainly function in cell cycle, cell adhesion/migration, and insulin signaling pathways. Furthermore, these events can serve as new molecular biomarkers to distinguish cancer from normal tissues, to separate cancer subtypes, and to predict patient survival. We also found that most genes whose expression is closely associated with cancer-specific splicing are key regulators of the cell cycle. This study uncovers a common set of cancer-specific AS events altered across multiple cancers, providing mechanistic insight into how splicing is mis-regulated in cancers.
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37
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Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets. Mol Genet Genomics 2015; 291:1035-51. [PMID: 26711644 DOI: 10.1007/s00438-015-1163-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/16/2015] [Indexed: 01/04/2023]
Abstract
Hepatocellular carcinoma (HCC) is an aggressive and deadly cancer. The molecular pathogenesis of the disease remains poorly understood. To better understand HCC biology and explore potential biomarkers and therapeutic targets, we investigated the whole transcriptome of HCC. Considering the genetic heterogeneity of HCC, four datasets from four studies consisting of 15 pairs of HCC and adjacent normal samples were analyzed. We observed that the number of lncRNAs expressed in each HCC sample was consistently greater than the adjacent normal sample. Moreover, 15 lncRNAs were identified expressed in five to seven HCC tissues but were not detected in any adjacent normal tissue. Differential expression analysis detected 35 up- and 80 down-regulated lncRNAs in HCC samples compared with adjacent normal samples. In addition, five differentially expressed lncRNAs were predicted to play a role in oxidation and reduction process. With regard to splicing alterations, we identified nine highly recurrent differential splicing events belonging to eight genes USO1, RPS24, CCDC50, THNSL2, NUMB, FN1 (two events), SLC39A14 and NR1I3. Of them, splicing alterations of SLC39A14 and NR1I3 were reported for the association with HCC for the first time. The splicing dysregulation in HCC may be influenced by three splicing factors ESRP2, CELF2 and SRSF5 which were significantly down-regulated in HCC samples. This study revealed uncharacterized aspects of HCC transcriptome and identified important lncRNAs and splicing isoforms with the potential to serve as biomarkers and therapeutic targets for the disease.
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38
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Splicing Regulators and Their Roles in Cancer Biology and Therapy. BIOMED RESEARCH INTERNATIONAL 2015; 2015:150514. [PMID: 26273588 PMCID: PMC4529883 DOI: 10.1155/2015/150514] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 03/10/2015] [Accepted: 04/01/2015] [Indexed: 12/17/2022]
Abstract
Alternative splicing allows cells to expand the encoding potential of their genomes. In this elegant mechanism, a single gene can yield protein isoforms with even antagonistic functions depending on the cellular physiological context. Alterations in splicing regulatory factors activity in cancer cells, however, can generate an abnormal protein expression pattern that promotes growth, survival, and other processes, which are relevant to tumor biology. In this review, we discuss dysregulated alternative splicing events and regulatory factors that impact pathways related to cancer. The SR proteins and their regulatory kinases SRPKs and CLKs have been frequently found altered in tumors and are examined in more detail. Finally, perspectives that support splicing machinery as target for the development of novel anticancer therapies are discussed.
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39
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Splicing Regulation: A Molecular Device to Enhance Cancer Cell Adaptation. BIOMED RESEARCH INTERNATIONAL 2015; 2015:543067. [PMID: 26273627 PMCID: PMC4529921 DOI: 10.1155/2015/543067] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/23/2015] [Indexed: 01/23/2023]
Abstract
Alternative splicing (AS) represents a major resource for eukaryotic cells to expand the coding potential of their genomes and to finely regulate gene expression in response to both intra- and extracellular cues. Cancer cells exploit the flexible nature of the mechanisms controlling AS in order to increase the functional diversity of their proteome. By altering the balance of splice isoforms encoded by human genes or by promoting the expression of aberrant oncogenic splice variants, cancer cells enhance their ability to adapt to the adverse growth conditions of the tumoral microenvironment. Herein, we will review the most relevant cancer-related splicing events and the underlying regulatory mechanisms allowing tumour cells to rapidly adapt to the harsh conditions they may face during the occurrence and development of cancer.
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40
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Kumar P, John V, Marathe S, Das G, Bhaskar S. Mycobacterium indicus pranii induces dendritic cell activation, survival, and Th1/Th17 polarization potential in a TLR-dependent manner. J Leukoc Biol 2015; 97:511-20. [PMID: 25593326 DOI: 10.1189/jlb.1a0714-361r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
MIP is a nonpathogenic, soil-borne predecessor of Mycobacterium avium. It has been reported previously that MIP possesses strong immunomodulatory properties and confers protection against experimental TB and tumor. DCs, by virtue of their unmatched antigen-presentation potential, play a critical role in activation of antitumor and antimycobacterial immune response. The effect of MIP on the behavior of DCs and the underlying mechanisms, however, have not been investigated so far. In the present study, we showed that MIP induces significant secretion of IL-6, IL-12p40, IL-10, and TNF-α by DCs and up-regulates the expression of costimulatory molecules CD40, CD80, and CD86. MIP(L) induced a significantly higher response compared with MIP(K). PI and Annexin V staining showed that MIP increases DC survival by inhibiting apoptosis. Consistently, higher expression of antiapoptotic proteins Bcl-2 and Bcl-xl was observed in MIP-stimulated DCs. Cytokines, produced by naïve T cells, cocultured with MIP-stimulated DCs, showed that MIP promotes Th1/Th17 polarization potential in DCs. Response to MIP was lost in MyD88(-/-)DCs, underscoring the critical role of TLRs in MIP-induced DC activation. Further studies revealed that TLR2 and TLR9 are involved in DC activation by MIP(L), whereas MIP(K) activates the DCs through TLR2. Our findings establish the DC activation by MIP, define the behavior of MIP-stimulated DCs, and highlight the role of TLRs in MIP-induced DC activation.
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Affiliation(s)
- Pawan Kumar
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Vini John
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Soumitra Marathe
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Gobardhan Das
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sangeeta Bhaskar
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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41
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Emerging technologies to map the protein methylome. J Mol Biol 2014; 426:3350-62. [PMID: 24805349 DOI: 10.1016/j.jmb.2014.04.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 01/26/2023]
Abstract
Protein methylation plays an integral role in cellular signaling, most notably by modulating proteins bound at chromatin and increasingly through regulation of non-histone proteins. One central challenge in understanding how methylation acts in signaling is identifying and measuring protein methylation. This includes locus-specific modification of histones, on individual non-histone proteins, and globally across the proteome. Protein methylation has been studied traditionally using candidate approaches such as methylation-specific antibodies, mapping of post-translational modifications by mass spectrometry, and radioactive labeling to characterize methylation on target proteins. Recent developments have provided new approaches to identify methylated proteins, measure methylation levels, identify substrates of methyltransferase enzymes, and match methylated proteins to methyl-specific reader domains. Methyl-binding protein domains and improved antibodies with broad specificity for methylated proteins are being used to characterize the "protein methylome". They also have the potential to be used in high-throughput assays for inhibitor screens and drug development. These tools are often coupled to improvements in mass spectrometry to quickly identify methylated residues, as well as to protein microarrays, where they can be used to screen for methylated proteins. Finally, new chemical biology strategies are being used to probe the function of methyltransferases, demethylases, and methyl-binding "reader" domains. These tools create a "system-level" understanding of protein methylation and integrate protein methylation into broader signaling processes.
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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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Oncogenic alternative splicing switches: role in cancer progression and prospects for therapy. Int J Cell Biol 2013; 2013:962038. [PMID: 24285959 PMCID: PMC3826442 DOI: 10.1155/2013/962038] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/12/2013] [Indexed: 01/30/2023] Open
Abstract
Alterations in the abundance or activities of alternative splicing regulators generate alternatively spliced variants that contribute to multiple aspects of tumor establishment, progression and resistance to therapeutic treatments. Notably, many cancer-associated genes are regulated through alternative splicing suggesting a significant role of this post-transcriptional regulatory mechanism in the production of oncogenes and tumor suppressors. Thus, the study of alternative splicing in cancer might provide a better understanding of the malignant transformation and identify novel pathways that are uniquely relevant to tumorigenesis. Understanding the molecular underpinnings of cancer-associated alternative splicing isoforms will not only help to explain many fundamental hallmarks of cancer, but will also offer unprecedented opportunities to improve the efficacy of anti-cancer treatments.
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Regulation of the Ras-MAPK and PI3K-mTOR Signalling Pathways by Alternative Splicing in Cancer. Int J Cell Biol 2013; 2013:568931. [PMID: 24078813 PMCID: PMC3775402 DOI: 10.1155/2013/568931] [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: 06/20/2013] [Accepted: 07/26/2013] [Indexed: 01/21/2023] Open
Abstract
Alternative splicing is a fundamental step in regulation of gene expression of many tumor suppressors and oncogenes in cancer. Signalling through the Ras-MAPK and PI3K-mTOR pathways is misregulated and hyperactivated in most types of cancer. However, the regulation of the Ras-MAPK and PI3K-mTOR signalling pathways by alternative splicing is less well established. Recent studies have shown the contribution of alternative splicing regulation of these signalling pathways which can lead to cellular transformation, cancer development, and tumor maintenance. This review will discuss findings in the literature which describe new modes of regulation of components of the Ras-MAPK and PI3K-mTOR signalling pathways by alternative splicing. We will also describe the mechanisms by which signals from extracellular stimuli can be communicated to the splicing machinery and to specific RNA-binding proteins that ultimately control exon definition events.
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Phosphorylation-mediated regulation of alternative splicing in cancer. Int J Cell Biol 2013; 2013:151839. [PMID: 24069033 PMCID: PMC3771450 DOI: 10.1155/2013/151839] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene. Splicing is mediated by a large macromolecular complex, the spliceosome, whose activity needs a fine regulation exerted by cis-acting RNA sequence elements and trans-acting RNA binding proteins (RBP). The activity of both core spliceosomal components and accessory splicing factors is modulated by their reversible phosphorylation. The kinases and phosphatases involved in these posttranslational modifications significantly contribute to AS regulation and to its integration in the complex regulative network that controls gene expression in eukaryotic cells. Herein, we will review the major canonical and noncanonical splicing factor kinases and phosphatases, focusing on those whose activity has been implicated in the aberrant splicing events that characterize neoplastic transformation.
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Lopez-Mejia IC, De Toledo M, Della Seta F, Fafet P, Rebouissou C, Deleuze V, Blanchard JM, Jorgensen C, Tazi J, Vignais ML. Tissue-specific and SRSF1-dependent splicing of fibronectin, a matrix protein that controls host cell invasion. Mol Biol Cell 2013; 24:3164-76. [PMID: 23966470 PMCID: PMC3806663 DOI: 10.1091/mbc.e13-03-0142] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Matching sets of human primary fibroblasts cocultured with placenta explants are used to compare tissue capacities to support trophoblast invasion. Substituting endometrium with dermis dramatically reduces EVCT interstitial invasion, a phenomenon related to the ECM fibronectin content, FN alternative splicing, and expression of the SR protein SRSF1. Cell invasion targets specific tissues in physiological placental implantation and pathological metastasis, which raises questions about how this process is controlled. We compare dermis and endometrium capacities to support trophoblast invasion, using matching sets of human primary fibroblasts in a coculture assay with human placental explants. Substituting endometrium, the natural trophoblast target, with dermis dramatically reduces trophoblast interstitial invasion. Our data reveal that endometrium expresses a higher rate of the fibronectin (FN) extra type III domain A+ (EDA+) splicing isoform, which displays stronger matrix incorporation capacity. We demonstrate that the high FN content of the endometrium matrix, and not specifically the EDA domain, supports trophoblast invasion by showing that forced incorporation of plasma FN (EDA–) promotes efficient trophoblast invasion. We further show that the serine/arginine-rich protein serine/arginine-rich splicing factor 1 (SRSF1) is more highly expressed in endometrium and, using RNA interference, that it is involved in the higher EDA exon inclusion rate in endometrium. Our data therefore show a mechanism by which tissues can be distinguished, for their capacity to support invasion, by their different rates of EDA inclusion, linked to their SRSF1 protein levels. In the broader context of cancer pathology, the results suggest that SRSF1 might play a central role not only in the tumor cells, but also in the surrounding stroma.
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Affiliation(s)
- Isabel Cristina Lopez-Mejia
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535/IFR122, Universities of Montpellier 1 and Montpellier 2, 34293 Montpellier Cedex 5, France Département de Physiologie, Université de Lausanne, CH-1015 Lausanne, Switzerland INSERM U844, Institut des Neurosciences de Montpellier, Centre Hospitalier Universitaire Saint Eloi, Université Montpellier 1, 34295 Montpellier Cedex 5, France Service Immuno-Rhumatologie, Centre Hospitalier Universitaire Lapeyronie, 34093 Montpellier Cedex, France
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Alternative splicing programs in prostate cancer. Int J Cell Biol 2013; 2013:458727. [PMID: 23983695 PMCID: PMC3747374 DOI: 10.1155/2013/458727] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/11/2013] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer (PCa) remains one of the most frequent causes of death for cancer in the male population. Although the initial antiandrogenic therapies are efficacious, PCa often evolves into a hormone-resistant, incurable disease. The genetic and phenotypic heterogeneity of this type of cancer renders its diagnosis and cure particularly challenging. Mounting evidence indicates that alternative splicing, the process that allows production of multiple mRNA variants from each gene, contributes to the heterogeneity of the disease. Key genes for the biology of normal and neoplastic prostate cells, such as those encoding for the androgen receptor and cyclin D1, are alternatively spliced to yield protein isoforms with different or even opposing functions. This review illustrates some examples of genes whose alternative splicing regulation is relevant to PCa biology and discusses the possibility to exploit alternative splicing regulation as a novel tool for prognosis, diagnosis, and therapeutic approaches to PCa.
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Liu Y, Conaway L, Rutherford Bethard J, Al-Ayoubi AM, Thompson Bradley A, Zheng H, Weed SA, Eblen ST. Phosphorylation of the alternative mRNA splicing factor 45 (SPF45) by Clk1 regulates its splice site utilization, cell migration and invasion. Nucleic Acids Res 2013; 41:4949-62. [PMID: 23519612 PMCID: PMC3643583 DOI: 10.1093/nar/gkt170] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Alternative mRNA splicing is a mechanism to regulate protein isoform expression and is regulated by alternative splicing factors. The alternative splicing factor 45 (SPF45) is overexpressed in cancer, although few biological effects of SPF45 are known, and few splicing targets have been identified. We previously showed that Extracellular Regulated Kinase 2 (ERK2) phosphorylation of SPF45 regulates cell proliferation and adhesion to fibronectin. In this work, we show that Cdc2-like kinase 1 (Clk1) phosphorylates SPF45 on eight serine residues. Clk1 expression enhanced, whereas Clk1 inhibition reduced, SPF45-induced exon 6 exclusion from Fas mRNA. Mutational analysis of the Clk1 phosphorylation sites on SPF45 showed both positive and negative regulation of splicing, with a net effect of inhibiting SPF45-induced exon 6 exclusion, correlating with reduced Fas mRNA binding. However, Clk1 enhanced SPF45 protein expression, but not mRNA expression, whereas inhibition of Clk1 increased SPF45 degradation through a proteasome-dependent pathway. Overexpression of SPF45 or a phospho-mimetic mutant, but not a phospho-inhibitory mutant, stimulated ovarian cancer cell migration and invasion, correlating with increased fibronectin expression, ERK activation and enhanced splicing and phosphorylation of full-length cortactin. Our results demonstrate for the first time that SPF45 overexpression enhances cell migration and invasion, dependent on biochemical regulation by Clk1.
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Affiliation(s)
- Yuying Liu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Ave, Charleston, SC 29425, USA
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