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Lozano-Vidal N, Stanicek L, Bink DI, Juni RP, Hooglugt A, Kremer V, Phelp P, van Bergen A, MacInnes AW, Dimmeler S, Boon RA. Aging-regulated PNUTS maintains endothelial barrier function via SEMA3B suppression. Commun Biol 2024; 7:541. [PMID: 38714838 PMCID: PMC11076560 DOI: 10.1038/s42003-024-06230-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Age-related diseases pose great challenges to health care systems worldwide. During aging, endothelial senescence increases the risk for cardiovascular disease. Recently, it was described that Phosphatase 1 Nuclear Targeting Subunit (PNUTS) has a central role in cardiomyocyte aging and homeostasis. Here, we determine the role of PNUTS in endothelial cell aging. We confirm that PNUTS is repressed in senescent endothelial cells (ECs). Moreover, PNUTS silencing elicits several of the hallmarks of endothelial aging: senescence, reduced angiogenesis and loss of barrier function. Findings are validate in vivo using endothelial-specific inducible PNUTS-deficient mice (Cdh5-CreERT2;PNUTSfl/fl), termed PNUTSEC-KO. Two weeks after PNUTS deletion, PNUTSEC-KO mice present severe multiorgan failure and vascular leakage. Transcriptomic analysis of PNUTS-silenced HUVECs and lungs of PNUTSEC-KO mice reveal that the PNUTS-PP1 axis tightly regulates the expression of semaphorin 3B (SEMA3B). Indeed, silencing of SEMA3B completely restores barrier function after PNUTS loss-of-function. These results reveal a pivotal role for PNUTS in endothelial homeostasis through a SEMA3B downstream pathway that provides a potential target against the effects of aging in ECs.
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Affiliation(s)
- Noelia Lozano-Vidal
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Laura Stanicek
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
- Institute of Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Diewertje I Bink
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Rio P Juni
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Aukie Hooglugt
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Veerle Kremer
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Philippa Phelp
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Anke van Bergen
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Alyson W MacInnes
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Potsdamer Strasse 58, 10785, Berlin, Germany
| | - Reinier A Boon
- Department of Physiology, Amsterdam UMC, VU University, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.
- Amsterdam Cardiovascular Sciences, Microcirculation, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
- Institute of Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Potsdamer Strasse 58, 10785, Berlin, Germany.
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2
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Verdugo-Sivianes EM, Carnero A. SPINOPHILIN: a multiplayer tumor suppressor. Genes Dis 2022; 10:187-198. [PMID: 37013033 PMCID: PMC10066247 DOI: 10.1016/j.gendis.2021.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/24/2021] [Indexed: 02/07/2023] Open
Abstract
SPINOPHILIN (SPN, PPP1R9B or NEURABIN-2) is a multifunctional protein that regulates protein-protein interactions in different cell signaling pathways. SPN is also one of the regulatory subunits of protein phosphatase 1 (PP1), implicated in the dephosphorylation of retinoblastoma protein (pRB) during cell cycle. The SPN gene has been described as a tumor suppressor in different human tumor contexts, in which low levels of SPN are correlated with a higher grade and worse prognosis. In addition, mutations of the SPN protein have been reported in human tumors. Recently, an oncogenic mutation of SPN, A566V, was described, which affects both the SPN-PP1 interaction and the phosphatase activity of the holoenzyme, and promotes p53-dependent tumorigenesis by increasing the cancer stem cell (CSC) pool in breast tumors. Thus, the loss or mutation of SPN could be late events that promotes tumor progression by increasing the CSC pool and, eventually, the malignant behavior of the tumor.
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Schreiter T, Gieseler RK, Vílchez-Vargas R, Jauregui R, Sowa JP, Klein-Scory S, Broering R, Croner RS, Treckmann JW, Link A, Canbay A. Transcriptome-Wide Analysis of Human Liver Reveals Age-Related Differences in the Expression of Select Functional Gene Clusters and Evidence for a PPP1R10-Governed 'Aging Cascade'. Pharmaceutics 2021; 13:pharmaceutics13122009. [PMID: 34959291 PMCID: PMC8709089 DOI: 10.3390/pharmaceutics13122009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 12/27/2022] Open
Abstract
A transcriptome-wide analysis of human liver for demonstrating differences between young and old humans has not yet been performed. However, identifying major age-related alterations in hepatic gene expression may pinpoint ontogenetic shifts with important hepatic and systemic consequences, provide novel pharmacogenetic information, offer clues to efficiently counteract symptoms of old age, and improve the overarching understanding of individual decline. Next-generation sequencing (NGS) data analyzed by the Mann-Whitney nonparametric test and Ensemble Feature Selection (EFS) bioinformatics identified 44 transcripts among 60,617 total and 19,986 protein-encoding transcripts that significantly (p = 0.0003 to 0.0464) and strikingly (EFS score > 0.3:16 transcripts; EFS score > 0.2:28 transcripts) differ between young and old livers. Most of these age-related transcripts were assigned to the categories 'regulome', 'inflammaging', 'regeneration', and 'pharmacogenes'. NGS results were confirmed by quantitative real-time polymerase chain reaction. Our results have important implications for the areas of ontogeny/aging and the age-dependent increase in major liver diseases. Finally, we present a broadly substantiated and testable hypothesis on a genetically governed 'aging cascade', wherein PPP1R10 acts as a putative ontogenetic master regulator, prominently flanked by IGFALS and DUSP1. This transcriptome-wide analysis of human liver offers potential clues towards developing safer and improved therapeutic interventions against major liver diseases and increased insights into key mechanisms underlying aging.
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Affiliation(s)
- Thomas Schreiter
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Robert K. Gieseler
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Ramiro Vílchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Ruy Jauregui
- Data Science Grasslands, Grasslands Research Centre, AgResearch, Palmerston North 4410, New Zealand;
| | - Jan-Peter Sowa
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Susanne Klein-Scory
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Ruth Broering
- Department of Gastroenterology and Hepatology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Roland S. Croner
- Department of General, Visceral, Vascular and Transplantation Surgery, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany;
| | - Jürgen W. Treckmann
- Department of General, Visceral and Transplantation Surgery, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Alexander Link
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Ali Canbay
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Section of Hepatology and Gastroenterology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
- Correspondence: ; Tel.: +49-234-299-3401
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Li Y, Kardell MB, Wang F, Wang L, Zhu S, Bessho T, Peng A. The Sm core components of small nuclear ribonucleoproteins promote homologous recombination repair. DNA Repair (Amst) 2021; 108:103244. [PMID: 34768043 DOI: 10.1016/j.dnarep.2021.103244] [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: 04/19/2021] [Revised: 10/01/2021] [Accepted: 10/29/2021] [Indexed: 11/17/2022]
Abstract
DNA Double strand breaks (DSBs) are highly hazardous to the cell, and are repaired predominantly via non-homologous end joining (NHEJ) and homologous recombination (HR). Using DSB-mimicking DNA templates, our proteomic studies identified a group of Sm core proteins of small nuclear ribonucleoproteins (snRNPs) as potential DSB-associated proteins. We further confirmed that these Sm proteins were recruited to laser-induced DNA damage sites, and co-localized with established DNA damage repair factors. Depletion of Sm-D3 or Sm-B induced accumulation of γ-H2AX, and impaired the repair efficiency of HR, but not NHEJ. Furthermore, disruption of Sm-D3 reduced the protein level of HR factors, especially RAD51 and CHK1, but caused no change in the expression of repair factors involved in NHEJ. Mechanistically, Sm-D3 proteins bound RAD51, suppressed the ubiquitination of RAD51, and mediated the stabilization of RAD51; Sm-D3 depletion particularly impacted the level of RAD51 and CHK1 on damaged chromatin. As such, our studies characterized a role of Sm proteins in HR repair, via a new mechanism that is distinct from their conventional functions in RNA processing and gene regulation, but consistent with their direct recruitment to DNA damage sites and association with repair factors.
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Affiliation(s)
- Yanqiu Li
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Mary Bridget Kardell
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Feifei Wang
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Ling Wang
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Songli Zhu
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Tadayoshi Bessho
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Aimin Peng
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA.
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Verdugo-Sivianes EM, Carnero A. Role of the Holoenzyme PP1-SPN in the Dephosphorylation of the RB Family of Tumor Suppressors During Cell Cycle. Cancers (Basel) 2021; 13:cancers13092226. [PMID: 34066428 PMCID: PMC8124259 DOI: 10.3390/cancers13092226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Cell cycle progression is highly regulated by modulating the phosphorylation status of retinoblastoma (RB) family proteins. This process is controlled by a balance in the action of kinases, such as the complexes formed by cyclin-dependent kinases (CDKs) and cyclins, and phosphatases, mainly the protein phosphatase 1 (PP1). However, while the phosphorylation of the RB family has been largely studied, its dephosphorylation is less known. Recently, the PP1-Spinophilin (SPN) holoenzyme has been described as the main phosphatase responsible for the dephosphorylation of RB proteins during the G0/G1 transition and at the end of G1. Here, we describe the regulation of the phosphorylation status of RB family proteins, giving importance not only to their inactivation by phosphorylation but also to their dephosphorylation to restore the cell cycle. Abstract Cell cycle progression is highly regulated by modulating the phosphorylation status of the retinoblastoma protein (pRB) and the other two members of the RB family, p107 and p130. This process is controlled by a balance in the action of kinases, such as the complexes formed by cyclin-dependent kinases (CDKs) and cyclins, and phosphatases, mainly the protein phosphatase 1 (PP1). However, while the phosphorylation of the RB family has been largely studied, its dephosphorylation is less known. Phosphatases are holoenzymes formed by a catalytic subunit and a regulatory protein with substrate specificity. Recently, the PP1-Spinophilin (SPN) holoenzyme has been described as the main phosphatase responsible for the dephosphorylation of RB proteins during the G0/G1 transition and at the end of G1. Moreover, SPN has been described as a tumor suppressor dependent on PP1 in lung and breast tumors, where it promotes tumorigenesis by increasing the cancer stem cell pool. Therefore, a connection between the cell cycle and stem cell biology has also been proposed via SPN/PP1/RB proteins.
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Affiliation(s)
- Eva M. Verdugo-Sivianes
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocio, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Avda. Manuel Siurot s/n, 41013 Seville, Spain;
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocio, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Avda. Manuel Siurot s/n, 41013 Seville, Spain;
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-955-92-31-11
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Verdugo-Sivianes EM, Rojas AM, Muñoz-Galván S, Otero-Albiol D, Carnero A. Mutation of SPINOPHILIN (PPP1R9B) found in human tumors promotes the tumorigenic and stemness properties of cells. Am J Cancer Res 2021; 11:3452-3471. [PMID: 33537097 PMCID: PMC7847670 DOI: 10.7150/thno.53572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/20/2020] [Indexed: 12/17/2022] Open
Abstract
Rationale: SPINOPHILIN (SPN, PPP1R9B) is an important tumor suppressor involved in the progression and malignancy of different tumors depending on its association with protein phosphatase 1 (PP1) and the ability of the PP1-SPN holoenzyme to dephosphorylate retinoblastoma (pRB). Methods: We performed a mutational analysis of SPN in human tumors, focusing on the region of interaction with PP1 and pRB. We explored the effect of the SPN-A566V mutation in an immortalized non-tumorigenic cell line of epithelial breast tissue, MCF10A, and in two different p53-mutated breast cancer cells lines, T47D and MDA-MB-468. Results: We characterized an oncogenic mutation of SPN found in human tumor samples, SPN-A566V, that affects both the SPN-PP1 interaction and its phosphatase activity. The SPN-A566V mutation does not affect the interaction of the PP1-SPN holoenzyme with pocket proteins pRB, p107 and p130, but it affects its ability to dephosphorylate them during G0/G1 and G1, indicating that the PP1-SPN holoenzyme regulates cell cycle progression. SPN-A566V also promoted stemness, establishing a connection between the cell cycle and stem cell biology via pocket proteins and PP1-SPN regulation. However, only cells with both SPN-A566V and mutant p53 have increased tumorigenic and stemness properties. Conclusions: SPN-A566V, or other equivalent mutations, could be late events that promote tumor progression by increasing the CSC pool and, eventually, the malignant behavior of the tumor.
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Essential role of GEXP15, a specific Protein Phosphatase type 1 partner, in Plasmodium berghei in asexual erythrocytic proliferation and transmission. PLoS Pathog 2019; 15:e1007973. [PMID: 31348803 PMCID: PMC6685639 DOI: 10.1371/journal.ppat.1007973] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/07/2019] [Accepted: 07/10/2019] [Indexed: 12/21/2022] Open
Abstract
The essential and distinct functions of Protein Phosphatase type 1 (PP1) catalytic subunit in eukaryotes are exclusively achieved through its interaction with a myriad of regulatory partners. In this work, we report the molecular and functional characterization of Gametocyte EXported Protein 15 (GEXP15), a Plasmodium specific protein, as a regulator of PP1. In vitro interaction studies demonstrated that GEXP15 physically interacts with PP1 through the RVxF binding motif in P. berghei. Functional assays showed that GEXP15 was able to increase PP1 activity and the mutation of the RVxF motif completely abolished this regulation. Immunoprecipitation assays of tagged GEXP15 or PP1 in P. berghei followed by immunoblot or mass spectrometry analyses confirmed their interaction and showed that they are present both in schizont and gametocyte stages in shared protein complexes involved in the spliceosome and proteasome pathways and known to play essential role in parasite development. Phenotypic analysis of viable GEXP15 deficient P. berghei blood parasites showed that they were unable to develop lethal infection in BALB/c mice or to establish experimental cerebral malaria in C57BL/6 mice. Further, although deficient parasites produced gametocytes they did not produce any oocysts/sporozoites indicating a high fitness cost in the mosquito. Global proteomic and phosphoproteomic analyses of GEXP15 deficient schizonts revealed a profound defect with a significant decrease in the abundance and an impact on phosphorylation status of proteins involved in regulation of gene expression or invasion. Moreover, depletion of GEXP15 seemed to impact mainly the abundance of some specific proteins of female gametocytes. Our study provides the first insight into the contribution of a PP1 regulator to Plasmodium virulence and suggests that GEXP15 affects both the asexual and sexual life cycle. In the absence of an effective vaccine and the emerging resistance to artemisinin combination therapy, malaria is still a significant threat to human health. Increasing our understanding of the specific mechanisms of the biology of Plasmodium is essential to propose new strategies to control this infection. Here, we demonstrated that GEXP15, a specific protein in Plasmodium, was able to interact with the Protein Phosphatase 1 and regulate its activity. We showed that both proteins are implicated in common protein complexes involved in the mRNA splicing and proteasome pathways. We reported that the deletion of GEXP15 leads to a loss of parasite virulence during asexual stages and a total abolishment of the capacity of deficient parasites to develop in the mosquito. We also found that this deletion affects both protein phosphorylation status and significantly decreases the expression of essential proteins in schizont and gametocyte stages. This study characterizes for the first time a novel molecular pathway through the control of PP1 by an essential and specific Plasmodium regulator, which may contribute to the discovery of new therapeutic targets to control malaria.
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Wang F, Zhu S, Fisher LA, Wang L, Eurek NJ, Wahl JK, Lan L, Peng A. Phosphatase 1 Nuclear Targeting Subunit Mediates Recruitment and Function of Poly (ADP-Ribose) Polymerase 1 in DNA Repair. Cancer Res 2019; 79:2526-2535. [PMID: 30733193 DOI: 10.1158/0008-5472.can-18-1673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/26/2018] [Accepted: 01/31/2019] [Indexed: 12/17/2022]
Abstract
PARP, particularly PARP1, plays an essential role in the detection and repair of DNA single-strand breaks and double-strand breaks. PARP1 accumulates at DNA damage sites within seconds after DNA damage to catalyze the massive induction of substrate protein poly ADP-ribosylation (PARylation). However, the molecular mechanisms underlying the recruitment and activation of PARP1 in DNA repair are not fully understood. Here we show that phosphatase 1 nuclear targeting subunit 1 (PNUTS) is a robust binding partner of PARP1. Inhibition of PNUTS led to strong accumulation of endogenous DNA damage and sensitized the cellular response to a wide range of DNA-damaging agents, implicating PNUTS as an essential and multifaceted regulator of DNA repair. Recruitment of PNUTS to laser-induced DNA damage was similar to that of PARP1, and depletion or inhibition of PARP1 abrogated recruitment of PNUTS to sites of DNA damage. Conversely, PNUTS was required for efficient induction of substrate PARylation after DNA damage. PNUTS bound the BRCA1 C-terminal (BRCT) domain of PARP1 and was required for the recruitment of PARP1 to sites of DNA damage. Finally, depletion of PNUTS rendered cancer cells hypersensitive to PARP inhibition. Taken together, our study characterizes PNUTS as an essential partner of PARP1 in DNA repair and a potential drug target in cancer therapy. SIGNIFICANCE: These findings reveal PNUTS as an essential functional partner of PARP1 in DNA repair and suggest its inhibition as a potential therapeutic strategy in conjunction with DNA-damaging agents or PARP inhibitors.See related commentary by Murai and Pommier, p. 2460.
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Affiliation(s)
- Feifei Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, P.R. China.,Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Songli Zhu
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Laura A Fisher
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Ling Wang
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Nicholas J Eurek
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - James K Wahl
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Li Lan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Aimin Peng
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska.
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Wang F, Wang L, Fisher LA, Li C, Wang W, Peng A. Phosphatase 1 Nuclear Targeting Subunit (PNUTS) Regulates Aurora Kinases and Mitotic Progression. Mol Cancer Res 2018; 17:10-19. [PMID: 30190438 DOI: 10.1158/1541-7786.mcr-17-0670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/31/2018] [Accepted: 08/27/2018] [Indexed: 11/16/2022]
Abstract
Mitotic progression is regulated largely by reversible phosphorylation events that are mediated by mitotic kinases and phosphatases. Protein phosphatase 1 (PP1) has been shown to play a crucial role in regulation of mitotic entry, progression, and exit. We previously observed, in Xenopus egg extracts, that phosphatase 1 nuclear targeting subunit (PPP1R10/PNUTS) acts as a mitotic regulator by negatively modulating PP1. This study investigates the role of PNUTS in mitotic progression in mammalian cells, and demonstrates that PNUTS expression is elevated in mitosis and depletion partially blocks mitotic entry. Cells that enter mitosis after PNUTS knockdown exhibit frequent chromosome mis-segregation. Aurora A/B kinase complexes and several kinetochore components are identified as PNUTS-associated proteins. PNUTS depletion suppresses the activation of Aurora A/B kinases, and disrupts the spatiotemporal regulation of the chromosomal passenger complex (CPC). PNUTS dynamically localizes to kinetochores, and is required for the activation of the spindle assembly checkpoint. Finally, PNUTS depletion sensitizes the tumor cell response to Aurora inhibition, suggesting that PNUTS is a potential drug target in combination anticancer therapy. IMPLICATIONS: Delineation of how PNUTS governs the mitotic activation and function of Aurora kinases will improve the understanding of the complex phospho-regulation in mitotic progression, and suggest new options to enhance the therapeutic efficacy of Aurora inhibitors.
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Affiliation(s)
- Feifei Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China.,Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska.,Institute of Hypertension, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ling Wang
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Laura A Fisher
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Chunling Li
- Institute of Hypertension, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Weidong Wang
- Institute of Hypertension, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Aimin Peng
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska.
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Vennin C, Adriaenssens E. Long non-coding RNA and messenger RNA-the meeting of two worlds. J Thorac Dis 2018; 10:544-546. [PMID: 29607108 DOI: 10.21037/jtd.2018.01.103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Constance Vennin
- Institute of Physiological Chemistry, University Medical Center of Johannes Gutenberg, University of Mainz, Mainz, Germany
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11
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Protein interactomes of protein phosphatase 2A B55 regulatory subunits reveal B55-mediated regulation of replication protein A under replication stress. Sci Rep 2018; 8:2683. [PMID: 29422626 PMCID: PMC5805732 DOI: 10.1038/s41598-018-21040-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/24/2018] [Indexed: 11/24/2022] Open
Abstract
The specific function of PP2A, a major serine/threonine phosphatase, is mediated by regulatory targeting subunits, such as members of the B55 family. Although implicated in cell division and other pathways, the specific substrates and functions of B55 targeting subunits are largely undefined. In this study we identified over 100 binding proteins of B55α and B55β in Xenopus egg extracts that are involved in metabolism, mitochondria function, molecular trafficking, cell division, cytoskeleton, DNA replication, DNA repair, and cell signaling. Among the B55α and B55β-associated proteins were numerous mitotic regulators, including many substrates of CDK1. Consistently, upregulation of B55α accelerated M-phase exit and inhibited M-phase entry. Moreover, specific substrates of CDK2, including factors of DNA replication and chromatin remodeling were identified within the interactomes of B55α and B55β, suggesting a role for these phosphatase subunits in DNA replication. In particular, we confirmed in human cells that B55α binds RPA and mediates the dephosphorylation of RPA2. The B55-RPA association is disrupted after replication stress, consistent with the induction of RPA2 phosphorylation. Thus, we report here a new mechanism that accounts for both how RPA phosphorylation is modulated by PP2A and how the phosphorylation of RPA2 is abruptly induced after replication stress.
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Zhu S, Fisher LA, Bessho T, Peng A. Protein phosphatase 1 and phosphatase 1 nuclear targeting subunit-dependent regulation of DNA-dependent protein kinase and non-homologous end joining. Nucleic Acids Res 2017; 45:10583-10594. [PMID: 28985363 PMCID: PMC5737533 DOI: 10.1093/nar/gkx686] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 07/28/2017] [Indexed: 12/29/2022] Open
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) plays a key role in mediating non-homologous end joining (NHEJ), a major repair pathway for DNA double-strand breaks (DSBs). The activation, function and dynamics of DNA-PKcs is regulated largely by its reversible phosphorylation at numerous residues, many of which are targeted by DNA-PKcs itself. Interestingly, these DNA-PKcs phosphorylation sites function in a distinct, and sometimes opposing manner, suggesting that they are differentially regulated via complex actions of both kinases and phosphatases. In this study we identified several phosphatase subunits as potential DSB-associated proteins. In particular, protein phosphatase 1 (PP1) is recruited to a DSB-mimicking substrate in Xenopus egg extracts and sites of laser microirradiation in human cells. Depletion of PP1 impairs NHEJ in both Xenopus egg extracts and human cells. PP1 binds multiple motifs of DNA-PKcs, regulates DNA-PKcs phosphorylation, and is required for DNA-PKcs activation after DNA damage. Interestingly, phosphatase 1 nuclear targeting subunit (PNUTS), an inhibitory regulator of PP1, is also recruited to DNA damage sites to promote NHEJ. PNUTS associates with the DNA-PK complex and is required for DNA-PKcs phosphorylation at Ser-2056 and Thr-2609. Thus, PNUTS and PP1 together fine-tune the dynamic phosphorylation of DNA-PKcs after DNA damage to mediate NHEJ.
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Affiliation(s)
- Songli Zhu
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Laura A Fisher
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Tadayoshi Bessho
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Aimin Peng
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
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Ren D, Fisher LA, Zhao J, Wang L, Williams BC, Goldberg ML, Peng A. Cell cycle-dependent regulation of Greatwall kinase by protein phosphatase 1 and regulatory subunit 3B. J Biol Chem 2017; 292:10026-10034. [PMID: 28446604 DOI: 10.1074/jbc.m117.778233] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/25/2017] [Indexed: 11/06/2022] Open
Abstract
Greatwall (Gwl) kinase plays an essential role in the regulation of mitotic entry and progression. Mitotic activation of Gwl requires both cyclin-dependent kinase 1 (CDK1)-dependent phosphorylation and its autophosphorylation at an evolutionarily conserved serine residue near the carboxyl terminus (Ser-883 in Xenopus). In this study we show that Gwl associates with protein phosphatase 1 (PP1), particularly PP1γ, which mediates the dephosphorylation of Gwl Ser-883. Consistent with the mitotic activation of Gwl, its association with PP1 is disrupted in mitotic cells and egg extracts. During mitotic exit, PP1-dependent dephosphorylation of Gwl Ser-883 occurs prior to dephosphorylation of other mitotic substrates; replacing endogenous Gwl with a phosphomimetic S883E mutant blocks mitotic exit. Moreover, we identified PP1 regulatory subunit 3B (PPP1R3B) as a targeting subunit that can direct PP1 activity toward Gwl. PPP1R3B bridges PP1 and Gwl association and promotes Gwl Ser-883 dephosphorylation. Consistent with the cell cycle-dependent association of Gwl and PP1, Gwl and PPP1R3B dissociate in M phase. Interestingly, up-regulation of PPP1R3B facilitates mitotic exit and blocks mitotic entry. Thus, our study suggests PPP1R3B as a new cell cycle regulator that functions by governing Gwl dephosphorylation.
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Affiliation(s)
- Dapeng Ren
- From the Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583 and
| | - Laura A Fisher
- From the Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583 and
| | - Jing Zhao
- From the Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583 and
| | - Ling Wang
- From the Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583 and
| | - Byron C Williams
- the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Michael L Goldberg
- the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Aimin Peng
- From the Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583 and
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14
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Biogenesis and activity regulation of protein phosphatase 1. Biochem Soc Trans 2017; 45:89-99. [DOI: 10.1042/bst20160154] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/06/2016] [Accepted: 11/16/2016] [Indexed: 01/01/2023]
Abstract
Protein phosphatase 1 (PP1) is expressed in all eukaryotic cells and catalyzes a substantial fraction of phosphoserine/threonine dephosphorylation reactions. It forms stable complexes with PP1-interacting proteins (PIPs) that guide the phosphatase throughout its life cycle and control its fate and function. The diversity of PIPs is huge (≈200 in vertebrates), and most of them combine short linear motifs to form large and unique interaction interfaces with PP1. Many PIPs have separate domains for PP1 anchoring, PP1 regulation, substrate recruitment and subcellular targeting, which enable them to direct associated PP1 to a specific subset of substrates and mediate acute activity control. Hence, PP1 functions as the catalytic subunit of a large number of multimeric holoenzymes, each with its own subset of substrates and mechanism(s) of regulation.
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15
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Zhu S, Peng A. Non-homologous end joining repair in Xenopus egg extract. Sci Rep 2016; 6:27797. [PMID: 27324260 PMCID: PMC4914968 DOI: 10.1038/srep27797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/25/2016] [Indexed: 11/09/2022] Open
Abstract
Non-homologous end joining (NHEJ) is a major DNA double-strand break (DSB) repair mechanism. We characterized here a series of plasmid-based DSB templates that were repaired in Xenopus egg extracts via the canonical, Ku-dependent NHEJ pathway. We showed that the template with compatible ends was efficiently repaired without end processing, in a manner that required the kinase activity of DNA-PKcs but not ATM. Moreover, non-compatible ends with blunt/3'-overhang, blunt/5'-overhang, and 3'-overhang/5'-overhang were predominantly repaired with fill-in and ligation without the removal of end nucleotides. In contrast, 3'-overhang/3'-overhang and 5'-overhang/5'-overhang templates were processed by resection of 3-5 bases and fill-in of 1-4 bases prior to end ligation. Therefore, the NHEJ machinery exhibited a strong preference for precise repair; the presence of neither non-compatible ends nor protruding single strand DNA sufficiently warranted the action of nucleases. ATM was required for the efficient repair of all non-compatible ends including those repaired without end processing by nucleases, suggesting its role beyond phosphorylation and regulation of Artemis. Finally, dephosphorylation of the 5'-overhang/3'-overhang template reduced the efficiency of DNA repair without increasing the risk of end resection, indicating that end protection via prompt end ligation is not the sole mechanism that suppresses the action of nucleases.
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Affiliation(s)
- Songli Zhu
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Aimin Peng
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
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McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A. Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs. Mol Cell Proteomics 2015; 14:2194-212. [PMID: 26055452 DOI: 10.1074/mcp.m114.046938] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 12/27/2022] Open
Abstract
Entry into mitosis is driven by the coordinated phosphorylation of thousands of proteins. For the cell to complete mitosis and divide into two identical daughter cells it must regulate dephosphorylation of these proteins in a highly ordered, temporal manner. There is currently a lack of a complete understanding of the phosphorylation changes that occur during the initial stages of mitotic exit in human cells. Therefore, we performed a large unbiased, global analysis to map the very first dephosphorylation events that occur as cells exit mitosis. We identified and quantified the modification of >16,000 phosphosites on >3300 unique proteins during early mitotic exit, providing up to eightfold greater resolution than previous studies. The data have been deposited to the ProteomeXchange with identifier PXD001559. Only a small fraction (∼ 10%) of phosphorylation sites were dephosphorylated during early mitotic exit and these occurred on proteins involved in critical early exit events, including organization of the mitotic spindle, the spindle assembly checkpoint, and reformation of the nuclear envelope. Surprisingly this enrichment was observed across all kinase consensus motifs, indicating that it is independent of the upstream phosphorylating kinase. Therefore, dephosphorylation of these sites is likely determined by the specificity of phosphatase/s rather than the activity of kinase/s. Dephosphorylation was significantly affected by the amino acids at and surrounding the phosphorylation site, with several unique evolutionarily conserved amino acids correlating strongly with phosphorylation status. These data provide a potential mechanism for the specificity of phosphatases, and how they co-ordinate the ordered events of mitotic exit. In summary, our results provide a global overview of the phosphorylation changes that occur during the very first stages of mitotic exit, providing novel mechanistic insight into how phosphatase/s specifically regulate this critical transition.
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Affiliation(s)
- Rachael A McCloy
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Benjamin L Parker
- §The Charles Perkins Center, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, NSW 2006, Australia
| | - Samuel Rogers
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Rima Chaudhuri
- §The Charles Perkins Center, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, NSW 2006, Australia
| | - Velimir Gayevskiy
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Nolan J Hoffman
- §The Charles Perkins Center, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, NSW 2006, Australia
| | - Naveid Ali
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - D Neil Watkins
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia; ¶St. Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, Australia; ‖Department of Thoracic Medicine, St Vincent's Hospital, Darlinghurst, NSW, 2010, Australia
| | - Roger J Daly
- **Department of Biochemistry and Molecular Biology, School of Biomedical Sciences Monash University, Clatyon, VIC, 3800, Australia
| | - David E James
- §The Charles Perkins Center, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, NSW 2006, Australia
| | - Thierry Lorca
- ‡‡Equipe Labellisée Ligue Nationale Contre le Cancer, Universités Montpellier 2 et 1, Centre de Recherche de Biochimie Macromoléculaire, CNRS UMR 5237, 1919 Route de Mende, 34293 Montpellier cedex 5, France
| | - Anna Castro
- ‡‡Equipe Labellisée Ligue Nationale Contre le Cancer, Universités Montpellier 2 et 1, Centre de Recherche de Biochimie Macromoléculaire, CNRS UMR 5237, 1919 Route de Mende, 34293 Montpellier cedex 5, France
| | - Andrew Burgess
- ¶St. Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, Australia; From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia;
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