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Al-Qadhi MA, Allam HA, Fahim SH, Yahya TAA, Ragab FAF. Design and synthesis of certain 7-Aryl-2-Methyl-3-Substituted Pyrazolo{1,5-a}Pyrimidines as multikinase inhibitors. Eur J Med Chem 2023; 262:115918. [PMID: 37922829 DOI: 10.1016/j.ejmech.2023.115918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Four new series 7a-e, 8a-e, 9a-e, and 10a-e of 7-aryl-3-substituted pyrazolo[1,5-a]pyrimidines were synthesized and tested for their RTK and STK inhibitory activity. Compound 7d demonstrated potent enzymatic inhibitory activity against TrkA and ALK2 with IC50 0.087and 0.105 μM, respectively, and potent antiproliferative activity against KM12 and EKVX cell lines with IC50 0.82 and 4.13 μM, respectively. Compound 10e showed good enzyme inhibitory activity against TrkA, ALK2, c-KIT, EGFR, PIM1, CK2α, CHK1, and CDK2 in submicromolar values. Additionally 10e revealed antiproliferative activity against MCF7, HCT116 and EKVX with IC50 3.36, 1.40 and 3.49 μM, respectively; with good safety profile. Moreover, 10e showed cell cycle arrest at the G1/S phase and G1 phase in MCF7 and HCT116 cells with good apoptotic effect. Molecular docking studies were fulfilled for compound 10e and illustrated good interaction with the hot spots of the active site of the tested enzymes.
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Affiliation(s)
- Mustafa A Al-Qadhi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Sana'a University, P.O. Box, 18084, Sana'a, Yemen
| | - Heba Abdelrasheed Allam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box, 11562, Egypt.
| | - Samar H Fahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box, 11562, Egypt
| | - Tawfeek A A Yahya
- Department of Medicinal Chemistry, Faculty of Pharmacy, Sana'a University, P.O. Box, 18084, Sana'a, Yemen
| | - Fatma A F Ragab
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box, 11562, Egypt
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2
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König S, Schmidt N, Bechberger K, Morris S, Priego M, Zaky H, Song Y, Pielage J, Brunholz S, Brady ST, Kins S, Morfini G. Axon-Autonomous Effects of the Amyloid Precursor Protein Intracellular Domain (AICD) on Kinase Signaling and Fast Axonal Transport. Cells 2023; 12:2403. [PMID: 37830617 PMCID: PMC10572015 DOI: 10.3390/cells12192403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
The amyloid precursor protein (APP) is a key molecular component of Alzheimer's disease (AD) pathogenesis. Proteolytic APP processing generates various cleavage products, including extracellular amyloid beta (Aβ) and the cytoplasmic APP intracellular domain (AICD). Although the role of AICD in the activation of kinase signaling pathways is well established in the context of full-length APP, little is known about intracellular effects of the AICD fragment, particularly within discrete neuronal compartments. Deficits in fast axonal transport (FAT) and axonopathy documented in AD-affected neurons prompted us to evaluate potential axon-autonomous effects of the AICD fragment for the first time. Vesicle motility assays using the isolated squid axoplasm preparation revealed inhibition of FAT by AICD. Biochemical experiments linked this effect to aberrant activation of selected axonal kinases and heightened phosphorylation of the anterograde motor protein conventional kinesin, consistent with precedents showing phosphorylation-dependent regulation of motors proteins powering FAT. Pharmacological inhibitors of these kinases alleviated the AICD inhibitory effect on FAT. Deletion experiments indicated this effect requires a sequence encompassing the NPTY motif in AICD and interacting axonal proteins containing a phosphotyrosine-binding domain. Collectively, these results provide a proof of principle for axon-specific effects of AICD, further suggesting a potential mechanistic framework linking alterations in APP processing, FAT deficits, and axonal pathology in AD.
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Affiliation(s)
- Svenja König
- Department for Human Biology and Human Genetics, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany (K.B.); (S.K.)
| | - Nadine Schmidt
- Department for Human Biology and Human Genetics, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany (K.B.); (S.K.)
| | - Karin Bechberger
- Department for Human Biology and Human Genetics, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany (K.B.); (S.K.)
| | - Sarah Morris
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA (S.T.B.)
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Mercedes Priego
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA (S.T.B.)
| | - Hannah Zaky
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA (S.T.B.)
| | - Yuyu Song
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02129, USA
| | - Jan Pielage
- Department of Zoology, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany;
| | - Silke Brunholz
- Department for Human Biology and Human Genetics, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany (K.B.); (S.K.)
| | - Scott T. Brady
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA (S.T.B.)
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Stefan Kins
- Department for Human Biology and Human Genetics, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany (K.B.); (S.K.)
| | - Gerardo Morfini
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA (S.T.B.)
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
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3
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Su X, Su Z, Xu W. ROS elevate HIF-1α phosphorylation for insect lifespan through the CK2-MKP3-p38 pathway. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119389. [PMID: 36372111 DOI: 10.1016/j.bbamcr.2022.119389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
Diapause in insects is akin to dauer in Caenorhabditis elegans and hibernation in vertebrates, characterized by metabolic depression and lifespan extension. Previous studies have shown that reactive oxygen species (ROS) and hypoxia-inducible factor-1α (HIF-1α) in brains of diapause-destined pupae are more abundant than those in nondiapause-destined pupae in Helicoverpa armigera, but the ROS regulating HIF-1α activity remain unknown. Here, we showed that high ROS levels in brains of diapause-destined pupae resulted in low casein kinase 2 (CK2) activity and that downregulation of CK2 caused low expression of mitogen-activated protein kinase phosphatase 3 (MKP3), which is an inhibitor of p-p38. Thus, high p-p38 levels accumulate to improve HIF-1α activity via activating HIF-1α phosphorylation at the S732 residue to regulate insect diapause. This is the first report showing that a new pathway, ROS-CK2-MKP3-p38, regulates HIF-1α activity for lifespan in insects.
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Affiliation(s)
- Xiaolong Su
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhiren Su
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Weihua Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China.
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4
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Staudt DE, Murray HC, Skerrett-Byrne DA, Smith ND, Jamaluddin MFB, Kahl RGS, Duchatel RJ, Germon ZP, McLachlan T, Jackson ER, Findlay IJ, Kearney PS, Mannan A, McEwen HP, Douglas AM, Nixon B, Verrills NM, Dun MD. Phospho-heavy-labeled-spiketide FAIMS stepped-CV DDA (pHASED) provides real-time phosphoproteomics data to aid in cancer drug selection. Clin Proteomics 2022; 19:48. [PMID: 36536316 PMCID: PMC9762002 DOI: 10.1186/s12014-022-09385-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Global high-throughput phosphoproteomic profiling is increasingly being applied to cancer specimens to identify the oncogenic signaling cascades responsible for promoting disease initiation and disease progression; pathways that are often invisible to genomics analysis. Hence, phosphoproteomic profiling has enormous potential to inform and improve individualized anti-cancer treatment strategies. However, to achieve the adequate phosphoproteomic depth and coverage necessary to identify the activated, and hence, targetable kinases responsible for driving oncogenic signaling pathways, affinity phosphopeptide enrichment techniques are required and often coupled with offline high-pressure liquid chromatographic (HPLC) separation prior to nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS). These complex and time-consuming procedures, limit the utility of phosphoproteomics for the analysis of individual cancer patient specimens in real-time, and restrict phosphoproteomics to specialized laboratories often outside of the clinical setting. To address these limitations, here we have optimized a new protocol, phospho-heavy-labeled-spiketide FAIMS Stepped-CV DDA (pHASED), that employs online phosphoproteome deconvolution using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and internal phosphopeptide standards to provide accurate label-free quantitation (LFQ) data in real-time. Compared with traditional single-shot LFQ phosphoproteomics workflows, pHASED provided increased phosphoproteomic depth and coverage (phosphopeptides = 4617 pHASED, 2789 LFQ), whilst eliminating the variability associated with offline prefractionation. pHASED was optimized using tyrosine kinase inhibitor (sorafenib) resistant isogenic FLT3-mutant acute myeloid leukemia (AML) cell line models. Bioinformatic analysis identified differential activation of the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) pathway, responsible for sensing and repairing DNA damage in sorafenib-resistant AML cell line models, thereby uncovering a potential therapeutic opportunity. Herein, we have optimized a rapid, reproducible, and flexible protocol for the characterization of complex cancer phosphoproteomes in real-time, a step towards the implementation of phosphoproteomics in the clinic to aid in the selection of anti-cancer therapies for patients.
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Affiliation(s)
- Dilana E. Staudt
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Heather C. Murray
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - David A. Skerrett-Byrne
- grid.266842.c0000 0000 8831 109XSchool of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cInfertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Nathan D. Smith
- grid.266842.c0000 0000 8831 109XAnalytical and Biomolecular Research Facility (ABRF), Research Services, University of Newcastle, NSW, Callaghan, 2308 Australia
| | - M. Fairuz B. Jamaluddin
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia
| | - Richard G. S. Kahl
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia
| | - Ryan J. Duchatel
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Zacary P. Germon
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Tabitha McLachlan
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Evangeline R. Jackson
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Izac J. Findlay
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Padraic S. Kearney
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Abdul Mannan
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Holly P. McEwen
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Alicia M. Douglas
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia
| | - Brett Nixon
- grid.266842.c0000 0000 8831 109XSchool of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cInfertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Nicole M. Verrills
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
| | - Matthew D. Dun
- grid.266842.c0000 0000 8831 109XSchool of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308 Australia ,grid.413648.cPrecision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305 Australia
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A complex of distal appendage-associated kinases linked to human disease regulates ciliary trafficking and stability. Proc Natl Acad Sci U S A 2021; 118:2018740118. [PMID: 33846249 PMCID: PMC8072220 DOI: 10.1073/pnas.2018740118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Primary cilia (PC) are sensory organelles essential for the development and maintenance of adult tissues. Accordingly, dysfunction of PC causes human disorders called ciliopathies. Hence, a thorough understanding of the molecular regulation of PC is critical. Our findings highlight CSNK2A1 as a modulator of cilia trafficking and stability, tightly related to TTBK2 function. Enriched at the centrosome, CSNK2A1 prevents abnormal accumulation of key ciliary proteins, instability at the tip, and aberrant activation of the Sonic Hedgehog pathway. Furthermore, we establish that Csnk2a1 mutations associated with Okur-Chung neurodevelopmental disorder (OCNDS) alter cilia morphology. Thus, we report a potential linkage between CSNK2A1 ciliary function and OCNDS. Cilia biogenesis is a complex, multistep process involving the coordination of multiple cellular trafficking pathways. Despite the importance of ciliogenesis in mediating the cellular response to cues from the microenvironment, we have only a limited understanding of the regulation of cilium assembly. We previously identified Tau tubulin kinase 2 (TTBK2) as a key regulator of ciliogenesis. Here, using CRISPR kinome and biotin identification screening, we identify the CK2 catalytic subunit CSNK2A1 as an important modulator of TTBK2 function in cilia trafficking. Superresolution microscopy reveals that CSNK2A1 is a centrosomal protein concentrated at the mother centriole and associated with the distal appendages. Csnk2a1 mutant cilia are longer than those of control cells, showing instability at the tip associated with ciliary actin cytoskeleton changes. These cilia also abnormally accumulate key cilia assembly and SHH-related proteins. De novo mutations of Csnk2a1 were recently linked to the human genetic disorder Okur-Chung neurodevelopmental syndrome (OCNDS). Consistent with the role of CSNK2A1 in cilium stability, we find that expression of OCNDS-associated Csnk2a1 variants in wild-type cells causes ciliary structural defects. Our findings provide insights into mechanisms involved in ciliary length regulation, trafficking, and stability that in turn shed light on the significance of cilia instability in human disease.
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Fatoki TH, Ibraheem O, Ogunyemi IO, Akinmoladun AC, Ugboko HU, Adeseko CJ, Awofisayo OA, Olusegun SJ, Enibukun JM. Network analysis, sequence and structure dynamics of key proteins of coronavirus and human host, and molecular docking of selected phytochemicals of nine medicinal plants. J Biomol Struct Dyn 2020; 39:6195-6217. [PMID: 32686993 DOI: 10.1080/07391102.2020.1794971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The novel coronavirus of 2019 (nCoV-19) has become a pandemic, affecting over 205 nations with over 7,410,000 confirmed cases which has resulted to over 418,000 deaths worldwide. This study aimed to identify potential therapeutic compounds and phytochemicals of medicinal plants that have potential to modulate the expression network of genes that are involve in SARS-CoV-2 pathology in human host and to understand the dynamics key proteins involved in the virus-host interactions. The method used include gene network analysis, molecular docking, and sequence and structure dynamics simulations. The results identified DNA-dependent protein kinase (DNA-PK) and Protein kinase CK2 as key players in SARS-CoV-2 lifecycle. Among the predicted drugs compounds, clemizole, monorden, spironolactone and tanespimycin showed high binding energies; among the studied repurposing compounds, remdesivir, simeprevir and valinomycin showed high binding energies; among the predicted acidic compounds, acetylursolic acid and hardwickiic acid gave high binding energies; while among the studied anthraquinones and glycosides compounds, ellagitannin and friedelanone showed high binding energies against 3-Chymotrypsin-like protease (3CLpro), Papain-like protease (PLpro), helicase (nsp13), RNA-dependent RNA polymerase (nsp12), 2'-O-ribose methyltransferase (nsp16) of SARS-CoV-2 and DNA-PK and CK2alpha in human. The order of affinity for CoV proteins is 5Y3E > 6NUS > 6JYT > 2XYR > 3VB6. Finally, medicinal plants with phytochemicals such as caffeine, ellagic acid, quercetin and their derivatives could possibly remediate COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Toluwase Hezekiah Fatoki
- Translational Bioinformatics Unit, Department of Biochemistry, Federal University Oye Ekiti, Oye Ekiti, Ekiti State, Nigeria
| | - Omodele Ibraheem
- Translational Bioinformatics Unit, Department of Biochemistry, Federal University Oye Ekiti, Oye Ekiti, Ekiti State, Nigeria
| | | | | | - Harriet U Ugboko
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Ota, Ogun State, Nigeria
| | | | - Oladoja A Awofisayo
- Department of Pharmaceutical and Medicinal Chemistry, University of Uyo, Uyo, Nigeria
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Niu X, Lin X, Chen X, Xu S, Huang Z, Tang Q. Long-wave Ultraviolet Ray Promotes Inflammation in Keloid-derived Fibroblasts by Activating P38-NFκB1 Signaling Pathway. J Burn Care Res 2020; 41:1231-1239. [PMID: 32433772 DOI: 10.1093/jbcr/iraa075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
One of the main mechanisms of keloid formation is the persistent chronic inflammation, which initiates the activation of keloid-derived fibroblasts (KFs) and boosts the production of extracellular matrix. Meanwhile, 95% of the ultraviolet rays that reach the earth are long-wave ultraviolet (UVA). However, the effect of UVA on keloids is currently unclear. The objective of our research is to investigate UVA's impact on keloids. Cell viability assay, migration assay, and cell cycle analysis were conducted. UVA's impacts on gene expressions were detected by real-time quantitative polymerase chain reaction, western blot analysis, enzyme-linked immunosorbent assay, and immunofluorescence. Our results indicated that UVA inhibited the proliferation and migration of KFs. In addition, after UVA irradiation, the expressions of matrix metallopeptidase 1 and matrix metallopeptidase 2 markedly increased in KFs. Moreover, the expression of α-smooth muscle actin and collagen I decreased. Furthermore, KFs with UVA irradiation secreted more interleukin-6 and interleukin-8 in the culture medium. And it was confirmed that the protein expressions of inflammation-related factors, including P38, CK2A, NFκB1, and P65, increased observably in KFs with UVA irradiation. The protein expression of IKBα, also known as NFκB inhibitor α, decreased. All these observations suggested that UVA irradiation could inhibit cellular activity and collagen production in KFs while promoting inflammation by activating P38-NFκB1 signal pathway.
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Affiliation(s)
- Xingtang Niu
- Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xunxun Lin
- Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaoqian Chen
- General Committee Office, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shuqia Xu
- Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhipeng Huang
- Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Qing Tang
- Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
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A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line. Sci Rep 2019; 9:11062. [PMID: 31363108 PMCID: PMC6667479 DOI: 10.1038/s41598-019-47343-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
The circadian clock regulates key cellular processes and its dysregulation is associated to several pathologies including cancer. Although the transcriptional regulation of gene expression by the clock machinery is well described, the role of the clock in the regulation of post-transcriptional processes, including splicing, remains poorly understood. In the present work, we investigated the putative interplay between the circadian clock and splicing in a cancer context. For this, we applied a computational pipeline to identify oscillating genes and alternatively spliced transcripts in time-course high-throughput data sets from normal cells and tissues, and cancer cell lines. We investigated the temporal phenotype of clock-controlled genes and splicing factors, and evaluated their impact in alternative splice patterns in the Hodgkin Lymphoma cell line HD-MY-Z. Our data points to a connection between clock-controlled genes and splicing factors, which correlates with temporal alternative splicing in several genes in the HD-MY-Z cell line. These include the genes DPYD, SS18, VIPR1 and IRF4, involved in metabolism, cell cycle, apoptosis and proliferation. Our results highlight a role for the clock as a temporal regulator of alternative splicing, which may impact malignancy in this cellular model.
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Erban T, Sopko B, Kadlikova K, Talacko P, Harant K. Varroa destructor parasitism has a greater effect on proteome changes than the deformed wing virus and activates TGF-β signaling pathways. Sci Rep 2019; 9:9400. [PMID: 31253851 PMCID: PMC6599063 DOI: 10.1038/s41598-019-45764-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/10/2019] [Indexed: 02/07/2023] Open
Abstract
Honeybee workers undergo metamorphosis in capped cells for approximately 13 days before adult emergence. During the same period, Varroa mites prick the defenseless host many times. We sought to identify proteome differences between emerging Varroa-parasitized and parasite-free honeybees showing the presence or absence of clinical signs of deformed wing virus (DWV) in the capped cells. A label-free proteomic analysis utilizing nanoLC coupled with an Orbitrap Fusion Tribrid mass spectrometer provided a quantitative comparison of 2316 protein hits. Redundancy analysis (RDA) showed that the combination of Varroa parasitism and DWV clinical signs caused proteome changes that occurred in the same direction as those of Varroa alone and were approximately two-fold higher. Furthermore, proteome changes associated with DWV signs alone were positioned above Varroa in the RDA. Multiple markers indicate that Varroa activates TGF-β-induced pathways to suppress wound healing and the immune response and that the collective action of stressors intensifies these effects. Furthermore, we indicate JAK/STAT hyperactivation, p53-BCL-6 feedback loop disruption, Wnt pathway activation, Wnt/Hippo crosstalk disruption, and NF-κB and JAK/STAT signaling conflict in the Varroa–honeybee–DWV interaction. These results illustrate the higher effect of Varroa than of DWV at the time of emergence. Markers for future research are provided.
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Affiliation(s)
- Tomas Erban
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia.
| | - Bruno Sopko
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia
| | - Klara Kadlikova
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia.,Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague 6-Suchdol, CZ-165 00, Czechia
| | - Pavel Talacko
- Proteomics Core Facility, Faculty of Science, Charles University, BIOCEV, Prumyslova 595, Vestec, CZ-25242, Czechia
| | - Karel Harant
- Proteomics Core Facility, Faculty of Science, Charles University, BIOCEV, Prumyslova 595, Vestec, CZ-25242, Czechia
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10
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Yogosawa S, Yoshida K. Tumor suppressive role for kinases phosphorylating p53 in DNA damage-induced apoptosis. Cancer Sci 2018; 109:3376-3382. [PMID: 30191640 PMCID: PMC6215896 DOI: 10.1111/cas.13792] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/23/2018] [Accepted: 09/02/2018] [Indexed: 12/20/2022] Open
Abstract
Tumor suppressor p53 plays an important role in cancer prevention. Under normal conditions, p53 is maintained at a low level. However, in response to various cellular stresses, p53 is stabilized and activated, which, in turn, initiates DNA repair, cell-cycle arrest, senescence and apoptosis. Post-translational modifications of p53 including phosphorylation, ubiquitination, and acetylation at multiple sites are important to regulate its activation and subsequent transcriptional gene expression. Particularly, phosphorylation of p53 plays a critical role in modulating its activation to induce apoptosis in cancer cells. In this context, previous studies show that several serine/threonine kinases regulate p53 phosphorylation and downstream gene expression. The molecular basis by which p53 and its kinases induce apoptosis for cancer prevention has been extensively studied. However, the relationship between p53 phosphorylation and its kinases and how the activity of kinases is controlled are still largely unclear; hence, they need to be investigated. In this review, we discuss various roles for p53 phosphorylation and its responsible kinases to induce apoptosis and a new therapeutic approach in a broad range of cancers.
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Affiliation(s)
- Satomi Yogosawa
- Department of Biochemistry, Jikei University School of Medicine, Tokyo, Japan
| | - Kiyotsugu Yoshida
- Department of Biochemistry, Jikei University School of Medicine, Tokyo, Japan
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11
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Lyons SP, Jenkins NP, Nasa I, Choy MS, Adamo ME, Page R, Peti W, Moorhead GB, Kettenbach AN. A Quantitative Chemical Proteomic Strategy for Profiling Phosphoprotein Phosphatases from Yeast to Humans. Mol Cell Proteomics 2018; 17:2448-2461. [PMID: 30228194 DOI: 10.1074/mcp.ra118.000822] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/21/2018] [Indexed: 11/06/2022] Open
Abstract
A "tug-of-war" between kinases and phosphatases establishes the phosphorylation states of proteins. While serine and threonine phosphorylation can be catalyzed by more than 400 protein kinases, the majority of serine and threonine dephosphorylation is carried out by seven phosphoprotein phosphatases (PPPs). The PPP family consists of protein phosphatases 1 (PP1), 2A (PP2A), 2B (PP2B), 4 (PP4), 5 (PP5), 6 (PP6), and 7 (PP7). The imbalance in numbers between serine- and threonine-directed kinases and phosphatases led to the early belief that PPPs are unspecific and that kinases are the primary determinants of protein phosphorylation. However, it is now clear that PPPs achieve specificity through association with noncatalytic subunits to form multimeric holoenzymes, which expands the number of functionally distinct signaling entities to several hundred. Although there has been great progress in deciphering signaling by kinases, much less is known about phosphatases.We have developed a chemical proteomic strategy for the systematic interrogation of endogenous PPP catalytic subunits and their interacting proteins, including regulatory and scaffolding subunits (the "PPPome"). PP1, PP2A, PP4, PP5, and PP6 were captured using an immobilized, specific but nonselective PPP inhibitor microcystin-LR (MCLR), followed by protein identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in a single analysis. Here, we combine this approach of phosphatase inhibitor bead profiling and mass spectrometry (PIB-MS) with label-free and tandem mass tag (TMT) quantification to map the PPPome in human cancer cell lines, mouse tissues, and yeast species, through which we identify cell- and tissue-type-specific PPP expression patterns and discover new PPP interacting proteins.
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Affiliation(s)
- Scott P Lyons
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Nicole P Jenkins
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA
| | - Isha Nasa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA; Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA
| | - Meng S Choy
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Mark E Adamo
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA
| | - Rebecca Page
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Greg B Moorhead
- Department of Biological Science, University of Calgary, Alberta, Canada
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA; Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA.
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12
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Canedo-Antelo M, Serrano MP, Manterola A, Ruiz A, Llavero F, Mato S, Zugaza JL, Pérez-Cerdá F, Matute C, Sánchez-Gómez MV. Inhibition of Casein Kinase 2 Protects Oligodendrocytes From Excitotoxicity by Attenuating JNK/p53 Signaling Cascade. Front Mol Neurosci 2018; 11:333. [PMID: 30271323 PMCID: PMC6146035 DOI: 10.3389/fnmol.2018.00333] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/27/2018] [Indexed: 12/12/2022] Open
Abstract
Oligodendrocytes are highly vulnerable to glutamate excitotoxicity, a central mechanism involved in tissue damage in Multiple Sclerosis (MS). Sustained activation of AMPA receptors in rat oligodendrocytes induces cytosolic calcium overload, mitochondrial depolarization, increase of reactive oxygen species, and activation of intracelular pathways resulting in apoptotic cell death. Although many signals driven by excitotoxicity have been identified, some of the key players are still under investigation. Casein kinase 2 (CK2) is a serine/threonine kinase, constitutively expressed in all eukaryotic tissues, involved in cell proliferation, malignant transformation and apoptosis. In this study, we identify CK2 as a critical regulator of oligodendrocytic death pathways and elucidate its role as a signal inductor following excitotoxic insults. We provide evidence that CK2 activity is up-regulated in AMPA-treated oligodendrocytes and CK2 inhibition significantly diminished AMPA receptor-induced oligodendroglial death. In addition, we analyzed mitogen-activated protein kinase (MAPK) signaling after excitotoxic insult. We observed that AMPA receptor activation induced a rapid increase in c-Jun N-terminal kinase (JNK) and p38 phosphorylation that was reduced after CK2 inhibition. Moreover, blocking their phosphorylation, we enhanced oligodendrocyte survival after excitotoxic insult. Finally, we observed that the tumor suppressor p53 is activated during AMPA receptor-induced cell death and, interestingly, down-regulated by JNK or CK2 inhibition. Together, these data indicate that the increase in CK2 activity induced by excitotoxic insults regulates MAPKs, triggers p53 activation and mediates subsequent oligodendroglial loss. Therefore, targeting CK2 may be a useful strategy to prevent oligodendrocyte death in MS and other diseases involving central nervous system (CNS) white matter.
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Affiliation(s)
- Manuel Canedo-Antelo
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), Leioa, Spain.,Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), Leioa, Spain
| | - Mari Paz Serrano
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), Leioa, Spain.,Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), Leioa, Spain
| | - Andrea Manterola
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), Leioa, Spain.,Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), Leioa, Spain
| | - Asier Ruiz
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), Leioa, Spain.,Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), Leioa, Spain
| | - Francisco Llavero
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Genética, Antropología Física y Fisiología Animal, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Susana Mato
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), Leioa, Spain.,Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), Leioa, Spain
| | - José Luis Zugaza
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Genética, Antropología Física y Fisiología Animal, Universidad del País Vasco (UPV/EHU), Leioa, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Fernando Pérez-Cerdá
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), Leioa, Spain.,Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), Leioa, Spain
| | - Carlos Matute
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), Leioa, Spain.,Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), Leioa, Spain
| | - María Victoria Sánchez-Gómez
- Achucarro Basque Center for Neuroscience, Leioa, Spain.,Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), Leioa, Spain.,Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), Leioa, Spain
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13
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Pozhitkov AE, Neme R, Domazet-Lošo T, Leroux BG, Soni S, Tautz D, Noble PA. Tracing the dynamics of gene transcripts after organismal death. Open Biol 2017; 7:160267. [PMID: 28123054 PMCID: PMC5303275 DOI: 10.1098/rsob.160267] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/12/2016] [Indexed: 12/13/2022] Open
Abstract
In life, genetic and epigenetic networks precisely coordinate the expression of genes-but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became significantly more abundant after death of healthy adult animals in a time series spanning up to 96 h postmortem. Ordination plots revealed non-random patterns in the profiles by time. While most of these transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h postmortem. Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regulation and cancer. The data suggest a step-wise shutdown occurs in organismal death that is manifested by the apparent increase of certain transcripts with various abundance maxima and durations.
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Affiliation(s)
- Alex E Pozhitkov
- Department of Oral Health Sciences, University of Washington, PO Box 357444, Seattle, WA 98195, USA
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen, Germany
| | - Rafik Neme
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen, Germany
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, 10002 Zagreb, Croatia
- Catholic University of Croatia, Ilica 242, Zagreb, Croatia
| | - Brian G Leroux
- Department of Oral Health Sciences, University of Washington, PO Box 357444, Seattle, WA 98195, USA
| | - Shivani Soni
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36101-0271, USA
| | - Diethard Tautz
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen, Germany
| | - Peter A Noble
- Department of Periodontics, University of Washington, PO Box 357444, Seattle, WA 98195, USA
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36101-0271, USA
- PhD Program in Microbiology, Alabama State University, Montgomery, AL 36101-0271, USA
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14
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Singh S, Colonna G, Di Bernardo G, Bergantino F, Cammarota M, Castello G, Costantini S. The gene expression profiling of hepatocellular carcinoma by a network analysis approach shows a dominance of intrinsically disordered proteins (IDPs) between hub nodes. MOLECULAR BIOSYSTEMS 2016; 11:2933-45. [PMID: 26267014 DOI: 10.1039/c5mb00434a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We have analyzed the transcriptomic data from patients with hepatocellular carcinoma (HCC) after viral HCV infection at the various stages of the disease by means of a networking analysis using the publicly available E-MTAB-950 dataset. The data was compared with those obtained in our group from HepG2 cells, a cancer cell line that lacks the viral infection. By sequential pruning of data, and also taking into account the data from cells of healthy patients as blanks, we were able to obtain a distribution of hub genes for the various stages that characterize the disease and finally, we isolated a metabolic sub-net specific to HCC alone. The general picture is that the basic organization to energetically and metabolically sustain the cells in both the normal and diseased conditions is the same, but a complex cluster of sub-networks controlled by hub genes drives the HCC progression with high metabolic flexibility and plasticity. In particular, we have extracted a sub-net of genes strictly correlated to other hub genes of the network from HepG2 cells, but specific for the HCC and mainly devoted to: (i) control at chromatin levels of cell division; (ii) control of ergastoplasmatic stress through protein degradation and misfolding; (iii) control of the immune response also through an increase of mature T-cells in the thymus. This sub-net is characterized by 26 hub genes coding for intrinsically disordered proteins with a high ability to interact with numerous molecular partners. Moreover, we have also noted that periphery molecules, that is, with one or very few interactions (e.g., cytokines or post-translational enzymes), which do not have a central role in the clusters that make up the global metabolic network, essentially have roles as information transporters. The results evidence a strong presence of intrinsically disordered proteins with key roles as hubs in the sub-networks that characterize the various stages of the disease, conferring a structural plasticity to the net nodes but an inherent functional versatility to the whole metabolic net. Thus, our present article provides a novel way of targeting the intrinsic disorder in HCC networks to dampen the cancer effects and provides new insight into the potential mechanisms of HCC. Taken together, the present findings suggest novel targets to design strategies for drug design and may support a rational intervention in the pharmacotherapy of HCC and other associated diseases.
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Affiliation(s)
- Sakshi Singh
- Dottorato in Biologia Computazionale, Dipartimento di Biochimica, Biofisica e Patologia generale, Seconda Università degli Studi di Napoli, Napoli, Italy
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15
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Desrochers GF, Sherratt AR, Blais DR, Nasheri N, Ning Z, Figeys D, Goto NK, Pezacki JP. Profiling Kinase Activity during Hepatitis C Virus Replication Using a Wortmannin Probe. ACS Infect Dis 2015; 1:443-52. [PMID: 27617927 DOI: 10.1021/acsinfecdis.5b00083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
To complete its life cycle, the hepatitis C virus (HCV) induces changes to numerous aspects of its host cell. As kinases act as regulators of many pathways utilized by HCV, they are likely enzyme targets for virally induced inhibition or activation. Herein, we used activity-based protein profiling (ABPP), which allows for the identification of active enzymes in complex protein samples and the quantification of their activity, to identify kinases that displayed differential activity in HCV-expressing cells. We utilized an ABPP probe, wortmannin-yne, based on the kinase inhibitor wortmannin, which contains a pendant alkyne group for bioconjugation using bioorthogonal chemistry. We observed changes in the activity of kinases involved in the mitogen-activated protein kinase pathway, apoptosis pathways, and cell cycle control. These results establish changes to the active kinome, as reported by wortmannin-yne, in the proteome of human hepatoma cells actively replicating HCV. The observed changes include kinase activity that affect viral entry, replication, assembly, and secretion, implying that HCV is regulating the pathways that it uses for its life cycle through modulation of the active kinome.
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Affiliation(s)
- Geneviève F. Desrochers
- Life Sciences Division, National Research Council of Canada, 100
Sussex Drive, Ottawa, Canada
| | - Allison R. Sherratt
- Life Sciences Division, National Research Council of Canada, 100
Sussex Drive, Ottawa, Canada
| | - David R. Blais
- Life Sciences Division, National Research Council of Canada, 100
Sussex Drive, Ottawa, Canada
| | - Neda Nasheri
- Life Sciences Division, National Research Council of Canada, 100
Sussex Drive, Ottawa, Canada
| | | | | | | | - John Paul Pezacki
- Life Sciences Division, National Research Council of Canada, 100
Sussex Drive, Ottawa, Canada
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16
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Bennett L, Kittas A, Liu S, Papageorgiou LG, Tsoka S. Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PLoS One 2014; 9:e112821. [PMID: 25412367 PMCID: PMC4239042 DOI: 10.1371/journal.pone.0112821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 10/15/2014] [Indexed: 12/05/2022] Open
Abstract
Community structure detection has proven to be important in revealing the underlying properties of complex networks. The standard problem, where a partition of disjoint communities is sought, has been continually adapted to offer more realistic models of interactions in these systems. Here, a two-step procedure is outlined for exploring the concept of overlapping communities. First, a hard partition is detected by employing existing methodologies. We then propose a novel mixed integer non linear programming (MINLP) model, known as OverMod, which transforms disjoint communities to overlapping. The procedure is evaluated through its application to protein-protein interaction (PPI) networks of the rat, E. coli, yeast and human organisms. Connector nodes of hard partitions exhibit topological and functional properties indicative of their suitability as candidates for multiple module membership. OverMod identifies two types of connector nodes, inter and intra-connector, each with their own particular characteristics pertaining to their topological and functional role in the organisation of the network. Inter-connector proteins are shown to be highly conserved proteins participating in pathways that control essential cellular processes, such as proliferation, differentiation and apoptosis and their differences with intra-connectors is highlighted. Many of these proteins are shown to possess multiple roles of distinct nature through their participation in different network modules, setting them apart from proteins that are simply ‘hubs’, i.e. proteins with many interaction partners but with a more specific biochemical role.
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Affiliation(s)
- Laura Bennett
- Centre for Process Systems Engineering, Department of Chemical Engineering, UCL (University College London), Torrington Place, WC1E 7JE, London, United Kingdom
| | - Aristotelis Kittas
- Department of Informatics, King's College London, Strand, WC2R 2LS, London, United Kingdom
| | - Songsong Liu
- Centre for Process Systems Engineering, Department of Chemical Engineering, UCL (University College London), Torrington Place, WC1E 7JE, London, United Kingdom
| | - Lazaros G. Papageorgiou
- Centre for Process Systems Engineering, Department of Chemical Engineering, UCL (University College London), Torrington Place, WC1E 7JE, London, United Kingdom
| | - Sophia Tsoka
- Department of Informatics, King's College London, Strand, WC2R 2LS, London, United Kingdom
- * E-mail:
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17
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Jaksch C, Thams P. A critical role for CK2 in cytokine-induced activation of NFκB in pancreatic β cell death. Endocrine 2014; 47:117-28. [PMID: 24366643 PMCID: PMC4145192 DOI: 10.1007/s12020-013-0133-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 11/22/2013] [Indexed: 12/22/2022]
Abstract
This study aimed to assess the role of constitutive protein kinase CK2 in cytokine-induced activation of NFκB in pancreatic β cell death. The CK2 inhibitors DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) (50 μM) and DMAT (2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole) (5 μM), which decreased CK2 activity by approx. 65 %, rescued INS-1E β cells and mouse islets from cytokine (IL-1β, TNF-α plus IFN-γ)-induced β cell death without affecting H2O2- or palmitate-induced β cell death. Western blot analysis revealed that while DRB or DMAT did not influence cytokine-induced IκBα degradation, they inhibited NFκB-dependent IκBα resynthesis, demonstrating that cytokine-induced NFκB activity is dependent on CK2. Both DRB and DMAT inhibited the constitutive phosphorylation of NFκB p65 at serine 529, while leaving cytokine-induced phosphorylations of NFκB p65 at serines 276 and 536 unaltered. In comparison, putative phosphorylation sites for CK2 on HDACs 1, 2, and 3 at serines 421/423, 394, and 424, respectively, which may stimulate NFκB transcriptional activity, were unchanged by cytokines and CK2 inhibitors. Whereas IL-1β and TNF-α stimulate IκBα degradation and NFκB activation, IFN-γ potentiates cytokine-induced β cell death through activation of STAT1. DRB and DMAT inhibited IFN-γ-stimulated phosphorylation of STAT1 at serine 727, while leaving IFN-γ-induced phosphorylation of STAT1 at tyrosine 701 unaffected. Inhibition of cytokine-induced β cell death by CK2 inhibitors was, however, not dependent on IFN-γ, and IFN-γ did not affect CK2-dependent IκBα turnover. In conclusion, it is suggested that cytokine-induced activation of NFκB in β cells is dependent on CK2 activity, which phosphorylates NFκB p65 at serine 529.
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Affiliation(s)
- Caroline Jaksch
- Department of Biomedical Sciences, University of Copenhagen, 3C Blegdamsvej, 2200 Copenhagen N, Denmark
| | - Peter Thams
- Department of Biomedical Sciences, University of Copenhagen, 3C Blegdamsvej, 2200 Copenhagen N, Denmark
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18
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Schumann M, Armen RS. Identification of distant drug off-targets by direct superposition of binding pocket surfaces. PLoS One 2013; 8:e83533. [PMID: 24391782 PMCID: PMC3877058 DOI: 10.1371/journal.pone.0083533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/04/2013] [Indexed: 01/23/2023] Open
Abstract
Correctly predicting off-targets for a given molecular structure, which would have the ability to bind a large range of ligands, is both particularly difficult and important if they share no significant sequence or fold similarity with the respective molecular target ("distant off-targets"). A novel approach for identification of off-targets by direct superposition of protein binding pocket surfaces is presented and applied to a set of well-studied and highly relevant drug targets, including representative kinases and nuclear hormone receptors. The entire Protein Data Bank is searched for similar binding pockets and convincing distant off-target candidates were identified that share no significant sequence or fold similarity with the respective target structure. These putative target off-target pairs are further supported by the existence of compounds that bind strongly to both with high topological similarity, and in some cases, literature examples of individual compounds that bind to both. Also, our results clearly show that it is possible for binding pockets to exhibit a striking surface similarity, while the respective off-target shares neither significant sequence nor significant fold similarity with the respective molecular target ("distant off-target").
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Affiliation(s)
- Marcel Schumann
- Department of Pharmaceutical Sciences, School of Pharmacy, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Roger S. Armen
- Department of Pharmaceutical Sciences, School of Pharmacy, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
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19
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Kim HS, Chang YG, Bae HJ, Eun JW, Shen Q, Park SJ, Shin WC, Lee EK, Park S, Ahn YM, Park WS, Lee JY, Nam SW. Oncogenic potential of CK2α and its regulatory role in EGF-induced HDAC2 expression in human liver cancer. FEBS J 2013; 281:851-61. [DOI: 10.1111/febs.12652] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hyung S. Kim
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Young G. Chang
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Hyun J. Bae
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Jung W. Eun
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Qingyu Shen
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Se J. Park
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Woo C. Shin
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Eun K. Lee
- Cancer Evolution Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
- Department of Biochemistry; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Soha Park
- Techno-Art Division; Underwood International College; Yonsei University; Seoul Korea
| | - Young M. Ahn
- Department of Kidney System; College of Oriental Medicine; Kyung Hee University; Seoul Korea
| | - Won S. Park
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Jung Y. Lee
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
| | - Suk W. Nam
- Laboratory of Oncogenomics; Department of Pathology; College of Medicine; Catholic University of Korea; Seoul Korea
- Functional RNomics Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
- Cancer Evolution Research Center; College of Medicine; Catholic University of Korea; Seoul Korea
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20
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Zhou N, Zhang J, Feng L, Lu B, Wang Z, Sun R, Wu C, Bao J. IntApop: a web service for predicting apoptotic protein interactions in humans. Biosystems 2013; 114:238-44. [PMID: 24120734 DOI: 10.1016/j.biosystems.2013.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/06/2013] [Accepted: 09/26/2013] [Indexed: 01/31/2023]
Abstract
Apoptosis, a type of cell death, is necessary for maintaining tissue homeostasis and removing malignant cells. Interrupted apoptosis process contributes to carcinogenesis, developmental defects, autoimmune diseases and neurological disorders. Due to the complexity of the process, the molecular dynamics and relative interactions of individual proteins responsible for the activation or inhibition of apoptosis should be researched systematically. In this study, we integrate known protein interactions from databases DIP, IntAct, MINT, HPRD and BioGRID by Naïve Bayes classifier. The receiver operation characteristic (ROC) curve with the area under the ROC curve (AUC) of 0.797 indicates it has a good performance in prediction. Then, we predict the global human apoptotic protein interactions network. Within it, we not only identify the already known interactions of caspases (caspase-8/-10, caspase-9, caspase-3/-6/-7) and Bcl-2 family, but also reveal that Bid can interact with casein kinases (CSK21/22/2B, KC1A, KC1E); both of B2LA1 and B2CL2 can interact with Bid, Bax and Bak; caspase-8 interacts with autophagic proteins (MLP3B, MLP3A and LRRk2). Consequently, we make an initial step to develop the web service IntApop that provides an appropriate platform for apoptosis researchers, systems biologists and translational clinician scientists to predict apoptotic protein interactions in human. In addition, the interaction network can be visualized online, making it a widely applicable systems biology tool for apoptosis and cancer researchers.
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Affiliation(s)
- Nan Zhou
- School of Life Sciences & Key Laboratory of Bio-resources, Ministry of Education, Sichuan University, Chengdu 610064, China
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Ethanol induces cell cycle arrest and triggers apoptosis via Sp1-dependent p75NTR expression in human neuroblastoma cells. Cell Biol Toxicol 2013; 29:365-80. [PMID: 24026251 DOI: 10.1007/s10565-013-9260-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 08/30/2013] [Indexed: 02/07/2023]
Abstract
Ethanol exposure has deleterious effects on the central nervous system. Although several mechanisms for ethanol-induced damage have been suggested, the precise mechanism underlying ethanol-induced neuronal cell death remains unclear. Recent studies indicate that the p75 neurotrophin receptor (p75NTR) has a critical role in the regulation of neuronal survival. This study was designed to examine the role of p75NTR in ethanol-induced apoptotic signaling in neuroblastoma cells. Ethanol caused highly increased level of p75NTR expression. The use of small interfering RNA to inhibit p75NTR expression markedly attenuated ethanol-induced cell cycle arrest and apoptosis. DNA binding activity of Sp1 was increased by ethanol, whereas inhibition of Sp1 activity by mithramycin, a Sp1 inhibitor, or short hairpin RNA suppressed ethanol-induced p75NTR expression. In addition, inhibitors of casein kinase 2 (CK2) and extracellular signal-regulated kinase (ERK) augmented ethanol-induced p75NTR expression. Our results also demonstrate that inhibition of ERK and CK2 caused a further increase in the activation of the p75NTR proximal promoter induced by ethanol. This increased activation was partially suppressed by the deletion of the Sp1 binding sites. These results suggest that Sp1-mediated p75NTR expression is regulated at least in part by ERK and CK2 pathways. The present study also showed that treatment with ethanol resulted in significant increases in the expression of p21, but not the levels of p53 and p53 target genes such as Bax, Puma, and Bcl-2. Furthermore, the inhibition of p75NTR expression or Sp1 activity suppressed ethanol-induced p21 expression, cell cycle arrest, and apoptosis. These data suggest that ethanol increases p75NTR expression, and CK2 and ERK signaling inversely regulate Sp1-mediated p75NTR expression in ethanol-treated neuroblastoma cells. Thus, our study provides more insight into the mechanisms underlying ethanol actions.
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Yan LB, Shi K, Bing ZT, Sun YL, Shen Y. Proteomic analysis of energy metabolism and signal transduction in irradiated melanoma cells. Int J Ophthalmol 2013; 6:286-94. [PMID: 23826520 DOI: 10.3980/j.issn.2222-3959.2013.03.06] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 05/06/2013] [Indexed: 02/04/2023] Open
Abstract
AIM To analyze proteomic and signal transduction alterations in irradiated melanoma cells. METHODS We combined stable isotope labeling with amino acids in cell culture (SILAC) with highly sensitive shotgun tandem mass spectrometry (MS) to create an efficient approach for protein quantification. Protein-protein interaction was used to analyze relationships among proteins. RESULTS Energy metabolism protein levels were significantly different in glycolysis and not significantly different in oxidative phosphorylation after irradiation. Conversely, tumor suppressor proteins related to cell growth and development were downregulated, and those related to cell death and cell cycle were upregulated in irradiated cells. CONCLUSION Our results indicate that irradiation induces differential expression of the 29 identified proteins closely related to cell survival, cell cycle arrest, and growth inhibition. The data may provide new insights into the pathogenesis of uveal melanoma and guide appropriate radiotherapy.
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Affiliation(s)
- Lu-Bin Yan
- Department of Surgery, the Second Hospital of Lanzhou University, Lanzhou 730030, Gansu Province, China
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23
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Alekseeva L, Rault L, Almeida S, Legembre P, Edmond V, Azevedo V, Miyoshi A, Even S, Taieb F, Arlot-Bonnemains Y, Le Loir Y, Berkova N. Staphylococcus aureus-induced G2/M phase transition delay in host epithelial cells increases bacterial infective efficiency. PLoS One 2013; 8:e63279. [PMID: 23717407 PMCID: PMC3662696 DOI: 10.1371/journal.pone.0063279] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 04/02/2013] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus aureus is a highly versatile, opportunistic pathogen and the etiological agent of a wide range of infections in humans and warm-blooded animals. The epithelial surface is its principal site of colonization and infection. In this work, we investigated the cytopathic effect of S. aureus strains from human and animal origins and their ability to affect the host cell cycle in human HeLa and bovine MAC-T epithelial cell lines. S. aureus invasion slowed down cell proliferation and induced a cytopathic effect, resulting in the enlargement of host cells. A dramatic decrease in the number of mitotic cells was observed in the infected cultures. Flow cytometry analysis revealed an S. aureus-induced delay in the G2/M phase transition in synchronous HeLa cells. This delay required the presence of live S. aureus since the addition of the heat-killed bacteria did not alter the cell cycle. The results of Western blot experiments showed that the G2/M transition delay was associated with the accumulation of inactive cyclin-dependent kinase Cdk1, a key inducer of mitosis entry, and with the accumulation of unphosphorylated histone H3, which was correlated with a reduction of the mitotic cell number. Analysis of S. aureus proliferation in asynchronous, G1- and G2-phase-enriched HeLa cells showed that the G2 phase was preferential for bacterial infective efficiency, suggesting that the G2 phase delay may be used by S. aureus for propagation within the host. Taken together, our results divulge the potential of S. aureus in the subversion of key cellular processes such as cell cycle progression, and shed light on the biological significance of S. aureus-induced host cell cycle alteration.
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Affiliation(s)
- Ludmila Alekseeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
- AGROCAMPUS OUEST, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
| | - Lucie Rault
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
- AGROCAMPUS OUEST, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
| | - Sintia Almeida
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
- AGROCAMPUS OUEST, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
- Universidade Federal de Minas Gerais, Instituto de Ciencias Biologicas, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brazil
| | - Patrick Legembre
- Institut de Recherche en Santé, Environnement et Travail, U1085, Université Rennes-1, Rennes, France
| | - Valérie Edmond
- Institut de Recherche en Santé, Environnement et Travail, U1085, Université Rennes-1, Rennes, France
| | - Vasco Azevedo
- Universidade Federal de Minas Gerais, Instituto de Ciencias Biologicas, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson Miyoshi
- Universidade Federal de Minas Gerais, Instituto de Ciencias Biologicas, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brazil
| | - Sergine Even
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
- AGROCAMPUS OUEST, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
| | - Frédéric Taieb
- Institut National de la Recherche Agronomique, USC U1043, Institut National de la Santé et de la Recherche Médicale, Toulouse, France
| | - Yannick Arlot-Bonnemains
- CNRS, Unité Mixte de Recherche 6290, Biologie, Santé, Innovation technologique, Université Rennes-1, Rennes, France
| | - Yves Le Loir
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
- AGROCAMPUS OUEST, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
| | - Nadia Berkova
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
- AGROCAMPUS OUEST, Unité Mixte de Recherche 1253, Science et Technologie du Lait et de l'Œuf, Rennes, France
- * E-mail:
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Solier S, Zhang YW, Ballestrero A, Pommier Y, Zoppoli G. DNA damage response pathways and cell cycle checkpoints in colorectal cancer: current concepts and future perspectives for targeted treatment. Curr Cancer Drug Targets 2012; 12:356-71. [PMID: 22385513 DOI: 10.2174/156800912800190901] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 07/05/2011] [Accepted: 12/22/2011] [Indexed: 01/28/2023]
Abstract
Although several drugs have been designed in the last few years to target specific key pathways and functions in colorectal cancer (CRC), the backbone of CRC treatment is still made up of compounds which rely on DNA damage to accomplish their role. DNA damage response (DDR) and checkpoint pathways are intertwined signaling networks that arrest cell cycle, recognize and repair genetic mistakes which arise during DNA replication and transcription, as well as through the exposure to chemical and physical agents that interact with nucleic acids. The good but highly variable activity of DNA damaging agents in the treatment of CRC suggests that intrinsic alterations in DDR pathways and cell cycle checkpoints may contribute differentially to the way cancer cells react to DNA damage. In the present review, our aim is to depict the recent advances in understanding the molecular basis of the activity of DNA damaging agents used for the treatment of CRC. We focus on the known and potential drug targets that are part of these complex and intertwined pathways. We describe the potential role of the checkpoints in CRC, and how their pharmacological manipulation could lead to chemopotentiation or synergism with currently used drugs. Novel therapeutic agents playing a role in DDR and checkpoint inhibition are assessed. We discuss the possible rationale for combining PARP inhibition with DNA damaging agents, and we address the link between DDR and EGFR pathways in CRC.
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Affiliation(s)
- S Solier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda (MD), USA
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25
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Identifying protein phosphorylation sites with kinase substrate specificity on human viruses. PLoS One 2012; 7:e40694. [PMID: 22844408 PMCID: PMC3402495 DOI: 10.1371/journal.pone.0040694] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/12/2012] [Indexed: 11/23/2022] Open
Abstract
Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM – a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD) is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific phosphorylation site prediction tools. In the independent testing, the high sensitivity and specificity of the proposed method demonstrate the predictive effectiveness of the identified substrate motifs and the importance of investigating potential kinases for viral protein phosphorylation sites.
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Lee WH, Lee HH, Vo MT, Kim HJ, Ko MS, Im YC, Min YJ, Lee BJ, Cho WJ, Park JW. Casein kinase 2 regulates the mRNA-destabilizing activity of tristetraprolin. J Biol Chem 2011; 286:21577-87. [PMID: 21507959 DOI: 10.1074/jbc.m110.201137] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Tristetraprolin (TTP) is an AU-rich element-binding protein that regulates mRNA stability. We previously showed that TTP acts as a negative regulator of VEGF gene expression in colon cancer cells. The p38 MAPK pathway is known to suppress the TTP activity. However, until now the signaling pathway to enhance TTP function is not well known. Here, we show that casein kinase 2 (CK2) enhances the TTP function in the regulation of the VEGF expression in colon cancer cells. CK2 increased TTP protein levels and enhanced VEGF mRNA decaying activity of TTP. TTP was not a direct target of CK2. Instead, CK2 increased the phosphorylation of MKP-1, which led to a decrease in the phosphorylation of p38 MAPK. Inhibition of MKP-1 by siRNA attenuated the increase in TTP function and the decrease of p38 phosphorylation induced by CK2α overexpression. TGF-β1 increased the expressions of CK2 and TTP and the TTP function. The siRNA against CK2α or TTP reversed TGF-β1-induced increases in the expression of CK2 and TTP and the TTP function. Our data suggest that CK2 enhances the protein level and activity of TTP via the modulation of the MKP-1-p38 MAPK signaling pathway and that TGF-β1 enhances the activity of CK2.
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Affiliation(s)
- Won Hyeok Lee
- Department of Biological Sciences, University of Ulsan, Ulsan 680-749, Korea
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27
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Shimada M, Yamamoto A, Murakami-Tonami Y, Nakanishi M, Yoshida T, Aiba H, Murakami H. Casein kinase II is required for the spindle assembly checkpoint by regulating Mad2p in fission yeast. Biochem Biophys Res Commun 2009; 388:529-32. [PMID: 19666000 DOI: 10.1016/j.bbrc.2009.08.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 08/05/2009] [Indexed: 10/20/2022]
Abstract
The spindle checkpoint is a surveillance mechanism that ensures the fidelity of chromosome segregation in mitosis. Here we show that fission yeast casein kinase II (CK2) is required for this checkpoint function. In the CK2 mutants mitosis occurs in the presence of a spindle defect, and the spindle checkpoint protein Mad2p fails to localize to unattached kinetochores. The CK2 mutants are sensitive to the microtubule depolymerising drug thiabendazole, which is counteracted by ectopic expression of mad2+. The level of Mad2p is low in the CK2 mutants. These results suggest that CK2 has a role in the spindle checkpoint by regulating Mad2p.
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Affiliation(s)
- Midori Shimada
- Department of Biochemistry and Cell Biology, Graduate School of Medicine, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
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28
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Hung MS, Xu Z, Lin YC, Mao JH, Yang CT, Chang PJ, Jablons DM, You L. Identification of hematein as a novel inhibitor of protein kinase CK2 from a natural product library. BMC Cancer 2009; 9:135. [PMID: 19419583 PMCID: PMC2696466 DOI: 10.1186/1471-2407-9-135] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 05/06/2009] [Indexed: 11/10/2022] Open
Abstract
Background Casein kinase 2 (CK2) is dysregulated in various human cancers and is a promising target for cancer therapy. To date, there is no small molecular CK2 inhibitor in clinical trial yet. With the aim to identify novel CK2 inhibitors, we screened a natural product library. Methods We adopted cell-based proliferation and CK2 kinase assays to screen CK2 inhibitors from a natural compound library. Dose-dependent response of CK2 inhibitors in vitro was determined by a radioisotope kinase assay. Western blot analysis was used to evaluate down stream Akt phosphorylation and apoptosis. Apoptosis was also evaluated by annexin-V/propidium iodide (PI) labeling method using flow cytometry. Inhibition effects of CK2 inhibitors on the growth of cancer and normal cells were evaluated by cell proliferation and viability assays. Results Hematein was identified as a novel CK2 inhibitor that is highly selective among a panel of kinases. It appears to be an ATP non-competitive and partially reversible CK2 inhibitor with an IC50 value of 0.55 μM. In addition, hematein inhibited cancer cell growth partially through down-regulation of Akt phosphorylation and induced apoptosis in these cells. Furthermore, hematein exerted stronger inhibition effects on the growth of cancer cells than in normal cells. Conclusion In this study, we showed that hematein is a novel selective and cell permeable small molecule CK2 inhibitor. Hematein showed stronger growth inhibition effects to cancer cells when compared to normal cells. This compound may represent a promising class of CK2 inhibitors.
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Affiliation(s)
- Ming-Szu Hung
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of California, San Francisco, CA 94115, USA.
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Evidence for regulation of mitotic progression through temporal phosphorylation and dephosphorylation of CK2alpha. Mol Cell Biol 2009; 29:2068-81. [PMID: 19188443 DOI: 10.1128/mcb.01563-08] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proper mitotic progression is crucial for maintenance of genomic integrity in proliferating cells and is regulated through an intricate series of events, including protein phosphorylation governed by a complex network of protein kinases. One kinase family implicated in the regulation of mitotic progression is protein kinase CK2, a small family of enzymes that is overexpressed in cancer and induces transformation in mice and cultured fibroblasts. CK2alpha, one isoform of the catalytic subunits of CK2, is maximally phosphorylated at four sites in nocodazole-treated cells. To investigate the effects of CK2alpha phosphorylation on mitotic progression, we generated phosphospecific antibodies against its mitotic phosphorylation sites. In U2OS cells released from S-phase arrest, these antibodies reveal that CK2alpha is most highly phosphorylated in prophase and metaphase. Phosphorylation gradually decreases during anaphase and becomes undetectable during telophase and cytokinesis. Stable expression of phosphomimetic CK2alpha (CK2alpha-4D, CK2alpha-4E) results in aberrant centrosome amplification and chromosomal segregation defects and loss of mitotic cells through mitotic catastrophe. Conversely, cells expressing nonphosphorylatable CK2alpha (CK2alpha-4A) show a decreased ability to arrest in mitosis following nocodazole treatment, suggesting involvement in the spindle assembly checkpoint. Collectively, these studies indicate that reversible phosphorylation of CK2alpha requires precise regulation to allow proper mitotic progression.
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30
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Sun L, Zhang G, Li Z, Song T, Huang C, Si L. In GFP with high risk HPV-18E6 fusion protein expressed 293T and MCF-7 cells, the endogenous wild-type p53 could be transiently phosphorylated at multiple sites. J Exp Clin Cancer Res 2008; 27:35. [PMID: 18778462 PMCID: PMC2546361 DOI: 10.1186/1756-9966-27-35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Accepted: 09/08/2008] [Indexed: 11/13/2022] Open
Abstract
Background Infected cells recognize viral replication as a DNA damage stress and elicit the host surveillance mechanism to anti-virus infection. Modulation of the activity of tumor suppressor p53 is a key event in the replication of many viruses. They could manipulate p53 function through phosphorylation modification for their own purpose. But there is rarely research about p53 phosphorylation status in the context of HPV-E6. Therefore, we investigated whether p53 could be phosphorylated by HPV-E6. Methods We used a mammalian green fluorescence protein (GFP) expression system to express HPV-18E6 with GFP fusion proteins (GFP-18E6) in wild-type (wt) p53 cell lines, such as 293T and MCF-7 cells to trace the traffic and subcellular location of E6 protein. By immunofluorescence technique and immunoblotting, we determined the positive phosphorylated sites of p53 and observed the distribution of phosphorylated p53 in the context of GFP-18E6. Results GFP-18E6 was predominantly located in nuclei of wt p53 cell lines, and it could induce transient phosphorylation of p53 at multiple sites, such as Ser15, Ser20, and Ser392. All the three sites of phosphorylated p53s were localized in nuclei together with GFP-18E6. Conclusion In GFP with high risk HPV-18E6 fusion protein expressed 293T and MCF-7 cells, the endogenous wt p53 could be transiently phosphorylated at multiple sites.
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Affiliation(s)
- Lina Sun
- Key Laboratory of Environment and Genes Related to Diseases of the Education Ministry, School of Medicine, Xi an Jiaotong University, Xi an, PR China.
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Abstract
Casein kinase 2 (CK2) is a highly conserved and ubiquitous eukaryotic Ser/Thr protein kinase. Genetic, biochemical, and cell biological studies have indicated the involvement of this enzyme in the control of cell proliferation and in signal transduction. The regulation of CK2 is not well defined, and it has been considered a constitutively non-regulated protein kinase. However, we show that CK2 activation occurred during the progression of cell cycle in response to FBS stimuli of G0 arrested cells. Importantly, we show that as the downstream target for CK2, the phosphorylation of eukaryotic translation-initiation factor eIF5 by CK2 may play a critical role in cell cycle progression. We find that eIF5 is associated with CK2 when the kinase activity is at the highest level in vivo, and is phosphorylated at Ser389 and Ser390 by CK2. Expression of eIF5 mutants that lack those phosphorylation sites reveals that these mutants have a dominant-negative effect on phosphorylation of endogenous eIF5, as well as a significant reduction in the formation of the mature complex, in the growth rate, and the expression of cell cycle-regulated proteins. Also, a pool of CK2 translocates into the nuclear fraction following its activation during the progression of the cell cycle. Consistent with these findings, we report that CK2 may be involved in the regulation of cell cycle progression through the phosphorylation of a key molecule for translation initiation and of nuclear substrates upon activation of CK2 by itself.
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32
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A novel benzotriazole derivative inhibits proliferation of human hepatocarcinoma cells by increasing oxidative stress concomitant mitochondrial damage. Eur J Pharmacol 2008; 584:144-52. [DOI: 10.1016/j.ejphar.2008.01.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 12/21/2007] [Accepted: 01/22/2008] [Indexed: 11/21/2022]
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Seeber S, Issinger OG, Holm T, Kristensen LP, Guerra B. Validation of protein kinase CK2 as oncological target. Apoptosis 2007; 10:875-85. [PMID: 16133877 DOI: 10.1007/s10495-005-0380-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Protein kinase CK2 is a highly conserved enzyme composed of two catalytic subunits alpha and/or alpha' and two regulatory subunits beta whose activity is elevated in diverse tumour types as well as in highly proliferating tissues. Several results suggest that the overexpression of either CK2 catalytic subunits or the CK2 holoenzyme contributes to cellular transformation. In a similar vein, experiments performed compromising the intracellular expression of CK2 has led to somehow contradictory results with respect to the ability of this enzyme to control survival and apoptosis. To better elucidate the role of CK2 in programmed cell death, we have depleted cells of CK2 catalytic subunits by the application of antisense oligodeoxynucleotides and siRNAs techniques, respectively. Our results indicate that protein kinase CK2 is characterized by an extremely high stability that might be due to its association with other intracellular proteins, enhanced half-life or lower vulnerability towards proteolytic degradation. In addition, we show that despite the effectiveness of the methods applied in lowering CK2 kinase activity in all cells investigated, CK2 might not by itself be sufficient to trigger enhanced drug-induced apoptosis in cells.
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Affiliation(s)
- S Seeber
- Roche Diagnostics GmbH, Pharma Research Penzberg, Nonnenwald 2, D-82377 Penzberg, Germany
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Parhar K, Morse J, Salh B. The role of protein kinase CK2 in intestinal epithelial cell inflammatory signaling. Int J Colorectal Dis 2007; 22:601-9. [PMID: 17009010 DOI: 10.1007/s00384-006-0193-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/17/2006] [Indexed: 02/04/2023]
Abstract
BACKGROUND The transcription factor NF-kappaB is believed to play a key pathophysiological role in chronic intestinal inflammation. Further characterization of its mechanism of regulation, predominantly through cell signaling pathways, may provide clues as to the means of its intervention. One such potential signaling candidate is the protein kinase CK2. Despite its known ability to influence NF-kappaB activation, it has received no attention in this particular setting. AIM To characterize the aspects of its activation in response to IL-1beta in the colonic cell lines Caco2 and HCT116. MATERIALS AND METHODS A biochemical analysis of kinase activation was performed using phospho-specific antibodies as well as immune complex kinase assays; transcription factor activity was measured by transient transfection and luciferase-based NF-kappaB reporter assays; pro-inflammatory molecule expression was determined using RT-PCR. RESULTS In this report, we show an enhanced activation of CK2 bound to IKKgamma or the p65 subunit of the NF-kappaB in response to IL-1beta stimulation of intestinal epithelial cells. Using two established NF-kappaB reporters, we demonstrate that CK2 is involved in NF-kappaB regulation through the p65 serine 529 site. Using co-immunoprecipitation studies, we also show that p65 is bound to CK2 predominantly in the nucleus. From a functional perspective, two CK2 specific inhibitors were then shown to attenuate IL-8 reporter activation. Finally, the expression of a series of pro-inflammatory molecules including IL-8, GRO-alpha, MCP-1, TNFalpha and iNOS were variably affected in response to CK2 inhibition. CONCLUSION CK2 plays an active role in NF-kappaB signaling in intestinal epithelial cell lines and may represent a possible target for intervention.
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Affiliation(s)
- Kuljit Parhar
- The Jack Bell Research Center, 2660 Oak Street, V6H 3Z6, Vancouver, British Columbia, Canada
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Abstract
How cells behave as they divide in the presence of chromosome (DNA) damage is only just beginning to be explored. It appears to depend on the cell type and organism, the stage of development, how extensive the damage is and when it occurs. The existing data support the conclusion that vertebrate somatic cells lack a conventional DNA damage checkpoint during mitosis, and that when damaged DNA does prolong mitosis it is mediated by the spindle assembly checkpoint. As a rule, in the presence of DNA damage cells ultimately undergo an aberrant mitosis and enter the ensuing G1. They then either die, via apoptosis or mitotic catastrophe, or survive with an altered genome. To avoid these outcomes, cells with DNA damage are normally prevented from entering mitosis by a number of G2 checkpoint control pathways.
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Affiliation(s)
- Ciaran Morrison
- Department of Biochemistry/NCBES, National University of Ireland-Galway, University Road, Galway, Ireland.
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36
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Grasselli E, Tomati V, Bernasconi MV, Nicolini C, Vergani L. C-terminal region of protein kinase CK2 alpha: How the structure can affect function and stability of the catalytic subunit. J Cell Biochem 2005; 92:270-84. [PMID: 15108354 DOI: 10.1002/jcb.20049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A novel mutant of the catalytic alpha subunit of human protein kinase CK2 (CK2 alpha) was designed in an attempt to clarify the role of the carboxylic-terminal segment characteristic of vertebrates, excluding fish. Starting from the sequence alignments, we constructed a phylogenetic tree of the primary structure of CK2 alpha. On this basis, we substituted two distal prolines with alanines (PA 382-384). Theoretical calculations and spectropolarimetry measurements, performed both on native and mutant subunits, indicate an increased content of alpha-helix after this double amino acidic substitution. In order to clarify the structure/function relationship of the C-terminal region, we verified if the structural change affects the catalytic activity of CK2 alpha. The mutant exhibits slightly increased phosphorylation efficiency, but reduced ability to transfer phosphate in comparison with the native subunit. At last, we compared the thermal stability of the mutant with respect to the native subunit and we tested the proteolytic degradability. The observation that the PA 382-384 mutant exhibits an increased thermal and proteolytic stability suggests that this mutant could be employed to solve the three-dimensional (3D) structure of human CK2 alpha and to overcome difficulties in crystallizing the native form.
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Affiliation(s)
- Elena Grasselli
- Department of Biophysical Sciences and Technologies M&O, School of Medicine, University of Genova, Genoa, Italy
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37
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Hilgard P, Czaja MJ, Gerken G, Stockert RJ. Proapoptotic function of protein kinase CK2alpha" is mediated by a JNK signaling cascade. Am J Physiol Gastrointest Liver Physiol 2004; 287:G192-201. [PMID: 14962846 DOI: 10.1152/ajpgi.00507.2003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Protein kinase CK2 (formerly casein kinase II) is a tetrameric enzyme constitutively expressed in all eurakyotic tissues that plays a significant role in the regulation of cell proliferation, malignant transformation, and apoptosis. The catalytic alpha-subunit of the enzyme is known to exist in three isoforms CK2alpha, CK2alpha' and CK2alpha". CK2alpha" is highly expressed in liver compared with other tissues and is required for the normal trafficking of several hepatocellular membrane proteins. Initial studies of dengue virus infection indicated that the CK2alpha"-deficient membrane trafficking mutant cell line (Trf1) was resistant to virus-induced cell death compared with the parental human hepatoma (HuH)-7 hepatoma line. Expression of recombinant CK2alpha" in Trf1 was capable of reverting this resistant phenotype. This study was extended to TNF-alpha in addition to other stimuli of cell death in an attempt to uncover common death pathways that might be modulated by CK2alpha". Evaluation of different pathways involved in death signaling suggest that the regulation of a critical proapoptotic step in HuH-7 cells by CK2alpha" is mediated by a JNK signaling cascade.
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Affiliation(s)
- Philip Hilgard
- Department for Gastroenterology and Hepatology, University-Hospital Essen, 45133 Essen, Germany
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38
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Lim ACB, Tiu SY, Li Q, Qi RZ. Direct Regulation of Microtubule Dynamics by Protein Kinase CK2. J Biol Chem 2004; 279:4433-9. [PMID: 14634006 DOI: 10.1074/jbc.m310563200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microtubule dynamics is essential for many vital cellular processes such as morphogenesis and motility. Protein kinase CK2 is a ubiquitous protein kinase that is involved in diverse cellular functions. CK2 holoenzyme is composed of two catalytic alpha or alpha' subunits and two regulatory beta subunits. We show that the alpha subunit of CK2 binds directly to both microtubules and tubulin heterodimers. CK2 holoenzyme but neither of its individual subunits exhibited a potent effect of inducing microtubule assembly and bundling. Moreover, the polymerized microtubules were strongly stabilized by CK2 against cold-induced depolymerization. Interestingly, the kinase activity of CK2 is not required for its microtubule-assembling and stabilizing function because a kinase-inactive mutant of CK2 displayed the same microtubule-assembling activity as the wild-type protein. Knockdown of CK2alpha/alpha' in cultured cells by RNA interference dramatically destabilized their microtubule networks, and the destabilized microtubules were readily destructed by colchicine at a very low concentration. Further, over-expression of chicken CK2alpha or its kinaseinactive mutant in the endogenous CK2alpha/alpha'-depleted cells fully restored the microtubule resistance to the low dose of colchicine. Taken together, CK2 is a microtubule-associated protein that confers microtubule stability in a phosphorylation-independent manner.
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Affiliation(s)
- Anthony C B Lim
- Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609
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39
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Le Masson I, Yu DY, Jensen K, Chevalier A, Courbeyrette R, Boulard Y, Smith MM, Mann C. Yaf9, a novel NuA4 histone acetyltransferase subunit, is required for the cellular response to spindle stress in yeast. Mol Cell Biol 2003; 23:6086-102. [PMID: 12917332 PMCID: PMC180919 DOI: 10.1128/mcb.23.17.6086-6102.2003] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yaf9 is one of three proteins in budding yeast containing a YEATS domain. We show that Yaf9 is part of a large complex and that it coprecipitates with three known subunits of the NuA4 histone acetyltransferase. Although Esa1, the catalytic subunit of NuA4, is essential for viability, we found that yaf9 Delta mutants are viable but hypersensitive to microtubule depolymerizing agents and synthetically lethal with two different mutants of the mitotic apparatus. Microtubules depolymerized more readily in the yaf9Delta mutant compared to the wild type in the presence of nocodazole, and recovery of microtubule polymerization and cell division from limiting concentrations of nocodazole was inhibited. Two other NuA4 mutants (esa1-1851 and yng2 Delta) and nonacetylatable histone H4 mutants were also sensitive to benomyl. Furthermore, wild-type budding yeast were more resistant to benomyl when grown in the presence of trichostatin A, a histone deacetylase inhibitor. These results strongly suggest that acetylation of histone H4 by NuA4 is required for the cellular resistance to spindle stress.
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Affiliation(s)
- Ivan Le Masson
- Service de Biochimie et de Génétique Moléculaire, CEA/Saclay, 91191 Gif-sur-Yvette, France
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40
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Heinloth AN, Shackelford RE, Innes CL, Bennett L, Li L, Amin RP, Sieber SO, Flores KG, Bushel PR, Paules RS. Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation. Mol Carcinog 2003; 37:65-82. [PMID: 12766906 DOI: 10.1002/mc.10122] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The human genome is exposed to many different kinds of DNA-damaging agents. While most damage is detected and repaired through complex damage recognition and repair machineries, some damage has the potential to escape these mechanisms. Unrepaired DNA damage can give rise to alterations and mutations in the genome in an individual cell, which can result in malignant transformation, especially when critical genes are deregulated. In this study, we investigated gene expression changes in response to oxidative stress, gamma (gamma) radiation, and ultraviolet (UV) radiation and their potential implications in cancer development. Doses were selected for each of the three treatments, based on their ability to cause a similar G(1) checkpoint induction and slow down in early S-phase progression, as reflected by a comparable reduction in cyclin E-associated kinase activity of at least 75% in logarithmically growing human dermal diploid fibroblasts. To investigate gene expression changes, logarithmically growing dermal diploid fibroblasts were exposed to either gamma radiation (5 Gy), oxidative stress (75 microM of tert-butyl hydroperoxide (t-butyl-OOH)), or UV radiation (UVC) (7.5 J/m(2)) and RNA was harvested 6 h after treatment. Gene expression was analyzed using the NIEHS Human ToxChip 2.0 with approximately 1901 cDNA clones representing known genes and expressed sequence tags (ESTs). We were able to identify common and distinct responses in dermal diploid fibroblasts to the three different stimuli used. Within our analysis, gene expression profiles in response to gamma radiation and oxidative stress appeared to be more similar than profiles expressed after UV radiation. Interestingly, equivalent cyclin E-associated kinase activity reduction with all the three treatments was associated with greater transcriptional changes after UV radiation than after gamma radiation and oxidative stress. While samples treated with UV radiation displayed modulations of their mitogen activated protein kinase (MAPK) pathway, gamma radiation had its major influence on cell-cycle progression in S-phase and mitosis. In addition, cell cultures from different individuals displayed significant differences in their gene expression responses to DNA damage.
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Affiliation(s)
- Alexandra N Heinloth
- Growth Control and Cancer Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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41
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Litchfield DW. Protein kinase CK2: structure, regulation and role in cellular decisions of life and death. Biochem J 2003; 369:1-15. [PMID: 12396231 PMCID: PMC1223072 DOI: 10.1042/bj20021469] [Citation(s) in RCA: 967] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2002] [Revised: 10/21/2002] [Accepted: 10/23/2002] [Indexed: 01/07/2023]
Abstract
Protein kinase CK2 ('casein kinase II') has traditionally been classified as a messenger-independent protein serine/threonine kinase that is typically found in tetrameric complexes consisting of two catalytic (alpha and/or alpha') subunits and two regulatory beta subunits. Accumulated biochemical and genetic evidence indicates that CK2 has a vast array of candidate physiological targets and participates in a complex series of cellular functions, including the maintenance of cell viability. This review summarizes current knowledge of the structural and enzymic features of CK2, and discusses advances that challenge traditional views of this enzyme. For example, the recent demonstrations that individual CK2 subunits exist outside tetrameric complexes and that CK2 displays dual-specificity kinase activity raises new prospects for the precise elucidation of its regulation and cellular functions. This review also discusses a number of the mechanisms that contribute to the regulation of CK2 in cells, and will highlight emerging insights into the role of CK2 in cellular decisions of life and death. In this latter respect, recent evidence suggests that CK2 can exert an anti-apoptotic role by protecting regulatory proteins from caspase-mediated degradation. The mechanistic basis of the observation that CK2 is essential for viability may reside in part in this ability to protect cellular proteins from caspase action. Furthermore, this anti-apoptotic function of CK2 may contribute to its ability to participate in transformation and tumorigenesis.
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Affiliation(s)
- David W Litchfield
- Department of Biochemistry, Siebens-Drake Research Institute, University of Western Ontario, London, Ontario, Canada N6A 5C1.
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42
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Zhang H, Shi X, Zhang QJ, Hampong M, Paddon H, Wahyuningsih D, Pelech S. Nocodazole-induced p53-dependent c-Jun N-terminal kinase activation reduces apoptosis in human colon carcinoma HCT116 cells. J Biol Chem 2002; 277:43648-58. [PMID: 12221076 DOI: 10.1074/jbc.m203214200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microtubule-interfering agents are widely used in cancer chemotherapy, and prognostic results vary significantly from tumor to tumor, depending on the p53 status. In preliminary experiments, we compared the expression and phosphorylation profiles of more than 100 protein kinases and protein phosphatases in human colorectal carcinoma cell line HCT116 between p53+/+ and p53-/- cells in response to short term nocodazole treatment through application of Kinetworks immunoblotting screens. Among the proteins tracked, the regulation of the phosphorylation of c-Jun N-terminal kinase (JNK)1/2 at Thr-183/Tyr-185 was the major difference between p53+/+ and p53-/- cells. With the loss of the p53 gene, the levels of phosphorylation of Ser-63 of c-Jun and Thr-183/Tyr-185 of JNK1/2 in p53-/- cells did not increase as markedly as in p53+/+ cells in response to a 1-h treatment with nocodazole or other microtubule-disrupting drugs such as vinblastine and colchicine. Similar observations were also made in MCF-7 and A549 tumor cells, which were rendered p53-deficient by E6 oncoprotein expression. However, arsenate-induced JNK activation in p53-/- cells was preserved. Inhibition of p53 expression by its antisense oligonucleotide also attenuated nocodazole-induced JNK activation in p53+/+ cells. Surprisingly, cotransfection of p53+/+ cells with dominant negative mutants of JNK isoforms and treatment of p53+/+ cells with the JNK inhibitor SP600125 actually further enhanced apoptosis in p53+/+ cells by up to 2-fold in response to nocodazole. These findings indicate that inhibition of p53-mediated JNK1/2 activity in certain tumor cells could serve to enhance the apoptosis-inducing actions of cancer chemotherapeutic agents that disrupt mitotic spindle function.
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Affiliation(s)
- Hong Zhang
- Department of Medicine and the Biomedical Research Centre, University of British Columbia, Vancouver, Canada
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43
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Li PF, Li J, Müller EC, Otto A, Dietz R, von Harsdorf R. Phosphorylation by protein kinase CK2: a signaling switch for the caspase-inhibiting protein ARC. Mol Cell 2002; 10:247-58. [PMID: 12191471 DOI: 10.1016/s1097-2765(02)00600-7] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Caspases play a central role in apoptosis, but their activity is under the control of caspase-inhibiting proteins. A characteristic of caspase-inhibiting proteins is direct caspase binding. It is yet unknown how the localization of caspase-inhibiting proteins is regulated and whether there are upstream signals controlling their function. Here we report that the function of ARC is regulated by protein kinase CK2. ARC at threonine 149 is phosphorylated by CK2. This phosphorylation targets ARC to mitochondria. ARC is able to bind to caspase-8 only when it is localized to mitochondria but not to the cytoplasm. Our results reveal a molecular mechanism by which a caspase-inhibiting protein requires phosphorylation in order to prevent apoptosis.
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Affiliation(s)
- Pei-Feng Li
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
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44
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Messenger MM, Saulnier RB, Gilchrist AD, Diamond P, Gorbsky GJ, Litchfield DW. Interactions between protein kinase CK2 and Pin1. Evidence for phosphorylation-dependent interactions. J Biol Chem 2002; 277:23054-64. [PMID: 11940573 DOI: 10.1074/jbc.m200111200] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The peptidyl-prolyl isomerase Pin1 interacts in a phosphorylation-dependent manner with several proteins involved in cell cycle events. In this study, we demonstrate that Pin1 interacts with protein kinase CK2, an enzyme that generally exists in tetrameric complexes composed of two catalytic CK2 alpha and/or CK2 alpha' subunits together with two regulatory CK2 beta subunits. Our results indicate that Pin1 can interact with CK2 complexes that contain CK2 alpha. Furthermore, Pin1 can interact directly with the C-terminal domain of CK2 alpha that contains residues that are phosphorylated in vitro by p34(Cdc2) and in mitotic cells. Substitution of the phosphorylation sites of CK2 alpha with alanines resulted in decreased interactions between Pin1 and CK2. The other catalytic isoform of CK2, designated CK2 alpha', is not phosphorylated in mitotic cells and does not interact with Pin1, but a chimeric protein consisting of CK2 alpha' with the C terminus of CK2 alpha was phosphorylated in mitotic cells and interacts with Pin1, further implicating the phosphorylation sites in the interaction. In vitro, Pin1 inhibits the phosphorylation of Thr-1342 on human topoisomerase II alpha by CK2. Topoisomerase II alpha also interacts with Pin1 suggesting that the effect of Pin1 on the phosphorylation of Thr-1342 could result from its interactions with CK2 and/or topoisomerase II alpha. As compared with wild-type Pin1, isomerase-deficient and WW domain-deficient mutants of Pin1 are impaired in their ability to interact with CK2 and to inhibit the CK2-catalyzed phosphorylation of topoisomerase II alpha. Collectively, these results indicate that Pin1 and CK2 alpha interact and suggest a possible role for Pin1 in the regulation of topoisomerase II alpha. Furthermore, these results provide new insights into the functional role of the mitotic phosphorylation of CK2 and provide a new mechanism for selectively regulating the ability of CK2 to phosphorylate one of its mitotic targets.
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Affiliation(s)
- Moira M Messenger
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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45
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Zhang C, Vilk G, Canton DA, Litchfield DW. Phosphorylation regulates the stability of the regulatory CK2beta subunit. Oncogene 2002; 21:3754-64. [PMID: 12032843 DOI: 10.1038/sj.onc.1205467] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2001] [Revised: 03/07/2002] [Accepted: 03/11/2002] [Indexed: 11/09/2022]
Abstract
Protein kinase CK2 is a protein serine/threonine kinase that exhibits elevated expression in a number of cancers and displays oncogenic activity in mice. The regulatory CK2beta subunit has a central role in assembly of functional tetrameric CK2 complexes where it participates in modulation of catalytic activity and substrate specificity. Since overexpression of CK2beta results in elevated levels of CK2 activity, we investigated the molecular mechanisms that control its degradation since perturbations in these pathways could contribute to elevated CK2 in cancer. In this study, we demonstrate that CK2beta is degraded by a proteasome-dependent pathway and that it is ubiquitinated. We have also investigated the role of phosphorylation and a putative destruction box in regulating its stability in cells. Importantly, replacement of three serine residues within the autophosphorylation site of CK2beta with glutamic acid residues resulted in a significant decrease in its degradation indicating that autophosphorylation is involved in regulating its stability. Notably, although the autophosphorylation site of CK2beta is remarkably conserved between species, this is the first functional role ascribed to this site. Furthermore, based on these results, we speculate that alterations in the phosphorylation or dephosphorylation of the regulatory CK2beta subunit could underlie the elevated expression of CK2 that is observed in cancer cells.
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Affiliation(s)
- Cunjie Zhang
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada N6A 5C1
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46
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Ruzzene M, Penzo D, Pinna LA. Protein kinase CK2 inhibitor 4,5,6,7-tetrabromobenzotriazole (TBB) induces apoptosis and caspase-dependent degradation of haematopoietic lineage cell-specific protein 1 (HS1) in Jurkat cells. Biochem J 2002; 364:41-7. [PMID: 11988074 PMCID: PMC1222543 DOI: 10.1042/bj3640041] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Incubation of Jurkat cells with 4,5,6,7-tetrabromobenzotriazole (TBB), a specific inhibitor of protein kinase CK2, induces dose-and time-dependent apoptosis as judged by several criteria. TBB-promoted apoptosis is preceded by inhibition of Ser/Thr phosphorylation of haematopoietic lineage cell-specific protein 1 (HS1) and is accompanied by caspase-dependent fragmentation of the same protein. Both effects are also observable if apoptosis is promoted by anti-Fas antibodies and by etoposide. Moreover, in vitro experiments show that HS1, once phosphorylated by CK2, becomes refractory to cleavage by caspase-3. These findings, in conjunction with similar data in the literature concerning two other CK2 protein substrates, Bid and Max, suggest that CK2 may play a general anti-apoptotic role through the generation of phosphorylated sites conferring resistance to caspase cleavage.
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Affiliation(s)
- Maria Ruzzene
- Dipartimento di Chimica Biologica, Università di Padova, Viale G. Colombo, 3-35121 Padova, Italy
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