1
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Hein JB, Nguyen HT, Garvanska DH, Nasa I, Kruse T, Feng Y, Lopez Mendez B, Davey N, Kettenbach AN, Fordyce PM, Nilsson J. Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification. Mol Syst Biol 2023; 19:e11782. [PMID: 37916966 PMCID: PMC10698503 DOI: 10.15252/msb.202311782] [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: 05/21/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Phosphoprotein phosphatases (PPPs) regulate major signaling pathways, but the determinants of phosphatase specificity are poorly understood. This is because methods to investigate this at scale are lacking. Here, we develop a novel in vitro assay, MRBLE:Dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase preferences. Using MRBLE:Dephos, we establish amino acid preferences of the residues surrounding the dephosphorylation site for PP1 and PP2A-B55, which reveals common and unique preferences. To compare the MRBLE:Dephos results to cellular substrates, we focused on mitotic exit that requires extensive dephosphorylation by PP1 and PP2A-B55. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with phosphoproteomics to identify more than 2,000 regulated sites. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with MRBLE:Dephos. Furthermore, integration of our phosphoproteomic data with mitotic interactomes of PP1 and PP2A-B55 provides insight into how binding of phosphatases to substrates shapes dephosphorylation. Collectively, we develop novel approaches to investigate protein phosphatases that provide insight into mitotic exit regulation.
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Affiliation(s)
- Jamin B Hein
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Hieu T Nguyen
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Isha Nasa
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Thomas Kruse
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Yinnian Feng
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Norman Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Arminja N Kettenbach
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Polly M Fordyce
- Department of BioengineeringStanford UniversityStanfordCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
- Sarafan ChEM‐HStanford UniversityStanfordCAUSA
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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2
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Kao DS, Du Y, DeMarco AG, Min S, Hall MC, Rochet JC, Tao WA. Identification of Novel Kinases of Tau Using Fluorescence Complementation Mass Spectrometry (FCMS). Mol Cell Proteomics 2022; 21:100441. [PMID: 36379402 PMCID: PMC9755369 DOI: 10.1016/j.mcpro.2022.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022] Open
Abstract
Hyperphosphorylation of the microtubule-associated protein Tau is a major hallmark of Alzheimer's disease and other tauopathies. Understanding the protein kinases that phosphorylate Tau is critical for the development of new drugs that target Tau phosphorylation. At present, the repertoire of the Tau kinases remains incomplete, and methods to uncover novel upstream protein kinases are still limited. Here, we apply our newly developed proteomic strategy, fluorescence complementation mass spectrometry, to identify novel kinase candidates of Tau. By constructing Tau- and kinase-fluorescent fragment library, we detected 59 Tau-associated kinases, including 23 known kinases of Tau and 36 novel candidate kinases. In the validation phase using in vitro phosphorylation, among 15 candidate kinases we attempted to purify and test, four candidate kinases, OXSR1 (oxidative-stress responsive gene 1), DAPK2 (death-associated protein kinase 2), CSK (C-terminal SRC kinase), and ZAP70 (zeta chain of T-cell receptor-associated protein kinase 70), displayed the ability to phosphorylate Tau in time-course experiments. Furthermore, coexpression of these four kinases along with Tau increased the phosphorylation of Tau in human neuroglioma H4 cells. We demonstrate that fluorescence complementation mass spectrometry is a powerful proteomic strategy to systematically identify potential kinases that can phosphorylate Tau in cells. Our discovery of new candidate kinases of Tau can present new opportunities for developing Alzheimer's disease therapeutic strategies.
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Affiliation(s)
- Der-Shyang Kao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Yanyan Du
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Andrew G DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Sehong Min
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA; Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA; Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA; Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA; Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
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3
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KITAGAWA F, HAYASHI A, NUKATSUKA I. LVSEP Analysis of Phosphopeptides in Dynamically PVP-Coated Capillaries and Microchannels. CHROMATOGRAPHY 2022. [DOI: 10.15583/jpchrom.2021.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Fumihiko KITAGAWA
- Department of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University
| | - Ayaka HAYASHI
- Department of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University
| | - Isoshi NUKATSUKA
- Department of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University
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4
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Musiani D, Giambruno R, Massignani E, Ippolito MR, Maniaci M, Jammula S, Manganaro D, Cuomo A, Nicosia L, Pasini D, Bonaldi T. PRMT1 Is Recruited via DNA-PK to Chromatin Where It Sustains the Senescence-Associated Secretory Phenotype in Response to Cisplatin. Cell Rep 2020; 30:1208-1222.e9. [DOI: 10.1016/j.celrep.2019.12.061] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/02/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
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5
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Hip2 ubiquitin-conjugating enzyme has a role in UV-induced G1/S arrest and re-entry. Genes Genomics 2018; 41:159-166. [PMID: 30264212 DOI: 10.1007/s13258-018-0747-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022]
Abstract
Regulation of cell cycle arrest and re-entry triggered by DNA damage is vital for cell division and growth and is also involved in cell survival. UV radiation can generate lesions in the DNA, which results in cell cycle arrest and the induction of the DNA repair process. However, the mechanism of promoting cell cycle progression following DNA repair is elusive. The primary aim of this study is to investigate whether Hip2 ubiquitin-conjugating enzyme has a role in UV-induced G1/S arrest and re-entry. The phase of HEK293 cells was synchronized at the G1/S border using thymidine. The synchronously proliferating cells were exposed to UV radiation to cause DNA damage. We investigated the expression of p53, Hip2, p21, cyclin D and E proteins that are involved in the cell cycle progression. Finally, we examined changes in the phosphorylation of Hip2 after UV radiation treatment using the pIMAGO™ assay. When cells were exposed to UV radiation, expression of p53 was elevated, and the cell cycle was arrested at the G1/S boundary. In response to the increased p53 level, Hip2 became phosphorylated and activated through the inhibition of its degradation. The phosphorylated Hip2 inhibited p53, thereby suppressing the expression of p21, a downstream signal, and sequentially stimulating cyclin D and cyclin E to induce re-entry to the cell cycle. Our studies demonstrate that Hip2 works as a regulator in UV-induced cell cycle arrest and re-entry.
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6
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Jung SH, Kwon MH, Lee SH, Han ET, Park WS, Hong SH, Kim YM, Ha KS. High-throughput investigation of transglutaminase 2 kinase regulation using a novel cysteine-modified peptide array. Anal Biochem 2018; 559:62-70. [PMID: 30165045 DOI: 10.1016/j.ab.2018.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/19/2022]
Abstract
Transglutaminase 2 (TGase2) kinase has emerged as an important regulator of apoptosis as well as chromatin structure and function; however, details about the pathophysiological functions of TGase2 kinase have been limited because of the lack of a suitable activity assay for systematic investigation of TGase2 kinase regulation in a high-throughput manner. Thus, we developed a novel on-chip TGase2 kinase activity assay using a cysteine-modified insulin-like growth factor-binding protein-3-derived peptide (CMI peptide) on an array platform. This peptide array-based activity assay was reproducible, with a detection limit of 2.127 μg/ml. We successfully applied this assay to investigate the effects of thiol-reactive compounds and divalent cations on TGase2 kinase by determining the half maximal inhibitory concentrations (IC50). Thiol-reactive compounds inhibited TGase2 kinase activity in a concentration-dependent manner, with IC50 values ranging from 0.125 to 5.550 mM. Divalent metal cations also showed a concentration-dependent inhibition, with IC50 values ranging from 0.005 to 1.937 mM; however, Ca2+ had no effect on TGase2 kinase activity. Thus, this novel kinase activity assay using the CMI peptide array described here is suitable for systematic investigation of TGase2 kinase regulation and may be useful for investigating the roles of TGase2 kinase in pathogenesis of kinase-mediated diseases.
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Affiliation(s)
- Se-Hui Jung
- Department of Molecular and Cellular Biochemistry, Kangwon National University School of Medicine, Chuncheon, Kangwon-Do, 200-701, South Korea
| | - Mi-Hye Kwon
- Department of Molecular and Cellular Biochemistry, Kangwon National University School of Medicine, Chuncheon, Kangwon-Do, 200-701, South Korea
| | - Seong-Hyeon Lee
- Department of Molecular and Cellular Biochemistry, Kangwon National University School of Medicine, Chuncheon, Kangwon-Do, 200-701, South Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon, Kangwon-Do, 200-701, South Korea
| | - Won Sun Park
- Department of Physiology, Kangwon National University School of Medicine, Chuncheon, Kangwon-Do, 200-701, South Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Kangwon-Do, 200-701, South Korea
| | - Young-Myeong Kim
- Department of Molecular and Cellular Biochemistry, Kangwon National University School of Medicine, Chuncheon, Kangwon-Do, 200-701, South Korea
| | - Kwon-Soo Ha
- Department of Molecular and Cellular Biochemistry, Kangwon National University School of Medicine, Chuncheon, Kangwon-Do, 200-701, South Korea.
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7
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Li Z, Kong Y, Song L, Luo Q, Liu J, Shao C, Hou X, Liu X. Plk1-Mediated Phosphorylation of TSC1 Enhances the Efficacy of Rapamycin. Cancer Res 2018; 78:2864-2875. [PMID: 29559472 PMCID: PMC5984699 DOI: 10.1158/0008-5472.can-17-3046] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/13/2018] [Accepted: 03/15/2018] [Indexed: 12/20/2022]
Abstract
The AKT/TSC/mTOR axis is an important pathway controlling cell growth, survival, and proliferation in response to extracellular cues. Recently, it was reported that AKT activity fluctuates across the cell cycle. However, it remains unclear whether downstream targets of AKT are also regulated by the cell cycle. Here, we report that mTORC1 activity inversely correlates with AKT activity during the cell cycle. Mechanistically, Plk1 phosphorylation of TSC1 at S467 and S578 interfered with TSC1/TSC2 binding, destabilized TSC1, promoted dissociation of the TSC complex from the lysosome, and eventually led to mTORC1 activation. Tumors derived from cancer cells expressing the TSC1-S467E/S578E mutant exhibited greater sensitivity to rapamycin than those expressing WT TSC1. Collectively, our data support a model in which Plk1, instead of AKT, regulates the TSC/mTORC1 pathway during mitosis, eventually regulating the efficacy of rapamycin.Significance: This seminal report shows that activation of mTORC1 can be independent of AKT during mitosis. Cancer Res; 78(11); 2864-75. ©2018 AACR.
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Affiliation(s)
- Zhiguo Li
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Yifan Kong
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Longzhen Song
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Qian Luo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Jinghui Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Chen Shao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Xianzeng Hou
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana.
- Center for Cancer Research, Purdue University, West Lafayette, Indiana
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8
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Liu T, Zhang W, Zhang Z, Chen M, Wang J, Qian X, Qin W. Sensitive Western-Blot Analysis of Azide-Tagged Protein Post Translational Modifications Using Thermoresponsive Polymer Self-Assembly. Anal Chem 2018; 90:2186-2192. [DOI: 10.1021/acs.analchem.7b04531] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tong Liu
- Research
Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, PR China
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Wanjun Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Zheng Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Mingli Chen
- Research
Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, PR China
| | - Jianhua Wang
- Research
Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, PR China
| | - Xiaohong Qian
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Weijie Qin
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
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9
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Li Z, Li J, Kong Y, Yan S, Ahmad N, Liu X. Plk1 Phosphorylation of Mre11 Antagonizes the DNA Damage Response. Cancer Res 2017; 77:3169-3180. [PMID: 28512243 PMCID: PMC5504882 DOI: 10.1158/0008-5472.can-16-2787] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 03/01/2017] [Accepted: 04/19/2017] [Indexed: 11/16/2022]
Abstract
The mitotic kinase Plk1 contributes to the DNA damage response (DDR) by targeting multiple factors downstream of the core responder kinase ATM/ATR. In this study, we show that Polo-like kinase 1 (Plk1) also phosphorylates key factors upstream of ATM/ATR and regulates their DDR-related functions. Plk1 phosphorylated Mre11, a component of the Mre11/Rad50/Nbs1 (MRN) complex, at serine 649 (S649) during DDR. Phosphorylation of Mre11-S649 by Plk1 primed subsequent CK2-mediated phosphorylation at Mre11-serine 688 (S688). Phosphorylation of Mre11 at S649/S688 inhibited loading of the MRN complex to damaged DNA, leading to both premature DNA damage checkpoint termination and inhibition of DNA repair. Tumors expressing phosphomimetic Mre11 were more sensitive to the PARP inhibitor olaparib, compared with those expressing unphosphorylatable Mre11, suggesting that patients with elevated Plk1 expression might benefit from olaparib treatment. Cancer Res; 77(12); 3169-80. ©2017 AACR.
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Affiliation(s)
- Zhiguo Li
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Jie Li
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Yifan Kong
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, Madison, Wisconsin
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana.
- Center for Cancer Research, Purdue University, West Lafayette, Indiana
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10
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Phosphoproteins in extracellular vesicles as candidate markers for breast cancer. Proc Natl Acad Sci U S A 2017; 114:3175-3180. [PMID: 28270605 DOI: 10.1073/pnas.1618088114] [Citation(s) in RCA: 304] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The state of protein phosphorylation can be a key determinant of cellular physiology such as early-stage cancer, but the development of phosphoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate a strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer compared with healthy controls. Several biomarkers were validated in individual patients using paralleled reaction monitoring for targeted quantitation. This study demonstrates that the development of phosphoproteins in plasma EV as disease biomarkers is highly feasible and may transform cancer screening and monitoring.
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11
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Li Y, Wang Y, Dong M, Zou H, Ye M. Sensitive Approaches for the Assay of the Global Protein Tyrosine Phosphorylation in Complex Samples Using a Mutated SH2 Domain. Anal Chem 2017; 89:2304-2311. [DOI: 10.1021/acs.analchem.6b03812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yanan Li
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Dong
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanfa Zou
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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KITAGAWA F, MATSUO A, SUEYOSHI K, OTSUKA K. Sensitivity Enhancement by Sweeping via Solid Phase Extraction Using Titania Nanoparticles in Capillary Electrophoretic Analysis of Phosphopeptides. CHROMATOGRAPHY 2017. [DOI: 10.15583/jpchrom.2016.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Fumihiko KITAGAWA
- Department of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University
| | - Asako MATSUO
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University
| | - Kenji SUEYOSHI
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Koji OTSUKA
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University
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13
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Iliuk A, Li L, Melesse M, Hall MC, Tao WA. Multiplexed Imaging of Protein Phosphorylation on Membranes Based on Ti(IV) Functionalized Nanopolymers. Chembiochem 2016; 17:900-3. [PMID: 27037847 PMCID: PMC4870103 DOI: 10.1002/cbic.201600068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Indexed: 01/10/2023]
Abstract
Accurate protein phosphorylation analysis reveals dynamic cellular signaling events not evident from protein expression levels. The most dominant biochemical assay, western blotting, suffers from the inadequate availability and poor quality of phospho-specific antibodies for phosphorylated proteins. Furthermore, multiplexed assays based on antibodies are limited by steric interference between the antibodies. Here we introduce a multifunctionalized nanopolymer for the universal detection of phosphoproteins that, in combination with regular antibodies, allows multiplexed imaging and accurate determination of protein phosphorylation on membranes.
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Affiliation(s)
- Anton Iliuk
- Department of Biochemistry, Purdue University, 201 S University, West Lafayette, IN, 47907, USA
- Tymora Analytical Operations, 3495 Kent Avenue, West Lafayette, IN, 47906, USA
| | - Li Li
- Department of Biochemistry, Purdue University, 201 S University, West Lafayette, IN, 47907, USA
- Tymora Analytical Operations, 3495 Kent Avenue, West Lafayette, IN, 47906, USA
| | - Michael Melesse
- Department of Biochemistry, Purdue University, 201 S University, West Lafayette, IN, 47907, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, 201 S University, West Lafayette, IN, 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, 201 S University, West Lafayette, IN, 47907, USA.
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA.
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14
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Mass spectrometric phosphoproteome analysis of small-sized samples of human neutrophils. Clin Chim Acta 2015; 451:199-207. [DOI: 10.1016/j.cca.2015.09.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/21/2015] [Accepted: 09/29/2015] [Indexed: 12/28/2022]
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15
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Li J, Karki A, Hodges KB, Ahmad N, Zoubeidi A, Strebhardt K, Ratliff TL, Konieczny SF, Liu X. Cotargeting Polo-Like Kinase 1 and the Wnt/β-Catenin Signaling Pathway in Castration-Resistant Prostate Cancer. Mol Cell Biol 2015; 35:4185-98. [PMID: 26438599 PMCID: PMC4648817 DOI: 10.1128/mcb.00825-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/15/2015] [Accepted: 09/25/2015] [Indexed: 01/07/2023] Open
Abstract
The Wnt/β-catenin signaling pathway has been identified as one of the predominantly upregulated pathways in castration-resistant prostate cancer (CRPC). However, whether targeting the β-catenin pathway will prove effective as a CRPC treatment remains unknown. Polo-like kinase 1 (Plk1) is a critical regulator in many cell cycle events, and its level is significantly elevated upon castration of mice carrying xenograft prostate tumors. Indeed, inhibition of Plk1 has been shown to inhibit tumor growth in several in vivo studies. Here, we show that Plk1 is a negative regulator of Wnt/β-catenin signaling. Plk1 inhibition or depletion enhances the level of cytosolic and nuclear β-catenin in human prostate cancer cells. Furthermore, inhibition of Wnt/β-catenin signaling significantly potentiates the antineoplastic activity of the Plk1 inhibitor BI2536 in both cultured prostate cancer cells and CRPC xenograft tumors. Mechanistically, axin2, a negative regulator of the β-catenin pathway, serves as a substrate of Plk1, and Plk1 phosphorylation of axin2 facilitates the degradation of β-catenin by enhancing binding between glycogen synthase kinase 3β (GSK3β) and β-catenin. Plk1-phosphorylated axin2 also exhibits resistance to Cdc20-mediated degradation. Overall, this study identifies a novel Plk1-Wnt signaling axis in prostate cancer, offering a promising new therapeutic option to treat CRPC.
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Affiliation(s)
- Jie Li
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Anju Karki
- Department of Biological Science, Purdue University, West Lafayette, Indiana, USA
| | - Kurt B Hodges
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, Madison, Madison, Wisconsin, USA
| | - Amina Zoubeidi
- The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Klaus Strebhardt
- Department of Obstetrics and Gynecology, J. W. Goethe University, Frankfurt, Germany
| | - Timothy L Ratliff
- Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Stephen F Konieczny
- Department of Biological Science, Purdue University, West Lafayette, Indiana, USA Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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16
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Ludwig KR, Sun L, Zhu G, Dovichi NJ, Hummon AB. Over 2300 phosphorylated peptide identifications with single-shot capillary zone electrophoresis-tandem mass spectrometry in a 100 min separation. Anal Chem 2015; 87:9532-7. [PMID: 26399161 PMCID: PMC4605816 DOI: 10.1021/acs.analchem.5b02457] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ultraperformance liquid chromatography (UPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) is typically employed for phosphoproteome analysis. Alternatively, capillary zone electrophoresis (CZE)-ESI-MS/MS has great potential for phosphoproteome analysis due to the significantly different migration times of phosphorylated and unphosphorylated forms of peptides. In this work, we systematically compared UPLC-MS/MS and CZE-MS/MS for phosphorylated peptide identifications (IDs) using an enriched phosphoproteome from the MCF-10A cell line. When the sample loading amount of UPLC was 10 times higher than that of CZE (2 μg vs 200 ng), UPLC generated more phosphorylated peptide IDs than CZE (3313 vs 1783). However, when the same sample loading amounts were used for CZE and UPLC (2-200 ng), CZE-MS/MS consistently and significantly outperformed UPLC-MS/MS in terms of phosphorylated peptide and total peptide IDs. This superior performance is most likely due to the higher peptide intensity generated by CZE-MS/MS. More importantly, compared with UPLC data from a 2 μg sample, CZE-MS/MS can identify over 500 unique phosphorylated peptides from a 200 ng sample, suggesting that CZE and UPLC are complementary for phosphorylated peptide IDs. With further improved loading capacity via a dynamic pH junction method, 2313 phosphorylated peptides were identified with single-shot CZE-MS/MS in a 100 min analysis. This number of phosphorylated peptide IDs is over 1 order of magnitude higher than the number of phosphorylated peptide IDs previously reported by single-shot CZE-MS/MS.
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Affiliation(s)
- Katelyn R. Ludwig
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
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17
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Pan L, Wang L, Hsu CC, Zhang J, Iliuk A, Tao WA. Sensitive measurement of total protein phosphorylation level in complex protein samples. Analyst 2015; 140:3390-6. [PMID: 25857711 PMCID: PMC4425989 DOI: 10.1039/c5an00365b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Measurement of protein phosphorylation plays an essential role in delineating cell signaling pathways. Although the detection of a specific phosphoprotein has been largely accomplished by immunological methods, a specific and sensitive assay to measure total protein phosphorylation level in complex samples such as whole cell extracts has yet to be established. Here, we present a sensitive phosphorylation assay on a microwell plate to determine total protein phosphorylation level calibrated to a phosphoprotein standard. The core of the assay is a reagent termed pIMAGO that is multi-functionalized with titanium ions for its superior selectivity towards phosphorylated proteins and with fluorophores for quantification. The specificity, sensitivity, and quantitative nature of the assay were demonstrated with standard proteins and whole cell lysates. The method was then employed to measure the overall protein phosphorylation level of human cells under different treatments. At last, we investigated the practicability of the assay to serve as a sensitive tool to estimate the amount of phosphorylated samples prior to a mass spectrometry-based phosphoproteomic analysis.
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Affiliation(s)
- Li Pan
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.
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18
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Iliuk AB, Tao WA. Universal non-antibody detection of protein phosphorylation using pIMAGO. ACTA ACUST UNITED AC 2015; 7:17-25. [PMID: 25727060 DOI: 10.1002/9780470559277.ch140208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This article describes methods for a new, non-antibody phosphorylation detection reagent, termed pIMAGO (phospho-imaging). This novel reagent takes advantage not only of the unique properties of the soluble nanoparticles, but also of the multiple functionalities of the molecule, allowing for highly selective, sensitive, and quantitative assessment of protein phosphorylation without using radioactive isotopes or phospho-specific antibodies. The methods allow for multiplexed detection of phosphorylation and total protein amount simultaneously. The straightforward and routine detection and quantitation of general phosphorylation on any site of any protein can be performed in western blot and ELISA formats.
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Affiliation(s)
- Anton B Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana; Tymora Analytical Operations, LLC, West Lafayette, Indiana
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19
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Shao T, Liu X. Identification of rictor as a novel substrate of Polo-like kinase 1. Cell Cycle 2015; 14:755-60. [PMID: 25714006 PMCID: PMC4615041 DOI: 10.1080/15384101.2014.998050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 10/23/2022] Open
Abstract
Plk1 has been essentially described as a critical regulator of many mitotic events. However, increasing evidence supports the notion that its molecular functions are not restricted to the cell cycle. In particular, recent reports suggest the existence of a molecular and functional link between Plk1 and the mammalian target of rapamycin (mTOR) pathway, which controls cell growth and proliferation via the raptor-mTOR (TORC1) and rictor-mTOR (TORC2) protein complexes. Herein, we have identified rapamycin-insensitive companion of mTOR (Rictor), a core component of mTORC2, as a new Plk1 substrate and have shown that Plk1 phosphorylates Rictor at Ser1162 in vitro and in vivo. Surprisingly, cells expressing the unphosphorylatable mutant (S1162A) of Rictor did not show any effect on well characterized canonical PI3K-mTOR pathway. However, we found that cells expressing the unphosphorylatable form of Rictor have an elevated level of mSin1 isoform (mSin1.5). Considering that mSin1.5-containing mTORC2 was reported to associate with stress signaling, we propose that phosphorylation of Rictor at Ser1162 by Plk1 might be involved in a novel signaling pathway by regulating the mSin1.5-defined mTORC2.
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Key Words
- 4E-BP1, eIF4E-binding protein 1
- GST, glutathione S-transferase
- IB, immunoblotting.
- IP, immunoprecipitation
- PDK1, 3-phophoinositide-dependent protein kinase 1 (PDK1)
- Plk1
- Plk1, polo-like kinase 1
- Raptor, regulatory-associated protein of mTOR
- Rictor
- Rictor, rapamycin-insensitive companion of mTOR
- S6K, S6 Kinase
- WT, wild type
- aa, amino acids
- cell cycle
- mSin1
- mSin1, mammalian stress-activated map kinase-interacting protein 1 (mSin1)
- mTOR, mammalian target of rapamycin
- mTORC
- mTORC1, mTOR complex 1
- mTORC2, mTOR complex 2
- phosphorylation
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Affiliation(s)
- Tian Shao
- Department of Biochemistry; Purdue University; West Lafayette, IN USA
| | - Xiaoqi Liu
- Department of Biochemistry; Purdue University; West Lafayette, IN USA
- Purdue Center for Cancer Research; Purdue University; West Lafayette, IN USA
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20
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Li Z, Li J, Bi P, Lu Y, Burcham G, Elzey BD, Ratliff T, Konieczny SF, Ahmad N, Kuang S, Liu X. Plk1 phosphorylation of PTEN causes a tumor-promoting metabolic state. Mol Cell Biol 2014; 34:3642-61. [PMID: 25047839 PMCID: PMC4187734 DOI: 10.1128/mcb.00814-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/17/2014] [Indexed: 11/20/2022] Open
Abstract
One outcome of activation of the phosphatidylinositol 3-kinase (PI3K) pathway is increased aerobic glycolysis, but the upstream signaling events that regulate the PI3K pathway, and thus the Warburg effect, are elusive. Increasing evidence suggests that Plk1, a cell cycle regulator, is also involved in cellular events in addition to mitosis. To test whether Plk1 contributes to activation of the PI3K pathway, and thus aerobic glycolysis, we examined potential targets of Plk1 and identified PTEN as a Plk1 substrate. We hypothesize that Plk1 phosphorylation of PTEN leads to its inactivation, activation of the PI3K pathway, and the Warburg effect. Our data show that overexpression of Plk1 leads to activation of the PI3K pathway and enhanced aerobic glycolysis. In contrast, inhibition of Plk1 causes markedly reduced glucose metabolism in mice. Mechanistically, we show that Plk1 phosphorylation of PTEN and Nedd4-1, an E3 ubiquitin ligase of PTEN, results in PTEN inactivation. Finally, we show that Plk1 phosphorylation of PTEN promotes tumorigenesis in both its phosphatase-dependent and -independent pathways, revealing potentially new drug targets to arrest tumor cell growth.
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Affiliation(s)
- Zhiguo Li
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Jie Li
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Pengpeng Bi
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ying Lu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Grant Burcham
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, USA
| | - Bennett D Elzey
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, USA
| | - Timothy Ratliff
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, USA Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Stephen F Konieczny
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, Madison, Wisconsin, USA
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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21
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Abstract
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The
applicability of gel-based proteomic strategies in phosphoproteomics
has been largely limited by the lack of technologies for specific
detection of phosphoproteins in gels. Here for the first time we report
a strategy for simultaneous visualization and identification of phosphoproteome
in gels (VIPing) through coupling specific detection of phosphoproteins
with protein identification and phosphorylation site mapping by tandem
mass spectrometry. The core of the strategy is a novel compound multifunctionalized
with a titanium ion(IV) for outstanding selectivity toward phosphorylated
residues, a fluorophore for visualization, and a biotin group for
phosphopeptide enrichment. The sensitivity and specificity of the
VIPing strategy was demonstrated using standard protein mixtures and
complex cell extracts, and the method was applied to study the phosphorylation
changes of an essential tyrosine kinase Syk and interacting proteins
upon B-cell stimulation. The novel technique provides a powerful platform
for gel-based phosphoproteomic studies.
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Affiliation(s)
- Linna Wang
- Department of Biochemistry, ‡Department of Medicinal Chemistry & Molecular Pharmacology, and §Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
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22
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Li X, Kong M, Dong A, Qian J, Jiang D. Polymer-based delivering of shRNA to rabbit aortic smooth muscle cells suppressed the expression of IGF-1R in vitro and in vivo. Acta Biochim Biophys Sin (Shanghai) 2014; 46:141-8. [PMID: 24374775 DOI: 10.1093/abbs/gmt139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Restenosis is one of clinical limitations for vein graft in coronary bypass graft. It has been proved that signal pathway IGF-1 and its receptor (IGF-1R) activated by hemodynamic mechanical stretch are responsible for the vascular smooth muscle cells proliferation in vein graft neointima formation. Unfortunately, there is no routinely successful method to resolve this problem. Gene delivering to vein graft possesses great therapeutic potential to prevent neointima formation. Polymer is one kind of nanoparticles, which can activate the process of endocytosis of cells. In this study, we evaluated the transfection efficiency and therapeutic potential of polymer-based transfection of plasmids expressing GFP and shRNAs targeting IGF-1R (pGFPshIGF-1Rs) to smooth muscle cells and rabbit external jugular vein graft. Results showed that polymer-based transfection provided high efficiency of transgene expression in smooth muscle cells in vitro. In vitro, IGF-1R-specific shRNA transfected by polymer inhibited IGF-1R protein expression by 52 ± 3.6%, when compared with mock transfected cells. In vivo delivering efficiency of pGFPshIGF-1R plasmid into the rabbit external jugular vein graft was significantly high in the polymer-based transfection group, when compared with negative control group. In vivo, polymer-based transfection IGF-1R-specific shRNA efficiently inhibited the expression of IGF-1R protein by 77 ± 3.6%, 65.6 ± 4.9%, and 76.7 ± 4.3% at 24, 48, and 72 h, respectively, when compared with negative control group. Our findings indicated that polymer-based transfection may be a promising technique that allows the targeting of gene therapy for vein graft restenosis.
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Affiliation(s)
- Xuebiao Li
- Department of Cardiothoracic Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
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23
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Yue XS, Hummon AB. Combination of Multistep IMAC Enrichment with High-pH Reverse Phase Separation for In-Depth Phosphoproteomic Profiling. J Proteome Res 2013; 12:4176-86. [DOI: 10.1021/pr4005234] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiao-Shan Yue
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall,
Notre Dame, Indiana 46556, United States
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall,
Notre Dame, Indiana 46556, United States
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24
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Iliuk AB, Tao WA. Is phosphoproteomics ready for clinical research? Clin Chim Acta 2012; 420:23-7. [PMID: 23159844 DOI: 10.1016/j.cca.2012.10.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 12/29/2022]
Abstract
BACKGROUND For many diseases such as cancer where phosphorylation-dependent signaling is the foundation of disease onset and progression, single-gene testing and genomic profiling alone are not sufficient in providing most critical information. The reason for this is that in these activated pathways the signaling changes and drug resistance are often not directly correlated with changes in protein expression levels. In order to obtain the essential information needed to evaluate pathway activation or the effects of certain drugs and therapies on the molecular level, the analysis of changes in protein phosphorylation is critical. METHODS Existing approaches do not differentiate clinical disease subtypes on the protein and signaling pathway level, and therefore hamper the predictive management of the disease and the selection of therapeutic targets. CONCLUSIONS The mini-review examines the impact of emerging systems biology tools and the possibility of applying phosphoproteomics to clinical research.
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Affiliation(s)
- Anton B Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, United States
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