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Wang J, Saltzman AB, Jaehnig EJ, Lei JT, Malovannaya A, Holt MV, Young MN, Rimawi MF, Ademuyiwa FO, Anurag M, Kim BJ, Ellis MJ. Kinase Inhibitor Pulldown Assay Identifies a Chemotherapy Response Signature in Triple-negative Breast Cancer Based on Purine-binding Proteins. CANCER RESEARCH COMMUNICATIONS 2023; 3:1551-1563. [PMID: 37587913 PMCID: PMC10426551 DOI: 10.1158/2767-9764.crc-22-0501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/10/2023] [Accepted: 06/21/2023] [Indexed: 08/18/2023]
Abstract
Triple-negative breast cancer (TNBC) constitutes 10%-15% of all breast tumors. The current standard of care is multiagent chemotherapy, which is effective in only a subset of patients. The original objective of this study was to deploy a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) to identify kinases elevated in non-pCR (pathologic complete response) cases for therapeutic targeting. Frozen optimal cutting temperature compound-embedded core needle biopsies were obtained from 43 patients with TNBC before docetaxel- and carboplatin-based neoadjuvant chemotherapy. KIPA was applied to the native tumor lysates that were extracted from samples with high tumor content. Seven percent of all identified proteins were kinases, and none were significantly associated with lack of pCR. However, among a large population of "off-target" purine-binding proteins (PBP) identified, seven were enriched in pCR-associated samples (P < 0.01). In orthogonal mRNA-based TNBC datasets, this seven-gene "PBP signature" was associated with chemotherapy sensitivity and favorable clinical outcomes. Functional annotation demonstrated IFN gamma response, nuclear import of DNA repair proteins, and cell death associations. Comparisons with standard tandem mass tagged-based discovery proteomics performed on the same samples demonstrated that KIPA-nominated pCR biomarkers were unique to the platform. KIPA is a novel biomarker discovery tool with unexpected utility for the identification of PBPs related to cytotoxic drug response. The PBP signature has the potential to contribute to clinical trials designed to either escalate or de-escalate therapy based on pCR probability. Significance The identification of pretreatment predictive biomarkers for pCR in response to neoadjuvant chemotherapy would advance precision treatment for TNBC. To complement standard proteogenomic discovery profiling, a KIPA was deployed and unexpectedly identified a seven-member non-kinase PBP pCR-associated signature. Individual members served diverse pathways including IFN gamma response, nuclear import of DNA repair proteins, and cell death.
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Affiliation(s)
- Junkai Wang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Alexander B. Saltzman
- Mass Spectrometry Proteomics Core, Advanced Technology Cores, Baylor College of Medicine, Houston, Texas
| | - Eric J. Jaehnig
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Jonathan T. Lei
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Anna Malovannaya
- Mass Spectrometry Proteomics Core, Advanced Technology Cores, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Matthew V. Holt
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Meggie N. Young
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Mothaffar F. Rimawi
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Foluso O. Ademuyiwa
- Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, Missouri
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- AstraZeneca, Gaithersburg, Maryland
| | - Matthew J. Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- AstraZeneca, Gaithersburg, Maryland
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Tian L, Wang L, Zhang X, Huang X, Wang F, Zhu S, Li X, Guan Y. Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:24284-24298. [PMID: 36334202 DOI: 10.1007/s11356-022-23539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.
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Affiliation(s)
- Lu Tian
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Lin Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.
| | - Xiaofeng Zhang
- Qingdao Water Development Service Center, Qingdao, 266071, China
| | - Xuda Huang
- Qingdao Water Development Service Center, Qingdao, 266071, China
| | - Fuhao Wang
- Qingdao Water Affairs Group, Environmental Energy Co., Ltd, Qingdao, 266075, China
| | - Sifu Zhu
- Qingdao Haibo River Water Operation Co., Ltd, Qingdao, 266021, China
| | - Xueqiang Li
- Qingdao Haibo River Water Operation Co., Ltd, Qingdao, 266021, China
| | - Ying Guan
- Qingdao Haibo River Water Operation Co., Ltd, Qingdao, 266021, China
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3
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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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4
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Wilkinson IVL, Pfanzelt M, Sieber SA. Functionalised Cofactor Mimics for Interactome Discovery and Beyond. Angew Chem Int Ed Engl 2022; 61:e202201136. [PMID: 35286003 PMCID: PMC9401033 DOI: 10.1002/anie.202201136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Indexed: 11/09/2022]
Abstract
Cofactors are required for almost half of all enzyme reactions, but their functions and binding partners are not fully understood even after decades of research. Functionalised cofactor mimics that bind in place of the unmodified cofactor can provide answers, as well as expand the scope of cofactor activity. Through chemical proteomics approaches such as activity-based protein profiling, the interactome and localisation of the native cofactor in its physiological environment can be deciphered and previously uncharacterised proteins annotated. Furthermore, cofactors that supply functional groups to substrate biomolecules can be hijacked by mimics to site-specifically label targets and unravel the complex biology of post-translational protein modification. The diverse activity of cofactors has inspired the design of mimics for use as inhibitors, antibiotic therapeutics, and chemo- and biosensors, and cofactor conjugates have enabled the generation of novel enzymes and artificial DNAzymes.
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Affiliation(s)
- Isabel V. L. Wilkinson
- Centre for Functional Protein AssembliesTechnical University of MunichErnst-Otto-Fischer-Straße 885748GarchingGermany
| | - Martin Pfanzelt
- Centre for Functional Protein AssembliesTechnical University of MunichErnst-Otto-Fischer-Straße 885748GarchingGermany
| | - Stephan A. Sieber
- Centre for Functional Protein AssembliesTechnical University of MunichErnst-Otto-Fischer-Straße 885748GarchingGermany
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5
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Wilkinson IVL, Pfanzelt M, Sieber SA. Funktionalisierte Cofaktor‐Analoga für die Erforschung von Interaktomen und darüber hinaus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Isabel V. L. Wilkinson
- Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
| | - Martin Pfanzelt
- Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
| | - Stephan A. Sieber
- Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
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6
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Pan M, Liu Y, Zheng X, Zhou M, You C, Dai X. Comprehensive profiling of CTP-binding proteins using a biotinylated CTP affinity probe. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.05.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Liu Y, Qu M, Pan M, Zheng X, Sheng Y, Ji Y, You C, Dai X. Chemical proteomic profiling of UTP-binding proteins in human cells. Anal Chim Acta 2021; 1168:338607. [PMID: 34052001 DOI: 10.1016/j.aca.2021.338607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/20/2022]
Abstract
Nucleotide-binding proteins play important roles in a variety of biological processes. While ATP- and GTP-binding proteins have been well studied, the systematical identification of UTP-interacting proteins remains under investigated. Here, we developed a chemical proteomic strategy using a biotinylated UTP affinity probe coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) method to enrich, identify and quantify UTP-binding proteins at the entire proteome scale. By performing labeling reactions with high vs low concentrations of UTP probe (100 and 10 μM) or with the UTP probe in the presence of free UTP in stable isotope labeling by amino acids in cell culture (SILAC) experiments, we identified more than 70 potential UTP-binding proteins which are involved in multiple cellular processes, such as translational elongation and protein folding. We also validated the UTP-binding capability of the cytoskeletal protein ACTB by using cellular thermal shift assay (CETSA). Together, we performed a high-throughput chemical proteomics-based analysis to identify, for the first time, UTP-binding proteins in human proteome, which should be applicable for the identification and quantification of UTP-binding proteins in other organisms.
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Affiliation(s)
- Yunming Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Minghui Qu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Mengting Pan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Xiaofang Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Yuwei Sheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Yongqin Ji
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Changjun You
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Xiaoxia Dai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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8
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James AM, Seal SE, Bailey AM, Foster GD. Viral inosine triphosphatase: A mysterious enzyme with typical activity, but an atypical function. MOLECULAR PLANT PATHOLOGY 2021; 22:382-389. [PMID: 33471956 PMCID: PMC7865087 DOI: 10.1111/mpp.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 05/03/2023]
Abstract
Plant viruses typically have highly condensed genomes, yet the plant-pathogenic viruses Cassava brown streak virus, Ugandan cassava brown streak virus, and Euphorbia ringspot virus are unusual in encoding an enzyme not yet found in any other virus, the "house-cleaning" enzyme inosine triphosphatase. Inosine triphosphatases (ITPases) are highly conserved enzymes that occur in all kingdoms of life and perform a house-cleaning function by hydrolysing the noncanonical nucleotide inosine triphosphate to inosine monophosphate. The ITPases encoded by cassava brown streak virus and Ugandan cassava brown streak virus have been characterized biochemically and are shown to have typical ITPase activity. However, their biological role in virus infection has yet to be elucidated. Here we review what is known of viral-encoded ITPases and speculate on potential roles in infection with the aim of generating a greater understanding of cassava brown streak viruses, a group of the world's most devastating viruses.
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Affiliation(s)
- Amy M. James
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Susan E. Seal
- Natural Resources Institute, Chatham MaritimeGillinghamUK
| | - Andy M. Bailey
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Gary D. Foster
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
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9
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Systems level profiling of arginine starvation reveals MYC and ERK adaptive metabolic reprogramming. Cell Death Dis 2020; 11:662. [PMID: 32814773 PMCID: PMC7438517 DOI: 10.1038/s41419-020-02899-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022]
Abstract
Arginine auxotrophy due to the silencing of argininosuccinate synthetase 1 (ASS1) occurs in many carcinomas and in the majority of sarcomas. Arginine deiminase (ADI-PEG20) therapy exploits this metabolic vulnerability by depleting extracellular arginine, causing arginine starvation. ASS1-negative cells develop resistance to ADI-PEG20 through a metabolic adaptation that includes re-expressing ASS1. As arginine-based multiagent therapies are being developed, further characterization of the changes induced by arginine starvation is needed. In order to develop a systems-level understanding of these changes, activity-based proteomic profiling (ABPP) and phosphoproteomic profiling were performed before and after ADI-PEG20 treatment in ADI-PEG20-sensitive and resistant sarcoma cells. When integrated with metabolomic profiling, this multi-omic analysis reveals that cellular response to arginine starvation is mediated by adaptive ERK signaling and activation of the Myc–Max transcriptional network. Concomitantly, these data elucidate proteomic changes that facilitate oxaloacetate production by enhancing glutamine and pyruvate anaplerosis and altering lipid metabolism to recycle citrate for oxidative glutaminolysis. Based on the complexity of metabolic and cellular signaling interactions, these multi-omic approaches could provide valuable tools for evaluating response to metabolically targeted therapies.
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10
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Hamza GM, Bergo VB, Mamaev S, Wojchowski DM, Toran P, Worsfold CR, Castaldi MP, Silva JC. Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics. Int J Mol Sci 2020; 21:E2016. [PMID: 32188029 PMCID: PMC7139916 DOI: 10.3390/ijms21062016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed "Affinity-Bead Assisted Mass Spectrometry" (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.
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Affiliation(s)
- Ghaith M. Hamza
- Discovery Sciences, BioPharmaceutical R&D, AstraZeneca, Boston, MA 02451, USA; (G.M.H.); (M.P.C.)
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | - Vladislav B. Bergo
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
| | - Sergey Mamaev
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
| | - Don M. Wojchowski
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | - Paul Toran
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | | | - M. Paola Castaldi
- Discovery Sciences, BioPharmaceutical R&D, AstraZeneca, Boston, MA 02451, USA; (G.M.H.); (M.P.C.)
| | - Jeffrey C. Silva
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
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11
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Alqahtani FM, Arivett BA, Taylor ZE, Handy ST, Farone AL, Farone MB. Chemogenomic profiling to understand the antifungal action of a bioactive aurone compound. PLoS One 2019; 14:e0226068. [PMID: 31825988 PMCID: PMC6905557 DOI: 10.1371/journal.pone.0226068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
Every year, more than 250,000 invasive candidiasis infections are reported with 50,000 deaths worldwide. The limited number of antifungal agents necessitates the need for alternative antifungals with potential novel targets. The 2-benzylidenebenzofuran-3-(2H)-ones have become an attractive scaffold for antifungal drug design. This study aimed to determine the antifungal activity of a synthetic aurone compound and characterize its mode of action. Using the broth microdilution method, aurone SH1009 exhibited inhibition against C. albicans, including resistant isolates, as well as C. glabrata, and C. tropicalis with IC50 values of 4-29 μM. Cytotoxicity assays using human THP-1, HepG2, and A549 human cell lines showed selective toxicity toward fungal cells. The mode of action for SH1009 was characterized using chemical-genetic interaction via haploinsufficiency (HIP) and homozygous (HOP) profiling of a uniquely barcoded Saccharomyces cerevisiae mutant collection. Approximately 5300 mutants were competitively treated with SH1009 followed by DNA extraction, amplification of unique barcodes, and quantification of each mutant using multiplexed next-generation sequencing. Barcode post-sequencing analysis revealed 238 sensitive and resistant mutants that significantly (FDR P values ≤ 0.05) responded to aurone SH1009. The enrichment analysis of KEGG pathways and gene ontology demonstrated the cell cycle pathway as the most significantly enriched pathway along with DNA replication, cell division, actin cytoskeleton organization, and endocytosis. Phenotypic studies of these significantly enriched responses were validated in C. albicans. Flow cytometric analysis of SH1009-treated C. albicans revealed a significant accumulation of cells in G1 phase, indicating cell cycle arrest. Fluorescence microscopy detected abnormally interrupted actin dynamics, resulting in enlarged, unbudded cells. RT-qPCR confirmed the effects of SH1009 in differentially expressed cell cycle, actin polymerization, and signal transduction genes. These findings indicate the target of SH1009 as a cell cycle-dependent organization of the actin cytoskeleton, suggesting a novel mode of action of the aurone compound as an antifungal inhibitor.
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Affiliation(s)
- Fatmah M. Alqahtani
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Brock A. Arivett
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Zachary E. Taylor
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Scott T. Handy
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Anthony L. Farone
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Mary B. Farone
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
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12
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Liu X, Miao W, Huang M, Li L, Dai X, Wang Y. Elevated Hexokinase II Expression Confers Acquired Resistance to 4-Hydroxytamoxifen in Breast Cancer Cells. Mol Cell Proteomics 2019; 18:2273-2284. [PMID: 31519767 PMCID: PMC6823848 DOI: 10.1074/mcp.ra119.001576] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/26/2019] [Indexed: 12/11/2022] Open
Abstract
Tamoxifen has been clinically used in treating estrogen receptor (ER)-positive breast cancer for over 30 years. The most challenging aspect associated with tamoxifen therapy is the development of resistance in initially responsive breast tumors. We applied a parallel-reaction monitoring (PRM)-based quantitative proteomic method to examine the differential expression of kinase proteins in MCF-7 and the isogenic tamoxifen-resistant (TamR) cells. We were able to quantify the relative protein expression levels of 315 kinases, among which hexokinase 2 (HK2) and mTOR were up-regulated in TamR MCF-7 cells. We also observed that the TamR MCF-7 cells exhibited elevated rate of glycolysis than the parental MCF-7 cells. In addition, we found that phosphorylation of S6K - a target of mTOR - was much lower in TamR MCF-7 cells, and this phosphorylation level could be restored upon genetic depletion or pharmacological inhibition of HK2. Reciprocally, the level of S6K phosphorylation was diminished upon overexpression of HK2 in MCF-7 cells. Moreover, we observed that HK2 interacts with mTOR, and this interaction inhibits mTOR activity. Lower mTOR activity led to augmented autophagy, which conferred resistance of MCF-7 cells toward tamoxifen. Together, our study demonstrates that elevated expression of HK2 promotes autophagy through inhibiting the mTOR-S6K signaling pathway and results in resistance of MCF-7 breast cancer cells toward tamoxifen; thus, our results uncovered, for the first time, HK2 as a potential therapeutic target for overcoming tamoxifen resistance.
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Affiliation(s)
- Xiaochuan Liu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521
| | - Weili Miao
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521
| | - Ming Huang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521
| | - Lin Li
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521
| | - Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521; Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521.
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13
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Bioinformatic Analysis of Transcriptomic Data Reveals Novel Key Genes Regulating Osteogenic Differentiation of Human Adipose Stem Cells. Stem Cells Int 2019; 2019:1705629. [PMID: 31467558 PMCID: PMC6701308 DOI: 10.1155/2019/1705629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/02/2019] [Accepted: 05/21/2019] [Indexed: 12/22/2022] Open
Abstract
Adipose stem cells (ASCs) are an attractive cell source for treating many human diseases including osteoporosis. However, the molecular mechanisms accounting for ASC osteogenesis are poorly known. In this study, ASCs were first isolated from the fat tissues from the patients with osteoporosis. The global transcriptome profile between osteogenic differentiated ASCs and undifferentiated ASCs was compared using RNA sequencing (RNA-seq). Then, bioinformatic analysis was performed to reveal the central genes and pathways that regulated the osteogenic differentiation of ASCs. One of the interested genes C5AR1 was chosen for further investigation. A total of 1521 upregulated and 3020 downregulated genes were identified between the ASCs with osteogenic induction and controls. Functional gene ontology analysis revealed that these significantly differentially expressed genes (DEGs) were associated with cell cycle, protein binding, and nucleotide binding. Pathway analysis showed that many canonical pathways, such as the MAPK signaling pathway and the PI3K-AKT pathway, might actively be involved in regulating osteogenic differentiation of ASCs. A total of three subnetworks and 20 central nodes were identified by the protein-protein interaction analysis. In addition, the expression level of C5AR1 was significantly increased during osteogenic differentiation of ASCs. The downregulation of C5AR1 dramatically reduced the expression levels of osteogenic differentiation biomarkers and calcium nodule formation capacity. Collectively, we have provided a number of novel genes and pathways that might be indispensable for ASC osteogenic differentiation. Manipulating the levels of this candidate gene might contribute to the osteoporosis therapy.
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14
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Vaz C, Reales-Calderon JA, Pitarch A, Vellosillo P, Trevisan M, Hernáez ML, Monteoliva L, Gil C. Enrichment of ATP Binding Proteins Unveils Proteomic Alterations in Human Macrophage Cell Death, Inflammatory Response, and Protein Synthesis after Interaction with Candida albicans. J Proteome Res 2019; 18:2139-2159. [PMID: 30985132 DOI: 10.1021/acs.jproteome.9b00032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Macrophages are involved in the primary human response to Candida albicans. After pathogen recognition, signaling pathways are activated, leading to the production of cytokines, chemokines, and antimicrobial peptides. ATP binding proteins are crucial for this regulation. Here, a quantitative proteomic and phosphoproteomic approach was carried out for the study of human macrophage ATP-binding proteins after interaction with C. albicans. From a total of 547 nonredundant quantified proteins, 137 were ATP binding proteins and 59 were detected as differentially abundant. From the differentially abundant ATP-binding proteins, 6 were kinases (MAP2K2, SYK, STK3, MAP3K2, NDKA, and SRPK1), most of them involved in signaling pathways. Furthermore, 85 phosphopeptides were quantified. Macrophage proteomic alterations including an increase of protein synthesis with a consistent decrease in proteolysis were observed. Besides, macrophages showed changes in proteins of endosomal trafficking together with mitochondrial proteins, including some involved in the response to oxidative stress. Regarding cell death mechanisms, an increase of antiapoptotic over pro-apoptotic signals is suggested. Furthermore, a high pro-inflammatory response was detected, together with no upregulation of key mi-RNAs involved in the negative feedback of this response. These findings illustrate a strategy to deepen the knowledge of the complex interactions between the host and the clinically important pathogen C. albicans.
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Affiliation(s)
- Catarina Vaz
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain
| | - Jose Antonio Reales-Calderon
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain
| | - Aida Pitarch
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain
| | - Perceval Vellosillo
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain
| | - Marco Trevisan
- Laboratorio de Proteómica Cardiovascular , Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid , Spain
| | - María Luisa Hernáez
- Unidad de Proteómica , Universidad Complutense de Madrid , 28040 Madrid , Spain
| | - Lucía Monteoliva
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain
| | - Concha Gil
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain.,Unidad de Proteómica , Universidad Complutense de Madrid , 28040 Madrid , Spain
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15
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Yan Z, Deng P, Liu Y. Recent Advances in Protein Kinase Activity Analysis Based on Nanomaterials. Int J Mol Sci 2019; 20:ijms20061440. [PMID: 30901923 PMCID: PMC6471164 DOI: 10.3390/ijms20061440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022] Open
Abstract
Protein phosphorylation regulated by protein kinases, as well as their dephosphorylation, is one of the most common post-translational modifications, and plays important roles in physiological activities, such as intracellular signal communications, gene transcription, cell proliferation and apoptosis. Over-expression of protein kinases is closely associated with various diseases. Consequently, accurate detection of protein kinases activities and their relevant inhibitors screening is critically important, not only to the biochemical research, but also to the clinical diagnosis and therapy. Nanomaterials, taking advantage of large surface areas, as well as excellent electrical, catalytic, magnetic and optical properties, have been utilized as target concentrators, recognition components, signal transducer or amplification elements in protein kinase related assays. This review summarizes the recent representative works to highlight the applications of nanomaterials in different biosensor technologies for protein kinases activities detection and their inhibitors screening. First, different nanomaterials developed for phosphoprotein/phosphopeptide enrichment and phosphate recognition are introduced. Next, representative works are selected that mainly focus on the utilization of nanomaterials as signal transducer or amplification elements in various protein kinases sensing platforms, such as electrochemical, colorimetric, fluorescent, and mass spectroscopy-based approaches. Finally, the major challenges and perspectives of nanomaterials being applied in protein kinases related assays are discussed.
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Affiliation(s)
- Zhiyong Yan
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology of Ministry of Education, Tsinghua University, Beijing 100084, China.
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Pingye Deng
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Yang Liu
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology of Ministry of Education, Tsinghua University, Beijing 100084, China.
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16
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Garcia L, Girod M, Rompais M, Dugourd P, Carapito C, Lemoine J. Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset. Anal Chem 2018; 90:3928-3935. [PMID: 29465226 DOI: 10.1021/acs.analchem.7b04821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Thanks to comprehensive and unbiased sampling of all precursor ions, the interest to move toward bottom-up proteomic with data-independent acquisition (DIA) is continuously growing. DIA offers precision and reproducibility performances comparable to true targeted methods but has the advantage of enabling retrospective data testing with the hypothetical presence of new proteins of interest. Nonetheless, the chimeric nature of DIA MS/MS spectra inherent to concomitant transmission of a multiplicity of precursor ions makes the confident identification of peptides often challenging, even with spectral library-based extraction strategy. The introduction of specificity at the fragmentation step upon ultraviolet or visible laser-induced dissociation (LID) range targeting only the subset of cysteine-containing peptides (Cys-peptide) has been proposed as an option to streamline and reduce the search space. Here, we describe the first coupling between DIA and visible LID at 473 nm to test for the presence of Cys-peptides with a peptide-centric approach. As a test run, a spectral library was built for a pool of Cys-synthetic peptides used as surrogates of human kinases (1 peptide per protein). By extracting ion chromatograms of query standard and kinase peptides spiked at different concentration levels in an Escherichia coli proteome lysate, DIA-LID demonstrates a dynamic range of detection of at least 3 decades and coefficients of precision better than 20%. Finally, the spectral library was used to search for endogenous kinases in human cellular extract.
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Affiliation(s)
- Lény Garcia
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , UMR 5280, 5 rue de la Doua , F-69100 Villeurbanne , France
| | - Marion Girod
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , UMR 5280, 5 rue de la Doua , F-69100 Villeurbanne , France
| | - Magali Rompais
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC , Université de Strasbourg, CNRS , UMR 7178, 25 rue Becquerel , 67087 Strasbourg , France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC , Université de Strasbourg, CNRS , UMR 7178, 25 rue Becquerel , 67087 Strasbourg , France
| | - Jérôme Lemoine
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , UMR 5280, 5 rue de la Doua , F-69100 Villeurbanne , France
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17
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Zeng L, Wang WH, Arrington J, Shao G, Geahlen RL, Hu CD, Tao WA. Identification of Upstream Kinases by Fluorescence Complementation Mass Spectrometry. ACS CENTRAL SCIENCE 2017; 3:1078-1085. [PMID: 29104924 PMCID: PMC5658758 DOI: 10.1021/acscentsci.7b00261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Indexed: 05/09/2023]
Abstract
Protein kinases and their substrates comprise extensive signaling networks that regulate many diverse cellular functions. However, methods and techniques to systematically identify kinases directly responsible for specific phosphorylation events have remained elusive. Here we describe a novel proteomic strategy termed fluorescence complementation mass spectrometry (FCMS) to identify kinase-substrate pairs in high throughput. The FCMS strategy employs a specific substrate and a kinase library, both of which are fused with fluorescence complemented protein fragments. Transient and weak kinase-substrate interactions in living cells are stabilized by the association of fluorescence protein fragments. These kinase-substrate pairs are then isolated with high specificity and are identified and quantified by LC-MS. FCMS was applied to the identification of both known and novel kinases of the transcription factor, cAMP response element-binding protein (CREB). Novel CREB kinases were validated by in vitro kinase assays, and the phosphorylation sites were unambiguously located. These results uncovered possible new roles for CREB in multiple important signaling pathways and demonstrated the great potential of this new proteomic strategy.
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Affiliation(s)
- Lingfei Zeng
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Wen-Horng Wang
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Justine Arrington
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Gengbao Shao
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Robert L. Geahlen
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue
Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chang-Deng Hu
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue
Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - W. Andy Tao
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department
of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue
Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- E-mail:
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18
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Caira S, Nicolai MA, Lilla S, Calabrese MG, Pinto G, Scaloni A, Chianese L, Addeo F. Eventual limits of the current EU official method for evaluating milk adulteration of water buffalo dairy products and potential proteomic solutions. Food Chem 2017; 230:482-490. [DOI: 10.1016/j.foodchem.2017.03.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/03/2017] [Accepted: 03/09/2017] [Indexed: 10/20/2022]
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19
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Werth EG, McConnell EW, Gilbert TSK, Couso Lianez I, Perez CA, Manley CK, Graves LM, Umen JG, Hicks LM. Probing the global kinome and phosphoproteome in Chlamydomonas reinhardtii via sequential enrichment and quantitative proteomics. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:416-426. [PMID: 27671103 DOI: 10.1111/tpj.13384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
The identification of dynamic protein phosphorylation events is critical for understanding kinase/phosphatase-regulated signaling pathways. To date, protein phosphorylation and kinase expression have been examined independently in photosynthetic organisms. Here we present a method to study the global kinome and phosphoproteome in tandem in a model photosynthetic organism, the alga Chlamydomonas reinhardtii (Chlamydomonas), using mass spectrometry-based label-free proteomics. A dual enrichment strategy targets intact protein kinases via capture on immobilized multiplexed inhibitor beads with subsequent proteolytic digestion of unbound proteins and peptide-based phosphorylation enrichment. To increase depth of coverage, both data-dependent and data-independent (via SWATH, Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra) mass spectrometric acquisitions were performed to obtain a more than 50% increase in coverage of the enriched Chlamydomonas kinome over coverage found with no enrichment. The quantitative phosphoproteomic dataset yielded 2250 phosphopeptides and 1314 localized phosphosites with excellent reproducibility across biological replicates (90% of quantified sites with coefficient of variation below 11%). This approach enables simultaneous investigation of kinases and phosphorylation events at the global level to facilitate understanding of kinase networks and their influence in cell signaling events.
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Affiliation(s)
- Emily G Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
| | - Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
| | - Thomas S Karim Gilbert
- The Department of Pharmacology, The University of North Carolina at Chapel Hill, NC 27599, USA
| | | | - Carlos A Perez
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
| | - Cherrel K Manley
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
| | - Lee M Graves
- The Department of Pharmacology, The University of North Carolina at Chapel Hill, NC 27599, USA
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
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20
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Yuan LL, Wauson E, Duric V. Kinase-mediated signaling cascades in mood disorders and antidepressant treatment. J Neurogenet 2016; 30:178-184. [PMID: 27785950 PMCID: PMC5590647 DOI: 10.1080/01677063.2016.1245303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/29/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
Abstract
Kinase-mediated signaling cascades regulate a number of different molecular mechanisms involved in cellular homeostasis, and are viewed as one of the most common intracellular processes that are robustly dysregulated in the pathophysiology of mood disorders such as depression. Newly emerged, rapid acting antidepressants are able to achieve therapeutic improvement, possibly in part, through stimulating activity of kinase-dependent signaling pathways. Thus, advancements in our understanding of how kinases may contribute to development and treatment of depression seem crucial. However, current investigations are limited to a single or small number of kinases and are unable to detect novel kinases. Here, we review fast developing kinome profiling approaches that allow identification of multiple kinases and kinase network connections simultaneously, analyze technical limitation and challenges, and discuss their future applications to mood disorders and antidepressant treatment.
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Affiliation(s)
- Li-Lian Yuan
- Department of Physiology and Pharmacology, Des Moines University, Des Moines, IA 50312, USA
| | - Eric Wauson
- Department of Physiology and Pharmacology, Des Moines University, Des Moines, IA 50312, USA
| | - Vanja Duric
- Department of Physiology and Pharmacology, Des Moines University, Des Moines, IA 50312, USA
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21
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Médard G, Pachl F, Ruprecht B, Klaeger S, Heinzlmeir S, Helm D, Qiao H, Ku X, Wilhelm M, Kuehne T, Wu Z, Dittmann A, Hopf C, Kramer K, Kuster B. Optimized chemical proteomics assay for kinase inhibitor profiling. J Proteome Res 2015; 14:1574-86. [PMID: 25660469 DOI: 10.1021/pr5012608] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Solid supported probes have proven to be an efficient tool for chemical proteomics. The kinobeads technology features kinase inhibitors covalently attached to Sepharose for affinity enrichment of kinomes from cell or tissue lysates. This technology, combined with quantitative mass spectrometry, is of particular interest for the profiling of kinase inhibitors. It often leads to the identification of new targets for medicinal chemistry campaigns where it allows a two-in-one binding and selectivity assay. The assay can also uncover resistance mechanisms and molecular sources of toxicity. Here we report on the optimization of the kinobead assay resulting in the combination of five chemical probes and four cell lines to cover half the human kinome in a single assay (∼ 260 kinases). We show the utility and large-scale applicability of the new version of kinobeads by reprofiling the small molecule kinase inhibitors Alvocidib, Crizotinib, Dasatinib, Fasudil, Hydroxyfasudil, Nilotinib, Ibrutinib, Imatinib, and Sunitinib.
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Affiliation(s)
- Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technische Universität München , Freising, Germany
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