1
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Russo GC, Crawford AJ, Clark D, Cui J, Carney R, Karl MN, Su B, Starich B, Lih TS, Kamat P, Zhang Q, Nair PR, Wu PH, Lee MH, Leong HS, Zhang H, Rebecca VW, Wirtz D. E-cadherin interacts with EGFR resulting in hyper-activation of ERK in multiple models of breast cancer. Oncogene 2024; 43:1445-1462. [PMID: 38509231 DOI: 10.1038/s41388-024-03007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024]
Abstract
The loss of intercellular adhesion molecule E-cadherin is a hallmark of the epithelial-mesenchymal transition (EMT), during which tumor cells transition into an invasive phenotype. Accordingly, E-cadherin has long been considered a tumor suppressor gene; however, E-cadherin expression is paradoxically correlated with breast cancer survival rates. Using novel multi-compartment organoids and multiple in vivo models, we show that E-cadherin promotes a hyper-proliferative phenotype in breast cancer cells via interaction with the transmembrane receptor EGFR. The E-cad and EGFR interaction results in activation of the MEK/ERK signaling pathway, leading to a significant increase in proliferation via activation of transcription factors, including c-Fos. Pharmacological inhibition of MEK activity in E-cadherin positive breast cancer significantly decreases both tumor growth and macro-metastasis in vivo. This work provides evidence for a novel role of E-cadherin in breast tumor progression and identifies a new target to treat hyper-proliferative E-cadherin-positive breast tumors, thus providing the foundation to utilize E-cadherin as a biomarker for specific therapeutic success.
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Affiliation(s)
- Gabriella C Russo
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
- Johns Hopkins Physical Sciences-Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Ashleigh J Crawford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
- Johns Hopkins Physical Sciences-Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - David Clark
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Julie Cui
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Ryan Carney
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Michelle N Karl
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
- Johns Hopkins Physical Sciences-Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Boyang Su
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Bartholomew Starich
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
- Johns Hopkins Physical Sciences-Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Tung-Shing Lih
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Pratik Kamat
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
- Johns Hopkins Physical Sciences-Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Qiming Zhang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Praful R Nair
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
- Johns Hopkins Physical Sciences-Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Pei-Hsun Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
- Johns Hopkins Physical Sciences-Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Meng-Horng Lee
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Hon S Leong
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Vito W Rebecca
- Department of Biochemistry and Molecular Biology, Johns Hopkins University School of Public Health, Baltimore, MD, 21231, USA
| | - Denis Wirtz
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA.
- Johns Hopkins Physical Sciences-Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA.
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2
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Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
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Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
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3
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Zittlau K, Nashier P, Cavarischia-Rega C, Macek B, Spät P, Nalpas N. Recent progress in quantitative phosphoproteomics. Expert Rev Proteomics 2023; 20:469-482. [PMID: 38116637 DOI: 10.1080/14789450.2023.2295872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Protein phosphorylation is a critical post-translational modification involved in the regulation of numerous cellular processes from signal transduction to modulation of enzyme activities. Knowledge of dynamic changes of phosphorylation levels during biological processes, under various treatments or between healthy and disease models is fundamental for understanding the role of each phosphorylation event. Thereby, LC-MS/MS based technologies in combination with quantitative proteomics strategies evolved as a powerful strategy to investigate the function of individual protein phosphorylation events. AREAS COVERED State-of-the-art labeling techniques including stable isotope and isobaric labeling provide precise and accurate quantification of phosphorylation events. Here, we review the strengths and limitations of recent quantification methods and provide examples based on current studies, how quantitative phosphoproteomics can be further optimized for enhanced analytic depth, dynamic range, site localization, and data integrity. Specifically, reducing the input material demands is key to a broader implementation of quantitative phosphoproteomics, not least for clinical samples. EXPERT OPINION Despite quantitative phosphoproteomics is one of the most thriving fields in the proteomics world, many challenges still have to be overcome to facilitate even deeper and more comprehensive analyses as required in the current research, especially at single cell levels and in clinical diagnostics.
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Affiliation(s)
- Katharina Zittlau
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Payal Nashier
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Claudia Cavarischia-Rega
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Boris Macek
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Philipp Spät
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Nicolas Nalpas
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
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4
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Mahumud RA, Shahjalal M. The Emerging Burden of Genetic Instability and Mutation in Melanoma: Role of Molecular Mechanisms. Cancers (Basel) 2022; 14:cancers14246202. [PMID: 36551688 PMCID: PMC9776466 DOI: 10.3390/cancers14246202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Melanoma is a severe skin cancer affecting thousands of people and a growing public health concern worldwide. The potential hallmarks of melanoma are genetic instability and mutation (GIAM), which are driving mechanisms for phenotypic variation and adaptation in melanoma. In metastatic melanoma, DNA repair-associated genes are frequently expressed at higher levels than in primary cancers, suggesting melanoma cells rely on genetic stability to spread distantly. The tumour microenvironment is affected by genomic instability and melanoma mutation (GIMM), which plays significant roles in developing GIMM and their contributions to the overall disease burden. The GIAM is the crucial vulnerability of cancer cells, determining their sensitivity to harmful treatments, including radiation and many chemotherapeutics. The high incidence of melanoma is typically associated with genetic modifications, and several clinical and genetic interventions have been critical in easing the burden.
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Affiliation(s)
- Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Correspondence:
| | - Md. Shahjalal
- Department of Public Health, North South University, Dhaka 1229, Bangladesh
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5
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Srinivasan A, Sing JC, Gingras AC, Röst HL. Improving Phosphoproteomics Profiling Using Data-Independent Mass Spectrometry. J Proteome Res 2022; 21:1789-1799. [PMID: 35877786 DOI: 10.1021/acs.jproteome.2c00172] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry-based profiling of the phosphoproteome is a powerful method of identifying phosphorylation events at a systems level. Most phosphoproteomics studies have used data-dependent acquisition (DDA) mass spectrometry as their method of choice. In this Perspective, we review some recent studies benchmarking DDA and DIA methods for phosphoproteomics and discuss data analysis options for DIA phosphoproteomics. In order to evaluate the impact of data-dependent and data-independent acquisition (DIA) on identification and quantification, we analyze a previously published phosphopeptide-enriched data set consisting of 10 replicates acquired by DDA and DIA each. We find that though more unique identifications are made in DDA data, phosphopeptides are identified more consistently across replicates in DIA. We further discuss the challenges of identifying chromatographically coeluting phosphopeptide isomers and investigate the impact on reproducibility of identifying high-confidence site-localized phosphopeptides in replicates.
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Affiliation(s)
- Aparna Srinivasan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Justin C Sing
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Hannes L Röst
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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6
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Cai W, Nguyen MQ, Wilski NA, Purwin TJ, Vernon M, Tiago M, Aplin AE. A Genome-Wide Screen Identifies PDPK1 as a Target to Enhance the Efficacy of MEK1/2 Inhibitors in NRAS Mutant Melanoma. Cancer Res 2022; 82:2625-2639. [PMID: 35657206 PMCID: PMC9298960 DOI: 10.1158/0008-5472.can-21-3217] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/22/2022] [Accepted: 05/31/2022] [Indexed: 01/21/2023]
Abstract
Melanomas frequently harbor activating NRAS mutations. However, limited advance has been made in developing targeted therapy options for patients with NRAS mutant melanoma. MEK inhibitors (MEKi) show modest efficacy in the clinic and their actions need to be optimized. In this study, we performed a genome-wide CRISPR-Cas9-based screen and demonstrated that loss of phosphoinositide-dependent kinase-1 (PDPK1) enhances the efficacy of MEKi. The synergistic effects of PDPK1 loss and MEKi was validated in NRAS mutant melanoma cell lines using pharmacologic and molecular approaches. Combined PDPK1 inhibitors (PDPK1i) with MEKi suppressed NRAS mutant xenograft growth and induced gasdermin E-associated pyroptosis. In an immune-competent allograft model, PDPK1i+MEKi increased the ratio of intratumoral CD8+ T cells, delayed tumor growth, and prolonged survival; the combination treatment was less effective against tumors in immune-deficient mice. These data suggest PDPK1i+MEKi as an efficient immunostimulatory strategy against NRAS mutant melanoma. SIGNIFICANCE Targeting PDPK1 stimulates antitumor immunity and sensitizes NRAS mutant melanoma to MEK inhibition, providing rationale for the clinical development of a combinatorial approach for treating patients with melanoma.
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Affiliation(s)
- Weijia Cai
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Mai Q. Nguyen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Nicole A. Wilski
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Timothy J. Purwin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Megane Vernon
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Manoela Tiago
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Andrew E. Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107
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7
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Lüke F, Harrer DC, Pantziarka P, Pukrop T, Ghibelli L, Gerner C, Reichle A, Heudobler D. Drug Repurposing by Tumor Tissue Editing. Front Oncol 2022; 12:900985. [PMID: 35814409 PMCID: PMC9270020 DOI: 10.3389/fonc.2022.900985] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
The combinatory use of drugs for systemic cancer therapy commonly aims at the direct elimination of tumor cells through induction of apoptosis. An alternative approach becomes the focus of attention if biological changes in tumor tissues following combinatory administration of regulatorily active drugs are considered as a therapeutic aim, e.g., differentiation, transdifferentiation induction, reconstitution of immunosurveillance, the use of alternative cell death mechanisms. Editing of the tumor tissue establishes new biological ‘hallmarks’ as a ‘pressure point’ to attenuate tumor growth. This may be achieved with repurposed, regulatorily active drug combinations, often simultaneously targeting different cell compartments of the tumor tissue. Moreover, tissue editing is paralleled by decisive functional changes in tumor tissues providing novel patterns of target sites for approved drugs. Thus, agents with poor activity in non-edited tissue may reveal new clinically meaningful outcomes. For tissue editing and targeting edited tissue novel requirements concerning drug selection and administration can be summarized according to available clinical and pre-clinical data. Monoactivity is no pre-requisite, but combinatory bio-regulatory activity. The regulatorily active dose may be far below the maximum tolerable dose, and besides inhibitory active drugs stimulatory drug activities may be integrated. Metronomic scheduling often seems to be of advantage. Novel preclinical approaches like functional assays testing drug combinations in tumor tissue are needed to select potential drugs for repurposing. The two-step drug repurposing procedure, namely establishing novel functional systems states in tumor tissues and consecutively providing novel target sites for approved drugs, facilitates the systematic identification of drug activities outside the scope of any original clinical drug approvals.
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Affiliation(s)
- Florian Lüke
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
- Division of Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine, Regensburg, Germany
| | - Dennis Christoph Harrer
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Pan Pantziarka
- The George Pantziarka TP53 Trust, London, United Kingdom
| | - Tobias Pukrop
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
- Bavarian Cancer Research Center (BZKF), University Hospital Regensburg, Regensburg, Germany
| | - Lina Ghibelli
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Albrecht Reichle
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Daniel Heudobler
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
- Bavarian Cancer Research Center (BZKF), University Hospital Regensburg, Regensburg, Germany
- *Correspondence: Daniel Heudobler, , orcid.org/0000-0002-8790-4584
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8
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Yunga ST, Gower AJ, Melrose AR, Fitzgerald MK, Rajendran A, Lusardi TA, Armstrong RJ, Minnier J, Jordan KR, McCarty OJT, David LL, Wilmarth PA, Reddy AP, Aslan JE. Effects of ex vivo blood anticoagulation and preanalytical processing time on the proteome content of platelets. J Thromb Haemost 2022; 20:1437-1450. [PMID: 35253976 PMCID: PMC9887642 DOI: 10.1111/jth.15694] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Ex vivo assays of platelet function critically inform mechanistic and clinical hematology studies, where effects of divergent blood processing methods on platelet composition are apparent, but unspecified. OBJECTIVE Here, we evaluate how different blood anticoagulation options and processing times affect platelet function and protein content ex vivo. METHODS Parallel blood samples were collected from healthy human donors into sodium citrate, acid citrate dextrose, EDTA or heparin, and processed over an extended time course for functional and biochemical experiments, including platelet proteome quantification with multiplexed tandem mass tag (TMT) labeling and triple quadrupole mass spectrometry (MS). RESULTS Each anticoagulant had time-dependent effects on platelet function in whole blood. For instance, heparin enhanced platelet agonist reactivity, platelet-monocyte aggregate formation and platelet extracellular vesicle release, while EDTA increased platelet α-granule secretion. Following platelet isolation, TMT-MS quantified 3357 proteins amongst all prepared platelet samples. Altogether, >400 proteins were differentially abundant in platelets isolated from blood processed at 24 h versus 1 h post-phlebotomy, including proteins pertinent to membrane trafficking and exocytosis. Anticoagulant-specific effects on platelet proteomes included increased complement system and decreased α-granule proteins in platelets from EDTA-anticoagulated blood. Platelets prepared from heparinized blood had higher levels of histone and neutrophil-associated proteins in a manner related to neutrophil extracellular trap (NET) formation and platelet:NET interactions in whole blood ex vivo. CONCLUSION Our results demonstrate that different anticoagulants routinely used for blood collection have varying effects on platelets ex vivo, where methodology-associated alterations in platelet proteome may influence mechanistic, translational and biomarker studies.
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Affiliation(s)
- Samuel Tassi Yunga
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Austin J. Gower
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Alexander R. Melrose
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Meghan K. Fitzgerald
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Ashmitha Rajendran
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Theresa A. Lusardi
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Randall J. Armstrong
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Jessica Minnier
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Kelley R. Jordan
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Owen J. T. McCarty
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Larry L. David
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Chemical Physiology & Biochemistry, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Ashok P. Reddy
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Joseph E. Aslan
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Chemical Physiology & Biochemistry, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
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9
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Paulo JA, Schweppe DK. Advances in quantitative high-throughput phosphoproteomics with sample multiplexing. Proteomics 2021; 21:e2000140. [PMID: 33455035 DOI: 10.1002/pmic.202000140] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
Eukaryotic protein phosphorylation modulates nearly every major biological process. Phosphorylation regulates protein activity, mediates cellular signal transduction, and manipulates cellular structure. Consequently, the dysregulation of kinase and phosphatase pathways has been linked to a multitude of diseases. Mass spectrometry-based proteomic techniques are increasingly used for the global interrogation of perturbations in phosphorylation-based cellular signaling. Strategies for studying phosphoproteomes require high-specificity enrichment, sensitive detection, and accurate localization of phosphorylation sites with advanced LC-MS/MS techniques and downstream informatics. Sample multiplexing with isobaric tags has also been integral to recent advancements in throughput and sensitivity for phosphoproteomic studies. Each of these facets of phosphoproteomics analysis present distinct challenges and thus opportunities for improvement and innovation. Here, we review current methodologies, explore persistent challenges, and discuss the outlook for isobaric tag-based quantitative phosphoproteomic analysis.
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Affiliation(s)
- Joao A Paulo
- Harvard Medical School, Boston, Massachusetts, USA
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10
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Gaun A, Lewis Hardell KN, Olsson N, O'Brien JJ, Gollapudi S, Smith M, McAlister G, Huguet R, Keyser R, Buffenstein R, McAllister FE. Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice. J Proteome Res 2021; 20:1280-1295. [PMID: 33499602 DOI: 10.1021/acs.jproteome.0c00681] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Performing large-scale plasma proteome profiling is challenging due to limitations imposed by lengthy preparation and instrument time. We present a fully automated multiplexed proteome profiling platform (AutoMP3) using the Hamilton Vantage liquid handling robot capable of preparing hundreds to thousands of samples. To maximize protein depth in single-shot runs, we combined 16-plex Tandem Mass Tags (TMTpro) with high-field asymmetric waveform ion mobility spectrometry (FAIMS Pro) and real-time search (RTS). We quantified over 40 proteins/min/sample, doubling the previously published rates. We applied AutoMP3 to investigate the naked mole-rat plasma proteome both as a function of the circadian cycle and in response to ultraviolet (UV) treatment. In keeping with the lack of synchronized circadian rhythms in naked mole-rats, we find few circadian patterns in plasma proteins over the course of 48 h. Furthermore, we quantify many disparate changes between mice and naked mole-rats at both 48 h and one week after UV exposure. These species differences in plasma protein temporal responses could contribute to the pronounced cancer resistance observed in naked mole-rats. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD022891.
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Affiliation(s)
- Aleksandr Gaun
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Kaitlyn N Lewis Hardell
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States.,Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892-7315, United States
| | - Niclas Olsson
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Jonathon J O'Brien
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Sudha Gollapudi
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Megan Smith
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Graeme McAlister
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Robert Keyser
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Rochelle Buffenstein
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Fiona E McAllister
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
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11
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Iizuka S, Quintavalle M, Navarro JC, Gribbin KP, Ardecky RJ, Abelman MM, Ma CT, Sergienko E, Zeng FY, Pass I, Thomas GV, McWeeney SK, Hassig CA, Pinkerton AB, Courtneidge SA. Serine-Threonine Kinase TAO3-Mediated Trafficking of Endosomes Containing the Invadopodia Scaffold TKS5α Promotes Cancer Invasion and Tumor Growth. Cancer Res 2021; 81:1472-1485. [PMID: 33414172 DOI: 10.1158/0008-5472.can-20-2383] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 11/16/2022]
Abstract
Invadopodia are actin-based proteolytic membrane protrusions required for invasive behavior and tumor growth. In this study, we used our high-content screening assay to identify kinases whose activity affects invadopodia formation. Among the top hits selected for further analysis was TAO3, an STE20-like kinase of the GCK subfamily. TAO3 was overexpressed in many human cancers and regulated invadopodia formation in melanoma, breast, and bladder cancers. Furthermore, TAO3 catalytic activity facilitated melanoma growth in three-dimensional matrices and in vivo. A novel, potent catalytic inhibitor of TAO3 was developed that inhibited invadopodia formation and function as well as tumor cell extravasation and growth. Treatment with this inhibitor demonstrated that TAO3 activity is required for endosomal trafficking of TKS5α, an obligate invadopodia scaffold protein. A phosphoproteomics screen for TAO3 substrates revealed the dynein subunit protein LIC2 as a relevant substrate. Knockdown of LIC2 or expression of a phosphomimetic form promoted invadopodia formation. Thus, TAO3 is a new therapeutic target with a distinct mechanism of action. SIGNIFICANCE: An unbiased screening approach identifies TAO3 as a regulator of invadopodia formation and function, supporting clinical development of this class of target.
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Affiliation(s)
- Shinji Iizuka
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.,Department of Cell Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | | | - Jose C Navarro
- Department of Cell Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Kyle P Gribbin
- Department of Cell Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Robert J Ardecky
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Matthew M Abelman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Chen-Ting Ma
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Eduard Sergienko
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Fu-Yue Zeng
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Ian Pass
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - George V Thomas
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.,Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon.,Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, Oregon
| | - Christian A Hassig
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | | | - Sara A Courtneidge
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. .,Department of Cell Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon.,Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon
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12
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Rabiee B, Anwar KN, Shen X, Putra I, Liu M, Jung R, Afsharkhamseh N, Rosenblatt MI, Fishman GA, Liu X, Ghassemi M, Djalilian AR. Gene dosage manipulation alleviates manifestations of hereditary PAX6 haploinsufficiency in mice. Sci Transl Med 2020; 12:eaaz4894. [PMID: 33298563 DOI: 10.1126/scitranslmed.aaz4894] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 04/16/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022]
Abstract
In autosomal dominant conditions with haploinsufficiency, a single functional allele cannot maintain sufficient dosage for normal function. We hypothesized that pharmacologic induction of the wild-type allele could lead to gene dosage compensation and mitigation of the disease manifestations. The paired box 6 (PAX6) gene is crucial in tissue development and maintenance particularly in eye, brain, and pancreas. Aniridia is a panocular condition with impaired eye development and limited vision due to PAX6 haploinsufficiency. To test our hypothesis, we performed a chemical screen and found mitogen-activated protein kinase kinase (MEK) inhibitors to induce PAX6 expression in normal and mutant corneal cells. Treatment of newborn Pax6-deficient mice (Pax6Sey-Neu/+ ) with topical or systemic MEK inhibitor PD0325901 led to increased corneal PAX6 expression, improved corneal morphology, reduced corneal opacity, and enhanced ocular function. These results suggest that induction of the wild-type allele by drug repurposing is a potential therapeutic strategy for haploinsufficiencies, which is not limited to specific mutations.
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Affiliation(s)
- Behnam Rabiee
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Khandaker N Anwar
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Xiang Shen
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Ilham Putra
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Mingna Liu
- Departments of Biology and Psychology, University of Virginia, Charlottesville, VA 22903, USA
| | - Rebecca Jung
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Neda Afsharkhamseh
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Mark I Rosenblatt
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Gerald A Fishman
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
- Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, IL 60608, USA
| | - Xiaorong Liu
- Departments of Biology and Psychology, University of Virginia, Charlottesville, VA 22903, USA
| | - Mahmood Ghassemi
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Ali R Djalilian
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA.
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13
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TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nat Methods 2020; 17:399-404. [PMID: 32203386 DOI: 10.1038/s41592-020-0781-4] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/12/2020] [Indexed: 02/07/2023]
Abstract
Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on an isobutyl-proline immonium ion reporter structure (TMTpro) is presented. These reagents have similar characteristics to existing tandem mass tag reagents but with increased fragmentation efficiency and signal. In a proteome-scale example dataset, we compared eight common cell lines with and without Torin1 treatment with three replicates, quantifying more than 8,800 proteins (mean of 7.5 peptides per protein) per replicate with an analysis time of only 1.1 h per proteome. Finally, we modified the thermal stability assay to examine proteome-wide melting shifts after treatment with DMSO, 1 or 20 µM staurosporine with five replicates. This assay identified and dose-stratified staurosporine binding to 228 cellular kinases in just one, 18-h experiment. TMTpro reagents allow complex experimental designs-all with essentially no missing values across the 16 samples and no loss in quantitative integrity.
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14
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Schweppe DK, Rusin SF, Gygi SP, Paulo JA. Optimized Workflow for Multiplexed Phosphorylation Analysis of TMT-Labeled Peptides Using High-Field Asymmetric Waveform Ion Mobility Spectrometry. J Proteome Res 2019; 19:554-560. [PMID: 31799850 DOI: 10.1021/acs.jproteome.9b00759] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Phosphorylation is a post-translational modification with a vital role in cellular signaling. Isobaric labeling-based strategies, such as tandem mass tags (TMT), can measure the relative phosphorylation states of peptides in a multiplexed format. However, the low stoichiometry of protein phosphorylation constrains the depth of phosphopeptide analysis by mass spectrometry. As such, robust and sensitive workflows are required. Here we evaluate and optimize high-Field Asymmetric waveform Ion Mobility Spectrometry (FAIMS) coupled to Orbitrap Tribrid mass spectrometers for the analysis of TMT-labeled phosphopeptides. We determined that using FAIMS-MS3 with three compensation voltages (CV) in a single method (e.g., CV = -40/-60/-80 V) maximizes phosphopeptide coverage while minimizing inter-CV overlap. Furthermore, consecutive analyses using MSA-CID (multistage activation collision-induced dissociation) and HCD (higher-energy collisional dissociation) fragmentation at the MS2 stage increases the depth of phosphorylation analysis. The methodology and results outlined herein provide a template for tailoring optimized FAIMS-based methods.
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Affiliation(s)
- Devin K Schweppe
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Scott F Rusin
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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15
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Pre-clinical effects of highly potent MEK1/2 inhibitors on rat cerebral vasculature after organ culture and subarachnoid haemorrhage. Clin Sci (Lond) 2019; 133:1797-1811. [DOI: 10.1042/cs20190636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Background: Aneurysmal subarachnoid haemorrhage (SAH) is a variant of haemorrhagic stroke with a striking 50% mortality rate. In addition to the initial insult, secondary delayed brain injury may occur days after the initial ischemic insult and is associated with vasospasms leading to delayed cerebral ischemia. We have previously shown that the MEK1/2 inhibitor U0126 improves neurological assessment after SAH in rats. Aim: The purpose of the present study was to analyse the impact of a broad selection of high potency MEK1/2 inhibitors in an organ culture model and use the IC50 values obtained from the organ culture to select highly potent inhibitors for pre-clinical in vivo studies. Results: Nine highly potent mitogen activated protein kinase kinase (MEK1/2) inhibitors were screened and the two most potent inhibitors from the organ culture screening, trametinib and PD0325901, were tested in an in vivo experimental rat SAH model with intrathecal injections. Subsequently, the successful inhibitor trametinib was administered intraperitoneally in a second in vivo study. In both regimens, trametinib treatment caused significant reductions in the endothelin-1 induced contractility after SAH, which is believed to be associated with endothelin B receptor up-regulation. Trametinib treated rats showed improved neurological scores, evaluated by the ability to traverse a rotating pole, after induced SAH. Conclusion: The PD0325901 treatment did not improve the neurological score after SAH, nor showed any beneficial therapeutic effect on the contractility, contrasting with the reduction in neurological deficits seen after trametinib treatment. These data show that trametinib might be a potential candidate for treatment of SAH.
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16
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Wakeham CM, Wilmarth PA, Cunliffe JM, Klimek JE, Ren G, David LL, Morgans CW. Identification of PKCα-dependent phosphoproteins in mouse retina. J Proteomics 2019; 206:103423. [PMID: 31255707 DOI: 10.1016/j.jprot.2019.103423] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 12/11/2022]
Abstract
Adjusting to a wide range of light intensities is an essential feature of retinal rod bipolar cell (RBC) function. While persuasive evidence suggests this modulation involves phosphorylation by protein kinase C-alpha (PKCα), the targets of PKCα phosphorylation in the retina have not been identified. PKCα activity and phosphorylation in RBCs was examined by immunofluorescence confocal microscopy using a conformation-specific PKCα antibody and antibodies to phosphorylated PKC motifs. PKCα activity was dependent on light and expression of TRPM1, and RBC dendrites were the primary sites of light-dependent phosphorylation. PKCα-dependent retinal phosphoproteins were identified using a phosphoproteomics approach to compare total protein and phosphopeptide abundance between phorbol ester-treated wild type and PKCα knockout (PKCα-KO) mouse retinas. Phosphopeptide mass spectrometry identified over 1100 phosphopeptides in mouse retina, with 12 displaying significantly greater phosphorylation in WT compared to PKCα-KO samples. The differentially phosphorylated proteins fall into the following functional groups: cytoskeleton/trafficking (4 proteins), ECM/adhesion (2 proteins), signaling (2 proteins), transcriptional regulation (3 proteins), and homeostasis/metabolism (1 protein). Two strongly differentially expressed phosphoproteins, BORG4 and TPBG, were localized to the synaptic layers of the retina, and may play a role in PKCα-dependent modulation of RBC physiology. Data are available via ProteomeXchange with identifier PXD012906. SIGNIFICANCE: Retinal rod bipolar cells (RBCs), the second-order neurons of the mammalian rod visual pathway, are able to modulate their sensitivity to remain functional across a wide range of light intensities, from starlight to daylight. Evidence suggests that this modulation requires the serine/threonine kinase, PKCα, though the specific mechanism by which PKCα modulates RBC physiology is unknown. This study examined PKCα phosophorylation patterns in mouse rod bipolar cells and then used a phosphoproteomics approach to identify PKCα-dependent phosphoproteins in the mouse retina. A small number of retinal proteins showed significant PKCα-dependent phosphorylation, including BORG4 and TPBG, suggesting a potential contribution to PKCα-dependent modulation of RBC physiology.
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Affiliation(s)
- Colin M Wakeham
- Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA
| | - Jennifer M Cunliffe
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA
| | - John E Klimek
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA
| | - Gaoying Ren
- Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA; Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Catherine W Morgans
- Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA.
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17
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Hafner M, Mills CE, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Liu C, Walmsley CS, Juric D, Sorger PK. Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity. Cell Chem Biol 2019; 26:1067-1080.e8. [PMID: 31178407 DOI: 10.1016/j.chembiol.2019.05.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/14/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
Abstract
The target profiles of many drugs are established early in their development and are not systematically revisited at the time of FDA approval. Thus, it is often unclear whether therapeutics with the same nominal targets but different chemical structures are functionally equivalent. In this paper we use five different phenotypic and biochemical assays to compare approved inhibitors of cyclin-dependent kinases 4/6-collectively regarded as breakthroughs in the treatment of hormone receptor-positive breast cancer. We find that transcriptional, proteomic, and phenotypic changes induced by palbociclib, ribociclib, and abemaciclib differ significantly; abemaciclib in particular has advantageous activities partially overlapping those of alvocidib, an older polyselective CDK inhibitor. In cells and mice, abemaciclib inhibits kinases other than CDK4/6 including CDK2/cyclin A/E-implicated in resistance to CDK4/6 inhibition-and CDK1/cyclin B. The multifaceted experimental and computational approaches described here therefore uncover underappreciated differences in CDK4/6 inhibitor activities with potential importance in treating human patients.
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Affiliation(s)
- Marc Hafner
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kartik Subramanian
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Chen
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mirra Chung
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Everley
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Changchang Liu
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Charlotte S Walmsley
- Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Dejan Juric
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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18
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Poulin EJ, Bera AK, Lu J, Lin YJ, Strasser SD, Paulo JA, Huang TQ, Morales C, Yan W, Cook J, Nowak JA, Brubaker DK, Joughin BA, Johnson CW, DeStefanis RA, Ghazi PC, Gondi S, Wales TE, Iacob RE, Bogdanova L, Gierut JJ, Li Y, Engen JR, Perez-Mancera PA, Braun BS, Gygi SP, Lauffenburger DA, Westover KD, Haigis KM. Tissue-Specific Oncogenic Activity of KRAS A146T. Cancer Discov 2019; 9:738-755. [PMID: 30952657 PMCID: PMC6548671 DOI: 10.1158/2159-8290.cd-18-1220] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/06/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
Abstract
KRAS is the most frequently mutated oncogene. The incidence of specific KRAS alleles varies between cancers from different sites, but it is unclear whether allelic selection results from biological selection for specific mutant KRAS proteins. We used a cross-disciplinary approach to compare KRASG12D, a common mutant form, and KRASA146T, a mutant that occurs only in selected cancers. Biochemical and structural studies demonstrated that KRASA146T exhibits a marked extension of switch 1 away from the protein body and nucleotide binding site, which activates KRAS by promoting a high rate of intrinsic and guanine nucleotide exchange factor-induced nucleotide exchange. Using mice genetically engineered to express either allele, we found that KRASG12D and KRASA146T exhibit distinct tissue-specific effects on homeostasis that mirror mutational frequencies in human cancers. These tissue-specific phenotypes result from allele-specific signaling properties, demonstrating that context-dependent variations in signaling downstream of different KRAS mutants drive the KRAS mutational pattern seen in cancer. SIGNIFICANCE: Although epidemiologic and clinical studies have suggested allele-specific behaviors for KRAS, experimental evidence for allele-specific biological properties is limited. We combined structural biology, mass spectrometry, and mouse modeling to demonstrate that the selection for specific KRAS mutants in human cancers from different tissues is due to their distinct signaling properties.See related commentary by Hobbs and Der, p. 696.This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Emily J Poulin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Asim K Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jia Lu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Yi-Jang Lin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Samantha Dale Strasser
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Tannie Q Huang
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Carolina Morales
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Wei Yan
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Joshua Cook
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Douglas K Brubaker
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christian W Johnson
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Rebecca A DeStefanis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Phaedra C Ghazi
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Lana Bogdanova
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Jessica J Gierut
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Yina Li
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Pedro A Perez-Mancera
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Benjamin S Braun
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.
| | - Kevin M Haigis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Harvard Digestive Disease Center, Harvard Medical School, Boston, Massachusetts
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19
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Pappireddi N, Martin L, Wühr M. A Review on Quantitative Multiplexed Proteomics. Chembiochem 2019; 20:1210-1224. [PMID: 30609196 PMCID: PMC6520187 DOI: 10.1002/cbic.201800650] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/27/2018] [Indexed: 12/11/2022]
Abstract
Over the last few decades, mass spectrometry-based proteomics has become an increasingly powerful tool that is now able to routinely detect and quantify thousands of proteins. A major advance for global protein quantification was the introduction of isobaric tags, which, in a single experiment, enabled the global quantification of proteins across multiple samples. Herein, these methods are referred to as multiplexed proteomics. The principles, advantages, and drawbacks of various multiplexed proteomics techniques are discussed and compared with alternative approaches. We also discuss how the emerging combination of multiplexing with targeted proteomics might enable the reliable and high-quality quantification of very low abundance proteins across multiple conditions. Lastly, we suggest that fusing multiplexed proteomics with data-independent acquisition approaches might enable the comparison of hundreds of different samples without missing values, while maintaining the superb measurement precision and accuracy obtainable with isobaric tag quantification.
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Affiliation(s)
- Nishant Pappireddi
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- The Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lance Martin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- The Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- The Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
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20
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Wu X, Xing X, Dowlut D, Zeng Y, Liu J, Liu X. Integrating phosphoproteomics into kinase-targeted cancer therapies in precision medicine. J Proteomics 2019; 191:68-79. [DOI: 10.1016/j.jprot.2018.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/20/2018] [Accepted: 03/31/2018] [Indexed: 12/12/2022]
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21
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Jones FK, Hardman GE, Ferries S, Eyers CE, Pisconti A. Myoblast Phosphoproteomics as a Tool to Investigate Global Signaling Events During Myogenesis. Methods Mol Biol 2019; 1889:301-317. [PMID: 30367422 DOI: 10.1007/978-1-4939-8897-6_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation is a universal covalent chemical modification of amino acids involved in a large number of biological processes including cell signaling, metabolism, proliferation, differentiation, survival/death, ageing, and many more. Regulation of protein phosphorylation is essential in myogenesis and indeed, when the enzymatic activity of protein kinases is distrupted in myoblasts, myogenesis is affected. In this chapter we describe a method to profile the phosphoproteome of myoblasts using mass spectrometry. Phosphate groups are labile and easily lost during the processing of samples for mass spectrometry. Thus, effective methods to enrich for phosphopeptides from protein extracts have been developed. Here, we discuss and present in detail two such methods that we routinely employ. These methods are based on a sample enrichment step performed on titanium dioxide matrices followed by label-free tandem mass spectrometry and semi-quantitation.
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Affiliation(s)
- Fiona K Jones
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gemma E Hardman
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Samantha Ferries
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Addolorata Pisconti
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
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22
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Targeting Epigenetic Crosstalk as a Therapeutic Strategy for EZH2-Aberrant Solid Tumors. Cell 2018; 175:186-199.e19. [DOI: 10.1016/j.cell.2018.08.058] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 07/23/2018] [Accepted: 08/24/2018] [Indexed: 12/24/2022]
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23
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Paulo JA, Navarrete-Perea J, Erickson AR, Knott J, Gygi SP. An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1505-1511. [PMID: 29671274 PMCID: PMC6004253 DOI: 10.1007/s13361-018-1946-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 06/08/2023]
Abstract
Phosphorylation-mediated signaling pathways have major implications in cellular regulation and disease. However, proteins with roles in these pathways are frequently less abundant and phosphorylation is often sub-stoichiometric. As such, the efficient enrichment, and subsequent recovery of phosphorylated peptides, is vital. Mass spectrometry-based proteomics is a well-established approach for quantifying thousands of phosphorylation events in a single experiment. We designed a peptide internal standard-based assay directed toward sample preparation strategies for mass spectrometry analysis to understand better phosphopeptide recovery from enrichment strategies. We coupled mass-differential tandem mass tag (mTMT) reagents (specifically, TMTzero and TMTsuper-heavy), nine mass spectrometry-amenable phosphopeptides (phos9), and peak area measurements from extracted ion chromatograms to determine phosphopeptide recovery. We showcase this mTMT/phos9 recovery assay by evaluating three phosphopeptide enrichment workflows. Our assay provides data on the recovery of phosphopeptides, which complement other metrics, namely the number of identified phosphopeptides and enrichment specificity. Our mTMT/phos9 assay is applicable to any enrichment protocol in a typical experimental workflow irrespective of sample origin or labeling strategy. Graphical Abstract ᅟ.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
| | - Jose Navarrete-Perea
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Alison R Erickson
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
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24
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Quantitative phosphoproteomic analysis of the molecular substrates of sleep need. Nature 2018; 558:435-439. [PMID: 29899451 DOI: 10.1038/s41586-018-0218-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 05/01/2018] [Indexed: 12/25/2022]
Abstract
Sleep and wake have global effects on brain physiology, from molecular changes1-4 and neuronal activities to synaptic plasticity3-7. Sleep-wake homeostasis is maintained by the generation of a sleep need that accumulates during waking and dissipates during sleep8-11. Here we investigate the molecular basis of sleep need using quantitative phosphoproteomic analysis of the sleep-deprived and Sleepy mouse models of increased sleep need. Sleep deprivation induces cumulative phosphorylation of the brain proteome, which dissipates during sleep. Sleepy mice, owing to a gain-of-function mutation in the Sik3 gene 12 , have a constitutively high sleep need despite increased sleep amount. The brain proteome of these mice exhibits hyperphosphorylation, similar to that seen in the brain of sleep-deprived mice. Comparison of the two models identifies 80 mostly synaptic sleep-need-index phosphoproteins (SNIPPs), in which phosphorylation states closely parallel changes of sleep need. SLEEPY, the mutant SIK3 protein, preferentially associates with and phosphorylates SNIPPs. Inhibition of SIK3 activity reduces phosphorylation of SNIPPs and slow wave activity during non-rapid-eye-movement sleep, the best known measurable index of sleep need, in both Sleepy mice and sleep-deprived wild-type mice. Our results suggest that phosphorylation of SNIPPs accumulates and dissipates in relation to sleep need, and therefore SNIPP phosphorylation is a molecular signature of sleep need. Whereas waking encodes memories by potentiating synapses, sleep consolidates memories and restores synaptic homeostasis by globally downscaling excitatory synapses4-6. Thus, the phosphorylation-dephosphorylation cycle of SNIPPs may represent a major regulatory mechanism that underlies both synaptic homeostasis and sleep-wake homeostasis.
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25
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Hong S, Song W, Zushin PJH, Liu B, Jedrychowski MP, Mina AI, Deng Z, Cabarkapa D, Hall JA, Palmer CJ, Aliakbarian H, Szpyt J, Gygi SP, Tavakkoli A, Lynch L, Perrimon N, Banks AS. Phosphorylation of Beta-3 adrenergic receptor at serine 247 by ERK MAP kinase drives lipolysis in obese adipocytes. Mol Metab 2018; 12:25-38. [PMID: 29661693 PMCID: PMC6001906 DOI: 10.1016/j.molmet.2018.03.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/21/2018] [Accepted: 03/24/2018] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE The inappropriate release of free fatty acids from obese adipose tissue stores has detrimental effects on metabolism, but key molecular mechanisms controlling FFA release from adipocytes remain undefined. Although obesity promotes systemic inflammation, we find activation of the inflammation-associated Mitogen Activated Protein kinase ERK occurs specifically in adipose tissues of obese mice, and provide evidence that adipocyte ERK activation may explain exaggerated adipose tissue lipolysis observed in obesity. METHODS AND RESULTS We provide genetic and pharmacological evidence that inhibition of the MEK/ERK pathway in human adipose tissue, mice, and flies all effectively limit adipocyte lipolysis. In complementary findings, we show that genetic and obesity-mediated activation of ERK enhances lipolysis, whereas adipose tissue specific knock-out of ERK2, the exclusive ERK1/2 protein in adipocytes, dramatically impairs lipolysis in explanted mouse adipose tissue. In addition, acute inhibition of MEK/ERK signaling also decreases lipolysis in adipose tissue and improves insulin sensitivity in obese mice. Mice with decreased rates of adipose tissue lipolysis in vivo caused by either MEK or ATGL pharmacological inhibition were unable to liberate sufficient White Adipose Tissue (WAT) energy stores to fuel thermogenesis from brown fat during a cold temperature challenge. To identify a molecular mechanism controlling these actions, we performed unbiased phosphoproteomic analysis of obese adipose tissue at different time points following acute pharmacological MEK/ERK inhibition. MEK/ERK inhibition decreased levels of adrenergic signaling and caused de-phosphorylation of the β3-adrenergic receptor (β3AR) on serine 247. To define the functional implications of this phosphorylation, we showed that CRISPR/Cas9 engineered cells expressing wild type β3AR exhibited β3AR phosphorylation by ERK2 and enhanced lipolysis, but this was not seen when serine 247 of β3AR was mutated to alanine. CONCLUSION Taken together, these data suggest that ERK activation in adipocytes and subsequent phosphorylation of the β3AR on S247 are critical regulatory steps in the enhanced adipocyte lipolysis of obesity.
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Affiliation(s)
- Shangyu Hong
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Wei Song
- Department of Genetics, Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Peter-James H Zushin
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Bingyang Liu
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Amir I Mina
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Zhaoming Deng
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Dimitrije Cabarkapa
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Jessica A Hall
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Colin J Palmer
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Hassan Aliakbarian
- Department of Surgery, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ali Tavakkoli
- Department of Surgery, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - Lydia Lynch
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Alexander S Banks
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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26
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Navarrete-Perea J, Yu Q, Gygi SP, Paulo JA. Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3. J Proteome Res 2018; 17:2226-2236. [PMID: 29734811 DOI: 10.1021/acs.jproteome.8b00217] [Citation(s) in RCA: 206] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands of peptides and, by inference, thousands of proteins from multiple samples in a single MS experiment. Accurate quantification demands a consistent and robust sample-preparation strategy. Here, we present a detailed workflow for SPS-MS3-based quantitative abundance profiling of tandem mass tag (TMT)-labeled proteins and phosphopeptides that we have named the streamlined (SL)-TMT protocol. We describe a universally applicable strategy that requires minimal individual sample processing and permits the seamless addition of a phosphopeptide enrichment step ("mini-phos") with little deviation from the deep proteome analysis. To showcase our workflow, we profile the proteome of wild-type Saccharomyces cerevisiae yeast grown with either glucose or pyruvate as the carbon source. Here, we have established a streamlined TMT protocol that enables deep proteome and medium-scale phosphoproteome analysis.
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Affiliation(s)
- José Navarrete-Perea
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Qing Yu
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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27
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Paulo JA, Jedrychowski MP, Chouchani ET, Kazak L, Gygi SP. Multiplexed Isobaric Tag-Based Profiling of Seven Murine Tissues Following In Vivo Nicotine Treatment Using a Minimalistic Proteomics Strategy. Proteomics 2018; 18:e1700326. [PMID: 29660237 PMCID: PMC5992107 DOI: 10.1002/pmic.201700326] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/24/2017] [Indexed: 12/18/2022]
Abstract
Nicotine is a major addictive compound in tobacco and a component of smoking-related products, such as e-cigarettes. Once internalized, nicotine can perturb many cellular pathways and can induce alterations in proteins across different cell types; however, the mechanisms thereof remain undetermined. The authors hypothesize that both tissue-specific and global protein abundance alterations result from nicotine exposure. Presented here is the first proteomic profiling of multiple tissues from mice treated orally with nicotine. Proteins extracted from seven tissues (brain, heart, kidney, liver, lung, pancreas, and spleen) from treated (n = 5) and untreated control (n = 5) mice are assembled into a TMT10-plex experiment. A minimalistic proteomics strategy is employed using TMT reagents efficiently and centrifugation-based reversed-phase columns to streamline sample preparation. Combined, over 11 000 non-redundant proteins from over 138 000 different peptides are quantified in seven TMT10-plex experiments. Between 7 and 126 proteins are significantly altered in tissues from nicotine-exposed mice, 11 which are altered in two or more tissues. Our data showcase the vast extent of nicotine exposure across murine tissue.
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Affiliation(s)
- Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Mark P. Jedrychowski
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Edward T. Chouchani
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Lawrence Kazak
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
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28
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Campo L, Breuer EK. Inhibition of TACC3 by a small molecule inhibitor in breast cancer. Biochem Biophys Res Commun 2018; 498:1085-1092. [PMID: 29555478 DOI: 10.1016/j.bbrc.2018.03.125] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
Abstract
Studies have shown that transforming acidic coiled-coil protein 3 (TACC3), a key component of centrosome-microtubule dynamic networks, is significantly associated with various types of human cancer. We have recently reported that high levels of TACC3 are found in breast cancer, lead to the accumulation of spontaneous DNA damage due to defective DNA damage response signaling, and confer cellular sensitivity to radiation and poly(ADP-ribose) polymerase (PARP) inhibitors. Although our study suggests a potential role of TACC3 as a biomarker in breast cancer detection and prediction of therapy outcome, its role as a therapeutic target in breast cancer is not well studied. In this study, we show that a small molecule TACC3 inhibitor, KHS101, suppresses cell growth, motility, epithelial-mesenchymal transition (EMT), and breast cancer cell stemness while it induces apoptotic cell death. Quantitative multiplexed proteomic analysis using tandem mass tags (TMTs) revealed that KHS101 alters multiple biological processes and signaling pathways, and significantly reduces the expression of mitotic kinases Aurora A and Polo-like kinase 1 (PLK1), which are closely associated with TACC3. Our findings therefore provide a new insight into the potential mechanisms of the action of KHS101 and suggest its possible use as a dual or multi-targeting mitotic inhibitor in breast cancer.
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Affiliation(s)
- Loredana Campo
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Eun-Kyoung Breuer
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
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29
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Berberich MJ, Paulo JA, Everley RA. MS3-IDQ: Utilizing MS3 Spectra beyond Quantification Yields Increased Coverage of the Phosphoproteome in Isobaric Tag Experiments. J Proteome Res 2018; 17:1741-1747. [PMID: 29461835 DOI: 10.1021/acs.jproteome.8b00006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein phosphorylation is critically important for many cellular processes, including progression through the cell cycle, cellular metabolism, and differentiation. Isobaric labeling, for example, tandem mass tags (TMT), in phosphoproteomics workflows enables both relative and absolute quantitation of these phosphorylation events. Traditional TMT workflows identify peptides using fragment ions at the MS2 level and quantify reporter ions at the MS3 level. However, in addition to the TMT reporter ions, MS3 spectra also include fragment ions that can be used to identify peptides. Here we describe using MS3 spectra for both phosphopeptide identification and quantification, a process that we term MS3-IDQ. To maximize quantified phosphopeptides, we optimize several instrument parameters, including the modality of mass analyzer (i.e., ion trap or Orbitrap), MS2 automatic gain control (AGC), and MS3 normalized collision energy (NCE), to achieve the best balance of identified and quantified peptides. Our optimized MS3-IDQ method included the following parameters for the MS3 scan: NCE = 37.5 and AGC target = 1.5 × 105, and scan range = 100-2000. Data from the MS3 scan were complementary to those of the MS2 scan, and the combination of these scans can increase phosphoproteome coverage by >50%, thereby yielding a greater number of quantified and accurately localized phosphopeptides.
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Affiliation(s)
- Matthew J Berberich
- Laboratory of Systems Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Robert A Everley
- Laboratory of Systems Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States.,Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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30
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Kwon Y, Ju S, Kaushal P, Lee JW, Lee C. Neutralizing the Detrimental Effect of an N-Hydroxysuccinimide Quenching Reagent on Phosphopeptide in Quantitative Proteomics. Anal Chem 2018; 90:3019-3023. [PMID: 29406695 DOI: 10.1021/acs.analchem.7b04678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the most common chemistries used to label primary amines utilizes N-hydroxysuccinimide (NHS), which is also structurally incorporated in various quantitative proteomic reagents such as isobaric tags for relative and absolute quantification (iTRAQ) and tandem mass tags (TMT). In this paper we report detrimental effect of hydroxylamine, a widely used quenching reagent for excess NHS, on phosphopeptides. We found an impairment in the degree of phosphopeptide identification when hydroxylamine-quenched TMT-labeled samples were vacuum-dried and desalted compared to the nondried (just diluted) and desalted ones prior to phosphoenrichment. We have also demonstrated that vacuum-drying in the presence of hydroxylamine promotes β-elimination of phosphate groups from phosphoserine and phosphothreonine while having a minimalistic effect on phosphotyrosine. Additionally, we herein report that this negative impact of hydroxylamine could be minimized by direct desalting after appropriate dilution of quenched samples. We also found a 1.6-fold increase in the number of phosphopeptide identifications after employing our optimized method. The above method was also successfully applied to human tumor tissues to quantify over 15000 phosphopeptides from 3 mg TMT 6-plex labeled-peptides.
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Affiliation(s)
- Yumi Kwon
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Shinyeong Ju
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Prashant Kaushal
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science and Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Cheolju Lee
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science and Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
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31
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Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. Nat Commun 2017; 8:1186. [PMID: 29084964 PMCID: PMC5662764 DOI: 10.1038/s41467-017-01383-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/14/2017] [Indexed: 01/04/2023] Open
Abstract
More effective use of targeted anti-cancer drugs depends on elucidating the connection between the molecular states induced by drug treatment and the cellular phenotypes controlled by these states, such as cytostasis and death. This is particularly true when mutation of a single gene is inadequate as a predictor of drug response. The current paper describes a data set of ~600 drug cell line pairs collected as part of the NIH LINCS Program ( http://www.lincsproject.org/ ) in which molecular data (reduced dimensionality transcript L1000 profiles) were recorded across dose and time in parallel with phenotypic data on cellular cytostasis and cytotoxicity. We report that transcriptional and phenotypic responses correlate with each other in general, but whereas inhibitors of chaperones and cell cycle kinases induce similar transcriptional changes across cell lines, changes induced by drugs that inhibit intra-cellular signaling kinases are cell-type specific. In some drug/cell line pairs significant changes in transcription are observed without a change in cell growth or survival; analysis of such pairs identifies drug equivalence classes and, in one case, synergistic drug interactions. In this case, synergy involves cell-type specific suppression of an adaptive drug response.
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32
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Susman MW, Karuna EP, Kunz RC, Gujral TS, Cantú AV, Choi SS, Jong BY, Okada K, Scales MK, Hum J, Hu LS, Kirschner MW, Nishinakamura R, Yamada S, Laird DJ, Jao LE, Gygi SP, Greenberg ME, Ho HYH. Kinesin superfamily protein Kif26b links Wnt5a-Ror signaling to the control of cell and tissue behaviors in vertebrates. eLife 2017; 6:e26509. [PMID: 28885975 PMCID: PMC5590807 DOI: 10.7554/elife.26509] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022] Open
Abstract
Wnt5a-Ror signaling constitutes a developmental pathway crucial for embryonic tissue morphogenesis, reproduction and adult tissue regeneration, yet the molecular mechanisms by which the Wnt5a-Ror pathway mediates these processes are largely unknown. Using a proteomic screen, we identify the kinesin superfamily protein Kif26b as a downstream target of the Wnt5a-Ror pathway. Wnt5a-Ror, through a process independent of the canonical Wnt/β-catenin-dependent pathway, regulates the cellular stability of Kif26b by inducing its degradation via the ubiquitin-proteasome system. Through this mechanism, Kif26b modulates the migratory behavior of cultured mesenchymal cells in a Wnt5a-dependent manner. Genetic perturbation of Kif26b function in vivo caused embryonic axis malformations and depletion of primordial germ cells in the developing gonad, two phenotypes characteristic of disrupted Wnt5a-Ror signaling. These findings indicate that Kif26b links Wnt5a-Ror signaling to the control of morphogenetic cell and tissue behaviors in vertebrates and reveal a new role for regulated proteolysis in noncanonical Wnt5a-Ror signal transduction.
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Affiliation(s)
- Michael W Susman
- Department of NeurobiologyHarvard Medical SchoolBostonUnited States
| | - Edith P Karuna
- Department of Cell Biology and Human AnatomyUniversity of California, Davis School of MedicineDavisUnited States
| | - Ryan C Kunz
- Department of Cell BiologyHarvard Medical SchoolBostonUnited States
| | - Taranjit S Gujral
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
- Division of Human BiologyFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Andrea V Cantú
- Department of Obstetrics, Gynecology and Reproductive SciencesCenter for Reproductive Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of CaliforniaSan FranciscoUnited States
| | - Shannon S Choi
- Department of Cell Biology and Human AnatomyUniversity of California, Davis School of MedicineDavisUnited States
| | - Brigette Y Jong
- Department of Cell Biology and Human AnatomyUniversity of California, Davis School of MedicineDavisUnited States
| | - Kyoko Okada
- Department of Cell Biology and Human AnatomyUniversity of California, Davis School of MedicineDavisUnited States
| | - Michael K Scales
- Department of Cell Biology and Human AnatomyUniversity of California, Davis School of MedicineDavisUnited States
| | - Jennie Hum
- Department of Cell Biology and Human AnatomyUniversity of California, Davis School of MedicineDavisUnited States
| | - Linda S Hu
- Department of NeurobiologyHarvard Medical SchoolBostonUnited States
| | - Marc W Kirschner
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Ryuichi Nishinakamura
- Department of Kidney DevelopmentInstitute of Molecular Embryology and Genetics, Kumamoto UniversityKumamotoJapan
| | - Soichiro Yamada
- Department of Biomedical EngineeringUniversity of CaliforniaDavisUnited States
| | - Diana J Laird
- Department of Obstetrics, Gynecology and Reproductive SciencesCenter for Reproductive Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of CaliforniaSan FranciscoUnited States
| | - Li-En Jao
- Department of Cell Biology and Human AnatomyUniversity of California, Davis School of MedicineDavisUnited States
| | - Steven P Gygi
- Department of Cell BiologyHarvard Medical SchoolBostonUnited States
| | | | - Hsin-Yi Henry Ho
- Department of NeurobiologyHarvard Medical SchoolBostonUnited States
- Department of Cell Biology and Human AnatomyUniversity of California, Davis School of MedicineDavisUnited States
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33
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Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J. Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome. Sci Rep 2017; 7:4513. [PMID: 28674419 PMCID: PMC5495806 DOI: 10.1038/s41598-017-04798-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/13/2017] [Indexed: 02/06/2023] Open
Abstract
Protein phosphorylation is involved in the regulation of most eukaryotic cells functions and mass spectrometry-based analysis has made major contributions to our understanding of this regulation. However, low abundance of phosphorylated species presents a major challenge in achieving comprehensive phosphoproteome coverage and robust quantification. In this study, we developed a workflow employing titanium dioxide phospho-enrichment coupled with isobaric labeling by Tandem Mass Tags (TMT) and high-resolution isoelectric focusing (HiRIEF) fractionation to perform in-depth quantitative phosphoproteomics starting with a low sample quantity. To benchmark the workflow, we analyzed HeLa cells upon pervanadate treatment or cell cycle arrest in mitosis. Analyzing 300 µg of peptides per sample, we identified 22,712 phosphorylation sites, of which 19,075 were localized with high confidence and 1,203 are phosphorylated tyrosine residues, representing 6.3% of all detected phospho-sites. HiRIEF fractions with the most acidic isoelectric points are enriched in multiply phosphorylated peptides, which represent 18% of all the phospho-peptides detected in the pH range 2.5–3.7. Cross-referencing with the PhosphoSitePlus database reveals 1,264 phosphorylation sites that have not been previously reported and kinase association analysis suggests that a subset of these may be functional during the mitotic phase.
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Affiliation(s)
- Elena Panizza
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Rui M M Branca
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Lukas M Orre
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Janne Lehtiö
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
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Mohideen F, Paulo JA, Ordureau A, Gygi SP, Harper JW. Quantitative Phospho-proteomic Analysis of TNFα/NFκB Signaling Reveals a Role for RIPK1 Phosphorylation in Suppressing Necrotic Cell Death. Mol Cell Proteomics 2017; 16:1200-1216. [PMID: 28539327 DOI: 10.1074/mcp.m117.068189] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/24/2017] [Indexed: 12/19/2022] Open
Abstract
TNFα is a potent inducer of inflammation due to its ability to promote gene expression, in part via the NFκB pathway. Moreover, in some contexts, TNFα promotes Caspase-dependent apoptosis or RIPK1/RIPK3/MLKL-dependent necrosis. Engagement of the TNF Receptor Signaling Complex (TNF-RSC), which contains multiple kinase activities, promotes phosphorylation of several downstream components, including TAK1, IKKα/IKKβ, IκBα, and NFκB. However, immediate downstream phosphorylation events occurring in response to TNFα signaling are poorly understood at a proteome-wide level. Here we use Tandem Mass Tagging-based proteomics to quantitatively characterize acute TNFα-mediated alterations in the proteome and phosphoproteome with or without inhibition of the cIAP-dependent survival arm of the pathway with a SMAC mimetic. We identify and quantify over 8,000 phosphorylated peptides, among which are numerous known sites in the TNF-RSC, NFκB, and MAP kinase signaling systems, as well as numerous previously unrecognized phosphorylation events. Functional analysis of S320 phosphorylation in RIPK1 demonstrates a role for this event in suppressing its kinase activity, association with CASPASE-8 and FADD proteins, and subsequent necrotic cell death during inflammatory TNFα stimulation. This study provides a resource for further elucidation of TNFα-dependent signaling pathways.
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Affiliation(s)
- Firaz Mohideen
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Joao A Paulo
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Alban Ordureau
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Steve P Gygi
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - J Wade Harper
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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35
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Chen LS, Wang J, Wang X, Wang P. A MIXED-EFFECTS MODEL FOR INCOMPLETE DATA FROM LABELING-BASED QUANTITATIVE PROTEOMICS EXPERIMENTS. Ann Appl Stat 2017; 11:114-138. [PMID: 29743963 PMCID: PMC5937554 DOI: 10.1214/16-aoas994] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In mass spectrometry (MS) based quantitative proteomics research, the emerging iTRAQ (isobaric tag for relative and absolute quantitation) and TMT (tandem mass tags) techniques have been widely adopted for high throughput protein profiling. In a typical iTRAQ/TMT proteomics study, samples are grouped into batches, and each batch is processed by one multiplex experiment, in which the abundances of thousands of proteins/peptides in a batch of samples can be measured simultaneously. The multiplex labeling technique greatly enhances the throughput of protein quantification. However, the technical variation across different iTRAQ/TMT multiplex experiments is often large due to the dynamic nature of MS instruments. This leads to strong batch effects in the iTRAQ/TMT data. Moreover, the iTRAQ/TMT data often contain substantial batch-level nonignorable missing entries. Specifically, the abundance measures of a given protein/peptide are often either observed or missing altogether in all the samples from the same batch, with the missing probability depending on the combined batch-level abundances. We term this unique missing-data mechanism as the Batch-level Abundance-Dependent Missing-data Mechanism (BADMM). We introduce a new method- mixEMM-for analyzing iTRAQ/TMT data with batch effects and batch-level nonignorable missingness. The mixEMM method employs a linear mixed-effects model and explicitly models the batch effects and the BADMM. With simulation studies, we showed that, compared with existing approaches that utilize relative abundances and ignore the missing batches under the missing-completely-at-random assumption, the mixEMM method achieves more accurate parameter estimation and inference. We applied the method to an iTRAQ proteomics data from a breast cancer study and identified phosphopeptides differentially expressed between different breast cancer subtypes. The method can be applied to general clustered data with cluster-level nonignorable missing-data mechanisms.
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Affiliation(s)
- Lin S Chen
- Department of Public Health Sciences, University of Chicago, 5841 S Maryland Ave, Chicago, Illinois, USA
| | - Jiebiao Wang
- Department of Public Health Sciences, University of Chicago, 5841 S Maryland Ave, Chicago, Illinois, USA
| | - Xianlong Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington 98109, USA
| | - Pei Wang
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, S8-102, New York, New York, USA
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36
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Possemato AP, Paulo JA, Mulhern D, Guo A, Gygi SP, Beausoleil SA. Multiplexed Phosphoproteomic Profiling Using Titanium Dioxide and Immunoaffinity Enrichments Reveals Complementary Phosphorylation Events. J Proteome Res 2017; 16:1506-1514. [PMID: 28171727 DOI: 10.1021/acs.jproteome.6b00905] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A comprehensive view of protein phosphorylation remains an unmet challenge in the field of cell biology. Mass spectrometry-based proteomics is one of the most promising approaches for identifying thousands of phosphorylation events in a single experiment, yet the full breadth of the phosphoproteome has yet to be elucidated. In this article, we examined the complementarity of two methods for phosphopeptide enrichment based on either titanium dioxide (TiO2) enrichment or phosphorylation motif-specific immunoaffinity precipitation (IAP) with four different antibodies. Each method identified nearly 2000 phosphoproteins. However, distinct populations of phosphopeptides were observed. Despite quantifying over 10 000 unique phosphorylation events using TiO2 and over 3900 with IAP, less than 5% of the sites were in common. Agreeing with published literature, the ratio of pS:pT:pY phosphorylation for the TiO2-enriched data set approximated 90:10:<1. In contrast, that ratio for the combined IAP data sets was 51:29:20. These differences not only suggest the complementarity between multiple enrichment methods but also emphasize their collective importance in obtaining a comprehensive view of the phosphoproteome.
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Affiliation(s)
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Daniel Mulhern
- Bluefin Biomedicine , Beverly, Massachusetts 01915, United States
| | - Ailan Guo
- Bluefin Biomedicine , Beverly, Massachusetts 01915, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
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37
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Ganter M, Goldberg JM, Dvorin JD, Paulo JA, King JG, Tripathi AK, Paul AS, Yang J, Coppens I, Jiang RH, Elsworth B, Baker DA, Dinglasan RR, Gygi SP, Duraisingh MT. Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nat Microbiol 2017; 2:17017. [PMID: 28211852 PMCID: PMC5328244 DOI: 10.1038/nmicrobiol.2017.17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 01/13/2017] [Indexed: 02/08/2023]
Abstract
Plasmodium parasites, the causative agents of malaria, have evolved a unique cell division cycle in the clinically relevant asexual blood stage of infection1. DNA replication commences approximately halfway through the intracellular development following invasion and parasite growth. The schizont stage is associated with multiple rounds of DNA replication and nuclear division without cytokinesis, resulting in a multinucleated cell. Nuclei divide asynchronously through schizogony, with only the final round of DNA replication and segregation being synchronous and coordinated with daughter cell assembly2,3. However, the control mechanisms for this divergent mode of replication are unknown. Here, we show that the Plasmodium-specific kinase PfCRK4 is a key cell-cycle regulator that orchestrates multiple rounds of DNA replication throughout schizogony in Plasmodium falciparum. PfCRK4 depletion led to a complete block in nuclear division and profoundly inhibited DNA replication. Quantitative phosphoproteomic profiling identified a set of PfCRK4-regulated phosphoproteins with greatest functional similarity to CDK2 substrates, particularly proteins involved in the origin of replication firing. PfCRK4 was required for initial and subsequent rounds of DNA replication during schizogony and, in addition, was essential for development in the mosquito vector. Our results identified an essential S-phase promoting factor of the unconventional P. falciparum cell cycle. PfCRK4 is required for both a prolonged period of the intraerythrocytic stage of Plasmodium infection, as well as for transmission, revealing a broad window for PfCRK4-targeted chemotherapeutics.
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Affiliation(s)
- Markus Ganter
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jonathan M. Goldberg
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeffrey D. Dvorin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Jonas G. King
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Abhai K. Tripathi
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Aditya S. Paul
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jing Yang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Isabelle Coppens
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rays H.Y. Jiang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David A. Baker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Rhoel R. Dinglasan
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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38
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Huang FK, Zhang G, Lawlor K, Nazarian A, Philip J, Tempst P, Dephoure N, Neubert TA. Deep Coverage of Global Protein Expression and Phosphorylation in Breast Tumor Cell Lines Using TMT 10-plex Isobaric Labeling. J Proteome Res 2017; 16:1121-1132. [PMID: 28102081 DOI: 10.1021/acs.jproteome.6b00374] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Labeling peptides with isobaric tags is a popular strategy in quantitative bottom-up proteomics. In this study, we labeled six breast tumor cell lysates (1.34 mg proteins per channel) using 10-plex tandem mass tag reagents and analyzed the samples on a Q Exactive HF Quadrupole-Orbitrap mass spectrometer. We identified a total of 8,706 proteins and 28,186 phosphopeptides, including 7,394 proteins and 23,739 phosphosites common to all channels. The majority of technical replicates correlated with a R2 ≥ 0.98, indicating minimum variability was introduced after labeling. Unsupervised hierarchical clustering of phosphopeptide data sets successfully classified the breast tumor samples into Her2 (epidermal growth factor receptor 2) positive and Her2 negative groups, whereas mRNA abundance did not. The tyrosine phosphorylation levels of receptor tyrosine kinases, phosphoinositide-3-kinase, protein kinase C delta, and Src homology 2, among others, were significantly higher in the Her2 positive than the Her2 negative group. Despite ratio compression in MS2-based experiments, we demonstrated the ratios calculated using an MS2 method are highly correlated (R2 > 0.65) with ratios obtained using MS3-based quantitation (using a Thermo Orbitrap Fusion mass spectrometer) with reduced ratio suppression. Given the deep coverage of global and phosphoproteomes, our data show that MS2-based quantitation using TMT can be successfully used for large-scale multiplexed quantitative proteomics.
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Affiliation(s)
- Fang-Ke Huang
- Kimmel Center for Biology and Medicine at the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, New York 10016, United States
| | - Guoan Zhang
- Kimmel Center for Biology and Medicine at the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, New York 10016, United States
| | - Kevin Lawlor
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Arpi Nazarian
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - John Philip
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Paul Tempst
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Noah Dephoure
- Sandra and Edward Meyer Cancer Center, Department of Biochemistry, Weill Cornell Medical College , New York, New York 10065, United States
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, New York 10016, United States
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39
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Abstract
OBJECTIVES Mass spectrometry-based proteomics enables near-comprehensive protein expression profiling. We aimed to compare quantitatively the relative expression levels of thousands of proteins across 5 pancreatic cell lines. METHODS Using tandem mass tags (TMT10-plex), we profiled the global proteomes of 5 cell lines in duplicate in a single multiplexed experiment. We selected cell lines commonly used in pancreatic research: CAPAN-1, HPAC, HPNE, PANC1, and PaSCs. In addition, we examined the effects of different proteases (Lys-C and Lys-C plus trypsin) on the dataset depth. RESULTS We quantified over 8000 proteins across the 5 cell lines. Analysis of variance testing of cell lines within each data set resulted in over 1400 statistically significant differences in protein expression levels. Comparing the data sets, 10% more proteins and 30% more peptides were identified in the Lys-C/trypsin data set than in the Lys-C-only data set. The correlation coefficient of quantified proteins common between the data sets was greater than 0.85. CONCLUSIONS We illustrate protein level differences across pancreatic cell lines. In addition, we highlight the advantages of Lys-C/trypsin over Lys-C-only digests for discovery proteomics. These data sets provide a valuable resource of cell line-dependent peptide and protein differences for future targeted analyses, including those investigating on- or off-target drug effects across cell lines.
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40
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Paulo JA, Gygi SP. Nicotine-induced protein expression profiling reveals mutually altered proteins across four human cell lines. Proteomics 2016; 17. [PMID: 27862958 DOI: 10.1002/pmic.201600319] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/11/2016] [Accepted: 11/10/2016] [Indexed: 11/10/2022]
Abstract
Mass spectrometry-based proteomic strategies can profile the expression level of proteins in response to external stimuli. Nicotine affects diverse cellular pathways, however, the nicotine-induced alterations on the global proteome across human cell lines have not been fully elucidated. We measured perturbations in protein levels resulting from nicotine treatment in four cell lines-HEK, HeLa, PaSC, and SH-SY5Y-in a single experiment using tandem mass tags (TMT10-plex) and high-resolution mass spectrometry. We quantified 8590 proteins across all cell lines. Of these, nicotine increased the abundance of 31 proteins 1.5-fold or greater in all cell lines. Likewise, considering proteins with altered levels in at least three of the four cell lines, 64 were up-regulated, while one was down-regulated. Gene ontology analysis revealed that ∼40% of these proteins were membrane bound, and functioned in transmembrane signaling and receptor activity. We highlighted proteins, including APP, APLP2, LAPTM4B, and NCOA4, which were dysregulated by nicotine in all cell lines investigated and may have implications in downstream signaling pathways, particularly autophagy. Using the outlined methodology, studies in additional (including primary) cell lines will provide further evidence that alterations in the levels of these proteins are indeed a general response to nicotine and thereby merit further investigation.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
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41
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Chan CYX, Gritsenko MA, Smith RD, Qian WJ. The current state of the art of quantitative phosphoproteomics and its applications to diabetes research. Expert Rev Proteomics 2016; 13:421-33. [PMID: 26960075 DOI: 10.1586/14789450.2016.1164604] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein phosphorylation is a fundamental regulatory mechanism in many cellular processes and aberrant perturbation of phosphorylation has been implicated in various human diseases. Kinases and their cognate inhibitors have been considered as hotspots for drug development. Therefore, the emerging tools, which enable a system-wide quantitative profiling of phosphoproteome, would offer a powerful impetus in unveiling novel signaling pathways, drug targets and/or biomarkers for diseases of interest. This review highlights recent advances in phosphoproteomics, the current state of the art of the technologies and the challenges and future perspectives of this research area. Finally, some exemplary applications of phosphoproteomics in diabetes research are underscored.
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Affiliation(s)
- Chi Yuet X'avia Chan
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Marina A Gritsenko
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Richard D Smith
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
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42
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Abe Y, Nagano M, Tada A, Adachi J, Tomonaga T. Deep Phosphotyrosine Proteomics by Optimization of Phosphotyrosine Enrichment and MS/MS Parameters. J Proteome Res 2016; 16:1077-1086. [PMID: 28152594 DOI: 10.1021/acs.jproteome.6b00576] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphorylation is a major post-translational modification that regulates protein function, with phosphotyrosine (pY) modifications being implicated in oncogenesis. However, global profiling of pY statuses without treatment with a tyrosine phosphatase inhibitor such as pervanadate is still challenging due to the low occupancy of pY sites. In this study, we greatly improved the identification of pY sites by liquid chromatography-tandem mass spectrometry (LC-MS/MS) by optimization of both the pY-immunoprecipitation (pY-IP) protocol and the LC-MS/MS parameters. Our highly sensitive method reproducibly identified more than 1000 pY sites from 8 mg of protein lysate without the need for tyrosine phosphatase inhibitor treatment. Furthermore, >30% of the identified pY sites were not assigned in the PhosphositePlus database. We further applied our method to the comparison of pY status between PC3 cells with and without treatment using the epidermal growth factor receptor (EGFR) inhibitor Erlotinib. Under Erlotinib treatment, we observed not only a decrease in well-known modes of EGFR downstream signaling but also modulations of kinases that are not relevant to the EGFR cascade, such as PTK6 and MAPK13. Our newly developed method for pY proteomics has the potential to reveal unknown pY signaling modes and to identify novel kinase anticancer targets.
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Affiliation(s)
- Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
| | - Maiko Nagano
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
| | - Asa Tada
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
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43
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Koch H, Wilhelm M, Ruprecht B, Beck S, Frejno M, Klaeger S, Kuster B. Phosphoproteome Profiling Reveals Molecular Mechanisms of Growth-Factor-Mediated Kinase Inhibitor Resistance in EGFR-Overexpressing Cancer Cells. J Proteome Res 2016; 15:4490-4504. [PMID: 27794612 DOI: 10.1021/acs.jproteome.6b00621] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Although substantial progress has been made regarding the use of molecularly targeted cancer therapies, resistance almost invariably develops and presents a major clinical challenge. The tumor microenvironment can rescue cancer cells from kinase inhibitors by growth-factor-mediated induction of pro-survival pathways. Here we show that epidermal growth factor receptor (EGFR) inhibition by Gefitinib is counteracted by growth factors, notably FGF2, and we assessed the global molecular consequences of this resistance at the proteome and phosphoproteome level in A431 cells. Tandem mass tag peptide labeling and quantitative mass spectrometry allowed the identification and quantification of 22 000 phosphopeptides and 8800 proteins in biological triplicates without missing values. The data show that FGF2 protects the cells from the antiproliferative effect of Gefitinib and largely prevents reprogramming of the proteome and phosphoproteome. Simultaneous EGFR/FGFR or EGFR/GSG2 (Haspin) inhibition overcomes this resistance, and the phosphoproteomic experiments further prioritized the RAS/MEK/ERK as well as the PI3K/mTOR axis for combination treatment. Consequently, the MEK inhibitor Trametinib prevented FGF2-mediated survival of EGFR inhibitor-resistant cells when used in combination with Gefitinib. Surprisingly, the PI3K/mTOR inhibitor Omipalisib reversed resistance mediated by all four growth factors tested, making it an interesting candidate for mitigating the effects of the tumor microenvironment.
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Affiliation(s)
- Heiner Koch
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,German Cancer Consortium (DKTK) , 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany
| | - Mathias Wilhelm
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany
| | - Benjamin Ruprecht
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,Center for Integrated Protein Science Munich (CIPSM) , 81377 Munich, Germany
| | - Scarlet Beck
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , 82152 Martinsried, Germany
| | - Martin Frejno
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,Department of Oncology, University of Oxford , OX3 7DQ Oxford, United Kingdom
| | - Susan Klaeger
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,German Cancer Consortium (DKTK) , 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany
| | - Bernhard Kuster
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,German Cancer Consortium (DKTK) , 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany.,Center for Integrated Protein Science Munich (CIPSM) , 81377 Munich, Germany.,Bavarian Biomolecular Mass Spectrometry Center, Technische Universität München , 85354 Freising, Germany
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44
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Strmiskova M, Desrochers GF, Shaw TA, Powdrill MH, Lafreniere MA, Pezacki JP. Chemical Methods for Probing Virus-Host Proteomic Interactions. ACS Infect Dis 2016; 2:773-786. [PMID: 27933785 DOI: 10.1021/acsinfecdis.6b00084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interactions between host and pathogen proteins constitute an important aspect of both infectivity and the host immune response. Different viruses have evolved complex mechanisms to hijack host-cell machinery and metabolic pathways to redirect resources and energy flow toward viral propagation. These interactions are often critical to the virus, and thus understanding these interactions at a molecular level gives rise to opportunities to develop novel antiviral strategies for therapeutic intervention. This review summarizes current advances in chemoproteomic methods for studying these molecular altercations between different viruses and their hosts.
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Affiliation(s)
- Miroslava Strmiskova
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew A. Lafreniere
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
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45
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Zou C, Wang P, Xu Y. Bulked sample analysis in genetics, genomics and crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1941-55. [PMID: 26990124 PMCID: PMC5043468 DOI: 10.1111/pbi.12559] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 05/18/2023]
Abstract
Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
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Affiliation(s)
- Cheng Zou
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pingxi Wang
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunbi Xu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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Paulo JA, O'Connell JD, Gygi SP. A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1620-5. [PMID: 27400695 PMCID: PMC5018445 DOI: 10.1007/s13361-016-1434-9] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/30/2016] [Accepted: 05/31/2016] [Indexed: 05/16/2023]
Abstract
Isobaric labeling is a powerful strategy for quantitative mass spectrometry-based proteomic investigations. A complication of such analyses has been the co-isolation of multiple analytes of similar mass-to-charge resulting in the distortion of relative protein abundance measurements across samples. When properly implemented, synchronous precursor selection and triple-stage mass spectrometry (SPS-MS3) can reduce the occurrence of this phenomenon, referred to as ion interference. However, no diagnostic tool is available currently to rapidly and accurately assess ion interference. To address this need, we developed a multiplexed tandem mass tag (TMT)-based standard, termed the triple knockout (TKO). This standard is comprised of three yeast proteomes in triplicate, each from a strain deficient in a highly abundant protein (Met6, Pfk2, or Ura2). The relative abundance patterns of these proteins, which can be inferred from dozens of peptide measurements can demonstrate ion interference in peptide quantification. We expect no signal in channels where the protein is knocked out, permitting maximum sensitivity for measurements of ion interference against a null background. Here, we emphasize the need to investigate further ion interference-generated ratio distortion and promote the TKO standard as a tool to investigate such issues. Graphical Abstract ᅟ.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Jeremy D O'Connell
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
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Paulo JA, O'Connell JD, Everley RA, O'Brien J, Gygi MA, Gygi SP. Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources. J Proteomics 2016; 148:85-93. [PMID: 27432472 DOI: 10.1016/j.jprot.2016.07.005] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/26/2016] [Accepted: 07/07/2016] [Indexed: 12/18/2022]
Abstract
UNLABELLED The budding yeast Saccharomyces cerevisiae is a model system for investigating biological processes. Cellular events are known to be dysregulated due to shifts in carbon sources. However, the comprehensive proteomic alterations thereof have not been fully investigated. Here we examined proteomic alterations in S. cerevisiae due to the adaptation of yeast from glucose to nine different carbon sources - maltose, trehalose, fructose, sucrose, glycerol, acetate, pyruvate, lactic acid, and oleate. Isobaric tag-based mass spectrometry techniques are at the forefront of global proteomic investigations. As such, we used a TMT10-plex strategy to study multiple growth conditions in a single experiment. The SPS-MS3 method on an Orbitrap Fusion Lumos mass spectrometer enabled the quantification of over 5000 yeast proteins across ten carbon sources at a 1% protein-level FDR. On average, the proteomes of yeast cultured in fructose and sucrose deviated the least from those cultured in glucose. As expected, gene ontology classification revealed the major alteration in protein abundances occurred in metabolic pathways and mitochondrial proteins. Our protocol lays the groundwork for further investigation of carbon source-induced protein alterations. Additionally, these data offer a hypothesis-generating resource for future studies aiming to investigate both characterized and uncharacterized genes. BIOLOGICAL SIGNIFICANCE We investigate the proteomic alterations in S. cerevisiae resulting from adaptation of yeast from glucose to nine different carbon sources - maltose, trehalose, fructose, sucrose, glycerol, acetate, pyruvate, lactic acid, and oleate. SPS-MS3 TMT10plex analysis is used for quantitative proteomic analysis. We showcase a technique that allows the quantification of over 5000 yeast proteins, the highest number to date in S. cerevisiae, across 10 growth conditions in a single experiment. As expected, gene ontology classification of proteins with the major alterations in abundances occurred in metabolic pathways and mitochondrial proteins, reflecting the degree of metabolic stress when cellular machinery shifts from growth on glucose to an alternative carbon source. Our protocol lays the groundwork for further investigation of carbon source-induced protein alterations. Improving depth of coverage - measuring abundance changes of over 5000 proteins - increases our understanding of difficult-to-study genes in the model system S. cerevisiae and by homology human cell biology. We submit this highly comprehensive dataset as a hypothesis generating resource for targeted studies on uncharacterized genes.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States.
| | - Jeremy D O'Connell
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Robert A Everley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Jonathon O'Brien
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Micah A Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States.
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Open-gate mutants of the mammalian proteasome show enhanced ubiquitin-conjugate degradation. Nat Commun 2016; 7:10963. [PMID: 26957043 PMCID: PMC4786872 DOI: 10.1038/ncomms10963] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/04/2016] [Indexed: 12/20/2022] Open
Abstract
When in the closed form, the substrate translocation channel of the proteasome core
particle (CP) is blocked by the convergent N termini of α-subunits. To
probe the role of channel gating in mammalian proteasomes, we deleted the N-terminal
tail of α3; the resulting α3ΔN proteasomes are intact
but hyperactive in the hydrolysis of fluorogenic peptide substrates and the
degradation of polyubiquitinated proteins. Cells expressing the hyperactive
proteasomes show markedly elevated degradation of many established proteasome
substrates and resistance to oxidative stress. Multiplexed quantitative proteomics
revealed ∼200 proteins with reduced levels in the mutant cells. Potentially
toxic proteins such as tau exhibit reduced accumulation and aggregate formation.
These data demonstrate that the CP gate is a key negative regulator of proteasome
function in mammals, and that opening the CP gate may be an effective strategy to
increase proteasome activity and reduce levels of toxic proteins in cells. The proteasome plays a key role in proteostasis by mediating the
degradation of ubiquitinated substrates. Here the authors show that an open-gate mutant
of the proteasome is hyperactive towards a subset of substrates and can effectively
delay the accumulation of toxic protein aggregates.
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Affiliation(s)
- Nicholas M. Riley
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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Paulo JA, O'Connell JD, Gaun A, Gygi SP. Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. Mol Biol Cell 2015; 26:4063-74. [PMID: 26399295 PMCID: PMC4710237 DOI: 10.1091/mbc.e15-07-0499] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/18/2015] [Indexed: 12/27/2022] Open
Abstract
A mass spectrometry–based tandem mass tag 9-plex strategy was used to determine alterations in relative protein abundance due to three carbon sources—glucose, galactose, and raffinose. More than 4700 proteins were quantified across all nine samples; 1003 demonstrated statistically significant differences in abundance in at least one condition. The global proteomic alterations in the budding yeast Saccharomyces cerevisiae due to differences in carbon sources can be comprehensively examined using mass spectrometry–based multiplexing strategies. In this study, we investigate changes in the S. cerevisiae proteome resulting from cultures grown in minimal media using galactose, glucose, or raffinose as the carbon source. We used a tandem mass tag 9-plex strategy to determine alterations in relative protein abundance due to a particular carbon source, in triplicate, thereby permitting subsequent statistical analyses. We quantified more than 4700 proteins across all nine samples; 1003 proteins demonstrated statistically significant differences in abundance in at least one condition. The majority of altered proteins were classified as functioning in metabolic processes and as having cellular origins of plasma membrane and mitochondria. In contrast, proteins remaining relatively unchanged in abundance included those having nucleic acid–related processes, such as transcription and RNA processing. In addition, the comprehensiveness of the data set enabled the analysis of subsets of functionally related proteins, such as phosphatases, kinases, and transcription factors. As a resource, these data can be mined further in efforts to understand better the roles of carbon source fermentation in yeast metabolic pathways and the alterations observed therein, potentially for industrial applications, such as biofuel feedstock production.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | | | - Aleksandr Gaun
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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