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Piersma SR, Valles-Marti A, Rolfs F, Pham TV, Henneman AA, Jiménez CR. Inferring kinase activity from phosphoproteomic data: Tool comparison and recent applications. MASS SPECTROMETRY REVIEWS 2024; 43:725-751. [PMID: 36156810 DOI: 10.1002/mas.21808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aberrant cellular signaling pathways are a hallmark of cancer and other diseases. One of the most important signaling mechanisms involves protein phosphorylation/dephosphorylation. Protein phosphorylation is catalyzed by protein kinases, and over 530 protein kinases have been identified in the human genome. Aberrant kinase activity is one of the drivers of tumorigenesis and cancer progression and results in altered phosphorylation abundance of downstream substrates. Upstream kinase activity can be inferred from the global collection of phosphorylated substrates. Mass spectrometry-based phosphoproteomic experiments nowadays routinely allow identification and quantitation of >10k phosphosites per biological sample. This substrate phosphorylation footprint can be used to infer upstream kinase activities using tools like Kinase Substrate Enrichment Analysis (KSEA), Posttranslational Modification Substrate Enrichment Analysis (PTM-SEA), and Integrative Inferred Kinase Activity Analysis (INKA). Since the topic of kinase activity inference is very active with many new approaches reported in the past 3 years, we would like to give an overview of the field. In this review, an inventory of kinase activity inference tools, their underlying algorithms, statistical frameworks, kinase-substrate databases, and user-friendliness is presented. The most widely-used tools are compared in-depth. Subsequently, recent applications of the tools are described focusing on clinical tissues and hematological samples. Two main application areas for kinase activity inference tools can be discerned. (1) Maximal biological insights can be obtained from large data sets with group comparisons using multiple complementary tools (e.g., PTM-SEA and KSEA or INKA). (2) In the oncology context where personalized treatment requires analysis of single samples, INKA for example, has emerged as tool that can prioritize actionable kinases for targeted inhibition.
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Affiliation(s)
- Sander R Piersma
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Andrea Valles-Marti
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Frank Rolfs
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex A Henneman
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
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2
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Duchatel RJ, Jackson ER, Parackal SG, Kiltschewskij D, Findlay IJ, Mannan A, Staudt DE, Thomas BC, Germon ZP, Laternser S, Kearney PS, Jamaluddin MFB, Douglas AM, Beitaki T, McEwen HP, Persson ML, Hocke EA, Jain V, Aksu M, Manning EE, Murray HC, Verrills NM, Sun CX, Daniel P, Vilain RE, Skerrett-Byrne DA, Nixon B, Hua S, de Bock CE, Colino-Sanguino Y, Valdes-Mora F, Tsoli M, Ziegler DS, Cairns MJ, Raabe EH, Vitanza NA, Hulleman E, Phoenix TN, Koschmann C, Alvaro F, Dayas CV, Tinkle CL, Wheeler H, Whittle JR, Eisenstat DD, Firestein R, Mueller S, Valvi S, Hansford JR, Ashley DM, Gregory SG, Kilburn LB, Nazarian J, Cain JE, Dun MD. PI3K/mTOR is a therapeutically targetable genetic dependency in diffuse intrinsic pontine glioma. J Clin Invest 2024; 134:e170329. [PMID: 38319732 PMCID: PMC10940093 DOI: 10.1172/jci170329] [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: 03/08/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Diffuse midline glioma (DMG), including tumors diagnosed in the brainstem (diffuse intrinsic pontine glioma; DIPG), are uniformly fatal brain tumors that lack effective treatment. Analysis of CRISPR/Cas9 loss-of-function gene deletion screens identified PIK3CA and MTOR as targetable molecular dependencies across patient derived models of DIPG, highlighting the therapeutic potential of the blood-brain barrier-penetrant PI3K/Akt/mTOR inhibitor, paxalisib. At the human-equivalent maximum tolerated dose, mice treated with paxalisib experienced systemic glucose feedback and increased insulin levels commensurate with patients using PI3K inhibitors. To exploit genetic dependence and overcome resistance while maintaining compliance and therapeutic benefit, we combined paxalisib with the antihyperglycemic drug metformin. Metformin restored glucose homeostasis and decreased phosphorylation of the insulin receptor in vivo, a common mechanism of PI3K-inhibitor resistance, extending survival of orthotopic models. DIPG models treated with paxalisib increased calcium-activated PKC signaling. The brain penetrant PKC inhibitor enzastaurin, in combination with paxalisib, synergistically extended the survival of multiple orthotopic patient-derived and immunocompetent syngeneic allograft models; benefits potentiated in combination with metformin and standard-of-care radiotherapy. Therapeutic adaptation was assessed using spatial transcriptomics and ATAC-Seq, identifying changes in myelination and tumor immune microenvironment crosstalk. Collectively, this study has identified what we believe to be a clinically relevant DIPG therapeutic combinational strategy.
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Affiliation(s)
- Ryan J. Duchatel
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Evangeline R. Jackson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Sarah G. Parackal
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Dylan Kiltschewskij
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Izac J. Findlay
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Abdul Mannan
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Dilana E. Staudt
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Bryce C. Thomas
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Zacary P. Germon
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Sandra Laternser
- DIPG/DMG Research Center Zurich, Children’s Research Center, Department of Pediatrics, University Children’s Hospital Zürich, Zurich, Switzerland
| | - Padraic S. Kearney
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - M. Fairuz B. Jamaluddin
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Alicia M. Douglas
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Tyrone Beitaki
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Holly P. McEwen
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Mika L. Persson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Emily A. Hocke
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Michael Aksu
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Elizabeth E. Manning
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Heather C. Murray
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Nicole M. Verrills
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Claire Xin Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Paul Daniel
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Ricardo E. Vilain
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - David A. Skerrett-Byrne
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Brett Nixon
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Susan Hua
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Charles E. de Bock
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Yolanda Colino-Sanguino
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Fatima Valdes-Mora
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Maria Tsoli
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - David S. Ziegler
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Murray J. Cairns
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Eric H. Raabe
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicholas A. Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, Washington, USA
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Timothy N. Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio, USA
| | - Carl Koschmann
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank Alvaro
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- John Hunter Children’s Hospital, New Lambton Heights, New South Wales, Australia
| | - Christopher V. Dayas
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Christopher L. Tinkle
- Department of Radiation Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Helen Wheeler
- Department of Radiation Oncology Northern Sydney Cancer Centre, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- The Brain Cancer group, St Leonards, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - James R. Whittle
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David D. Eisenstat
- Children’s Cancer Centre, The Royal Children’s Hospital Melbourne, Parkville, Victoria, Australia
- Neuro-Oncology Laboratory, Murdoch Children’s Research Institute, Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Sabine Mueller
- DIPG/DMG Research Center Zurich, Children’s Research Center, Department of Pediatrics, University Children’s Hospital Zürich, Zurich, Switzerland
- Department of Neurology, Neurosurgery, and Pediatrics, University of California, San Francisco, California, USA
| | - Santosh Valvi
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children’s Hospital, Nedlands, Washington, Australia
- Brain Tumour Research Laboratory, Telethon Kids Institute, Nedlands, Washington, Australia
- Division of Paediatrics, University of Western Australia Medical School, Nedlands, Western Australia, Australia
| | - Jordan R. Hansford
- Michael Rice Centre for Hematology and Oncology, Women’s and Children’s Hospital, North Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - David M. Ashley
- The Preston Robert Tisch Brain Tumor Center at Duke, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
- The Preston Robert Tisch Brain Tumor Center at Duke, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | - Lindsay B. Kilburn
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- The George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Javad Nazarian
- DIPG/DMG Research Center Zurich, Children’s Research Center, Department of Pediatrics, University Children’s Hospital Zürich, Zurich, Switzerland
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- The George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Jason E. Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Matthew D. Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
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3
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Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
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Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
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4
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Delgado M, Washam CL, Urbaniak A, Heflin B, Storey AJ, Lan RS, Mackintosh SG, Tackett AJ, Byrum SD, Chambers TC. Phosphoproteomics Provides Novel Insights into the Response of Primary Acute Lymphoblastic Leukemia Cells to Microtubule Depolymerization in G1 Phase of the Cell Cycle. ACS OMEGA 2021; 6:24949-24959. [PMID: 34604676 PMCID: PMC8482483 DOI: 10.1021/acsomega.1c03936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Microtubule targeting agents (MTAs) have been used for the treatment of cancer for many decades and are among the most successful chemotherapeutic agents. However, their application and effectiveness are limited because of toxicity and resistance as well as a lack of knowledge of molecular mechanisms downstream of microtubule inhibition. Insights into key pathways that link microtubule disruption to cell death is critical for optimal use of these drugs, for defining biomarkers useful in patient stratification, and for informed design of drug combinations. Although MTAs characteristically induce death in mitosis, microtubule destabilizing agents such as vincristine also induce death directly in G1 phase in primary acute lymphoblastic leukemia (ALL) cells. Because many signaling pathways regulating cell survival and death involve changes in protein expression and phosphorylation, we undertook a comprehensive quantitative proteomic study of G1 phase ALL cells treated with vincristine. The results revealed distinct alterations associated with c-Jun N-terminal kinase signaling, anti-proliferative signaling, the DNA damage response, and cytoskeletal remodeling. Signals specifically associated with cell death were identified by pre-treatment with the CDK4/6 inhibitor palbociclib, which caused G1 arrest and precluded death induction. These results provide insights into signaling mechanisms regulating cellular responses to microtubule inhibition and provide a foundation for a better understanding of the clinical mechanisms of MTAs and for the design of novel drug combinations. The mass spectrometry proteomics data have been deposited to the PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) via the PRIDE partner repository with the data set identifier PXD027190 and 10.6019/PXD027190.
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Affiliation(s)
- Magdalena Delgado
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Charity L. Washam
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Alicja Urbaniak
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Billie Heflin
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Aaron J. Storey
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Renny S. Lan
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Samuel G. Mackintosh
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Alan J. Tackett
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States
- Winthrop
P. Rockefeller Cancer Institute, 449 Jack Stephens Dr, Little Rock, Arkansas 72205, United
States
| | - Stephanie D. Byrum
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States
- Winthrop
P. Rockefeller Cancer Institute, 449 Jack Stephens Dr, Little Rock, Arkansas 72205, United
States
| | - Timothy C. Chambers
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Winthrop
P. Rockefeller Cancer Institute, 449 Jack Stephens Dr, Little Rock, Arkansas 72205, United
States
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5
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Rada CC, Mejia-Pena H, Grimsey NJ, Cordova IC, Olson J, Wozniak J, Gonzalez DJ, Nizet V, Trejo J. Heat shock protein 27 activity is linked to endothelial barrier recovery after proinflammatory GPCR-induced disruption. Sci Signal 2021; 14:eabc1044. [PMID: 34516752 PMCID: PMC8538426 DOI: 10.1126/scisignal.abc1044] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Vascular inflammation causes endothelial barrier disruption and tissue edema. Several inflammatory mediators act through G protein–coupled receptors (GPCRs), including protease-activated receptor-1 (PAR1), to elicit inflammatory responses. The activation of PAR1 by its ligand thrombin stimulates proinflammatory, p38 mitogen-activated protein kinase (MAPK) signaling that promotes endothelial barrier disruption. Through mass spectrometry phosphoproteomics, we identified heat shock protein 27 (HSP27), which exists as a large oligomer that binds to actin, as a promising candidate for the p38-mediated regulation of barrier integrity. Depletion of HSP27 by siRNA enhanced endothelial cell barrier permeability and slowed recovery after thrombin stimulation. We further showed that two effector kinases of p38 MAPK, MAPKAPK2 (MK2) and MAPKAPK3 (MK3), differentially phosphorylated HSP27 at Ser15, Ser78, and Ser82. Whereas inhibition of thrombin-stimulated p38 activation blocked HSP27 phosphorylation at all three sites, inhibition of MK2 reduced the phosphorylation of only Ser15 and Ser78. Inhibition of both MK2 and MK3 was necessary to attenuate Ser82 phosphorylation. Thrombin-stimulated p38-MK2-MK3 signaling induced HSP27 oligomer disassembly. However, a phosphorylation-deficient mutant of HSP27 exhibited defective oligomer disassembly and altered the dynamics of barrier recovery after thrombin stimulation. Moreover, blocking HSP27 oligomer reassembly with the small-molecule inhibitor J2 enhanced endothelial barrier permeability in vitro and vascular leakage in vivo in response to PAR1 activation. These studies reveal the distinct regulation of HSP27 phosphorylation and function induced by the GPCR-stimulated p38-MK2-MK3 signaling axis that controls the dynamics of endothelial barrier recovery in vitro and vascular leakage in vivo.
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Affiliation(s)
- Cara C. Rada
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hilda Mejia-Pena
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neil J. Grimsey
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30682, USA
| | - Isabel Canto Cordova
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joshua Olson
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jacob Wozniak
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J. Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Victor Nizet
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - JoAnn Trejo
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
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6
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Leeming MG, O'Callaghan S, Licata L, Iannuccelli M, Lo Surdo P, Micarelli E, Ang CS, Nie S, Varshney S, Ameen S, Cheng HC, Williamson NA. Phosphomatics: interactive interrogation of substrate-kinase networks in global phosphoproteomics datasets. Bioinformatics 2021; 37:1635-1636. [PMID: 33119075 DOI: 10.1093/bioinformatics/btaa916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/14/2020] [Accepted: 10/15/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Mass spectrometry-based phosphoproteomics can routinely identify and quantify thousands of phosphorylated peptides from a single experiment. However interrogating possible upstream kinases and identifying key literature for phosphorylation sites is laborious and time-consuming. RESULTS Here, we present Phosphomatics-a publicly available web resource for interrogating phosphoproteomics data. Phosphomatics allows researchers to upload phosphoproteomics data and interrogate possible relationships from a substrate-, kinase- or pathway-centric viewpoint. AVAILABILITY AND IMPLEMENTATION Phosphomatics is freely available via the internet at: https://phosphomatics.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael G Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Luana Licata
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marta Iannuccelli
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Prisca Lo Surdo
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Elisa Micarelli
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Ching-Seng Ang
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Swati Varshney
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sadia Ameen
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Heung-Chin Cheng
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Nicholas A Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
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7
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Chappell K, Manna K, Washam CL, Graw S, Alkam D, Thompson MD, Zafar MK, Hazeslip L, Randolph C, Gies A, Bird JT, Byrd AK, Miah S, Byrum SD. Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer. Mol Omics 2021; 17:677-691. [PMID: 34142686 PMCID: PMC8504614 DOI: 10.1039/d1mo00117e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triple negative breast cancer (TNBC) is an aggressive type of breast cancer with very little treatment options. TNBC is very heterogeneous with large alterations in the genomic, transcriptomic, and proteomic landscapes leading to various subtypes with differing responses to therapeutic treatments. We applied a multi-omics data integration method to evaluate the correlation of important regulatory features in TNBC BRCA1 wild-type MDA-MB-231 and TNBC BRCA1 5382insC mutated HCC1937 cells compared with non-tumorigenic epithelial breast MCF10A cells. The data includes DNA methylation, RNAseq, protein, phosphoproteomics, and histone post-translational modification. Data integration methods identified regulatory features from each omics method that had greater than 80% positive correlation within each TNBC subtype. Key regulatory features at each omics level were identified distinguishing the three cell lines and were involved in important cancer related pathways such as TGFβ signaling, PI3K/AKT/mTOR, and Wnt/beta-catenin signaling. We observed overexpression of PTEN, which antagonizes the PI3K/AKT/mTOR pathway, and MYC, which downregulates the same pathway in the HCC1937 cells relative to the MDA-MB-231 cells. The PI3K/AKT/mTOR and Wnt/beta-catenin pathways are both downregulated in HCC1937 cells relative to MDA-MB-231 cells, which likely explains the divergent sensitivities of these cell lines to inhibitors of downstream signaling pathways. The DNA methylation and RNAseq data is freely available via GEO GSE171958 and the proteomics data is available via the ProteomeXchange PXD025238.
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Affiliation(s)
- Kevin Chappell
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Kanishka Manna
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Charity L Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
| | - Stefan Graw
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA and Emory University, Atlanta, GA, USA
| | - Duah Alkam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Matthew D Thompson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Maroof Khan Zafar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Lindsey Hazeslip
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Christopher Randolph
- Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
| | - Allen Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Jordan T Bird
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Winthrop P. Rockefeller Cancer Institute, 449 Jack Stephens Dr, Little Rock, AR 72205, USA
| | - Sayem Miah
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Winthrop P. Rockefeller Cancer Institute, 449 Jack Stephens Dr, Little Rock, AR 72205, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA and Winthrop P. Rockefeller Cancer Institute, 449 Jack Stephens Dr, Little Rock, AR 72205, USA
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8
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Chen YJ, Roumeliotis TI, Chang YH, Chen CT, Han CL, Lin MH, Chen HW, Chang GC, Chang YL, Wu CT, Lin MW, Hsieh MS, Wang YT, Chen YR, Jonassen I, Ghavidel FZ, Lin ZS, Lin KT, Chen CW, Sheu PY, Hung CT, Huang KC, Yang HC, Lin PY, Yen TC, Lin YW, Wang JH, Raghav L, Lin CY, Chen YS, Wu PS, Lai CT, Weng SH, Su KY, Chang WH, Tsai PY, Robles AI, Rodriguez H, Hsiao YJ, Chang WH, Sung TY, Chen JS, Yu SL, Choudhary JS, Chen HY, Yang PC, Chen YJ. Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression. Cell 2021; 182:226-244.e17. [PMID: 32649875 DOI: 10.1016/j.cell.2020.06.012] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/13/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022]
Abstract
Lung cancer in East Asia is characterized by a high percentage of never-smokers, early onset and predominant EGFR mutations. To illuminate the molecular phenotype of this demographically distinct disease, we performed a deep comprehensive proteogenomic study on a prospectively collected cohort in Taiwan, representing early stage, predominantly female, non-smoking lung adenocarcinoma. Integrated genomic, proteomic, and phosphoproteomic analysis delineated the demographically distinct molecular attributes and hallmarks of tumor progression. Mutational signature analysis revealed age- and gender-related mutagenesis mechanisms, characterized by high prevalence of APOBEC mutational signature in younger females and over-representation of environmental carcinogen-like mutational signatures in older females. A proteomics-informed classification distinguished the clinical characteristics of early stage patients with EGFR mutations. Furthermore, integrated protein network analysis revealed the cellular remodeling underpinning clinical trajectories and nominated candidate biomarkers for patient stratification and therapeutic intervention. This multi-omic molecular architecture may help develop strategies for management of early stage never-smoker lung adenocarcinoma.
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Affiliation(s)
- Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Theodoros I Roumeliotis
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, UK
| | - Ya-Hsuan Chang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Ching-Tai Chen
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| | - Miao-Hsia Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Huei-Wen Chen
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Gee-Chen Chang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yih-Leong Chang
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chen-Tu Wu
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mong-Wei Lin
- Division of Thoracic Surgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Min-Shu Hsieh
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Tai Wang
- National Applied Research Laboratories, National Center for High-performance Computing, Hsinchu, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Inge Jonassen
- Computational Biology Unit (CBU), Informatics Department, University of Bergen, Bergen, Norway
| | | | - Ze-Shiang Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kuen-Tyng Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ching-Wen Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Yuan Sheu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chen-Ting Hung
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | | | - Hao-Chin Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ta-Chi Yen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yi-Wei Lin
- Division of Thoracic Surgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Jen-Hung Wang
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Lovely Raghav
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan; Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Bioinformatics Program, Taiwan International Graduate Program, Hsinchu, Taiwan
| | - Chien-Yu Lin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yan-Si Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Pei-Shan Wu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chi-Ting Lai
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Hung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Pang-Yan Tsai
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yi-Jing Hsiao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Hsin Chang
- Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica, Taipei, Taiwan.
| | - Jin-Shing Chen
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan.
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Jyoti S Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, UK.
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan; Ph.D. Program in Microbial Genomics, National Chung Hsing University, Taichung, Taiwan.
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University, Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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9
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Mantini G, Pham TV, Piersma SR, Jimenez CR. Computational Analysis of Phosphoproteomics Data in Multi-Omics Cancer Studies. Proteomics 2020; 21:e1900312. [PMID: 32875713 DOI: 10.1002/pmic.201900312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/09/2020] [Indexed: 12/24/2022]
Abstract
Multiple types of molecular data for the same set of clinical samples are increasingly available and may be analyzed jointly in an integrative analysis to maximize comprehensive biological insight. This analysis is important as separate analyses of individual omics data types usually do not fully explain disease phenotypes. An increasing number of studies have now been focusing on multi-omics data integration, yet not many studies have included phosphoproteomics data, an important layer for understanding signaling pathways. Multi-omics integration methods with phosphoproteomics data are reviewed in the context of cancer research as well as multi-omics methods papers that would be promising to apply to phosphoproteomics data. Analysis of individual data types is still the major approach even in large cohort proteogenomics studies. Hence, a section is dedicated on possible integrative methods for multi-omics and phosphoproteomics data. In summary, this review provides the readers with both currently used integrative methods previously applied to phosphoproteomics and multi-omics data integration and other algorithms for multi-omics data integration promising for future application to phosphoproteomics data.
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Affiliation(s)
- Giulia Mantini
- Department of Medical Oncology, OncoProteomics Laboratory, CCA 1-60, Amsterdam UMC VUmc-location, De Boelelaan 1117, Amsterdam, 1081 HV, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, OncoProteomics Laboratory, CCA 1-60, Amsterdam UMC VUmc-location, De Boelelaan 1117, Amsterdam, 1081 HV, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, CCA 1-60, Amsterdam UMC VUmc-location, De Boelelaan 1117, Amsterdam, 1081 HV, The Netherlands
| | - Connie R Jimenez
- Department of Medical Oncology, OncoProteomics Laboratory, CCA 1-60, Amsterdam UMC VUmc-location, De Boelelaan 1117, Amsterdam, 1081 HV, The Netherlands
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10
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Savage SR, Zhang B. Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. Clin Proteomics 2020; 17:27. [PMID: 32676006 PMCID: PMC7353784 DOI: 10.1186/s12014-020-09290-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 07/04/2020] [Indexed: 12/19/2022] Open
Abstract
Mass spectrometry-based phosphoproteomics is becoming an essential methodology for the study of global cellular signaling. Numerous bioinformatics resources are available to facilitate the translation of phosphopeptide identification and quantification results into novel biological and clinical insights, a critical step in phosphoproteomics data analysis. These resources include knowledge bases of kinases and phosphatases, phosphorylation sites, kinase inhibitors, and sequence variants affecting kinase function, and bioinformatics tools that can predict phosphorylation sites in addition to the kinase that phosphorylates them, infer kinase activity, and predict the effect of mutations on kinase signaling. However, these resources exist in silos and it is challenging to select among multiple resources with similar functions. Therefore, we put together a comprehensive collection of resources related to phosphoproteomics data interpretation, compared the use of tools with similar functions, and assessed the usability from the standpoint of typical biologists or clinicians. Overall, tools could be improved by standardization of enzyme names, flexibility of data input and output format, consistent maintenance, and detailed manuals.
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Affiliation(s)
- Sara R. Savage
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
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11
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Katrancha SM, Shaw JE, Zhao AY, Myers SA, Cocco AR, Jeng AT, Zhu M, Pittenger C, Greer CA, Carr SA, Xiao X, Koleske AJ. Trio Haploinsufficiency Causes Neurodevelopmental Disease-Associated Deficits. Cell Rep 2020; 26:2805-2817.e9. [PMID: 30840899 PMCID: PMC6436967 DOI: 10.1016/j.celrep.2019.02.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 12/22/2018] [Accepted: 02/06/2019] [Indexed: 12/31/2022] Open
Abstract
Heterozygous coding mutations in TRIO are associated with neurodevelopmental disorders, including autism, schizophrenia, bipolar disorder, and epilepsy, and impair TRIO's biochemical activities. To model mutant alleles, we ablated one or both Trio alleles from excitatory neurons in the cortex and hippocampus of mice. Trio haploinsufficiency increases anxiety and impairs social preference and motor coordination. Trio loss reduces forebrain size and dendritic arborization but increases dendritic spine densities. Cortical synapses in Trio haploinsufficient mice are small, exhibit pre- and postsynaptic deficits, and cannot undergo long-term potentiation. Similar phenotypes are observed in Trio knockout mice. Overall, Trio haploinsufficiency causes severe disease-relevant deficits in behavior and neuronal structure and function. Interestingly, phosphodiesterase 4A5 (PDE4A5) levels are reduced and protein kinase A (PKA) signaling is increased when TRIO levels are reduced. Elevation of PDE4A5 and drug-based attenuation of PKA signaling rescue Trio haploinsufficiency-related dendritic spine defects, suggesting an avenue for therapeutic intervention for TRIO-related neurodevelopmental disorders.
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Affiliation(s)
- Sara Marie Katrancha
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA; Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Juliana E Shaw
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Amy Y Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA; Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Samuel A Myers
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Amanda T Jeng
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA
| | - Minsheng Zhu
- Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Christopher Pittenger
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA; Department of Psychiatry, Yale University, New Haven, CT 06510, USA; Child Study Center, Yale University, New Haven, CT 06510, USA
| | - Charles A Greer
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA; Department of Neuroscience, Yale University, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xiao Xiao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai 200433, China.
| | - Anthony J Koleske
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06510, USA; Department of Neuroscience, Yale University, New Haven, CT 06510, USA.
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12
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CIGB-300 anticancer peptide regulates the protein kinase CK2-dependent phosphoproteome. Mol Cell Biochem 2020; 470:63-75. [PMID: 32405972 DOI: 10.1007/s11010-020-03747-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022]
Abstract
Casein-kinase CK2 is a Ser/Thr protein kinase that fosters cell survival and proliferation of malignant cells. The CK2 holoenzyme, formed by the association of two catalytic alpha/alpha' (CK2α/CK2α') and two regulatory beta subunits (CK2β), phosphorylates diverse intracellular proteins partaking in key cellular processes. A handful of such CK2 substrates have been identified as targets for the substrate-binding anticancer peptide CIGB-300. However, since CK2β also contains a CK2 phosphorylation consensus motif, this peptide may also directly impinge on CK2 enzymatic activity, thus globally modifying the CK2-dependent phosphoproteome. To address such a possibility, firstly, we evaluated the potential interaction of CIGB-300 with CK2 subunits, both in cell-free assays and cellular lysates, as well as its effect on CK2 enzymatic activity. Then, we performed a phosphoproteomic survey focusing on early inhibitory events triggered by CIGB-300 and identified those CK2 substrates significantly inhibited along with disturbed cellular processes. Altogether, we provided here the first evidence for a direct impairment of CK2 enzymatic activity by CIGB-300. Of note, both CK2-mediated inhibitory mechanisms of this anticancer peptide (i.e., substrate- and enzyme-binding mechanism) may run in parallel in tumor cells and help to explain the different anti-neoplastic effects exerted by CIGB-300 in preclinical cancer models.
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13
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Schäfer A, Gjerga E, Welford RW, Renz I, Lehembre F, Groenen PM, Saez-Rodriguez J, Aebersold R, Gstaiger M. Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data. Mol Syst Biol 2020; 15:e8828. [PMID: 31464372 PMCID: PMC6683863 DOI: 10.15252/msb.20198828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 01/31/2023] Open
Abstract
Endothelins (EDN) are peptide hormones that activate a GPCR signalling system and contribute to several diseases, including hypertension and cancer. Current knowledge about EDN signalling is fragmentary, and no systems level understanding is available. We investigated phosphoproteomic changes caused by endothelin B receptor (ENDRB) activation in the melanoma cell lines UACC257 and A2058 and built an integrated model of EDNRB signalling from the phosphoproteomics data. More than 5,000 unique phosphopeptides were quantified. EDN induced quantitative changes in more than 800 phosphopeptides, which were all strictly dependent on EDNRB. Activated kinases were identified based on high confidence EDN target sites and validated by Western blot. The data were combined with prior knowledge to construct the first comprehensive logic model of EDN signalling. Among the kinases predicted by the signalling model, AKT, JNK, PKC and AMP could be functionally linked to EDN‐induced cell migration. The model contributes to the system‐level understanding of the mechanisms underlying the pleiotropic effects of EDN signalling and supports the rational selection of kinase inhibitors for combination treatments with EDN receptor antagonists.
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Affiliation(s)
- Alexander Schäfer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Enio Gjerga
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
| | | | - Imke Renz
- Idorsia Pharmaceuticals, Allschwil, Switzerland
| | | | | | - Julio Saez-Rodriguez
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany.,Faculty of Medicine, Institute for Computational Biomedicine, Heidelberg University Hospital, Bioquant, Heidelberg University, Heidelberg, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zürich, Zürich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Competence Center Personalized Medicine UZH/ETH, Zürich, Switzerland
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14
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Zhang B, Whiteaker JR, Hoofnagle AN, Baird GS, Rodland KD, Paulovich AG. Clinical potential of mass spectrometry-based proteogenomics. Nat Rev Clin Oncol 2019; 16:256-268. [PMID: 30487530 PMCID: PMC6448780 DOI: 10.1038/s41571-018-0135-7] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cancer genomics research aims to advance personalized oncology by finding and targeting specific genetic alterations associated with cancers. In genome-driven oncology, treatments are selected for individual patients on the basis of the findings of tumour genome sequencing. This personalized approach has prolonged the survival of subsets of patients with cancer. However, many patients do not respond to the predicted therapies based on the genomic profiles of their tumours. Furthermore, studies pairing genomic and proteomic analyses of samples from the same tumours have shown that the proteome contains novel information that cannot be discerned through genomic analysis alone. This observation has led to the concept of proteogenomics, in which both types of data are leveraged for a more complete view of tumour biology that might enable patients to be more successfully matched to effective treatments than they would using genomics alone. In this Perspective, we discuss the added value of proteogenomics over the current genome-driven approach to the clinical characterization of cancers and summarize current efforts to incorporate targeted proteomic measurements based on selected/multiple reaction monitoring (SRM/MRM) mass spectrometry into the clinical laboratory to facilitate clinical proteogenomics.
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Affiliation(s)
- Bing Zhang
- Department of Molecular and Human Genetics, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Geoffrey S Baird
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Cell, Development and Cancer Biology, Oregon Health & Sciences University, Portland, OR, USA
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA.
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15
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Krug K, Mertins P, Zhang B, Hornbeck P, Raju R, Ahmad R, Szucs M, Mundt F, Forestier D, Jane-Valbuena J, Keshishian H, Gillette MA, Tamayo P, Mesirov JP, Jaffe JD, Carr SA, Mani DR. A Curated Resource for Phosphosite-specific Signature Analysis. Mol Cell Proteomics 2019; 18:576-593. [PMID: 30563849 PMCID: PMC6398202 DOI: 10.1074/mcp.tir118.000943] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/13/2018] [Indexed: 12/28/2022] Open
Abstract
Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. However, pathway analysis of PTM data sets generated by mass spectrometry (MS)-based proteomics is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases and bioinformatic tools that leverage PTM site-specific information. Here we present the first version of PTMsigDB, a database of modification site-specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications. We adapted the widely used single sample Gene Set Enrichment Analysis approach to utilize PTMsigDB, enabling PTMSignature Enrichment Analysis (PTM-SEA) of quantitative MS data. We used a well-characterized data set of epidermal growth factor (EGF)-perturbed cancer cells to evaluate our approach and demonstrated better representation of signaling events compared with gene-centric methods. We then applied PTM-SEA to analyze the phosphoproteomes of cancer cells treated with cell-cycle inhibitors and detected mechanism-of-action specific signatures of cell cycle kinases. We also applied our methods to analyze the phosphoproteomes of PI3K-inhibited human breast cancer cells and detected signatures of compounds inhibiting PI3K as well as targets downstream of PI3K (AKT, MAPK/ERK) covering a substantial fraction of the PI3K pathway. PTMsigDB and PTM-SEA can be freely accessed at https://github.com/broadinstitute/ssGSEA2.0.
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Affiliation(s)
- Karsten Krug
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
| | - Philipp Mertins
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
- §Proteomics Platform, Max Delbrück Center for Molecular Medicine, Berlin, Germany 13092
- ¶Berlin Institute of Health, Berlin, Germany 10178
| | - Bin Zhang
- ‖Cell Signaling Technology, Danvers Massachusetts 01923
| | | | - Rajesh Raju
- **Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India 695014
| | - Rushdy Ahmad
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
| | - Matthew Szucs
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
- ‡‡University of Colorado, Denver Colorado 80204
| | - Filip Mundt
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
| | - Dominique Forestier
- §§Department of Oncology, Novartis Institute of Biomedical Research, Cambridge Massachusetts 02139
| | | | - Hasmik Keshishian
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
| | - Michael A Gillette
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
- ¶¶Massachusetts General Hospital, Boston Massachusetts 02114
| | - Pablo Tamayo
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
- ‖‖Department of Medicine, UCSD, La Jolla Califorrnia 92093
- ***Moores Cancer Center, UCSD, La Jolla California 92093
| | - Jill P Mesirov
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
- ‖‖Department of Medicine, UCSD, La Jolla Califorrnia 92093
- ***Moores Cancer Center, UCSD, La Jolla California 92093
| | - Jacob D Jaffe
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
| | - Steven A Carr
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142
| | - D R Mani
- From the ‡Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142;
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Kaur S, Baldi B, Vuong J, O'Donoghue SI. Visualization and Analysis of Epiproteome Dynamics. J Mol Biol 2019; 431:1519-1539. [PMID: 30769119 DOI: 10.1016/j.jmb.2019.01.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 12/28/2022]
Abstract
The epiproteome describes the set of all post-translational modifications (PTMs) made to the proteins comprising a cell or organism. The extent of the epiproteome is still largely unknown; however, advances in experimental techniques are beginning to produce a deluge of data, tracking dynamic changes to the epiproteome in response to cellular stimuli. These data have potential to revolutionize our understanding of biology and disease. This review covers a range of recent visualization methods and tools developed specifically for dynamic epiproteome data sets. These methods have been designed primarily for data sets on phosphorylation, as this the most studied PTM; however, most of these methods are also applicable to other types of PTMs. Unfortunately, the currently available methods are often inadequate for existing data sets; thus, realizing the potential buried in epiproteome data sets will require new, tailored bioinformatics methods that will help researchers analyze, visualize, and interactively explore these complex data sets.
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Affiliation(s)
- Sandeep Kaur
- University of New South Wales (UNSW), Kensington, NSW 2052, Australia; Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
| | - Benedetta Baldi
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Data 61, CSIRO, Eveleigh, NSW 2015, Australia.
| | - Jenny Vuong
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Data 61, CSIRO, Eveleigh, NSW 2015, Australia.
| | - Seán I O'Donoghue
- University of New South Wales (UNSW), Kensington, NSW 2052, Australia; Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Data 61, CSIRO, Eveleigh, NSW 2015, Australia.
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17
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Mohl BP, Emmott E, Roy P. Phosphoproteomic Analysis Reveals the Importance of Kinase Regulation During Orbivirus Infection. Mol Cell Proteomics 2017; 16:1990-2005. [PMID: 28851738 PMCID: PMC5672004 DOI: 10.1074/mcp.m117.067355] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 08/08/2017] [Indexed: 01/03/2023] Open
Abstract
Bluetongue virus (BTV) causes infections in wild and domesticated ruminants with high morbidity and mortality and is responsible for significant economic losses in both developing and developed countries. BTV serves as a model for the study of other members of the Orbivirus genus. Previously, the importance of casein kinase 2 for BTV replication was demonstrated. To identify intracellular signaling pathways and novel host-cell kinases involved during BTV infection, the phosphoproteome of BTV infected cells was analyzed. Over 1000 phosphosites were identified using mass spectrometry, which were then used to determine the corresponding kinases involved during BTV infection. This analysis yielded protein kinase A (PKA) as a novel kinase activated during BTV infection. Subsequently, the importance of PKA for BTV infection was validated using a PKA inhibitor and activator. Our data confirmed that PKA was essential for efficient viral growth. Further, we showed that PKA is also required for infection of equid cells by African horse sickness virus, another member of the Orbivirus genus. Thus, despite their preference in specific host species, orbiviruses may utilize the same host signaling pathways during their replication.
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Affiliation(s)
- Bjorn-Patrick Mohl
- From the ‡Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Edward Emmott
- §University of Cambridge, Division of Virology, Department of Pathology, Lab block level 5, Box 237, Addenbrookes Hospital, Cambridge, UK
| | - Polly Roy
- From the ‡Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK;
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18
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Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics 2017; 16:959-981. [PMID: 28456751 DOI: 10.1074/mcp.mr117.000024] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 12/20/2022] Open
Abstract
With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e. the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease. Many methods and tools have been developed or adapted to enable an array of integrative proteogenomic approaches and in this article, we systematically classify published methods and tools into four major categories, (1) Sequence-centric proteogenomics; (2) Analysis of proteogenomic relationships; (3) Integrative modeling of proteogenomic data; and (4) Data sharing and visualization. We provide a comprehensive review of methods and available tools in each category and highlight their typical applications.
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Affiliation(s)
- Kelly V Ruggles
- From the ‡Department of Medicine, New York University School of Medicine, New York, New York 10016
| | - Karsten Krug
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Xiaojing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Karl R Clauser
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Jing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Samuel H Payne
- **Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - David Fenyö
- ‡‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016; .,§§Institute for Systems Genetics, New York University School of Medicine, New York, New York 10016
| | - Bing Zhang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030; .,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - D R Mani
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
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Murray HC, Dun MD, Verrills NM. Harnessing the power of proteomics for identification of oncogenic, druggable signalling pathways in cancer. Expert Opin Drug Discov 2017; 12:431-447. [PMID: 28286965 DOI: 10.1080/17460441.2017.1304377] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Genomic and transcriptomic profiling of tumours has revolutionised our understanding of cancer. However, the majority of tumours possess multiple mutations, and determining which oncogene, or even which pathway, to target is difficult. Proteomics is emerging as a powerful approach to identify the functionally important pathways driving these cancers, and how they can be targeted therapeutically. Areas covered: The authors provide a technical overview of mass spectrometry based approaches for proteomic profiling, and review the current and emerging strategies available for the identification of dysregulated networks, pathways, and drug targets in cancer cells, with a key focus on the ability to profile cancer kinomes. The potential applications of mass spectrometry in the clinic are also highlighted. Expert opinion: The addition of proteomic information to genomic platforms - 'proteogenomics' - is providing unparalleled insight in cancer cell biology. Application of improved mass spectrometry technology and methodology, in particular the ability to analyse post-translational modifications (the PTMome), is providing a more complete picture of the dysregulated networks in cancer, and uncovering novel therapeutic targets. While the application of proteomics to discovery research will continue to rise, improved workflow standardisation and reproducibility is required before mass spectrometry can enter routine clinical use.
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Affiliation(s)
- Heather C Murray
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
| | - Matthew D Dun
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
| | - Nicole M Verrills
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
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20
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Sauer S, Luge T. Nutriproteomics: Facts, concepts, and perspectives. Proteomics 2015; 15:997-1013. [DOI: 10.1002/pmic.201400383] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/03/2014] [Accepted: 11/27/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Sascha Sauer
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Toni Luge
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
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