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Higgins L, Gerdes H, Cutillas PR. Principles of phosphoproteomics and applications in cancer research. Biochem J 2023; 480:403-420. [PMID: 36961757 PMCID: PMC10212522 DOI: 10.1042/bcj20220220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation capabilities and sensitivity, in biochemical methods for sample preparation and in computational pipelines are enabling an increasingly deep analysis of the phosphoproteome, where previous bottlenecks in data acquisition, processing and interpretation are being relieved. These powerful hardware and algorithmic innovations are not only providing exciting new mechanistic insights into tumour biology, from where new drug targets may be derived, but are also leading to the discovery of phosphoproteins as mediators of drug sensitivity and resistance and as classifiers of disease subtypes. These studies are, therefore, uncovering phosphoproteins as a new generation of disruptive biomarkers to improve personalised anti-cancer therapies.
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Affiliation(s)
- Luke Higgins
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Henry Gerdes
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Pedro R. Cutillas
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
- Alan Turing Institute, The British Library, London, U.K
- Digital Environment Research Institute, Queen Mary University of London, London, U.K
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2
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Hayat A, Carter EP, King HW, Ors A, Doe A, Teijeiro SA, Charrot S, Godinho S, Cutillas P, Mohammed H, Grose RP, Ficz G. Low HER2 expression in normal breast epithelium enables dedifferentiation and malignant transformation via chromatin opening. Dis Model Mech 2023; 16:dmm049894. [PMID: 36661191 PMCID: PMC9922733 DOI: 10.1242/dmm.049894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
Overexpression of the HER2 protein in breast cancer patients is a predictor of poor prognosis and resistance to therapies. We used an inducible breast cancer transformation system that allows investigation of early molecular changes. HER2 overexpression to similar levels as those observed in a subtype of HER2-positive breast cancer patients induced transformation of MCF10A cells and resulted in gross morphological changes, increased anchorage-independent growth of cells, and altered the transcriptional programme of genes associated with oncogenic transformation. Global phosphoproteomic analysis during HER2 induction predominantly detected an increase in protein phosphorylation. Intriguingly, this correlated with chromatin opening, as measured by ATAC-seq on acini isolated from 3D cell culture. HER2 overexpression resulted in opening of many distal regulatory regions and promoted reprogramming-associated heterogeneity. We found that a subset of cells acquired a dedifferentiated breast stem-like phenotype, making them likely candidates for malignant transformation. Our data show that this population of cells, which counterintuitively enriches for relatively low HER2 protein abundance and increased chromatin accessibility, possesses transformational drive, resulting in increased anchorage-independent growth in vitro compared to cells not displaying a stem-like phenotype.
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Affiliation(s)
- Ateequllah Hayat
- Institute of Medical and Biomedical Education, St George’s, University of London, Cranmer Terrace, Tooting, London SW17 0RE, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Edward P. Carter
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Hamish W. King
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, VIC 3052, Australia
| | - Aysegul Ors
- Knight Cancer Institute, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Aaron Doe
- Knight Cancer Institute, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Saul A. Teijeiro
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Sarah Charrot
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Susana Godinho
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Pedro Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Hisham Mohammed
- Knight Cancer Institute, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
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3
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Prieto-Fernandez L, Villaronga MDLA, Hermida-Prado F, Hijazi M, Montoro-Jimenez I, Pevida M, Llames S, Rodrigo JP, Cutillas P, Calvo F, Garcia-Pedrero JM, Alvarez-Teijeiro S. Driving role of head and neck cancer cell secretome on the invasion of stromal fibroblasts: Mechanistic insights by phosphoproteomics. Biomed Pharmacother 2023; 158:114176. [PMID: 36916400 DOI: 10.1016/j.biopha.2022.114176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) are major players in tumor-stroma communication, and participate in several cancer hallmarks to drive tumor progression and metastatic dissemination. This study investigates the driving effects of tumor-secreted factors on CAF biology, with the ultimate goal of identifying effective therapeutic targets/strategies for head and neck squamous cell carcinomas (HNSCC). METHODS Functionally, conditioned media (CM) from different HNSCC-derived cell lines and normal keratinocytes (Kc) were tested on the growth and invasion of populations of primary CAFs and normal fibroblasts (NFs) using 3D invasion assays in collagen matrices. The changes in MMPs expression were evaluated by RT-qPCR and kinase enrichment was analyzed using mass spectrometry phosphoproteomics. RESULTS Our results consistently demonstrate that HNSCC-secreted factors (but not Kc CM) specifically and robustly promoted pro-invasive properties in both CAFs and NFs, thereby reflecting the plasticity of fibroblast subtypes. Concomitantly, HNSCC-secreted factors massively increased metalloproteinases levels in CAFs and NFs. By contrast, HNSCC CM and Kc CM exhibited comparable growth-promoting effects on stromal fibroblasts. Mechanistically, phosphoproteomic analysis predominantly revealed phosphorylation changes in fibroblasts upon treatment with HNSCC CM, and various promising kinases were identified: MKK7, MKK4, ASK1, RAF1, BRAF, ARAF, COT, PDK1, RSK2 and AKT1. Interestingly, pharmacologic inhibition of RAF1/BRAF using sorafenib emerged as the most effective drug to block tumor-promoted fibroblast invasion without affecting fibroblast viability CONCLUSIONS: Our findings demonstrate that HNSCC-secreted factors specifically fine tune the invasive potential of stromal fibroblasts, thereby generating tumor-driven pro-invasive niches, which in turn to ultimately facilitate cancer cell dissemination. Furthermore, the RAF/BRAF inhibitor sorafenib was identified as a promising candidate to effectively target the onset of pro-invasive clusters of stromal fibroblasts in the HNSCC microenvironment.
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Affiliation(s)
- Llara Prieto-Fernandez
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria de Los Angeles Villaronga
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Hermida-Prado
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Maruan Hijazi
- Cell Signalling & Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Irene Montoro-Jimenez
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Pevida
- Tissue engineering unit, Centro Comunitario Sangre y Tejidos de Asturias (CCST), Oviedo, Spain; Instituto Universitario Fernández-Vega, Fundación de Investigación Oftalmológica, University of Oviedo, Oviedo, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Sara Llames
- Tissue engineering unit, Centro Comunitario Sangre y Tejidos de Asturias (CCST), Oviedo, Spain; Instituto Universitario Fernández-Vega, Fundación de Investigación Oftalmológica, University of Oviedo, Oviedo, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Juan Pablo Rodrigo
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Cutillas
- Cell Signalling & Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Fernando Calvo
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom; Instituto de Biomedicina y Biotecnología de Cantabria (Consejo Superior de Investigaciones Científicas, Universidad de Cantabria), Santander, Spain
| | - Juana Maria Garcia-Pedrero
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Saul Alvarez-Teijeiro
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
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4
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Newport E, Pedrosa AR, Lees D, Dukinfield M, Carter E, Gomez-Escudero J, Casado P, Rajeeve V, Reynolds LE, R Cutillas P, Duffy SW, De Luxán Delgado B, Hodivala-Dilke K. Elucidating the role of the kinase activity of endothelial cell focal adhesion kinase in angiocrine signalling and tumour growth. J Pathol 2022; 256:235-247. [PMID: 34743335 DOI: 10.1002/path.5833] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/21/2021] [Accepted: 11/03/2021] [Indexed: 11/08/2022]
Abstract
A common limitation of cancer treatments is chemotherapy resistance. We have previously identified that endothelial cell (EC)-specific deletion of focal adhesion kinase (FAK) sensitises tumour cells to DNA-damaging therapies, reducing tumour growth in mice. The present study addressed the kinase activity dependency of EC FAK sensitisation to the DNA-damaging chemotherapeutic drug, doxorubicin. FAK is recognised as a therapeutic target in tumour cells, leading to the development of a range of inhibitors, the majority being ATP competitive kinase inhibitors. We demonstrate that inactivation of EC FAK kinase domain (kinase dead; EC FAK-KD) in established subcutaneous B16F0 tumours improves melanoma cell sensitisation to doxorubicin. Doxorubicin treatment in EC FAK-KD mice reduced the percentage change in exponential B16F0 tumour growth further than in wild-type mice. There was no difference in tumour blood vessel numbers, vessel perfusion or doxorubicin delivery between genotypes, suggesting a possible angiocrine effect on the regulation of tumour growth. Doxorubicin reduced perivascular malignant cell proliferation, while enhancing perivascular tumour cell apoptosis and DNA damage in tumours grown in EC FAK-KD mice 48 h after doxorubicin injection. Human pulmonary microvascular ECs treated with the pharmacological FAK kinase inhibitors defactinib, PF-562,271 or PF-573,228 in combination with doxorubicin also reduced cytokine expression levels. Together, these data suggest that targeting EC FAK kinase activity may alter angiocrine signals that correlate with improved acute tumour cell chemosensitisation. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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MESH Headings
- Angiogenesis Inhibitors/pharmacology
- Animals
- Antibiotics, Antineoplastic/pharmacology
- Apoptosis
- Cell Line, Tumor
- Cell Proliferation
- Cytokines/metabolism
- Doxorubicin/pharmacology
- Drug Resistance, Neoplasm
- Endothelial Cells/enzymology
- Female
- Focal Adhesion Kinase 1/antagonists & inhibitors
- Focal Adhesion Kinase 1/genetics
- Focal Adhesion Kinase 1/metabolism
- Humans
- Male
- Melanoma, Experimental/drug therapy
- Melanoma, Experimental/enzymology
- Melanoma, Experimental/genetics
- Melanoma, Experimental/pathology
- Mice, Inbred C57BL
- Mice, Knockout
- Neovascularization, Physiologic
- Protein Kinase Inhibitors/pharmacology
- Signal Transduction
- Skin Neoplasms/drug therapy
- Skin Neoplasms/enzymology
- Skin Neoplasms/genetics
- Skin Neoplasms/pathology
- Tumor Burden
- Mice
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Affiliation(s)
- Emma Newport
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Ana Rita Pedrosa
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Delphine Lees
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Matthew Dukinfield
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Edward Carter
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Jesus Gomez-Escudero
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Pedro Casado
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Vinothini Rajeeve
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Louise E Reynolds
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Pedro R Cutillas
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | | | - Beatriz De Luxán Delgado
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Kairbaan Hodivala-Dilke
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
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5
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Lan Y, Zeng X, Xiao J, Hu L, Tan L, Liang M, Wang X, Lu S, Long F, Peng T. New advances in quantitative proteomics research and current applications in asthma. Expert Rev Proteomics 2021; 18:1045-1057. [PMID: 34890515 DOI: 10.1080/14789450.2021.2017777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Asthma is the most common chronic respiratory disease and has been declared a global public health problem by the World Health Organization. Due to the high heterogeneity and complexity, asthma can be classified into different 'phenotypes' and it is still difficult to assess the phenotypes and stages of asthma by traditional methods. In recent years, mass spectrometry-based proteomics studies have made significant progress in sensitivity and accuracy of protein identification and quantitation, and are able to obtain differences in protein expression across samples, which provides new insights into the mechanisms and classification of asthma. AREAS COVERED In this article, we summarize research strategies in quantitative proteomics, including labeled, label-free and targeted quantification, and highlight the advantages and disadvantages of each. In addition, new applications of quantitative proteomics and the current status of research in asthma have also been discussed. In this study, online resources such as PubMed and Google Scholar were used for literature retrieval. EXPERT OPINION The application of quantitative proteomics in asthma has an important role in identifying asthma subphenotypes, revealing potential pathogenesis and therapeutic targets. But the proteomic studies on asthma are not sufficient, as most of them are in the phase of biomarker discovery.
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Affiliation(s)
- Yanting Lan
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xiaoyin Zeng
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jing Xiao
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Longbo Hu
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Long Tan
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Mengdi Liang
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xufei Wang
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Shaohua Lu
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Fei Long
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China.,Guangdong South China Vaccine Co. Ltd, Guangzhou, China
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6
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Casado P, Hijazi M, Gerdes H, Cutillas PR. Implementation of Clinical Phosphoproteomics and Proteomics for Personalized Medicine. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:87-106. [PMID: 34905168 DOI: 10.1007/978-1-0716-1936-0_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The identification of biomarkers for companion diagnostics is revolutionizing the development of treatments tailored to individual patients in different disease areas including cancer. Precision medicine is most frequently based on the detection of genomic markers that correlate with the efficacy of selected targeted therapies. However, since nongenetic mechanisms also contribute to disease biology, there is a considerable interest of using proteomic techniques as additional source of biomarkers to personalize therapies. In this chapter, we describe label-free mass spectrometry methods for proteomic and phosphoproteomic analysis compatible with routine analysis of clinical samples. We also outline bioinformatic pipelines based on statistical learning that use these proteomics datasets as input to quantify kinase activities and predict drug responses in cancer cells.
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Affiliation(s)
- Pedro Casado
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Maruan Hijazi
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Henry Gerdes
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Pedro R Cutillas
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK.
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7
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Hashimoto A, Sarker D, Reebye V, Jarvis S, Sodergren MH, Kossenkov A, Sanseviero E, Raulf N, Vasara J, Andrikakou P, Meyer T, Huang KW, Plummer R, Chee CE, Spalding D, Pai M, Khan S, Pinato DJ, Sharma R, Basu B, Palmer D, Ma YT, Evans J, Habib R, Martirosyan A, Elasri N, Reynaud A, Rossi JJ, Cobbold M, Habib NA, Gabrilovich DI. Upregulation of C/EBPα Inhibits Suppressive Activity of Myeloid Cells and Potentiates Antitumor Response in Mice and Patients with Cancer. Clin Cancer Res 2021; 27:5961-5978. [PMID: 34407972 PMCID: PMC8756351 DOI: 10.1158/1078-0432.ccr-21-0986] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/21/2021] [Accepted: 08/16/2021] [Indexed: 01/09/2023]
Abstract
PURPOSE To evaluate the mechanisms of how therapeutic upregulation of the transcription factor, CCAAT/enhancer-binding protein alpha (C/EBPα), prevents tumor progression in patients with advanced hepatocellular carcinoma (HCC) and in different mouse tumor models. EXPERIMENTAL DESIGN We conducted a phase I trial in 36 patients with HCC (NCT02716012) who received sorafenib as part of their standard care, and were given therapeutic C/EBPα small activating RNA (saRNA; MTL-CEBPA) as either neoadjuvant or adjuvant treatment. In the preclinical setting, the effects of MTL-CEBPA were assessed in several mouse models, including BNL-1ME liver cancer, Lewis lung carcinoma (LLC), and colon adenocarcinoma (MC38). RESULTS MTL-CEBPA treatment caused radiologic regression of tumors in 26.7% of HCC patients with an underlying viral etiology with 3 complete responders. MTL-CEBPA treatment in those patients caused a marked decrease in peripheral blood monocytic myeloid-derived suppressor cell (M-MDSC) numbers and an overall reduction in the numbers of protumoral M2 tumor-associated macrophages (TAM). Gene and protein analysis of patient leukocytes following treatment showed CEBPA activation affected regulation of factors involved in immune-suppressive activity. To corroborate this observation, treatment of all the mouse tumor models with MTL-CEBPA led to a reversal in the suppressive activity of M-MDSCs and TAMs, but not polymorphonuclear MDSCs (PMN-MDSC). The antitumor effects of MTL-CEBPA in these tumor models showed dependency on T cells. This was accentuated when MTL-CEBPA was combined with checkpoint inhibitors or with PMN-MDSC-targeted immunotherapy. CONCLUSIONS This report demonstrates that therapeutic upregulation of the transcription factor C/EBPα causes inactivation of immune-suppressive myeloid cells with potent antitumor responses across different tumor models and in cancer patients. MTL-CEBPA is currently being investigated in combination with pembrolizumab in a phase I/Ib multicenter clinical study (NCT04105335).
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Affiliation(s)
- Ayumi Hashimoto
- Wistar Institute, Philadelphia, Pennsylvania
- AstraZeneca, Gaithersburg, Maryland
| | | | - Vikash Reebye
- Imperial College London, London, UK.
- MiNA Therapeutics Ltd, London, UK
| | | | | | | | | | | | | | | | - Tim Meyer
- University College London Cancer Institute, London, UK
| | | | - Ruth Plummer
- Northern Centre for Cancer Care and Newcastle University, Newcastle upon Tyne, UK
| | - Cheng E Chee
- National University Cancer Institute Singapore, Singapore
| | | | | | | | | | | | | | - Daniel Palmer
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool and Clatterbridge Cancer Centre, Liverpool, UK
| | - Yuk-Ting Ma
- University of Birmingham and University Hospitals Birmingham NHS Trust, Birmingham, UK
| | - Jeff Evans
- University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow, UK
| | | | | | | | | | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California
| | | | - Nagy A Habib
- Imperial College London, London, UK.
- MiNA Therapeutics Ltd, London, UK
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8
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Zaghdoudi S, Decaup E, Belhabib I, Samain R, Cassant‐Sourdy S, Rochotte J, Brunel A, Schlaepfer D, Cros J, Neuzillet C, Strehaiano M, Alard A, Tomasini R, Rajeeve V, Perraud A, Mathonnet M, Pearce OMT, Martineau Y, Pyronnet S, Bousquet C, Jean C. FAK activity in cancer-associated fibroblasts is a prognostic marker and a druggable key metastatic player in pancreatic cancer. EMBO Mol Med 2020; 12:e12010. [PMID: 33025708 PMCID: PMC7645544 DOI: 10.15252/emmm.202012010] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 12/22/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs) are considered the most abundant type of stromal cells in pancreatic ductal adenocarcinoma (PDAC), playing a critical role in tumour progression and chemoresistance; however, a druggable target on CAFs has not yet been identified. Here we report that focal adhesion kinase (FAK) activity (evaluated based on 397 tyrosine phosphorylation level) in CAFs is highly increased compared to its activity in fibroblasts from healthy pancreas. Fibroblastic FAK activity is an independent prognostic marker for disease-free and overall survival of PDAC patients (cohort of 120 PDAC samples). Genetic inactivation of FAK within fibroblasts (FAK kinase-dead, KD) reduces fibrosis and immunosuppressive cell number within primary tumours and dramatically decreases tumour spread. FAK pharmacologic or genetic inactivation reduces fibroblast migration/invasion, decreases extracellular matrix (ECM) expression and deposition by CAFs, modifies ECM track generation and negatively impacts M2 macrophage polarization and migration. Thus, FAK activity within CAFs appears as an independent PDAC prognostic marker and a druggable driver of tumour cell invasion.
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Affiliation(s)
- Sonia Zaghdoudi
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Emilie Decaup
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Ismahane Belhabib
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Rémi Samain
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Stéphanie Cassant‐Sourdy
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Julia Rochotte
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Alexia Brunel
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - David Schlaepfer
- Department of Reproductive Medicine Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Jérome Cros
- Department of PathologyBeaujon HospitalINSERM U1149ClichyFrance
| | - Cindy Neuzillet
- Medical Oncology DepartmentCurie InstituteVersailles Saint‐Quentin UniversitySaint‐CloudFrance
| | - Manon Strehaiano
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Amandine Alard
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | | | - Vinothini Rajeeve
- Centre for Genomics and Computational BiologyBarts Cancer InstituteQueen Mary University of LondonLondonUK
| | - Aurélie Perraud
- EA 3842 Laboratory, Medicine and Pharmacy FacultiesLimoges UniversityLimogesFrance
| | - Muriel Mathonnet
- EA 3842 Laboratory, Medicine and Pharmacy FacultiesLimoges UniversityLimogesFrance
| | - Oliver MT Pearce
- Centre for Tumour MicroenvironmentBarts Cancer InstituteLondonUK
| | - Yvan Martineau
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Stéphane Pyronnet
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Corinne Bousquet
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
| | - Christine Jean
- Cancer Research Center of Toulouse (CRCT)team 6 “Protein synthesis & secretion in carcinogenesis”Equipe labellisée Ligue Contre Le CancerLabex TOUCANINSERM UMR 1037‐ University Toulouse III Paul SabatierToulouseFrance
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9
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Xu R, Jones W, Wilcz-Villega E, Costa AS, Rajeeve V, Bentham RB, Bryson K, Nagano A, Yaman B, Olendo Barasa S, Wang Y, Chelala C, Cutillas P, Szabadkai G, Frezza C, Bianchi K. The breast cancer oncogene IKKε coordinates mitochondrial function and serine metabolism. EMBO Rep 2020; 21:e48260. [PMID: 32783398 PMCID: PMC7116048 DOI: 10.15252/embr.201948260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/29/2020] [Accepted: 07/09/2020] [Indexed: 12/25/2022] Open
Abstract
IκB kinase ε (IKKε) is a key molecule at the crossroads of inflammation and cancer. Known to regulate cytokine secretion via NFκB and IRF3, the kinase is also a breast cancer oncogene, overexpressed in a variety of tumours. However, to what extent IKKε remodels cellular metabolism is currently unknown. Here, we used metabolic tracer analysis to show that IKKε orchestrates a complex metabolic reprogramming that affects mitochondrial metabolism and consequently serine biosynthesis independently of its canonical signalling role. We found that IKKε upregulates the serine biosynthesis pathway (SBP) indirectly, by limiting glucose‐derived pyruvate utilisation in the TCA cycle, inhibiting oxidative phosphorylation. Inhibition of mitochondrial function induces activating transcription factor 4 (ATF4), which in turn drives upregulation of the expression of SBP genes. Importantly, pharmacological reversal of the IKKε‐induced metabolic phenotype reduces proliferation of breast cancer cells. Finally, we show that in a highly proliferative set of ER negative, basal breast tumours, IKKε and PSAT1 are both overexpressed, corroborating the link between IKKε and the SBP in the clinical context.
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Affiliation(s)
- Ruoyan Xu
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - William Jones
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Ewa Wilcz-Villega
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Ana Sh Costa
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Vinothini Rajeeve
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Robert B Bentham
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, UK.,Francis Crick Institute, London, UK
| | - Kevin Bryson
- Department of Computer Sciences, University College London, London, UK
| | - Ai Nagano
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Busra Yaman
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Sheila Olendo Barasa
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Yewei Wang
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - Pedro Cutillas
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gyorgy Szabadkai
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, UK.,Francis Crick Institute, London, UK.,Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
| | - Katiuscia Bianchi
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
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10
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Hijazi M, Smith R, Rajeeve V, Bessant C, Cutillas PR. Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring. Nat Biotechnol 2020; 38:493-502. [PMID: 31959955 DOI: 10.1038/s41587-019-0391-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
Abstract
Understanding how oncogenic mutations rewire regulatory-protein networks is important for rationalizing the mechanisms of oncogenesis and for individualizing anticancer treatments. We report a chemical phosphoproteomics method to elucidate the topology of kinase-signaling networks in mammalian cells. We identified >6,000 protein phosphorylation sites that can be used to infer >1,500 kinase-kinase interactions and devised algorithms that can reconstruct kinase network topologies from these phosphoproteomics data. Application of our methods to primary acute myeloid leukemia and breast cancer tumors quantified the relationship between kinase expression and activity, and enabled the identification of hitherto unknown kinase network topologies associated with drug-resistant phenotypes or specific genetic mutations. Using orthogonal methods we validated that PIK3CA wild-type cells adopt MAPK-dependent circuitries in breast cancer cells and that the kinase TTK is important in acute myeloid leukemia. Our phosphoproteomic signatures of network circuitry can identify kinase topologies associated with both phenotypes and genotypes of cancer cells.
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Affiliation(s)
- Maruan Hijazi
- Signalling and Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ryan Smith
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Vinothini Rajeeve
- Signalling and Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Conrad Bessant
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- The Alan Turing Institute, British Library, London, UK
| | - Pedro R Cutillas
- Signalling and Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, UK.
- The Alan Turing Institute, British Library, London, UK.
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11
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Carvajal S, Perramón M, Casals G, Oró D, Ribera J, Morales-Ruiz M, Casals E, Casado P, Melgar-Lesmes P, Fernández-Varo G, Cutillas P, Puntes V, Jiménez W. Cerium Oxide Nanoparticles Protect against Oxidant Injury and Interfere with Oxidative Mediated Kinase Signaling in Human-Derived Hepatocytes. Int J Mol Sci 2019; 20:ijms20235959. [PMID: 31783479 PMCID: PMC6928882 DOI: 10.3390/ijms20235959] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 12/15/2022] Open
Abstract
Cerium oxide nanoparticles (CeO2NPs) possess powerful antioxidant properties, thus emerging as a potential therapeutic tool in non-alcoholic fatty liver disease (NAFLD) progression, which is characterized by a high presence of reactive oxygen species (ROS). The aim of this study was to elucidate whether CeO2NPs can prevent or attenuate oxidant injury in the hepatic human cell line HepG2 and to investigate the mechanisms involved in this phenomenon. The effect of CeO2NPs on cell viability and ROS scavenging was determined, the differential expression of pro-inflammatory and oxidative stress-related genes was analyzed, and a proteomic analysis was performed to assess the impact of CeO2NPs on cell phosphorylation in human hepatic cells under oxidative stress conditions. CeO2NPs did not modify HepG2 cell viability in basal conditions but reduced H2O2- and lipopolysaccharide (LPS)-induced cell death and prevented H2O2-induced overexpression of MPO, PTGS1 and iNOS. Phosphoproteomic analysis showed that CeO2NPs reverted the H2O2-mediated increase in the phosphorylation of peptides related to cellular proliferation, stress response, and gene transcription regulation, and interfered with H2O2 effects on mTOR, MAPK/ERK, CK2A1 and PKACA signaling pathways. In conclusion, CeO2NPs protect HepG2 cells from cell-induced oxidative damage, reducing ROS generation and inflammatory gene expression as well as regulation of kinase-driven cell survival pathways.
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Affiliation(s)
- Silvia Carvajal
- Biochemistry and Molecular Genetics Service, Hospital Clínic Universitari, IDIBAPS, CIBERehd, 08036 Barcelona, Spain; (S.C.); (M.P.); (D.O.); (J.R.); (M.M.-R.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Meritxell Perramón
- Biochemistry and Molecular Genetics Service, Hospital Clínic Universitari, IDIBAPS, CIBERehd, 08036 Barcelona, Spain; (S.C.); (M.P.); (D.O.); (J.R.); (M.M.-R.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Gregori Casals
- Biochemistry and Molecular Genetics Service, Hospital Clínic Universitari, IDIBAPS, CIBERehd, 08036 Barcelona, Spain; (S.C.); (M.P.); (D.O.); (J.R.); (M.M.-R.); (P.M.-L.); (G.F.-V.); (W.J.)
- Correspondence: ; Tel.: +34-932275400-2667
| | - Denise Oró
- Biochemistry and Molecular Genetics Service, Hospital Clínic Universitari, IDIBAPS, CIBERehd, 08036 Barcelona, Spain; (S.C.); (M.P.); (D.O.); (J.R.); (M.M.-R.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Jordi Ribera
- Biochemistry and Molecular Genetics Service, Hospital Clínic Universitari, IDIBAPS, CIBERehd, 08036 Barcelona, Spain; (S.C.); (M.P.); (D.O.); (J.R.); (M.M.-R.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Manuel Morales-Ruiz
- Biochemistry and Molecular Genetics Service, Hospital Clínic Universitari, IDIBAPS, CIBERehd, 08036 Barcelona, Spain; (S.C.); (M.P.); (D.O.); (J.R.); (M.M.-R.); (P.M.-L.); (G.F.-V.); (W.J.)
- Department of Biomedicine, University of Barcelona, 08036 Barcelona, Spain
| | - Eudald Casals
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China;
| | - Pedro Casado
- Cell Signalling and Proteomics Group, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (P.C.); (P.C.)
| | - Pedro Melgar-Lesmes
- Biochemistry and Molecular Genetics Service, Hospital Clínic Universitari, IDIBAPS, CIBERehd, 08036 Barcelona, Spain; (S.C.); (M.P.); (D.O.); (J.R.); (M.M.-R.); (P.M.-L.); (G.F.-V.); (W.J.)
- Department of Biomedicine, University of Barcelona, 08036 Barcelona, Spain
| | - Guillermo Fernández-Varo
- Biochemistry and Molecular Genetics Service, Hospital Clínic Universitari, IDIBAPS, CIBERehd, 08036 Barcelona, Spain; (S.C.); (M.P.); (D.O.); (J.R.); (M.M.-R.); (P.M.-L.); (G.F.-V.); (W.J.)
- Department of Biomedicine, University of Barcelona, 08036 Barcelona, Spain
| | - Pedro Cutillas
- Cell Signalling and Proteomics Group, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (P.C.); (P.C.)
| | - Victor Puntes
- Institut Català de Recerca i Estudis Avançats, (ICREA), 08010 Barcelona, Spain;
- Vall d’Hebron Insitute of Research (VHIR), 08035 Barcelona, Spain
- Institut Català de Nanociència i Nanotecnologia (ICN2), 08193 Bellaterra, Spain
| | - Wladimiro Jiménez
- Biochemistry and Molecular Genetics Service, Hospital Clínic Universitari, IDIBAPS, CIBERehd, 08036 Barcelona, Spain; (S.C.); (M.P.); (D.O.); (J.R.); (M.M.-R.); (P.M.-L.); (G.F.-V.); (W.J.)
- Department of Biomedicine, University of Barcelona, 08036 Barcelona, Spain
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12
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Liver Activation of Hepatocellular Nuclear Factor-4α by Small Activating RNA Rescues Dyslipidemia and Improves Metabolic Profile. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 19:361-370. [PMID: 31877412 PMCID: PMC6938799 DOI: 10.1016/j.omtn.2019.10.044] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/11/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) culminates in insulin resistance and metabolic syndrome. Because there are no approved pharmacological treatment agents for non-alcoholic steatohepatitis (NASH) and NAFLD, different signaling pathways are under investigation for drug development with the focus on metabolic pathways. Hepatocyte nuclear factor 4-alpha (HNF4A) is at the center of a complex transcriptional network where its disruption is directly linked to glucose and lipid metabolism. Resetting HNF4A expression in NAFLD is therefore crucial for re-establishing normal liver function. Here, small activating RNA (saRNA) specific for upregulating HNF4A was injected into rats fed a high-fat diet for 16 weeks. Intravenous delivery was carried out using 5-(G5)-triethanolamine-core polyamidoamine (PAMAM) dendrimers. We observed a significant reduction in liver triglyceride, increased high-density lipoprotein/low-density lipoprotein (HDL/LDL) ratio, and decreased white adipose tissue/body weight ratio, all parameters to suggest that HNF4A-saRNA treatment induced a favorable metabolic profile. Proteomic analysis showed significant regulation of genes involved in sphingolipid metabolism, fatty acid β-oxidation, ketogenesis, detoxification of reactive oxygen species, and lipid transport. We demonstrate that HNF4A activation by oligonucleotide therapy may represent a novel single agent for the treatment of NAFLD and insulin resistance.
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13
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Martín-Guerrero SM, Casado P, Muñoz-Gámez JA, Carrasco MC, Navascués J, Cuadros MA, López-Giménez JF, Cutillas PR, Martín-Oliva D. Poly(ADP-Ribose) Polymerase-1 inhibition potentiates cell death and phosphorylation of DNA damage response proteins in oxidative stressed retinal cells. Exp Eye Res 2019; 188:107790. [DOI: 10.1016/j.exer.2019.107790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/24/2019] [Accepted: 09/02/2019] [Indexed: 10/26/2022]
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14
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Host-directed kinase inhibitors act as novel therapies against intracellular Staphylococcus aureus. Sci Rep 2019; 9:4876. [PMID: 30890742 PMCID: PMC6425000 DOI: 10.1038/s41598-019-41260-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/05/2019] [Indexed: 01/09/2023] Open
Abstract
Host-directed therapeutics are a promising anti-infective strategy against intracellular bacterial pathogens. Repurposing host-targeted drugs approved by the FDA in the US, the MHRA in the UK and/or regulatory equivalents in other countries, is particularly interesting because these drugs are commercially available, safe doses are documented and they have been already approved for other clinical purposes. In this study, we aimed to identify novel therapies against intracellular Staphylococcus aureus, an opportunistic pathogen that is able to exploit host molecular and metabolic pathways to support its own intracellular survival. We screened 133 host-targeting drugs and found three host-directed tyrosine kinase inhibitors (Ibrutinib, Dasatinib and Crizotinib) that substantially impaired intracellular bacterial survival. We found that Ibrutinib significantly increased host cell viability after S. aureus infection via inhibition of cell invasion and intracellular bacterial proliferation. Using phosphoproteomics data, we propose a putative mechanism of action of Ibrutinib involving several host factors, including EPHA2, C-JUN and NWASP. We confirmed the importance of EPHA2 for staphylococcal infection in an EPHA2-knock-out cell line. Our study serves as an important example of feasibility for identifying host-directed therapeutics as candidates for repurposing.
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15
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Álvarez-Teijeiro S, García-Inclán C, Villaronga MÁ, Casado P, Hermida-Prado F, Granda-Díaz R, Rodrigo JP, Calvo F, Del-Río-Ibisate N, Gandarillas A, Morís F, Hermsen M, Cutillas P, García-Pedrero JM. Factors Secreted by Cancer-Associated Fibroblasts that Sustain Cancer Stem Properties in Head and Neck Squamous Carcinoma Cells as Potential Therapeutic Targets. Cancers (Basel) 2018; 10:cancers10090334. [PMID: 30227608 PMCID: PMC6162704 DOI: 10.3390/cancers10090334] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/09/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022] Open
Abstract
This study investigates for the first time the crosstalk between stromal fibroblasts and cancer stem cell (CSC) biology in head and neck squamous cell carcinomas (HNSCC), with the ultimate goal of identifying effective therapeutic targets. The effects of conditioned media from cancer-associated fibroblasts (CAFs) and normal fibroblasts (NFs) on the CSC phenotype were assessed by combining functional and expression analyses in HNSCC-derived cell lines. Further characterization of CAFs and NFs secretomes by mass spectrometry was followed by pharmacologic target inhibition. We demonstrate that factors secreted by CAFs but not NFs, in the absence of serum/supplements, robustly increased anchorage-independent growth, tumorsphere formation, and CSC-marker expression. Modulators of epidermal growth factor receptor (EGFR), insulin-like growth factor receptor (IGFR), and platelet-derived growth factor receptor (PDGFR) activity were identified as paracrine cytokines/factors differentially secreted between CAFs and NFs, in a mass spectrometry analysis. Furthermore, pharmacologic inhibition of EGFR, IGFR, and PDGFR significantly reduced CAF-induced tumorsphere formation and anchorage-independent growth suggesting a role of these receptor tyrosine kinases in sustaining the CSC phenotype. These findings provide novel insights into tumor stroma⁻CSC communication, and potential therapeutic targets to effectively block the CAF-enhanced CSC niche signaling circuit.
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Affiliation(s)
- Saúl Álvarez-Teijeiro
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias; Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011 Oviedo, Spain.
- CIBERONC, 28029 Madrid, Spain.
| | - Cristina García-Inclán
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias; Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011 Oviedo, Spain.
| | - M Ángeles Villaronga
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias; Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011 Oviedo, Spain.
- CIBERONC, 28029 Madrid, Spain.
| | - Pedro Casado
- Cell Signalling & Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.
| | - Francisco Hermida-Prado
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias; Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011 Oviedo, Spain.
| | - Rocío Granda-Díaz
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias; Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011 Oviedo, Spain.
| | - Juan P Rodrigo
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias; Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011 Oviedo, Spain.
- CIBERONC, 28029 Madrid, Spain.
| | - Fernando Calvo
- Tumour Microenvironment Team, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
| | - Nagore Del-Río-Ibisate
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias; Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011 Oviedo, Spain.
| | - Alberto Gandarillas
- Cell Cycle, Stem Cell Fate and Cancer Lab Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain.
| | - Francisco Morís
- EntreChem SL, Vivero Ciencias de la Salud, 33011 Oviedo, Spain.
| | - Mario Hermsen
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias; Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011 Oviedo, Spain.
- CIBERONC, 28029 Madrid, Spain.
| | - Pedro Cutillas
- Cell Signalling & Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.
| | - Juana M García-Pedrero
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias; Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011 Oviedo, Spain.
- CIBERONC, 28029 Madrid, Spain.
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16
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Abstract
Cellular signaling, predominantly mediated by phosphorylation through protein kinases, is found to be deregulated in most cancers. Accordingly, protein kinases have been subject to intense investigations in cancer research, to understand their role in oncogenesis and to discover new therapeutic targets. Despite great advances, an understanding of kinase dysfunction in cancer is far from complete.A powerful tool to investigate phosphorylation is mass-spectrometry (MS)-based phosphoproteomics, which enables the identification of thousands of phosphorylated peptides in a single experiment. Since every phosphorylation event results from the activity of a protein kinase, high-coverage phosphoproteomics data should indirectly contain comprehensive information about the activity of protein kinases.In this chapter, we discuss the use of computational methods to predict kinase activity scores from MS-based phosphoproteomics data. We start with a short explanation of the fundamental features of the phosphoproteomics data acquisition process from the perspective of the computational analysis. Next, we briefly review the existing databases with experimentally verified kinase-substrate relationships and present a set of bioinformatic tools to discover novel kinase targets. We then introduce different methods to infer kinase activities from phosphoproteomics data and these kinase-substrate relationships. We illustrate their application with a detailed protocol of one of the methods, KSEA (Kinase Substrate Enrichment Analysis). This method is implemented in Python within the framework of the open-source Kinase Activity Toolbox (kinact), which is freely available at http://github.com/saezlab/kinact/ .
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Affiliation(s)
- Jakob Wirbel
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, MTZ Pauwelsstrasse 19, D-52074, Aachen, Germany
- Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, 69120, Heidelberg, Germany
| | - Pedro Cutillas
- Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Julio Saez-Rodriguez
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, MTZ Pauwelsstrasse 19, D-52074, Aachen, Germany.
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
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17
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Schmitz M, Ziv T, Admon A, Baekelandt S, Mandiki SN, L'Hoir M, Kestemont P. Salinity stress, enhancing basal and induced immune responses in striped catfish Pangasianodon hypophthalmus (Sauvage). J Proteomics 2017; 167:12-24. [DOI: 10.1016/j.jprot.2017.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 12/12/2022]
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18
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Dermit M, Dokal A, Cutillas PR. Approaches to identify kinase dependencies in cancer signalling networks. FEBS Lett 2017; 591:2577-2592. [DOI: 10.1002/1873-3468.12748] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/27/2017] [Accepted: 07/03/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Maria Dermit
- Cell Signalling & Proteomics Group; Barts Cancer Institute (CRUK Centre); Queen Mary University of London; UK
| | - Arran Dokal
- Cell Signalling & Proteomics Group; Barts Cancer Institute (CRUK Centre); Queen Mary University of London; UK
| | - Pedro R. Cutillas
- Cell Signalling & Proteomics Group; Barts Cancer Institute (CRUK Centre); Queen Mary University of London; UK
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19
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Wilkes EH, Casado P, Rajeeve V, Cutillas PR. Kinase activity ranking using phosphoproteomics data (KARP) quantifies the contribution of protein kinases to the regulation of cell viability. Mol Cell Proteomics 2017; 16:1694-1704. [PMID: 28674151 DOI: 10.1074/mcp.o116.064360] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 02/05/2017] [Indexed: 12/17/2022] Open
Abstract
Cell survival is regulated by a signaling network driven by the activity of protein kinases; however, determining the contribution that each kinase in the network makes to such regulation remains challenging. Here, we report a computational approach that uses mass spectrometry-based phosphoproteomics data to rank protein kinases based on their contribution to cell regulation. We found that the scores returned by this algorithm, which we have termed kinase activity ranking using phosphoproteomics data (KARP), were a quantitative measure of the contribution that individual kinases make to the signaling output. Application of KARP to the analysis of eight hematological cell lines revealed that cyclin-dependent kinase (CDK) 1/2, casein kinase (CK) 2, extracellular signal-related kinase (ERK), and p21-activated kinase (PAK) were the most frequently highly ranked kinases in these cell models. The patterns of kinase activation were cell-line specific yet showed a significant association with cell viability as a function of kinase inhibitor treatment. Thus, our study exemplifies KARP as an untargeted approach to empirically and systematically identify regulatory kinases within signaling networks.
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Affiliation(s)
- Edmund H Wilkes
- From the ‡Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ
| | - Pedro Casado
- From the ‡Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ
| | - Vinothini Rajeeve
- From the ‡Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ
| | - Pedro R Cutillas
- From the ‡Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ
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20
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Abstract
Phosphoproteomics is a powerful platform for the unbiased profiling of kinase-driven signaling pathways. Quantitation of phosphorylation can be performed by means of either labeling or label-free mass spectrometry (MS) methods. Because of their simplicity and universality, label-free methodology is gaining acceptance and popularity in molecular biology research. Analytical workflows for label-free quantification of phosphorylation, however, need to overcome several hurdles for the technique to be accurate and precise. These include the use of biochemical extraction procedures that efficiently and reproducibly isolate phosphopeptides from complex peptide matrices and an analytical strategy that can cope with missing MS/MS phosphopeptide spectra in a subset of the samples being compared. Testing the accuracy of the developed workflows is an essential prerequisite in the analysis of small molecules by MS, and this is achieved by constructing calibration curves to demonstrate linearity of quantification for each analyte. This level of analytical rigor is rarely shown in large-scale quantification of proteins using either label-based or label-free techniques. In this chapter we show an approach to test linearity of quantification of each phosphopeptide quantified by liquid chromatography (LC)-MS without the need to synthesize standards or label proteins. We further describe the appropriate sample handling techniques required for the reproducible recovery of phosphopeptides and explore the essential algorithmic features that enable the handling of missing MS/MS spectra and thus make label-free data suitable for such analyses. The combined technology described in this chapter expands the applicability of phosphoproteomics to questions not previously tractable with other methodologies.
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21
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Afzal TA, Luong LA, Chen D, Zhang C, Yang F, Chen Q, An W, Wilkes E, Yashiro K, Cutillas PR, Zhang L, Xiao Q. NCK Associated Protein 1 Modulated by miRNA-214 Determines Vascular Smooth Muscle Cell Migration, Proliferation, and Neointima Hyperplasia. J Am Heart Assoc 2016; 5:e004629. [PMID: 27927633 PMCID: PMC5210428 DOI: 10.1161/jaha.116.004629] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/28/2016] [Indexed: 11/16/2022]
Abstract
BACKGROUND MicroRNA miR-214 has been implicated in many biological cellular functions, but the impact of miR-214 and its target genes on vascular smooth muscle cell (VSMC) proliferation, migration, and neointima smooth muscle cell hyperplasia is unknown. METHODS AND RESULTS Expression of miR-214 was closely regulated by different pathogenic stimuli in VSMCs through a transcriptional mechanism and decreased in response to vascular injury. Overexpression of miR-214 in serum-starved VSMCs significantly decreased VSMC proliferation and migration, whereas knockdown of miR-214 dramatically increased VSMC proliferation and migration. Gene and protein biochemical assays, including proteomic analyses, showed that NCK associated protein 1 (NCKAP1)-a major component of the WAVE complex that regulates lamellipodia formation and cell motility-was negatively regulated by miR-214 in VSMCs. Luciferase assays showed that miR-214 substantially repressed wild-type but not the miR-214 binding site mutated version of NCKAP1 3' untranslated region luciferase activity in VSMCs. This result confirmed that NCKAP1 is the functional target of miR-214 in VSMCs. NCKAP1 knockdown in VSMCs recapitulates the inhibitory effects of miR-214 overexpression on actin polymerization, cell migration, and proliferation. Data from cotransfection experiments also revealed that inhibition of NCKAP1 is required for miR-214-mediated lamellipodia formation, cell motility, and growth. Importantly, locally enforced expression of miR-214 in the injured vessels significantly reduced NCKAP1 expression levels, inhibited VSMC proliferation, and prevented neointima smooth muscle cell hyperplasia after injury. CONCLUSIONS We uncovered an important role of miR-214 and its target gene NCKAP1 in modulating VSMC functions and neointima hyperplasia. Our findings suggest that miR-214 represents a potential therapeutic target for vascular diseases.
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Affiliation(s)
- Tayyab Adeel Afzal
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Le Anh Luong
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Dan Chen
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Cheng Zhang
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Feng Yang
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qishan Chen
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weiwei An
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Edmund Wilkes
- Centre for Haemato-Oncology, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Kenta Yashiro
- Translational Medicine & Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Pedro R Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Li Zhang
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qingzhong Xiao
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
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22
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Cutillas PR. Targeted In-Depth Quantification of Signaling Using Label-Free Mass Spectrometry. Methods Enzymol 2016; 585:245-268. [PMID: 28109432 DOI: 10.1016/bs.mie.2016.09.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein phosphorylation encodes information on the activity of kinase-driven signaling pathways that regulate cell biology. This chapter discusses an approach, named TIQUAS (targeted in-depth quantification of signaling), to quantify cell signaling comprehensively and without bias. The workflow-based on mass spectrometry (MS) and computational science-consists of targeting the analysis of phosphopeptides previously identified by shotgun liquid chromatography tandem MS (LC-MS/MS) across the samples that are being compared. TIQUAS therefore takes advantage of concepts derived from both targeted (data-independent) and data-dependent acquisition methods; phosphorylation sites are quantified in all experimental samples regardless of whether or not these phosphopeptides were identified by MS/MS in all runs. As a result, datasets are obtained containing quantitative information on several thousand phosphorylation sites in as many samples and replicates as required in the experimental design, and these rich datasets are devoid of a significant number of missing data points. This chapter discussed the biochemical, analytical, and computational procedures required to apply the approach and for obtaining a biological interpretation of the data in the context of our understanding of cell signaling regulation and kinase-substrate relationships.
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Affiliation(s)
- P R Cutillas
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom.
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23
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Sciacovelli M, Gonçalves E, Johnson TI, Zecchini VR, da Costa ASH, Gaude E, Drubbel AV, Theobald SJ, Abbo SR, Tran MGB, Rajeeve V, Cardaci S, Foster S, Yun H, Cutillas P, Warren A, Gnanapragasam V, Gottlieb E, Franze K, Huntly B, Maher ER, Maxwell PH, Saez-Rodriguez J, Frezza C. Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition. Nature 2016; 537:544-547. [PMID: 27580029 PMCID: PMC5136292 DOI: 10.1038/nature19353] [Citation(s) in RCA: 396] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/10/2016] [Indexed: 12/18/2022]
Abstract
Mutations of the tricarboxylic acid cycle enzyme fumarate hydratase cause hereditary leiomyomatosis and renal cell cancer. Fumarate hydratase-deficient renal cancers are highly aggressive and metastasize even when small, leading to a very poor clinical outcome. Fumarate, a small molecule metabolite that accumulates in fumarate hydratase-deficient cells, plays a key role in cell transformation, making it a bona fide oncometabolite. Fumarate has been shown to inhibit α-ketoglutarate-dependent dioxygenases that are involved in DNA and histone demethylation. However, the link between fumarate accumulation, epigenetic changes, and tumorigenesis is unclear. Here we show that loss of fumarate hydratase and the subsequent accumulation of fumarate in mouse and human cells elicits an epithelial-to-mesenchymal-transition (EMT), a phenotypic switch associated with cancer initiation, invasion, and metastasis. We demonstrate that fumarate inhibits Tet-mediated demethylation of a regulatory region of the antimetastatic miRNA cluster mir-200ba429, leading to the expression of EMT-related transcription factors and enhanced migratory properties. These epigenetic and phenotypic changes are recapitulated by the incubation of fumarate hydratase-proficient cells with cell-permeable fumarate. Loss of fumarate hydratase is associated with suppression of miR-200 and the EMT signature in renal cancer and is associated with poor clinical outcome. These results imply that loss of fumarate hydratase and fumarate accumulation contribute to the aggressive features of fumarate hydratase-deficient tumours.
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Affiliation(s)
- Marco Sciacovelli
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Emanuel Gonçalves
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Cambridge CB10 1SD, UK
| | - Timothy Isaac Johnson
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | | | | | - Edoardo Gaude
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | | | | | - Sandra Riekje Abbo
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Maxine Gia Binh Tran
- Department of Oncology, Uro-Oncology Research Group, University of Cambridge, Cambridge CB2 0Ql, UK
| | - Vinothini Rajeeve
- Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, John Vane Science Centre, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Simone Cardaci
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Sarah Foster
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Haiyang Yun
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0XY, UK
| | - Pedro Cutillas
- Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, John Vane Science Centre, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Anne Warren
- Department of Pathology, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Vincent Gnanapragasam
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Eyal Gottlieb
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Brian Huntly
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0XY, UK
| | - Eamonn Richard Maher
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Patrick Henry Maxwell
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Cambridge CB10 1SD, UK
- RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen 52074, Germany
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
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24
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Synergic stress in striped catfish (Pangasianodon hypophthalmus, S.) exposed to chronic salinity and bacterial infection: Effects on kidney protein expression profile. J Proteomics 2016; 142:91-101. [DOI: 10.1016/j.jprot.2016.04.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 12/14/2022]
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25
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Kulbe H, Iorio F, Chakravarty P, Milagre CS, Moore R, Thompson RG, Everitt G, Canosa M, Montoya A, Drygin D, Braicu I, Sehouli J, Saez-Rodriguez J, Cutillas PR, Balkwill FR. Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells. Oncotarget 2016; 7:15648-61. [PMID: 26871292 PMCID: PMC4941267 DOI: 10.18632/oncotarget.7255] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/26/2016] [Indexed: 01/07/2023] Open
Abstract
We previously showed how key pathways in cancer-related inflammation and Notch signaling are part of an autocrine malignant cell network in ovarian cancer. This network, which we named the "TNF network", has paracrine actions within the tumor microenvironment, influencing angiogenesis and the immune cell infiltrate.The aim of this study was to identify critical regulators in the signaling pathways of the TNF network in ovarian cancer cells that might be therapeutic targets. To achieve our aim, we used a systems biology approach, combining data from phospho-proteomic mass spectrometry and gene expression array analysis. Among the potential therapeutic kinase targets identified was the protein kinase Casein kinase II (CK2).Knockdown of CK2 expression in malignant cells by siRNA or treatment with the specific CK2 inhibitor CX-4945 significantly decreased Notch signaling and reduced constitutive cytokine release in ovarian cancer cell lines that expressed the TNF network as well as malignant cells isolated from high grade serous ovarian cancer ascites. The expression of the same cytokines was also inhibited after treatment with CX-4945 in a 3D organotypic model. CK2 inhibition was associated with concomitant inhibition of proliferative activity, reduced angiogenesis and experimental peritoneal ovarian tumor growth.In conclusion, we have identified kinases, particularly CK2, associated with the TNF network that may play a central role in sustaining the cytokine network and/or mediating its effects in ovarian cancer.
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Affiliation(s)
- Hagen Kulbe
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Gynecology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Francesco Iorio
- European Molecular Biology Laboratory – European Bioinformatics Institute, EMBL-EBI, Cambridge, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - Carla S. Milagre
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Robert Moore
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Richard G. Thompson
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Gemma Everitt
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Monica Canosa
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alexander Montoya
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Ioana Braicu
- Tumorbank Ovarian Cancer Network, Department of Gynecology, Charité Universitätsmedizin Berlin, Berlin, Germany
- Department of Gynecology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jalid Sehouli
- Tumorbank Ovarian Cancer Network, Department of Gynecology, Charité Universitätsmedizin Berlin, Berlin, Germany
- Department of Gynecology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory – European Bioinformatics Institute, EMBL-EBI, Cambridge, UK
| | - Pedro R. Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Frances R. Balkwill
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, London, UK
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26
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Cutillas PR, Crnogorac-Jurcevic T. Application of Proteomics in Cancer Biomarker Discovery: GeLC-MS/MS. Methods Mol Biol 2016; 1381:201-209. [PMID: 26667462 DOI: 10.1007/978-1-4939-3204-7_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteomic approaches are being increasingly applied to study multiple facets of healthy and diseased processes. In particular, the application of global proteome profiling in the field of oncology is already starting to shape the diagnostic, prognostic, monitoring, and therapeutic approaches. At the heart of such approaches lies a quest for clinically relevant biomarkers, particularly arising from global analyses of body fluids, as, in major part, they represent easily accessible and noninvasive matrices. A detailed protocol of one of the popular approaches for global proteome profiling, SDS-PAGE-liquid chromatography-tandem mass spectrometry or GeLC-MS/MS, and its application for biomarker discovery in urine is provided here.
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Affiliation(s)
- Pedro R Cutillas
- Centre for Haemato-Oncology, Bart Cancer Institute, Queen Mary University of London, 3rd Floor, John Vane Science Centre, John Vane Science Building, Charterhouse Square, London, EC1 6BQ, UK.
| | - Tatjana Crnogorac-Jurcevic
- Molecular Oncology Centre, Bart Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1 6BQ, UK
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27
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Dammeier S, Nahnsen S, Veit J, Wehner F, Ueffing M, Kohlbacher O. Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence. J Proteome Res 2015; 15:182-92. [DOI: 10.1021/acs.jproteome.5b00704] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Sascha Dammeier
- Institute
for Ophthalmic Research, Medical Proteome Center, University Hospital Tuebingen, Naegelestrasse 5, 72074 Tuebingen, Germany
| | - Sven Nahnsen
- Quantitative
Biology Center, Eberhard Karls University of Tuebingen, Auf der
Morgenstelle 10, 72076 Tuebingen, Germany
| | - Johannes Veit
- Center
for Bioinformatics and Department of Computer Science, Eberhard Karls University of Tuebingen, Sand 14, 72076 Tuebingen, Germany
| | - Frank Wehner
- Institute
for Forensic Medicine, Eberhard Karls University of Tuebingen, Naegelestrasse
5, 72074 Tuebingen, Germany
| | - Marius Ueffing
- Institute
for Ophthalmic Research, Medical Proteome Center, University Hospital Tuebingen, Naegelestrasse 5, 72074 Tuebingen, Germany
| | - Oliver Kohlbacher
- Quantitative
Biology Center, Eberhard Karls University of Tuebingen, Auf der
Morgenstelle 10, 72076 Tuebingen, Germany
- Center
for Bioinformatics and Department of Computer Science, Eberhard Karls University of Tuebingen, Sand 14, 72076 Tuebingen, Germany
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28
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Terfve CDA, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J. Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data. Nat Commun 2015; 6:8033. [PMID: 26354681 PMCID: PMC4579397 DOI: 10.1038/ncomms9033] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/09/2015] [Indexed: 12/27/2022] Open
Abstract
Mass spectrometry is widely used to probe the proteome and its modifications in an untargeted manner, with unrivalled coverage. Applied to phosphoproteomics, it has tremendous potential to interrogate phospho-signalling and its therapeutic implications. However, this task is complicated by issues of undersampling of the phosphoproteome and challenges stemming from its high-content but low-sample-throughput nature. Hence, methods using such data to reconstruct signalling networks have been limited to restricted data sets and insights (for example, groups of kinases likely to be active in a sample). We propose a new method to handle high-content discovery phosphoproteomics data on perturbation by putting it in the context of kinase/phosphatase-substrate knowledge, from which we derive and train logic models. We show, on a data set obtained through perturbations of cancer cells with small-molecule inhibitors, that this method can study the targets and effects of kinase inhibitors, and reconcile insights obtained from multiple data sets, a common issue with these data. Phosphoproteomics can offer significant insight into cell signalling and how signalling is modified in response to perturbations. Here the authors develop a new tool for the analysis of high-content phosphoproteomics in the context of kinase/phosphatase-substrate knowledge, which is used to train logic models.
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Affiliation(s)
- Camille D A Terfve
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Edmund H Wilkes
- Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Pedro Casado
- Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Pedro R Cutillas
- Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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29
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Herranz N, Gallage S, Mellone M, Wuestefeld T, Klotz S, Hanley CJ, Raguz S, Acosta JC, Innes AJ, Banito A, Georgilis A, Montoya A, Wolter K, Dharmalingam G, Faull P, Carroll T, Martínez-Barbera JP, Cutillas P, Reisinger F, Heikenwalder M, Miller RA, Withers D, Zender L, Thomas GJ, Gil J. mTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype. Nat Cell Biol 2015; 17:1205-17. [PMID: 26280535 PMCID: PMC4589897 DOI: 10.1038/ncb3225] [Citation(s) in RCA: 501] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/20/2015] [Indexed: 12/15/2022]
Abstract
Senescent cells secrete a combination of factors collectively known as the senescence-associated secretory phenotype (SASP). The SASP reinforces senescence and activates an immune surveillance response, but it can also show pro-tumorigenic properties and contribute to age-related pathologies. In a drug screen to find new SASP regulators, we uncovered the mTOR inhibitor rapamycin as a potent SASP suppressor. Here we report a mechanism by which mTOR controls the SASP by differentially regulating the translation of the MK2 (also known as MAPKAPK2) kinase through 4EBP1. In turn, MAPKAPK2 phosphorylates the RNA-binding protein ZFP36L1 during senescence, inhibiting its ability to degrade the transcripts of numerous SASP components. Consequently, mTOR inhibition or constitutive activation of ZFP36L1 impairs the non-cell-autonomous effects of senescent cells in both tumour-suppressive and tumour-promoting contexts. Altogether, our results place regulation of the SASP as a key mechanism by which mTOR could influence cancer, age-related diseases and immune responses.
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Affiliation(s)
- Nicolás Herranz
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Suchira Gallage
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Metabolic Signalling Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Massimiliano Mellone
- Cancer Sciences Unit, Cancer Research UK Centre, Somers Building, University of Southampton, Southampton SO16 6YD, UK
| | - Torsten Wuestefeld
- Division of Molecular Oncology of Solid Tumors, Dept. of Internal Medicine I, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Sabrina Klotz
- Division of Molecular Oncology of Solid Tumors, Dept. of Internal Medicine I, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Christopher J. Hanley
- Cancer Sciences Unit, Cancer Research UK Centre, Somers Building, University of Southampton, Southampton SO16 6YD, UK
| | - Selina Raguz
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Juan Carlos Acosta
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Andrew J Innes
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Ana Banito
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Athena Georgilis
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Alex Montoya
- Proteomics Facility; MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Katharina Wolter
- Division of Molecular Oncology of Solid Tumors, Dept. of Internal Medicine I, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Gopuraja Dharmalingam
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Peter Faull
- Proteomics Facility; MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Thomas Carroll
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | | | - Pedro Cutillas
- Proteomics Facility; MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Florian Reisinger
- Institute for Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Mathias Heikenwalder
- Institute for Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research (DKFZ), Heidelberg, Germany
| | - Richard A. Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Dominic Withers
- Metabolic Signalling Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Lars Zender
- Division of Molecular Oncology of Solid Tumors, Dept. of Internal Medicine I, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Gareth J. Thomas
- Cancer Sciences Unit, Cancer Research UK Centre, Somers Building, University of Southampton, Southampton SO16 6YD, UK
| | - Jesús Gil
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
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30
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Song W, Yu L, Peng Z. Targeted label-free approach for quantification of epoxide hydrolase and glutathione transferases in microsomes. Anal Biochem 2015; 478:8-13. [PMID: 25769418 DOI: 10.1016/j.ab.2015.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 02/24/2015] [Accepted: 03/02/2015] [Indexed: 11/29/2022]
Abstract
The aim of this study was to investigate the expression and organ distribution of cytochrome P450 (CYP450) enzymes, microsomal epoxide hydrolase (MEH), and microsomal glutathione-S-transferase (MGST 1, 2, 3) in human liver, lung, intestinal, and kidney microsomes by targeted peptide-based quantification using nano liquid chromatography-tandem multiple reaction monitoring (nano LC-MRM). Applying this method, we analyzed 16 human liver microsomes and pooled lung, kidney, and intestine microsomes. Nine of the CYP450s (CYP1A2, 2B6, 2C8, 2C9, 2C19, 2D6, 2E1, 3A4, 3A5) could be quantified in liver. Except for CYP3A4 and 3A5 existing in intestine, other CYP450s had little content (<0.1 pmol/mg protein) in extrahepatic tissues. MEH and MGSTs could be quantified both in hepatic and in extrahepatic tissues. The highest concentrations of MEH and MGST 1, 2 were found in liver; conversely MGST 3 was abundant in human kidney and intestine compared to liver. The targeted proteomics assay described here can be broadly and efficiently utilized as a tool for investigating the targeted proteins. The method also provides novel CYP450s, MEH, and MGSTs expression data in human hepatic and extrahepatic tissues that will benefit rational approaches to evaluate metabolism in drug development.
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Affiliation(s)
- Wei Song
- Institute of Resource Biology and Biotechnology, Department of biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Zhihong Peng
- Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, Hubei University, Wuhan 430062, China.
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31
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Hall AM, Vilasi A, Garcia-Perez I, Lapsley M, Alston CL, Pitceathly RDS, McFarland R, Schaefer AM, Turnbull DM, Beaumont NJ, Hsuan JJ, Cutillas PR, Lindon JC, Holmes E, Unwin RJ, Taylor RW, Gorman GS, Rahman S, Hanna MG. The urinary proteome and metabonome differ from normal in adults with mitochondrial disease. Kidney Int 2015; 87:610-22. [PMID: 25207879 DOI: 10.1038/ki.2014.297] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/27/2014] [Accepted: 07/10/2014] [Indexed: 02/08/2023]
Abstract
We studied the extent and nature of renal involvement in a cohort of 117 adult patients with mitochondrial disease, by measuring urinary retinol-binding protein (RBP) and albumin; established markers of tubular and glomerular dysfunction, respectively. Seventy-five patients had the m.3243A>G mutation and the most frequent phenotypes within the entire cohort were 14 with MELAS, 33 with MIDD, and 17 with MERRF. Urinary RBP was increased in 29 of 75 of m.3243A>G patients, whereas albumin was increased in 23 of the 75. The corresponding numbers were 16 and 14, respectively, in the 42 non-m.3243A>G patients. RBP and albumin were higher in diabetic m.3243A>G patients than in nondiabetics, but there were no significant differences across the three major clinical phenotypes. The urine proteome (mass spectrometry) and metabonome (nuclear magnetic resonance) in a subset of the m.3243A>G patients were markedly different from controls, with the most significant alterations occurring in lysosomal proteins, calcium-binding proteins, and antioxidant defenses. Differences were also found between asymptomatic m.3243A>G carriers and controls. No patients had an elevated serum creatinine level, but 14% had hyponatremia, 10% had hypophosphatemia, and 14% had hypomagnesemia. Thus, abnormalities in kidney function are common in adults with mitochondrial disease, exist in the absence of elevated serum creatinine, and are not solely explained by diabetes.
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Affiliation(s)
- Andrew M Hall
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Annalisa Vilasi
- Laboratory of Mass Spectrometry and Proteomics, Institute of Protein Biochemistry-CNR, Naples, Italy
| | - Isabel Garcia-Perez
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Marta Lapsley
- South West Thames Institute for Renal Research, St Helier University Hospitals, Surrey, UK
| | - Charlotte L Alston
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Robert D S Pitceathly
- Medical Research Council Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, University College London Institute of Neurology, London, UK
| | - Robert McFarland
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew M Schaefer
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Doug M Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Nick J Beaumont
- Division of Medicine, Institute for Liver & Digestive Health, University College London, London, UK
| | - Justin J Hsuan
- Division of Medicine, Institute for Liver & Digestive Health, University College London, London, UK
| | - Pedro R Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary, University of London, London, UK
| | - John C Lindon
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Elaine Holmes
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Robert J Unwin
- UCL Centre for Nephrology, Royal Free Hospital, London, UK
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Grainne S Gorman
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | | | - Michael G Hanna
- Medical Research Council Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, University College London Institute of Neurology, London, UK
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32
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Cutillas PR. Role of phosphoproteomics in the development of personalized cancer therapies. Proteomics Clin Appl 2015; 9:383-95. [PMID: 25488289 DOI: 10.1002/prca.201400104] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/20/2014] [Accepted: 11/18/2014] [Indexed: 01/08/2023]
Abstract
Cell signalling pathways driven by protein and lipid kinases contribute to the onset and progression of virtually all cancer types. Consequently, several inhibitors against these enzymes have clinical utility for the treatment of different forms of cancer. A problem that hampers further development is that not all patients respond equally well to kinase inhibitors and a significant proportion of those that initially respond eventually develop resistance. This review considers how an integrative analysis of kinase signalling may be used to address this issue. Advances in the biophysics of mass spectrometry, in biochemical procedures for phosphopeptide enrichment, and in computational approaches for label-free quantification have contributed to the development of phosphoproteomics workflows compatible with the analysis of clinical material. These developments, together with new bioinformatics tools to derive information on signalling circuitry from phosphoproteomics data, allow investigating kinase networks with unprecedented depth. Phosphoproteomics technology is starting to be used in translational research and, with further developments, such methods may also be able to measure the circuitry of cancer signalling networks in routine clinical assays. This review reflects on how this information could be used to accurately predict the best kinase inhibitor for each individual cancer patient.
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Affiliation(s)
- Pedro R Cutillas
- Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, John Vane Science Centre, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
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33
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Ai Q, Sun G, Luo Y, Dong X, Hu R, Meng X, Sun X. Ginsenoside Rb1 prevents hypoxia-reoxygenation-induced apoptosis in H9c2 cardiomyocytes via an estrogen receptor-dependent crosstalk among the Akt, JNK, and ERK 1/2 pathways using a label-free quantitative proteomics analysis. RSC Adv 2015. [DOI: 10.1039/c5ra02432c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Rb1 prevents H/R-induced apoptosis of H9c2 cells via an estrogen receptor-dependent crosstalk among the Akt, JNK, and ERK 1/2 pathways.
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Affiliation(s)
- Qidi Ai
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine
- Ministry of Education
- Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing
| | - Guibo Sun
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine
- Ministry of Education
- Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing
| | - Yun Luo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine
- Ministry of Education
- Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing
| | - Xi Dong
- Wenzhou Medical University
- Wenzhou
- P. R. China
| | - Ruifeng Hu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine
- Ministry of Education
- Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing
| | - Xiangbao Meng
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine
- Ministry of Education
- Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing
| | - Xiaobo Sun
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine
- Ministry of Education
- Institute of Medicinal Plant Development
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing
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34
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Rotival M, Ko JH, Srivastava PK, Kerloc'h A, Montoya A, Mauro C, Faull P, Cutillas PR, Petretto E, Behmoaras J. Integrating phosphoproteome and transcriptome reveals new determinants of macrophage multinucleation. Mol Cell Proteomics 2014; 14:484-98. [PMID: 25532521 PMCID: PMC4349971 DOI: 10.1074/mcp.m114.043836] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Macrophage multinucleation (MM) is essential for various biological processes such as osteoclast-mediated bone resorption and multinucleated giant cell-associated inflammatory reactions. Here we study the molecular pathways underlying multinucleation in the rat through an integrative approach combining MS-based quantitative phosphoproteomics (LC-MS/MS) and transcriptome (high-throughput RNA-sequencing) to identify new regulators of MM. We show that a strong metabolic shift toward HIF1-mediated glycolysis occurs at transcriptomic level during MM, together with modifications in phosphorylation of over 50 proteins including several ARF GTPase activators and polyphosphate inositol phosphatases. We use shortest-path analysis to link differential phosphorylation with the transcriptomic reprogramming of macrophages and identify LRRFIP1, SMARCA4, and DNMT1 as novel regulators of MM. We experimentally validate these predictions by showing that knock-down of these latter reduce macrophage multinucleation. These results provide a new framework for the combined analysis of transcriptional and post-translational changes during macrophage multinucleation, prioritizing essential genes, and revealing the sequential events leading to the multinucleation of macrophages.
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Affiliation(s)
- Maxime Rotival
- From the ‡Integrative Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, UK
| | - Jeong-Hun Ko
- §Centre for Complement and Inflammation Research (CCIR), Imperial College London, UK
| | - Prashant K Srivastava
- From the ‡Integrative Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, UK
| | - Audrey Kerloc'h
- §Centre for Complement and Inflammation Research (CCIR), Imperial College London, UK
| | - Alex Montoya
- ‖Biological Mass Spectrometry and Proteomics Laboratory, MRC Clinical Sciences Centre, Imperial College London, UK
| | - Claudio Mauro
- ¶William Harvey Research Institute, Queen Mary University of London, UK
| | - Peter Faull
- ‖Biological Mass Spectrometry and Proteomics Laboratory, MRC Clinical Sciences Centre, Imperial College London, UK
| | - Pedro R Cutillas
- **Integrative Cell Signaling and Proteomics, Barts Cancer Institute, Queen Mary University of London, UK
| | - Enrico Petretto
- From the ‡Integrative Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, UK;
| | - Jacques Behmoaras
- §Centre for Complement and Inflammation Research (CCIR), Imperial College London, UK;
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35
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Rajeeve V, Vendrell I, Wilkes E, Torbett N, Cutillas PR. Cross-species proteomics reveals specific modulation of signaling in cancer and stromal cells by phosphoinositide 3-kinase (PI3K) inhibitors. Mol Cell Proteomics 2014; 13:1457-70. [PMID: 24648465 DOI: 10.1074/mcp.m113.035204] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The tumor microenvironment plays key roles in cancer biology, but its impact on the regulation of signaling pathway activity in cancer cells has not been systemically investigated. We designed an analytical strategy that allows differential analysis of signaling between cancer and stromal cells present in tumor xenografts. We used this approach to investigate how in vivo growth conditions and PI3K inhibitors regulate pathway activities in both cancer and stromal cell populations. We found that, despite inducing more modest changes in protein expression, in vivo growing conditions extensively rewired protein kinase networks in cancer cells. As a result, different sets of phosphorylation sites were modulated by PI3K inhibitors in cancer cells growing in tumors relative to when these cells were in culture. The p110δ PI3K-selective compound CAL-101 (Idelalisib) did not inhibit markers of PI3K activity in cancer or stromal cells; however, unexpectedly, it induced phosphorylation on SQ motifs in both subpopulations of tumor cells in vivo but not in vitro. Thus, the interaction between cancer cells and the stroma modulated the ability of PI3K inhibitors to induce the activation of apoptosis in solid tumors. Our study provides proof-of-principle of a proteomics workflow for measuring signaling specifically in cancer and stromal cells and for investigating how cancer biochemistry is modulated in vivo.
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Affiliation(s)
- Vinothini Rajeeve
- From the ‡Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Barts School of Medicine and Dentistry, UK
| | | | - Edmund Wilkes
- From the ‡Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Barts School of Medicine and Dentistry, UK
| | - Neil Torbett
- §Activiomics Ltd, Charterhouse Square, London, UK
| | - Pedro R Cutillas
- From the ‡Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Barts School of Medicine and Dentistry, UK;
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36
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Casado P, Bilanges B, Rajeeve V, Vanhaesebroeck B, Cutillas PR. Environmental stress affects the activity of metabolic and growth factor signaling networks and induces autophagy markers in MCF7 breast cancer cells. Mol Cell Proteomics 2014; 13:836-48. [PMID: 24425749 PMCID: PMC3945912 DOI: 10.1074/mcp.m113.034751] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/13/2013] [Indexed: 11/06/2022] Open
Abstract
Phosphoproteomic techniques are contributing to our understanding of how signaling pathways interact and regulate biological processes. This technology is also being used to characterize how signaling networks are remodeled during disease progression and to identify biomarkers of signaling pathway activity and of responses to cancer therapy. A potential caveat in these studies is that phosphorylation is a very dynamic modification that can substantially change during the course of an experiment or the retrieval and processing of cellular samples. Here, we investigated how exposure of cells to ambient conditions modulates phosphorylation and signaling pathway activity in the MCF7 breast cancer cell line. About 1.5% of 3,500 sites measured showed a significant change in phosphorylation extent upon exposure of cells to ambient conditions for 15 min. The effects of this perturbation in modifying phosphorylation patterns did not involve random changes due to stochastic activation of kinases and phosphatases. Instead, exposure of cells to ambient conditions elicited an environmental stress reaction that involved a coordinated response to a metabolic stress situation, which included: (1) the activation of AMPK; (2) the inhibition of PI3K, AKT, and ERK; (3) an increase in markers of protein synthesis inhibition at the level of translation elongation; and (4) an increase in autophagy markers. We also observed that maintaining cells in ice modified but did not completely abolish this metabolic stress response. In summary, exposure of cells to ambient conditions affects the activity of signaling networks previously implicated in metabolic and growth factor signaling. Mass spectrometry data have been deposited to the ProteomeXchange with identifier PXD000472.
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Affiliation(s)
- Pedro Casado
- From the ‡Analytical Signalling Group and
- ¶ Current affiliation: Integrative Cell Signaling and Proteomics Group, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry
| | - Benoit Bilanges
- §Cell Signalling Group, Centre for Cell Signalling, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London EC1B 6BQ, UK
| | - Vinothini Rajeeve
- From the ‡Analytical Signalling Group and
- ¶ Current affiliation: Integrative Cell Signaling and Proteomics Group, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry
| | - Bart Vanhaesebroeck
- §Cell Signalling Group, Centre for Cell Signalling, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London EC1B 6BQ, UK
| | - Pedro R. Cutillas
- From the ‡Analytical Signalling Group and
- ¶ Current affiliation: Integrative Cell Signaling and Proteomics Group, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Barts and the London School of Medicine and Dentistry
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37
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Mermelekas G, Makridakis M, Koeck T, Vlahou A. Redox proteomics: from residue modifications to putative biomarker identification by gel- and LC-MS-based approaches. Expert Rev Proteomics 2014; 10:537-49. [DOI: 10.1586/14789450.2013.855611] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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38
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Li KW, Jimenez CR. Synapse proteomics: current status and quantitative applications. Expert Rev Proteomics 2014; 5:353-60. [DOI: 10.1586/14789450.5.2.353] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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39
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Park E, Drakakaki G. Proteomics of endosomal compartments from plants case study: isolation of trans-Golgi network vesicles. Methods Mol Biol 2014; 1209:179-187. [PMID: 25117284 DOI: 10.1007/978-1-4939-1420-3_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A detailed understanding of endomembrane processes and their biological roles is vital for a complete picture of plant growth and development; however their highly dynamic nature has complicated comprehensive and rigorous studies so far. Recent pioneering efforts have demonstrated that isolation of vesicles in their native state, paired with a quantitative identification of their cargo, offers a viable and practicable approach for the dissection of endomembrane trafficking pathways. The protocol presented in this chapter describes in detail the isolation of the SYP61 trans-Golgi network vesicles from Arabidopsis. With minor alterations, in a few key parameters, it can be adopted to yield a universal procedure for the broad spectrum of plant vesicles.
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Affiliation(s)
- Eunsook Park
- Department of Plant sciences, University of California Davis, Asmundson Hall, One Shields Avenue, Davis, CA, 95616, USA
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40
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Sacchi R, Li J, Villarreal F, Gardell AM, Kültz D. Salinity-induced regulation of the myo-inositol biosynthesis pathway in tilapia gill epithelium. ACTA ACUST UNITED AC 2013; 216:4626-38. [PMID: 24072791 DOI: 10.1242/jeb.093823] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The myo-inositol biosynthesis (MIB) pathway converts glucose-6-phosphate to the compatible osmolyte myo-inositol that protects cells from osmotic stress. Using proteomics, the enzymes that constitute the MIB pathway, myo-inositol phosphate synthase (MIPS) and inositol monophosphatase 1 (IMPA1), are identified in tilapia (Oreochromis mossambicus) gill epithelium. Targeted, quantitative, label-free proteomics reveals that they are both upregulated during salinity stress. Upregulation is stronger when fish are exposed to severe (34 ppt acute and 90 ppt gradual) relative to moderate (70 ppt gradual) salinity stress. IMPA1 always responds more strongly than MIPS, suggesting that MIPS is more stable during salinity stress. MIPS is N-terminally acetylated and the corresponding peptide increases proportionally to MIPS protein, while non-acetylated N-terminal peptide is not detectable, indicating that MIPS acetylation is constitutive and may serve to stabilize the protein. Hyperosmotic induction of MIPS and IMPA1 is confirmed using western blot and real-time qPCR and is much higher at the mRNA than at the protein level. Two distinct MIPS mRNA variants are expressed in the gill, but one is more strongly regulated by salinity than the other. A single MIPS gene is encoded in the tilapia genome whereas the zebrafish genome lacks MIPS entirely. The genome of euryhaline tilapia contains four IMPA genes, two of which are expressed, but only one is salinity regulated in gill epithelium. The genome of stenohaline zebrafish contains a single IMPA gene. We conclude that the MIB pathway represents a major salinity stress coping mechanism that is regulated at multiple levels in euryhaline fish but absent in stenohaline zebrafish.
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Affiliation(s)
- Romina Sacchi
- Physiological Genomics Group, Department of Animal Sciences, University of California, Davis, One Shields Avenue, Meyer Hall, Davis, CA 95616, USA
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41
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Kültz D, Li J, Gardell A, Sacchi R. Quantitative molecular phenotyping of gill remodeling in a cichlid fish responding to salinity stress. Mol Cell Proteomics 2013; 12:3962-75. [PMID: 24065692 DOI: 10.1074/mcp.m113.029827] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A two-tiered label-free quantitative (LFQ) proteomics workflow was used to elucidate how salinity affects the molecular phenotype, i.e. proteome, of gills from a cichlid fish, the euryhaline tilapia (Oreochromis mossambicus). The workflow consists of initial global profiling of relative tryptic peptide abundances in treated versus control samples followed by targeted identification (by MS/MS) and quantitation (by chromatographic peak area integration) of validated peptides for each protein of interest. Fresh water acclimated tilapia were independently exposed in separate experiments to acute short-term (34 ppt) and gradual long-term (70 ppt, 90 ppt) salinity stress followed by molecular phenotyping of the gill proteome. The severity of salinity stress can be deduced with high technical reproducibility from the initial global label-free quantitative profiling step alone at both peptide and protein levels. However, an accurate regulation ratio can only be determined by targeted label-free quantitative profiling because not all peptides used for protein identification are also valid for quantitation. Of the three salinity challenges, gradual acclimation to 90 ppt has the most pronounced effect on gill molecular phenotype. Known salinity effects on tilapia gills, including an increase in the size and number of mitochondria-rich ionocytes, activities of specific ion transporters, and induction of specific molecular chaperones are reflected in the regulation of abundances of the corresponding proteins. Moreover, specific protein isoforms that are responsive to environmental salinity change are resolved and it is revealed that salinity effects on the mitochondrial proteome are nonuniform. Furthermore, protein NDRG1 has been identified as a novel key component of molecular phenotype restructuring during salinity-induced gill remodeling. In conclusion, besides confirming known effects of salinity on gills of euryhaline fish, molecular phenotyping reveals novel insight into proteome changes that underlie the remodeling of tilapia gill epithelium in response to environmental salinity change.
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Affiliation(s)
- Dietmar Kültz
- Physiological Genomics Group, Department of Animal Sciences, University of California Davis, One Shields Avenue, Davis, California 95616
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42
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Bateman NW, Goulding SP, Shulman NJ, Gadok AK, Szumlinski KK, MacCoss MJ, Wu CC. Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA). Mol Cell Proteomics 2013; 13:329-38. [PMID: 23820513 DOI: 10.1074/mcp.m112.026500] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Current analytical strategies for collecting proteomic data using data-dependent acquisition (DDA) are limited by the low analytical reproducibility of the method. Proteomic discovery efforts that exploit the benefits of DDA, such as providing peptide sequence information, but that enable improved analytical reproducibility, represent an ideal scenario for maximizing measureable peptide identifications in "shotgun"-type proteomic studies. Therefore, we propose an analytical workflow combining DDA with retention time aligned extracted ion chromatogram (XIC) areas obtained from high mass accuracy MS1 data acquired in parallel. We applied this workflow to the analyses of sample matrixes prepared from mouse blood plasma and brain tissues and observed increases in peptide detection of up to 30.5% due to the comparison of peptide MS1 XIC areas following retention time alignment of co-identified peptides. Furthermore, we show that the approach is quantitative using peptide standards diluted into a complex matrix. These data revealed that peptide MS1 XIC areas provide linear response of over three orders of magnitude down to low femtomole (fmol) levels. These findings argue that augmenting "shotgun" proteomic workflows with retention time alignment of peptide identifications and comparative analyses of corresponding peptide MS1 XIC areas improve the analytical performance of global proteomic discovery methods using DDA.
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Affiliation(s)
- Nicholas W Bateman
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
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Craft GE, Chen A, Nairn AC. Recent advances in quantitative neuroproteomics. Methods 2013; 61:186-218. [PMID: 23623823 PMCID: PMC3891841 DOI: 10.1016/j.ymeth.2013.04.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 03/29/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023] Open
Abstract
The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.
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Affiliation(s)
- George E Craft
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Anshu Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Angus C Nairn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
- Yale/NIDA Neuroproteomics Center, Yale University School of Medicine, New Haven, CT, 06508
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Zhang W, Zhang J, Xu C, Li N, Liu H, Ma J, Zhu Y, Xie H. LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data. Proteomics 2013; 12:3475-84. [PMID: 23081734 DOI: 10.1002/pmic.201200017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 09/25/2012] [Accepted: 10/01/2012] [Indexed: 11/09/2022]
Abstract
Database searching based methods for label-free quantification aim to reconstruct the peptide extracted ion chromatogram based on the identification information, which can limit the search space and thus make the data processing much faster. The random effect of the MS/MS sampling can be remedied by cross-assignment among different runs. Here, we present a new label-free fast quantitative analysis tool, LFQuant, for high-resolution LC-MS/MS proteomics data based on database searching. It is designed to accept raw data in two common formats (mzXML and Thermo RAW), and database search results from mainstream tools (MASCOT, SEQUEST, and X!Tandem), as input data. LFQuant can handle large-scale label-free data with fractionation such as SDS-PAGE and 2D LC. It is easy to use and provides handy user interfaces for data loading, parameter setting, quantitative analysis, and quantitative data visualization. LFQuant was compared with two common quantification software packages, MaxQuant and IDEAL-Q, on the replication data set and the UPS1 standard data set. The results show that LFQuant performs better than them in terms of both precision and accuracy, and consumes significantly less processing time. LFQuant is freely available under the GNU General Public License v3.0 at http://sourceforge.net/projects/lfquant/.
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Affiliation(s)
- Wei Zhang
- Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, PR China
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 970] [Impact Index Per Article: 88.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Casado P, Rodriguez-Prados JC, Cosulich SC, Guichard S, Vanhaesebroeck B, Joel S, Cutillas PR. Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells. Sci Signal 2013; 6:rs6. [PMID: 23532336 DOI: 10.1126/scisignal.2003573] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Kinases determine the phenotypes of many cancer cells, but the frequency with which individual kinases are activated in primary tumors remains largely unknown. We used a computational approach, termed kinase-substrate enrichment analysis (KSEA), to systematically infer the activation of given kinase pathways from mass spectrometry-based phosphoproteomic analysis of acute myeloid leukemia (AML) cells. Experiments conducted in cell lines validated the approach and, furthermore, revealed that DNA-dependent protein kinase (DNA-PK) was activated as a result of inhibiting the phosphoinositide 3-kinase (PI3K)-mammalian target of rapamycin (mTOR) signaling pathway. Application of KSEA to primary AML cells identified PI3K, casein kinases (CKs), cyclin-dependent kinases (CDKs), and p21-activated kinases (PAKs) as the kinase substrate groups most frequently enriched in this cancer type. Substrates phosphorylated by extracellular signal-regulated kinase (ERK) and cell division cycle 7 (CDC7) were enriched in primary AML cells that were resistant to inhibition of PI3K-mTOR signaling, whereas substrates of the kinases Abl, Lck, Src, and CDK1 were increased in abundance in inhibitor-sensitive cells. Modeling based on the abundances of these substrate groups accurately predicted sensitivity to a dual PI3K and mTOR inhibitor in two independent sets of primary AML cells isolated from patients. Thus, our study demonstrates KSEA as an untargeted method for the systematic profiling of kinase pathway activities and for increasing our understanding of diseases caused by the dysregulation of signaling pathways.
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Affiliation(s)
- Pedro Casado
- Analytical Signalling Group, Centre for Cell Signalling, Barts Cancer Institute, Queen Mary University of London, London EC1B 6BQ, UK.
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Martyniuk CJ, Alvarez S. Proteome analysis of the fathead minnow (Pimephales promelas) reproductive testes. J Proteomics 2012; 79:28-42. [PMID: 23234800 DOI: 10.1016/j.jprot.2012.11.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/31/2012] [Accepted: 11/17/2012] [Indexed: 11/28/2022]
Abstract
Proteomics is becoming more widely used as a tool in fish physiology and toxicology and can offer mechanistic insight into organism responses to environmental signals and stressors. Using a LTQ Orbitrap Velos MS/MS, we detected 1075 proteins in the reproductive testis of fathead minnow. Proteins localized to the testis included those with a role in spermatogenesis, DNA repair, gamete meiosis, and proteins that have methylation and phosporylation activity, which are important regulatory mechanisms required for sperm maturation. Enrichment analysis revealed that proteins involved in translation, excision DNA repair, and chromatin remodeling were significantly enriched in the testis (>25% protein coverage of the cellular pathways). Proteins involved in RNA metabolism, spliceosome assembly, metabolism, and DNA unwinding were localized to the testis, and the DEAD (Asp-Glu-Ala-Asp) box RNA-dependent helicase family was well represented in this reproductive tissue. Based upon common detected proteins and functional processes between FHMs and the more ancient sharks, other ray-finned fishes, and mammals, we hypothesize that biological processes involved in the testis (DNA unwinding, RNA processing, spliceosome assembly) have been conserved throughout vertebrate evolution. This study provides the foundation for more in depth proteomics studies investigating the effects of hormones and endocrine disruptors in the teleostean testes.
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Affiliation(s)
- Christopher J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada E2L 4L5.
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Beltran L, Casado P, Rodríguez-Prados JC, Cutillas PR. Global profiling of protein kinase activities in cancer cells by mass spectrometry. J Proteomics 2012; 77:492-503. [DOI: 10.1016/j.jprot.2012.09.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 09/03/2012] [Accepted: 09/24/2012] [Indexed: 01/15/2023]
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Cappadona S, Baker PR, Cutillas PR, Heck AJR, van Breukelen B. Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids 2012. [PMID: 22821268 DOI: 10.1007/s00726-012-1289-1288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often considered the main bottleneck for proteomics development. This review highlights important issues that directly impact the effectiveness of proteomic quantitation and educates software developers and end-users on available computational solutions to correct for the occurrence of these factors. Potential sources of errors specific for stable isotope-based methods or label-free approaches are explicitly outlined. The overall aim focuses on a generic proteomic workflow.
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Affiliation(s)
- Salvatore Cappadona
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, The Netherlands
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50
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Cappadona S, Baker PR, Cutillas PR, Heck AJR, van Breukelen B. Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids 2012; 43:1087-108. [PMID: 22821268 PMCID: PMC3418498 DOI: 10.1007/s00726-012-1289-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 04/03/2012] [Indexed: 10/31/2022]
Abstract
Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often considered the main bottleneck for proteomics development. This review highlights important issues that directly impact the effectiveness of proteomic quantitation and educates software developers and end-users on available computational solutions to correct for the occurrence of these factors. Potential sources of errors specific for stable isotope-based methods or label-free approaches are explicitly outlined. The overall aim focuses on a generic proteomic workflow.
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Affiliation(s)
- Salvatore Cappadona
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Peter R. Baker
- Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, University of California San Francisco, San Francisco, USA
| | - Pedro R. Cutillas
- Analytical Signalling Group, Centre for Cell Signalling, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bas van Breukelen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Bioinformatics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
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