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Casado P, Cutillas PR. Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine. Mol Cell Proteomics 2023; 22:100517. [PMID: 36805445 PMCID: PMC10152134 DOI: 10.1016/j.mcpro.2023.100517] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous cancer of the hematopoietic system with no cure for most patients. In addition to chemotherapy, treatment options for AML include recently approved therapies that target proteins with roles in AML pathobiology, such as FLT3, BLC2, and IDH1/2. However, due to disease complexity, these therapies produce very diverse responses, and survival rates are still low. Thus, despite considerable advances, there remains a need for therapies that target different aspects of leukemic biology and for associated biomarkers that define patient populations likely to respond to each available therapy. To meet this need, drugs that target different AML vulnerabilities are currently in advanced stages of clinical development. Here, we review proteomics and phosphoproteomics studies that aimed to provide insights into AML biology and clinical disease heterogeneity not attainable with genomic approaches. To place the discussion in context, we first provide an overview of genetic and clinical aspects of the disease, followed by a summary of proteins targeted by compounds that have been approved or are under clinical trials for AML treatment and, if available, the biomarkers that predict responses. We then discuss proteomics and phosphoproteomics studies that provided insights into AML pathogenesis, from which potential biomarkers and drug targets were identified, and studies that aimed to rationalize the use of synergistic drug combinations. When considered as a whole, the evidence summarized here suggests that proteomics and phosphoproteomics approaches can play a crucial role in the development and implementation of precision medicine for AML patients.
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Affiliation(s)
- Pedro Casado
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Pedro R Cutillas
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; The Alan Turing Institute, The British Library, London, United Kingdom; Digital Environment Research Institute (DERI), Queen Mary University of London, London, United Kingdom.
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2
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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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3
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Andrés-Benito P, Flores Á, Busquet-Areny S, Carmona M, Ausín K, Cartas-Cejudo P, Lachén-Montes M, Del Rio JA, Fernández-Irigoyen J, Santamaría E, Ferrer I. Deregulated Transcription and Proteostasis in Adult mapt Knockout Mouse. Int J Mol Sci 2023; 24:ijms24076559. [PMID: 37047532 PMCID: PMC10095510 DOI: 10.3390/ijms24076559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Transcriptomics and phosphoproteomics were carried out in the cerebral cortex of B6.Cg-Mapttm1(EGFP)Klt (tau knockout: tau-KO) and wild-type (WT) 12 month-old mice to learn about the effects of tau ablation. Compared with WT mice, tau-KO mice displayed reduced anxiety-like behavior and lower fear expression induced by aversive conditioning, whereas recognition memory remained unaltered. Cortical transcriptomic analysis revealed 69 downregulated and 105 upregulated genes in tau-KO mice, corresponding to synaptic structures, neuron cytoskeleton and transport, and extracellular matrix components. RT-qPCR validated increased mRNA levels of col6a4, gabrq, gad1, grm5, grip2, map2, rab8a, tubb3, wnt16, and an absence of map1a in tau-KO mice compared with WT mice. A few proteins were assessed with Western blotting to compare mRNA expression with corresponding protein levels. Map1a mRNA and protein levels decreased. However, β-tubulin III and GAD1 protein levels were reduced in tau-KO mice. Cortical phosphoproteomics revealed 121 hypophosphorylated and 98 hyperphosphorylated proteins in tau-KO mice. Deregulated phosphoproteins were categorized into cytoskeletal (n = 45) and membrane proteins, including proteins of the synapses and vesicles, myelin proteins, and proteins linked to membrane transport and ion channels (n = 84), proteins related to DNA and RNA metabolism (n = 36), proteins connected to the ubiquitin-proteasome system (UPS) (n = 7), proteins with kinase or phosphatase activity (n = 21), and 22 other proteins related to variegated pathways such as metabolic pathways, growth factors, or mitochondrial function or structure. The present observations reveal a complex altered brain transcriptome and phosphoproteome in tau-KO mice with only mild behavioral alterations.
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Affiliation(s)
- Pol Andrés-Benito
- Neurologic Diseases and Neurogenetics Group, Bellvitge Institute for Biomedical Research (IDIBELL), 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - África Flores
- Neuropharmacology & Pain Group, Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sara Busquet-Areny
- Neuropathology Group, Bellvitge Institute for Biomedical Research (IDIBELL), 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Margarita Carmona
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Neuropathology Group, Bellvitge Institute for Biomedical Research (IDIBELL), 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Karina Ausín
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, 31008 Pamplona, Navarra, Spain
| | - Paz Cartas-Cejudo
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, 31008 Pamplona, Navarra, Spain
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, 31008 Pamplona, Navarra, Spain
| | - José Antonio Del Rio
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Molecular and Cellular Neurobiotechnology Group, Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute for Science and Technology, Science Park Barcelona (PCB), 08028 Barcelona, Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, 31008 Pamplona, Navarra, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, 31008 Pamplona, Navarra, Spain
| | - Isidro Ferrer
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Neuropathology Group, Bellvitge Institute for Biomedical Research (IDIBELL), 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapeutics, University of Barcelona, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Emeritus Researcher, Bellvitge Biomedical Research Institute (IDIBELL), Emeritus Professor, University of Barcelona, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
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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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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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Rejeeth C, Sharma A. Label-free designed nanomaterials enrichment and separation techniques for phosphoproteomics based on mass spectrometry. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.1047055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The surface chemical characteristics of nanomaterials have a substantial impact on the affinity probe used to enrich proteins and peptides for MALDI-MS analysis of a real human sample. Detecting phosphoproteins involved in signalling is always difficult, even with recent developments in mass spectrometry, because protein phosphorylation is often temporary from complicated mixtures. This review summarizes current research on the successful enrichment of various intriguing glycoproteins and glycol peptides using surface affinity materials with distinctive qualities such as low cost, excellent structural stability, diversity, and multifunction. As a consequence, this review will provide a quick overview of the scholars from various backgrounds who are working in this intriguing interdisciplinary field. Label-free cancer biomarkers and other diseases will benefit from future challenges.
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Ferrer I, Andrés-Benito P, Ausín K, Cartas-Cejudo P, Lachén-Montes M, Del Rio JA, Fernández-Irigoyen J, Santamaría E. Dysregulated Protein Phosphorylation in a Mouse Model of FTLD-Tau. J Neuropathol Exp Neurol 2022; 81:696-706. [PMID: 35848963 DOI: 10.1093/jnen/nlac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The neocortex of P301S mice, used as a model of fronto-temporal lobar degeneration linked to tau mutation (FTLD-tau), and wild-type mice, both aged 9 months, were analyzed with conventional label-free phosphoproteomics and SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry) to assess the (phospho)proteomes. The total number of identified dysregulated phosphoproteins was 328 corresponding to 524 phosphorylation sites. The majority of dysregulated phosphoproteins, most of them hyperphosphorylated, were proteins of the membranes, synapses, membrane trafficking, membrane vesicles linked to endo- and exocytosis, cytoplasmic vesicles, and cytoskeleton. Another group was composed of kinases. In contrast, proteins linked to DNA, RNA metabolism, RNA splicing, and protein synthesis were hypophosphorylated. Other pathways modulating energy metabolism, cell signaling, Golgi apparatus, carbohydrates, and lipids are also targets of dysregulated protein phosphorylation in P301S mice. The present results, together with accompanying immunohistochemical and Western-blotting studies, show widespread abnormal phosphorylation of proteins, in addition to protein tau, in P301S mice. These observations point to dysregulated protein phosphorylation as a relevant contributory pathogenic component of tauopathies.
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Affiliation(s)
- Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, Barcelona, Spain.,Bellvitge University Hospital/Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Pol Andrés-Benito
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, Barcelona, Spain.,Bellvitge University Hospital/Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Karina Ausín
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Paz Cartas-Cejudo
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain (PC-C, ML-M, ES)
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain (PC-C, ML-M, ES)
| | - José Antonio Del Rio
- Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute for Science and Technology, Science Park Barcelona (PCB), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain (PC-C, ML-M, ES)
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8
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Thompson EM, Patel V, Rajeeve V, Cutillas PR, Stoker AW. The cytotoxic action of BCI is not dependent on its stated DUSP1 or DUSP6 targets in neuroblastoma cells. FEBS Open Bio 2022; 12:1388-1405. [PMID: 35478300 PMCID: PMC9249316 DOI: 10.1002/2211-5463.13418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/04/2022] [Accepted: 04/26/2022] [Indexed: 12/04/2022] Open
Abstract
Neuroblastoma (NB) is a heterogeneous cancer of the sympathetic nervous system, which accounts for 7-10% of paediatric malignancies worldwide. Due to the lack of targetable molecular aberrations in NB, most treatment options remain relatively nonspecific. Here, we investigated the therapeutic potential of BCI, an inhibitor of DUSP1 and DUSP6, in cultured NB cells. BCI was cytotoxic in a range of NB cell lines and induced a short-lived activation of the AKT and stress-inducible MAP kinases, although ERK phosphorylation was unaffected. Furthermore, a phosphoproteomic screen identified significant upregulation of JNK signalling components and suppression in mTOR and R6K signalling. To assess the specificity of BCI, CRISPR-Cas9 was employed to introduce insertions and deletions in the DUSP1 and DUSP6 genes. Surprisingly, BCI remained fully cytotoxic in NB cells with complete loss of DUSP6 and partial depletion of DUSP1, suggesting that BCI exerts cytotoxicity in NB cells through a complex mechanism that is unrelated to these phosphatases. Overall, these data highlight the risk of using an inhibitor such as BCI as supposedly specific DUSP1/6, without understanding its full range of targets in cancer cells.
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Affiliation(s)
- Elliott M. Thompson
- Developmental Biology & Cancer Research and Teaching DepartmentUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Vruti Patel
- Developmental Biology & Cancer Research and Teaching DepartmentUCL Great Ormond Street Institute of Child HealthLondonUK
- Present address:
Current Address: Discovery Research MRL UKMSDThe London Bioscience Innovation Centre (LBIC)LondonUK
| | - Vinothini Rajeeve
- Mass Spectrometry LaboratoryBarts Cancer InstituteQueen Mary University of LondonUK
| | - Pedro R Cutillas
- Mass Spectrometry LaboratoryBarts Cancer InstituteQueen Mary University of LondonUK
| | - Andrew W. Stoker
- Developmental Biology & Cancer Research and Teaching DepartmentUCL Great Ormond Street Institute of Child HealthLondonUK
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Comprehensive Evaluation of Different TiO2-Based Phosphopeptide Enrichment and Fractionation Methods for Phosphoproteomics. Cells 2022; 11:cells11132047. [PMID: 35805136 PMCID: PMC9265536 DOI: 10.3390/cells11132047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Protein phosphorylation is an essential post-translational modification that regulates multiple cellular processes. Due to their low stoichiometry and ionization efficiency, it is critical to efficiently enrich phosphopeptides for phosphoproteomics. Several phosphopeptide enrichment methods have been reported; however, few studies have comprehensively compared different TiO2-based phosphopeptide enrichment methods using complex proteomic samples. Here, we compared four TiO2-based phosphopeptide enrichment methods that used four non-phosphopeptide excluders (glutamic acid, lactic acid, glycolic acid, and DHB). We found that these four TiO2-based phosphopeptide enrichment methods had different enrichment specificities and that phosphopeptides enriched by the four methods had different physicochemical characteristics. More importantly, we discovered that phosphopeptides had a higher deamidation ratio than peptides from cell lysate and that phosphopeptides enriched using the glutamic acid method had a higher deamidation ratio than the other three methods. We then compared two phosphopeptide fractionation methods: ammonia- or TEA-based high pH reversed-phase (HpH-RP). We found that fewer phosphopeptides, especially multi-phosphorylated peptides, were identified using the ammonia-based method than using the TEA-based method. Therefore, the TEA-based HpH-RP fractionation method performed better than the ammonia method. In conclusion, we comprehensively evaluated different TiO2-based phosphopeptide enrichment and fractionation methods, providing a basis for selecting the proper protocols for comprehensive phosphoproteomics.
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Dysregulated Brain Protein Phosphorylation Linked to Increased Human Tau Expression in the hTau Transgenic Mouse Model. Int J Mol Sci 2022; 23:ijms23126427. [PMID: 35742871 PMCID: PMC9223516 DOI: 10.3390/ijms23126427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Altered protein phosphorylation is a major pathologic modification in tauopathies and Alzheimer’s disease (AD) linked to abnormal tau fibrillar deposits in neurofibrillary tangles (NFTs) and pre-tangles and β-amyloid deposits in AD. hTau transgenic mice, which express 3R and less 4R human tau with no mutations in a murine knock-out background, show increased tau deposition in neurons but not NFTs and pre-tangles at the age of nine months. Label-free (phospho)proteomics and SWATH-MS identified 2065 proteins in hTau and wild-type (WT) mice. Only six proteins showed increased levels in hTau; no proteins were down-regulated. Increased tau phosphorylation in hTau was detected at Ser199, Ser202, Ser214, Ser396, Ser400, Thr403, Ser404, Ser413, Ser416, Ser422, Ser491, and Ser494, in addition to Thr181, Thr231, Ser396/Ser404, but not at Ser202/Thr205. In addition, 4578 phosphopeptides (corresponding to 1622 phosphoproteins) were identified in hTau and WT mice; 64 proteins were differentially phosphorylated in hTau. Sixty proteins were grouped into components of membranes, membrane signaling, synapses, vesicles, cytoskeleton, DNA/RNA/protein metabolism, ubiquitin/proteasome system, cholesterol and lipid metabolism, and cell signaling. These results showed that over-expression of human tau without pre-tangle and NFT formation preferentially triggers an imbalance in the phosphorylation profile of specific proteins involved in the cytoskeletal–membrane-signaling axis.
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Hijazi M, Casado P, Akhtar N, Alvarez-Teijeiro S, Rajeeve V, Cutillas PR. eEF2K Activity Determines Synergy to Cotreatment of Cancer Cells With PI3K and MEK Inhibitors. Mol Cell Proteomics 2022; 21:100240. [PMID: 35513296 PMCID: PMC9184568 DOI: 10.1016/j.mcpro.2022.100240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/17/2022] [Accepted: 04/25/2022] [Indexed: 10/31/2022] Open
Abstract
PI3K-mammalian target of rapamycin and MAPK/ERK kinase (MEK)/mitogen-activated protein kinase (MAPK) are the most frequently dysregulated signaling pathways in cancer. A problem that limits the success of therapies that target individual PI3K-MAPK members is that these pathways converge to regulate downstream functions and often compensate each other, leading to drug resistance and transient responses to therapy. In order to overcome resistance, therapies based on cotreatments with PI3K/AKT and MEK/MAPK inhibitors are now being investigated in clinical trials, but the mechanisms of sensitivity to cotreatment are not fully understood. Using LC-MS/MS-based phosphoproteomics, we found that eukaryotic elongation factor 2 kinase (eEF2K), a key convergence point downstream of MAPK and PI3K pathways, mediates synergism to cotreatment with trametinib plus pictilisib (which target MEK1/2 and PI3Kα/δ, respectively). Inhibition of eEF2K by siRNA or with a small molecule inhibitor reversed the antiproliferative effects of the cotreatment with PI3K plus MEK inhibitors in a cell model-specific manner. Systematic analysis in 12 acute myeloid leukemia cell lines revealed that eEF2K activity was increased in cells for which PI3K plus MEKi cotreatment is synergistic, while PKC potentially mediated resistance to such cotreatment. Together, our study uncovers eEF2K activity as a key mediator of responses to PI3Ki plus MEKi and as a potential biomarker to predict synergy to cotreatment in cancer cells.
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Affiliation(s)
- Maruan Hijazi
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
| | - Pedro Casado
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Nosheen Akhtar
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Saul Alvarez-Teijeiro
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Vinothini Rajeeve
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Pedro R Cutillas
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; The Alan Turing Institute, British Library, London, United Kingdom.
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12
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Pistorius K, Ly L, Souza PR, Gomez EA, Koenis DS, Rodriguez AR, Foster J, Sosabowski J, Hopkinson M, Rajeeve V, Spur BW, Pitsillides A, Pitzalis C, Dalli J. MCTR3 reprograms arthritic monocytes to upregulate Arginase-1 and exert pro-resolving and tissue-protective functions in experimental arthritis. EBioMedicine 2022; 79:103974. [PMID: 35430453 PMCID: PMC9038546 DOI: 10.1016/j.ebiom.2022.103974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a progressive degenerative disorder that leads to joint destruction. Available treatments only target the inflammatory component with minimal impact on joint repair. We recently uncovered a previously unappreciated family of pro-resolving mediators, the maresin conjugate in tissue regeneration (MCTR), that display both immunoregulatory and tissue-protective activities. Thus, we queried whether the production of these autacoids is disrupted in RA patients and whether they can be useful in treating joint inflammation and promoting joint repair. METHODS Using a highly phenotyped RA cohort we evaluated plasma MCTR concentrations and correlated these to clinical markers of disease activity. To evaluate the immunoregulatory and tissue reparative activities we employed both in vivo models of arthritis and organ culture models. FINDINGS Herein, we observed that plasma MCTR3 concentrations were negatively correlated with joint disease activity and severity in RA patients. Evaluation of the mechanisms engaged by this mediator in arthritic mice demonstrated that MCTR3 reprograms monocytes to confer enduring joint protective properties. Single cell transcriptomic profiling and flow cytometric evaluation of macrophages from mice treated with MCTR3-reprogrammed monocytes revealed a role for Arginase-1 (Arg-1) in mediating their joint reparative and pro-resolving activities. Arg-1 inhibition reversed both the anti-arthritic and tissue reparative actions of MCTR3-reprogrammed monocytes. INTERPRETATION Our findings demonstrate that circulating MCTR3 levels are negatively correlated with disease in RA. When administered to mice in vivo, MCTR3 displayed both anti-inflammatory and joint reparative activities, protecting both cartilage and bone in murine arthritis. These activities were, at least in part, mediated via the reprogramming of mononuclear phagocyte responses. FUNDING This work was supported by funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant no: 677542) and the Barts Charity (grant no: MGU0343) to J.D. J.D. is also supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant 107613/Z/15/Z).
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Affiliation(s)
- Kimberly Pistorius
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Lucy Ly
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Patricia R Souza
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Esteban A Gomez
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Duco S Koenis
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Ana R Rodriguez
- Rowan University School of Osteopathic Medicine, Department of Cell Biology & Neuroscience, 2 Medical Centre Drive, Stratford NJ 08084, USA
| | - Julie Foster
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Jane Sosabowski
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Mark Hopkinson
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Vinothini Rajeeve
- Mass spectrometry Laboratory, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, United Kingdom
| | - Bernd W Spur
- Rowan University School of Osteopathic Medicine, Department of Cell Biology & Neuroscience, 2 Medical Centre Drive, Stratford NJ 08084, USA
| | - Andrew Pitsillides
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Costantino Pitzalis
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Jesmond Dalli
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK; Centre for Inflammation and Therapeutic Innovation, Queen Mary University of London, London, UK.
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13
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Thongboonkerd V, Chaiyarit S. Gel-Based and Gel-Free Phosphoproteomics to Measure and Characterize Mitochondrial Phosphoproteins. Curr Protoc 2022; 2:e390. [PMID: 35275445 DOI: 10.1002/cpz1.390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mitochondrion is a key intracellular organelle regulating metabolic processes, oxidative stress, energy production, calcium homeostasis, and cell survival. Protein phosphorylation plays an important role in regulating mitochondrial functions and cellular signaling pathways. Dysregulation of protein phosphorylation status can cause protein malfunction and abnormal signal transduction, leading to organ dysfunction and disease. Investigating the mitochondrial phosphoproteins is therefore crucial to better understand the molecular and pathogenic mechanisms of many metabolic disorders. Conventional analyses of phosphoproteins, for instance, via western blotting, can be done only for proteins for which specific antibodies to their phosphorylated forms are available. Moreover, such an approach is not suitable for large-scale study of phosphoproteins. Currently, proteomics represents an important tool for large-scale analysis of proteins and their post-translational modifications, including phosphorylation. Here, we provide step-by-step protocols for the proteomics analysis of mitochondrial phosphoproteins (the phosphoproteome), using renal tubular cells as an example. These protocols include methods to effectively isolate mitochondria and to validate the efficacy of mitochondrial enrichment as well as its purity. We also provide detailed protocols for performing both gel-based and gel-free phosphoproteome analyses. The gel-based analysis involves two-dimensional gel electrophoresis and phosphoprotein-specific staining, followed by protein identification via mass spectrometry, whereas the gel-free approach is based on in-solution mass spectrometric identification of specific phosphorylation sites and residues. In all, these approaches allow large-scale analyses of mitochondrial phosphoproteins that can be applied to other cells and tissues of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Mitochondrial isolation/purification from renal tubular cells Support Protocol: Validation of enrichment efficacy and purity of mitochondrial isolation Basic Protocol 2: Gel-based phosphoproteome analysis Basic Protocol 3: Gel-free phosphoproteome analysis.
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Affiliation(s)
- Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sakdithep Chaiyarit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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14
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Synthesis of a metal oxide affinity chromatography magnetic mesoporous nanomaterial and development of a one-step selective phosphopeptide enrichment strategy for analysis of phosphorylated proteins. Anal Chim Acta 2022; 1195:339430. [DOI: 10.1016/j.aca.2022.339430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/05/2021] [Accepted: 01/01/2022] [Indexed: 11/23/2022]
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15
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Ryzhakov G, Almuttaqi H, Corbin AL, Berthold DL, Khoyratty T, Eames HL, Bullers S, Pearson C, Ai Z, Zec K, Bonham S, Fischer R, Jostins-Dean L, Travis SPL, Kessler BM, Udalova IA. Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation. Nat Commun 2021; 12:6702. [PMID: 34795257 PMCID: PMC8602323 DOI: 10.1038/s41467-021-27038-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Interferon regulating factor 5 (IRF5) is a multifunctional regulator of immune responses, and has a key pathogenic function in gut inflammation, but how IRF5 is modulated is still unclear. Having performed a kinase inhibitor library screening in macrophages, here we identify protein-tyrosine kinase 2-beta (PTK2B/PYK2) as a putative IRF5 kinase. PYK2-deficient macrophages display impaired endogenous IRF5 activation, leading to reduction of inflammatory gene expression. Meanwhile, a PYK2 inhibitor, defactinib, has a similar effect on IRF5 activation in vitro, and induces a transcriptomic signature in macrophages similar to that caused by IRF5 deficiency. Finally, defactinib reduces pro-inflammatory cytokines in human colon biopsies from patients with ulcerative colitis, as well as in a mouse colitis model. Our results thus implicate a function of PYK2 in regulating the inflammatory response in the gut via the IRF5 innate sensing pathway, thereby opening opportunities for related therapeutic interventions for inflammatory bowel diseases and other inflammatory conditions.
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Affiliation(s)
- Grigory Ryzhakov
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, Basel, Switzerland
| | - Hannah Almuttaqi
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Alastair L Corbin
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Dorothée L Berthold
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Tariq Khoyratty
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Hayley L Eames
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Samuel Bullers
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Claire Pearson
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Zhichao Ai
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Kristina Zec
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Luke Jostins-Dean
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Simon P L Travis
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Irina A Udalova
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom.
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16
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Khorsandi SE, Dokal AD, Rajeeve V, Britton DJ, Illingworth MS, Heaton N, Cutillas PR. Computational Analysis of Cholangiocarcinoma Phosphoproteomes Identifies Patient-Specific Drug Targets. Cancer Res 2021; 81:5765-5776. [PMID: 34551960 PMCID: PMC9397618 DOI: 10.1158/0008-5472.can-21-0955] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/11/2021] [Accepted: 09/20/2021] [Indexed: 01/07/2023]
Abstract
Cholangiocarcinoma is a form of hepatobiliary cancer with an abysmal prognosis. Despite advances in our understanding of cholangiocarcinoma pathophysiology and its genomic landscape, targeted therapies have not yet made a significant impact on its clinical management. The low response rates of targeted therapies in cholangiocarcinoma suggest that patient heterogeneity contributes to poor clinical outcome. Here we used mass spectrometry-based phosphoproteomics and computational methods to identify patient-specific drug targets in patient tumors and cholangiocarcinoma-derived cell lines. We analyzed 13 primary tumors of patients with cholangiocarcinoma with matched nonmalignant tissue and 7 different cholangiocarcinoma cell lines, leading to the identification and quantification of more than 13,000 phosphorylation sites. The phosphoproteomes of cholangiocarcinoma cell lines and patient tumors were significantly correlated. MEK1, KIT, ERK1/2, and several cyclin-dependent kinases were among the protein kinases most frequently showing increased activity in cholangiocarcinoma relative to nonmalignant tissue. Application of the Drug Ranking Using Machine Learning (DRUML) algorithm selected inhibitors of histone deacetylase (HDAC; belinostat and CAY10603) and PI3K pathway members as high-ranking therapies to use in primary cholangiocarcinoma. The accuracy of the computational drug rankings based on predicted responses was confirmed in cell-line models of cholangiocarcinoma. Together, this study uncovers frequently activated biochemical pathways in cholangiocarcinoma and provides a proof of concept for the application of computational methodology to rank drugs based on efficacy in individual patients. SIGNIFICANCE: Phosphoproteomic and computational analyses identify patient-specific drug targets in cholangiocarcinoma, supporting the potential of a machine learning method to predict personalized therapies.
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Affiliation(s)
- Shirin Elizabeth Khorsandi
- Institute of Liver Studies, Kings College Hospital, London, United Kingdom.,The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, United Kingdom.,Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom.,Corresponding Authors: Pedro R. Cutillas, Cell Signaling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom. Phone: 207-882-5555; E-mail: ; and Shirin Elizabeth Khorsandi, The Roger Williams Institute of Hepatology, 111 Coldharbor Lane, London SE5 9NT, United Kingdom. E-mail:
| | - Arran D. Dokal
- Cell Signaling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Mass Spectrometry Laboratory, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Kinomica Ltd, Cheshire, United Kingdom
| | - Vinothini Rajeeve
- Cell Signaling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Mass Spectrometry Laboratory, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - David J. Britton
- Cell Signaling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Mass Spectrometry Laboratory, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Kinomica Ltd, Cheshire, United Kingdom
| | - Megan S. Illingworth
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, United Kingdom.,Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Nigel Heaton
- Institute of Liver Studies, Kings College Hospital, London, United Kingdom
| | - Pedro R. Cutillas
- Cell Signaling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Mass Spectrometry Laboratory, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Kinomica Ltd, Cheshire, United Kingdom.,The Alan Turing Institute, The British Library, London, United Kingdom.,Corresponding Authors: Pedro R. Cutillas, Cell Signaling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom. Phone: 207-882-5555; E-mail: ; and Shirin Elizabeth Khorsandi, The Roger Williams Institute of Hepatology, 111 Coldharbor Lane, London SE5 9NT, United Kingdom. E-mail:
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17
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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: 44] [Impact Index Per Article: 14.7] [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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18
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Ferrer I, Andrés-Benito P, Ausín K, Pamplona R, Del Rio JA, Fernández-Irigoyen J, Santamaría E. Dysregulated protein phosphorylation: A determining condition in the continuum of brain aging and Alzheimer's disease. Brain Pathol 2021; 31:e12996. [PMID: 34218486 PMCID: PMC8549032 DOI: 10.1111/bpa.12996] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 01/09/2023] Open
Abstract
Tau hyperphosphorylation is the first step of neurofibrillary tangle (NFT) formation. In the present study, samples of the entorhinal cortex (EC) and frontal cortex area 8 (FC) of cases with NFT pathology classified as stages I-II, III-IV, and V-VI without comorbidities, and of middle-aged (MA) individuals with no NFT pathology, were analyzed by conventional label-free and SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry) to assess the (phospho)proteomes. The total number of identified dysregulated phosphoproteins was 214 in the EC, 65 of which were dysregulated at the first stages (I-II) of NFT pathology; 167 phosphoproteins were dysregulated in the FC, 81 of them at stages I-II of NFT pathology. A large percentage of dysregulated phosphoproteins were identified in the two regions and at different stages of NFT progression. The main group of dysregulated phosphoproteins was made up of components of the membranes, cytoskeleton, synapses, proteins linked to membrane transport and ion channels, and kinases. The present results show abnormal phosphorylation of proteins at the first stages of NFT pathology in the elderly (in individuals clinically considered representative of normal aging) and sporadic Alzheimer's disease (sAD). Dysregulated protein phosphorylation in the FC precedes the formation of NFTs and SPs. The most active period of dysregulated phosphorylation is at stages III-IV when a subpopulation of individuals might be clinically categorized as suffering from mild cognitive impairment which is a preceding determinant stage in the progression to dementia. Altered phosphorylation of selected proteins, carried out by activation of several kinases, may alter membrane and cytoskeletal functions, among them synaptic transmission and membrane/cytoskeleton signaling. Besides their implications in sAD, the present observations suggest a molecular substrate for "benign" cognitive deterioration in "normal" brain aging.
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Affiliation(s)
- Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, Hospitalet de Llobregat, Spain.,Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL, Hospitalet de Llobregat, Spain
| | - Pol Andrés-Benito
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, Hospitalet de Llobregat, Spain.,Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL, Hospitalet de Llobregat, Spain
| | - Karina Ausín
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA, IdiSNA, Pamplona, Spain
| | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida, Lleida, Spain
| | - José Antonio Del Rio
- Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute for Science and Technology, Science Park Barcelona (PCB, Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA, IdiSNA, Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA, IdiSNA, Pamplona, Spain
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19
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Quantitative Phosphoproteomic Comparison of Lens Proteins in Highly Myopic Cataract and Age-Related Cataract. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6668845. [PMID: 34055996 PMCID: PMC8130905 DOI: 10.1155/2021/6668845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/23/2021] [Accepted: 04/02/2021] [Indexed: 11/17/2022]
Abstract
Purpose To investigate and compare the lens phosphoproteomes in patients with highly myopic cataract (HMC) or age-related cataract (ARC). Methods In this study, we undertook a comparative phosphoproteome analysis of the lenses from patients with HMC or ARC. Intact lenses from ARC and HMC patients were separated into the cortex and nucleus. After protein digestion, the phosphopeptides were quantitatively analyzed with TiO2 enrichment and liquid chromatography-mass spectrometry. The potential functions of different phosphopeptides were assessed by Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Results In total, 522 phosphorylation sites in 164 phosphoproteins were identified. The number of phosphorylation sites was significantly higher in the cortex than in the nucleus, in both ARC and HMC lenses. The differentially phosphorylated peptides in the lens cortex and nucleus in HMC eyes were significantly involved in the glutathione metabolism pathway. The KEGG pathway enrichment analysis indicated that the differences in phosphosignaling mediators between the ARC and HMC lenses were associated with glycolysis and the level of phosphorylated phosphoglycerate kinase 1 was lower in HMC lenses than in ARC lenses. Conclusions We provide an overview of the differential phosphoproteomes of HMC and ARC lenses that can be used to clarify the molecular mechanisms underlying their different phenotypes.
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20
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Song B, Liu D, Greco TM, Cristea IM. Post-translational modification control of viral DNA sensors and innate immune signaling. Adv Virus Res 2021; 109:163-199. [PMID: 33934827 PMCID: PMC8489191 DOI: 10.1016/bs.aivir.2021.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The vertebrate innate immune system confers host cells with mechanisms to protect against both evolutionarily ancient pathogens and newly emerging pathogenic strains. Innate immunity relies on the host cell's ability to distinguish between self and pathogen-derived molecules. To achieve this, the innate immune system uses germline encoded receptors called pattern recognition receptors (PRRs), which recognize various molecular signatures, including nucleic acids, proteins, lipids, glycans and glycolipids. Among these molecules, the recognition of pathogenic, mislocalized, or damaged DNA by cellular protein receptors, commonly called DNA sensors, represents a major surveillance pathway for initiating immune signaling. The ability of cells to temporally regulate DNA sensor activation and subsequent signal termination is critical for effective immune signaling. These same mechanisms are also co-opted by pathogens to promote their replication. Therefore, there is significant interest in understanding DNA sensor regulatory networks during microbial infections and autoimmune disease. One emerging aspect of DNA sensor regulation is through post-translational modifications (PTMs), including phosphorylation, acetylation, ubiquitination, ADP-ribosylation, SUMOylation, methylation, deamidation, glutamylation. In this chapter, we discuss how PTMs have been shown to positively or negatively impact DNA sensor functions via diverse mechanisms, including direct regulation of enzymatic activity, protein-protein and protein-DNA interactions, protein translocations and protein turnover. In addition, we highlight the ability of virus-induced PTMs to promote immune evasion. We also discuss the recent evidence linking PTMs on DNA sensors with human diseases and more broadly, highlight promising directions for future research on PTM-mediated regulation of DNA sensor-dependent immune signaling.
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Affiliation(s)
- Bokai Song
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Dawei Liu
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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21
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Gerdes H, Casado P, Dokal A, Hijazi M, Akhtar N, Osuntola R, Rajeeve V, Fitzgibbon J, Travers J, Britton D, Khorsandi S, Cutillas PR. Drug ranking using machine learning systematically predicts the efficacy of anti-cancer drugs. Nat Commun 2021; 12:1850. [PMID: 33767176 PMCID: PMC7994645 DOI: 10.1038/s41467-021-22170-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Artificial intelligence and machine learning (ML) promise to transform cancer therapies by accurately predicting the most appropriate therapies to treat individual patients. Here, we present an approach, named Drug Ranking Using ML (DRUML), which uses omics data to produce ordered lists of >400 drugs based on their anti-proliferative efficacy in cancer cells. To reduce noise and increase predictive robustness, instead of individual features, DRUML uses internally normalized distance metrics of drug response as features for ML model generation. DRUML is trained using in-house proteomics and phosphoproteomics data derived from 48 cell lines, and it is verified with data comprised of 53 cellular models from 12 independent laboratories. We show that DRUML predicts drug responses in independent verification datasets with low error (mean squared error < 0.1 and mean Spearman's rank 0.7). In addition, we demonstrate that DRUML predictions of cytarabine sensitivity in clinical leukemia samples are prognostic of patient survival (Log rank p < 0.005). Our results indicate that DRUML accurately ranks anti-cancer drugs by their efficacy across a wide range of pathologies.
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Affiliation(s)
- Henry Gerdes
- Cell Signalling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Pedro Casado
- Cell Signalling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Arran Dokal
- Cell Signalling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
- Kinomica Ltd, Alderley Park, Alderley Edge, Macclesfield, UK
| | - Maruan Hijazi
- Cell Signalling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Nosheen Akhtar
- Cell Signalling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Ruth Osuntola
- Mass spectrometry Laboratory, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Vinothini Rajeeve
- Mass spectrometry Laboratory, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Jude Fitzgibbon
- Personalised Medicine Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Jon Travers
- Astra Zeneca Ltd, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - David Britton
- Cell Signalling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
- Kinomica Ltd, Alderley Park, Alderley Edge, Macclesfield, UK
| | | | - Pedro R Cutillas
- Cell Signalling & Proteomics Group, Centre for Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK.
- Mass spectrometry Laboratory, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK.
- The Alan Turing Institute, The British Library, 2QR, London, UK.
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22
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Abstract
Phosphopeptide enrichment is a commonly used sample preparation step for investigating phosphorylation. TiO2-based enrichment has been demonstrated to have excellent performance both for large amounts of complex and for small amounts of simple samples. However, it has not yet been studied for complex samples in the nanogram range. Our objective was to develop a methodology applicable for complex samples in the low nanogram range, useful for mass spectrometry analysis of tissue microarrays. The selectivity and performance of two stationary phases (TiO2 nanoparticle-coated monolithic column and spin tip filled with TiO2 microspheres) and several loading solvents were studied. Based on this study, we developed an effective and robust method, based on a spin tip with a non-conventional 50 mM citric acid-based loading solvent. It gave excellent results for phosphopeptide enrichment from samples containing a few nanograms of a complex protein mixture.
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23
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Robinson AE, Binek A, Venkatraman V, Searle BC, Holewinski RJ, Rosenberger G, Parker SJ, Basisty N, Xie X, Lund PJ, Saxena G, Mato JM, Garcia BA, Schilling B, Lu SC, Van Eyk JE. Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease. J Proteome Res 2020; 19:4163-4178. [PMID: 32966080 DOI: 10.1021/acs.jproteome.0c00685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Proteoforms containing post-translational modifications (PTMs) represent a degree of functional diversity only harnessed through analytically precise simultaneous quantification of multiple PTMs. Here we present a method to accurately differentiate an unmodified peptide from its PTM-containing counterpart through data-independent acquisition-mass spectrometry, leveraging small precursor mass windows to physically separate modified peptidoforms from each other during MS2 acquisition. We utilize a lysine and arginine PTM-enriched peptide assay library and site localization algorithm to simultaneously localize and quantify seven PTMs including mono-, di-, and trimethylation, acetylation, and succinylation in addition to total protein quantification in a single MS run without the need to enrich experimental samples. To evaluate biological relevance, this method was applied to liver lysate from differentially methylated nonalcoholic steatohepatitis (NASH) mouse models. We report that altered methylation and acetylation together with total protein changes drive the novel hypothesis of a regulatory function of PTMs in protein synthesis and mRNA stability in NASH.
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Affiliation(s)
- Aaron E Robinson
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandra Binek
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Vidya Venkatraman
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Brian C Searle
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Ronald J Holewinski
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - George Rosenberger
- Department of Systems Biology, Columbia University, New York, New York 10027, United States
| | - Sarah J Parker
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Xueshu Xie
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Peder J Lund
- Department of Biochemistry and Biophysics, Epigenetics Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | | | - José M Mato
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Epigenetics Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Shelly C Lu
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
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24
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Zeneyedpour L, Stingl C, Dekker LJM, Mustafa DAM, Kros JM, Luider TM. Phosphorylation Ratio Determination in Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Tissue with Targeted Mass Spectrometry. J Proteome Res 2020; 19:4179-4190. [PMID: 32811146 DOI: 10.1021/acs.jproteome.0c00354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are routinely prepared and collected for diagnostics in pathology departments. These are, therefore, the most accessible research sources in pathology archives. In this study we investigated whether we can apply a targeted and quantitative parallel reaction monitoring (PRM) method for FFPE tissue samples in a sensitive and reproducible way. The feasibility of this technical approach was demonstrated for normal brain and glioblastoma multiforme tissues. Two methods were used: PRM measurement of a tryptic digest without phosphopeptide enrichment (Direct-PRM) and after Fe-NTA phosphopeptide enrichment (Fe-NTA-PRM). With these two methods, the phosphorylation ratio could be determined for four selected peptide pairs that originate from neuroblast differentiation-associated protein (AHNAK S5448-p), calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D T337-p), eukaryotic translation initiation factor 4B (EIF4B S93-p), and epidermal growth factor receptor (EGFR S1166-p). In normal brain FFPE tissues, the Fe-NTA-PRM method enabled the quantification of targeted phosphorylated peptides with high reproducibility (CV < 14%). Our results indicate that formalin fixation does not impede relative quantification of a phospho-site and its phosphorylation ratio in FFPE tissues. The developed workflow combining these methods opens ways to study archival FFPE tissues for phosphorylation ratio determination in proteins.
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Affiliation(s)
- Lona Zeneyedpour
- Department of Neurology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Christoph Stingl
- Department of Neurology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | | | - Dana A M Mustafa
- Department of Pathology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
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25
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Kostaras E, Kaserer T, Lazaro G, Heuss SF, Hussain A, Casado P, Hayes A, Yandim C, Palaskas N, Yu Y, Schwartz B, Raynaud F, Chung YL, Cutillas PR, Vivanco I. A systematic molecular and pharmacologic evaluation of AKT inhibitors reveals new insight into their biological activity. Br J Cancer 2020; 123:542-555. [PMID: 32439931 PMCID: PMC7435276 DOI: 10.1038/s41416-020-0889-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 04/07/2020] [Accepted: 04/24/2020] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND AKT, a critical effector of the phosphoinositide 3-kinase (PI3K) signalling cascade, is an intensely pursued therapeutic target in oncology. Two distinct classes of AKT inhibitors have been in clinical development, ATP-competitive and allosteric. Class-specific differences in drug activity are likely the result of differential structural and conformational requirements governing efficient target binding, which ultimately determine isoform-specific potency, selectivity profiles and activity against clinically relevant AKT mutant variants. METHODS We have carried out a systematic evaluation of clinical AKT inhibitors using in vitro pharmacology, molecular profiling and biochemical assays together with structural modelling to better understand the context of drug-specific and drug-class-specific cell-killing activity. RESULTS Our data demonstrate clear differences between ATP-competitive and allosteric AKT inhibitors, including differential effects on non-catalytic activity as measured by a novel functional readout. Surprisingly, we found that some mutations can cause drug resistance in an isoform-selective manner despite high structural conservation across AKT isoforms. Finally, we have derived drug-class-specific phosphoproteomic signatures and used them to identify effective drug combinations. CONCLUSIONS These findings illustrate the utility of individual AKT inhibitors, both as drugs and as chemical probes, and the benefit of AKT inhibitor pharmacological diversity in providing a repertoire of context-specific therapeutic options.
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Affiliation(s)
- Eleftherios Kostaras
- Division of Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG, London, UK
| | - Teresa Kaserer
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, SW7 3RP, UK
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, A-6020, Austria
| | - Glorianne Lazaro
- Division of Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG, London, UK
| | - Sara Farrah Heuss
- Division of Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG, London, UK
| | - Aasia Hussain
- Division of Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG, London, UK
| | - Pedro Casado
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Angela Hayes
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Cihangir Yandim
- Division of Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG, London, UK
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, 35330, Balçova, Izmir, Turkey
| | - Nicolaos Palaskas
- Division of Hematology and Oncology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Yi Yu
- ArQule, Inc. (a wholly-owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA), Burlington, MA, 01803, USA
| | - Brian Schwartz
- ArQule, Inc. (a wholly-owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA), Burlington, MA, 01803, USA
| | - Florence Raynaud
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Yuen-Li Chung
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research London and Royal Marsden Hospital, London, SW7 3RP, UK
| | - Pedro R Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Igor Vivanco
- Division of Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG, London, UK.
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26
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Wong PP, Muñoz-Félix JM, Hijazi M, Kim H, Robinson SD, De Luxán-Delgado B, Rodríguez-Hernández I, Maiques O, Meng YM, Meng Q, Bodrug N, Dukinfield MS, Reynolds LE, Elia G, Clear A, Harwood C, Wang Y, Campbell JJ, Singh R, Zhang P, Schall TJ, Matchett KP, Henderson NC, Szlosarek PW, Dreger SA, Smith S, Jones JL, Gribben JG, Cutillas PR, Meier P, Sanz-Moreno V, Hodivala-Dilke KM. Cancer Burden Is Controlled by Mural Cell-β3-Integrin Regulated Crosstalk with Tumor Cells. Cell 2020; 181:1346-1363.e21. [PMID: 32473126 DOI: 10.1016/j.cell.2020.02.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/21/2019] [Accepted: 01/31/2020] [Indexed: 02/07/2023]
Abstract
Enhanced blood vessel (BV) formation is thought to drive tumor growth through elevated nutrient delivery. However, this observation has overlooked potential roles for mural cells in directly affecting tumor growth independent of BV function. Here we provide clinical data correlating high percentages of mural-β3-integrin-negative tumor BVs with increased tumor sizes but no effect on BV numbers. Mural-β3-integrin loss also enhances tumor growth in implanted and autochthonous mouse tumor models with no detectable effects on BV numbers or function. At a molecular level, mural-cell β3-integrin loss enhances signaling via FAK-p-HGFR-p-Akt-p-p65, driving CXCL1, CCL2, and TIMP-1 production. In particular, mural-cell-derived CCL2 stimulates tumor cell MEK1-ERK1/2-ROCK2-dependent signaling and enhances tumor cell survival and tumor growth. Overall, our data indicate that mural cells can control tumor growth via paracrine signals regulated by β3-integrin, providing a previously unrecognized mechanism of cancer growth control.
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Affiliation(s)
- Ping-Pui Wong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.
| | - José M Muñoz-Félix
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.
| | - Maruan Hijazi
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Hyojin Kim
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, Mary-Jean Mitchell Green Building, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
| | - Stephen D Robinson
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Beatriz De Luxán-Delgado
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Irene Rodríguez-Hernández
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Oscar Maiques
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Ya-Ming Meng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Qiong Meng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Natalia Bodrug
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Matthew Scott Dukinfield
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Louise E Reynolds
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - George Elia
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Andrew Clear
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Catherine Harwood
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Yu Wang
- ChemoCentryx Inc., 850 Maude Ave., Mountain View, CA 94043, USA
| | | | - Rajinder Singh
- ChemoCentryx Inc., 850 Maude Ave., Mountain View, CA 94043, USA
| | - Penglie Zhang
- ChemoCentryx Inc., 850 Maude Ave., Mountain View, CA 94043, USA
| | - Thomas J Schall
- ChemoCentryx Inc., 850 Maude Ave., Mountain View, CA 94043, USA
| | - Kylie P Matchett
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Peter W Szlosarek
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Sally A Dreger
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Sally Smith
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - J Louise Jones
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - John G Gribben
- 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
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, Mary-Jean Mitchell Green Building, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
| | - Victoria Sanz-Moreno
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Kairbaan M Hodivala-Dilke
- Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.
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27
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Venkadakrishnan VB, Ben-Salem S, Heemers HV. AR-dependent phosphorylation and phospho-proteome targets in prostate cancer. Endocr Relat Cancer 2020; 27:R193-R210. [PMID: 32276264 PMCID: PMC7583603 DOI: 10.1530/erc-20-0048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/17/2022]
Abstract
Prostate cancer (CaP) is the second leading cause of cancer-related deaths in Western men. Because androgens drive CaP by activating the androgen receptor (AR), blocking AR's ligand activation, known as androgen deprivation therapy (ADT), is the default treatment for metastatic CaP. Despite an initial remission, CaP eventually develops resistance to ADT and progresses to castration-recurrent CaP (CRPC). CRPC continues to rely on aberrantly activated AR that is no longer inhibited effectively by available therapeutics. Interference with signaling pathways downstream of activated AR that mediate aggressive CRPC behavior may lead to alternative CaP treatments. Developing such therapeutic strategies requires a thorough mechanistic understanding of the most clinically relevant and druggable AR-dependent signaling events. Recent proteomics analyses of CRPC clinical specimens indicate a shift in the phosphoproteome during CaP progression. Kinases and phosphatases represent druggable entities, for which clinically tested inhibitors are available, some of which are incorporated already in treatment plans for other human malignancies. Here, we reviewed the AR-associated transcriptome and translational regulon, and AR interactome involved in CaP phosphorylation events. Novel and for the most part mutually exclusive AR-dependent transcriptional and post-transcriptional control over kinase and phosphatase expression was found, with yet other phospho-regulators interacting with AR. The multiple mechanisms by which AR can shape and fine-tune the CaP phosphoproteome were reflected in diverse aspects of CaP biology such as cell cycle progression and cell migration. Furthermore, we examined the potential, limitations and challenges of interfering with AR-mediated phosphorylation events as alternative strategy to block AR function during CaP progression.
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Affiliation(s)
- Varadha Balaji Venkadakrishnan
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
| | - Salma Ben-Salem
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
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28
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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: 53] [Impact Index Per Article: 13.3] [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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29
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Matthiesen R, Carvalho AS. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry. Methods Mol Biol 2020; 2051:161-197. [PMID: 31552629 DOI: 10.1007/978-1-4939-9744-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.
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Affiliation(s)
- Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal.
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30
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Li B, Guo F, Hu H, Liu P, Tan M, Pan J, Zhai L. The characterization of column heating effect in nanoflow liquid chromatography mass spectrometry (nanoLC-MS)-based proteomics. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4441. [PMID: 31840882 DOI: 10.1002/jms.4441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 09/06/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Column heating strategy is often applied in nano-high-performance liquid chromatography-mass spectrometer (nanoHPLC-MS) platform for enhancing the analytical efficiency of peptides or proteins. Nonetheless, the influence effects of column heating in peptides or proteins identification still lack of deep understanding. In this study, a systematic comparison of room temperature (RT) and column heating of nanoHPLC was done. Based on the data, under column heating condition, the backpressure of nanoHPLC can be decreased. Due to the increase of resolution, the peak widths of precursor ion were narrowed. As a result, in MS/MS data acquisition part, more time was spared for MS1 detecting and MS2 fragmenting, which eventually resulted in increased identification of peptides and proteins. Moreover, we also proposed the application scope of column heating by evaluating its influence on sample detection. On one hand, column heating significantly increased the identification of membrane proteins due to more efficient elution of highly hydrophobic peptides compared with RT. On the other hand, heating was not suitable for analyzing short or/and hydrophilic peptides with low retention time, which would be eluted out during sample loading process under high temperature and missed by mass spectrometric detection. In conclusion, our study provides a reference for rational application of column heating in proteomics research.
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Affiliation(s)
- Bolin Li
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Fang Guo
- Shanghai Easymass Co., Ltd., Shanghai, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ping Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jianyi Pan
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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31
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Cao L, Zhao Y, Chu Z, Zhang X, Zhang W. Core-shell magnetic bimetallic MOF material for synergistic enrichment of phosphopeptides. Talanta 2020; 206:120165. [DOI: 10.1016/j.talanta.2019.120165] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 02/07/2023]
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32
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Andaluz Aguilar H, Iliuk AB, Chen IH, Tao WA. Sequential phosphoproteomics and N-glycoproteomics of plasma-derived extracellular vesicles. Nat Protoc 2019; 15:161-180. [PMID: 31863077 DOI: 10.1038/s41596-019-0260-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/16/2019] [Indexed: 12/22/2022]
Abstract
Extracellular vesicles (EVs) are increasingly being recognized as important vehicles for intercellular communication and as promising sources for biomarker discovery. Because the state of protein post-translational modifications (PTMs) such as phosphorylation and glycosylation can be a key determinant of cellular physiology, comprehensive characterization of protein PTMs in EVs can be particularly valuable for early-stage diagnostics and monitoring of disease status. However, the analysis of PTMs in EVs has been complicated by limited amounts of purified EVs, low-abundance PTM proteins, and interference from proteins and metabolites in biofluids. Recently, we developed an approach to isolate phosphoproteins and glycoproteins in EVs from small volumes of human plasma that enabled us to identify nearly 10,000 unique phosphopeptides and 1,500 unique N-glycopeptides. The approach demonstrated the feasibility of using these data to identify potential markers to differentiate disease from healthy states. Here we present an updated workflow to sequentially isolate phosphopeptides and N-glycopeptides, enabling multiple PTM analyses of the same clinical samples. In this updated workflow, we have improved the reproducibility and efficiency of EV isolation, protein extraction, and phosphopeptide/N-glycopeptide enrichment to achieve sensitive analyses of low-abundance PTMs in EVs isolated from 1 mL of plasma. The modularity of the workflow also allows for the characterization of phospho- or glycopeptides only and enables additional analysis of total proteomes and other PTMs of interest. After blood collection, the protocol takes 2 d, including EV isolation, PTM/peptide enrichment, mass spectrometry analysis, and data quantification.
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Affiliation(s)
| | - Anton B Iliuk
- Tymora Analytical Operations, West Lafayette, IN, USA.,Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - I-Hsuan Chen
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - W Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA. .,Tymora Analytical Operations, West Lafayette, IN, USA. .,Department of Biochemistry, Purdue University, West Lafayette, IN, USA. .,Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA.
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33
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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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34
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Ndika J, Seemab U, Poon WL, Fortino V, El-Nezami H, Karisola P, Alenius H. Silver, titanium dioxide, and zinc oxide nanoparticles trigger miRNA/isomiR expression changes in THP-1 cells that are proportional to their health hazard potential. Nanotoxicology 2019; 13:1380-1395. [PMID: 31519129 DOI: 10.1080/17435390.2019.1661040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
After over a decade of nanosafety research, it is indisputable that the vast majority of nano-sized particles induce a plethora of adverse cellular responses - the severity of which is linked to the material's physicochemical properties. Differentiated THP-1 cells were previously exposed for 6 h and 24 h to silver, titanium dioxide, and zinc oxide nanoparticles at the maximum molar concentration at which no more than 15% cellular cytotoxicity was observed. All three nanoparticles differed in extent of induction of biological pathways corresponding to immune response signaling and metal ion homeostasis. In this study, we integrated gene and miRNA expression profiles from the same cells to propose miRNA biomarkers of adverse exposure to metal-based nanoparticles. We employed RNA sequencing together with a quantitative strategy that also enables analysis of the overlooked repertoire of length and sequence miRNA variants called isomiRs. Whilst only modest changes in expression were observed within the first 6 h of exposure, the miRNA/isomiR (miR) profiles of each nanoparticle were unique. Via canonical correlation and pathway enrichment analyses, we identified a co-regulated miR-mRNA cluster, predicted to be highly relevant for cellular response to metal ion homeostasis. These miRs were annotated to be canonical or variant isoforms of hsa-miR-142-5p, -342-3p, -5100, -6087, -6894-3p, and -7704. Hsa-miR-5100 was differentially expressed in response to each nanoparticle in both the 6 h and 24 h exposures. Taken together, this co-regulated miR-mRNA cluster could represent potential biomarkers of sub-toxic metal-based nanoparticle exposure.
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Affiliation(s)
- Joseph Ndika
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Umair Seemab
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Wing-Lam Poon
- School of Biological Sciences, the University of Hong Kong, Hong Kong, Hong Kong
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Hani El-Nezami
- School of Biological Sciences, the University of Hong Kong, Hong Kong, Hong Kong.,Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Piia Karisola
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Harri Alenius
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Institute of Environmental Medicine (IMM), Karolinska Institutet, Stockholm, Sweden
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35
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Chatzifrangkeskou M, Pefani D, Eyres M, Vendrell I, Fischer R, Pankova D, O'Neill E. RASSF1A is required for the maintenance of nuclear actin levels. EMBO J 2019; 38:e101168. [PMID: 31414556 PMCID: PMC6694222 DOI: 10.15252/embj.2018101168] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/23/2019] [Accepted: 05/14/2019] [Indexed: 01/19/2023] Open
Abstract
Nuclear actin participates in many essential cellular processes including gene transcription, chromatin remodelling and mRNA processing. Actin shuttles into and out the nucleus through the action of dedicated transport receptors importin-9 and exportin-6, but how this transport is regulated remains unclear. Here, we show that RASSF1A is a novel regulator of actin nucleocytoplasmic trafficking and is required for the active maintenance of nuclear actin levels through supporting binding of exportin-6 (XPO6) to RAN GTPase. RASSF1A (Ras association domain family 1 isoform A) is a tumour suppressor gene frequently silenced by promoter hypermethylation in all major solid cancers. Specifically, we demonstrate that endogenous RASSF1A localises to the nuclear envelope (NE) and is required for nucleocytoplasmic actin transport and the concomitant regulation of myocardin-related transcription factor A (MRTF-A), a co-activator of the transcription factor serum response factor (SRF). The RASSF1A/RAN/XPO6/nuclear actin pathway is aberrant in cancer cells where RASSF1A expression is lost and correlates with reduced MRTF-A/SRF activity leading to cell adhesion defects. Taken together, we have identified a previously unknown mechanism by which the nuclear actin pool is regulated and uncovered a previously unknown link of RASSF1A and MRTF-A/SRF in tumour suppression.
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Affiliation(s)
| | - Dafni‐Eleftheria Pefani
- Department of OncologyUniversity of OxfordOxfordUK
- Laboratory of BiologyMedical SchoolNational and Kapodistrian University of AthensAthensGreece
- Biomedical Research Foundation of the Academy of AthensAthensGreece
| | | | - Iolanda Vendrell
- Department of OncologyUniversity of OxfordOxfordUK
- Nuffield Department of MedicineTarget Discovery InstituteUniversity of OxfordOxfordUK
| | - Roman Fischer
- Nuffield Department of MedicineTarget Discovery InstituteUniversity of OxfordOxfordUK
| | | | - Eric O'Neill
- Department of OncologyUniversity of OxfordOxfordUK
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36
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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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37
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Dziomba S, Pawelec A, Ciura K, Dolegowska M, Klimowska A, Rodzaj W, Guerrouache M, Carbonnier B, Wielgomas B. Low-cost and green dispersive solid phase extraction of hydrophilic compounds using titanium dioxide nanoparticles. Microchem J 2019. [DOI: 10.1016/j.microc.2018.11.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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38
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Ippoushi K, Wakagi M, Hashimoto N, Takano-Ishikawa Y. Absolute quantification of the α, α', and β subunits of β-conglycinin from soybeans by liquid chromatography/tandem mass spectrometry using stable isotope-labelled peptides. Food Res Int 2019; 116:1223-1228. [PMID: 30716909 DOI: 10.1016/j.foodres.2018.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 09/26/2018] [Accepted: 10/02/2018] [Indexed: 01/21/2023]
Abstract
β-Conglycinin, a major protein in soybeans, shows improvement effect of lipid metabolism. Moreover, this protein influences the processing properties of soybeans. β-Conglycinin is a hetero-trimer constituted by α, α', and β subunits. In this work, a method for the selective quantification of these subunits was developed by means of protein absolute quantification (AQUA) technology using liquid chromatography/tandem mass spectrometry with the stable isotope-labelled internal standard peptides LQSGDALR[13C6,15N4], NILEASYDTK[13C6,15N2], and NPIYSNNFGK[13C6,15N2]. This method exhibited linear relationships (r2 > 0.99) in the concentration range of 1.2-300 fmol/μL for LQSGDALR[13C6,15N4] and NILEASYDTK[13C6,15N2], and of 4.7-300 fmol/μL for NPIYSNNFGK[13C6,15N2]. As a result, the content of these subunits in β-conglycinin-rich and both α and α' subunit-deficient soybean cultivars was successfully determined. This quantitative assay is promising for the evaluation of the food functionality and processing properties of soybeans.
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Affiliation(s)
- Katsunari Ippoushi
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
| | - Manabu Wakagi
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Naoto Hashimoto
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Yuko Takano-Ishikawa
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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39
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Wu X, Xing X, Dowlut D, Zeng Y, Liu J, Liu X. Integrating phosphoproteomics into kinase-targeted cancer therapies in precision medicine. J Proteomics 2019; 191:68-79. [DOI: 10.1016/j.jprot.2018.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/20/2018] [Accepted: 03/31/2018] [Indexed: 12/12/2022]
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40
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Galán A, Horvatić A, Kuleš J, Bilić P, Gotić J, Mrljak V. LC-MS/MS analysis of the dog serum phosphoproteome reveals novel and conserved phosphorylation sites: Phosphoprotein patterns in babesiosis caused by Babesia canis, a case study. PLoS One 2018; 13:e0207245. [PMID: 30485286 PMCID: PMC6261647 DOI: 10.1371/journal.pone.0207245] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/26/2018] [Indexed: 12/30/2022] Open
Abstract
Phosphorylation is the most commonly studied protein post-translational modification (PTM) in biological systems due to its importance in controlling cell division, survival, growth, etc. Despite the thorough research in phosphoproteomics of cells and tissues there is little information on circulating phosphoproteins. We compared serum from 10 healthy dogs and 10 dogs affected by B. canis-caused babesiosis with no organ dysfunctions by employing gel-free LC-MS/MS analysis of individual samples and tandem mass tag (TMT) label-based quantitative analyses of pools, both supported by phosphopeptide enrichment. Results showed a moderate number of phosphorylated proteins (50-55), with 89 phosphorylation sites not previously published for dogs although a number of them matched phosphorylation sites found in mammalian orthologs. Three phosphopeptides showed significant variation in babesiosis-affected dog sera compared to controls: Serum amyloid A (SAA) phosphorylated at serine 101 (up-regulation), kininogen 1 phosphorylated at threonine 326, and fibrinogen α phosphorylated at both threonine 20 and serine 22 (down-regulation). 71.9% of the detected phosphorylated sites were phosphoserine, 16.8% phosphothreonine and only 11.2% phosphotyrosine residues. TMT label-based quantitative analysis showed α-2-HS-glycoprotein / Fetuin A to be the most abundant phosphoprotein (50-70% of all phosphoproteins) followed by kininogen-1 (10-20%). The alterations of phosphorylated proteins observed in canine babesiosis caused by Babesia canis suggest new insights into the largely neglected role of extracellular protein phosphorylation in health and disease, encouraging urgent further research on this area. To the best of our knowledge the present study represents the first attempt to characterize canine serum phosphoproteome.
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Affiliation(s)
- Asier Galán
- ERA Chair”VetMedZg”, Clinic for Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
| | - Anita Horvatić
- ERA Chair”VetMedZg”, Clinic for Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
| | - Josipa Kuleš
- ERA Chair”VetMedZg”, Clinic for Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
| | - Petra Bilić
- ERA Chair”VetMedZg”, Clinic for Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
| | - Jelena Gotić
- Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
| | - Vladimir Mrljak
- ERA Chair”VetMedZg”, Clinic for Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
- Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
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41
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Angulo-Urarte A, Casado P, Castillo SD, Kobialka P, Kotini MP, Figueiredo AM, Castel P, Rajeeve V, Milà-Guasch M, Millan J, Wiesner C, Serra H, Muixi L, Casanovas O, Viñals F, Affolter M, Gerhardt H, Huveneers S, Belting HG, Cutillas PR, Graupera M. Endothelial cell rearrangements during vascular patterning require PI3-kinase-mediated inhibition of actomyosin contractility. Nat Commun 2018; 9:4826. [PMID: 30446640 PMCID: PMC6240100 DOI: 10.1038/s41467-018-07172-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
Angiogenesis is a dynamic process relying on endothelial cell rearrangements within vascular tubes, yet the underlying mechanisms and functional relevance are poorly understood. Here we show that PI3Kα regulates endothelial cell rearrangements using a combination of a PI3Kα-selective inhibitor and endothelial-specific genetic deletion to abrogate PI3Kα activity during vessel development. Quantitative phosphoproteomics together with detailed cell biology analyses in vivo and in vitro reveal that PI3K signalling prevents NUAK1-dependent phosphorylation of the myosin phosphatase targeting-1 (MYPT1) protein, thereby allowing myosin light chain phosphatase (MLCP) activity and ultimately downregulating actomyosin contractility. Decreased PI3K activity enhances actomyosin contractility and impairs junctional remodelling and stabilization. This leads to overstretched endothelial cells that fail to anastomose properly and form aberrant superimposed layers within the vasculature. Our findings define the PI3K/NUAK1/MYPT1/MLCP axis as a critical pathway to regulate actomyosin contractility in endothelial cells, supporting vascular patterning and expansion through the control of cell rearrangement. Angiogenesis requires dynamic endothelial rearrangements and relative position changes within the vascular tubes. Here the authors show that a PI3K/NUAK1/MYPT1/MLCP pathway regulates actomyosin contractility in endothelial cells and cellular rearrangement during vascular patterning.
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Affiliation(s)
- Ana Angulo-Urarte
- Vascular Signalling Laboratory, ProCURE, Oncobell Program, Institut d´Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Pedro Casado
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sandra D Castillo
- Vascular Signalling Laboratory, ProCURE, Oncobell Program, Institut d´Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Piotr Kobialka
- Vascular Signalling Laboratory, ProCURE, Oncobell Program, Institut d´Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain
| | | | - Ana M Figueiredo
- Vascular Signalling Laboratory, ProCURE, Oncobell Program, Institut d´Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Vinothini Rajeeve
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Maria Milà-Guasch
- Vascular Signalling Laboratory, ProCURE, Oncobell Program, Institut d´Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Jaime Millan
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Calle Nicolás Cabrera, 28049, Madrid, Spain
| | - Cora Wiesner
- Biozentrum der Universität Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Helena Serra
- Vascular Signalling Laboratory, ProCURE, Oncobell Program, Institut d´Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Muixi
- Vascular Signalling Laboratory, ProCURE, Oncobell Program, Institut d´Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Oriol Casanovas
- Translation Research Laboratory, ProCURE, Oncobell Program, IDIBELL, Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Francesc Viñals
- Translation Research Laboratory, ProCURE, Oncobell Program, IDIBELL, Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain.,Departament de Ciències Fisiològiques II, Universitat de Barcelona, Carrer de la Feixa Llarga, 08907, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Markus Affolter
- Biozentrum der Universität Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Holger Gerhardt
- Max-Delbrueck Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125, Berlin, Germany.,The German Center for Cardiovascular Research (DZHK), Oudenarder Str. 16, 13347, Berlin, Germany.,The Berlin Institute of Health (BIH), Berlin, 10178, Germany
| | - Stephan Huveneers
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105 AZ, Amsterdam, Netherlands
| | - Heinz-Georg Belting
- Biozentrum der Universität Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Pedro R Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Mariona Graupera
- Vascular Signalling Laboratory, ProCURE, Oncobell Program, Institut d´Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de l'Hospitalet 199, 08908, L´Hospitalet de Llobregat, Barcelona, Spain. .,CIBERONC, Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain.
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42
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Tan HT, Chung MCM. Label-Free Quantitative Phosphoproteomics Reveals Regulation of Vasodilator-Stimulated Phosphoprotein upon Stathmin-1 Silencing in a Pair of Isogenic Colorectal Cancer Cell Lines. Proteomics 2018; 18:e1700242. [PMID: 29460479 DOI: 10.1002/pmic.201700242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 02/10/2018] [Indexed: 02/06/2023]
Abstract
In this communication, we present the phosphoproteome changes in an isogenic pair of colorectal cancer cell lines, viz., the poorly metastatic HCT-116 and the highly metastatic derivative E1, upon stathmin-1 (STMN1) knockdown. The aim was to better understand how the alterations of the phosphoproteins in these cells are involved in cancer metastasis. After the phosphopeptides were enriched using the TiO2 HAMMOC approach, comparative proteomics analysis was carried out using sequential window acquisition of all theoretical mass spectra-MS. Following bioinformatics analysis using MarkerView and OneOmics platforms, we identified a list of regulated phosphoproteins that may play a potential role in signaling, maintenance of cytoskeletal structure, and focal adhesion. Among these phosphoproteins, was the actin cytoskeleton regulator protein, vasodilator-stimulated phosphoprotein (VASP), where its change in phosphorylation status was found to be concomitant with STMN1-associated roles in metastasis. We further showed that silencing of stathmin-1 altered the expression, subcellular localization and phosphorylation status of VASP, which suggested that it might be associated with remodeling of the cell cytoskeleton in colorectal cancer metastasis.
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Affiliation(s)
- Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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43
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Dekker LJM, Zeneyedpour L, Snoeijers S, Joore J, Leenstra S, Luider TM. Determination of Site-Specific Phosphorylation Ratios in Proteins with Targeted Mass Spectrometry. J Proteome Res 2018; 17:1654-1663. [PMID: 29457462 DOI: 10.1021/acs.jproteome.7b00911] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We show that parallel reaction monitoring (PRM) can be used for exact quantification of phosphorylation ratios of proteins using stable-isotope-labeled peptides. We have compared two different PRM approaches on a digest of a U87 cell culture, namely, direct-PRM (tryptic digest measured by PRM without any further sample preparation) and TiO2-PRM (tryptic digest enriched with TiO2 cartridges, followed by PRM measurement); these approaches are compared for the following phosphorylation sites: neuroblast differentiation-associated protein (AHNAK S5480-p), calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D T337-p), and epidermal growth factor receptor (EGFR S1166-p). A reproducible percentage of phosphorylation could be determined (CV 6-13%) using direct-PRM or TiO2-PRM. In addition, we tested the approaches in a cell culture experiment in which U87 cells were deprived of serum. As a "gold standard" we included immune precipitation of EGFR followed by PRM (IP-PRM). For EGFR (S1166) and AHNAK (S5480) a statistical significant change in the percentage of phosphorylation could be observed as a result of serum deprivation; for EGFR (S1166) this change was observed for both TiO2-PRM and IP-PRM. The presented approach has the potential to multiplex and to quantify the ratio of phosphorylation in a single analysis.
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Affiliation(s)
- Lennard J M Dekker
- Erasmus MC , Department of Neurology , Wytemaweg 80 , 3015 CN Rotterdam , The Netherlands
| | - Lona Zeneyedpour
- Erasmus MC , Department of Neurology , Wytemaweg 80 , 3015 CN Rotterdam , The Netherlands
| | | | - Jos Joore
- Pepscope , Dantelaan 83 , 3533 VB Utrecht , The Netherlands
| | - Sieger Leenstra
- Erasmus MC , Department of Neurosurgery , 3015 CN Rotterdam , The Netherlands
| | - Theo M Luider
- Erasmus MC , Department of Neurology , Wytemaweg 80 , 3015 CN Rotterdam , The Netherlands
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44
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Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J. Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells. Metab Eng 2018; 45:149-157. [PMID: 29191787 PMCID: PMC5805855 DOI: 10.1016/j.ymben.2017.11.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/15/2017] [Accepted: 11/24/2017] [Indexed: 12/31/2022]
Abstract
Deregulated signal transduction and energy metabolism are hallmarks of cancer and both play a fundamental role in tumorigenesis. While it is increasingly recognised that signalling and metabolism are highly interconnected, the underpinning mechanisms of their co-regulation are still largely unknown. Here we designed and acquired proteomics, phosphoproteomics, and metabolomics experiments in fumarate hydratase (FH) deficient cells and developed a computational modelling approach to identify putative regulatory phosphorylation-sites of metabolic enzymes. We identified previously reported functionally relevant phosphosites and potentially novel regulatory residues in enzymes of the central carbon metabolism. In particular, we showed that pyruvate dehydrogenase (PDHA1) enzymatic activity is inhibited by increased phosphorylation in FH-deficient cells, restricting carbon entry from glucose to the tricarboxylic acid cycle. Moreover, we confirmed PDHA1 phosphorylation in human FH-deficient tumours. Our work provides a novel approach to investigate how post-translational modifications of enzymes regulate metabolism and could have important implications for understanding the metabolic transformation of FH-deficient cancers with potential clinical applications.
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Affiliation(s)
- Emanuel Gonçalves
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Marco Sciacovelli
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Ana S H Costa
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Maxine Gia Binh Tran
- UCL Division of Surgery and Interventional Science, Specialist Center for Kidney Cancer, Royal Free Hospital, Pond Street, London NW3 2QG, UK
| | - Timothy Isaac Johnson
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Daniel Machado
- European Molecular Biology Laboratory, EMBL, Heidelberg, Germany; Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK.
| | - Julio Saez-Rodriguez
- RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen, Germany.
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45
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Gedik N, Krüger M, Thielmann M, Kottenberg E, Skyschally A, Frey UH, Cario E, Peters J, Jakob H, Heusch G, Kleinbongard P. Proteomics/phosphoproteomics of left ventricular biopsies from patients with surgical coronary revascularization and pigs with coronary occlusion/reperfusion: remote ischemic preconditioning. Sci Rep 2017; 7:7629. [PMID: 28794502 PMCID: PMC5550488 DOI: 10.1038/s41598-017-07883-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/22/2017] [Indexed: 12/18/2022] Open
Abstract
Remote ischemic preconditioning (RIPC) by repeated brief cycles of limb ischemia/reperfusion reduces myocardial ischemia/reperfusion injury. In left ventricular (LV) biopsies from patients undergoing coronary artery bypass grafting (CABG), only the activation of signal transducer and activator of transcription 5 was associated with RIPC’s cardioprotection. We have now used an unbiased, non-hypothesis-driven proteomics and phosphoproteomics approach to analyze LV biopsies from patients undergoing CABG and from pigs undergoing coronary occlusion/reperfusion without (sham) and with RIPC. False discovery rate-based statistics identified a higher prostaglandin reductase 2 expression at early reperfusion with RIPC than with sham in patients. In pigs, the phosphorylation of 116 proteins was different between baseline and early reperfusion with RIPC and/or with sham. The identified proteins were not identical for patients and pigs, but in-silico pathway analysis of proteins with ≥2-fold higher expression/phosphorylation at early reperfusion with RIPC in comparison to sham revealed a relation to mitochondria and cytoskeleton in both species. Apart from limitations of the proteomics analysis per se, the small cohorts, the sampling/sample processing and the number of uncharacterized/unverifiable porcine proteins may have contributed to this largely unsatisfactory result.
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Affiliation(s)
- Nilgün Gedik
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Marcus Krüger
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Matthias Thielmann
- Department of Thoracic and Cardiovascular Surgery, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg- Essen, Essen, Germany
| | - Eva Kottenberg
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Andreas Skyschally
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Ulrich H Frey
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Elke Cario
- Experimental Gastroenterology, Department of Gastroenterology and Hepatology, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Jürgen Peters
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Heinz Jakob
- Department of Thoracic and Cardiovascular Surgery, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg- Essen, Essen, Germany
| | - Gerd Heusch
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Petra Kleinbongard
- Institute for Pathophysiology, West German Heart and Vascular Center Essen, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.
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46
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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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47
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Guerreiro JF, Mira NP, Santos AXS, Riezman H, Sá-Correia I. Membrane Phosphoproteomics of Yeast Early Response to Acetic Acid: Role of Hrk1 Kinase and Lipid Biosynthetic Pathways, in Particular Sphingolipids. Front Microbiol 2017; 8:1302. [PMID: 28747907 PMCID: PMC5506226 DOI: 10.3389/fmicb.2017.01302] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/28/2017] [Indexed: 01/02/2023] Open
Abstract
Saccharomyces cerevisiae response and tolerance to acetic acid is critical in industrial biotechnology and in acidic food and beverages preservation. The HRK1 gene, encoding a protein kinase of unknown function belonging to the “Npr1-family” of kinases known to be involved in the regulation of plasma membrane transporters, is an important determinant of acetic acid tolerance. This study was performed to identify the alterations occurring in yeast membrane phosphoproteome profile during the adaptive early response to acetic acid stress (following 1 h of exposure to a sub-lethal inhibitory concentration; 50 mM at pH 4.0) and the effect of HRK1 expression on the phosphoproteome. Results from mass spectrometry analysis following the prefractionation and specific enrichment of phosphorylated peptides using TiO2 beads highlight the contribution of processes related with translation, protein folding and processing, transport, and cellular homeostasis in yeast response to acetic acid stress, with particular relevance for changes in phosphorylation of transport-related proteins, found to be highly dependent on the Hrk1 kinase. Twenty different phosphoproteins known to be involved in lipid and sterol metabolism were found to be differently phosphorylated in response to acetic acid stress, including several phosphopeptides that had not previously been described as being phosphorylated. The suggested occurrence of cellular lipid composition remodeling during the short term yeast response to acetic acid was confirmed: Hrk1 kinase-independent reduction in phytoceramide levels and a reduction in phosphatidylcholine and phosphatidylinositol levels under acetic acid stress in the more susceptible hrk1Δ strain were revealed by a lipidomic analysis.
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Affiliation(s)
- Joana F Guerreiro
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
| | - Nuno P Mira
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
| | - Aline X S Santos
- Department of Biochemistry, University of GenevaGeneva, Switzerland
| | - Howard Riezman
- Department of Biochemistry, University of GenevaGeneva, Switzerland
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
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48
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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: 15] [Impact Index Per Article: 2.1] [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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49
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Labots M, van der Mijn JC, Beekhof R, Piersma SR, de Goeij-de Haas RR, Pham TV, Knol JC, Dekker H, van Grieken NC, Verheul HM, Jiménez CR. Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection. J Proteomics 2017; 162:99-107. [DOI: 10.1016/j.jprot.2017.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/28/2017] [Accepted: 04/12/2017] [Indexed: 12/17/2022]
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50
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Moniz LS, Surinova S, Ghazaly E, Velasco LG, Haider S, Rodríguez-Prados JC, Berenjeno IM, Chelala C, Vanhaesebroeck B. Phosphoproteomic comparison of Pik3ca and Pten signalling identifies the nucleotidase NT5C as a novel AKT substrate. Sci Rep 2017; 7:39985. [PMID: 28059163 PMCID: PMC5216349 DOI: 10.1038/srep39985] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 11/30/2016] [Indexed: 12/16/2022] Open
Abstract
To identify novel effectors and processes regulated by PI3K pathway activation, we performed an unbiased phosphoproteomic screen comparing two common events of PI3K deregulation in cancer: oncogenic Pik3ca mutation (Pik3caH1047R) and deletion of Pten. Using mouse embryonic fibroblast (MEF) models that generate inducible, low-level pathway activation as observed in cancer, we quantified 7566 unique phosphopeptides from 3279 proteins. A number of proteins were found to be differentially-regulated by Pik3caH1047R and Pten loss, suggesting unique roles for these two events in processes such as vesicular trafficking, DNA damage repair and RNA splicing. We also identified novel PI3K effectors that were commonly-regulated, including putative AKT substrates. Validation of one of these hits, confirmed NT5C (5',3'-Nucleotidase, Cytosolic) as a novel AKT substrate, with an unexpected role in actin cytoskeleton regulation via an interaction with the ARP2/3 complex. This study has produced a comprehensive data resource and identified a new link between PI3K pathway activation and actin regulation.
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Affiliation(s)
- Larissa S. Moniz
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
| | - Silvia Surinova
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
| | - Essam Ghazaly
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Lorena Gonzalez Velasco
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
| | - Syed Haider
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Inma M. Berenjeno
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
| | - Claude Chelala
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Bart Vanhaesebroeck
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street London WC1E 6DD, UK
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