1
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Zribi I, Ghorbel M, Haddaji N, Besbes M, Brini F. Genome-Wide Identification and Expression Profiling of Pathogenesis-Related Protein 1 ( PR-1) Genes in Durum Wheat ( Triticum durum Desf.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1998. [PMID: 37653915 PMCID: PMC10223549 DOI: 10.3390/plants12101998] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 07/30/2023]
Abstract
Pathogen-related proteins (PRs) are diversified proteins with a low molecular weight implicated in plant response to biotic and abiotic stress as well in regulating different functions in plant maturation. Interestingly, no systematical study has been conducted in durum wheat (Triticum turgidum subsp. durum). In the present study, 12 PR-1 genes encoding a CAP superfamily domain were identified in the genome of Triticum turgidum subsp. durum, which is an important cereal, using in silico approaches. Additionally, phylogenetic analysis showed that the PR-1 genes were classified into three groups based on their isoelectric point and the conserved motif domain. Moreover, our analysis showed that most of the TdPR-1 proteins presented an N-terminal signal peptide. Expression patterns analysis showed that the PR-1 gene family presented temporal and spatial specificity and was induced by different abiotic stresses. This is the first report describing the genome-scale analysis of the durum wheat PR-1 gene family, and these data will help further study the roles of PR-1 genes during stress responses, leading to crop improvement.
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Affiliation(s)
- Ikram Zribi
- Laboratory of Biotechnology and Plant Improvement, Centre of Biotechnology of Sfax, P.O. Box 1177, Sfax 3018, Tunisia;
| | - Mouna Ghorbel
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (M.B.)
| | - Najla Haddaji
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (M.B.)
| | - Malek Besbes
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (M.B.)
| | - Faiçal Brini
- Laboratory of Biotechnology and Plant Improvement, Centre of Biotechnology of Sfax, P.O. Box 1177, Sfax 3018, Tunisia;
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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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Madison I, Amin F, Song K, Sozzani R, Van den Broeck L. A Data-Driven Signaling Network Inference Approach for Phosphoproteomics. Methods Mol Biol 2023; 2690:335-354. [PMID: 37450158 DOI: 10.1007/978-1-0716-3327-4_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Proteins are rapidly and dynamically post-transcriptionally modified as cells respond to changes in their environment. For example, protein phosphorylation is mediated by kinases while dephosphorylation is mediated by phosphatases. Quantifying and predicting interactions between kinases, phosphatases, and target proteins over time will aid the study of signaling cascades under a variety of environmental conditions. Here, we describe methods to statistically analyze label-free phosphoproteomic data and infer posttranscriptional regulatory networks over time. We provide an R-based method that can be used to normalize and analyze label-free phosphoproteomic data using variance stabilizing normalization and a linear mixed model across multiple time points and conditions. We also provide a method to infer regulator-target interactions over time using a discretization scheme followed by dynamic Bayesian modeling computations to validate our conclusions. Overall, this pipeline is designed to perform functional analyses and predictions of phosphoproteomic signaling cascades.
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Affiliation(s)
- Imani Madison
- Department of Plant and Microbial Biology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, USA
| | - Fin Amin
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA
| | - Kuncheng Song
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, USA.
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, USA.
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4
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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: 4] [Impact Index Per Article: 2.0] [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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5
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Roy-Luzarraga M, Reynolds LE, de Luxán-Delgado B, Maiques O, Wisniewski L, Newport E, Rajeeve V, Drake RJ, Gómez-Escudero J, Richards FM, Weller C, Dormann C, Meng YM, Vermeulen PB, Saur D, Sanz-Moreno V, Wong PP, Géraud C, Cutillas PR, Hodivala-Dilke K. Suppression of Endothelial Cell FAK Expression Reduces Pancreatic Ductal Adenocarcinoma Metastasis after Gemcitabine Treatment. Cancer Res 2022; 82:1909-1925. [PMID: 35350066 PMCID: PMC9381116 DOI: 10.1158/0008-5472.can-20-3807] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/07/2022] [Accepted: 03/25/2022] [Indexed: 02/02/2023]
Abstract
Despite substantial advances in the treatment of solid cancers, resistance to therapy remains a major obstacle to prolonged progression-free survival. Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers, with a high level of liver metastasis. Primary PDAC is highly hypoxic, and metastases are resistant to first-line treatment, including gemcitabine. Recent studies have indicated that endothelial cell (EC) focal adhesion kinase (FAK) regulates DNA-damaging therapy-induced angiocrine factors and chemosensitivity in primary tumor models. Here, we show that inducible loss of EC-FAK in both orthotopic and spontaneous mouse models of PDAC is not sufficient to affect primary tumor growth but reduces liver and lung metastasis load and improves survival rates in gemcitabine-treated, but not untreated, mice. EC-FAK loss did not affect primary tumor angiogenesis, tumor blood vessel leakage, or early events in metastasis, including the numbers of circulating tumor cells, tumor cell homing, or metastatic seeding. Phosphoproteomics analysis showed a downregulation of the MAPK, RAF, and PAK signaling pathways in gemcitabine-treated FAK-depleted ECs compared with gemcitabine-treated wild-type ECs. Moreover, low levels of EC-FAK correlated with increased survival and reduced relapse in gemcitabine-treated patients with PDAC, supporting the clinical relevance of these findings. Altogether, we have identified a new role of EC-FAK in regulating PDAC metastasis upon gemcitabine treatment that impacts outcome. SIGNIFICANCE These findings establish the potential utility of combinatorial endothelial cell FAK targeting together with gemcitabine in future clinical applications to control metastasis in patients with pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Marina Roy-Luzarraga
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Louise E. Reynolds
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Beatriz de Luxán-Delgado
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Oscar Maiques
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Laura Wisniewski
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Emma Newport
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Vinothini Rajeeve
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Rebecca J.G. Drake
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Jesús Gómez-Escudero
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Frances M. Richards
- Translational Medicine Operations, Astrazeneca Oncology, Darwin Building, Cambridge Science Park, Milton Road, Cambridge, United Kingdom
| | - Céline Weller
- Department of Dermatology, Section of Clinical and Molecular Dermatology, Venereology and Allergology, University Medical Center and European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christof Dormann
- Department of Dermatology, Section of Clinical and Molecular Dermatology, Venereology and Allergology, University Medical Center and European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ya-Ming Meng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Peter B. Vermeulen
- Department of Oncological Research, Translational Cancer Research Unit, Oncology Center GZA—GZA Hospitals St. Augustinus and University of Antwerp, Antwerp, Belgium
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg and Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, München, Germany
| | - Victoria Sanz-Moreno
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Ping-Pui Wong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cyrill Géraud
- Department of Dermatology, Section of Clinical and Molecular Dermatology, Venereology and Allergology, University Medical Center and European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Pedro R. Cutillas
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
| | - Kairbaan Hodivala-Dilke
- Barts Cancer Institute—A CR-UK Center of Excellence, Queen Mary University of London, John Vane Science Center, Charterhouse Square, London, United Kingdom
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6
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Heydt Q, Xintaropoulou C, Clear A, Austin M, Pislariu I, Miraki-Moud F, Cutillas P, Korfi K, Calaminici M, Cawthorn W, Suchacki K, Nagano A, Gribben JG, Smith M, Cavenagh JD, Oakervee H, Castleton A, Taussig D, Peck B, Wilczynska A, McNaughton L, Bonnet D, Mardakheh F, Patel B. Adipocytes disrupt the translational programme of acute lymphoblastic leukaemia to favour tumour survival and persistence. Nat Commun 2021; 12:5507. [PMID: 34535653 PMCID: PMC8448863 DOI: 10.1038/s41467-021-25540-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 08/17/2021] [Indexed: 11/09/2022] Open
Abstract
The specific niche adaptations that facilitate primary disease and Acute Lymphoblastic Leukaemia (ALL) survival after induction chemotherapy remain unclear. Here, we show that Bone Marrow (BM) adipocytes dynamically evolve during ALL pathogenesis and therapy, transitioning from cellular depletion in the primary leukaemia niche to a fully reconstituted state upon remission induction. Functionally, adipocyte niches elicit a fate switch in ALL cells towards slow-proliferation and cellular quiescence, highlighting the critical contribution of the adipocyte dynamic to disease establishment and chemotherapy resistance. Mechanistically, adipocyte niche interaction targets posttranscriptional networks and suppresses protein biosynthesis in ALL cells. Treatment with general control nonderepressible 2 inhibitor (GCN2ib) alleviates adipocyte-mediated translational repression and rescues ALL cell quiescence thereby significantly reducing the cytoprotective effect of adipocytes against chemotherapy and other extrinsic stressors. These data establish how adipocyte driven restrictions of the ALL proteome benefit ALL tumours, preventing their elimination, and suggest ways to manipulate adipocyte-mediated ALL resistance.
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Affiliation(s)
- Q Heydt
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - C Xintaropoulou
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - A Clear
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - M Austin
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - I Pislariu
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - F Miraki-Moud
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - P Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - K Korfi
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - M Calaminici
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - W Cawthorn
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, Scotland, UK
| | - K Suchacki
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, Scotland, UK
| | - A Nagano
- Centre for Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - J G Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - M Smith
- Department of Haemato-Oncology, St Bartholomew's Hospital, West Smithfield, London, UK
| | - J D Cavenagh
- Department of Haemato-Oncology, St Bartholomew's Hospital, West Smithfield, London, UK
| | - H Oakervee
- Department of Haemato-Oncology, St Bartholomew's Hospital, West Smithfield, London, UK
| | - A Castleton
- Christie NHS Foundation Trust, Manchester, UK
| | - D Taussig
- Haemato-oncology Unit, The Royal Marsden Hospital, Sutton, UK
| | - B Peck
- Centre for Tumour Biology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - A Wilczynska
- CRUK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - L McNaughton
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - D Bonnet
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - F Mardakheh
- Centre for Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK
| | - B Patel
- Centre for Haemato-Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, UK.
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7
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Arabia S, Sami AA, Akhter S, Sarker RH, Islam T. Comprehensive in silico Characterization of Universal Stress Proteins in Rice ( Oryza sativa L.) With Insight Into Their Stress-Specific Transcriptional Modulation. FRONTIERS IN PLANT SCIENCE 2021; 12:712607. [PMID: 34394169 PMCID: PMC8355530 DOI: 10.3389/fpls.2021.712607] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 06/10/2023]
Abstract
In a world where climate change is real and its consequences are unprecedented, understanding of the plant adaptive capacity and native stress-responsive machinery is crucial. In recent years, universal stress proteins (USPs) have received much attention in the field of plant science due to their stress-specific transcriptional regulation. This study focuses on the extensive characterization of the USP gene family members in the monocot crop rice (Oryza sativa L. var. japonica). Here, we report a total of 44 USP genes in the rice genome. In silico characterization of these genes showed that domain architecture played a major role in the functional diversification of the USP gene family which holds for all plant USPs. On top of that, a higher conservation of OsUSP members has been exhibited with a monocot genome (Zea mays L.) as compared to a dicot genome (Arabidopsis thaliana L.). Expression profiling of the identified genes led to the discovery of multiple OsUSP genes that showed pronounced transcript alteration under various abiotic stress conditions, indicating their potential role as multi-functional stress-specific modules. Furthermore, expression validation of OsUSP genes using qRT-PCR provided a strong evidence for the utility OsUSP genes in building multi-stress tolerant plants. Altogether, this study provides leads to suitable USP candidates that could be targeted for plant breeding and genetic engineering experiments to develop stress resilient crop species.
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8
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Badodi S, Pomella N, Zhang X, Rosser G, Whittingham J, Niklison-Chirou MV, Lim YM, Brandner S, Morrison G, Pollard SM, Bennett CD, Clifford SC, Peet A, Basson MA, Marino S. Inositol treatment inhibits medulloblastoma through suppression of epigenetic-driven metabolic adaptation. Nat Commun 2021; 12:2148. [PMID: 33846320 PMCID: PMC8042111 DOI: 10.1038/s41467-021-22379-7] [Citation(s) in RCA: 15] [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: 09/01/2020] [Accepted: 03/12/2021] [Indexed: 12/11/2022] Open
Abstract
Deregulation of chromatin modifiers plays an essential role in the pathogenesis of medulloblastoma, the most common paediatric malignant brain tumour. Here, we identify a BMI1-dependent sensitivity to deregulation of inositol metabolism in a proportion of medulloblastoma. We demonstrate mTOR pathway activation and metabolic adaptation specifically in medulloblastoma of the molecular subgroup G4 characterised by a BMI1High;CHD7Low signature and show this can be counteracted by IP6 treatment. Finally, we demonstrate that IP6 synergises with cisplatin to enhance its cytotoxicity in vitro and extends survival in a pre-clinical BMI1High;CHD7Low xenograft model.
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Affiliation(s)
- Sara Badodi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nicola Pomella
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Xinyu Zhang
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Gabriel Rosser
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - John Whittingham
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Maria Victoria Niklison-Chirou
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Centre for Therapeutic Innovation (CTI-Bath), Department of Pharmacy & Pharmacology, University of Bath, Bath, UK
| | - Yau Mun Lim
- UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Sebastian Brandner
- UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Gillian Morrison
- Centre for Regenerative Medicine & Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine & Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Christopher D Bennett
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Birmingham Women and Children's Hospital, Birmingham, UK
| | - Steven C Clifford
- Newcastle University Centre for Cancer, Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Andrew Peet
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Birmingham Women and Children's Hospital, Birmingham, UK
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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9
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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: 49] [Impact Index Per Article: 16.3] [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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10
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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: 52] [Impact Index Per Article: 13.0] [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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11
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Demircioglu F, Wang J, Candido J, Costa ASH, Casado P, de Luxan Delgado B, Reynolds LE, Gomez-Escudero J, Newport E, Rajeeve V, Baker AM, Roy-Luzarraga M, Graham TA, Foster J, Wang Y, Campbell JJ, Singh R, Zhang P, Schall TJ, Balkwill FR, Sosabowski J, Cutillas PR, Frezza C, Sancho P, Hodivala-Dilke K. Cancer associated fibroblast FAK regulates malignant cell metabolism. Nat Commun 2020; 11:1290. [PMID: 32157087 PMCID: PMC7064590 DOI: 10.1038/s41467-020-15104-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/18/2020] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence suggests that cancer cell metabolism can be regulated by cancer-associated fibroblasts (CAFs), but the mechanisms are poorly defined. Here we show that CAFs regulate malignant cell metabolism through pathways under the control of FAK. In breast and pancreatic cancer patients we find that low FAK expression, specifically in the stromal compartment, predicts reduced overall survival. In mice, depletion of FAK in a subpopulation of CAFs regulates paracrine signals that increase malignant cell glycolysis and tumour growth. Proteomic and phosphoproteomic analysis in our mouse model identifies metabolic alterations which are reflected at the transcriptomic level in patients with low stromal FAK. Mechanistically we demonstrate that FAK-depletion in CAFs increases chemokine production, which via CCR1/CCR2 on cancer cells, activate protein kinase A, leading to enhanced malignant cell glycolysis. Our data uncover mechanisms whereby stromal fibroblasts regulate cancer cell metabolism independent of genetic mutations in cancer cells.
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Affiliation(s)
- Fevzi Demircioglu
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jun Wang
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Juliana Candido
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Pedro Casado
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Beatriz de Luxan Delgado
- Centre for Stem Cells in Cancer and Ageing, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Louise E Reynolds
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jesus Gomez-Escudero
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Emma Newport
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Vinothini Rajeeve
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Ann-Marie Baker
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Marina Roy-Luzarraga
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Trevor A Graham
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Julie Foster
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Yu Wang
- ChemoCentryx Inc., 850 Maude Ave, Mountain View, CA94043, USA
| | | | - Rajinder Singh
- ChemoCentryx Inc., 850 Maude Ave, Mountain View, CA94043, USA
| | - Penglie Zhang
- ChemoCentryx Inc., 850 Maude Ave, Mountain View, CA94043, USA
| | - Thomas J Schall
- ChemoCentryx Inc., 850 Maude Ave, Mountain View, CA94043, USA
| | - Frances R Balkwill
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jane Sosabowski
- Centre for Molecular 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
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Patricia Sancho
- Centre for Stem Cells in Cancer and Ageing, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
- IIS Aragon, Hospital Universitario Miguel Servet, Zaragoza, 50009, Spain
| | - Kairbaan Hodivala-Dilke
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK.
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12
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Post-Translational Modification-Dependent Activity of Matrix Metalloproteinases. Int J Mol Sci 2019; 20:ijms20123077. [PMID: 31238509 PMCID: PMC6627178 DOI: 10.3390/ijms20123077] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/16/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022] Open
Abstract
Due to their capacity to process different proteins of the extracellular matrix (ECM), matrix metalloproteinases (MMPs) were initially described as a family of secreted proteases, functioning as main ECM regulators. However, through proteolytic processing of various biomolecules, MMPs also modulate intra- and extracellular pathways and networks. Thereby, they are functionally implicated in the regulation of multiple physiological and pathological processes. Consequently, MMP activity is tightly regulated through a combination of epigenetic, transcriptional, and post-transcriptional control of gene expression, proteolytic activation, post-translational modifications (PTMs), and extracellular inhibition. In addition, MMPs, their substrates and ECM binding partners are frequently modified by PTMs, which suggests an important role of PTMs in modulating the pleiotropic activities of these proteases. This review summarizes the recent progress towards understanding the role of PTMs (glycosylation, phosphorylation, glycosaminoglycans) on the activity of several members of the MMP family.
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13
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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: 45] [Impact Index Per Article: 7.5] [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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