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Adderley J, O'Donoghue F, Doerig C, Davis S. MAPPINGS, a tool for network analysis of large phospho-signalling datasets: application to host erythrocyte response to Plasmodium infection. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100149. [PMID: 35909628 PMCID: PMC9325900 DOI: 10.1016/j.crmicr.2022.100149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/12/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022] Open
Abstract
The complexity of signal transduction networks in eukaryotic cells, superimposed to very large datasets generated by “omics” approaches (notably phosphor-proteomics), calls for tools to identify pathways that are mobilised under specific conditions, including infection by intracellular pathogens. This has become a bottleneck in various biology fields, from cancer through developmental biology to infectious diseases. We developed MAPPINGS, a computational tool to extract meaning from large phosphosignalling datasets, and used it to analyse host erythrocyte response to infection with malaria parasites, leading to the identification of host cell pathways that are activated by Plasmodium. MAPPINGS uses random walks to identify chains of phosphorylation events occurring much more or much less frequently than expected, and highlights pathways of phosphorylation that work synergistically, providing a rapid interpretation of the most critical pathways in any phosphosiganlling dataset.
Large datasets of phosphorylation interactions are constantly being generated, but deciphering the complex network structure hidden in these datasets remains challenging. Many phosphorylation interactions occurring in human cells have been identified and constitute the basis for the known phosphorylation interaction network. We overlayed onto this network phosphorylation datasets obtained from an antibody microarray approach aimed at determining changes in phospho-signalling of host erythrocytes, during infection with the malaria parasite Plasmodium falciparum. We designed a pathway analysis tool denoted MAPPINGS that uses random walks to identify chains of phosphorylation events occurring much more or much less frequently than expected. MAPPINGS highlights pathways of phosphorylation that work synergistically, providing a rapid interpretation of the most critical pathways in each dataset. MAPPINGS confirmed several signalling interactions previously shown to be modulated by infection, and revealed additional interactions which could form the basis of numerous future studies. The MAPPINGS analysis strategy described here is widely applicable to comparative phosphorylation datasets in any context, such as response of cells to infection, treatment, or comparison between differentiation stages of any cellular population.
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Affiliation(s)
- Jack Adderley
- School of Health and Biomedical Sciences, RMIT University, Bundoora VIC 3083, Australia
- Corresponding authors.
| | - Finn O'Donoghue
- School of Science, RMIT University, Melbourne, VIC 3053, Australia
| | - Christian Doerig
- School of Health and Biomedical Sciences, RMIT University, Bundoora VIC 3083, Australia
- Corresponding authors.
| | - Stephen Davis
- School of Science, RMIT University, Melbourne, VIC 3053, Australia
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Adderley JD, John von Freyend S, Jackson SA, Bird MJ, Burns AL, Anar B, Metcalf T, Semblat JP, Billker O, Wilson DW, Doerig C. Analysis of erythrocyte signalling pathways during Plasmodium falciparum infection identifies targets for host-directed antimalarial intervention. Nat Commun 2020; 11:4015. [PMID: 32782246 PMCID: PMC7419518 DOI: 10.1038/s41467-020-17829-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/16/2020] [Indexed: 02/08/2023] Open
Abstract
Intracellular pathogens mobilize host signaling pathways of their host cell to promote their own survival. Evidence is emerging that signal transduction elements are activated in a-nucleated erythrocytes in response to infection with malaria parasites, but the extent of this phenomenon remains unknown. Here, we fill this knowledge gap through a comprehensive and dynamic assessment of host erythrocyte signaling during infection with Plasmodium falciparum. We used arrays of 878 antibodies directed against human signaling proteins to interrogate the activation status of host erythrocyte phospho-signaling pathways at three blood stages of parasite asexual development. This analysis reveals a dynamic modulation of many host signalling proteins across parasite development. Here we focus on the hepatocyte growth factor receptor (c-MET) and the MAP kinase pathway component B-Raf, providing a proof of concept that human signaling kinases identified as activated by malaria infection represent attractive targets for antimalarial intervention. Plasmodium infection activates signaling pathways in a-nucleated erythrocytes. Here, Adderley et al. use a comprehensive antibody microarray to show that infection extensively modulates host cell signalling and that the host receptor tyrosine kinase c-MET supports Plasmodium falciparum proliferation.
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Affiliation(s)
- Jack D Adderley
- Centre for Chronic Inflammatory and Infectious and Diseases, Biomedical Sciences Cluster, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, 3083, Australia
| | - Simona John von Freyend
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Sarah A Jackson
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Megan J Bird
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Amy L Burns
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Burcu Anar
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Tom Metcalf
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jean-Philippe Semblat
- Institut National de la Transfusion Sanguine, Inserm UMR S1134, 75015, Paris, France
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.,Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.,Burnet Institute, Melbourne, VIC, 3004, Australia
| | - Christian Doerig
- Centre for Chronic Inflammatory and Infectious and Diseases, Biomedical Sciences Cluster, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, 3083, Australia.
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Pumilacidins from the Octocoral-Associated Bacillus sp. DT001 Display Anti-Proliferative Effects in Plasmodium falciparum. Molecules 2018; 23:molecules23092179. [PMID: 30158478 PMCID: PMC6225264 DOI: 10.3390/molecules23092179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/24/2018] [Accepted: 08/25/2018] [Indexed: 12/03/2022] Open
Abstract
Chemical examination of the octocoral-associated Bacillus species (sp.) DT001 led to the isolation of pumilacidins A (1) and C (2). We investigated the effect of these compounds on the viability of Plasmodium falciparum and the mechanism of pumilacidin-induced death. The use of inhibitors of protein kinase C (PKC) and phosphoinositide 3-kinase (PI3K) was able to prevent the effects of pumilacidins A and C. The results indicated also that pumilacidins inhibit parasite growth via mitochondrial dysfunction and decreased cytosolic Ca2+.
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Carvalho TG, Morahan B, John von Freyend S, Boeuf P, Grau G, Garcia-Bustos J, Doerig C. The ins and outs of phosphosignalling in Plasmodium: Parasite regulation and host cell manipulation. Mol Biochem Parasitol 2016; 208:2-15. [PMID: 27211241 DOI: 10.1016/j.molbiopara.2016.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 05/16/2016] [Indexed: 12/15/2022]
Abstract
Signal transduction and kinomics have been rapidly expanding areas of investigation within the malaria research field. Here, we provide an overview of phosphosignalling pathways that operate in all stages of the Plasmodium life cycle. We review signalling pathways in the parasite itself, in the cells it invades, and in other cells of the vertebrate host with which it interacts. We also discuss the potential of these pathways as novel targets for antimalarial intervention.
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Affiliation(s)
- Teresa Gil Carvalho
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Belinda Morahan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Simona John von Freyend
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Philippe Boeuf
- Burnet Institute, Melbourne, Victoria 3004, Australia; The University of Melbourne, Department of Medicine, Melbourne, Victoria 3010, Australia; Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Victoria 3010, Australia
| | - Georges Grau
- Vascular Immunology Unit, Department of Pathology, Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Jose Garcia-Bustos
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Christian Doerig
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia.
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Abstract
Eukaryotic, prokaryotic and viral pathogens are known to interfere with signaling pathways of their host to promote their own survival and proliferation. Here, we present selected examples of modulation of PAK activity in human cells by both intracellular and extracellular pathogens, focusing on one eukaryotic pathogen, the human malaria parasite Plasmodium falciparum, two Gram-negative bacteria (Helicobacter pylori and Pseudomonas aeruginosa), and two viruses belonging to distinct groups, the lentivirus HIV and the orthomyxovirus Influenza virus A.
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Pantaleo A, Ferru E, Carta F, Mannu F, Giribaldi G, Vono R, Lepedda AJ, Pippia P, Turrini F. Analysis of changes in tyrosine and serine phosphorylation of red cell membrane proteins induced by P. falciparum
growth. Proteomics 2010; 10:3469-79. [DOI: 10.1002/pmic.201000269] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Leroy D, Doerig C. Drugging the Plasmodium kinome: the benefits of academia-industry synergy. Trends Pharmacol Sci 2008; 29:241-9. [PMID: 18394721 DOI: 10.1016/j.tips.2008.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 02/25/2008] [Accepted: 02/25/2008] [Indexed: 01/21/2023]
Abstract
Malaria remains a major killer in many parts of the world. Recently, the development of nonprofit organisations aimed at fighting this deadly scourge incited academic and industrial scientists to merge their expertise in drug-target validation and lead discovery. Expectations are clear: identification and characterisation of new molecules showing high efficacy, low toxicity and little propensity to induce resistance in the parasite. In this context, protein kinase inhibitors represent an attractive possibility. Here, we compare traditional target-based drug-discovery approaches with innovative exploratory paths (parallel screening, cell-based assays, integrated systems biology and allosteric inhibition) and discuss the benefits of acadaemia-industry cooperation. Early characterisation of distribution, metabolism, pharmacokinetic (DMPK) and toxicology parameters are considered as well.
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Affiliation(s)
- Didier Leroy
- Merck-Serono International S.A., Geneva Research Center, 9, Chemin des Mines, Case postale 54, CH-1211 Genève 20, Switzerland.
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Abstract
Protein kinases (PKs) are prime targets for drug discovery in a variety of diseases, including cancer and neurodegenerative pathologies. The characterisation of the kinome of the human malaria parasite Plasmodium falciparum has revealed profound divergences, at several levels, between PKs of the parasite and those of its host. Here, the authors review the major issues and recent advances regarding the development of Plasmodium-selective PK inhibitors, with emphasis on target identification and validation, and on structure-based design. The authors also discuss the possibility of interfering with: i) Plasmodium PKs regulating transmission to the mosquito vector; and ii) host PKs that may be required for parasite survival.
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Affiliation(s)
- Christian Doerig
- INSERM U609, Wellcome Centre for Molecular Parasitology, Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow, UK.
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Doerig C, Billker O, Pratt D, Endicott J. Protein kinases as targets for antimalarial intervention: Kinomics, structure-based design, transmission-blockade, and targeting host cell enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1754:132-50. [PMID: 16271522 DOI: 10.1016/j.bbapap.2005.08.027] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Revised: 08/20/2005] [Accepted: 08/25/2005] [Indexed: 12/31/2022]
Abstract
The surge of interest in protein kinases as targets for chemotherapeutic intervention in a number of diseases such as cancer and neurodegenerative disorders has stimulated research aimed at determining whether enzymes of this class might also be considered as targets in the context of diseases caused by parasitic protists. Here, we present an overview of recent developments in this field, concentrating (i) on the benefits gained from the availability of genomic databases for a number of parasitic protozoa, (ii) on the emerging field of structure-aided design of inhibitors targeting protein kinases of parasitic protists, (iii) on the concept known as transmission-blockade, whereby kinases implicated in the development of the parasite in their arthropod vector might be targeted to interfere with disease transmission, and (iv) on the possibility of controlling parasitic diseases through the inhibition of host cell protein kinases that are required for the establishment of infection by the parasites.
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Affiliation(s)
- Christian Doerig
- INSERM U609, Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 Glasgow University Place, Glasgow G12 8TA, Scotland, UK.
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Abstract
Parasitic protozoa are surrounded by membrane structures that have a different lipid and protein composition relative to membranes of the host. The parasite membranes are essential structurally and also for parasite specific processes, like host cell invasion, nutrient acquisition or protection against the host immune system. Furthermore, intracellular parasites can modulate membranes of their host, and trafficking of membrane components occurs between host membranes and those of the intracellular parasite. Phospholipids are major membrane components and, although many parasites scavenge these phospholipids from their host, most parasites also synthesise phospholipids de novo, or modify a large part of the scavenged phospholipids. It was recently shown that some parasites like Plasmodium have unique phospholipid metabolic pathways. This review will focus on new developments in research on phospholipid metabolism of parasitic protozoa in relation to parasite-specific membrane structures and function, as well as on several targets for interference with the parasite phospholipid metabolism with a view to developing new anti-parasitic drugs.
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Affiliation(s)
- Henri J Vial
- Dynamique Moléculaire des Interactions Membranaires, CNRS UMR 5539, cc107, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier, France.
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Al-Khedery B, Barnwell JW, Galinski MR. Stage-specific expression of 14-3-3 in asexual blood-stage Plasmodium. Mol Biochem Parasitol 1999; 102:117-30. [PMID: 10477181 DOI: 10.1016/s0166-6851(99)00090-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper reports the identification of 14-3-3 in Plasmodium. 14-3-3 is an evolutionarily conserved protein that is most noted as a mediator in signal transduction events and cell cycle regulation. The complete cDNA (approximately 2.6 kb) and gDNA (approximately 3.4 kb) of a Plasmodium knowlesi 14-3-3 (Pk14-3-3) is reported. The gene has three introns; two near the beginning and one close to the end of the coding sequence. Also reported, is the gDNA of the Plasmodium falciparum homologue (Pf14-3-3). Unlike in many other organisms, where multiple gene copies and different functional isoforms exist, Plasmodium 14-3-3 is encoded as a single-copy gene. Northern blot analyses show that the Pk14-3-3 transcript in asexual blood stages begins to be expressed in the ring-stage, predominates in young trophozoites, and thereafter declines. An antiserum produced against recombinant Pk14-3-3 reacts via immunoblot and immunoprecipitation with the approximately 30 kDa and the approximately 32 kDa Pk14-3-3 and Pf14-3-3 proteins, respectively. Protein expression in P. knowlesi closely mimics the pattern of the transcript.
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Affiliation(s)
- B Al-Khedery
- Department of Medical and Molecular Parasitology, New York University School of Medicine, NY 10010, USA
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