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Fernández-García M, Mesquita I, Ferreira C, Araújo M, Saha B, Rey-Stolle MF, García A, Silvestre R, Barbas C. Leishmania donovani Induces Multiple Dynamic Responses in the Metabolome Associated with Amastigote Differentiation and Maturation Inside the Human Macrophage. J Proteome Res 2023. [PMID: 37339249 DOI: 10.1021/acs.jproteome.2c00845] [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: 06/22/2023]
Abstract
Leishmania donovani infection of macrophages drives profound changes in the metabolism of both the host macrophage and the parasite, which undergoes different phases of development culminating in replication and propagation. However, the dynamics of this parasite-macrophage cometabolome are poorly understood. In this study, a multiplatform metabolomics pipeline combining untargeted, high-resolution CE-TOF/MS and LC-QTOF/MS with targeted LC-QqQ/MS was followed to characterize the metabolome alterations induced in L. donovani-infected human monocyte-derived macrophages from different donors at 12, 36, and 72 h post-infection. The set of alterations known to occur during Leishmania infection of macrophages, substantially expanded in this investigation, characterized the dynamics of the glycerophospholipid, sphingolipid, purine, pentose phosphate, glycolytic, TCA, and amino acid metabolism. Our results showed that only citrulline, arginine, and glutamine exhibited constant trends across all studied infection time points, while most metabolite alterations underwent a partial recovery during amastigote maturation. We determined a major metabolite response pointing to an early induction of sphingomyelinase and phospholipase activities and correlated with amino acid depletion. These data represent a comprehensive overview of the metabolome alterations occurring during promastigote-to-amastigote differentiation and maturation of L. donovani inside macrophages that contributes to our understanding of the relationship between L. donovani pathogenesis and metabolic dysregulation.
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Affiliation(s)
- Miguel Fernández-García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
| | - Inês Mesquita
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Carolina Ferreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Marta Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Bhaskar Saha
- National Centre for Cell Science, 411007 Pune, India
| | - Ma Fernanda Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
| | - Antonia García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
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Tagliazucchi L, Perea-Martinez A, Fiorini G, Manzano JI, Genovese F, García-Hernández R, Pinetti D, Gamarro F, Costi MP. Label-Free Mass Spectrometry Proteomics Reveals Different Pathways Modulated in THP-1 Cells Infected with Therapeutic Failure and Drug Resistance Leishmania infantum Clinical Isolates. ACS Infect Dis 2023; 9:470-485. [PMID: 36762976 PMCID: PMC10012269 DOI: 10.1021/acsinfecdis.2c00457] [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: 02/11/2023]
Abstract
As the world is facing increasing difficulties to treat leishmaniasis with current therapies, deeper investigation into the molecular mechanisms responsible for both drug resistance and treatment failure (TF) is essential in drug discovery and development. So far, few available drugs cause severe side effects and have developed several resistance mechanisms. Drug resistance and TF parasite strains from clinical isolates may have acquired altered expression of proteins that characterize specific mechanisms leading to therapy inefficacy. This work aims to identify the biochemical pathways of THP-1 human monocytes infected by different Leishmania infantum clinical isolates from patients with either resistance or with TF outcome, using whole cell differential Mass Spectrometry proteomics. We have adopted network enrichment analysis to integrate the transcriptomics and the proteomic results of infected cells studies. Transferrin receptor C (TFRC) and nucleoside diphosphate kinase 3 (NDK3) were discovered as overexpressed proteins in THP-1 cells infected with paromomycin, antimony, and miltefosine resistant L. infantum lines. The overall achievements represent founding concepts to confirm new targets involved in the parasitic drug resistance and TF mechanisms, and to consider in perspective the importance of a dual host-guest pharmacological approach to treat the acute stage of the disease.
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Affiliation(s)
- Lorenzo Tagliazucchi
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.,Clinical and Experimental Medicine (CEM) Ph.D. Program, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Ana Perea-Martinez
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Greta Fiorini
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - José Ignacio Manzano
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Filippo Genovese
- Centro Interdipartimentale Grandi Strumenti (CIGS), University of Modena and Reggio Emilia, Via Campi 213/A, 41125 Modena, Italy
| | - Raquel García-Hernández
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Diego Pinetti
- Centro Interdipartimentale Grandi Strumenti (CIGS), University of Modena and Reggio Emilia, Via Campi 213/A, 41125 Modena, Italy
| | - Francisco Gamarro
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Maria Paola Costi
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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Omics Approaches in Drug Development against Leishmaniasis: Current Scenario and Future Prospects. Pathogens 2022; 12:pathogens12010039. [PMID: 36678387 PMCID: PMC9866966 DOI: 10.3390/pathogens12010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
Leishmaniasis is a zoonotic disease transmitted in humans by the bite of Leishmania-infected phlebotomine sandflies. Each year approximately 58,500 cases of leishmaniasis are diagnosed across the globe, with a mortality rate of nearly seven percent. There are over 20 parasitic strains of Leishmania which are known to cause distinct types of leishmaniasis and pose an endemic threat to humans worldwide. Therefore, it is crucial to develop potential medications and vaccines to combat leishmaniasis. However, the task of developing therapeutic solutions is challenging due to Leishmania's digenetic lifecycle. The challenge is further intensified by cases of resistance against the available drugs. Owing to these challenges, the conventional drug development regimen is further limited by target discovery and ligand suitability for the targets. On the other hand, as an added advantage, the emergence of omics-based tools, such as high-end proteomics, transcriptomics and genomics, has hastened the pace of target discovery and target-based drug development. It is now becoming apparent that multi-omics convergence and an inter-connected systems approach is less time-consuming and more cost-effective for any drug-development process. This comprehensive review is an attempt to summarize the current knowledge on the muti-omics approach in drug development against leishmaniasis. In particular, it elaborates the potential target identification from secreted proteins in various stages of Leishmania infection and also illustrates the convergence of transcriptomic and genomic data towards the collective goal of drug discovery. This review also provides an understanding of the potential parasite's drug targets and drug resistance characteristics of the parasite, which can be used in designing effective and specific therapeutics.
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Chaparro V, Graber TE, Alain T, Jaramillo M. Transcriptional profiling of macrophages reveals distinct parasite stage-driven signatures during early infection by Leishmania donovani. Sci Rep 2022; 12:6369. [PMID: 35430587 PMCID: PMC9013368 DOI: 10.1038/s41598-022-10317-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/05/2022] [Indexed: 12/22/2022] Open
Abstract
Macrophages undergo swift changes in mRNA abundance upon pathogen invasion. Herein we describe early remodelling of the macrophage transcriptome during infection by amastigotes or promastigotes of Leishmania donovani. Approximately 10–16% of host mRNAs were differentially modulated in L. donovani-infected macrophages when compared to uninfected controls. This response was partially stage-specific as a third of changes in mRNA abundance were either exclusively driven by one of the parasite forms or significantly different between them. Gene ontology analyses identified categories associated with immune functions (e.g. antigen presentation and leukocyte activation) among significantly downregulated mRNAs during amastigote infection while cytoprotective-related categories (e.g. DNA repair and apoptosis inhibition) were enriched in upregulated transcripts. Interestingly a combination of upregulated (e.g. cellular response to IFNβ) and repressed (e.g. leukocyte activation, chemotaxis) immune-related transcripts were overrepresented in the promastigote-infected dataset. In addition, Ingenuity Pathway Analysis (IPA) associated specific mRNA subsets with a number of upstream transcriptional regulators predicted to be modulated in macrophages infected with L. donovani amastigotes (e.g. STAT1 inhibition) or promastigotes (e.g. NRF2, IRF3, and IRF7 activation). Overall, our results indicate that early parasite stage-driven transcriptional remodelling in macrophages contributes to orchestrate both protective and deleterious host cell responses during L. donovani infection.
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Silvestre A, Shintre SS, Rachidi N. Released Parasite-Derived Kinases as Novel Targets for Antiparasitic Therapies. Front Cell Infect Microbiol 2022; 12:825458. [PMID: 35252034 PMCID: PMC8893276 DOI: 10.3389/fcimb.2022.825458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
The efficient manipulation of their host cell is an essential feature of intracellular parasites. Most molecular mechanisms governing the subversion of host cell by protozoan parasites involve the release of parasite-derived molecules into the host cell cytoplasm and direct interaction with host proteins. Among these released proteins, kinases are particularly important as they govern the subversion of important host pathways, such as signalling or metabolic pathways. These enzymes, which catalyse the transfer of a phosphate group from ATP onto serine, threonine, tyrosine or histidine residues to covalently modify proteins, are involved in numerous essential biological processes such as cell cycle or transport. Although little is known about the role of most of the released parasite-derived kinases in the host cell, they are examples of kinases hijacking host cellular pathways such as signal transduction or apoptosis, which are essential for immune response evasion as well as parasite survival and development. Here we present the current knowledge on released protozoan kinases and their involvement in host-pathogen interactions. We also highlight the knowledge gaps remaining before considering those kinases - involved in host signalling subversion - as antiparasitic drug targets.
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Affiliation(s)
- Anne Silvestre
- INRAE, Université de Tours, ISP, Nouzilly, France
- *Correspondence: Anne Silvestre, ; Najma Rachidi,
| | - Sharvani Shrinivas Shintre
- INRAE, Université de Tours, ISP, Nouzilly, France
- Institut Pasteur, Université de Paris and INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Najma Rachidi
- Institut Pasteur, Université de Paris and INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
- *Correspondence: Anne Silvestre, ; Najma Rachidi,
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Smirlis D, Dingli F, Sabatet V, Roth A, Knippschild U, Loew D, Späth GF, Rachidi N. Identification of the Host Substratome of Leishmania-Secreted Casein Kinase 1 Using a SILAC-Based Quantitative Mass Spectrometry Assay. Front Cell Dev Biol 2022; 9:800098. [PMID: 35047509 PMCID: PMC8762337 DOI: 10.3389/fcell.2021.800098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022] Open
Abstract
Leishmaniasis is a severe public health problem, caused by the protozoan Leishmania. This parasite has two developmental forms, extracellular promastigote in the insect vector and intracellular amastigote in the mammalian host where it resides inside the phagolysosome of macrophages. Little is known about the virulence factors that regulate host-pathogen interactions and particularly host signalling subversion. All the proteomes of Leishmania extracellular vesicles identified the presence of Leishmania casein kinase 1 (L-CK1.2), a signalling kinase. L-CK1.2 is essential for parasite survival and thus might be essential for host subversion. To get insights into the functions of L-CK1.2 in the macrophage, the systematic identification of its host substrates is crucial, we thus developed an easy method to identify substrates, combining phosphatase treatment, in vitro kinase assay and Stable Isotope Labelling with Amino acids in Cell (SILAC) culture-based mass spectrometry. Implementing this approach, we identified 225 host substrates as well as a potential novel phosphorylation motif for CK1. We confirmed experimentally the enrichment of our substratome in bona fide L-CK1.2 substrates and showed they were also phosphorylated by human CK1δ. L-CK1.2 substratome is enriched in biological processes such as "viral and symbiotic interaction," "actin cytoskeleton organisation" and "apoptosis," which are consistent with the host pathways modified by Leishmania upon infection, suggesting that L-CK1.2 might be the missing link. Overall, our results generate important mechanistic insights into the signalling of host subversion by these parasites and other microbial pathogens adapted for intracellular survival.
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Affiliation(s)
- Despina Smirlis
- Institut Pasteur, Université de Paris, Institut National de Santé et Recherche Médicale INSERM U1201, Unité de parasitologie Moléculaire et Signalisation, Paris, France.,Hellenic Pasteur Institute, Athens, Greece
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse Protéomique (LSMP), Centre de Recherche, Institut Curie, PSL Research University, Paris, France
| | - Valentin Sabatet
- Laboratoire de Spectrométrie de Masse Protéomique (LSMP), Centre de Recherche, Institut Curie, PSL Research University, Paris, France
| | - Aileen Roth
- Department of General and Visceral Surgery, Centre of Surgery, University Hospital Ulm, Ulm, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Centre of Surgery, University Hospital Ulm, Ulm, Germany
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique (LSMP), Centre de Recherche, Institut Curie, PSL Research University, Paris, France
| | - Gerald F Späth
- Institut Pasteur, Université de Paris, Institut National de Santé et Recherche Médicale INSERM U1201, Unité de parasitologie Moléculaire et Signalisation, Paris, France
| | - Najma Rachidi
- Institut Pasteur, Université de Paris, Institut National de Santé et Recherche Médicale INSERM U1201, Unité de parasitologie Moléculaire et Signalisation, Paris, France
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7
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Zilberstein D. Lysosome Sensing Is a Key Mechanism in Leishmania Intracellular Development. Front Microbiol 2021; 12:667807. [PMID: 34025623 PMCID: PMC8137843 DOI: 10.3389/fmicb.2021.667807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/25/2021] [Indexed: 01/01/2023] Open
Abstract
Phagolysosomes of macrophages are the niche where the parasitic protozoan Leishmania resides and causes human leishmaniasis. During infection, this organism encounters dramatic environmental changes. These include heat shock (from 26°C in the vector to 33°C or 37°C in the host, for cutaneous and visceral species, respectively) and acidic pH typical to the lysosome and nutrient availability. Leishmania cells developed ways to sense the lysosome-specific environment (acidic pH and body temperature) as means of recognition and, subsequently, initiation of differentiation into the intracellular form. Recent studies have indicated that protein kinase A plays a role as the gatekeeper that enables differentiation initiation. This review provides an update on the lysosome signaling pathway-mediated Leishmania intracellular development.
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Affiliation(s)
- Dan Zilberstein
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa, Israel
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Xue X, Ren S, Yang X, Masoudi A, Hu Y, Wang X, Li H, Zhang X, Wang M, Wang H, Liu J. Protein regulation strategies of the mouse spleen in response to Babesia microti infection. Parasit Vectors 2021; 14:61. [PMID: 33468223 PMCID: PMC7814643 DOI: 10.1186/s13071-020-04574-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/29/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Babesia is a protozoan parasite that infects red blood cells in some vertebrates. Some species of Babesia can induce zoonoses and cause considerable harm. As the largest immune organ in mammals, the spleen plays an important role in defending against Babesia infection. When infected with Babesia, the spleen is seriously injured but still actively initiates immunomodulatory responses. METHODS To explore the molecular mechanisms underlying the immune regulation and self-repair of the spleen in response to infection, this study used data-independent acquisition (DIA) quantitative proteomics to analyse changes in expression levels of global proteins and in phosphorylation modification in spleen tissue after Babesia microti infection in mice. RESULTS After mice were infected with B. microti, their spleens were seriously damaged. Using bioinformatics methods to analyse dynamic changes in a large number of proteins, we found that the spleen still initiated immune responses to combat the infection, with immune-related proteins playing an important role, including cathepsin D (CTSD), interferon-induced protein 44 (IFI44), interleukin-2 enhancer-binding factor 2 (ILF2), interleukin enhancer-binding factor 3 (ILF3) and signal transducer and activator of transcription 5A (STAT5A). In addition, some proteins related to iron metabolism were also involved in the repair of the spleen after B. microti infection, including serotransferrin, lactoferrin, transferrin receptor protein 1 (TfR1) and glutamate-cysteine ligase (GCL). At the same time, the expression and phosphorylation of proteins related to the growth and development of the spleen also changed, including protein kinase C-δ (PKC-δ), mitogen-activated protein kinase (MAPK) 3/1, growth factor receptor-bound protein 2 (Grb2) and P21-activated kinase 2 (PAK2). CONCLUSIONS Immune-related proteins, iron metabolism-related proteins and growth and development-related proteins play an important role in the regulation of spleen injury and maintenance of homeostasis. This study provides an important basis for the diagnosis and treatment of babesiosis.
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Affiliation(s)
- Xiaomin Xue
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Shuguang Ren
- The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, Hebei, People's Republic of China
| | - Xiaohong Yang
- Department of Pathogenic Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, People's Republic of China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Yuhong Hu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.,Instrumental Analysis Center, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Xiaoshuang Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Hongxia Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Xiaojing Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Minjing Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Hui Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.
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