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Diotallevi A, Bruno F, Castelli G, Persico G, Buffi G, Ceccarelli M, Ligi D, Mannello F, Vitale F, Magnani M, Galluzzi L. Transcriptional signatures in human macrophage-like cells infected by Leishmania infantum, Leishmania major and Leishmania tropica. PLoS Negl Trop Dis 2024; 18:e0012085. [PMID: 38578804 PMCID: PMC11023634 DOI: 10.1371/journal.pntd.0012085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/17/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND In the Mediterranean basin, three Leishmania species have been identified: L. infantum, L. major and L. tropica, causing zoonotic visceral leishmaniasis (VL), zoonotic cutaneous leishmaniasis (CL) and anthroponotic CL, respectively. Despite animal models and genomic/transcriptomic studies provided important insights, the pathogenic determinants modulating the development of VL and CL are still poorly understood. This work aimed to identify host transcriptional signatures shared by cells infected with L. infantum, L. major, and L. tropica, as well as specific transcriptional signatures elicited by parasites causing VL (i.e., L. infantum) and parasites involved in CL (i.e., L. major, L. tropica). METHODOLOGY/PRINCIPAL FINDINGS U937 cells differentiated into macrophage-like cells were infected with L. infantum, L. major and L. tropica for 24h and 48h, and total RNA was extracted. RNA sequencing, performed on an Illumina NovaSeq 6000 platform, was used to evaluate the transcriptional signatures of infected cells with respect to non-infected cells at both time points. The EdgeR package was used to identify differentially expressed genes (fold change > 2 and FDR-adjusted p-values < 0.05). Then, functional enrichment analysis was employed to identify the enriched ontology terms in which these genes are involved. At 24h post-infection, a common signature of 463 dysregulated genes shared among all infection conditions was recognized, while at 48h post-infection the common signature was reduced to 120 genes. Aside from a common transcriptional response, we evidenced different upregulated functional pathways characterizing L. infantum-infected cells, such as VEGFA-VEGFR2 and NFE2L2-related pathways, indicating vascular remodeling and reduction of oxidative stress as potentially important factors for visceralization. CONCLUSIONS The identification of pathways elicited by parasites causing VL or CL could lead to new therapeutic strategies for leishmaniasis, combining the canonical anti-leishmania compounds with host-directed therapy.
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Affiliation(s)
- Aurora Diotallevi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Federica Bruno
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia A Mirri, Palermo, Italy
| | - Germano Castelli
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia A Mirri, Palermo, Italy
| | - Giuseppe Persico
- Department of Experimental Oncology, IRCCS, European Institute of Oncology, Milan, Italy
| | - Gloria Buffi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Marcello Ceccarelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Daniela Ligi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Ferdinando Mannello
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Fabrizio Vitale
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia A Mirri, Palermo, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Luca Galluzzi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
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Moradimotlagh A, Chen S, Koohbor S, Moon KM, Foster LJ, Reiner N, Nandan D. Leishmania infection upregulates and engages host macrophage Argonaute 1, and system-wide proteomics reveals Argonaute 1-dependent host response. Front Immunol 2023; 14:1287539. [PMID: 38098491 PMCID: PMC10720368 DOI: 10.3389/fimmu.2023.1287539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/26/2023] [Indexed: 12/17/2023] Open
Abstract
Leishmania donovani, an intracellular protozoan parasite, is the causative agent of visceral leishmaniasis, the most severe form of leishmaniasis in humans. It is becoming increasingly clear that several intracellular pathogens target host cell RNA interference (RNAi) pathways to promote their survival. Complexes of Argonaute proteins with small RNAs are core components of the RNAi. In this study, we investigated the potential role of host macrophage Argonautes in Leishmania pathogenesis. Using Western blot analysis of Leishmania donovani-infected macrophages, we show here that Leishmania infection selectively increased the abundance of host Argonaute 1 (Ago1). This increased abundance of Ago1 in infected cells also resulted in higher levels of Ago1 in active Ago-complexes, suggesting the preferred use of Ago1 in RNAi in Leishmania-infected cells. This analysis used a short trinucleotide repeat containing 6 (TNRC6)/glycine-tryptophan repeat protein (GW182) protein-derived peptide fused to Glutathione S-transferase as an affinity matrix to capture mature Ago-small RNAs complexes from the cytosol of non-infected and Leishmania-infected cells. Furthermore, Ago1 silencing significantly reduced intracellular survival of Leishmania, demonstrating that Ago1 is essential for Leishmania pathogenesis. To investigate the role of host Ago1 in Leishmania pathogenesis, a quantitative whole proteome approach was employed, which showed that expression of several previously reported Leishmania pathogenesis-related proteins was dependent on the level of macrophage Ago1. Together, these findings identify Ago1 as the preferred Argonaute of RNAi machinery in infected cells and a novel and essential virulence factor by proxy that promotes Leishmania survival.
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Affiliation(s)
- Atieh Moradimotlagh
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stella Chen
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sara Koohbor
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Neil Reiner
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Devki Nandan
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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Pouyabahar D, Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, McGilvray ID, MacParland SA, Bader GD. A rat liver cell atlas reveals intrahepatic myeloid heterogeneity. iScience 2023; 26:108213. [PMID: 38026201 PMCID: PMC10651689 DOI: 10.1016/j.isci.2023.108213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/20/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
The large size and vascular accessibility of the laboratory rat (Rattus norvegicus) make it an ideal hepatic animal model for diseases that require surgical manipulation. Often, the disease susceptibility and outcomes of inflammatory pathologies vary significantly between strains. This study uses single-cell transcriptomics to better understand the complex cellular network of the rat liver, as well as to unravel the cellular and molecular sources of inter-strain hepatic variation. We generated single-cell and single-nucleus transcriptomic maps of the livers of healthy Dark Agouti and Lewis rat strains and developed a factor analysis-based bioinformatics analysis pipeline to study data covariates, such as strain and batch. Using this approach, we discovered transcriptomic variation within the hepatocyte and myeloid populations that underlie distinct cell states between rat strains. This finding will help provide a reference for future investigations on strain-dependent outcomes of surgical experiment models.
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Affiliation(s)
- Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Sai W. Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Olivia I. Pezzutti
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Catia T. Perciani
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xinle Wang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xue-Zhong Ma
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Chao Jiang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Damra Camat
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Trevor Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Manmeet Sekhon
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Justin Manuel
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xu-Chun Chen
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Ian D. McGilvray
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Sonya A. MacParland
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, ON, Canada
- The Multiscale Human Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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Tarannum A, Rodríguez-Almonacid CC, Salazar-Bravo J, Karamysheva ZN. Molecular Mechanisms of Persistence in Protozoan Parasites. Microorganisms 2023; 11:2248. [PMID: 37764092 PMCID: PMC10534552 DOI: 10.3390/microorganisms11092248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Protozoan parasites are known for their remarkable capacity to persist within the bodies of vertebrate hosts, which frequently results in prolonged infections and the recurrence of diseases. Understanding the molecular mechanisms that underlie the event of persistence is of paramount significance to develop innovative therapeutic approaches, given that these pathways still need to be thoroughly elucidated. The present article provides a comprehensive overview of the latest developments in the investigation of protozoan persistence in vertebrate hosts. The focus is primarily on the function of persisters, their formation within the host, and the specific molecular interactions between host and parasite while they persist. Additionally, we examine the metabolomic, transcriptional, and translational changes that protozoan parasites undergo during persistence within vertebrate hosts, focusing on major parasites such as Plasmodium spp., Trypanosoma spp., Leishmania spp., and Toxoplasma spp. Key findings of our study suggest that protozoan parasites deploy several molecular and physiological strategies to evade the host immune surveillance and sustain their persistence. Furthermore, some parasites undergo stage differentiation, enabling them to acclimate to varying host environments and immune challenges. More often, stressors such as drug exposure were demonstrated to impact the formation of protozoan persisters significantly. Understanding the molecular mechanisms regulating the persistence of protozoan parasites in vertebrate hosts can reinvigorate our current insights into host-parasite interactions and facilitate the development of more efficacious disease therapeutics.
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Affiliation(s)
| | | | | | - Zemfira N. Karamysheva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (A.T.); (C.C.R.-A.); (J.S.-B.)
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5
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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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6
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Goto Y, Mizobuchi H. Pathological roles of macrophages in Leishmania infections. Parasitol Int 2023; 94:102738. [PMID: 36738983 DOI: 10.1016/j.parint.2023.102738] [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] [Received: 10/27/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Macrophages are the major host cells for Leishmania parasites, and determine the fate of infection by either limiting or allowing growth of the parasites, resulting in development or control of leishmaniasis, respectively. They also play important roles in causing pathological outcomes during Leishmania infection. The pathophysiology is complex and include a wide variety of molecular and cellular responses including enhancement of inflammatory responses by releasing cytokines, causing damages to surrounding cells by reactive oxygen species, or disordered phagocytosis of other cells. It is of note that disease severity in leishmaniasis sometimes does not correlate with parasite burdens, indicating that pathological roles of macrophages are not necessarily linked to their parasite-killing activities that are often defined by M1/M2 status. Here, we review the roles of macrophages in leishmaniasis with a focus on their pathological mechanisms in disease development.
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Affiliation(s)
- Yasuyuki Goto
- Laboratory of Molecular Immunology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Haruka Mizobuchi
- Laboratory of Molecular Immunology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Venugopal G, Bird JT, Roys H, Bowlin A, Fry L, Byrum SD, Weinkopff T. BOTH THE INFECTION STATUS AND INFLAMMATORY MICROENVIRONMENT INDUCE TRANSCRIPTIONAL REMODELING IN MACROPHAGES IN MURINE LEISHMANIAL LESIONS. J Parasitol 2023; 109:200-210. [PMID: 37270767 DOI: 10.1645/22-94] [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: 06/05/2023] Open
Abstract
Cutaneous leishmaniasis is caused by infection with the protozoan parasite Leishmania, which resides intracellularly in dermal macrophages (Mø), producing lesions. The skin lesions are characterized by proinflammatory cytokines and growth factors as well as inflammatory hypoxia, creating a stressful microenvironment for Mø. Of importance, not all Mø in lesions harbor parasites. To distinguish the influence of the parasite from the inflammatory microenvironment after Leishmania major (LM) infection on the Mø, we performed single-cell RNA sequencing and compared Mø associated with LM transcripts (or 'infected' Mø) with Mø not associated with LM transcripts (or 'bystander' Mø) within the lesions. Our findings show coordinated lysosomal expression and regulation signaling with increased cathepsin and H+-ATPase transcripts are upregulated in infected compared with bystander Mø. Additionally, eukaryotic initiation factor 2 (EIF2) signaling is downregulated in infected compared with bystander Mø, which includes many small and large ribosomal subunit (Rps and Rpl) transcripts being decreased in Mø harboring parasites. Furthermore, we also find EIF2 signaling including EIF, Rps, and Rpl transcripts being downregulated in bystander Mø compared with Mø from naïve skin. These data suggest that both the parasite and the inflammatory host microenvironment affect the transcription of ribosomal machinery in lesional Mø, thereby potentially affecting the ability of these cells to perform translation, protein synthesis, and thus function. Altogether, these results suggest that both the parasite and host inflammatory microenvironment independently drive transcriptional remodeling in Mø during LM infection in vivo.
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Affiliation(s)
- Gopinath Venugopal
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Jordan T Bird
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
- Arkansas Children's Research Institute, Little Rock, Arkansas 72202
| | - Hayden Roys
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Anne Bowlin
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Lucy Fry
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
- Arkansas Children's Research Institute, Little Rock, Arkansas 72202
| | - Tiffany Weinkopff
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
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Bouabid C, Rabhi S, Thedinga K, Barel G, Tnani H, Rabhi I, Benkahla A, Herwig R, Guizani-Tabbane L. Host M-CSF induced gene expression drives changes in susceptible and resistant mice-derived BMdMs upon Leishmania major infection. Front Immunol 2023; 14:1111072. [PMID: 37187743 PMCID: PMC10175952 DOI: 10.3389/fimmu.2023.1111072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Leishmaniases are a group of diseases with different clinical manifestations. Macrophage-Leishmania interactions are central to the course of the infection. The outcome of the disease depends not only on the pathogenicity and virulence of the parasite, but also on the activation state, the genetic background, and the underlying complex interaction networks operative in the host macrophages. Mouse models, with mice strains having contrasting behavior in response to parasite infection, have been very helpful in exploring the mechanisms underlying differences in disease progression. We here analyzed previously generated dynamic transcriptome data obtained from Leishmania major (L. major) infected bone marrow derived macrophages (BMdMs) from resistant and susceptible mouse. We first identified differentially expressed genes (DEGs) between the M-CSF differentiated macrophages derived from the two hosts, and found a differential basal transcriptome profile independent of Leishmania infection. These host signatures, in which 75% of the genes are directly or indirectly related to the immune system, may account for the differences in the immune response to infection between the two strains. To gain further insights into the underlying biological processes induced by L. major infection driven by the M-CSF DEGs, we mapped the time-resolved expression profiles onto a large protein-protein interaction (PPI) network and performed network propagation to identify modules of interacting proteins that agglomerate infection response signals for each strain. This analysis revealed profound differences in the resulting responses networks related to immune signaling and metabolism that were validated by qRT-PCR time series experiments leading to plausible and provable hypotheses for the differences in disease pathophysiology. In summary, we demonstrate that the host's gene expression background determines to a large degree its response to L. major infection, and that the gene expression analysis combined with network propagation is an effective approach to help identifying dynamically altered mouse strain-specific networks that hold mechanistic information about these contrasting responses to infection.
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Affiliation(s)
- Cyrine Bouabid
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
- Faculty of Sciences of Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Sameh Rabhi
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Kristina Thedinga
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gal Barel
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hedia Tnani
- Laboratory de BioInformatic, BioMathematic and BioStatistic (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Imen Rabhi
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
- Higher Institute of Biotechnology at Sidi-Thabet (ISBST), Biotechnopole Sidi-Thabet- University of Manouba, Sidi-Thabet, Tunisia
| | - Alia Benkahla
- Laboratory de BioInformatic, BioMathematic and BioStatistic (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Ralf Herwig
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lamia Guizani-Tabbane
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
- *Correspondence: Lamia Guizani-Tabbane,
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Bekkar A, Isorce N, Snäkä T, Claudinot S, Desponds C, Kopelyanskiy D, Prével F, Reverte M, Xenarios I, Fasel N, Teixeira F. Dissection of the macrophage response towards infection by the Leishmania-viral endosymbiont duo and dynamics of the type I interferon response. Front Cell Infect Microbiol 2022; 12:941888. [PMID: 35992159 PMCID: PMC9386148 DOI: 10.3389/fcimb.2022.941888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Abstract
Leishmania RNA virus 1 (LRV1) is a double-stranded RNA virus found in some strains of the human protozoan parasite Leishmania, the causative agent of leishmaniasis, a neglected tropical disease. Interestingly, the presence of LRV1 inside Leishmania constitutes an important virulence factor that worsens the leishmaniasis outcome in a type I interferon (IFN)–dependent manner and contributes to treatment failure. Understanding how macrophages respond toward Leishmania alone or in combination with LRV1 as well as the role that type I IFNs may play during infection is fundamental to oversee new therapeutic strategies. To dissect the macrophage response toward infection, RNA sequencing was performed on murine wild-type and Ifnar-deficient bone marrow–derived macrophages infected with Leishmania guyanensis (Lgy) devoid or not of LRV1. Additionally, macrophages were treated with poly I:C (mimetic virus) or with type I IFNs. By implementing a weighted gene correlation network analysis, the groups of genes (modules) with similar expression patterns, for example, functionally related, coregulated, or the members of the same functional pathway, were identified. These modules followed patterns dependent on Leishmania, LRV1, or Leishmania exacerbated by the presence of LRV1. Not only the visualization of how individual genes were embedded to form modules but also how different modules were related to each other were observed. Thus, in the context of the observed hyperinflammatory phenotype associated to the presence of LRV1, it was noted that the biomarkers tumor-necrosis factor α (TNF-α) and the interleukin 6 (IL-6) belonged to different modules and that their regulating specific Src-family kinases were segregated oppositely. In addition, this network approach revealed the strong and sustained effect of LRV1 on the macrophage response and genes that had an early, late, or sustained impact during infection, uncovering the dynamics of the IFN response. Overall, this study contributed to shed light and dissect the intricate macrophage response toward infection by the Leishmania-LRV1 duo and revealed the crosstalk between modules made of coregulated genes and provided a new resource that can be further explored to study the impact of Leishmania on the macrophage response.
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Affiliation(s)
- Amel Bekkar
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Nathalie Isorce
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Tiia Snäkä
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | | | - Chantal Desponds
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | | | - Florence Prével
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Marta Reverte
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Ioannis Xenarios
- Agora Center, Center Hospitalier Universitaire (CHUV), Lausanne, Switzerland
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Fasel
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
- *Correspondence: Nicolas Fasel, ; Filipa Teixeira,
| | - Filipa Teixeira
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
- *Correspondence: Nicolas Fasel, ; Filipa Teixeira,
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