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Cosgrove J, Marçais A, Hartmann FJ, Bergthaler A, Zanoni I, Corrado M, Perié L, Cabezas-Wallscheid N, Bousso P, Alexandrov T, Kielian T, Martínez-Martín N, Opitz CA, Lyssiotis CA, Argüello RJ, Van den Bossche J. A call for accessible tools to unlock single-cell immunometabolism research. Nat Metab 2024; 6:779-782. [PMID: 38605184 DOI: 10.1038/s42255-024-01031-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Antoine Marçais
- CIRI, Centre International de Recherche en Infectiologie, (Team Lyacts), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Felix J Hartmann
- German Cancer Research Center (DKFZ), Heidelberg, Systems Immunology & Single-Cell Biology, Germany and German Cancer Consortium (DKTK), DKFZ, Core Center Heidelberg, Heidelberg, Germany
| | - Andreas Bergthaler
- Institute of Hygiene and Applied Immunology, Department of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ivan Zanoni
- Division of Immunology, Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mauro Corrado
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Institute for Genetics, University of Cologne, Cologne, Germany
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | | | - Philippe Bousso
- Institut Pasteur, Université Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Paris, France
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Bio Studio, BioInnovation Institute, Copenhagen, Denmark
| | - Tammy Kielian
- Department of Pathology, Microbiology, and Immunology University of Nebraska Medical Center, Omaha, NE, USA
| | - Nuria Martínez-Martín
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
| | - Christiane A Opitz
- German Cancer Research Center (DKFZ), Heidelberg, Division of Metabolic Crosstalk in Cancer and the German Cancer Consortium (DKTK), DKFZ Core Center Heidelberg, Heidelberg, Germany
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, Department of Internal Medicine, Division of Gastroenterology and Hepatology, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Rafael J Argüello
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Centre for Living Systems, Marseille, France
| | - Jan Van den Bossche
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Institute for Infection and Immunity, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
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Rinaldi G, Loukas A, Sotillo J. Trematode Genomics and Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1454:507-539. [PMID: 39008274 DOI: 10.1007/978-3-031-60121-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Trematode infections stand out as one of the frequently overlooked tropical diseases, despite their wide global prevalence and remarkable capacity to parasitize diverse host species and tissues. Furthermore, these parasites hold significant socio-economic, medical, veterinary and agricultural implications. Over the past decades, substantial strides have been taken to bridge the information gap concerning various "omic" tools, such as proteomics and genomics, in this field. In this edition of the book, we highlight recent progress in genomics and proteomics concerning trematodes with a particular focus on the advances made in the past 5 years. Additionally, we present insights into cutting-edge technologies employed in studying trematode biology and shed light on the available resources for exploring the molecular facets of this particular group of parasitic helminths.
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Affiliation(s)
- Gabriel Rinaldi
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Javier Sotillo
- Laboratorio de Referencia e Investigación en Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain.
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Bennett CL, Perona-Wright G. Metabolic adaption of mucosal macrophages: Is metabolism a driver of persistence across tissues? Mucosal Immunol 2023; 16:753-763. [PMID: 37385586 PMCID: PMC10564628 DOI: 10.1016/j.mucimm.2023.06.006] [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: 02/21/2023] [Revised: 05/27/2023] [Accepted: 06/17/2023] [Indexed: 07/01/2023]
Abstract
Macrophages play essential roles in tissue homeostasis, defense, and repair. Their functions are highly tissue-specific, and when damage and inflammation stimulate repopulation by circulating monocytes, the incoming monocytes rapidly acquire the same, tissue-specific functions as the previous, resident macrophages. Several environmental factors are thought to guide the functional differentiation of recruited monocytes, including metabolic pressures imposed by the fuel sources available in each tissue. Here we discuss whether such a model of metabolic determinism can be applied to macrophage differentiation across barrier sites, from the lung to the skin. We suggest an alternative model, in which metabolic phenotype is a consequence of macrophage longevity rather than an early driver of tissue-specific adaption.
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Affiliation(s)
- Clare L Bennett
- Department of Haematology, UCL Cancer Institute, University College London, London, UK.
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Baquer G, Sementé L, Ràfols P, Martín-Saiz L, Bookmeyer C, Fernández JA, Correig X, García-Altares M. rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation. J Cheminform 2023; 15:80. [PMID: 37715285 PMCID: PMC10504721 DOI: 10.1186/s13321-023-00756-2] [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: 04/03/2023] [Accepted: 08/29/2023] [Indexed: 09/17/2023] Open
Abstract
Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) spatially resolves the chemical composition of tissues. Lipids are of particular interest, as they influence important biological processes in health and disease. However, the identification of lipids in MALDI-MSI remains a challenge due to the lack of chromatographic separation or untargeted tandem mass spectrometry. Recent studies have proposed the use of MALDI in-source fragmentation to infer structural information and aid identification. Here we present rMSIfragment, an open-source R package that exploits known adducts and fragmentation pathways to confidently annotate lipids in MALDI-MSI. The annotations are ranked using a novel score that demonstrates an area under the curve of 0.7 in ROC analyses using HPLC-MS and Target-Decoy validations. rMSIfragment applies to multiple MALDI-MSI sample types and experimental setups. Finally, we demonstrate that overlooking in-source fragments increases the number of incorrect annotations. Annotation workflows should consider in-source fragmentation tools such as rMSIfragment to increase annotation confidence and reduce the number of false positives.
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Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain.
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain.
| | - Lucía Martín-Saiz
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Christoph Bookmeyer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Institute of Hygiene, University of Münster, Münster, Germany
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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Forrester S, Goundry A, Dias BT, Leal-Calvo T, Moraes MO, Kaye PM, Mottram JC, Lima APCA. Tissue Specific Dual RNA-Seq Defines Host-Parasite Interplay in Murine Visceral Leishmaniasis Caused by Leishmania donovani and Leishmania infantum. Microbiol Spectr 2022; 10:e0067922. [PMID: 35384718 PMCID: PMC9045295 DOI: 10.1128/spectrum.00679-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 01/22/2023] Open
Abstract
Visceral leishmaniasis is associated with hepato-splenomegaly and altered immune and hematological parameters in both preclinical animal models and humans. We studied mouse experimental visceral leishmaniasis caused by Leishmania infantum and Leishmania donovani in BALB/c mice using dual RNA-seq to investigate the transcriptional response of host and parasite in liver and spleen. We identified only 4 species-specific parasite expressed genes (SSPEGs; log2FC >1, FDR <0.05) in the infected spleen, and none in the infected liver. For the host transcriptome, we found 789 differentially expressed genes (DEGs; log2FC >1, FDR <0.05) in the spleen that were common to both infections, with IFNγ signaling and complement and coagulation cascade pathways highly enriched, and an additional 286 and 186 DEGs that were selective to L. donovani and L. infantum infection, respectively. Among those, there were network interactions between genes of amino acid metabolism and PPAR signaling in L. donovani infection and increased IL1β and positive regulation of fatty acid transport in L. infantum infection, although no pathway enrichment was observed. In the liver, there were 1,939 DEGs in mice infected with either L. infantum or L. donovani in comparison to uninfected mice, and the most enriched pathways were IFNγ signaling, neutrophil mediated immunity, complement and coagulation, cytokine-chemokine responses, and hemostasis. Additionally, 221 DEGs were selective in L. donovani and 429 DEGs in L. infantum infections. These data show that the host response for these two visceral leishmaniasis infection models is broadly similar, and ∼10% of host DEGs vary in infections with either parasite species. IMPORTANCE Visceral leishmaniasis (VL) is caused by two species of Leishmania parasites, L. donovani in the Old World and L. infantum in the New World and countries bordering the Mediterranean. Although cardinal features such as hepato-splenomegaly and alterations in blood and immune function are evident, clinical presentation may vary by geography, with for example severe bleeding often associated with VL in Brazil. Although animal models of both L. donovani and L. infantum have been widely used to study disease pathogenesis, a direct side-by-side comparison of how these parasites species impact the infected host and/or how they might respond to the stresses of mammalian infection has not been previously reported. Identifying common and distinct pathways to pathogenesis will be important to ensure that new therapeutic or prophylactic approaches will be applicable across all forms of VL.
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Affiliation(s)
- Sarah Forrester
- York Biomedical Research Institute, Department of Biology, University of York, York, England, United Kingdom
| | - Amy Goundry
- York Biomedical Research Institute, Department of Biology, University of York, York, England, United Kingdom
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruna Torres Dias
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Paul M. Kaye
- York Biomedical Research Institute, Hull York Medical School, University of York, York, England, United Kingdom
| | - Jeremy C. Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, England, United Kingdom
| | - Ana Paula C. A. Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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