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Dunican C, Andradi-Brown C, Ebmeier S, Georgiadou A, Cunnington AJ. The malarial blood transcriptome: translational applications. Biochem Soc Trans 2024; 52:651-660. [PMID: 38421063 PMCID: PMC11088907 DOI: 10.1042/bst20230497] [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: 11/09/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
The blood transcriptome of malaria patients has been used extensively to elucidate the pathophysiological mechanisms and host immune responses to disease, identify candidate diagnostic and prognostic biomarkers, and reveal new therapeutic targets for drug discovery. This review gives a high-level overview of the three main translational applications of these studies (diagnostics, prognostics, and therapeutics) by summarising recent literature and outlining the main limitations and future directions of each application. It highlights the need for consistent and accurate definitions of disease states and subject groups and discusses how prognostic studies must distinguish clearly between analyses that attempt to predict future disease states and those which attempt to discriminate between current disease states (classification). Lastly it examines how many promising therapeutics fail due to the choice of imperfect animal models for pre-clinical testing and lack of appropriate validation studies in humans, and how future transcriptional studies may be utilised to overcome some of these limitations.
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Affiliation(s)
- Claire Dunican
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
| | - Clare Andradi-Brown
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
| | - Stefan Ebmeier
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
| | - Athina Georgiadou
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
| | - Aubrey J. Cunnington
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, U.K
- Centre for Paediatrics and Child Health, Imperial College London, London, U.K
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2
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Nikulkova M, Abdrabou W, Carlton JM, Idaghdour Y. Exploiting integrative metabolomics to study host-parasite interactions in Plasmodium infections. Trends Parasitol 2024; 40:313-323. [PMID: 38508901 PMCID: PMC10994734 DOI: 10.1016/j.pt.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
Despite years of research, malaria remains a significant global health burden, with poor diagnostic tests and increasing antimalarial drug resistance challenging diagnosis and treatment. While 'single-omics'-based approaches have been instrumental in gaining insight into the biology and pathogenicity of the Plasmodium parasite and its interaction with the human host, a more comprehensive understanding of malaria pathogenesis can be achieved through 'multi-omics' approaches. Integrative methods, which combine metabolomics, lipidomics, transcriptomics, and genomics datasets, offer a holistic systems biology approach to studying malaria. This review highlights recent advances, future directions, and challenges involved in using integrative metabolomics approaches to interrogate the interactions between Plasmodium and the human host, paving the way towards targeted antimalaria therapeutics and control intervention methods.
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Affiliation(s)
- Maria Nikulkova
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 11101, USA; Johns Hopkins Malaria Research Institute, Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Wael Abdrabou
- Program in Biology, Division of Science and Mathematics, New York University, Abu Dhabi, United Arab Emirates
| | - Jane M Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 11101, USA; Johns Hopkins Malaria Research Institute, Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University, Abu Dhabi, United Arab Emirates
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3
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Tebben K, Yirampo S, Coulibaly D, Koné AK, Laurens MB, Stucke EM, Dembélé A, Tolo Y, Traoré K, Niangaly A, Berry AA, Kouriba B, Plowe CV, Doumbo OK, Lyke KE, Takala-Harrison S, Thera MA, Travassos MA, Serre D. Gene expression analyses reveal differences in children's response to malaria according to their age. Nat Commun 2024; 15:2021. [PMID: 38448421 PMCID: PMC10918175 DOI: 10.1038/s41467-024-46416-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
In Bandiagara, Mali, children experience on average two clinical malaria episodes per year. However, even in the same transmission area, the number of uncomplicated symptomatic infections, and their parasitemia, can vary dramatically among children. We simultaneously characterize host and parasite gene expression profiles from 136 Malian children with symptomatic falciparum malaria and examine differences in the relative proportion of immune cells and parasite stages, as well as in gene expression, associated with infection and or patient characteristics. Parasitemia explains much of the variation in host and parasite gene expression, and infections with higher parasitemia display proportionally more neutrophils and fewer T cells, suggesting parasitemia-dependent neutrophil recruitment and/or T cell extravasation to secondary lymphoid organs. The child's age also strongly correlates with variations in gene expression: Plasmodium falciparum genes associated with age suggest that older children carry more male gametocytes, while variations in host gene expression indicate a stronger innate response in younger children and stronger adaptive response in older children. These analyses highlight the variability in host responses and parasite regulation during P. falciparum symptomatic infections and emphasize the importance of considering the children's age when studying and treating malaria infections.
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Affiliation(s)
- Kieran Tebben
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Salif Yirampo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Abdoulaye K Koné
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Matthew B Laurens
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emily M Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ahmadou Dembélé
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Youssouf Tolo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Karim Traoré
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Andrea A Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Christopher V Plowe
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Kirsten E Lyke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mahamadou A Thera
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Mark A Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
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4
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Andradi-Brown C, Wichers-Misterek JS, von Thien H, Höppner YD, Scholz JAM, Hansson H, Filtenborg Hocke E, Gilberger TW, Duffy MF, Lavstsen T, Baum J, Otto TD, Cunnington AJ, Bachmann A. A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture. eLife 2024; 12:RP87726. [PMID: 38270586 PMCID: PMC10945709 DOI: 10.7554/elife.87726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
The pathogenesis of severe Plasmodium falciparum malaria involves cytoadhesive microvascular sequestration of infected erythrocytes, mediated by P. falciparum erythrocyte membrane protein 1 (PfEMP1). PfEMP1 variants are encoded by the highly polymorphic family of var genes, the sequences of which are largely unknown in clinical samples. Previously, we published new approaches for var gene profiling and classification of predicted binding phenotypes in clinical P. falciparum isolates (Wichers et al., 2021), which represented a major technical advance. Building on this, we report here a novel method for var gene assembly and multidimensional quantification from RNA-sequencing that outperforms the earlier approach of Wichers et al., 2021, on both laboratory and clinical isolates across a combination of metrics. Importantly, the tool can interrogate the var transcriptome in context with the rest of the transcriptome and can be applied to enhance our understanding of the role of var genes in malaria pathogenesis. We applied this new method to investigate changes in var gene expression through early transition of parasite isolates to in vitro culture, using paired sets of ex vivo samples from our previous study, cultured for up to three generations. In parallel, changes in non-polymorphic core gene expression were investigated. Modest but unpredictable var gene switching and convergence towards var2csa were observed in culture, along with differential expression of 19% of the core transcriptome between paired ex vivo and generation 1 samples. Our results cast doubt on the validity of the common practice of using short-term cultured parasites to make inferences about in vivo phenotype and behaviour.
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Affiliation(s)
- Clare Andradi-Brown
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Department of Life Sciences, Imperial College London, South KensingtonLondonUnited Kingdom
- Centre for Paediatrics and Child Health, Imperial College LondonLondonUnited Kingdom
| | - Jan Stephan Wichers-Misterek
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Heidrun von Thien
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Yannick D Höppner
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Judith AM Scholz
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
| | - Helle Hansson
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
- Department of Infectious Diseases, Copenhagen University HospitalCopenhagenDenmark
| | - Emma Filtenborg Hocke
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
- Department of Infectious Diseases, Copenhagen University HospitalCopenhagenDenmark
| | - Tim Wolf Gilberger
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Michael F Duffy
- Department of Microbiology and Immunology, University of MelbourneMelbourneAustralia
| | - Thomas Lavstsen
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
- Department of Infectious Diseases, Copenhagen University HospitalCopenhagenDenmark
| | - Jake Baum
- Department of Life Sciences, Imperial College London, South KensingtonLondonUnited Kingdom
- School of Biomedical Sciences, Faculty of Medicine & Health, UNSW, KensingtonSydneyUnited Kingdom
| | - Thomas D Otto
- School of Infection & Immunity, MVLS, University of GlasgowGlasgowUnited Kingdom
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Centre for Paediatrics and Child Health, Imperial College LondonLondonUnited Kingdom
| | - Anna Bachmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-RiemsHamburgGermany
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5
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Mura M, Misganaw B, Gautam A, Robinson T, Chaudhury S, Bansal N, Martins AJ, Tsang J, Hammamieh R, Bergmann-Leitner E. Human transcriptional signature of protection after Plasmodium falciparum immunization and infectious challenge via mosquito bites. Hum Vaccin Immunother 2023; 19:2282693. [PMID: 38010150 PMCID: PMC10760396 DOI: 10.1080/21645515.2023.2282693] [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: 09/14/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
The identification of immune correlates of protection against infectious pathogens will accelerate the design and optimization of recombinant and subunit vaccines. Systematic analyses such as immunoprofiling including serological, cellular, and molecular assessments supported by computational tools are key to not only identify correlates of protection but also biomarkers of disease susceptibility. The current study expands our previous cellular and serological profiling of vaccine-induced responses to a whole parasite malaria vaccine. The irradiated sporozoite model was chosen as it is considered the most effective vaccine against malaria. In contrast to whole blood transcriptomics analysis, we stimulated peripheral blood mononuclear cells (PBMC) with sporozoites and enriched for antigen-specific cells prior to conducting transcriptomics analysis. By focusing on transcriptional events triggered by antigen-specific stimulation, we were able to uncover quantitative and qualitative differences between protected and non-protected individuals to controlled human malaria infections and identified differentially expressed genes associated with sporozoite-specific responses. Further analyses including pathway and gene set enrichment analysis revealed that vaccination with irradiated sporozoites induced a transcriptomic profile associated with Th1-responses, Interferon-signaling, antigen-presentation, and inflammation. Analyzing longitudinal time points not only post-vaccination but also post-controlled human malaria infection further revealed that the transcriptomic profile of protected vs non-protected individuals was not static but continued to diverge over time. The results lay the foundation for comparing protective immune signatures induced by various vaccine platforms to uncover immune correlates of protection that are common across platforms.
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Affiliation(s)
- Marie Mura
- Immunology Core, Biologics Research & Development, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Host-Pathogen Interactions, Microbiology and Infectious Diseases, IRBA-Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Burook Misganaw
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Vysnova Inc, Landover, MD, USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Tanisha Robinson
- Immunology Core, Biologics Research & Development, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sidhartha Chaudhury
- Center of Enabling Capabilties, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - John Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Elke Bergmann-Leitner
- Immunology Core, Biologics Research & Development, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Moradi Marjaneh M, Challenger JD, Salas A, Gómez-Carballa A, Sivananthan A, Rivero-Calle I, Barbeito-Castiñeiras G, Foo CY, Wu Y, Liew F, Jackson HR, Habgood-Coote D, D'Souza G, Nichols SJ, Wright VJ, Levin M, Kaforou M, Thwaites RS, Okell LC, Martinón-Torres F, Cunnington AJ. Analysis of blood and nasal epithelial transcriptomes to identify mechanisms associated with control of SARS-CoV-2 viral load in the upper respiratory tract. J Infect 2023; 87:538-550. [PMID: 37863321 DOI: 10.1016/j.jinf.2023.10.009] [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: 07/14/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
OBJECTIVES The amount of SARS-CoV-2 detected in the upper respiratory tract (URT viral load) is a key driver of transmission of infection. Current evidence suggests that mechanisms constraining URT viral load are different from those controlling lower respiratory tract viral load and disease severity. Understanding such mechanisms may help to develop treatments and vaccine strategies to reduce transmission. Combining mathematical modelling of URT viral load dynamics with transcriptome analyses we aimed to identify mechanisms controlling URT viral load. METHODS COVID-19 patients were recruited in Spain during the first wave of the pandemic. RNA sequencing of peripheral blood and targeted NanoString nCounter transcriptome analysis of nasal epithelium were performed and gene expression analysed in relation to paired URT viral load samples collected within 15 days of symptom onset. Proportions of major immune cells in blood were estimated from transcriptional data using computational differential estimation. Weighted correlation network analysis (adjusted for cell proportions) and fixed transcriptional repertoire analysis were used to identify associations with URT viral load, quantified as standard deviations (z-scores) from an expected trajectory over time. RESULTS Eighty-two subjects (50% female, median age 54 years (range 3-73)) with COVID-19 were recruited. Paired URT viral load samples were available for 16 blood transcriptome samples, and 17 respiratory epithelial transcriptome samples. Natural Killer (NK) cells were the only blood cell type significantly correlated with URT viral load z-scores (r = -0.62, P = 0.010). Twenty-four blood gene expression modules were significantly correlated with URT viral load z-score, the most significant being a module of genes connected around IFNA14 (Interferon Alpha-14) expression (r = -0.60, P = 1e-10). In fixed repertoire analysis, prostanoid-related gene expression was significantly associated with higher viral load. In nasal epithelium, only GNLY (granulysin) gene expression showed significant negative correlation with viral load. CONCLUSIONS Correlations between the transcriptional host response and inter-individual variations in SARS-CoV-2 URT viral load, revealed many molecular mechanisms plausibly favouring or constraining viral replication. Existing evidence corroborates many of these mechanisms, including likely roles for NK cells, granulysin, prostanoids and interferon alpha-14. Inhibition of prostanoid production and administration of interferon alpha-14 may be attractive transmission-blocking interventions.
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Affiliation(s)
- Mahdi Moradi Marjaneh
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Imperial College London, London, UK; Section of Virology, Department of Infectious Diseases, Imperial College London, London, UK.
| | - Joseph D Challenger
- Medical Research Council Centre for Global Infections Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Abilash Sivananthan
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Gema Barbeito-Castiñeiras
- Servicio de Microbiología y Parasitología, Complejo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Cher Y Foo
- School of Medicine, Imperial College London, London, UK
| | - Yue Wu
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, UK
| | - Felicity Liew
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Heather R Jackson
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Dominic Habgood-Coote
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Giselle D'Souza
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Samuel J Nichols
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Victoria J Wright
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Lucy C Okell
- Medical Research Council Centre for Global Infections Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Imperial College London, London, UK.
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7
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Tebben K, Yirampo S, Coulibaly D, Koné A, Laurens M, Stucke E, Dembélé A, Tolo Y, Traoré K, Niangaly A, Berry A, Kouriba B, Plowe C, Doumbo O, Lyke K, Takala-Harrison S, Thera M, Travassos M, Serre D. Gene expression analyses reveal differences in children's response to malaria according to their age. RESEARCH SQUARE 2023:rs.3.rs-3487114. [PMID: 37961587 PMCID: PMC10635353 DOI: 10.21203/rs.3.rs-3487114/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In Bandiagara, Mali, children experience on average two clinical malaria episodes per season. However, even in the same transmission area, the number of uncomplicated symptomatic infections, and their parasitemia, vary dramatically among children. To examine the factors contributing to these variations, we simultaneously characterized the host and parasite gene expression profiles from 136 children with symptomatic falciparum malaria and analyzed the expression of 9,205 human and 2,484 Plasmodium genes. We used gene expression deconvolution to estimate the relative proportion of immune cells and parasite stages in each sample and to adjust the differential gene expression analyses. Parasitemia explained much of the variation in both host and parasite gene expression and revealed that infections with higher parasitemia had more neutrophils and fewer T cells, suggesting parasitemia-dependent neutrophil recruitment and/or T cell extravasation to secondary lymphoid organs. The child's age was also strongly correlated with gene expression variations. Plasmodium falciparum genes associated with age suggested that older children carried more male gametocytes, while host genes associated with age indicated a stronger innate response (through TLR and NLR signaling) in younger children and stronger adaptive immunity (through TCR and BCR signaling) in older children. These analyses highlight the variability in host responses and parasite regulation during P. falciparum symptomatic infections and emphasize the importance of considering the children's age when studying and treating malaria infections.
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Affiliation(s)
| | - Salif Yirampo
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Drissa Coulibaly
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Abdoulaye Koné
- Universite des Sciences des Techniques et des Technologies de Bamako
| | | | | | - Ahmadou Dembélé
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Youssouf Tolo
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Karim Traoré
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Ahmadou Niangaly
- Universite des Sciences des Techniques et des Technologies de Bamako
| | | | - Bourema Kouriba
- Universite des Sciences des Techniques et des Technologies de Bamako
| | | | - Ogobara Doumbo
- Universite des Sciences des Techniques et des Technologies de Bamako
| | | | | | - Mahamadou Thera
- Malaria Research and Training Centre-International Center for Excellence in Research (MRTC-ICER)
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8
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Tebben K, Yirampo S, Coulibaly D, Koné AK, Laurens MB, Stucke EM, Dembélé A, Tolo Y, Traoré K, Niangaly A, Berry AA, Kouriba B, Plowe CV, Doumbo OK, Lyke KE, Takala-Harrison S, Thera MA, Travassos MA, Serre D. Gene expression analyses reveal differences in children's response to malaria according to their age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563751. [PMID: 37961701 PMCID: PMC10634788 DOI: 10.1101/2023.10.24.563751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In Bandiagara, Mali, children experience on average two clinical malaria episodes per season. However, even in the same transmission area, the number of uncomplicated symptomatic infections, and their parasitemia, vary dramatically among children. To examine the factors contributing to these variations, we simultaneously characterized the host and parasite gene expression profiles from 136 children with symptomatic falciparum malaria and analyzed the expression of 9,205 human and 2,484 Plasmodium genes. We used gene expression deconvolution to estimate the relative proportion of immune cells and parasite stages in each sample and to adjust the differential gene expression analyses. Parasitemia explained much of the variation in both host and parasite gene expression and revealed that infections with higher parasitemia had more neutrophils and fewer T cells, suggesting parasitemia-dependent neutrophil recruitment and/or T cell extravasation to secondary lymphoid organs. The child's age was also strongly correlated with gene expression variations. Plasmodium falciparum genes associated with age suggested that older children carried more male gametocytes, while host genes associated with age indicated a stronger innate response (through TLR and NLR signaling) in younger children and stronger adaptive immunity (through TCR and BCR signaling) in older children. These analyses highlight the variability in host responses and parasite regulation during P. falciparum symptomatic infections and emphasize the importance of considering the children's age when studying and treating malaria infections.
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Affiliation(s)
- Kieran Tebben
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine; Baltimore, USA
| | - Salif Yirampo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Abdoulaye K. Koné
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Matthew B. Laurens
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Emily M. Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Ahmadou Dembélé
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Youssouf Tolo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Karim Traoré
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Andrea A. Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Christopher V. Plowe
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Kirsten E. Lyke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Mahamadou A. Thera
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Mark A. Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine; Baltimore, USA
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9
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Kioko M, Pance A, Mwangi S, Goulding D, Kemp A, Rono M, Ochola-Oyier LI, Bull PC, Bejon P, Rayner JC, Abdi AI. Extracellular vesicles could be a putative posttranscriptional regulatory mechanism that shapes intracellular RNA levels in Plasmodium falciparum. Nat Commun 2023; 14:6447. [PMID: 37833314 PMCID: PMC10575976 DOI: 10.1038/s41467-023-42103-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Plasmodium falciparum secretes extracellular vesicles (PfEVs) that contain parasite-derived RNA. However, the significance of the secreted RNA remains unexplored. Here, we compare secreted and intracellular RNA from asexual cultures of six P. falciparum lines. We find that secretion of RNA via extracellular vesicles is not only periodic throughout the asexual intraerythrocytic developmental cycle but is also highly conserved across P. falciparum isolates. We further demonstrate that the phases of RNA secreted via extracellular vesicles are discernibly shifted compared to those of the intracellular RNA within the secreting whole parasite. Finally, transcripts of genes with no known function during the asexual intraerythrocytic developmental cycle are enriched in PfEVs compared to the whole parasite. We conclude that the secretion of extracellular vesicles could be a putative posttranscriptional RNA regulation mechanism that is part of or synergise the classic RNA decay processes to maintain intracellular RNA levels in P. falciparum.
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Affiliation(s)
- Mwikali Kioko
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Open University, Milton Keynes, UK
| | - Alena Pance
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
- School of Life and Medical Science, University of Hertfordshire, Hatfield, UK
| | - Shaban Mwangi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - David Goulding
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Alison Kemp
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Martin Rono
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
| | | | - Pete C Bull
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philip Bejon
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C Rayner
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Abdirahman I Abdi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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10
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Habgood-Coote D, Wilson C, Shimizu C, Barendregt AM, Philipsen R, Galassini R, Calle IR, Workman L, Agyeman PKA, Ferwerda G, Anderson ST, van den Berg JM, Emonts M, Carrol ED, Fink CG, de Groot R, Hibberd ML, Kanegaye J, Nicol MP, Paulus S, Pollard AJ, Salas A, Secka F, Schlapbach LJ, Tremoulet AH, Walther M, Zenz W, Van der Flier M, Zar HJ, Kuijpers T, Burns JC, Martinón-Torres F, Wright VJ, Coin LJM, Cunnington AJ, Herberg JA, Levin M, Kaforou M. Diagnosis of childhood febrile illness using a multi-class blood RNA molecular signature. MED 2023; 4:635-654.e5. [PMID: 37597512 DOI: 10.1016/j.medj.2023.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND Appropriate treatment and management of children presenting with fever depend on accurate and timely diagnosis, but current diagnostic tests lack sensitivity and specificity and are frequently too slow to inform initial treatment. As an alternative to pathogen detection, host gene expression signatures in blood have shown promise in discriminating several infectious and inflammatory diseases in a dichotomous manner. However, differential diagnosis requires simultaneous consideration of multiple diseases. Here, we show that diverse infectious and inflammatory diseases can be discriminated by the expression levels of a single panel of genes in blood. METHODS A multi-class supervised machine-learning approach, incorporating clinical consequence of misdiagnosis as a "cost" weighting, was applied to a whole-blood transcriptomic microarray dataset, incorporating 12 publicly available datasets, including 1,212 children with 18 infectious or inflammatory diseases. The transcriptional panel identified was further validated in a new RNA sequencing dataset comprising 411 febrile children. FINDINGS We identified 161 transcripts that classified patients into 18 disease categories, reflecting individual causative pathogen and specific disease, as well as reliable prediction of broad classes comprising bacterial infection, viral infection, malaria, tuberculosis, or inflammatory disease. The transcriptional panel was validated in an independent cohort and benchmarked against existing dichotomous RNA signatures. CONCLUSIONS Our data suggest that classification of febrile illness can be achieved with a single blood sample and opens the way for a new approach for clinical diagnosis. FUNDING European Union's Seventh Framework no. 279185; Horizon2020 no. 668303 PERFORM; Wellcome Trust (206508/Z/17/Z); Medical Research Foundation (MRF-160-0008-ELP-KAFO-C0801); NIHR Imperial BRC.
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Affiliation(s)
- Dominic Habgood-Coote
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Clare Wilson
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Chisato Shimizu
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Anouk M Barendregt
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Ria Philipsen
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Rachel Galassini
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Irene Rivero Calle
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Lesley Workman
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Philipp K A Agyeman
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gerben Ferwerda
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Suzanne T Anderson
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - J Merlijn van den Berg
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Marieke Emonts
- Great North Children's Hospital, Department of Paediatric Immunology, Infectious Diseases & Allergy and NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Enitan D Carrol
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Colin G Fink
- Micropathology Ltd Research and Diagnosis, Coventry, UK; University of Warwick, Coventry, UK
| | - Ronald de Groot
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - John Kanegaye
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Mark P Nicol
- Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Stéphane Paulus
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Antonio Salas
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Fatou Secka
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Luregn J Schlapbach
- Pediatric and Neonatal Intensive Care Unit, and Children`s Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Child Health Research Centre, The University of Queensland, and Paediatric Intensive Care Unit, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Adriana H Tremoulet
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Walther
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Werner Zenz
- University Clinic of Paediatrics and Adolescent Medicine, Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Michiel Van der Flier
- Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Paediatric Infectious Diseases and Immunology Amalia Children's Hospital, Radboudumc, Nijmegen, the Netherlands
| | - Heather J Zar
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands; Department of Blood Cell Research, Sanquin Blood Supply, Division Research and Landsteiner Laboratory of Amsterdam UMC (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Jane C Burns
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Federico Martinón-Torres
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Victoria J Wright
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Jethro A Herberg
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK.
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11
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Prah DA, Dunican C, Amoah LE, Marjaneh MM, Kaforou M, Nordgren A, Jones-Warner W, Aniweh Y, Awandare GA, Cunnington AJ, Hafalla JC. Asymptomatic Plasmodium falciparum infection evades triggering a host transcriptomic response. J Infect 2023; 87:259-262. [PMID: 37356628 DOI: 10.1016/j.jinf.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/17/2023] [Accepted: 06/21/2023] [Indexed: 06/27/2023]
Affiliation(s)
- Diana Ahu Prah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana; Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Claire Dunican
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom
| | - Linda Eva Amoah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana; Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Mahdi Moradi Marjaneh
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, United Kingdom
| | - Asa Nordgren
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom
| | - William Jones-Warner
- Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, United Kingdom.
| | - Julius Clemence Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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12
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Li H, Yang S, Zeng K, Guo J, Wu J, Jiang H, Xie Y, Hu Z, Lu J, Yang J, Su XZ, Cui J, Yu X. SHIP1 modulates antimalarial immunity by bridging the crosstalk between type I IFN signaling and autophagy. mBio 2023; 14:e0351222. [PMID: 37366613 PMCID: PMC10470592 DOI: 10.1128/mbio.03512-22] [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: 12/15/2022] [Accepted: 04/24/2023] [Indexed: 06/28/2023] Open
Abstract
Stringent control of the type I interferon (IFN-I) signaling is critical for host immune defense against infectious diseases, yet the molecular mechanisms that regulate this pathway remain elusive. Here, we show that Src homology 2 containing inositol phosphatase 1 (SHIP1) suppresses IFN-I signaling by promoting IRF3 degradation during malaria infection. Genetic ablation of Ship1 in mice leads to high levels of IFN-I and confers resistance to Plasmodium yoelii nigeriensis (P.y.) N67 infection. Mechanistically, SHIP1 promotes the selective autophagic degradation of IRF3 by enhancing K63-linked ubiquitination of IRF3 at lysine 313, which serves as a recognition signal for NDP52-mediated selective autophagic degradation. In addition, SHIP1 is downregulated by IFN-I-induced miR-155-5p upon P.y. N67 infection and severs as a feedback loop of the signaling crosstalk. This study reveals a regulatory mechanism between IFN-I signaling and autophagy, and verifies SHIP1 can be a potential target for therapeutic intervention against malaria and other infectious diseases. IMPORTANCE Malaria remains a serious disease affecting millions of people worldwide. Malaria parasite infection triggers tightly controlled type I interferon (IFN-I) signaling that plays a critical role in host innate immunity; however, the molecular mechanisms underlying the immune responses are still elusive. Here, we discover a host gene [Src homology 2-containing inositol phosphatase 1 (SHIP1)] that can regulate IFN-I signaling by modulating NDP52-mediated selective autophagic degradation of IRF3 and significantly affect parasitemia and resistance of Plasmodium-infected mice. This study identifies SHIP1 as a potential target for immunotherapies in malaria and highlights the crosstalk between IFN-I signaling and autophagy in preventing related infectious diseases. SHIP1 functions as a negative regulator during malaria infection by targeting IRF3 for autophagic degradation.
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Affiliation(s)
- Hongyu Li
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Shuai Yang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ke Zeng
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiayin Guo
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Wu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Huaji Jiang
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Yue Bei People's Hospital Postdoctoral Innovation Practice Base, Southern Medical University, Guangzhou, Guangdong, China
| | - Yingchao Xie
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhiqiang Hu
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiansen Lu
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Department of Joint Surgery, the Fifth Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Jianwu Yang
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xin-zhuan Su
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jun Cui
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao Yu
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, China
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13
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Lansink LIM, Skinner OP, Engel JA, Lee HJ, Soon MSF, Williams CG, SheelaNair A, Pernold CPS, Laohamonthonkul P, Akter J, Stoll T, Hill MM, Talman AM, Russell A, Lawniczak M, Jia X, Chua B, Anderson D, Creek DJ, Davenport MP, Khoury DS, Haque A. Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites. mBio 2023; 14:e0112923. [PMID: 37449844 PMCID: PMC10470790 DOI: 10.1128/mbio.01129-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
Maturation rates of malaria parasites within red blood cells (RBCs) can be influenced by host nutrient status and circadian rhythm; whether host inflammatory responses can also influence maturation remains less clear. Here, we observed that systemic host inflammation induced in mice by an innate immune stimulus, lipopolysaccharide (LPS), or by ongoing acute Plasmodium infection, slowed the progression of a single cohort of parasites from one generation of RBC to the next. Importantly, plasma from LPS-conditioned or acutely infected mice directly inhibited parasite maturation during in vitro culture, which was not rescued by supplementation, suggesting the emergence of inhibitory factors in plasma. Metabolomic assessments confirmed substantial alterations to the plasma of LPS-conditioned and acutely infected mice, and identified a small number of candidate inhibitory metabolites. Finally, we confirmed rapid parasite responses to systemic host inflammation in vivo using parasite scRNA-seq, noting broad impairment in transcriptional activity and translational capacity specifically in trophozoites but not rings or schizonts. Thus, we provide evidence that systemic host inflammation rapidly triggered transcriptional alterations in circulating blood-stage Plasmodium trophozoites and predict candidate inhibitory metabolites in the plasma that may impair parasite maturation in vivo. IMPORTANCE Malaria parasites cyclically invade, multiply, and burst out of red blood cells. We found that a strong inflammatory response can cause changes to the composition of host plasma, which directly slows down parasite maturation. Thus, our work highlights a new mechanism that limits malaria parasite growth in the bloodstream.
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Affiliation(s)
- Lianne I. M. Lansink
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Department of Biology, University of York, Wentworth Way, York, Yorkshire, United Kingdom
| | - Oliver P. Skinner
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jessica A. Engel
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Hyun Jae Lee
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Megan S. F. Soon
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Cameron G. Williams
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Arya SheelaNair
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Clara P. S. Pernold
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | | | - Jasmin Akter
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Thomas Stoll
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Michelle M. Hill
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Arthur M. Talman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- MIVEGEC, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Andrew Russell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mara Lawniczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Brendon Chua
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Dovile Anderson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Darren J. Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Miles P. Davenport
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
| | - David S. Khoury
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
| | - Ashraful Haque
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
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14
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Anyona S, Cheng Q, Guo Y, Raballah E, Hurwitz I, Onyango C, Seidenberg P, Schneider K, Lambert C, McMahon B, Ouma C, Perkins D. Entire Expressed Peripheral Blood Transcriptome in Pediatric Severe Malarial Anemia. RESEARCH SQUARE 2023:rs.3.rs-3150748. [PMID: 37503086 PMCID: PMC10371159 DOI: 10.21203/rs.3.rs-3150748/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
This study on severe malarial anemia (SMA: Hb < 6.0 g/dL), a leading global cause of childhood morbidity and mortality, analyzed the entire expressed transcriptome in whole blood from children with non-SMA (Hb ≥ 6.0 g/dL, n = 41) and SMA (n = 25). Analyses revealed 3,420 up-regulated and 3,442 down-regulated transcripts, signifying impairments in host inflammasome activation, cell death, innate immune responses, and cellular stress responses in SMA. Immune cell profiling showed a decreased antigenic and immune priming response in children with SMA, favoring polarization toward cellular proliferation and repair. Enrichment analysis further identified altered neutrophil and autophagy-related processes, consistent with neutrophil degranulation and altered ubiquitination and proteasome degradation. Pathway analyses highlighted SMA-related alterations in cellular homeostasis, signaling, response to environmental cues, and cellular and immune stress responses. Validation with a qRT-PCR array showed strong concordance with the sequencing data. These findings identify key molecular themes in SMA pathogenesis, providing potential targets for new malaria therapies.
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Affiliation(s)
| | | | | | - Evans Raballah
- School of Public Health, Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology
| | - Ivy Hurwitz
- Center for Global Health, University of New Mexico
| | - Clinton Onyango
- School of Public Health and Community Development, Maseno University
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15
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Muppidi P, Wright E, Wassmer SC, Gupta H. Diagnosis of cerebral malaria: Tools to reduce Plasmodium falciparum associated mortality. Front Cell Infect Microbiol 2023; 13:1090013. [PMID: 36844403 PMCID: PMC9947298 DOI: 10.3389/fcimb.2023.1090013] [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: 11/04/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Cerebral malaria (CM) is a major cause of mortality in Plasmodium falciparum (Pf) infection and is associated with the sequestration of parasitised erythrocytes in the microvasculature of the host's vital organs. Prompt diagnosis and treatment are key to a positive outcome in CM. However, current diagnostic tools remain inadequate to assess the degree of brain dysfunction associated with CM before the window for effective treatment closes. Several host and parasite factor-based biomarkers have been suggested as rapid diagnostic tools with potential for early CM diagnosis, however, no specific biomarker signature has been validated. Here, we provide an updated review on promising CM biomarker candidates and evaluate their applicability as point-of-care tools in malaria-endemic areas.
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Affiliation(s)
- Pranavi Muppidi
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Emily Wright
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Samuel C. Wassmer
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Himanshu Gupta
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom,Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, UP, India,*Correspondence: Himanshu Gupta, ;
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16
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Jackson H, Rivero Calle I, Broderick C, Habgood-Coote D, D’Souza G, Nichols S, Vito O, Gómez-Rial J, Rivero-Velasco C, Rodríguez-Núñez N, Barbeito-Castiñeiras G, Pérez-Freixo H, Barreiro-de Acosta M, Cunnington AJ, Herberg JA, Wright VJ, Gómez-Carballa A, Salas A, Levin M, Martinon-Torres F, Kaforou M, Jackson H, Calle IR, Habgood-Coote D, D’Souza G, Nichols S, Gómez-Rial J, Cunnington AJ, Herberg JA, Wright VJ, Gómez-Carballa A, Salas A, Levin M, Martinon-Torres F, Kaforou M, Antonio AG, Julián ÁE, Antonio AL, Gema BC, Xabier BP, Miriam BG, María Victoria CG, Miriam CL, Amparo CN, Mónica CP, José Javier CA, María José CT, Ana Isabel DU, Blanca DE, María Jesús DS, Cristina FP, Juan FV, Cristóbal GR, José Luis GA, Luisa GV, Elena GV, Alberto GC, José GR, Francisco Javier GB, Beatriz GL, Pilar LI, Beatriz LM, Marta LF, Montserrat LF, Ana LL, Federico MT, De la Cruz Daniel N, Eloína NM, Juan Bautista OD, Jacobo PS, María PN, del Molino Bernal Marisa P, Hugo PF, Lidia PR, Sara P, Manuel PR, Antonio PR, Gloria María PH, Teresa QV, Lorenzo RC, Patricia RC, Susana RG, Sara RV, Vanessa RB, Irene RC, Carmen RV, Nuria RN, Carmen RTS, Eva SP, José Miguel SO, Carla SV, Sonia SF, Pablo SS, Manuel TM, Rocío TP, Mercedes TC, Luis VC, Pablo VG, Soledad VIM, Sandra VL, Rocio FI, Iria BR, Cristina CS. Characterisation of the blood RNA host response underpinning severity in COVID-19 patients. Sci Rep 2022; 12:12216. [PMID: 35844004 PMCID: PMC9288817 DOI: 10.1038/s41598-022-15547-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/24/2022] [Indexed: 01/08/2023] Open
Abstract
Infection with SARS-CoV-2 has highly variable clinical manifestations, ranging from asymptomatic infection through to life-threatening disease. Host whole blood transcriptomics can offer unique insights into the biological processes underpinning infection and disease, as well as severity. We performed whole blood RNA Sequencing of individuals with varying degrees of COVID-19 severity. We used differential expression analysis and pathway enrichment analysis to explore how the blood transcriptome differs between individuals with mild, moderate, and severe COVID-19, performing pairwise comparisons between groups. Increasing COVID-19 severity was characterised by an abundance of inflammatory immune response genes and pathways, including many related to neutrophils and macrophages, in addition to an upregulation of immunoglobulin genes. In this study, for the first time, we show how immunomodulatory treatments commonly administered to COVID-19 patients greatly alter the transcriptome. Our insights into COVID-19 severity reveal the role of immune dysregulation in the progression to severe disease and highlight the need for further research exploring the interplay between SARS-CoV-2 and the inflammatory immune response.
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17
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Zhang YH, Su XZ, Li J, Shi JJ, Xie LH. Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections. Malar J 2022; 21:333. [PMID: 36380373 PMCID: PMC9664782 DOI: 10.1186/s12936-022-04374-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022] Open
Abstract
Background To understand how Plasmodium falciparum malaria is controlled, it is essential to elucidate the transcriptomic responses of the human host in naturally-exposed populations. Various individual studies of the human transcriptomic responses to naturally transmitted P. falciparum infections have been reported with varying results. Multicohort gene expression analysis by aggregating data from diverse populations into a single analysis will increase the reproducibility and reliability of the results. Methods In this study, discovery cohorts GSE1124-GPL96, GSE34404, GSE117613, and validation cohort GSE35858 were obtained from the Gene Expression Omnibus. A meta-analysis using data from the multicohort studies was performed to identify the differentially expressed genes (DEGs) between malaria-infected and noninfected individuals using the MetaIntegrator R package. Subsequently, the protein–protein interaction (PPI) networks of the DEGs were constructed using Cytoscape software. Significant modules were selected, and the hub genes were identified using the CytoHubba and MCODE plug-ins. Multicohort WGCNA was conducted to find a correlation between modules and malaria infection. Furthermore, the immune cell profile of the peripheral blood in different groups was identified using ssGSEA. Results These analyses reveal that neutrophil activation, neutrophil-mediated immunity, and neutrophil degranulation are involved in the human response to natural malaria infection. However, neutrophil cell enrichment and activation were not significantly different between mild malaria and severe malaria groups. Malaria infection also downregulates host genes in ribosome synthesis and protein translation and upregulates host cell division-related genes. Furthermore, immune cell profiling analysis shows that activated dendritic cells and type 2 T helper cells are upregulated, while activated B cells, immature B cells, and monocytes are downregulated in the malaria-infected patients relative to the noninfected individuals. Significantly higher enrichment of activated dendritic cell-related genes and significantly lower enrichment of monocyte-related genes are also observed in the peripheral blood of the severe malaria group than in the mild malaria group. Conclusion These results reveal important molecular signatures of host responses to malaria infections, providing some bases for developing malaria control strategies and protective vaccines. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04374-5.
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Affiliation(s)
- Yan-hui Zhang
- grid.419897.a0000 0004 0369 313XKey Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
| | - Xin-zhuan Su
- grid.94365.3d0000 0001 2297 5165Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD USA
| | - Jian Li
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian China
| | - Jia-jian Shi
- grid.419897.a0000 0004 0369 313XKey Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
| | - Li-hua Xie
- grid.419897.a0000 0004 0369 313XKey Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
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18
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Thomson-Luque R, Votborg-Novél L, Osório NS, Portugal S. Reply to: Relationship of circulating Plasmodium falciparum lifecycle stage to circulating parasitemia and total parasite biomass. Nat Commun 2022; 13:5558. [PMID: 36151088 PMCID: PMC9508074 DOI: 10.1038/s41467-022-32998-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/26/2022] [Indexed: 12/05/2022] Open
Affiliation(s)
- Richard Thomson-Luque
- Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Lasse Votborg-Novél
- Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Portugal and ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal
| | - Silvia Portugal
- Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany. .,Max Planck Institute for Infection Biology, Berlin, Germany.
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19
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Abstract
Malaria symptoms are caused by the development of the parasites within the blood of an infected host. Bulk RNA sequencing (RNA-seq) of infected blood can reveal interactions between parasites and the host immune system during an infection, but because multiple developmental stages with distinct transcriptional profiles are concurrently present in infected blood, it is necessary to correct such analyses for differences in cell composition among samples. Gene expression deconvolution is a statistical approach that has been developed for inferring the cell composition of complex tissues characterized by bulk RNA-seq using gene expression profiles from reference cell types. Here, we describe the evaluation of a species-agnostic reference data set that can be used for efficient and accurate gene expression deconvolution of bulk RNA-seq data generated from any Plasmodium species and for correct gene expression analyses for biases caused by differences in stage composition among samples. IMPORTANCE Differences in cell type proportions among samples can introduce artifacts in gene expression analyses and mask genuine differences in gene regulation. Gene expression deconvolution allows estimation of the proportion of each cell type present in one sample directly from bulk RNA sequencing data, but this approach requires a reference data set with the signature profile of each cell type. Here, we evaluate the suitability of a rodent malaria parasite gene expression data set for estimating the proportions of each parasite developmental stage present in bulk RNA sequencing data generated from blood-stage infections with the human parasites Plasmodium falciparum and Plasmodium vivax. These analyses provide a species-agnostic approach for reliably estimating stage proportions in infected human blood and correcting subsequent gene expression analyses for these variations.
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20
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Highly Variable Expression of Merozoite Surface Protein MSPDBL2 in Diverse Plasmodium falciparum Clinical Isolates and Transcriptome Scans for Correlating Genes. mBio 2022; 13:e0194822. [PMID: 35950755 PMCID: PMC9426457 DOI: 10.1128/mbio.01948-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The merozoite surface protein MSPDBL2 of Plasmodium falciparum is under strong balancing selection and is a target of naturally acquired antibodies. Remarkably, MSPDBL2 is expressed in only a minority of mature schizonts of any cultured parasite line, and mspdbl2 gene transcription increases in response to overexpression of the gametocyte development inducer GDV1, so it is important to understand its natural expression. Here, MSPDBL2 in mature schizonts was analyzed in the first ex vivo culture cycle of 96 clinical isolates from 4 populations with various levels of infection endemicity in different West African countries, by immunofluorescence microscopy with antibodies against a conserved region of the protein. In most isolates, less than 1% of mature schizonts were positive for MSPDBL2, but the frequency distribution was highly skewed, as nine isolates had more than 3% schizonts positive and one had 73% positive. To investigate whether the expression of other gene loci correlated with MSPDBL2 expression, whole-transcriptome sequencing was performed on schizont-enriched material from 17 of the isolates with a wide range of proportions of schizonts positive. Transcripts of particular genes were highly significantly positively correlated with MSPDBL2 positivity in schizonts as well as with mspdbl2 gene transcript levels, showing overrepresentation of genes implicated previously as involved in gametocytogenesis but not including the gametocytogenesis master regulator ap2-g. Single-cell transcriptome analysis of a laboratory-adapted clone showed that most individual parasites expressing mspdbl2 did not express ap2-g, consistent with MSPDBL2 marking a developmental subpopulation that is distinct but likely to co-occur alongside sexual commitment. IMPORTANCE These findings contribute to understanding malaria parasite antigenic and developmental variation, focusing on the merozoite surface protein encoded by the single locus under strongest balancing selection. Analyzing the initial ex vivo generation of parasites grown from a wide sample of clinical infections, we show a unique and highly skewed pattern of natural expression frequencies of MSPDBL2, distinct from that of any other antigen. Bulk transcriptome analysis of a range of clinical isolates showed significant overrepresentation of sexual development genes among those positively correlated with MSPDBL2 protein and mspdbl2 gene expression, indicating the MSPDBL2-positive subpopulation to be often coincident with parasites developing sexually in preparation for transmission. Single-cell transcriptome data confirm the absence of a direct correlation with the ap2-g master regulator of sexual development, indicating that the MSPDBL2-positive subpopulation has a separate function in asexual survival and replication under conditions that promote terminal sexual differentiation.
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21
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Babatunde KA, Adenuga OF. Neutrophils in malaria: A double-edged sword role. Front Immunol 2022; 13:922377. [PMID: 35967409 PMCID: PMC9367684 DOI: 10.3389/fimmu.2022.922377] [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: 04/17/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Neutrophils are the most abundant leukocytes in human peripheral blood. They form the first line of defense against invading foreign pathogens and might play a crucial role in malaria. According to World Health Organization (WHO), malaria is a globally significant disease caused by protozoan parasites from the Plasmodium genus, and it’s responsible for 627,000 deaths in 2020. Neutrophils participate in the defense response against the malaria parasite via phagocytosis and reactive oxygen species (ROS) production. Neutrophils might also be involved in the pathogenesis of malaria by the release of toxic granules and the release of neutrophil extracellular traps (NETs). Intriguingly, malaria parasites inhibit the anti-microbial function of neutrophils, thus making malaria patients more susceptible to secondary opportunistic Salmonella infections. In this review, we will provide a summary of the role of neutrophils during malaria infection, some contradicting mouse model neutrophil data and neutrophil-related mechanisms involved in malaria patients’ susceptibility to bacterial infection.
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Affiliation(s)
- Kehinde Adebayo Babatunde
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- Department of Pathology & Laboratory Medicine, University of Wisconsin, Madison, WI, United States
- *Correspondence: Kehinde Adebayo Babatunde,
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22
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Studniberg SI, Ioannidis LJ, Utami RAS, Trianty L, Liao Y, Abeysekera W, Li‐Wai‐Suen CSN, Pietrzak HM, Healer J, Puspitasari AM, Apriyanti D, Coutrier F, Poespoprodjo JR, Kenangalem E, Andries B, Prayoga P, Sariyanti N, Smyth GK, Cowman AF, Price RN, Noviyanti R, Shi W, Garnham AL, Hansen DS. Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria. Mol Syst Biol 2022; 18:e10824. [PMID: 35475529 PMCID: PMC9045086 DOI: 10.15252/msb.202110824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/12/2023] Open
Abstract
Clinical immunity to P. falciparum malaria is non-sterilizing, with adults often experiencing asymptomatic infection. Historically, asymptomatic malaria has been viewed as beneficial and required to help maintain clinical immunity. Emerging views suggest that these infections are detrimental and constitute a parasite reservoir that perpetuates transmission. To define the impact of asymptomatic malaria, we pursued a systems approach integrating antibody responses, mass cytometry, and transcriptional profiling of individuals experiencing symptomatic and asymptomatic P. falciparum infection. Defined populations of classical and atypical memory B cells and a TH2 cell bias were associated with reduced risk of clinical malaria. Despite these protective responses, asymptomatic malaria featured an immunosuppressive transcriptional signature with upregulation of pathways involved in the inhibition of T-cell function, and CTLA-4 as a predicted regulator in these processes. As proof of concept, we demonstrated a role for CTLA-4 in the development of asymptomatic parasitemia in infection models. The results suggest that asymptomatic malaria is not innocuous and might not support the induction of immune processes to fully control parasitemia or efficiently respond to malaria vaccines.
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Affiliation(s)
- Stephanie I Studniberg
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,Department of Medical BiologyThe University of MelbourneParkvilleVic.Australia
| | - Lisa J Ioannidis
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,Department of Medical BiologyThe University of MelbourneParkvilleVic.Australia
| | - Retno A S Utami
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,Department of Medical BiologyThe University of MelbourneParkvilleVic.Australia,Eijkman Institute for Molecular BiologyJakartaIndonesia
| | - Leily Trianty
- Eijkman Institute for Molecular BiologyJakartaIndonesia
| | - Yang Liao
- Olivia Newton‐John Cancer Research InstituteHeidelbergVic.Australia
| | - Waruni Abeysekera
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,School of Mathematics and StatisticsThe University of MelbourneParkvilleVic.Australia
| | - Connie S N Li‐Wai‐Suen
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,School of Mathematics and StatisticsThe University of MelbourneParkvilleVic.Australia
| | - Halina M Pietrzak
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,Department of Medical BiologyThe University of MelbourneParkvilleVic.Australia
| | - Julie Healer
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,Department of Medical BiologyThe University of MelbourneParkvilleVic.Australia
| | | | - Dwi Apriyanti
- Eijkman Institute for Molecular BiologyJakartaIndonesia
| | | | | | | | | | - Pak Prayoga
- Papuan Health and Community FoundationPapuaIndonesia
| | | | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,School of Mathematics and StatisticsThe University of MelbourneParkvilleVic.Australia
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,Department of Medical BiologyThe University of MelbourneParkvilleVic.Australia
| | - Ric N Price
- Global and Tropical Health DivisionMenzies School of Health Research and Charles Darwin UniversityDarwinNTAustralia,Centre for Tropical Medicine and Global HealthNuffield Department of MedicineUniversity of OxfordOxfordUK,Mahidol‐Oxford Tropical Medicine Research UnitMahidol UniversityBangkokThailand
| | | | - Wei Shi
- Olivia Newton‐John Cancer Research InstituteHeidelbergVic.Australia
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,School of Mathematics and StatisticsThe University of MelbourneParkvilleVic.Australia
| | - Diana S Hansen
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia,Department of Medical BiologyThe University of MelbourneParkvilleVic.Australia
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23
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Liu W, Rodgers GP. Olfactomedin 4 Is a Biomarker for the Severity of Infectious Diseases. Open Forum Infect Dis 2022; 9:ofac061. [PMID: 35291445 PMCID: PMC8918383 DOI: 10.1093/ofid/ofac061] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/07/2022] [Indexed: 09/05/2023] Open
Abstract
Biomarkers of infectious diseases are essential tools for patient monitoring, diagnostics, and prognostics. Here we review recent advances in our understanding of olfactomedin 4 (OLFM4) in neutrophil biology and of OLFM4 as a new biomarker for certain infectious diseases. OLFM4 is a neutrophil-specific granule protein that is expressed in a subset of human and mouse neutrophils. OLFM4 expression is upregulated in many viral and bacterial infections, as well as in malaria. OLFM4 appears to play an important role in regulating host innate immunity against bacterial infection. Further, higher expression of OLFM4 is associated with severity of disease for dengue virus, respiratory syncytial virus, and malaria infections. In addition, higher expression of OLFM4 or a higher percentage of OLFM4 + neutrophils is associated with poorer outcomes in septic patients. OLFM4 is a promising biomarker and potential therapeutic target in certain infectious diseases.
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Affiliation(s)
- Wenli Liu
- Molecular and Clinical Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Griffin P Rodgers
- Molecular and Clinical Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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24
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Pollenus E, Gouwy M, Van den Steen PE. Neutrophils in malaria: the good, the bad or the ugly? Parasite Immunol 2022; 44:e12912. [PMID: 35175636 DOI: 10.1111/pim.12912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/09/2022] [Accepted: 02/13/2022] [Indexed: 11/30/2022]
Abstract
Neutrophils are the most abundant circulating leukocytes in human peripheral blood. They are often the first cells to respond to an invading pathogen and might therefore play an important role in malaria. Malaria is a globally important disease caused by Plasmodium parasites, responsible for more than 400 000 deaths each year. Most of these deaths are caused by complications, including cerebral malaria, severe malarial anemia, placental malaria, renal injury, metabolic problems and malaria-associated acute respiratory distress syndrome. Neutrophils contribute in the immune defense against malaria, through clearance of parasites via phagocytosis, production of reactive oxygen species and release of neutrophil extracellular traps (NETs). However, Plasmodium parasites diminish antibacterial functions of neutrophils, making patients more susceptible to other infections. Neutrophils might also be involved in the development of malaria complications, for example via the release of toxic granules and NETs. However, technical pitfalls in the determination of the roles of neutrophils have caused contradicting results. Further investigations need to consider these pitfalls, in order to elucidate the role of neutrophils in malaria complications.
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Affiliation(s)
- Emilie Pollenus
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, University of Leuven, Leuven, Belgium
| | - Mieke Gouwy
- Laboratory of Molecular immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, University of Leuven, Leuven, Belgium
| | - Philippe E Van den Steen
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, University of Leuven, Leuven, Belgium
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25
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Gupta A, Galinski MR, Voit EO. Dynamic Control Balancing Cell Proliferation and Inflammation is Crucial for an Effective Immune Response to Malaria. Front Mol Biosci 2022; 8:800721. [PMID: 35242812 PMCID: PMC8886244 DOI: 10.3389/fmolb.2021.800721] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria has a complex pathology with varying manifestations and symptoms, effects on host tissues, and different degrees of severity and ultimate outcome, depending on the causative Plasmodium pathogen and host species. Previously, we compared the peripheral blood transcriptomes of two macaque species (Macaca mulatta and Macaca fascicularis) in response to acute primary infection by Plasmodium knowlesi. Although these two species are very closely related, the infection in M. mulatta is fatal, unless aggressively treated, whereas M. fascicularis develops a chronic, but tolerable infection in the blood. As a reason for this stark difference, our analysis suggests delayed pathogen detection in M. mulatta followed by extended inflammation that eventually overwhelms this monkey’s immune response. By contrast, the natural host M. fascicularis detects the pathogen earlier and controls the inflammation. Additionally, M. fascicularis limits cell proliferation pathways during the log phase of infection, presumably in an attempt to control inflammation. Subsequent cell proliferation suggests a cell-mediated adaptive immune response. Here, we focus on molecular mechanisms underlying the key differences in the host and parasite responses and their coordination. SICAvar Type 1 surface antigens are highly correlated with pattern recognition receptor signaling and important inflammatory genes for both hosts. Analysis of pathogen detection pathways reveals a similar signaling mechanism, but with important differences in the glutamate G-protein coupled receptor (GPCR) signaling pathway. Furthermore, differences in inflammasome assembly processes suggests an important role of S100 proteins in balancing inflammation and cell proliferation. Both differences point to the importance of Ca2+ homeostasis in inflammation. Additionally, the kynurenine-to-tryptophan ratio, a known inflammatory biomarker, emphasizes higher inflammation in M. mulatta during log phase. Transcriptomics-aided metabolic modeling provides a functional method for evaluating these changes and understanding downstream changes in NAD metabolism and aryl hydrocarbon receptor (AhR) signaling, with enhanced NAD metabolism in M. fascicularis and stronger AhR signaling in M. mulatta. AhR signaling controls important immune genes like IL6, IFNγ and IDO1. However, direct changes due to AhR signaling could not be established due to complicated regulatory feedback mechanisms associated with the AhR repressor (AhRR). A complete understanding of the exact dynamics of the immune response is difficult to achieve. Nonetheless, our comparative analysis provides clear suggestions of processes that underlie an effective immune response. Thus, our study identifies multiple points of intervention that are apparently responsible for a balanced and effective immune response and thereby paves the way toward future immune strategies for treating malaria.
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Affiliation(s)
- Anuj Gupta
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Mary R. Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA, United States
| | - Eberhard O. Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
- *Correspondence: Eberhard O. Voit,
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Schwartz SL, Dey D, Tanquary J, Bair CR, Lowen AC, Conn GL. Role of helical structure and dynamics in oligoadenylate synthetase 1 (OAS1) mismatch tolerance and activation by short dsRNAs. Proc Natl Acad Sci U S A 2022; 119:e2107111119. [PMID: 35017296 PMCID: PMC8784149 DOI: 10.1073/pnas.2107111119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022] Open
Abstract
The 2'-5'-oligoadenylate synthetases (OAS) are innate immune sensors of cytosolic double-stranded RNA (dsRNA) that play a critical role in limiting viral infection. How these proteins are able to avoid aberrant activation by cellular RNAs is not fully understood, but adenosine-to-inosine (A-to-I) editing has been proposed to limit accumulation of endogenous RNAs that might otherwise cause stimulation of the OAS/RNase L pathway. Here, we aim to uncover whether and how such sequence modifications can restrict the ability of short, defined dsRNAs to activate the single-domain form of OAS, OAS1. Unexpectedly, we find that all tested inosine-containing dsRNAs have an increased capacity to activate OAS1, whether in a destabilizing (I•U) or standard Watson-Crick-like base pairing (I-C) context. Additional variants with strongly destabilizing A•C mismatches or stabilizing G-C pairs also exhibit increased capacity to activate OAS1, eliminating helical stability as a factor in the relative ability of the dsRNAs to activate OAS1. Using thermal difference spectra and molecular dynamics simulations, we identify both increased helical dynamics and specific local changes in helical structure as important factors in the capacity of short dsRNAs to activate OAS1. These helical features may facilitate more ready adoption of the distorted OAS1-bound conformation or stabilize important structures to predispose the dsRNA for optimal binding and activation of OAS1. These studies thus reveal the molecular basis for the greater capacity of some short dsRNAs to activate OAS1 in a sequence-independent manner.
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Affiliation(s)
- Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Julia Tanquary
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Camden R Bair
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322;
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
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Wei W, Cheng W, Dai W, Lu F, Cheng Y, Jiang T, Ren Z, Xie Y, Xu J, Zhao Q, Yu X, Yin Y, Li J, Dong H. A Nanodrug Coated with Membrane from Brain Microvascular Endothelial Cells Protects against Experimental Cerebral Malaria. NANO LETTERS 2022; 22:211-219. [PMID: 34967631 DOI: 10.1021/acs.nanolett.1c03514] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Human malaria is a global life-threatening infectious disease. Cerebral malaria (CM) induced by Plasmodium falciparum parasites accounts for 90% of malaria deaths. Treating CM is challenging due to inadequate treatment options and the development of drug resistance. We describe a nanoparticle formulation of the antimalarial drug dihydroartemisinin that is coated in a biomimetic membrane derived from brain microvascular endothelial cells (BMECs) and test its therapeutic efficacy in a mouse model of experimental cerebral malaria (ECM). The membrane-coated nanoparticle drug has a prolonged drug-release profile and enhanced dual targeting killing efficacy toward parasites residing in red blood cells (iRBCs) and iRBCs obstructed in the BMECs (for both rodent and human). In a mice ECM model, the nanodrug protects the brain, liver, and spleen from infection-induced damage and improves the survival rate of mice. This so-called nanodrug offers new insight into engineering nanoparticle-based therapeutics for malaria and other parasitic pathogen infections.
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Affiliation(s)
- Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Weijia Cheng
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Feng Lu
- School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Yaru Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Tingting Jiang
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - Zhenyu Ren
- School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Yiting Xie
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - Jiahui Xu
- School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Qun Zhao
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - Xianjun Yu
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - Yi Yin
- School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Jian Li
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing, Beijing 100083, China
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
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28
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Georgiadou A, Dunican C, Soro-Barrio P, Lee HJ, Kaforou M, Cunnington AJ. Comparative transcriptomic analysis reveals translationally relevant processes in mouse models of malaria. eLife 2022; 11:e70763. [PMID: 35006075 PMCID: PMC8747512 DOI: 10.7554/elife.70763] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/22/2021] [Indexed: 02/07/2023] Open
Abstract
Recent initiatives to improve translation of findings from animal models to human disease have focussed on reproducibility but quantifying the relevance of animal models remains a challenge. Here, we use comparative transcriptomics of blood to evaluate the systemic host response and its concordance between humans with different clinical manifestations of malaria and five commonly used mouse models. Plasmodium yoelii 17XL infection of mice most closely reproduces the profile of gene expression changes seen in the major human severe malaria syndromes, accompanied by high parasite biomass, severe anemia, hyperlactatemia, and cerebral microvascular pathology. However, there is also considerable discordance of changes in gene expression between the different host species and across all models, indicating that the relevance of biological mechanisms of interest in each model should be assessed before conducting experiments. These data will aid the selection of appropriate models for translational malaria research, and the approach is generalizable to other disease models.
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Affiliation(s)
- Athina Georgiadou
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Centre for Paediatrics and Child Health, Imperial College LondonLondonUnited Kingdom
| | - Claire Dunican
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Centre for Paediatrics and Child Health, Imperial College LondonLondonUnited Kingdom
| | - Pablo Soro-Barrio
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
| | - Hyun Jae Lee
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Centre for Paediatrics and Child Health, Imperial College LondonLondonUnited Kingdom
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Centre for Paediatrics and Child Health, Imperial College LondonLondonUnited Kingdom
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Mandala WL. Expression of CD11a, CD11b, CD11c, and CD18 on Neutrophils from Different Clinical Types of Malaria in Malawian Children. J Blood Med 2022; 13:1-10. [PMID: 35018127 PMCID: PMC8742601 DOI: 10.2147/jbm.s343109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/15/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Malaria in individuals who have never had an infection before is usually characterized by an inflammatory response that is linked to the expression of specific activation markers on cells of the innate immune system. METHODS This study investigated absolute white blood cell (WBC) and neutrophil counts and expression of several adhesion markers on neutrophils from HIV-uninfected children who were suffering from cerebral malaria (n=35), severe malarial anemia (SMA, n=39), and uncomplicated malaria (n=49) and healthy aparasitemic children (n=33) in Blantyre, Malawi. RESULTS All clinical malaria groups had higher WBC and neutrophil counts compared to healthy controls, with the acute SMA group having significantly (p<0.0001) higher WBC counts than the controls. These elevated counts normalized during recovery. Surprisingly, in all clinical malaria groups, the surface expression of CD11b, CD11c, and CD18 on neutrophils was lower than in healthy controls, again normalizing during convalescence. CONCLUSION In areas where Plasmodium falciparum malaria is hyperendemic, such as where this study was conducted, neutrophils have reduced expression of adhesion molecules and activation markers during acute stages of the infection, regardless of the clinical type of malaria. This reduced expression could be due to an individual's past exposure to P. falciparum or other parasite-related factors that manifest during active malaria that still need to be investigated.
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Affiliation(s)
- Wilson Lewis Mandala
- Academy of Medical Sciences, Malawi University of Science and Technology (MUST), Thyolo, Malawi
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Basic Sciences Department, College of Medicine, University of Malawi, Blantyre, Malawi
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30
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Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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31
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Nguyen HHT, Azizan S, Yeoh LM, Tang J, Duffy MF. RNAseq of Infected Erythrocyte Surface Antigen-Encoding Genes. Methods Mol Biol 2022; 2470:185-209. [PMID: 35881347 DOI: 10.1007/978-1-0716-2189-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Massive parallel sequencing technology has greatly increased the breadth and depth of transcriptomic data that can be captured from P. falciparum samples. This has revolutionized in vitro studies but uptake has been slower in the analysis of clinical samples. The principal barriers are the removal of contaminating white blood cells in a malaria endemic setting and preservation of the RNA. We provide here detailed methods for the collection of purified infected erythrocytes and the preservation and extraction of RNA. We also provide methods for assessing and addressing contaminating RNA from erythroid cells, and a protocol for RNAseq library preparation optimized to maximize yield from low amounts of parasite mRNA. Finally, we provide some examples of RNAseq library characteristics that may fail quality control for other species but are in fact satisfactory for P. falciparum RNAseq.
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Affiliation(s)
- Hanh Hong Thi Nguyen
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Peter Doherty Institute, Melbourne, VIC, Australia
- Bio21 Institute, Parkville, VIC, Australia
| | - Suffian Azizan
- Bio21 Institute, Parkville, VIC, Australia
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Lee Ming Yeoh
- Peter Doherty Institute, Melbourne, VIC, Australia
- Bio21 Institute, Parkville, VIC, Australia
- Department of Microbiology and Immunology, School of Biomedical Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jingyi Tang
- School of Medicine, Faculty of Health, Deakin University, Waurn Ponds, VIC, Australia
| | - Michael F Duffy
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia.
- Peter Doherty Institute, Melbourne, VIC, Australia.
- Bio21 Institute, Parkville, VIC, Australia.
- Department of Microbiology and Immunology, School of Biomedical Sciences, The University of Melbourne, Parkville, VIC, Australia.
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32
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Impact of Sickle Cell Trait Hemoglobin on the Intraerythrocytic Transcriptional Program of Plasmodium falciparum. mSphere 2021; 6:e0075521. [PMID: 34668757 PMCID: PMC8527989 DOI: 10.1128/msphere.00755-21] [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] [Indexed: 11/20/2022] Open
Abstract
Sickle-trait hemoglobin (HbAS) confers nearly complete protection from severe, life-threatening falciparum malaria in African children. Despite this clear protection, the molecular mechanisms by which HbAS confers these protective phenotypes remain incompletely understood. As a forward genetic screen for aberrant parasite transcriptional responses associated with parasite neutralization in HbAS red blood cells (RBCs), we performed comparative transcriptomic analyses of Plasmodium falciparum in normal (HbAA) and HbAS erythrocytes during both in vitro cultivation of reference parasite strains and naturally occurring P. falciparum infections in Malian children with HbAA or HbAS. During in vitro cultivation, parasites matured normally in HbAS RBCs, and the temporal expression was largely unperturbed of the highly ordered transcriptional program that underlies the parasite’s maturation throughout the intraerythrocytic development cycle (IDC). However, differential expression analysis identified hundreds of transcripts aberrantly expressed in HbAS, largely occurring late in the IDC. Surprisingly, transcripts encoding members of the Maurer’s clefts were overexpressed in HbAS despite impaired parasite protein export in these RBCs, while parasites in HbAS RBCs underexpressed transcripts associated with the endoplasmic reticulum and those encoding serine repeat antigen proteases that promote parasite egress. Analyses of P. falciparum transcriptomes from 32 children with uncomplicated malaria identified stage-specific differential expression: among infections composed of ring-stage parasites, only cyclophilin 19B was underexpressed in children with HbAS, while trophozoite-stage infections identified a range of differentially expressed transcripts, including downregulation in HbAS of several transcripts associated with severe malaria in collateral studies. Collectively, our comparative transcriptomic screen in vitro and in vivo indicates that P. falciparum adapts to HbAS by altering its protein chaperone and folding machinery, oxidative stress response, and protein export machinery. Because HbAS consistently protects from severe P. falciparum, modulation of these responses may offer avenues by which to neutralize P. falciparum parasites. IMPORTANCE Sickle-trait hemoglobin (HbAS) confers nearly complete protection from severe, life-threatening malaria, yet the molecular mechanisms that underlie HbAS protection from severe malaria remain incompletely understood. Here, we used transcriptome sequencing (RNA-seq) to measure the impact of HbAS on the blood-stage transcriptome of Plasmodium falciparum in in vitro time series experiments and in vivo samples from natural infections. Our in vitro time series data reveal that, during its blood stage, P. falciparum’s gene expression in HbAS is impacted primarily through alterations in the abundance of gene products as opposed to variations in the timing of gene expression. Collectively, our in vitro and in vivo data indicate that P. falciparum adapts to HbAS by altering its protein chaperone and folding machinery, oxidative stress response, and protein export machinery. Due to the persistent association of HbAS and protection from severe disease, these processes that are modified in HbAS may offer strategies to neutralize P. falciparum.
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33
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Sahu PK, Duffy FJ, Dankwa S, Vishnyakova M, Majhi M, Pirpamer L, Vigdorovich V, Bage J, Maharana S, Mandala W, Rogerson SJ, Seydel KB, Taylor TE, Kim K, Sather DN, Mohanty A, Mohanty RR, Mohanty A, Pattnaik R, Aitchison JD, Hoffman A, Mohanty S, Smith JD, Bernabeu M, Wassmer SC. Determinants of brain swelling in pediatric and adult cerebral malaria. JCI Insight 2021; 6:145823. [PMID: 34549725 PMCID: PMC8492338 DOI: 10.1172/jci.insight.145823] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
Cerebral malaria (CM) affects children and adults, but brain swelling is more severe in children. To investigate features associated with brain swelling in malaria, we performed blood profiling and brain MRI in a cohort of pediatric and adult patients with CM in Rourkela, India, and compared them with an African pediatric CM cohort in Malawi. We determined that higher plasma Plasmodium falciparum histidine rich protein 2 (PfHRP2) levels and elevated var transcripts that encode for binding to endothelial protein C receptor (EPCR) were linked to CM at both sites. Machine learning models trained on the African pediatric cohort could classify brain swelling in Indian children CM cases but had weaker performance for adult classification, due to overall lower parasite var transcript levels in this age group and more severe thrombocytopenia in Rourkela adults. Subgrouping of patients with CM revealed higher parasite biomass linked to severe thrombocytopenia and higher Group A–EPCR var transcripts in mild thrombocytopenia. Overall, these findings provide evidence that higher parasite biomass and a subset of Group A–EPCR binding variants are common features in children and adult CM cases, despite age differences in brain swelling.
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Affiliation(s)
- Praveen K Sahu
- Center for the Study of Complex Malaria in India, Ispat General Hospital (IGH), Rourkela, Odisha, India
| | - Fergal J Duffy
- Seattle Children's Research Institute, Seattle, Washington, USA
| | - Selasi Dankwa
- Seattle Children's Research Institute, Seattle, Washington, USA
| | | | | | - Lukas Pirpamer
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Jabamani Bage
- Center for the Study of Complex Malaria in India, Ispat General Hospital (IGH), Rourkela, Odisha, India
| | - Sameer Maharana
- Center for the Study of Complex Malaria in India, Ispat General Hospital (IGH), Rourkela, Odisha, India
| | - Wilson Mandala
- Malawi University of Science and Technology, Limbe, Malawi
| | - Stephen J Rogerson
- Department of Medicine, The Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Karl B Seydel
- Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, USA.,Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Terrie E Taylor
- Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, USA.,Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Kami Kim
- Division of Infectious Diseases and International Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - D Noah Sather
- Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Akshaya Mohanty
- Infectious Diseases Biology Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | | | - Anita Mohanty
- Department of Intensive Care, IGH, Rourkela, Odisha, India
| | | | - John D Aitchison
- Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Angelika Hoffman
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany.,University Institute of Diagnostic and Interventional Neuroradiology, University Hospital Bern, Inselspital, University of Bern, Switzerland
| | - Sanjib Mohanty
- Center for the Study of Complex Malaria in India, Ispat General Hospital (IGH), Rourkela, Odisha, India
| | - Joseph D Smith
- Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Maria Bernabeu
- Seattle Children's Research Institute, Seattle, Washington, USA.,European Molecular Biology Laboratory (EMBL), Barcelona, Spain
| | - Samuel C Wassmer
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Dos Santos BM, Pereira PH, Garcia CR. Molecular basis of synchronous replication of malaria parasites in the blood stage. Curr Opin Microbiol 2021; 63:210-215. [PMID: 34428626 DOI: 10.1016/j.mib.2021.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
The search for host factors that leads to malaria parasite synchronization has been the focus of several laboratories. The host hormone melatonin synchronizes Plasmodium falciparum in culture by increasing the number of mature parasite stages through a PLC-IP3 activation. Melatonin signaling is linked to crosstalk between Ca2+-cAMP that results in PKA activation. Two other kinases, PfPK7 and PfeIK1, and the nuclear protein PfMORC that lacks melatonin sensitivity in the inducible knock-down parasites are also identified as part of the hormone-signal transduction pathways. Melatonin also modulates P. falciparum mitochondrial fission genes FIS1, DYN1, and DYN2 in a stage-specific manner. How these multiple molecular mechanisms are orchestrated to lead to parasite synchronization is a fascinating and opened biological question.
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Affiliation(s)
- Benedito M Dos Santos
- Laboratory of Functional Genomics and Antimalarial Discovery, Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, 05508-000, São Paulo, Brazil
| | - Pedro Hs Pereira
- Laboratory of Functional Genomics and Antimalarial Discovery, Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, 05508-000, São Paulo, Brazil
| | - Célia Rs Garcia
- Laboratory of Functional Genomics and Antimalarial Discovery, Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, 05508-000, São Paulo, Brazil.
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35
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Plasmodium falciparum transcription in different clinical presentations of malaria associates with circulation time of infected erythrocytes. Nat Commun 2021; 12:4711. [PMID: 34330920 PMCID: PMC8324851 DOI: 10.1038/s41467-021-25062-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023] Open
Abstract
Following Plasmodium falciparum infection, individuals can remain asymptomatic, present with mild fever in uncomplicated malaria cases, or show one or more severe malaria symptoms. Several studies have investigated associations between parasite transcription and clinical severity, but no broad conclusions have yet been drawn. Here, we apply a series of bioinformatic approaches based on P. falciparum's tightly regulated transcriptional pattern during its ~48-hour intraerythrocytic developmental cycle (IDC) to publicly available transcriptomes of parasites obtained from malaria cases of differing clinical severity across multiple studies. Our analysis shows that within each IDC, the circulation time of infected erythrocytes without sequestering to endothelial cells decreases with increasing parasitaemia or disease severity. Accordingly, we find that the size of circulating infected erythrocytes is inversely related to parasite density and disease severity. We propose that enhanced adhesiveness of infected erythrocytes leads to a rapid increase in parasite burden, promoting higher parasitaemia and increased disease severity.
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36
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Gnangnon B, Duraisingh MT, Buckee CO. Deconstructing the parasite multiplication rate of Plasmodium falciparum. Trends Parasitol 2021; 37:922-932. [PMID: 34119440 DOI: 10.1016/j.pt.2021.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 01/22/2023]
Abstract
Epidemiological indicators describing population-level malaria transmission dynamics are widely used to guide policy recommendations. However, the determinants of malaria outcomes within individuals are still poorly understood. This conceptual gap partly reflects the fact that there are few indicators that robustly predict the trajectory of individual infections or clinical outcomes. The parasite multiplication rate (PMR) is a widely used indicator for the Plasmodium intraerythrocytic development cycle (IDC), for example, but its relationship to clinical outcomes is complex. Here, we review its calculation and use in P. falciparum malaria research, as well as the parasite and host factors that impact it. We also provide examples of metrics that can help to link within-host dynamics to malaria clinical outcomes when used alongside the PMR.
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Affiliation(s)
- Bénédicte Gnangnon
- Center for Communicable Diseases Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Immunology & Infectious Diseases Department, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Manoj T Duraisingh
- Immunology & Infectious Diseases Department, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Caroline O Buckee
- Center for Communicable Diseases Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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37
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Georgiadou A, Naidu P, Walsh S, Kamiza S, Barrera V, Harding SP, Moxon CA, Cunnington AJ. Localised release of matrix metallopeptidase 8 in fatal cerebral malaria. Clin Transl Immunology 2021; 10:e1263. [PMID: 33968402 PMCID: PMC8082700 DOI: 10.1002/cti2.1263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVE Cerebral malaria (CM) is a complication of Plasmodium falciparum malaria, in which progressive brain swelling is associated with sequestration of parasites and impaired barrier function of the cerebral microvascular endothelium. To test the hypothesis that localised release of matrix metallopeptidase 8 (MMP8) within the retina is implicated in microvascular leak in CM, we examined its expression and association with extravascular fibrinogen leak in a case-control study of post-mortem retinal samples from 13 Malawian children who met the clinical case definition of CM during life. Cases were seven children who were found on post-mortem examination to have 'true-CM' (parasite sequestration in brain blood vessels), whilst controls were six children who had alternative causes of death ('faux-CM', no parasite sequestration in blood vessels). METHODS We used immunofluorescence microscopy and independent scoring, by two assessors blinded to the CM status, to assess MMP8 expression, extravascular fibrinogen as an indicator of vascular leak and their co-localisation in the retinal microvasculature. RESULTS In 'true-CM' subjects, MMP8 staining was invariably associated with sequestered parasites and a median of 88% (IQR = 74-91%) of capillaries showed MMP8 staining, compared with 14% (IQR = 3.8-24%) in 'faux-CM' (P-value = 0.001). 41% (IQR = 28-49%) of capillaries in 'true-CM' subjects showed co-localisation of extravascular fibrinogen leak and MMP8 staining, compared with 1.8% of capillaries in 'faux-CM' (IQR = 0-3.9%, P-value = 0.01). Vascular leak was rare in the absence of MMP8 staining. CONCLUSION Matrix metallopeptidase 8 was extensively expressed in retinal capillaries of Malawian children with malarial retinopathy and strongly associated with vascular leak. Our findings implicate MMP8 as a cause of the vascular endothelial barrier disruption in CM, which may precipitate fatal brain swelling.
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Affiliation(s)
- Athina Georgiadou
- Department of Infectious DiseaseSection of Paediatric Infectious DiseaseImperial College LondonLondonUK
- Centre for Paediatrics and Child HealthImperial College LondonLondonUK
| | - Praveena Naidu
- Department of Infectious DiseaseSection of Paediatric Infectious DiseaseImperial College LondonLondonUK
| | - Sophie Walsh
- Department of Infectious DiseaseSection of Paediatric Infectious DiseaseImperial College LondonLondonUK
| | - Steve Kamiza
- Department of PathologyCollege of MedicineUniversity of MalawiBlantyreMalawi
| | - Valentina Barrera
- Department of Eye and Vision ScienceInstitute of Life Course and Medical SciencesLiverpool University Hospitals Foundation TrustMembers of Liverpool Health PartnersUniversity of LiverpoolLiverpoolUK
| | - Simon P Harding
- Department of Eye and Vision ScienceInstitute of Life Course and Medical SciencesLiverpool University Hospitals Foundation TrustMembers of Liverpool Health PartnersUniversity of LiverpoolLiverpoolUK
| | - Christopher A Moxon
- Wellcome Centre for Integrative ParasitologyInstitute of Infection, Immunity and InflammationUniversity of GlasgowGlasgowUK
- Department of PaediatricsCollege of MedicineUniversity of MalawiBlantyreMalawi
- Malawi‐Liverpool Wellcome Clinical Research ProgrammeCollege of MedicineUniversity of MalawiBlantyreMalawi
| | - Aubrey J Cunnington
- Department of Infectious DiseaseSection of Paediatric Infectious DiseaseImperial College LondonLondonUK
- Centre for Paediatrics and Child HealthImperial College LondonLondonUK
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38
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Mukherjee P, Burgio G, Heitlinger E. Dual RNA Sequencing Meta-analysis in Plasmodium Infection Identifies Host-Parasite Interactions. mSystems 2021; 6:e00182-21. [PMID: 33879496 PMCID: PMC8546971 DOI: 10.1128/msystems.00182-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/04/2021] [Indexed: 11/20/2022] Open
Abstract
Dual RNA sequencing (RNA-Seq) is the simultaneous transcriptomic analysis of interacting symbionts, for example, in malaria. Potential cross-species interactions identified by correlated gene expression might highlight interlinked signaling, metabolic, or gene regulatory pathways in addition to physically interacting proteins. Often, malaria studies address one of the interacting organisms-host or parasite-rendering the other "contamination." Here we perform a meta-analysis using such studies for cross-species expression analysis. We screened experiments for gene expression from host and Plasmodium. Out of 171 studies in Homo sapiens, Macaca mulatta, and Mus musculus, we identified 63 potential studies containing host and parasite data. While 16 studies (1,950 samples) explicitly performed dual RNA-Seq, 47 (1,398 samples) originally focused on one organism. We found 915 experimental replicates from 20 blood studies to be suitable for coexpression analysis and used orthologs for meta-analysis across different host-parasite systems. Centrality metrics from the derived gene expression networks correlated with gene essentiality in the parasites. We found indications of host immune response to elements of the Plasmodium protein degradation system, an antimalarial drug target. We identified well-studied immune responses in the host with our coexpression networks, as our approach recovers known broad processes interlinked between hosts and parasites in addition to individual host and parasite protein associations. The set of core interactions represents commonalities between human malaria and its model systems for prioritization in laboratory experiments. Our approach might also allow insights into the transferability of model systems for different pathways in malaria studies.IMPORTANCE Malaria still causes about 400,000 deaths a year and is one of the most studied infectious diseases. The disease is studied in mice and monkeys as lab models to derive potential therapeutic intervention in human malaria. Interactions between Plasmodium spp. and its hosts are either conserved across different host-parasite systems or idiosyncratic to those systems. Here we use correlation of gene expression from different RNA-Seq studies to infer common host-parasite interactions across human, mouse, and monkey studies. First, we find a set of very conserved interactors, worth further scrutiny in focused laboratory experiments. Second, this work might help assess to which extent experiments and knowledge on different pathways can be transferred from models to humans for potential therapy.
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Affiliation(s)
- Parnika Mukherjee
- Department of Molecular Parasitology, Humboldt University, Berlin, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Gaétan Burgio
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Emanuel Heitlinger
- Department of Molecular Parasitology, Humboldt University, Berlin, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
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39
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Tennessen JA, Duraisingh MT. Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes. Mol Biol Evol 2021; 38:1356-1371. [PMID: 33185667 PMCID: PMC8042748 DOI: 10.1093/molbev/msaa294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host-parasite coevolutionary dynamics.
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40
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Bioengineered 3D Microvessels for Investigating Plasmodium falciparum Pathogenesis. Trends Parasitol 2021; 37:401-413. [PMID: 33485788 DOI: 10.1016/j.pt.2020.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/15/2020] [Accepted: 12/25/2020] [Indexed: 12/18/2022]
Abstract
Plasmodium falciparum pathogenesis is complex and intimately connected to vascular physiology. This is exemplified by cerebral malaria (CM), a neurovascular complication that accounts for most of the malaria deaths worldwide. P. falciparum sequestration in the brain microvasculature is a hallmark of CM and is not replicated in animal models. Numerous aspects of the disease are challenging to fully understand from clinical studies, such as parasite binding tropism or causal pathways in blood-brain barrier breakdown. Recent bioengineering approaches allow for the generation of 3D microvessels and organ-specific vasculature that provide precise control of vessel architecture and flow dynamics, and hold great promise for malaria research. Here, we discuss recent and future applications of bioengineered microvessels in malaria pathogenesis research.
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Abstract
Lactic acidosis and hyperlactatemia are common metabolic disturbances in patients with severe malaria. Lactic acidosis causes physiological adverse effects, which can aggravate the outcome of malaria. Despite its clear association with mortality in malaria patients, the etiology of lactic acidosis is not completely understood. In this review, the possible contributors to lactic acidosis and hyperlactatemia in patients with malaria are discussed. Both increased lactate production and impaired lactate clearance may play a role in the pathogenesis of lactic acidosis. The increased lactate production is caused by several factors, including the metabolism of intraerythrocytic Plasmodium parasites, aerobic glycolysis by activated immune cells, and an increase in anaerobic glycolysis in hypoxic cells and tissues as a consequence of parasite sequestration and anemia. Impaired hepatic and renal lactate clearance, caused by underlying liver and kidney disease, might further aggravate hyperlactatemia. Multiple factors thus participate in the etiology of lactic acidosis in malaria, and further investigations are required to fully understand their relative contributions and the consequences of this major metabolic disturbance.
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Affiliation(s)
- Hendrik Possemiers
- Laboratory of Immunoparasitology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, University of Leuven, Belgium
| | - Leen Vandermosten
- Laboratory of Immunoparasitology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, University of Leuven, Belgium
| | - Philippe E. Van den Steen
- Laboratory of Immunoparasitology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, University of Leuven, Belgium
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42
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He X, Xia L, Tumas KC, Wu J, Su XZ. Type I Interferons and Malaria: A Double-Edge Sword Against a Complex Parasitic Disease. Front Cell Infect Microbiol 2020; 10:594621. [PMID: 33344264 PMCID: PMC7738626 DOI: 10.3389/fcimb.2020.594621] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022] Open
Abstract
Type I interferons (IFN-Is) are important cytokines playing critical roles in various infections, autoimmune diseases, and cancer. Studies have also shown that IFN-Is exhibit 'conflicting' roles in malaria parasite infections. Malaria parasites have a complex life cycle with multiple developing stages in two hosts. Both the liver and blood stages of malaria parasites in a vertebrate host stimulate IFN-I responses. IFN-Is have been shown to inhibit liver and blood stage development, to suppress T cell activation and adaptive immune response, and to promote production of proinflammatory cytokines and chemokines in animal models. Different parasite species or strains trigger distinct IFN-I responses. For example, a Plasmodium yoelii strain can stimulate a strong IFN-I response during early infection, whereas its isogenetic strain does not. Host genetic background also greatly influences IFN-I production during malaria infections. Consequently, the effects of IFN-Is on parasitemia and disease symptoms are highly variable depending on the combination of parasite and host species or strains. Toll-like receptor (TLR) 7, TLR9, melanoma differentiation-associated protein 5 (MDA5), and cyclic GMP-AMP synthase (cGAS) coupled with stimulator of interferon genes (STING) are the major receptors for recognizing parasite nucleic acids (RNA/DNA) to trigger IFN-I responses. IFN-I levels in vivo are tightly regulated, and various novel molecules have been identified to regulate IFN-I responses during malaria infections. Here we review the major findings and progress in ligand recognition, signaling pathways, functions, and regulation of IFN-I responses during malaria infections.
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Affiliation(s)
- Xiao He
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States
| | - Lu Xia
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Keyla C. Tumas
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States
| | - Jian Wu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States
| | - Xin-Zhuan Su
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States
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43
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Su XZ, Zhang C, Joy DA. Host-Malaria Parasite Interactions and Impacts on Mutual Evolution. Front Cell Infect Microbiol 2020; 10:587933. [PMID: 33194831 PMCID: PMC7652737 DOI: 10.3389/fcimb.2020.587933] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
Malaria is the most deadly parasitic disease, affecting hundreds of millions of people worldwide. Malaria parasites have been associated with their hosts for millions of years. During the long history of host-parasite co-evolution, both parasites and hosts have applied pressure on each other through complex host-parasite molecular interactions. Whereas the hosts activate various immune mechanisms to remove parasites during an infection, the parasites attempt to evade host immunity by diversifying their genome and switching expression of targets of the host immune system. Human intervention to control the disease such as antimalarial drugs and vaccination can greatly alter parasite population dynamics and evolution, particularly the massive applications of antimalarial drugs in recent human history. Vaccination is likely the best method to prevent the disease; however, a partially protective vaccine may have unwanted consequences that require further investigation. Studies of host-parasite interactions and co-evolution will provide important information for designing safe and effective vaccines and for preventing drug resistance. In this essay, we will discuss some interesting molecules involved in host-parasite interactions, including important parasite antigens. We also discuss subjects relevant to drug and vaccine development and some approaches for studying host-parasite interactions.
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Affiliation(s)
- Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Cui Zhang
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Deirdre A Joy
- Parasitology and International Programs Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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44
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Andrade CM, Fleckenstein H, Thomson-Luque R, Doumbo S, Lima NF, Anderson C, Hibbert J, Hopp CS, Tran TM, Li S, Niangaly M, Cisse H, Doumtabe D, Skinner J, Sturdevant D, Ricklefs S, Virtaneva K, Asghar M, Homann MV, Turner L, Martins J, Allman EL, N'Dri ME, Winkler V, Llinás M, Lavazec C, Martens C, Färnert A, Kayentao K, Ongoiba A, Lavstsen T, Osório NS, Otto TD, Recker M, Traore B, Crompton PD, Portugal S. Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season. Nat Med 2020; 26:1929-1940. [PMID: 33106664 DOI: 10.1038/s41591-020-1084-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022]
Abstract
The dry season is a major challenge for Plasmodium falciparum parasites in many malaria endemic regions, where water availability limits mosquito vectors to only part of the year. How P. falciparum bridges two transmission seasons months apart, without being cleared by the human host or compromising host survival, is poorly understood. Here we show that low levels of P. falciparum parasites persist in the blood of asymptomatic Malian individuals during the 5- to 6-month dry season, rarely causing symptoms and minimally affecting the host immune response. Parasites isolated during the dry season are transcriptionally distinct from those of individuals with febrile malaria in the transmission season, coinciding with longer circulation within each replicative cycle of parasitized erythrocytes without adhering to the vascular endothelium. Low parasite levels during the dry season are not due to impaired replication but rather to increased splenic clearance of longer-circulating infected erythrocytes, which likely maintain parasitemias below clinical and immunological radar. We propose that P. falciparum virulence in areas of seasonal malaria transmission is regulated so that the parasite decreases its endothelial binding capacity, allowing increased splenic clearance and enabling several months of subclinical parasite persistence.
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Affiliation(s)
- Carolina M Andrade
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hannah Fleckenstein
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Richard Thomson-Luque
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Safiatou Doumbo
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nathalia F Lima
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carrie Anderson
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Julia Hibbert
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christine S Hopp
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Tuan M Tran
- Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shanping Li
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Moussa Niangaly
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Hamidou Cisse
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Didier Doumtabe
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jeff Skinner
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Dan Sturdevant
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Stacy Ricklefs
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kimmo Virtaneva
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Muhammad Asghar
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Manijeh Vafa Homann
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Louise Turner
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, København N, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Joana Martins
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Portugal and ICVS/3B's -PT Government Associate Laboratory, Braga, Portugal
| | - Erik L Allman
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, State College, PA, USA
| | | | - Volker Winkler
- Institute of Global Health, Heidelberg University Hospital, Heidelberg, Germany
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, State College, PA, USA.,Department of Chemistry, The Pennsylvania State University, State College, PA, USA
| | | | - Craig Martens
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Anna Färnert
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Kassoum Kayentao
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Aissata Ongoiba
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Thomas Lavstsen
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, København N, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Portugal and ICVS/3B's -PT Government Associate Laboratory, Braga, Portugal
| | - Thomas D Otto
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
| | - Mario Recker
- Centre for Mathematics & the Environment, University of Exeter, Penryn Campus, Penryn, UK
| | - Boubacar Traore
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Silvia Portugal
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany. .,German Center for Infection Research (DZIF), Heidelberg, Heidelberg, Germany. .,Max Planck Institute for Infection Biology, Berlin, Germany.
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45
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Prah DA, Amoah LE, Gibbins MP, Bediako Y, Cunnington AJ, Awandare GA, Hafalla JCR. Comparison of leucocyte profiles between healthy children and those with asymptomatic and symptomatic Plasmodium falciparum infections. Malar J 2020; 19:364. [PMID: 33036624 PMCID: PMC7547495 DOI: 10.1186/s12936-020-03435-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/01/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The immune mechanisms that determine whether a Plasmodium falciparum infection would be symptomatic or asymptomatic are not fully understood. Several studies have been carried out to characterize the associations between disease outcomes and leucocyte numbers. However, the majority of these studies have been conducted in adults with acute uncomplicated malaria, despite children being the most vulnerable group. METHODS Peripheral blood leucocyte subpopulations were characterized in children with acute uncomplicated (symptomatic; n = 25) or asymptomatic (n = 67) P. falciparum malaria, as well as malaria-free (uninfected) children (n = 16) from Obom, a sub-district of Accra, Ghana. Leucocyte subpopulations were enumerated by flow cytometry and correlated with two measures of parasite load: (a) plasma levels of P. falciparum histidine-rich protein 2 (PfHRP2) as a proxy for parasite biomass and (b) peripheral blood parasite densities determined by microscopy. RESULTS In children with symptomatic P. falciparum infections, the proportions and absolute cell counts of total (CD3 +) T cells, CD4 + T cells, CD8 + T cells, CD19 + B cells and CD11c + dendritic cells (DCs) were significantly lower as compared to asymptomatic P. falciparum-infected and uninfected children. Notably, CD15 + neutrophil proportions and cell counts were significantly increased in symptomatic children. There was no significant difference in the proportions and absolute counts of CD14 + monocytes amongst the three study groups. As expected, measures of parasite load were significantly higher in symptomatic cases. Remarkably, PfHRP2 levels and parasite densities negatively correlated with both the proportions and absolute numbers of peripheral leucocyte subsets: CD3 + T, CD4 + T, CD8 + T, CD19 + B, CD56 + NK, γδ + T and CD11c + cells. In contrast, both PfHRP2 levels and parasite densities positively correlated with the proportions and absolute numbers of CD15 + cells. CONCLUSIONS Symptomatic P. falciparum infection is correlated with an increase in the levels of peripheral blood neutrophils, indicating a role for this cell type in disease pathogenesis. Parasite load is a key determinant of peripheral cell numbers during malaria infections.
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Affiliation(s)
- Diana Ahu Prah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, UK
| | - Linda Eva Amoah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Matthew P Gibbins
- Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, UK
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation,, University of Glasgow, Glasgow, UK
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | | | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Julius Clemence R Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, UK.
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Kucharski M, Tripathi J, Nayak S, Zhu L, Wirjanata G, van der Pluijm RW, Dhorda M, Dondorp A, Bozdech Z. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 2020; 19:363. [PMID: 33036628 PMCID: PMC7547485 DOI: 10.1186/s12936-020-03436-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Background Sequencing technology advancements opened new opportunities to use transcriptomics for studying malaria pathology and epidemiology. Even though in recent years the study of whole parasite transcriptome proved to be essential in understanding parasite biology there is no compiled up-to-date reference protocol for the efficient generation of transcriptome data from growing number of samples. Here, a comprehensive methodology on how to preserve, extract, amplify, and sequence full-length mRNA transcripts from Plasmodium-infected blood samples is presented that can be fully streamlined for high-throughput studies. Results The utility of various commercially available RNA-preserving reagents in a range of storage conditions was evaluated. Similarly, several RNA extraction protocols were compared and the one most suitable method for the extraction of high-quality total RNA from low-parasitaemia and low-volume blood samples was established. Furthermore, the criteria needed to evaluate the quality and integrity of Plasmodium RNA in the presence of human RNA was updated. Optimization of SMART-seq2 amplification method to better suit AT-rich Plasmodium falciparum RNA samples allowed us to generate high-quality transcriptomes from as little as 10 ng of total RNA and a lower parasitaemia limit of 0.05%. Finally, a modified method for depletion of unwanted human haemoglobin transcripts using in vitro CRISPR-Cas9 treatment was designed, thus improving parasite transcriptome coverage in low parasitaemia samples. To prove the functionality of the pipeline for both laboratory and field strains, the highest 2-hour resolution RNA-seq transcriptome for P. falciparum 3D7 intraerythrocytic life cycle available to date was generated, and the entire protocol was applied to create the largest transcriptome data from Southeast Asian field isolates. Conclusions Overall, the presented methodology is an inclusive pipeline for generation of good quality transcriptomic data from a diverse range of Plasmodium-infected blood samples with varying parasitaemia and RNA inputs. The flexibility of this pipeline to be adapted to robotic handling will facilitate both small and large-scale future transcriptomic studies in the field of malaria.
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Affiliation(s)
- Michal Kucharski
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
| | - Jaishree Tripathi
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
| | - Sourav Nayak
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Rob W van der Pluijm
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mehul Dhorda
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,WorldWide Antimalarial Resistance Network-Asia Regional Centre, Bangkok, Thailand
| | - Arjen Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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47
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Noreikiene K, Ozerov M, Ahmad F, Kõiv T, Kahar S, Gross R, Sepp M, Pellizzone A, Vesterinen EJ, Kisand V, Vasemägi A. Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding. Parasit Vectors 2020; 13:433. [PMID: 32859251 PMCID: PMC7456052 DOI: 10.1186/s13071-020-04306-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/16/2020] [Indexed: 01/09/2023] Open
Abstract
Background Next generation sequencing (NGS) technologies are extensively used to dissect the molecular mechanisms of host-parasite interactions in human pathogens. However, ecological studies have yet to fully exploit the power of NGS as a rich source for formulating and testing new hypotheses. Methods We studied Eurasian perch (Perca fluviatilis) and its eye parasite (Trematoda, Diplostomidae) communities in 14 lakes that differed in humic content in order to explore host-parasite-environment interactions. We hypothesised that high humic content along with low pH would decrease the abundance of the intermediate hosts (gastropods), thus limiting the occurrence of diplostomid parasites in humic lakes. This hypothesis was initially invoked by whole eye RNA-seq data analysis and subsequently tested using PCR-based detection and a novel targeted metabarcoding approach. Results Whole eye transcriptome results revealed overexpression of immune-related genes and the presence of eye parasite sequences in RNA-seq data obtained from perch living in clear-water lakes. Both PCR-based and targeted-metabarcoding approach showed that perch from humic lakes were completely free from diplostomid parasites, while the prevalence of eye flukes in clear-water lakes that contain low amounts of humic substances was close to 100%, with the majority of NGS reads assigned to Tylodelphys clavata. Conclusions High intraspecific diversity of T. clavata indicates that massively parallel sequencing of naturally pooled samples represents an efficient and powerful strategy for shedding light on cryptic diversity of eye parasites. Our results demonstrate that perch populations in clear-water lakes experience contrasting eye parasite pressure compared to those from humic lakes, which is reflected by prevalent differences in the expression of immune-related genes in the eye. This study highlights the utility of NGS to discover novel host-parasite-environment interactions and provide unprecedented power to characterize the molecular diversity of cryptic parasites.![]()
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Affiliation(s)
- Kristina Noreikiene
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006, Tartu, Estonia.
| | - Mikhail Ozerov
- Department of Biology, University of Turku, 20014, Turku, Finland.,Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893, Drottningholm, Sweden.,Biodiversity Unit, University of Turku, 20014, Turku, Finland
| | - Freed Ahmad
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Toomas Kõiv
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, 51006, Tartu, Estonia
| | - Siim Kahar
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006, Tartu, Estonia
| | - Riho Gross
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006, Tartu, Estonia
| | - Margot Sepp
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, 51006, Tartu, Estonia
| | - Antonia Pellizzone
- Department of Biology, University of Turku, 20014, Turku, Finland.,Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy
| | - Eero J Vesterinen
- Biodiversity Unit, University of Turku, 20014, Turku, Finland.,Department of Ecology, Swedish University of Agricultural Sciences, 75651, Uppsala, Sweden
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Anti Vasemägi
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006, Tartu, Estonia. .,Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893, Drottningholm, Sweden.
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48
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Montaldo P, Cunnington A, Oliveira V, Swamy R, Bandya P, Pant S, Lally PJ, Ivain P, Mendoza J, Atreja G, Padmesh V, Baburaj M, Sebastian M, Yasashwi I, Kamalarathnam C, Chandramohan R, Mangalabharathi S, Kumaraswami K, Kumar S, Benakappa N, Manerkar S, Mondhkar J, Prakash V, Sajjid M, Seeralar A, Jahan I, Moni SC, Shahidullah M, Sujatha R, Chandrasekaran M, Ramji S, Shankaran S, Kaforou M, Herberg J, Thayyil S. Transcriptomic profile of adverse neurodevelopmental outcomes after neonatal encephalopathy. Sci Rep 2020; 10:13100. [PMID: 32753750 PMCID: PMC7403382 DOI: 10.1038/s41598-020-70131-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/16/2020] [Indexed: 12/20/2022] Open
Abstract
A rapid and early diagnostic test to identify the encephalopathic babies at risk of adverse outcome may accelerate the development of neuroprotectants. We examined if a whole blood transcriptomic signature measured soon after birth, predicts adverse neurodevelopmental outcome eighteen months after neonatal encephalopathy. We performed next generation sequencing on whole blood ribonucleic acid obtained within six hours of birth from the first 47 encephalopathic babies recruited to the Hypothermia for Encephalopathy in Low and middle-income countries (HELIX) trial. Two infants with blood culture positive sepsis were excluded, and the data from remaining 45 were analysed. A total of 855 genes were significantly differentially expressed between the good and adverse outcome groups, of which RGS1 and SMC4 were the most significant. Biological pathway analysis adjusted for gender, trial randomisation allocation (cooling therapy versus usual care) and estimated blood leukocyte proportions revealed over-representation of genes from pathways related to melatonin and polo-like kinase in babies with adverse outcome. These preliminary data suggest that transcriptomic profiling may be a promising tool for rapid risk stratification in neonatal encephalopathy. It may provide insights into biological mechanisms and identify novel therapeutic targets for neuroprotection.
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Affiliation(s)
- Paolo Montaldo
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK. .,Neonatal Unit, Università Degli Studi Della Campania "Luigi Vanvitelli", Naples, Italy.
| | - Aubrey Cunnington
- Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK
| | - Vania Oliveira
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK
| | - Ravi Swamy
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK
| | - Prathik Bandya
- Neonatal Medicine, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Stuti Pant
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK
| | - Peter J Lally
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK
| | - Phoebe Ivain
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK
| | - Josephine Mendoza
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK
| | - Gaurav Atreja
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK
| | - Vadakepat Padmesh
- Neonatal Medicine, Institute of Obstetrics and Gynaecology, Madras Medical College, Chennai, Tamil Nadu, India
| | - Mythili Baburaj
- Neonatal Medicine, Institute of Obstetrics and Gynaecology, Madras Medical College, Chennai, Tamil Nadu, India
| | - Monica Sebastian
- Neonatal Medicine, Institute of Child Health, Madras Medical College, Tamil Nadu, Chennai, India
| | - Indiramma Yasashwi
- Neonatal Medicine, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Chinnathambi Kamalarathnam
- Neonatal Medicine, Institute of Obstetrics and Gynaecology, Madras Medical College, Chennai, Tamil Nadu, India
| | - Rema Chandramohan
- Neonatal Medicine, Institute of Obstetrics and Gynaecology, Madras Medical College, Chennai, Tamil Nadu, India
| | - Sundaram Mangalabharathi
- Neonatal Medicine, Institute of Obstetrics and Gynaecology, Madras Medical College, Chennai, Tamil Nadu, India
| | - Kumutha Kumaraswami
- Neonatal Medicine, Institute of Obstetrics and Gynaecology, Madras Medical College, Chennai, Tamil Nadu, India
| | - Shobha Kumar
- Neonatal Medicine, Institute of Obstetrics and Gynaecology, Madras Medical College, Chennai, Tamil Nadu, India
| | - Naveen Benakappa
- Neonatal Medicine, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | | | | | - Vinayagam Prakash
- Neonatal Medicine, Institute of Obstetrics and Gynaecology, Madras Medical College, Chennai, Tamil Nadu, India
| | - Mohammed Sajjid
- Neonatal Medicine, Institute of Obstetrics and Gynaecology, Madras Medical College, Chennai, Tamil Nadu, India
| | - Arasar Seeralar
- Neonatal Medicine, Institute of Child Health, Madras Medical College, Tamil Nadu, Chennai, India
| | - Ismat Jahan
- Neonatal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | | | - Mohammod Shahidullah
- Neonatal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Radhika Sujatha
- Neonatal Medicine, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Manigandan Chandrasekaran
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK
| | - Siddarth Ramji
- Neonatal Medicine, Maulana Azad Medical College, New Delhi, Delhi, India
| | - Seetha Shankaran
- Neonatal-Perinatal Medicine, Wayne State University, Detroit, MI, USA
| | - Myrsini Kaforou
- Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK
| | - Jethro Herberg
- Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK
| | - Sudhin Thayyil
- Department of Brain Sciences, Centre for Perinatal Neuroscience, Imperial College London, London, UK
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Host and Parasite Transcriptomic Changes upon Successive Plasmodium falciparum Infections in Early Childhood. mSystems 2020; 5:5/4/e00116-20. [PMID: 32636334 PMCID: PMC7343306 DOI: 10.1128/msystems.00116-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We show that dual RNA-seq from patient blood samples allows characterization of host/parasite interactions during malaria infections and can provide a solid framework to study the acquisition of antimalarial immunity, as well as the adaptations of P. falciparum to malaria-experienced hosts. Children are highly susceptible to clinical malaria, and in regions where malaria is endemic, their immune systems must face successive encounters with Plasmodium falciparum parasites before they develop immunity, first against severe disease and later against uncomplicated malaria. Understanding cellular and molecular interactions between host and parasites during an infection could provide insights into the processes underlying this gradual acquisition of immunity, as well as to how parasites adapt to infect hosts that are successively more malaria experienced. Here, we describe methods to analyze the host and parasite gene expression profiles generated simultaneously from blood samples collected from five consecutive symptomatic P. falciparum infections in three Malian children. We show that the data generated enable statistical assessment of the proportions of (i) each white blood cell subset and (ii) the parasite developmental stages, as well as investigations of host-parasite gene coexpression. We also use the sequences generated to analyze allelic variations in transcribed regions and determine the complexity of each infection. While limited by the modest sample size, our analyses suggest that host gene expression profiles primarily clustered by individual, while the parasite gene expression profiles seemed to differentiate early from late infections. Overall, this study provides a solid framework to examine the mechanisms underlying acquisition of immunity to malaria infections using whole-blood transcriptome sequencing (RNA-seq). IMPORTANCE We show that dual RNA-seq from patient blood samples allows characterization of host/parasite interactions during malaria infections and can provide a solid framework to study the acquisition of antimalarial immunity, as well as the adaptations of P. falciparum to malaria-experienced hosts.
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50
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Paraburkholderia Symbionts Display Variable Infection Patterns That Are Not Predictive of Amoeba Host Outcomes. Genes (Basel) 2020; 11:genes11060674. [PMID: 32575747 PMCID: PMC7349545 DOI: 10.3390/genes11060674] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/07/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022] Open
Abstract
Symbiotic interactions exist within a parasitism to mutualism continuum that is influenced, among others, by genes and context. Dynamics of intracellular invasion, replication, and prevalence may underscore both host survivability and symbiont stability. More infectious symbionts might exert higher corresponding costs to hosts, which could ultimately disadvantage both partners. Here, we quantify infection patterns of diverse Paraburkholderia symbiont genotypes in their amoeba host Dictyostelium discoideum and probe the relationship between these patterns and host outcomes. We exposed D. discoideum to thirteen strains of Paraburkholderia each belonging to one of the three symbiont species found to naturally infect D. discoideum: Paraburkholderia agricolaris, Paraburkholderia hayleyella, and Paraburkholderia bonniea. We quantified the infection prevalence and intracellular density of fluorescently labeled symbionts along with the final host population size using flow cytometry and confocal microscopy. We find that infection phenotypes vary across symbiont strains. Symbionts belonging to the same species generally display similar infection patterns but are interestingly distinct when it comes to host outcomes. This results in final infection loads that do not strongly correlate to final host outcomes, suggesting other genetic factors that are not a direct cause or consequence of symbiont abundance impact host fitness.
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