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Hviid L, Jensen AR, Deitsch KW. PfEMP1 and var genes - Still of key importance in Plasmodium falciparum malaria pathogenesis and immunity. ADVANCES IN PARASITOLOGY 2024; 125:53-103. [PMID: 39095112 DOI: 10.1016/bs.apar.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The most severe form of malaria, caused by infection with Plasmodium falciparum parasites, continues to be an important cause of human suffering and poverty. The P. falciparum erythrocyte membrane protein 1 (PfEMP1) family of clonally variant antigens, which mediates the adhesion of infected erythrocytes to the vascular endothelium in various tissues and organs, is a central component of the pathogenesis of the disease and a key target of the acquired immune response to malaria. Much new knowledge has accumulated since we published a systematic overview of the PfEMP1 family almost ten years ago. In this chapter, we therefore aim to summarize research progress since 2015 on the structure, function, regulation etc. of this key protein family of arguably the most important human parasite. Recent insights regarding PfEMP1-specific immune responses and PfEMP1-specific vaccination against malaria, as well as an outlook for the coming years are also covered.
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Affiliation(s)
- Lars Hviid
- Centre for translational Medicine and Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.
| | - Anja R Jensen
- Centre for translational Medicine and Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States
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2
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Lenz T, Zhang X, Chakraborty A, Ardakany AR, Prudhomme J, Ay F, Deitsch K, Le Roch KG. Chromatin structure and var2csa - a tango in regulation of var gene expression in the human malaria parasite, Plasmodium falciparum? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580059. [PMID: 38405848 PMCID: PMC10888805 DOI: 10.1101/2024.02.13.580059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Over the last few decades, novel methods have been developed to study how chromosome positioning within the nucleus may play a role in gene regulation. Adaptation of these methods in the human malaria parasite, Plasmodium falciparum, has recently led to the discovery that the three-dimensional structure of chromatin within the nucleus may be critical in controlling expression of virulence genes (var genes). Recent work has implicated an unusual, highly conserved var gene called var2csa in contributing to coordinated transcriptional switching, however how this gene functions in this capacity is unknown. To further understand how var2csa influences var gene switching, targeted DNA double-strand breaks (DSBs) within the sub-telomeric region of chromosome 12 were used to delete the gene and the surrounding chromosomal region. To characterize the changes in chromatin architecture stemming from this deletion and how these changes could affect var gene expression, we used a combination of RNA-seq, Chip-seq and Hi-C to pinpoint epigenetic and chromatin structural modifications in regions of differential gene expression. We observed a net gain of interactions in sub-telomeric regions and internal var gene regions following var2csa knockout, indicating an increase of tightly controlled heterochromatin structures. Our results suggest that disruption of var2csa results not only in changes in var gene transcriptional regulation but also a significant tightening of heterochromatin clusters thereby disrupting coordinated activation of var genes throughout the genome. Altogether our result confirms a strong link between the var2csa locus, chromatin structure and var gene expression.
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Affiliation(s)
- Todd Lenz
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Xu Zhang
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Abhijit Chakraborty
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | | | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Ferhat Ay
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Kirk Deitsch
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
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3
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Reyser T, Paloque L, Augereau JM, Di Stefano L, Benoit-Vical F. Epigenetic regulation as a therapeutic target in the malaria parasite Plasmodium falciparum. Malar J 2024; 23:44. [PMID: 38347549 PMCID: PMC10863139 DOI: 10.1186/s12936-024-04855-9] [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: 07/28/2023] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Over the past thirty years, epigenetic regulation of gene expression has gained increasing interest as it was shown to be implicated in illnesses ranging from cancers to parasitic diseases. In the malaria parasite, epigenetics was shown to be involved in several key steps of the complex life cycle of Plasmodium, among which asexual development and sexual commitment, but also in major biological processes like immune evasion, response to environmental changes or DNA repair. Because epigenetics plays such paramount roles in the Plasmodium parasite, enzymes involved in these regulating pathways represent a reservoir of potential therapeutic targets. This review focuses on epigenetic regulatory processes and their effectors in the malaria parasite, as well as the inhibitors of epigenetic pathways and their potential as new anti-malarial drugs. Such types of drugs could be formidable tools that may contribute to malaria eradication in a context of widespread resistance to conventional anti-malarials.
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Affiliation(s)
- Thibaud Reyser
- LCC-CNRS, Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, Toulouse, France
- MAAP, Inserm ERL 1289, Team "New Antiplasmodial Molecules and Pharmacological Approaches", Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Lucie Paloque
- LCC-CNRS, Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, Toulouse, France
- MAAP, Inserm ERL 1289, Team "New Antiplasmodial Molecules and Pharmacological Approaches", Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Jean-Michel Augereau
- LCC-CNRS, Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, Toulouse, France
- MAAP, Inserm ERL 1289, Team "New Antiplasmodial Molecules and Pharmacological Approaches", Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Luisa Di Stefano
- MCD, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Françoise Benoit-Vical
- LCC-CNRS, Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, Toulouse, France.
- MAAP, Inserm ERL 1289, Team "New Antiplasmodial Molecules and Pharmacological Approaches", Toulouse, France.
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, UPS, Université de Toulouse, Toulouse, France.
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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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Barcons-Simon A, Carrington M, Siegel TN. Decoding the impact of nuclear organization on antigenic variation in parasites. Nat Microbiol 2023; 8:1408-1418. [PMID: 37524976 DOI: 10.1038/s41564-023-01424-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Antigenic variation as a strategy to evade the host adaptive immune response has evolved in divergent pathogens. Antigenic variation involves restricted, and often mutually exclusive, expression of dominant antigens and a periodic switch in antigen expression during infection. In eukaryotes, nuclear compartmentalization, including three-dimensional folding of the genome and physical separation of proteins in compartments or condensates, regulates mutually exclusive gene expression and chromosomal translocations. In this Review, we discuss the impact of nuclear organization on antigenic variation in the protozoan pathogens Trypanosoma brucei and Plasmodium falciparum. In particular, we highlight the relevance of nuclear organization in both mutually exclusive antigen expression and genome stability, which underlie antigenic variation.
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Affiliation(s)
- Anna Barcons-Simon
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - T Nicolai Siegel
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.
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6
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Thompson TA, Chahine Z, Le Roch KG. The role of long noncoding RNAs in malaria parasites. Trends Parasitol 2023; 39:517-531. [PMID: 37121862 DOI: 10.1016/j.pt.2023.03.016] [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: 02/01/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 05/02/2023]
Abstract
The human malaria parasites, including Plasmodium falciparum, persist as a major cause of global morbidity and mortality. The recent stalling of progress toward malaria elimination substantiates a need for novel interventions. Controlled gene expression is central to the parasite's numerous life cycle transformations and adaptation. With few specific transcription factors (TFs) identified, crucial roles for chromatin states and epigenetics in parasite transcription have become evident. Although many chromatin-modifying enzymes are known, less is known about which factors mediate their impacts on transcriptional variation. Like those of higher eukaryotes, long noncoding RNAs (lncRNAs) have recently been shown to have integral roles in parasite gene regulation. This review aims to summarize recent developments and key findings on the role of lncRNAs in P. falciparum.
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Affiliation(s)
- Trevor A Thompson
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA.
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7
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Wichers-Misterek JS, Krumkamp R, Held J, von Thien H, Wittmann I, Höppner YD, Ruge JM, Moser K, Dara A, Strauss J, Esen M, Fendel R, Sulyok Z, Jeninga MD, Kremsner PG, Sim BKL, Hoffman SL, Duffy MF, Otto TD, Gilberger TW, Silva JC, Mordmüller B, Petter M, Bachmann A. The exception that proves the rule: Virulence gene expression at the onset of Plasmodium falciparum blood stage infections. PLoS Pathog 2023; 19:e1011468. [PMID: 37384799 DOI: 10.1371/journal.ppat.1011468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Controlled human malaria infections (CHMI) are a valuable tool to study parasite gene expression in vivo under defined conditions. In previous studies, virulence gene expression was analyzed in samples from volunteers infected with the Plasmodium falciparum (Pf) NF54 isolate, which is of African origin. Here, we provide an in-depth investigation of parasite virulence gene expression in malaria-naïve European volunteers undergoing CHMI with the genetically distinct Pf 7G8 clone, originating in Brazil. Differential expression of var genes, encoding major virulence factors of Pf, PfEMP1s, was assessed in ex vivo parasite samples as well as in parasites from the in vitro cell bank culture that was used to generate the sporozoites (SPZ) for CHMI (Sanaria PfSPZ Challenge (7G8)). We report broad activation of mainly B-type subtelomeric located var genes at the onset of a 7G8 blood stage infection in naïve volunteers, mirroring the NF54 expression study and suggesting that the expression of virulence-associated genes is generally reset during transmission from the mosquito to the human host. However, in 7G8 parasites, we additionally detected a continuously expressed single C-type variant, Pf7G8_040025600, that was most highly expressed in both pre-mosquito cell bank and volunteer samples, suggesting that 7G8, unlike NF54, maintains expression of some previously expressed var variants during transmission. This suggests that in a new host, the parasite may preferentially express the variants that previously allowed successful infection and transmission. Trial registration: ClinicalTrials.gov - NCT02704533; 2018-004523-36.
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Affiliation(s)
- Jan Stephan Wichers-Misterek
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Ralf Krumkamp
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Heidrun von Thien
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Irene Wittmann
- Institute of Microbiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Yannick Daniel Höppner
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
| | - Julia M Ruge
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
| | - Kara Moser
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Antoine Dara
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Jan Strauss
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Meral Esen
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Zita Sulyok
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Myriam D Jeninga
- Institute of Microbiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Peter G Kremsner
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - B Kim Lee Sim
- Sanaria Inc., Rockville, Maryland, United States of America
| | | | - Michael F Duffy
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas D Otto
- School of Infection & Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Tim-Wolf Gilberger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisboa, Portugal
| | - Benjamin Mordmüller
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Michaela Petter
- Institute of Microbiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anna Bachmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
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8
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Schneider V, Visone J, Harris C, Florini F, Hadjimichael E, Zhang X, Gross M, Rhee K, Ben Mamoun C, Kafsack B, Deitsch K. The human malaria parasite Plasmodium falciparum can sense environmental changes and respond by antigenic switching. Proc Natl Acad Sci U S A 2023; 120:e2302152120. [PMID: 37068249 PMCID: PMC10151525 DOI: 10.1073/pnas.2302152120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
The primary antigenic and virulence determinant of the human malaria parasite Plasmodium falciparum is a variant surface protein called PfEMP1. Different forms of PfEMP1 are encoded by a multicopy gene family called var, and switching between active genes enables the parasites to evade the antibody response of their human hosts. var gene switching is key for the maintenance of chronic infections; however, what controls switching is unknown, although it has been suggested to occur at a constant frequency with little or no environmental influence. var gene transcription is controlled epigenetically through the activity of histone methyltransferases (HMTs). Studies in model systems have shown that metabolism and epigenetic control of gene expression are linked through the availability of intracellular S-adenosylmethionine (SAM), the principal methyl donor in biological methylation modifications, which can fluctuate based on nutrient availability. To determine whether environmental conditions and changes in metabolism can influence var gene expression, P. falciparum was cultured in media with altered concentrations of nutrients involved in SAM metabolism. We found that conditions that influence lipid metabolism induce var gene switching, indicating that parasites can respond to changes in their environment by altering var gene expression patterns. Genetic modifications that directly modified expression of the enzymes that control SAM levels similarly led to profound changes in var gene expression, confirming that changes in SAM availability modulate var gene switching. These observations directly challenge the paradigm that antigenic variation in P. falciparum follows an intrinsic, programed switching rate, which operates independently of any external stimuli.
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Affiliation(s)
- Victoria M. Schneider
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
- Laboratory of Chemical Biology and Microbial Pathogenesis, Rockefeller University, New York, NY 10065
| | - Joseph E. Visone
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Chantal T. Harris
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Francesca Florini
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Evi Hadjimichael
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Xu Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Mackensie R. Gross
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Kyu Y. Rhee
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Choukri Ben Mamoun
- Section of Infectious Disease, Department of Microbial Pathogenesis, Yale School of Medicine, Yale University New Haven, CT 06510
| | - Björn F. C. Kafsack
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Kirk W. Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
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9
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Establishment and validation of a plasma oncofetal chondroitin sulfated proteoglycan for pan-cancer detection. Nat Commun 2023; 14:645. [PMID: 36746966 PMCID: PMC9902466 DOI: 10.1038/s41467-023-36374-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Various biomarkers targeting cell-free DNA (cfDNA) and circulating proteins have been tested for pan-cancer detection. Oncofetal chondroitin sulfate (ofCS), which distinctively modifies proteoglycans (PGs) of most cancer cells and binds specifically to the recombinant Plasmodium falciparum VAR2CSA proteins (rVAR2), is explored for its potential as a plasma biomarker in pan-cancer detection. To quantitate the plasma ofCS/ofCSPGs, we optimized an ELISA using different capture/detection pairs (rVAR2/anti-CD44, -SDC1, and -CSPG4) in a case-control study with six cancer types. We show that the plasma levels of ofCS/ofCSPGs are significantly higher in cancer patients (P values, 1.2 × 10-2 to 4.4 × 10-10). Validation studies are performed with two independent cohorts covering 11 malignant tumors. The individuals in the top decile of ofCS-CD44 have more than 27-fold cancer risk (OR = 27.8, 95%CI = 18.8-41.4, P = 2.72 × 10-62) compared with the lowest 20%. Moreover, the elevated plasma ofCS-CD44 could be detected at the early stage of pan-cancer with strong dose-dependent odds risk prediction.
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10
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A nuclear redox sensor modulates gene activation and var switching in Plasmodium falciparum. Proc Natl Acad Sci U S A 2022; 119:e2201247119. [PMID: 35939693 PMCID: PMC9388093 DOI: 10.1073/pnas.2201247119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The virulence of Plasmodium falciparum, which causes the deadliest form of human malaria, is attributed to its ability to evade the human immune response. These parasites "choose" to express a single variant from a repertoire of surface antigens called PfEMP1, which are placed on the surface of the infected red cell. Immune evasion is achieved by switches in expression between var genes, each encoding a different PfEMP1 variant. While the mechanisms that regulate mutually exclusive expression of var genes are still elusive, antisense long-noncoding RNAs (lncRNAs) transcribed from the intron of the active var gene were implicated in the "choice" of the single active var gene. Here, we show that this lncRNA colocalizes with the site of var mRNA transcription and is anchored to the var locus via DNA:RNA interactions. We define the var lncRNA interactome and identify a redox sensor, P. falciparum thioredoxin peroxidase I (PfTPx-1), as one of the proteins associated with the var antisense lncRNA. We show that PfTPx-1 localizes to a nuclear subcompartment associated with active transcription on the nuclear periphery, in ring-stage parasite, when var transcription occurs. In addition, PfTPx-1 colocalizes with S-adenosylmethionine synthetase (PfSAMS) in the nucleus, and its overexpression leads to activation of var2csa, similar to overexpression of PfSAMS. Furthermore, we show that PfTPx-1 knockdown alters the var switch rate as well as activation of additional gene subsets. Taken together, our data indicate that nuclear PfTPx-1 plays a role in gene activation possibly by providing a redox-controlled nuclear microenvironment ideal for active transcription.
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11
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Florini F, Visone JE, Deitsch KW. Shared Mechanisms for Mutually Exclusive Expression and Antigenic Variation by Protozoan Parasites. Front Cell Dev Biol 2022; 10:852239. [PMID: 35350381 PMCID: PMC8957917 DOI: 10.3389/fcell.2022.852239] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/17/2022] [Indexed: 01/05/2023] Open
Abstract
Cellular decision-making at the level of gene expression is a key process in the development and evolution of every organism. Variations in gene expression can lead to phenotypic diversity and the development of subpopulations with adaptive advantages. A prime example is the mutually exclusive activation of a single gene from within a multicopy gene family. In mammals, this ranges from the activation of one of the two immunoglobulin (Ig) alleles to the choice in olfactory sensory neurons of a single odorant receptor (OR) gene from a family of more than 1,000. Similarly, in parasites like Trypanosoma brucei, Giardia lamblia or Plasmodium falciparum, the process of antigenic variation required to escape recognition by the host immune system involves the monoallelic expression of vsg, vsp or var genes, respectively. Despite the importance of this process, understanding how this choice is made remains an enigma. The development of powerful techniques such as single cell RNA-seq and Hi-C has provided new insights into the mechanisms these different systems employ to achieve monoallelic gene expression. Studies utilizing these techniques have shown how the complex interplay between nuclear architecture, physical interactions between chromosomes and different chromatin states lead to single allele expression. Additionally, in several instances it has been observed that high-level expression of a single gene is preceded by a transient state where multiple genes are expressed at a low level. In this review, we will describe and compare the different strategies that organisms have evolved to choose one gene from within a large family and how parasites employ this strategy to ensure survival within their hosts.
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12
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Zhang X, Florini F, Visone JE, Lionardi I, Gross MR, Patel V, Deitsch KW. A coordinated transcriptional switching network mediates antigenic variation of human malaria parasites. eLife 2022; 11:83840. [PMID: 36515978 PMCID: PMC9833823 DOI: 10.7554/elife.83840] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022] Open
Abstract
Malaria parasites avoid immune clearance through their ability to systematically alter antigens exposed on the surface of infected red blood cells. This is accomplished by tightly regulated transcriptional control of individual members of a large, multicopy gene family called var and is the key to both the virulence and chronic nature of malaria infections. Expression of var genes is mutually exclusive and controlled epigenetically, however how large populations of parasites coordinate var gene switching to avoid premature exposure of the antigenic repertoire is unknown. Here, we provide evidence for a transcriptional network anchored by a universally conserved gene called var2csa that coordinates the switching process. We describe a structured switching bias that shifts overtime and could shape the pattern of var expression over the course of a lengthy infection. Our results provide an explanation for a previously mysterious aspect of malaria infections and shed light on how parasites possessing a relatively small repertoire of variant antigen-encoding genes can coordinate switching events to limit antigen exposure, thereby maintaining chronic infections.
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Affiliation(s)
- Xu Zhang
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Francesca Florini
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Joseph E Visone
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Irina Lionardi
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical CollegeNew YorkUnited States
| | - Mackensie R Gross
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Valay Patel
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
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13
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McLeod DV, Wild G, Úbeda F. Epigenetic memories and the evolution of infectious diseases. Nat Commun 2021; 12:4273. [PMID: 34257309 PMCID: PMC8277771 DOI: 10.1038/s41467-021-24580-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Genes with identical DNA sequence may show differential expression because of epigenetic marks. Where epigenetic marks respond to past conditions, they represent a form of "memory". Despite their medical relevance, the impact of memories on the evolution of infectious diseases has rarely been considered. Here we explore the evolution of virulence in pathogens that carry memories of the sex of their previous host. We show that this form of memory provides information about the sex of present and future hosts when the sexes differ in their pathogen's transmission pattern. Memories of past hosts enable the evolution of greater virulence in infections originating from one sex and infections transmitted across sexes. Thus, our results account for patterns of virulence that have, to date, defied medical explanation. In particular, it has been observed that girls infected by boys (or boys infected by girls) are more likely to die from measles, chickenpox and polio than girls infected by girls (or boys infected by boys). We also evaluate epigenetic therapies that tamper with the memories of infecting pathogens. More broadly, our findings imply that pathogens can be selected to carry memories of past environments other than sex. This identifies new directions in personalised medicine.
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Affiliation(s)
- David V McLeod
- Centre D'Ecologie Fonctionnelle & Evolutive, CNRS, Montpellier, France
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Geoff Wild
- Department of Applied Mathematics, The University of Western Ontario, London, ON, Canada
| | - Francisco Úbeda
- Department of Biology, Royal Holloway University of London, Egham, Surrey, UK.
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14
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Gross MR, Hsu R, Deitsch KW. Evolution of transcriptional control of antigenic variation and virulence in human and ape malaria parasites. BMC Ecol Evol 2021; 21:139. [PMID: 34238209 PMCID: PMC8265125 DOI: 10.1186/s12862-021-01872-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
Background The most severe form of human malaria is caused by the protozoan parasite Plasmodium falciparum. This unicellular organism is a member of a subgenus of Plasmodium called the Laverania that infects apes, with P. falciparum being the only member that infects humans. The exceptional virulence of this species to humans can be largely attributed to a family of variant surface antigens placed by the parasites onto the surface of infected red blood cells that mediate adherence to the vascular endothelium. These proteins are encoded by a large, multicopy gene family called var, with each var gene encoding a different form of the protein. By changing which var gene is expressed, parasites avoid immune recognition, a process called antigenic variation that underlies the chronic nature of malaria infections. Results Here we show that the common ancestor of the branch of the Laverania lineage that includes the human parasite underwent a remarkable change in the organization and structure of elements linked to the complex transcriptional regulation displayed by the var gene family. Unlike the other members of the Laverania, the clade that gave rise to P. falciparum evolved distinct subsets of var genes distinguishable by different upstream transcriptional regulatory regions that have been associated with different expression profiles and virulence properties. In addition, two uniquely conserved var genes that have been proposed to play a role in coordinating transcriptional switching similarly arose uniquely within this clade. We hypothesize that these changes originated at a time of dramatic climatic change on the African continent that is predicted to have led to significant changes in transmission dynamics, thus selecting for patterns of antigenic variation that enabled lengthier, more chronic infections. Conclusions These observations suggest that changes in transmission dynamics selected for significant alterations in the transcriptional regulatory mechanisms that mediate antigenic variation in the parasite lineage that includes P. falciparum. These changes likely underlie the chronic nature of these infections as well as their exceptional virulence. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01872-z.
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Affiliation(s)
- Mackensie R Gross
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Rosie Hsu
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.
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15
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Vaccination with rEGVac elicits immunoprotection against different stages of Echinococcus granulosus life cycle: A pilot study. Acta Trop 2021; 218:105883. [PMID: 33676937 DOI: 10.1016/j.actatropica.2021.105883] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022]
Abstract
Vaccination against dog-sheep transmission cycle is necessary to control cystic echinococcosis (CE) infection. A multi-epitope multi-antigenic recombinant vaccine was developed-comprising the three putative vaccine antigens EG95, Eg14-3-3 and EgEnolase-was cloned and expressed. In a pilot experiment, the multi-antigen vaccine was assessed in 15 dogs and 15 sheep (five experimental groups and three animals in each group) by two subcutaneous doses 28 days apart. To evaluate the efficacy of the vaccine candidate first immunological analysis were done comprising IgG and IgE antibodies and the cytokine IL-4 in sera of the immunized dogs and sheep. Serum IgG, IgE, and IL-4, in particular in the dogs, were increased after the two rounds of vaccine candidate injection, while the total number of hydatid cysts was reduced (~85.43%). This pilot trial indicated significant immune protection efficacy against E. granulosus especially in dogs, while its efficacy in sheep was not as high as dogs. The multi-antigenic candidate vaccine is proposed as a protective vaccine modality in both dogs and sheep.
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16
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Activity of Epigenetic Inhibitors against Plasmodium falciparum Asexual and Sexual Blood Stages. Antimicrob Agents Chemother 2020; 64:AAC.02523-19. [PMID: 32366713 DOI: 10.1128/aac.02523-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
Earlier genetic and inhibitor studies showed that epigenetic regulation of gene expression is critical for malaria parasite survival in multiple life stages and a promising target for new antimalarials. We therefore evaluated the activity of 350 diverse epigenetic inhibitors against multiple stages of Plasmodium falciparum We observed ≥90% inhibition at 10 μM for 28% of compounds against asexual blood stages and early gametocytes, of which a third retained ≥90% inhibition at 1 μM.
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17
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A Histone Methyltransferase Inhibitor Can Reverse Epigenetically Acquired Drug Resistance in the Malaria Parasite Plasmodium falciparum. Antimicrob Agents Chemother 2020; 64:AAC.02021-19. [PMID: 32179524 DOI: 10.1128/aac.02021-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/08/2020] [Indexed: 01/14/2023] Open
Abstract
Malaria parasites invade and replicate within red blood cells (RBCs), extensively modifying their structure and gaining access to the extracellular environment by placing the plasmodial surface anion channel (PSAC) into the RBC membrane. Expression of members of the cytoadherence linked antigen gene 3 (clag3) family is required for PSAC activity, a process that is regulated epigenetically. PSAC is a well-established route of uptake for large, hydrophilic antimalarial compounds, and parasites can acquire resistance by silencing clag3 gene expression, thereby reducing drug uptake. We found that exposure to sub-IC50 concentrations of the histone methyltransferase inhibitor chaetocin caused substantial changes in both clag3 gene expression and RBC permeability, and reversed acquired resistance to the antimalarial compound blasticidin S that is transported through PSACs. Chaetocin treatment also altered progression of parasites through their replicative cycle, presumably by changing their ability to modify chromatin appropriately to enable DNA replication. These results indicate that targeting histone modifiers could represent a novel tool for reversing epigenetically acquired drug resistance in P. falciparum.
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18
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Coetzee N, von Grüning H, Opperman D, van der Watt M, Reader J, Birkholtz LM. Epigenetic inhibitors target multiple stages of Plasmodium falciparum parasites. Sci Rep 2020; 10:2355. [PMID: 32047203 PMCID: PMC7012883 DOI: 10.1038/s41598-020-59298-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022] Open
Abstract
The epigenome of the malaria parasite, Plasmodium falciparum, is associated with regulation of various essential processes in the parasite including control of proliferation during asexual development as well as control of sexual differentiation. The unusual nature of the epigenome has prompted investigations into the potential to target epigenetic modulators with novel chemotypes. Here, we explored the diversity within a library of 95 compounds, active against various epigenetic modifiers in cancerous cells, for activity against multiple stages of P. falciparum development. We show that P. falciparum is differentially susceptible to epigenetic perturbation during both asexual and sexual development, with early stage gametocytes particularly sensitive to epi-drugs targeting both histone and non-histone epigenetic modifiers. Moreover, 5 compounds targeting histone acetylation and methylation show potent multistage activity against asexual parasites, early and late stage gametocytes, with transmission-blocking potential. Overall, these results warrant further examination of the potential antimalarial properties of these hit compounds.
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Affiliation(s)
- Nanika Coetzee
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Hilde von Grüning
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Daniel Opperman
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Mariette van der Watt
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa.
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19
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Otto TD, Assefa SA, Böhme U, Sanders MJ, Kwiatkowski D, Berriman M, Newbold C. Evolutionary analysis of the most polymorphic gene family in falciparum malaria. Wellcome Open Res 2019; 4:193. [PMID: 32055709 PMCID: PMC7001760 DOI: 10.12688/wellcomeopenres.15590.1] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
The var gene family of the human malaria parasite Plasmodium falciparum encode proteins that are crucial determinants of both pathogenesis and immune evasion and are highly polymorphic. Here we have assembled nearly complete var gene repertoires from 2398 field isolates and analysed a normalised set of 714 from across 12 countries. This therefore represents the first large scale attempt to catalogue the worldwide distribution of var gene sequences We confirm the extreme polymorphism of this gene family but also demonstrate an unexpected level of sequence sharing both within and between continents. We show that this is likely due to both the remnants of selective sweeps as well as a worrying degree of recent gene flow across continents with implications for the spread of drug resistance. We also address the evolution of the var repertoire with respect to the ancestral genes within the Laverania and show that diversity generated by recombination is concentrated in a number of hotspots. An analysis of the subdomain structure indicates that some existing definitions may need to be revised From the analysis of this data, we can now understand the way in which the family has evolved and how the diversity is continuously being generated. Finally, we demonstrate that because the genes are distributed across the genome, sequence sharing between genotypes acts as a useful population genetic marker.
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Affiliation(s)
- Thomas D. Otto
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
| | - Sammy A. Assefa
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ulrike Böhme
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Dominic Kwiatkowski
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Pf3k consortium
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Matt Berriman
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Chris Newbold
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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20
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Gangnard S, Chêne A, Dechavanne S, Srivastava A, Avril M, Smith JD, Gamain B. VAR2CSA binding phenotype has ancient origin and arose before Plasmodium falciparum crossed to humans: implications in placental malaria vaccine design. Sci Rep 2019; 9:16978. [PMID: 31740695 PMCID: PMC6861233 DOI: 10.1038/s41598-019-53334-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/24/2019] [Indexed: 11/09/2022] Open
Abstract
VAR2CSA is a leading candidate for developing a placental malaria (PM) vaccine that would protect pregnant women living in malaria endemic areas against placental infections and improve birth outcomes. Two VAR2CSA-based PM vaccines are currently under clinical trials, but it is still unclear if the use of a single VAR2CSA variant will be sufficient to induce a broad enough humoral response in humans to cross-react with genetically diverse parasite populations. Additional immuno-focusing vaccine strategies may therefore be required to identify functionally conserved antibody epitopes in VAR2CSA. We explored the possibility that conserved epitopes could exist between VAR2CSA from the chimpanzee parasite Plasmodium reichenowi and Plasmodium falciparum sequences. Making use of VAR2CSA recombinant proteins originating from both species, we showed that VAR2CSA from P. reichenowi (Pr-VAR2CSA) binds to the placental receptor CSA with high specificity and affinity. Antibodies raised against Pr-VAR2CSA were able to recognize native VAR2CSA from different P. falciparum genotypes and to inhibit the interaction between CSA and P. falciparum-infected erythrocytes expressing different VAR2CSA variants. Our work revealed the existence of cross-species inhibitory epitopes in VAR2CSA and calls for pre-clinical studies assessing the efficacy of novel VAR2CSA-based cross-species boosting regimens.
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Affiliation(s)
- Stéphane Gangnard
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France.,Institut National de la Transfusion Sanguine, F-75015, Paris, France.,Laboratory of excellence GR-Ex, F-75015, Paris, France
| | - Arnaud Chêne
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France.,Institut National de la Transfusion Sanguine, F-75015, Paris, France.,Laboratory of excellence GR-Ex, F-75015, Paris, France
| | - Sébastien Dechavanne
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France.,Institut National de la Transfusion Sanguine, F-75015, Paris, France.,Laboratory of excellence GR-Ex, F-75015, Paris, France
| | - Anand Srivastava
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France.,Institut National de la Transfusion Sanguine, F-75015, Paris, France.,Laboratory of excellence GR-Ex, F-75015, Paris, France
| | - Marion Avril
- Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Joseph D Smith
- Seattle Children's Research Institute, Seattle, WA, 98109, USA.,Department of Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Benoît Gamain
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France. .,Institut National de la Transfusion Sanguine, F-75015, Paris, France. .,Laboratory of excellence GR-Ex, F-75015, Paris, France.
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21
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Bachmann A, Bruske E, Krumkamp R, Turner L, Wichers JS, Petter M, Held J, Duffy MF, Sim BKL, Hoffman SL, Kremsner PG, Lell B, Lavstsen T, Frank M, Mordmüller B, Tannich E. Controlled human malaria infection with Plasmodium falciparum demonstrates impact of naturally acquired immunity on virulence gene expression. PLoS Pathog 2019; 15:e1007906. [PMID: 31295334 PMCID: PMC6650087 DOI: 10.1371/journal.ppat.1007906] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/23/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
The pathogenesis of Plasmodium falciparum malaria is linked to the variant surface antigen PfEMP1, which mediates tethering of infected erythrocytes to the host endothelium and is encoded by approximately 60 var genes per parasite genome. Repeated episodes of malaria infection result in the gradual acquisition of protective antibodies against PfEMP1 variants. The antibody repertoire is believed to provide a selective pressure driving the clonal expansion of parasites expressing unrecognized PfEMP1 variants, however, due to the lack of experimental in vivo models there is only limited experimental evidence in support of this concept. To get insight into the impact of naturally acquired immunity on the expressed var gene repertoire early during infection we performed controlled human malaria infections of 20 adult African volunteers with life-long malaria exposure using aseptic, purified, cryopreserved P. falciparum sporozoites (Sanaria PfSPZ Challenge) and correlated serological data with var gene expression patterns from ex vivo parasites. Among the 10 African volunteers who developed patent infections, individuals with low antibody levels showed a steep rise in parasitemia accompanied by broad activation of multiple, predominantly subtelomeric var genes, similar to what we previously observed in naïve volunteers. In contrast, individuals with intermediate antibody levels developed asymptomatic infections and the ex vivo parasite populations expressed only few var gene variants, indicative of clonal selection. Importantly, in contrast to parasites from naïve volunteers, expression of var genes coding for endothelial protein C receptor (EPCR)-binding PfEMP1 that are associated with severe childhood malaria was rarely detected in semi-immune adult African volunteers. Moreover, we followed var gene expression for up to six parasite replication cycles and demonstrated for the first time in vivo a shift in the dominant var gene variant. In conclusion, our data suggest that P. falciparum activates multiple subtelomeric var genes at the onset of blood stage infection facilitating rapid expansion of parasite clones which express PfEMP1 variants unrecognized by the host's immune system, thus promoting overall parasite survival in the face of host immunity.
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Affiliation(s)
- Anna Bachmann
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Germany
| | - Ellen Bruske
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Ralf Krumkamp
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Germany
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Louise Turner
- Centre for Medical Parasitology, University of Copenhagen, Copenhagen K, Denmark
| | - J. Stephan Wichers
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Michaela Petter
- Mikrobiologisches Institut–Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jana Held
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Michael F. Duffy
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | | | | | - Peter G. Kremsner
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Bertrand Lell
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
| | - Thomas Lavstsen
- Centre for Medical Parasitology, University of Copenhagen, Copenhagen K, Denmark
| | - Matthias Frank
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Benjamin Mordmüller
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Egbert Tannich
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Germany
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22
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Silva Pereira S, Casas-Sánchez A, Haines LR, Ogugo M, Absolomon K, Sanders M, Kemp S, Acosta-Serrano Á, Noyes H, Berriman M, Jackson AP. Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs. Genome Res 2018; 28:1383-1394. [PMID: 30006414 PMCID: PMC6120623 DOI: 10.1101/gr.234146.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/12/2018] [Indexed: 11/25/2022]
Abstract
African trypanosomes are vector-borne hemoparasites of humans and animals. In the mammal, parasites evade the immune response through antigenic variation. Periodic switching of the variant surface glycoprotein (VSG) coat covering their cell surface allows sequential expansion of serologically distinct parasite clones. Trypanosome genomes contain many hundreds of VSG genes, subject to rapid changes in nucleotide sequence, copy number, and chromosomal position. Thus, analyzing, or even quantifying, VSG diversity over space and time presents an enormous challenge to conventional techniques. Indeed, previous population genomic studies have overlooked this vital aspect of pathogen biology for lack of analytical tools. Here we present a method for analyzing population-scale VSG diversity in Trypanosoma congolense from deep sequencing data. Previously, we suggested that T. congolense VSGs segregate into defined “phylotypes” that do not recombine. In our data set comprising 41 T. congolense genome sequences from across Africa, these phylotypes are universal and exhaustive. Screening sequence contigs with diagnostic protein motifs accurately quantifies relative phylotype frequencies, providing a metric of VSG diversity, called the “variant antigen profile.” We applied our metric to VSG expression in the tsetse fly, showing that certain, rare VSG phylotypes may be preferentially expressed in infective, metacyclic-stage parasites. Hence, variant antigen profiling accurately and rapidly determines the T. congolense VSG gene and transcript repertoire from sequence data, without need for manual curation or highly contiguous sequences. It offers a tractable approach to measuring VSG diversity across strains and during infections, which is imperative to understanding the host–parasite interaction at population and individual scales.
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Affiliation(s)
- Sara Silva Pereira
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Aitor Casas-Sánchez
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Lee R Haines
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Moses Ogugo
- International Livestock Research Institute, Nairobi 00100, Kenya
| | - Kihara Absolomon
- International Livestock Research Institute, Nairobi 00100, Kenya
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Steve Kemp
- International Livestock Research Institute, Nairobi 00100, Kenya
| | - Álvaro Acosta-Serrano
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Harry Noyes
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Andrew P Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
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23
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Remodeling of the malaria parasite and host human red cell by vesicle amplification that induces artemisinin resistance. Blood 2018; 131:1234-1247. [PMID: 29363540 DOI: 10.1182/blood-2017-11-814665] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/12/2018] [Indexed: 12/25/2022] Open
Abstract
Artemisinin resistance threatens worldwide malaria control and elimination. Elevation of phosphatidylinositol-3-phosphate (PI3P) can induce resistance in blood stages of Plasmodium falciparum The parasite unfolded protein response (UPR) has also been implicated as a proteostatic mechanism that may diminish artemisinin-induced toxic proteopathy. How PI3P acts and its connection to the UPR remain unknown, although both are conferred by mutation in P falciparum Kelch13 (K13), the marker of artemisinin resistance. Here we used cryoimmunoelectron microscopy to show that K13 concentrates at PI3P tubules/vesicles of the parasite's endoplasmic reticulum (ER) in infected red cells. K13 colocalizes and copurifies with the major virulence adhesin PfEMP1. The PfEMP1-K13 proteome is comprehensively enriched in multiple proteostasis systems of protein export, quality control, and folding in the ER and cytoplasm and UPR. Synthetic elevation of PI3P that induces resistance in absence of K13 mutation also yields signatures of proteostasis and clinical resistance. These findings imply a key role for PI3P-vesicle amplification as a mechanism of resistance of infected red cells. As validation, the major resistance mutation K13C580Y quantitatively increased PI3P tubules/vesicles, exporting them throughout the parasite and the red cell. Chemical inhibitors and fluorescence microscopy showed that alterations in PfEMP1 export to the red cell and cytoadherence of infected cells to a host endothelial receptor are features of multiple K13 mutants. Together these data suggest that amplified PI3P vesicles disseminate widespread proteostatic capacity that may neutralize artemisinins toxic proteopathy and implicate a role for the host red cell in artemisinin resistance. The mechanistic insights generated will have an impact on malaria drug development.
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24
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Abstract
Protozoan parasites colonize numerous metazoan hosts and insect vectors through their life cycles, with the need to respond quickly and reversibly while encountering diverse and often hostile ecological niches. To succeed, parasites must also persist within individuals until transmission between hosts is achieved. Several parasitic protozoa cause a huge burden of disease in humans and livestock, and here we focus on the parasites that cause malaria and African trypanosomiasis. Efforts to understand how these pathogens adapt to survive in varied host environments, cause disease, and transmit between hosts have revealed a wealth of epigenetic phenomena. Epigenetic switching mechanisms appear to be ideally suited for the regulation of clonal antigenic variation underlying successful parasitism. We review the molecular players and complex mechanistic layers that mediate the epigenetic regulation of virulence gene expression. Understanding epigenetic processes will aid the development of antiparasitic therapeutics.
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Affiliation(s)
- Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA.
| | - David Horn
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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25
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Abstract
Malaria is a significant threat throughout the developing world. Among the most fascinating aspects of the protozoan parasites responsible for this disease are the methods they employ to avoid the immune system and perpetuate chronic infections. Key among these is antigenic variation: By systematically altering antigens that are displayed to the host's immune system, the parasite renders the adaptive immune response ineffective. For Plasmodium falciparum, the species responsible for the most severe form of human malaria, this process involves a complicated molecular mechanism that results in continuously changing patterns of variant-antigen-encoding gene expression. Although many features of this process remain obscure, significant progress has been made in recent years to decipher various molecular aspects of the regulatory cascade that causes chronic infection.
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Affiliation(s)
- Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065;
| | - Ron Dzikowski
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada and Kuvin Center for the Study of Infectious and Tropical Diseases, Hebrew University Hadassah Medical School, Jerusalem 91120, Israel;
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26
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CRISPR/Cas9 Genome Editing Reveals That the Intron Is Not Essential for var2csa Gene Activation or Silencing in Plasmodium falciparum. mBio 2017; 8:mBio.00729-17. [PMID: 28698275 PMCID: PMC5513710 DOI: 10.1128/mbio.00729-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Plasmodium falciparum relies on monoallelic expression of 1 of 60 var virulence genes for antigenic variation and host immune evasion. Each var gene contains a conserved intron which has been implicated in previous studies in both activation and repression of transcription via several epigenetic mechanisms, including interaction with the var promoter, production of long noncoding RNAs (lncRNAs), and localization to repressive perinuclear sites. However, functional studies have relied primarily on artificial expression constructs. Using the recently developed P. falciparum clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, we directly deleted the var2csa P. falciparum 3D7_1200600 (Pf3D7_1200600) endogenous intron, resulting in an intronless var gene in a natural, marker-free chromosomal context. Deletion of the var2csa intron resulted in an upregulation of transcription of the var2csa gene in ring-stage parasites and subsequent expression of the PfEMP1 protein in late-stage parasites. Intron deletion did not affect the normal temporal regulation and subsequent transcriptional silencing of the var gene in trophozoites but did result in increased rates of var gene switching in some mutant clones. Transcriptional repression of the intronless var2csa gene could be achieved via long-term culture or panning with the CD36 receptor, after which reactivation was possible with chondroitin sulfate A (CSA) panning. These data suggest that the var2csa intron is not required for silencing or activation in ring-stage parasites but point to a subtle role in regulation of switching within the var gene family.IMPORTANCEPlasmodium falciparum is the most virulent species of malaria parasite, causing high rates of morbidity and mortality in those infected. Chronic infection depends on an immune evasion mechanism termed antigenic variation, which in turn relies on monoallelic expression of 1 of ~60 var genes. Understanding antigenic variation and the transcriptional regulation of monoallelic expression is important for developing drugs and/or vaccines. The var gene family encodes the antigenic surface proteins that decorate infected erythrocytes. Until recently, studying the underlying genetic elements that regulate monoallelic expression in P. falciparum was difficult, and most studies relied on artificial systems such as episomal reporter genes. Our study was the first to use CRISPR/Cas9 genome editing for the functional study of an important, conserved genetic element of var genes-the intron-in an endogenous, episome-free manner. Our findings shed light on the role of the var gene intron in transcriptional regulation of monoallelic expression.
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27
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Abstract
Organisms with identical genome sequences can show substantial differences in their phenotypes owing to epigenetic changes that result in different use of their genes. Epigenetic regulation of gene expression plays a key role in the control of several fundamental processes in the biology of malaria parasites, including antigenic variation and sexual differentiation. Some of the histone modifications and chromatin-modifying enzymes that control the epigenetic states of malaria genes have been characterized, and their functions are beginning to be unraveled. The fundamental principles of epigenetic regulation of gene expression appear to be conserved between malaria parasites and model eukaryotes, but important peculiarities exist. Here, we review the current knowledge of malaria epigenetics and discuss how it can be exploited for the development of new molecular markers and new types of drugs that may contribute to malaria eradication efforts.
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Affiliation(s)
- Alfred Cortés
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain.,ICREA, Barcelona, Catalonia 08010, Spain
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York 10065
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28
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Zuma AA, Santos JDO, Mendes I, de Souza W, Machado CR, Motta MCM. Chaetocin-A histone methyltransferase inhibitor-Impairs proliferation, arrests cell cycle and induces nucleolar disassembly in Trypanosoma cruzi. Acta Trop 2017; 170:149-160. [PMID: 28185826 DOI: 10.1016/j.actatropica.2017.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/12/2017] [Accepted: 02/06/2017] [Indexed: 12/15/2022]
Abstract
The Trypanosomatidae family includes pathogenic species of medical and veterinary interest. Chagas disease is endemic in Latin America, and about 8 million people are infected worldwide. There is a need for more effective drugs for the acute, undetermined and chronic phases of the disease that, in addition, do not cause side effects, stimulating the search for identification of new drug targets, as well as new chemotherapeutic targets. Trypanosomatids contain characteristic structures, such as the nucleus that undergoes a closed mitosis without chromosome formation and variations of chromatin packing in the different protozoa developmental stages. The nuclear DNA is condensed by histones that suffer post-translational modifications, such as addition of methyl groups by histone methyltransferases (MHT) and addition of acetyl groups by acetyltransferases. These processes modulate gene expression and chromatin organization, which are crucial to transcription, replication, repair and recombination. In the present study, the effects of chaetocin, a HMT inhibitor, on T. cruzi epimastigote proliferation, viability, ultrastructure and cell cycle were investigated. Results indicate that chaetocin promoted irreversible inhibition of protozoa growth, evident unpacking of nuclear heterochromatin and intense nucleolus fragmentation, which is associated with parasite cell cycle arrest and RNA transcription blockage. Taken together, data obtained with chaetocin treatment stimulate the use of histone methyltransferase inhibitors against pathogenic trypanosomatids.
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29
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Chan S, Frasch A, Mandava CS, Ch'ng JH, Quintana MDP, Vesterlund M, Ghorbal M, Joannin N, Franzén O, Lopez-Rubio JJ, Barbieri S, Lanzavecchia A, Sanyal S, Wahlgren M. Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor. Nat Microbiol 2017; 2:17068. [PMID: 28481333 DOI: 10.1038/nmicrobiol.2017.68] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/29/2017] [Indexed: 12/22/2022]
Abstract
Pregnancy-associated malaria commonly involves the binding of Plasmodium falciparum-infected erythrocytes to placental chondroitin sulfate A (CSA) through the PfEMP1-VAR2CSA protein. VAR2CSA is translationally repressed by an upstream open reading frame. In this study, we report that the P. falciparum translation enhancing factor (PTEF) relieves upstream open reading frame repression and thereby facilitates VAR2CSA translation. VAR2CSA protein levels in var2csa-transcribing parasites are dependent on the expression level of PTEF, and the alleviation of upstream open reading frame repression requires the proteolytic processing of PTEF by PfCalpain. Cleavage generates a C-terminal domain that contains a sterile-alpha-motif-like domain. The C-terminal domain is permissive to cytoplasmic shuttling and interacts with ribosomes to facilitate translational derepression of the var2csa coding sequence. It also enhances translation in a heterologous translation system and thus represents the first non-canonical translation enhancing factor to be found in a protozoan. Our results implicate PTEF in regulating placental CSA binding of infected erythrocytes.
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Affiliation(s)
- Sherwin Chan
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
| | - Alejandra Frasch
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Uppsala University, Box-596, 751 24 Uppsala, Sweden
| | - Jun-Hong Ch'ng
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden.,Department of Microbiology, National University of Singapore 117545, Singapore
| | - Maria Del Pilar Quintana
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden.,Escuela de Medicina y Ciencias de la Salud, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Calle 12C No. 6-25, Bogotá, Colombia
| | - Mattias Vesterlund
- Cancer Proteomics, Department of Oncology-Pathology, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Mehdi Ghorbal
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier F34090, France.,CNRS - 5290, IRD 224 - University of Montpellier (UMR 'MiVEGEC'), Montpellier, France
| | - Nicolas Joannin
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
| | - Oscar Franzén
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jose-Juan Lopez-Rubio
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier F34090, France.,CNRS - 5290, IRD 224 - University of Montpellier (UMR 'MiVEGEC'), Montpellier, France
| | - Sonia Barbieri
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, 751 24 Uppsala, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
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30
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Duffy MF, Tang J, Sumardy F, Nguyen HHT, Selvarajah SA, Josling GA, Day KP, Petter M, Brown GV. Activation and clustering of a Plasmodium falciparum var gene are affected by subtelomeric sequences. FEBS J 2016; 284:237-257. [PMID: 27860263 DOI: 10.1111/febs.13967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/12/2016] [Accepted: 11/15/2016] [Indexed: 11/30/2022]
Abstract
The Plasmodium falciparum var multigene family encodes the cytoadhesive, variant antigen PfEMP1. P. falciparum antigenic variation and cytoadhesion specificity are controlled by epigenetic switching between the single, or few, simultaneously expressed var genes. Most var genes are maintained in perinuclear clusters of heterochromatic telomeres. The active var gene(s) occupy a single, perinuclear var expression site. It is unresolved whether the var expression site forms in situ at a telomeric cluster or whether it is an extant compartment to which single chromosomes travel, thus controlling var switching. Here we show that transcription of a var gene did not require decreased colocalisation with clusters of telomeres, supporting var expression site formation in situ. However following recombination within adjacent subtelomeric sequences, the same var gene was persistently activated and did colocalise less with telomeric clusters. Thus, participation in stable, heterochromatic, telomere clusters and var switching are independent but are both affected by subtelomeric sequences. The var expression site colocalised with the euchromatic mark H3K27ac to a greater extent than it did with heterochromatic H3K9me3. H3K27ac was enriched within the active var gene promoter even when the var gene was transiently repressed in mature parasites and thus H3K27ac may contribute to var gene epigenetic memory.
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Affiliation(s)
- Michael F Duffy
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Jingyi Tang
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Fransisca Sumardy
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Hanh H T Nguyen
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Shamista A Selvarajah
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Gabrielle A Josling
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA, USA
| | - Karen P Day
- The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Michaela Petter
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Graham V Brown
- The Nossal Institute for Global Health, The University of Melbourne, Victoria, Australia
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31
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Jackson AP. Gene family phylogeny and the evolution of parasite cell surfaces. Mol Biochem Parasitol 2016; 209:64-75. [DOI: 10.1016/j.molbiopara.2016.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/18/2016] [Accepted: 03/19/2016] [Indexed: 11/30/2022]
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32
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Dimonte S, Bruske EI, Hass J, Supan C, Salazar CL, Held J, Tschan S, Esen M, Flötenmeyer M, Koch I, Berger J, Bachmann A, Sim BKL, Hoffman SL, Kremsner PG, Mordmüller B, Frank M. Sporozoite Route of Infection Influences In Vitro var Gene Transcription of Plasmodium falciparum Parasites From Controlled Human Infections. J Infect Dis 2016; 214:884-94. [PMID: 27279526 DOI: 10.1093/infdis/jiw225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/19/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Antigenic variation in Plasmodium falciparum is mediated by the multicopy var gene family. Each parasite possesses about 60 var genes, and switching between active var loci results in antigenic variation. In the current study, the effect of mosquito and host passage on in vitro var gene transcription was investigated. METHODS Thirty malaria-naive individuals were inoculated by intradermal or intravenous injection with cryopreserved, isogenic NF54 P. falciparum sporozoites (PfSPZ) generated from 1 premosquito culture. Microscopic parasitemia developed in 22 individuals, and 21 in vitro cultures were established. The var gene transcript levels were determined in early and late postpatient cultures and in the premosquito culture. RESULTS At the early time point, all cultures preferentially transcribed 8 subtelomeric var genes. Intradermal infections had higher var gene transcript levels than intravenous infections and a significantly longer intrahost replication time (P = .03). At the late time point, 9 subtelomeric and 8 central var genes were transcribed at the same levels in almost all cultures. Premosquito and late postpatient cultures transcribed the same subtelomeric and central var genes, except for var2csa CONCLUSIONS The duration of intrahost replication influences in vitro var gene transcript patterns. Differences between premosquito and postpatient cultures decrease with prolonged in vitro growth.
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Affiliation(s)
- Sandra Dimonte
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
| | - Ellen I Bruske
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
| | - Johanna Hass
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
| | - Christian Supan
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
| | - Carmen L Salazar
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
| | - Jana Held
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
| | - Serena Tschan
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
| | - Meral Esen
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
| | | | - Iris Koch
- Max Planck Institute for Developmental Biology, Tübingen
| | - Jürgen Berger
- Max Planck Institute for Developmental Biology, Tübingen
| | - Anna Bachmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Peter G Kremsner
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen Centre de Recherches Médicales de Lambaréné (CERMEL), Fondation Internationale de l'Hôpital Albert Schweitzer, Lambaréné, Gabon
| | - Benjamin Mordmüller
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
| | - Matthias Frank
- Institute of Tropical Medicine University of Tübingen and German Center for Infection Research, Partner Site Tübingen
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