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Tan MH, Tiedje KE, Feng Q, Zhan Q, Pascual M, Shim H, Chan YB, Day KP. A paradoxical population structure of var DBLα types in Africa. bioRxiv 2023:2023.11.05.565723. [PMID: 37986738 PMCID: PMC10659346 DOI: 10.1101/2023.11.05.565723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The var multigene family encodes the P. falciparum erythrocyte membrane protein 1 (PfEMP1), which is important in host-parasite interaction as a virulence factor and major surface antigen of the blood stages of the parasite, responsible for maintaining chronic infection. Whilst important in the biology of P. falciparum, these genes (50 to 60 genes per parasite genome) are routinely excluded from whole genome analyses due to their hyper-diversity, achieved primarily through recombination. The PfEMP1 head structure almost always consists of a DBLα-CIDR tandem. Categorised into different groups (upsA, upsB, upsC), different head structures have been associated with different ligand-binding affinities and disease severities. We study how conserved individual DBLα types are at the country, regional, and local scales in Sub-Saharan Africa. Using publicly-available sequence datasets and a novel ups classification algorithm, cUps, we performed an in silico exploration of DBLα conservation through time and space in Africa. In all three ups groups, the population structure of DBLα types in Africa consists of variants occurring at rare, low, moderate, and high frequencies. Non-rare variants were found to be temporally stable in a local area in endemic Ghana. When inspected across different geographical scales, we report different levels of conservation; while some DBLα types were consistently found in high frequencies in multiple African countries, others were conserved only locally, signifying local preservation of specific types. Underlying this population pattern is the composition of DBLα types within each isolate DBLα repertoire, revealed to also consist of a mix of types found at rare, low, moderate, and high frequencies in the population. We further discuss the adaptive forces and balancing selection, including host genetic factors, potentially shaping the evolution and diversity of DBLα types in Africa.
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Affiliation(s)
- Mun Hua Tan
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, AU
| | - Kathryn E Tiedje
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, AU
| | - Qian Feng
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Qi Zhan
- Department of Ecology and Evolution, University of Chicago; Chicago, Illinois, USA
| | - Mercedes Pascual
- Department of Ecology and Evolution, University of Chicago; Chicago, Illinois, USA
| | - Heejung Shim
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Yao-Ban Chan
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Karen P Day
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, AU
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Tiedje KE, Zhan Q, Ruybal-Pésantez S, Tonkin-Hill G, He Q, Tan MH, Argyropoulos DC, Deed SL, Ghansah A, Bangre O, Oduro AR, Koram KA, Pascual M, Day KP. Measuring changes in Plasmodium falciparum census population size in response to sequential malaria control interventions. medRxiv 2023:2023.05.18.23290210. [PMID: 37292908 PMCID: PMC10246142 DOI: 10.1101/2023.05.18.23290210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Here we introduce a new endpoint "census population size" to evaluate the epidemiology and control of Plasmodium falciparum infections, where the parasite, rather than the infected human host, is the unit of measurement. To calculate census population size, we rely on a definition of parasite variation known as multiplicity of infection (M O I v a r ), based on the hyper-diversity of the v a r multigene family. We present a Bayesian approach to estimate M O I v a r from sequencing and counting the number of unique DBLα tags (or DBLα types) of v a r genes, and derive from it census population size by summation of M O I v a r in the human population. We track changes in this parasite population size and structure through sequential malaria interventions by indoor residual spraying (IRS) and seasonal malaria chemoprevention (SMC) from 2012 to 2017 in an area of high-seasonal malaria transmission in northern Ghana. Following IRS, which reduced transmission intensity by > 90% and decreased parasite prevalence by ~40-50%, significant reductions in v a r diversity, M O I v a r , and population size were observed in ~2,000 humans across all ages. These changes, consistent with the loss of diverse parasite genomes, were short lived and 32-months after IRS was discontinued and SMC was introduced, v a r diversity and population size rebounded in all age groups except for the younger children (1-5 years) targeted by SMC. Despite major perturbations from IRS and SMC interventions, the parasite population remained very large and retained the v a r population genetic characteristics of a high-transmission system (high v a r diversity; low v a r repertoire similarity) demonstrating the resilience of P. falciparum to short-term interventions in high-burden countries of sub-Saharan Africa.
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Affiliation(s)
- Kathryn E. Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
| | - Qi Zhan
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago; Chicago, Illinois, USA
- Department of Ecology and Evolution, The University of Chicago; Chicago, Illinois, USA
| | - Shazia Ruybal-Pésantez
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
| | - Gerry Tonkin-Hill
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute; Melbourne, Australia
| | - Qixin He
- Department of Ecology and Evolution, The University of Chicago; Chicago, Illinois, USA
| | - Mun Hua Tan
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
| | - Dionne C. Argyropoulos
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
| | - Samantha L. Deed
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana; Legon, Ghana
| | - Oscar Bangre
- Navrongo Health Research Centre, Ghana Health Service; Navrongo, Ghana
| | - Abraham R. Oduro
- Navrongo Health Research Centre, Ghana Health Service; Navrongo, Ghana
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana; Legon, Ghana
| | - Mercedes Pascual
- Department of Ecology and Evolution, The University of Chicago; Chicago, Illinois, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Karen P. Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
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3
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Abstract
The enormous diversity and complexity of var genes that diversify rapidly by recombination has led to the exclusion of assembly of these genes from major genome initiatives (e.g., Pf6). A scalable solution in epidemiological surveillance of var genes is to use a small ‘tag’ region encoding the immunogenic DBLα domain as a marker to estimate var diversity. As var genes diversify by recombination, it is not clear the extent to which the same tag can appear in multiple var genes. This relationship between marker and gene has not been investigated in natural populations. Analyses of in vitro recombination within and between var genes have suggested that this relationship would not be exclusive. Using a dataset of publicly-available assembled var sequences, we test this hypothesis by studying DBLα-var relationships for four study sites in four countries: Pursat (Cambodia) and Mae Sot (Thailand), representing low malaria transmission, and Navrongo (Ghana) and Chikwawa (Malawi), representing high malaria transmission. In all study sites, DBLα-var relationships were shown to be predominantly 1-to-1, followed by a second largest proportion of 1-to-2 DBLα-var relationships. This finding indicates that DBLα tags can be used to estimate not just DBLα diversity but var gene diversity when applied in a local endemic area. Epidemiological applications of this result are discussed.
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Affiliation(s)
- Mun Hua Tan
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute, Melbourne, VIC, Australia
| | - Heejung Shim
- School of Mathematics and Statistics/Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Yao-ban Chan
- School of Mathematics and Statistics/Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Karen P. Day
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute, Melbourne, VIC, Australia
- CORRESPONDENCE Karen P. Day,
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Labbé F, He Q, Zhan Q, Tiedje KE, Argyropoulos DC, Tan MH, Ghansah A, Day KP, Pascual M. Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections. PLoS Comput Biol 2023; 19:e1010816. [PMID: 36595546 PMCID: PMC9838855 DOI: 10.1371/journal.pcbi.1010816] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 01/13/2023] [Accepted: 12/14/2022] [Indexed: 01/04/2023] Open
Abstract
At a time when effective tools for monitoring malaria control and eradication efforts are crucial, the increasing availability of molecular data motivates their application to epidemiology. The multiplicity of infection (MOI), defined as the number of genetically distinct parasite strains co-infecting a host, is one key epidemiological parameter for evaluating malaria interventions. Estimating MOI remains a challenge for high-transmission settings where individuals typically carry multiple co-occurring infections. Several quantitative approaches have been developed to estimate MOI, including two cost-effective ones relying on molecular data: i) THE REAL McCOIL method is based on putatively neutral single nucleotide polymorphism loci, and ii) the varcoding method is a fingerprinting approach that relies on the diversity and limited repertoire overlap of the var multigene family encoding the major Plasmodium falciparum blood-stage antigen PfEMP1 and is therefore under selection. In this study, we assess the robustness of the MOI estimates generated with these two approaches by simulating P. falciparum malaria dynamics under three transmission conditions using an extension of a previously developed stochastic agent-based model. We demonstrate that these approaches are complementary and best considered across distinct transmission intensities. While varcoding can underestimate MOI, it allows robust estimation, especially under high transmission where repertoire overlap is extremely limited from frequency-dependent selection. In contrast, THE REAL McCOIL often considerably overestimates MOI, but still provides reasonable estimates for low and moderate transmission. Regardless of transmission intensity, results for THE REAL McCOIL indicate that an inaccurate tail at high MOI values is generated, and that at high transmission, an apparently reasonable estimated MOI distribution can arise from some degree of compensation between overestimation and underestimation. As many countries pursue malaria elimination targets, defining the most suitable approach to estimate MOI based on sample size and local transmission intensity is highly recommended for monitoring the impact of intervention programs.
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Affiliation(s)
- Frédéric Labbé
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, Indianapolis, United States of America
| | - Qi Zhan
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Kathryn E. Tiedje
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Dionne C. Argyropoulos
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Mun Hua Tan
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Science, University of Ghana, Legon, Ghana
| | - Karen P. Day
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Mercedes Pascual
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
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Bachmann A, Metwally NG, Allweier J, Cronshagen J, Del Pilar Martinez Tauler M, Murk A, Roth LK, Torabi H, Wu Y, Gutsmann T, Bruchhaus I. CD36-A Host Receptor Necessary for Malaria Parasites to Establish and Maintain Infection. Microorganisms 2022; 10. [PMID: 36557610 DOI: 10.3390/microorganisms10122356] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/21/2022] [Accepted: 11/27/2022] [Indexed: 11/30/2022] Open
Abstract
Plasmodium falciparum-infected erythrocytes (PfIEs) present P. falciparum erythrocyte membrane protein 1 proteins (PfEMP1s) on the cell surface, via which they cytoadhere to various endothelial cell receptors (ECRs) on the walls of human blood vessels. This prevents the parasite from passing through the spleen, which would lead to its elimination. Each P. falciparum isolate has about 60 different PfEMP1s acting as ligands, and at least 24 ECRs have been identified as interaction partners. Interestingly, in every parasite genome sequenced to date, at least 75% of the encoded PfEMP1s have a binding domain for the scavenger receptor CD36 widely distributed on host endothelial cells and many other cell types. Here, we discuss why the interaction between PfIEs and CD36 is optimal to maintain a finely regulated equilibrium that allows the parasite to multiply and spread while causing minimal harm to the host in most infections.
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7
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Johnson EK, Larremore DB. Bayesian estimation of community size and overlap from random subsamples. PLoS Comput Biol 2022; 18:e1010451. [PMID: 36121879 PMCID: PMC9522272 DOI: 10.1371/journal.pcbi.1010451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/29/2022] [Accepted: 07/28/2022] [Indexed: 11/19/2022] Open
Abstract
Counting the number of species, items, or genes that are shared between two groups, sets, or communities is a simple calculation when sampling is complete. However, when only partial samples are available, quantifying the overlap between two communities becomes an estimation problem. Furthermore, to calculate normalized measures of β-diversity, such as the Jaccard and Sorenson-Dice indices, one must also estimate the total sizes of the communities being compared. Previous efforts to address these problems have assumed knowledge of total community sizes and then used Bayesian methods to produce unbiased estimates with quantified uncertainty. Here, we address communities of unknown size and show that this produces systematically better estimates—both in terms of central estimates and quantification of uncertainty in those estimates. We further show how to use species, item, or gene count data to refine estimates of community size in a Bayesian joint model of community size and overlap.
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Affiliation(s)
- Erik K. Johnson
- Department of Applied Mathematics, University of Colorado Boulder, Boulder, Colorado, United States of America
- * E-mail: (EKJ); (DBL)
| | - Daniel B. Larremore
- Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
- * E-mail: (EKJ); (DBL)
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8
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Indari O, Sk MF, Jakhmola S, Jonniya NA, Jha HC, Kar P. Decoding the Host-Parasite Protein Interactions Involved in Cerebral Malaria Through Glares of Molecular Dynamics Simulations. J Phys Chem B 2022; 126:387-402. [PMID: 34989590 DOI: 10.1021/acs.jpcb.1c07850] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Malaria causes millions of deaths every year. The malaria parasite spends a substantial part of its life cycle inside human erythrocytes. Inside erythrocytes, it synthesizes and displays various proteins onto the erythrocyte surface, such as Plasmodium falciparum erythrocytic membrane protein-1 (PfEMP1). This protein contains cysteine-rich interdomain region (CIDR) domains which have many subtypes based on sequence diversity and can cross-talk with host molecules. The CIDRα1.4 subtype can attach host endothelial protein C receptor (EPCR). This interaction facilitates infected erythrocyte adherence to brain endothelium and subsequent development of cerebral malaria. Through molecular dynamics simulations in conjunction with the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, we explored the mechanism of interaction in the CIDRα1-EPCR complex. We examined the structural behavior of two CIDRα1 molecules (encoded by HB3-isolate var03-gene and IT4-isolate var07-gene) with EPCR unbound and bound (complex) forms. HB3var03CIDRα1 in apo and complexed with EPCR was comparatively more stable than IT4var07CIDRα1. Both of the complexes adopted two distinct conformational energy states. The hydrophobic residues played a crucial role in the binding of both complexes. For HB3var03CIDRα1-EPCR, the dominant energetic components were total polar interactions, while in IT4var07CIDRα1-EPCR, the primary interaction was van der Waals and nonpolar solvation energy. The study also revealed details such as correlated conformational motions and secondary structure evolution. Further, it elucidated various hotspot residues involved in protein-protein recognition. Overall, our study provides additional information on the structural behavior of CIDR molecules in unbound and receptor-bound states, which will help to design potent inhibitors.
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Affiliation(s)
- Omkar Indari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, MP 453552, India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, MP 453552, India
| | - Shweta Jakhmola
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, MP 453552, India
| | - Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, MP 453552, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, MP 453552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, MP 453552, India
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9
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Feng Q, Tiedje KE, Ruybal-Pesántez S, Tonkin-Hill G, Duffy MF, Day KP, Shim H, Chan YB. An accurate method for identifying recent recombinants from unaligned sequences. Bioinformatics 2022; 38:1823-1829. [PMID: 35025988 PMCID: PMC8963311 DOI: 10.1093/bioinformatics/btac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/18/2021] [Indexed: 11/12/2022] Open
Abstract
Abstract
Motivation
Recombination is a fundamental process in molecular evolution, and the identification of recombinant sequences is thus of major interest. However, current methods for detecting recombinants are primarily designed for aligned sequences. Thus they struggle with analyses of highly diverse genes, such as the var genes of the malaria parasite Plasmodium falciparum, which are known to diversify primarily through recombination.
Results
We introduce an algorithm to detect recent recombinant sequences from a dataset without a full multiple alignment. Our algorithm can handle thousands of gene-length sequences without the need for a reference panel. We demonstrate the accuracy of our algorithm through extensive numerical simulations; in particular, it maintains its effectiveness in the presence of insertions and deletions. We apply our algorithm to a dataset of 17,335 DBLα types in var genes from Ghana, observing that sequences belonging to the same ups group or domain subclass recombine amongst themselves more frequently, and that non-recombinant DBLα types are more conserved than recombinant ones.
Availability
Source code is freely available at https://github.com/qianfeng2/detREC_program.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qian Feng
- Melbourne Integrative Genomics/School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Kathryn E Tiedje
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3010, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity and Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3000, Australia
| | - Shazia Ruybal-Pesántez
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3010, Australia
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Burnet Institute, Melbourne, VIC, 3004, Australia
| | - Gerry Tonkin-Hill
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3010, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Michael F Duffy
- Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3004, Australia
| | - Karen P Day
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3010, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity and Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3000, Australia
| | - Heejung Shim
- Melbourne Integrative Genomics/School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Yao-Ban Chan
- Melbourne Integrative Genomics/School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
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10
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Andisi KC, Abdi AI. Analysis of var Gene Transcription Pattern Using DBLα Tags. Methods Mol Biol 2022; 2470:173-184. [PMID: 35881346 PMCID: PMC7613572 DOI: 10.1007/978-1-0716-2189-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
AbstractThe Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) antigens, which are encoded by a multigene family called var genes, are exported and inserted onto the surface of the infected erythrocytes. PfEMP1 plays a key role in the pathogenesis of severe malaria and are major targets of naturally acquired immunity. Studying the expression pattern of var genes in P. falciparum clinical isolates is crucial for understanding disease mechanism and immunity to malaria. However, var genes are highly variable, which makes it difficult to study their expression in clinical isolates obtained directly from malaria patients. In this chapter, we describe an approach for analysis of var gene expression that targets a region referred to as DBLα tag, which is relatively conserved in all var genes.
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11
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Abstract
The virulence of Plasmodium falciparum has been attributed in large part to the expression on the surface of infected red blood cells of the variant surface antigen Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1). Different forms of this protein are encoded by individual members of the multicopy gene family called var. Two attributes of the var gene family are key to the pathogenesis of malaria caused by P. falciparum; the hyperrecombinogenic nature of the var gene family that continuously generates antigenic diversity within parasite populations, and the ability of parasites to express only a single var gene at a time and to switch which gene is expressed over the course of an infection. The unique attributes of CRISPR-Cas9 have been applied to help decipher the molecular mechanisms underlying these unusual properties of the var gene family, both as a source of the DNA double strand breaks that initiate var gene recombination and as a way to recruit molecular probes to specific regions of the genome. In this chapter, we describe these somewhat unusual applications of the CRISPR-Cas9 system.
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Affiliation(s)
- Xu Zhang
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Kirk William Deitsch
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Ron Dzikowski
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Bourgard C, Lopes SCP, Lacerda MVG, Albrecht L, Costa FTM. A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax-infected patients. Sci Rep 2021; 11:5089. [PMID: 33658571 PMCID: PMC7930272 DOI: 10.1038/s41598-021-84607-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/06/2021] [Indexed: 12/03/2022] Open
Abstract
Plasmodium vivax is a world-threatening human malaria parasite, whose biology remains elusive. The unavailability of in vitro culture, and the difficulties in getting a high number of pure parasites makes RNA isolation in quantity and quality a challenge. Here, a methodological outline for RNA-seq from P. vivax isolates with low parasitemia is presented, combining parasite maturation and enrichment with efficient RNA extraction, yielding ~ 100 pg.µL−1 of RNA, suitable for SMART-Seq Ultra-Low Input RNA library and Illumina sequencing. Unbiased coding transcriptome of ~ 4 M reads was achieved for four patient isolates with ~ 51% of transcripts mapped to the P. vivax P01 reference genome, presenting heterogeneous profiles of expression among individual isolates. Amongst the most transcribed genes in all isolates, a parasite-staged mixed repertoire of conserved parasite metabolic, membrane and exported proteins was observed. Still, a quarter of transcribed genes remain functionally uncharacterized. In parallel, a P. falciparum Brazilian isolate was also analyzed and 57% of its transcripts mapped against IT genome. Comparison of transcriptomes of the two species revealed a common trophozoite-staged expression profile, with several homologous genes being expressed. Collectively, these results will positively impact vivax research improving knowledge of P. vivax biology.
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Affiliation(s)
- Catarina Bourgard
- Laboratory of Tropical Diseases, Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Stefanie C P Lopes
- Instituto Leônidas & Maria Deane, Fundação Oswaldo Cruz-Fiocruz, Manaus, AM, Brazil.,Fundação de Medicina Tropical Dr. Heitor Vieira Dourado-FMT-HVD, Gerência de Malária, Manaus, AM, Brazil
| | - Marcus V G Lacerda
- Instituto Leônidas & Maria Deane, Fundação Oswaldo Cruz-Fiocruz, Manaus, AM, Brazil.,Fundação de Medicina Tropical Dr. Heitor Vieira Dourado-FMT-HVD, Gerência de Malária, Manaus, AM, Brazil
| | - Letusa Albrecht
- Laboratory of Tropical Diseases, Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, Brazil. .,Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil.
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, Brazil.
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14
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Tabassum W, Bhattacharyya S, Varunan SM, Bhattacharyya MK. Febrile temperature causes transcriptional downregulation of Plasmodium falciparum Sirtuins through Hsp90-dependent epigenetic modification. Mol Microbiol 2021; 115:1025-1038. [PMID: 33538363 DOI: 10.1111/mmi.14692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/30/2021] [Accepted: 01/30/2021] [Indexed: 11/28/2022]
Abstract
Sirtuins (PfSIR2A and PfSIR2B) are implicated to play pivotal roles in the silencing of sub-telomeric genes and the maintenance of telomere length in P. falciparum 3D7 strain. Here, we identify the key factors that regulate the cellular abundance and activity of these two histone deacetylases. Our results demonstrate that PfSIR2A and PfSIR2B are transcriptionally downregulated at the mid-ring stage in response to febrile temperature. We found that the molecular chaperone PfHsp90 acts as a repressor of PfSIR2A & B transcription. By virtue of its presence in the PfSIR2A & B promoter proximal regions PfHsp90 helps recruiting H3K9me3, conferring heterochromatic state, and thereby leading to the downregulation of PfSIR2A & B transcription. Such transcriptional downregulation can be reversed by the addition of 17-(allylamino)-17-demethoxygeldanamycin or Radicicol, two potent inhibitors of PfHsp90. The reduced occupancy of PfSir2 at sub-telomeric var promoters leads to the de-repression of var genes. Thus, here we uncover how exposure to febrile temperature, a hallmark of malaria, enables the parasites to manipulate the expression of the two prominent epigenetic modifiers PfSir2A and PfSir2B.
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Affiliation(s)
- Wahida Tabassum
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sunanda Bhattacharyya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Shalu M Varunan
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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15
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Zhang X, Deitsch KW, Kirkman LA. The contribution of extrachromosomal DNA to genome plasticity in malaria parasites. Mol Microbiol 2020; 115:503-507. [PMID: 33103309 DOI: 10.1111/mmi.14632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 01/20/2023]
Abstract
Malaria caused by the protozoan parasite Plasmodium falciparum continues to impose significant morbidity and mortality, despite substantial investment into drug and vaccine development and deployment. Underlying the resilience of this parasite is its remarkable ability to undergo genome modifications, thus, providing parasite populations with extensive genetic variability that accelerates selection of drug resistance and limits the efficacy of most vaccines. This genome plasticity is rooted in the mechanisms of DNA repair that parasites employ to maintain genome integrity, a process skewed toward homologous recombination through the evolutionary loss of classical nonhomologous end joining. Repair of DNA double-strand breaks have been shown to enable "shuffling" of antigen-encoding gene sequences to vastly increase antigen diversity and to enable copy number expansion of genes that contribute to drug resistance. The latter phenomenon has been proposed to be a major contributor to the rise of resistance to several classes of antimalarial drugs. In this issue of Molecular Microbiology, McDaniels and colleagues add yet another mechanism that malaria parasites use to reduce drug susceptibility by demonstrating that P. falciparum can maintain expanded arrays of drug resistance cassettes as stably replicating, circular, extrachromosomal DNAs, thus, expanding genome plasticity beyond the parasite's 14 nuclear chromosomes.
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Affiliation(s)
- Xu Zhang
- 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
| | - Laura A Kirkman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.,Department of Internal Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, USA
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16
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Aguilar M, Prieto P. Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes. Plant Genome 2020; 13:e20065. [PMID: 33029942 DOI: 10.1002/tpg2.20065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/20/2020] [Accepted: 09/08/2020] [Indexed: 05/23/2023]
Abstract
Bread wheat, Triticum aestivum L., is one of the most important crops in the world. Understanding its genome organization (allohexaploid; AABBDD; 2n = 6x = 42) is essential for geneticists and plant breeders. Particularly, the knowledge of how homologous chromosomes (equivalent chromosomes from the same genome) specifically recognize each other to pair at the beginning of meiosis, the cellular process to generate gametes in sexually reproducing organisms, is fundamental for plant breeding and has a big influence on the fertility of wheat plants. Initial homologous chromosome interactions contribute to specific recognition and pairing between homologues at the onset of meiosis. Understanding the molecular basis of these critical processes can help to develop genetic tools in a breeding context to promote interspecific chromosome associations in hybrids or interspecific genetic crosses to facilitate the transfer of desirable agronomic traits from related species into a crop like wheat. The terminal regions of chromosomes, which include telomeres and subtelomeres, participate in chromosome recognition and pairing. We present a detailed molecular analysis of subtelomeres of wheat chromosome arms 1AS, 4AS, 7AS, 7BS and 7DS. Results showed a high polymorphism in the subtelomeric region among homoeologues (equivalent chromosomes from related genomes) for all the features analyzed, including genes, transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots and targeted sequence motifs for relevant DNA-binding proteins. These polymorphisms might be the molecular basis for the specificity of homologous recognition and pairing in initial chromosome interactions at the beginning of meiosis in wheat.
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Affiliation(s)
- Miguel Aguilar
- Área de Fisiología Vegetal. Universidad de Córdoba. Campus de Rabanales, edif. C4, 3a planta, Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4084, Córdoba, 14080, Spain
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17
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Gazanion E, Lacroix L, Alberti P, Gurung P, Wein S, Cheng M, Mergny JL, Gomes AR, Lopez-Rubio JJ. Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites. PLoS Genet 2020; 16:e1008917. [PMID: 32628663 PMCID: PMC7365481 DOI: 10.1371/journal.pgen.1008917] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/16/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
Mechanisms of transcriptional control in malaria parasites are still not fully understood. The positioning patterns of G-quadruplex (G4) DNA motifs in the parasite's AT-rich genome, especially within the var gene family which encodes virulence factors, and in the vicinity of recombination hotspots, points towards a possible regulatory role of G4 in gene expression and genome stability. Here, we carried out the most comprehensive genome-wide survey, to date, of G4s in the Plasmodium falciparum genome using G4Hunter, which identifies G4 forming sequences (G4FS) considering their G-richness and G-skewness. We show an enrichment of G4FS in nucleosome-depleted regions and in the first exon of var genes, a pattern that is conserved within the closely related Laverania Plasmodium parasites. Under G4-stabilizing conditions, i.e., following treatment with pyridostatin (a high affinity G4 ligand), we show that a bona fide G4 found in the non-coding strand of var promoters modulates reporter gene expression. Furthermore, transcriptional profiling of pyridostatin-treated parasites, shows large scale perturbations, with deregulation affecting for instance the ApiAP2 family of transcription factors and genes involved in ribosome biogenesis. Overall, our study highlights G4s as important DNA secondary structures with a role in Plasmodium gene expression regulation, sub-telomeric recombination and var gene biology.
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Affiliation(s)
- Elodie Gazanion
- MIVEGEC UMR IRD 224, CNRS 5290, Montpellier University, Montpellier, France
| | - Laurent Lacroix
- IBENS, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Patrizia Alberti
- "Structure and Instability of Genomes" laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, Paris, France
| | - Pratima Gurung
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Sharon Wein
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Mingpan Cheng
- ARNA Laboratory, IECB, CNRS UMR5320, INSERM U1212, Bordeaux University, Pessac, France
| | - Jean-Louis Mergny
- ARNA Laboratory, IECB, CNRS UMR5320, INSERM U1212, Bordeaux University, Pessac, France
- Institute of Biophysics of the Czech Academy of Sciences, Czech Republic
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, France
| | - Ana Rita Gomes
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Jose-Juan Lopez-Rubio
- MIVEGEC UMR IRD 224, CNRS 5290, Montpellier University, Montpellier, France
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
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18
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Siao MC, Borner J, Perkins SL, Deitsch KW, Kirkman LA. Evolution of Host Specificity by Malaria Parasites through Altered Mechanisms Controlling Genome Maintenance. mBio 2020; 11:e03272-19. [PMID: 32184256 DOI: 10.1128/mBio.03272-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Malaria remains one of the most prevalent and deadly infectious diseases of the developing world, causing approximately 228 million clinical cases and nearly half a million deaths annually. The disease is caused by protozoan parasites of the genus Plasmodium, and of the five species capable of infecting humans, infections with P. falciparum are the most severe. In addition to the parasites that infect people, there are hundreds of additional species that infect birds, reptiles, and other mammals, each exquisitely evolved to meet the specific challenges inherent to survival within their respective hosts. By comparing the unique strategies that each species has evolved, key insights into host-parasite interactions can be gained, including discoveries regarding the pathogenesis of human disease. Here, we describe the surprising observation that closely related parasites with different hosts have evolved remarkably different methods for repairing their genomes. This observation has important implications for the ability of parasites to maintain chronic infections and for the development of host immunity. The protozoan parasites that cause malaria infect a wide variety of vertebrate hosts, including birds, reptiles, and mammals, and the evolutionary pressures inherent to the host-parasite relationship have profoundly shaped the genomes of both host and parasite. Here, we report that these selective pressures have resulted in unexpected alterations to one of the most basic aspects of eukaryotic biology, the maintenance of genome integrity through DNA repair. Malaria parasites that infect humans continuously generate genetic diversity within their antigen-encoding gene families through frequent ectopic recombination between gene family members, a process that is a crucial feature of the persistence of malaria globally. The continuous generation of antigen diversity ensures that different parasite isolates are antigenically distinct, thus preventing extensive cross-reactive immunity and enabling parasites to maintain stable transmission within human populations. However, the molecular basis of the recombination between gene family members is not well understood. Through computational analyses of the antigen-encoding, multicopy gene families of different Plasmodium species, we report the unexpected observation that malaria parasites that infect rodents do not display the same degree of antigen diversity as observed in Plasmodium falciparum and appear to undergo significantly less ectopic recombination. Using comparative genomics, we also identify key molecular components of the diversification process, thus shedding new light on how malaria parasites balance the maintenance of genome integrity with the requirement for continuous genetic diversification.
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19
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Tessema SK, Nakajima R, Jasinskas A, Monk SL, Lekieffre L, Lin E, Kiniboro B, Proietti C, Siba P, Felgner PL, Doolan DL, Mueller I, Barry AE. Protective Immunity against Severe Malaria in Children Is Associated with a Limited Repertoire of Antibodies to Conserved PfEMP1 Variants. Cell Host Microbe 2020; 26:579-590.e5. [PMID: 31726028 DOI: 10.1016/j.chom.2019.10.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/08/2019] [Accepted: 10/18/2019] [Indexed: 01/31/2023]
Abstract
Extreme diversity of the major Plasmodium falciparum antigen, PfEMP1, poses a barrier to identifying targets of immunity to malaria. Here, we used protein microarrays containing hundreds of variants of the DBLα domain of PfEMP1 to cover the diversity of Papua New Guinean (PNG) parasites. Probing the plasma of a longitudinal cohort of malaria-exposed PNG children showed that group 2 DBLα antibodies were moderately associated with a lower risk of uncomplicated malaria, whereas individual variants were only weakly associated with clinical immunity. In contrast, antibodies to 85 individual group 1 and 2 DBLα variants were associated with a 70%-100% reduction in severe malaria. Of these, 17 variants were strong predictors of severe malaria. Analysis of full-length PfEMP1 sequences from PNG samples shows that these 17 variants are linked to pathogenic CIDR domains. This suggests that whereas immunity to uncomplicated malaria requires a broad repertoire of antibodies, immunity to severe malaria targets a subset of conserved variants. These findings provide insights into antimalarial immunity and potential antibody biomarkers for disease risk.
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Affiliation(s)
- Sofonias K Tessema
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne 3000, VIC, Australia
| | - Rie Nakajima
- Physiology & Biophysics Department, Vaccine R&D Center, University of California, Irvine, Irvine 92697, CA, USA
| | - Algis Jasinskas
- Physiology & Biophysics Department, Vaccine R&D Center, University of California, Irvine, Irvine 92697, CA, USA
| | - Stephanie L Monk
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne 3000, VIC, Australia
| | - Lea Lekieffre
- Infectious Diseases Programme, QIMR Berghofer Medical Research Institute, Brisbane 4006, QLD, Australia
| | - Enmoore Lin
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Goroka 441, EHG, Papua New Guinea
| | - Benson Kiniboro
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Goroka 441, EHG, Papua New Guinea
| | - Carla Proietti
- Infectious Diseases Programme, QIMR Berghofer Medical Research Institute, Brisbane 4006, QLD, Australia; Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, QLD, Australia
| | - Peter Siba
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Goroka 441, EHG, Papua New Guinea
| | - Philip L Felgner
- Physiology & Biophysics Department, Vaccine R&D Center, University of California, Irvine, Irvine 92697, CA, USA
| | - Denise L Doolan
- Infectious Diseases Programme, QIMR Berghofer Medical Research Institute, Brisbane 4006, QLD, Australia; Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, QLD, Australia
| | - Ivo Mueller
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne 3000, VIC, Australia; Department of Parasites and Insect Vectors, Institut Pasteur, Paris 75015, France
| | - Alyssa E Barry
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne 3000, VIC, Australia.
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20
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Pilosof S, He Q, Tiedje KE, Ruybal-Pesántez S, Day KP, Pascual M. Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum. PLoS Biol 2019; 17:e3000336. [PMID: 31233490 PMCID: PMC6611651 DOI: 10.1371/journal.pbio.3000336] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 07/05/2019] [Accepted: 06/05/2019] [Indexed: 01/14/2023] Open
Abstract
In their competition for hosts, parasites with antigens that are novel to the host immune system will be at a competitive advantage. The resulting frequency-dependent selection can structure parasite populations into strains of limited genetic overlap. For the causative agent of malaria, Plasmodium falciparum, the high recombination rates and associated vast diversity of its highly antigenic and multicopy var genes preclude such clear clustering in endemic regions. This undermines the definition of strains as specific, temporally persisting gene variant combinations. We use temporal multilayer networks to analyze the genetic similarity of parasites in both simulated data and in an extensively and longitudinally sampled population in Ghana. When viewed over time, populations are structured into modules (i.e., groups) of parasite genomes whose var gene combinations are more similar within than between the modules and whose persistence is much longer than that of the individual genomes that compose them. Comparison to neutral models that retain parasite population dynamics but lack competition reveals that the selection imposed by host immunity promotes the persistence of these modules. The modular structure is, in turn, associated with a slower acquisition of immunity by individual hosts. Modules thus represent dynamically generated niches in host immune space, which can be interpreted as strains. Negative frequency-dependent selection therefore shapes the organization of the var diversity into parasite genomes, leaving a persistence signature over ecological time scales. Multilayer networks extend the scope of phylodynamics analyses by allowing quantification of temporal genetic structure in organisms that generate variation via recombination or other non-bifurcating processes. A strain structure similar to the one described here should apply to other pathogens with large antigenic spaces that evolve via recombination. For malaria, the temporal modular structure should enable the formulation of tractable epidemiological models that account for parasite antigenic diversity and its influence on intervention outcomes. A combination of computational modeling and empirical data reveals persistent strain structure despite vast antigenic diversity in the human malaria parasite Plasmodium falciparum, with potential consequences for the acquisition of immunity.
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Affiliation(s)
- Shai Pilosof
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Qixin He
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Kathryn E. Tiedje
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | | | - Karen P. Day
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | - Mercedes Pascual
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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21
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Zhang X, Alexander N, Leonardi I, Mason C, Kirkman LA, Deitsch KW. Rapid antigen diversification through mitotic recombination in the human malaria parasite Plasmodium falciparum. PLoS Biol 2019; 17:e3000271. [PMID: 31083650 PMCID: PMC6532940 DOI: 10.1371/journal.pbio.3000271] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/23/2019] [Accepted: 04/30/2019] [Indexed: 11/18/2022] Open
Abstract
Malaria parasites possess the remarkable ability to maintain chronic infections that fail to elicit a protective immune response, characteristics that have stymied vaccine development and cause people living in endemic regions to remain at risk of malaria despite previous exposure to the disease. These traits stem from the tremendous antigenic diversity displayed by parasites circulating in the field. For Plasmodium falciparum, the most virulent of the human malaria parasites, this diversity is exemplified by the variant gene family called var, which encodes the major surface antigen displayed on infected red blood cells (RBCs). This gene family exhibits virtually limitless diversity when var gene repertoires from different parasite isolates are compared. Previous studies indicated that this remarkable genome plasticity results from extensive ectopic recombination between var genes during mitotic replication; however, the molecular mechanisms that direct this process to antigen-encoding loci while the rest of the genome remains relatively stable were not determined. Using targeted DNA double-strand breaks (DSBs) and long-read whole-genome sequencing, we show that a single break within an antigen-encoding region of the genome can result in a cascade of recombination events leading to the generation of multiple chimeric var genes, a process that can greatly accelerate the generation of diversity within this family. We also found that recombinations did not occur randomly, but rather high-probability, specific recombination products were observed repeatedly. These results provide a molecular basis for previously described structured rearrangements that drive diversification of this highly polymorphic gene family.
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Affiliation(s)
- Xu Zhang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Irina Leonardi
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, New York, New York, United States of America
| | - Christopher Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
- Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, New York, United States of America
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medical College, New York, New York, United States of America
| | - Laura A. Kirkman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- Department of Internal Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, New York, United States of America
| | - Kirk W. Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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22
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Quintana MDP, Ecklu-Mensah G, Tcherniuk SO, Ditlev SB, Oleinikov AV, Hviid L, Lopez-Perez M. Comprehensive analysis of Fc-mediated IgM binding to the Plasmodium falciparum erythrocyte membrane protein 1 family in three parasite clones. Sci Rep 2019; 9:6050. [PMID: 30988351 PMCID: PMC6465264 DOI: 10.1038/s41598-019-42585-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/03/2019] [Indexed: 12/14/2022] Open
Abstract
PfEMP1 is a family of adhesive proteins expressed on the surface of Plasmodium falciparum-infected erythrocytes (IEs), where they mediate adhesion of IEs to a range of host receptors. Efficient PfEMP1-dependent IE sequestration often depends on soluble serum proteins, including IgM. Here, we report a comprehensive investigation of which of the about 60 var gene-encoded PfEMP1 variants per parasite genome can bind IgM via the Fc part of the antibody molecule, and which of the constituent domains of those PfEMP1 are involved. We erased the epigenetic memory of var gene expression in three distinct P. falciparum clones, 3D7, HB3, and IT4/FCR3 by promoter titration, and then isolated individual IEs binding IgM from malaria-unexposed individuals by fluorescence-activated single-cell sorting. The var gene transcription profiles of sub-clones measured by real-time qPCR were used to identify potential IgM-binding PfEMP1 variants. Recombinant DBL and CIDR domains corresponding to those variants were tested by ELISA and protein arrays to confirm their IgM-binding capacity. Selected DBL domains were used to raise specific rat anti-sera to select IEs with uniform expression of candidate PfEMP1 proteins. Our data document that IgM-binding PfEMP1 proteins are common in each of the three clones studied, and that the binding epitopes are mainly found in DBLε and DBLζ domains near the C-terminus.
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Affiliation(s)
- Maria Del Pilar Quintana
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gertrude Ecklu-Mensah
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Sergey O Tcherniuk
- Charles E Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Sisse Bolm Ditlev
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrew V Oleinikov
- Charles E Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Lars Hviid
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark.
| | - Mary Lopez-Perez
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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23
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Waltmann A, Patel JC, Thwai KL, Hathaway NJ, Parobek CM, Massougbodji A, Fievet N, Bailey JA, Deloron P, Juliano JJ, Ndam NT, Meshnick SR. Matched Placental and Circulating Plasmodium falciparum Parasites are Genetically Homologous at the var2csa ID1-DBL2X Locus by Deep Sequencing. Am J Trop Med Hyg 2018; 98:77-82. [PMID: 29342401 DOI: 10.4269/ajtmh.17-0529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In pregnancy-associated malaria, infected erythrocytes accumulate in the placenta. It is unclear if in polyclonal infections this results in distinct peripheral and placental parasite populations. We used long amplicon deep sequencing of Plasmodium falciparum var2csa ID1-DBL2X from 15 matched peripheral and placental samples collected at delivery from a high transmission area to determine genetic homology. Despite substantial sequence variation and detecting 23 haplotypes, the matched pairs mostly contained the same genetic variants, with 11 pairs sharing 100% of their variants, whereas others showed some heterogeneity. Thus, at delivery, peripheral and placental parasites appear to intermix and placental genotypes can be inferred through peripheral sampling.
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Affiliation(s)
- Andreea Waltmann
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Jaymin C Patel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Kyaw L Thwai
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Nicholas J Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester, Massachusetts
| | - Christian M Parobek
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le paludisme associé à la Grossesse et à l'Enfance, Université d'Abomey-Calavi, Cotonou, Benin
| | - Nadine Fievet
- UMR216 - MERIT, Institut de Recherche pour le Développement, COMUE Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - Jeffery A Bailey
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts, Worcester, Massachusetts.,Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester, Massachusetts
| | - Philippe Deloron
- UMR216 - MERIT, Institut de Recherche pour le Développement, COMUE Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - Jonathan J Juliano
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina.,Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Nicaise Tuikue Ndam
- UMR216 - MERIT, Institut de Recherche pour le Développement, COMUE Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina.,Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
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24
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Ecklu-Mensah G, Olsen RW, Bengtsson A, Ofori MF, Hviid L, Jensen ATR, Adams Y. Blood outgrowth endothelial cells (BOECs) as a novel tool for studying adhesion of Plasmodium falciparum-infected erythrocytes. PLoS One 2018; 13:e0204177. [PMID: 30300360 PMCID: PMC6177148 DOI: 10.1371/journal.pone.0204177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/03/2018] [Indexed: 11/19/2022] Open
Abstract
The lack of suitable animal models for the study of cytoadhesion of P. falciparum-infected erythrocytes (IEs) has necessitated in vitro studies employing a range of cell lines of either human tumour origin (e.g., BeWo and C32 cells) or non-human origin (e.g., CHO cells). Of the human cells available, many were isolated from adults, or derived from a pool of donors (e.g., HBEC-5i). Here we demonstrate, for the first time, the successful isolation of blood outgrowth endothelial cells (BOECs) from frozen stabilates of peripheral blood mononuclear cells obtained from small-volume peripheral blood samples from paediatric malaria patients. BOECs are a sub-population of human endothelial cells, found within the peripheral blood. We demonstrate that these cells express receptors such as Intercellular Adhesion Molecule 1 (ICAM-1/CD54), Endothelial Protein C Receptor (EPCR/CD201), platelet/endothelial cell adhesion molecule 1 (PECAM-1/CD31), Thrombomodulin (CD141), and support adhesion of P. falciparum IEs.
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Affiliation(s)
- Gertrude Ecklu-Mensah
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Centre for Medical Parasitology at Department of Immunology and Microbiology (ISIM), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca W. Olsen
- Centre for Medical Parasitology at Department of Immunology and Microbiology (ISIM), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anja Bengtsson
- Centre for Medical Parasitology at Department of Immunology and Microbiology (ISIM), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael F. Ofori
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Lars Hviid
- Centre for Medical Parasitology at Department of Immunology and Microbiology (ISIM), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Anja T. R. Jensen
- Centre for Medical Parasitology at Department of Immunology and Microbiology (ISIM), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yvonne Adams
- Centre for Medical Parasitology at Department of Immunology and Microbiology (ISIM), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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25
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Abstract
Antigenic diversity is commonly used by pathogens to enhance their
transmission success. Within-host clonal antigenic variation helps to maintain
long infectious periods, whereas high levels of allelic diversity at the
population level significantly expand the pool of susceptible individuals.
Diversity, however, is not necessarily a static property of a pathogen
population but in many cases is generated by the very act of infection and
transmission, and it is therefore expected to respond dynamically to changes in
transmission and immune selection. We hypothesized that this coupling creates a
positive feedback whereby infection and disease transmission promote the
generation of diversity, which itself facilitates immune evasion and further
infections. To investigate this link in more detail, we considered the human
malaria parasite Plasmodium falciparum, one of the most
important antigenically diverse pathogens. We developed an individual-based
model in which antigenic diversity emerges as a dynamic property from the
underlying transmission processes. Our results show that the balance between
stochastic extinction and the generation of new antigenic variants is
intrinsically linked to within-host and between-host immune selection. This in
turn determines the level of diversity that can be maintained in a given
population. Furthermore, the transmission-diversity feedback can lead to
temporal lags in the response to natural or intervention-induced perturbations
in transmission rates. Our results therefore have important implications for
monitoring and assessing the effectiveness of disease control efforts.
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26
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Claessens A, Harris LM, Stanojcic S, Chappell L, Stanton A, Kuk N, Veneziano-Broccia P, Sterkers Y, Rayner JC, Merrick CJ. RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics. PLoS Genet 2018; 14:e1007490. [PMID: 29965959 PMCID: PMC6044543 DOI: 10.1371/journal.pgen.1007490] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 07/13/2018] [Accepted: 06/13/2018] [Indexed: 11/18/2022] Open
Abstract
The malaria parasite Plasmodium falciparum has evolved an unusual genome structure. The majority of the genome is relatively stable, with mutation rates similar to most eukaryotic species. However, some regions are very unstable with high recombination rates, driving the generation of new immune evasion-associated var genes. The molecular factors controlling the inconsistent stability of this genome are not known. Here we studied the roles of the two putative RecQ helicases in P. falciparum, PfBLM and PfWRN. When PfWRN was knocked down, recombination rates increased four-fold, generating chromosomal abnormalities, a high rate of chimeric var genes and many microindels, particularly in known ‘fragile sites’. This is the first identification of a gene involved in suppressing recombination and maintaining genome stability in Plasmodium. By contrast, no change in mutation rate appeared when the second RecQ helicase, PfBLM, was mutated. At the transcriptional level, however, both helicases evidently modulate the transcription of large cohorts of genes, with several hundred genes—including a large proportion of vars—showing deregulated expression in each RecQ mutant. Aberrant processing of stalled replication forks is a possible mechanism underlying elevated mutation rates and this was assessed by measuring DNA replication dynamics in the RecQ mutant lines. Replication forks moved slowly and stalled at elevated rates in both mutants, confirming that RecQ helicases are required for efficient DNA replication. Overall, this work identifies the Plasmodium RecQ helicases as major players in DNA replication, antigenic diversification and genome stability in the most lethal human malaria parasite, with important implications for genome evolution in this pathogen. Human malaria is caused by Plasmodium parasites, with most of the mortality (almost half a million deaths each year) being caused by one species, Plasmodium falciparum. This parasite has an unusual genome: it is exceptionally biased towards A and T nucleotides rather than G and C, and it contains specific areas rich in hypervariable virulence-associated genes which evolve very rapidly to produce new variants. This evolution is probably vital for the parasite to evade the human immune system and maintain chronic infections, but how it is controlled at a molecular level remains unknown. We have identified a helicase in the parasite with a huge influence on genome stability and the rate of genome evolution. It appears to function by unwinding various unusual DNA structures, and if this fails then the genome becomes unstable. In addition, the transcription of many genes whose DNA tends to form secondary structures is affected, and DNA replication is impeded. If this helicase was expressed variably in different parasite strains infecting humans, it could influence the parasites’ ability to grow and replicate efficiently, and also, crucially, its ability to evolve and thus evade the human immune system.
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Affiliation(s)
- Antoine Claessens
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Medical Research Council Unit The Gambia, Fajara, Banjul, The Gambia
| | - Lynne M. Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Slavica Stanojcic
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France
| | - Lia Chappell
- Malaria Programme, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Adam Stanton
- School of Computing and Mathematics, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Nada Kuk
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France
| | - Pamela Veneziano-Broccia
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Yvon Sterkers
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France
- CNRS 5290 - IRD 224 - University of Montpellier (UMR “MiVEGEC”), Montpellier, France
- University Hospital Centre (CHU), Department of Parasitology-Mycology, Montpellier, France
| | - Julian C. Rayner
- Malaria Programme, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Catherine J. Merrick
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
- * E-mail:
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27
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He Q, Pilosof S, Tiedje KE, Ruybal-Pesántez S, Artzy-Randrup Y, Baskerville EB, Day KP, Pascual M. Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum. Nat Commun 2018; 9:1817. [PMID: 29739937 DOI: 10.1038/s41467-018-04219-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 04/12/2018] [Indexed: 11/09/2022] Open
Abstract
Pathogens compete for hosts through patterns of cross-protection conferred by immune responses to antigens. In Plasmodium falciparum malaria, the var multigene family encoding for the major blood-stage antigen PfEMP1 has evolved enormous genetic diversity through ectopic recombination and mutation. With 50-60 var genes per genome, it is unclear whether immune selection can act as a dominant force in structuring var repertoires of local populations. The combinatorial complexity of the var system remains beyond the reach of existing strain theory and previous evidence for non-random structure cannot demonstrate immune selection without comparison with neutral models. We develop two neutral models that encompass malaria epidemiology but exclude competitive interactions between parasites. These models, combined with networks of genetic similarity, reveal non-neutral strain structure in both simulated systems and an extensively sampled population in Ghana. The unique population structure we identify underlies the large transmission reservoir characteristic of highly endemic regions in Africa.
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28
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Abstract
The time it takes for malaria parasites to develop within a mosquito, and become transmissible, is known as the extrinsic incubation period, or EIP. EIP is a key parameter influencing transmission intensity as it combines with mosquito mortality rate and competence to determine the number of mosquitoes that ultimately become infectious. In spite of its epidemiological significance, data on EIP are scant. Current approaches to estimate EIP are largely based on temperature-dependent models developed from data collected on parasite development within a single mosquito species in the 1930s. These models assume that the only factor affecting EIP is mean environmental temperature. Here, we review evidence to suggest that in addition to mean temperature, EIP is likely influenced by genetic diversity of the vector, diversity of the parasite, and variation in a range of biotic and abiotic factors that affect mosquito condition. We further demonstrate that the classic approach of measuring EIP as the time at which mosquitoes first become infectious likely misrepresents EIP for a mosquito population. We argue for a better understanding of EIP to improve models of transmission, refine predictions of the possible impacts of climate change, and determine the potential evolutionary responses of malaria parasites to current and future mosquito control tools.
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Affiliation(s)
- Johanna R Ohm
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA.
| | - Francesco Baldini
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
| | - Priscille Barreaux
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Thierry Lefevre
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Penelope A Lynch
- College of Life and Environmental Sciences, Penryn Campus, University of Exeter, Cornwall, UK
| | - Eunho Suh
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Shelley A Whitehead
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Matthew B Thomas
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
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29
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Tonkin-Hill GQ, Trianty L, Noviyanti R, Nguyen HHT, Sebayang BF, Lampah DA, Marfurt J, Cobbold SA, Rambhatla JS, McConville MJ, Rogerson SJ, Brown GV, Day KP, Price RN, Anstey NM, Papenfuss AT, Duffy MF. The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen-encoding var genes. PLoS Biol 2018; 16:e2004328. [PMID: 29529020 DOI: 10.1371/journal.pbio.2004328] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/22/2018] [Accepted: 02/16/2018] [Indexed: 01/13/2023] Open
Abstract
Within the human host, the malaria parasite Plasmodium falciparum is exposed to multiple selection pressures. The host environment changes dramatically in severe malaria, but the extent to which the parasite responds to-or is selected by-this environment remains unclear. From previous studies, the parasites that cause severe malaria appear to increase expression of a restricted but poorly defined subset of the PfEMP1 variant, surface antigens. PfEMP1s are major targets of protective immunity. Here, we used RNA sequencing (RNAseq) to analyse gene expression in 44 parasite isolates that caused severe and uncomplicated malaria in Papuan patients. The transcriptomes of 19 parasite isolates associated with severe malaria indicated that these parasites had decreased glycolysis without activation of compensatory pathways; altered chromatin structure and probably transcriptional regulation through decreased histone methylation; reduced surface expression of PfEMP1; and down-regulated expression of multiple chaperone proteins. Our RNAseq also identified novel associations between disease severity and PfEMP1 transcripts, domains, and smaller sequence segments and also confirmed all previously reported associations between expressed PfEMP1 sequences and severe disease. These findings will inform efforts to identify vaccine targets for severe malaria and also indicate how parasites adapt to-or are selected by-the host environment in severe malaria.
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30
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Rorick MM, Artzy-Randrup Y, Ruybal-Pesántez S, Tiedje KE, Rask TS, Oduro A, Ghansah A, Koram K, Day KP, Pascual M. Signatures of competition and strain structure within the major blood-stage antigen of Plasmodium falciparum in a local community in Ghana. Ecol Evol 2018; 8:3574-3588. [PMID: 29686839 PMCID: PMC5901166 DOI: 10.1002/ece3.3803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/31/2017] [Accepted: 12/06/2017] [Indexed: 11/12/2022] Open
Abstract
The concept of niche partitioning has received considerable theoretical attention at the interface of ecology and evolution of infectious diseases. Strain theory postulates that pathogen populations can be structured into distinct nonoverlapping strains by frequency-dependent selection in response to intraspecific competition for host immune space. The malaria parasite Plasmodium falciparum presents an opportunity to investigate this phenomenon in nature, under conditions of high recombination rate and extensive antigenic diversity. The parasite's major blood-stage antigen, Pf EMP1, is encoded by the hyperdiverse var genes. With a dataset that includes thousands of var DBLα sequence types sampled from asymptomatic cases within an area of high endemicity in Ghana, we address how var diversity is distributed within isolates and compare this to the distribution of microsatellite allelic diversity within isolates to test whether antigenic and neutral regions of the genome are structured differently. With respect to var DBLα sequence types, we find that on average isolates exhibit significantly lower overlap than expected randomly, but that there also exists frequent pairs of isolates that are highly related. Furthermore, the linkage network of var DBLα sequence types reveals a pattern of nonrandom modularity unique to these antigenic genes, and we find that modules of highly linked DBLα types are not explainable by neutral forces related to var recombination constraints, microsatellite diversity, sampling location, host age, or multiplicity of infection. These findings of reduced overlap and modularity among the var antigenic genes are consistent with a role for immune selection as proposed by strain theory. Identifying the evolutionary and ecological dynamics that are responsible for the nonrandom structure in P. falciparum antigenic diversity is important for designing effective intervention in endemic areas.
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Affiliation(s)
- Mary M Rorick
- Department of Ecology and Evolution University of Chicago Chicago IL USA.,Department of Biology University of Utah Salt Lake City UT USA
| | - Yael Artzy-Randrup
- Theoretical Ecology Group Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Shazia Ruybal-Pesántez
- School of Biosciences Bio21 Institute The University of Melbourne Melbourne Vic. Australia.,Department of Microbiology New York University New York NY USA
| | - Kathryn E Tiedje
- School of Biosciences Bio21 Institute The University of Melbourne Melbourne Vic. Australia.,Department of Microbiology New York University New York NY USA
| | - Thomas S Rask
- School of Biosciences Bio21 Institute The University of Melbourne Melbourne Vic. Australia.,Department of Microbiology New York University New York NY USA
| | | | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research University of Ghana Legon Ghana
| | - Kwadwo Koram
- Noguchi Memorial Institute for Medical Research University of Ghana Legon Ghana
| | - Karen P Day
- School of Biosciences Bio21 Institute The University of Melbourne Melbourne Vic. Australia.,Department of Microbiology New York University New York NY USA
| | - Mercedes Pascual
- Department of Ecology and Evolution University of Chicago Chicago IL USA.,The Santa Fe Institute Santa Fe NM USA
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31
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Carrington E, Otto TD, Szestak T, Lennartz F, Higgins MK, Newbold CI, Craig AG. In silico guided reconstruction and analysis of ICAM-1-binding var genes from Plasmodium falciparum. Sci Rep 2018; 8:3282. [PMID: 29459671 PMCID: PMC5818487 DOI: 10.1038/s41598-018-21591-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/07/2018] [Indexed: 11/23/2022] Open
Abstract
The Plasmodium falciparum variant surface antigen PfEMP1 expressed on the surface of infected erythrocytes is thought to play a major role in the pathology of severe malaria. As the sequence pool of the var genes encoding PfEMP1 expands there are opportunities, despite the high degree of sequence diversity demonstrated by this gene family, to reconstruct full-length var genes from small sequence tags generated from patient isolates. To test whether this is possible we have used a set of recently laboratory adapted ICAM-1-binding parasite isolates to generate sequence tags and, from these, to identify the full-length PfEMP1 being expressed by them. In a subset of the strains available we were able to produce validated, full-length var gene sequences and use these to conduct biophysical analyses of the ICAM-1 binding regions.
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Affiliation(s)
- Eilidh Carrington
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Malaria Gene Regulation Lab, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Tadge Szestak
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Frank Lennartz
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Matt K Higgins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Chris I Newbold
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
| | - Alister G Craig
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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32
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Githinji G, Bull PC. A re-assessment of gene-tag classification approaches for describing var gene expression patterns during human Plasmodium falciparum malaria parasite infections. Wellcome Open Res 2017; 2:86. [PMID: 29062916 PMCID: PMC5635463 DOI: 10.12688/wellcomeopenres.12053.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2017] [Indexed: 11/20/2022] Open
Abstract
PfEMP1 are variant parasite antigens that are inserted on the surface of Plasmodium falciparum infected erythrocytes (IE). Through interactions with various host molecules, PfEMP1 mediate IE sequestration in tissues and play a key role in the pathology of severe malaria. PfEMP1 is encoded by a diverse multi-gene family called var. Previous studies have shown that that expression of specific subsets of var genes are associated with low levels of host immunity and severe malaria. However, in most clinical studies to date, full-length var gene sequences were unavailable and various approaches have been used to make comparisons between var gene expression profiles in different parasite isolates using limited information. Several studies have relied on the classification of a 300 - 500 base-pair "DBLα tag" region in the DBLα domain located at the 5' end of most var genes. We assessed the relationship between various DBLα tag classification methods, and sequence features that are only fully assessable through full-length var gene sequences. We compared these different sequence features in full-length var gene from six fully sequenced laboratory isolates. These comparisons show that despite a long history of recombination, DBLα sequence tag classification can provide functional information on important features of full-length var genes. Notably, a specific subset of DBLα tags previously defined as "group A-like" is associated with CIDRα1 domains proposed to bind to endothelial protein C receptor. This analysis helps to bring together different sources of data that have been used to assess var gene expression in clinical parasite isolates.
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Affiliation(s)
- George Githinji
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Peter C Bull
- Department of Pathology, University of Cambridge, Cambridge, UK
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33
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Ruybal-Pesántez S, Tiedje KE, Tonkin-Hill G, Rask TS, Kamya MR, Greenhouse B, Dorsey G, Duffy MF, Day KP. Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda. Sci Rep 2017; 7:11810. [PMID: 28924231 PMCID: PMC5603532 DOI: 10.1038/s41598-017-11814-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/30/2017] [Indexed: 12/18/2022] Open
Abstract
Plasmodium falciparum causes a spectrum of malarial disease from asymptomatic to uncomplicated through to severe. Investigations of parasite virulence have associated the expression of distinct variants of the major surface antigen of the blood stages known as Pf EMP1 encoded by up to 60 var genes per genome. Looking at the population genomics of var genes in cases of uncomplicated malaria, we set out to determine if there was any evidence of a selective sweep of specific var genes or clonal epidemic structure related to the incidence of uncomplicated disease in children. By sequencing the conserved DBLα domain of var genes from six sentinel sites in Uganda we found that the parasites causing uncomplicated P. falciparum disease in children were highly diverse and that every child had a unique var DBLα repertoire. Despite extensive var DBLα diversity and minimal overlap between repertoires, specific DBLα types and groups were conserved at the population level across Uganda. This pattern was the same regardless of the geographic distance or malaria transmission intensity. These data lead us to propose that any parasite can cause uncomplicated malarial disease and that these diverse parasite repertoires are composed of both upsA and non-upsA var gene groups.
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Affiliation(s)
- Shazia Ruybal-Pesántez
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia.,Department of Microbiology, New York University, New York, USA
| | - Kathryn E Tiedje
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia.,Department of Microbiology, New York University, New York, USA
| | | | - Thomas S Rask
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia.,Department of Microbiology, New York University, New York, USA
| | - Moses R Kamya
- School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, USA
| | - Grant Dorsey
- Department of Medicine, University of California, San Francisco, USA
| | - Michael F Duffy
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | - Karen P Day
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia. .,Department of Microbiology, New York University, New York, USA.
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Metwally NG, Tilly AK, Lubiana P, Roth LK, Dörpinghaus M, Lorenzen S, Schuldt K, Witt S, Bachmann A, Tidow H, Gutsmann T, Burmester T, Roeder T, Tannich E, Bruchhaus I. Characterisation of Plasmodium falciparum populations selected on the human endothelial receptors P-selectin, E-selectin, CD9 and CD151. Sci Rep 2017. [PMID: 28642573 PMCID: PMC5481354 DOI: 10.1038/s41598-017-04241-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The ability of the parasite Plasmodium falciparum to evade the immune system and be sequestered within human small blood vessels is responsible for severe forms of malaria. The sequestration depends on the interaction between human endothelial receptors and P. falciparum erythrocyte membrane protein 1 (PfEMP1) exposed on the surface of the infected erythrocytes (IEs). In this study, the transcriptomes of parasite populations enriched for parasites that bind to human P-selectin, E-selectin, CD9 and CD151 receptors were analysed. IT4_var02 and IT4_var07 were specifically expressed in IT4 parasite populations enriched for P-selectin-binding parasites; eight var genes (IT4_var02/07/09/13/17/41/44/64) were specifically expressed in isolate populations enriched for CD9-binding parasites. Interestingly, IT4 parasite populations enriched for E-selectin- and CD151-binding parasites showed identical expression profiles to those of a parasite population exposed to wild-type CHO-745 cells. The same phenomenon was observed for the 3D7 isolate population enriched for binding to P-selectin, E-selectin, CD9 and CD151. This implies that the corresponding ligands for these receptors have either weak binding capacity or do not exist on the IE surface. Conclusively, this work expanded our understanding of P. falciparum adhesive interactions, through the identification of var transcripts that are enriched within the selected parasite populations.
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Affiliation(s)
- Nahla Galal Metwally
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Medical Parasitology Department, Faculty of Medicine-Suez Canal University, Ismailia, Egypt
| | | | - Pedro Lubiana
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Lisa K Roth
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Stephan Lorenzen
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Kathrin Schuldt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Susanne Witt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anna Bachmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Henning Tidow
- Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Thomas Gutsmann
- Division of Biophysics, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Thorsten Burmester
- Institute of Zoology, Biocenter Grindel, University of Hamburg, Hamburg, Germany
| | - Thomas Roeder
- Zoological Institute, Department of Molecular Physiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Egbert Tannich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
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Abstract
INTRODUCTION Malaria during pregnancy is a massive health problem in endemic areas. Placental malaria infections caused by Plasmodium falciparum are responsible for up to one million babies being born with a low birth weight every year. Significant efforts have been invested into preventing the condition. Areas covered: Pub Med was searched using the broad terms 'malaria parasite placenta' to identify studies of interactions between parasite and host, 'prevention of placental malaria' to identify current strategies to prevent placental malaria, and 'placental malaria vaccine' to identify pre-clinical vaccine development. However, all papers from these searches were not systematically included. Expert commentary: The first phase I clinical trials of vaccines are well underway. Trials testing efficacy are more complicated to carry out as only women that are exposed to parasites during pregnancy will contribute to endpoint measurements, further it may require extensive follow-up to establish protection. Future second generation vaccines may overcome the inherent challenges in making an effective placental malaria vaccine.
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Affiliation(s)
- Caroline Pehrson
- a Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science , University of Copenhagen , Copenhagen , Denmark.,b Department of Infectious Diseases , Copenhagen University Hospital (Rigshospitalet) , Copenhagen , Denmark
| | - Ali Salanti
- a Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science , University of Copenhagen , Copenhagen , Denmark.,b Department of Infectious Diseases , Copenhagen University Hospital (Rigshospitalet) , Copenhagen , Denmark
| | - Thor G Theander
- a Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science , University of Copenhagen , Copenhagen , Denmark.,b Department of Infectious Diseases , Copenhagen University Hospital (Rigshospitalet) , Copenhagen , Denmark
| | - Morten A Nielsen
- a Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science , University of Copenhagen , Copenhagen , Denmark.,b Department of Infectious Diseases , Copenhagen University Hospital (Rigshospitalet) , Copenhagen , Denmark
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36
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Dara A, Drábek EF, Travassos MA, Moser KA, Delcher AL, Su Q, Hostelley T, Coulibaly D, Daou M, Dembele A, Diarra I, Kone AK, Kouriba B, Laurens MB, Niangaly A, Traore K, Tolo Y, Fraser CM, Thera MA, Djimde AA, Doumbo OK, Plowe CV, Silva JC. New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali. Genome Med 2017; 9:30. [PMID: 28351419 PMCID: PMC5368897 DOI: 10.1186/s13073-017-0422-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/02/2017] [Indexed: 11/10/2022] Open
Abstract
Background Encoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion and severe malaria disease. Sequencing and assembling the 40–60 var gene complement for individual infections has been notoriously difficult, impeding molecular epidemiological studies and the assessment of particular var elements as subunit vaccine candidates. Methods We developed and validated a novel algorithm, Exon-Targeted Hybrid Assembly (ETHA), to perform targeted assembly of var gene sequences, based on a combination of Pacific Biosciences and Illumina data. Results Using ETHA, we characterized the repertoire of var genes in 12 samples from uncomplicated malaria infections in children from a single Malian village and showed them to be as genetically diverse as vars from isolates from around the globe. The gene var2csa, a member of the var family associated with placental malaria pathogenesis, was present in each genome, as were vars previously associated with severe malaria. Conclusion ETHA, a tool to discover novel var sequences from clinical samples, will aid the understanding of malaria pathogenesis and inform the design of malaria vaccines based on PfEMP1. ETHA is available at: https://sourceforge.net/projects/etha/. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0422-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antoine Dara
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elliott F Drábek
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark A Travassos
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kara A Moser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Arthur L Delcher
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Qi Su
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Timothy Hostelley
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Modibo Daou
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Ahmadou Dembele
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Issa Diarra
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Abdoulaye K Kone
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Matthew B Laurens
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Karim Traore
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Youssouf Tolo
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Claire M Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mahamadou A Thera
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Abdoulaye A Djimde
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali
| | - Christopher V Plowe
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
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37
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Bruske EI, Dimonte S, Enderes C, Tschan S, Flötenmeyer M, Koch I, Berger J, Kremsner P, Frank M. In Vitro Variant Surface Antigen Expression in Plasmodium falciparum Parasites from a Semi-Immune Individual Is Not Correlated with Var Gene Transcription. PLoS One 2016; 11:e0166135. [PMID: 27907004 PMCID: PMC5132323 DOI: 10.1371/journal.pone.0166135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/24/2016] [Indexed: 12/17/2022] Open
Abstract
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is considered to be the main variant surface antigen (VSA) of Plasmodium falciparum and is mainly localized on electron-dense knobs in the membrane of the infected erythrocyte. Switches in PfEMP1 expression provide the basis for antigenic variation and are thought to be critical for parasite persistence during chronic infections. Recently, strain transcending anti-PfEMP1 immunity has been shown to develop early in life, challenging the role of PfEMP1 in antigenic variation during chronic infections. In this work we investigate how P. falciparum achieves persistence during a chronic asymptomatic infection. The infected individual (MOA) was parasitemic for 42 days and multilocus var gene genotyping showed persistence of the same parasite population throughout the infection. Parasites from the beginning of the infection were adapted to tissue culture and cloned by limiting dilution. Flow cytometry using convalescent serum detected a variable surface recognition signal on isogenic clonal parasites. Quantitative real-time PCR with a field isolate specific var gene primer set showed that the surface recognition signal was not correlated with transcription of individual var genes. Strain transcending anti-PfEMP1 immunity of the convalescent serum was demonstrated with CD36 selected and PfEMP1 knock-down NF54 clones. In contrast, knock-down of PfEMP1 did not have an effect on the antibody recognition signal in MOA clones. Trypsinisation of the membrane surface proteins abolished the surface recognition signal and immune electron microscopy revealed that antibodies from the convalescent serum bound to membrane areas without knobs and with knobs. Together the data indicate that PfEMP1 is not the main variable surface antigen during a chronic infection and suggest a role for trypsin sensitive non-PfEMP1 VSAs for parasite persistence in chronic infections.
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Affiliation(s)
- Ellen Inga Bruske
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
| | - Sandra Dimonte
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
| | - Corinna Enderes
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
| | - Serena Tschan
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
| | | | - Iris Koch
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Jürgen Berger
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Peter Kremsner
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
- CERMEL (Centre de Recherche Médicale de Lambaréné), Lambaréné, Gabon
| | - Matthias Frank
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
- CERMEL (Centre de Recherche Médicale de Lambaréné), Lambaréné, Gabon
- * E-mail:
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38
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Stanton A, Harris LM, Graham G, Merrick CJ. Recombination events among virulence genes in malaria parasites are associated with G-quadruplex-forming DNA motifs. BMC Genomics 2016; 17:859. [PMID: 27809775 PMCID: PMC5093961 DOI: 10.1186/s12864-016-3183-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/21/2016] [Indexed: 11/10/2022] Open
Abstract
Background Malaria parasites of the genus Plasmodium possess large hyper-variable families of antigen-encoding genes. These are often variantly-expressed and are major virulence factors for immune evasion and the maintenance of chronic infections. Recombination and diversification of these gene families occurs readily, and may be promoted by G-quadruplex (G4) DNA motifs within and close to the variant genes. G4s have been shown to cause replication fork stalling, DNA breakage and recombination in model systems, but these motifs remain largely unstudied in Plasmodium. Results We examined the nature and distribution of putative G4-forming sequences in multiple Plasmodium genomes, finding that their co-distribution with variant gene families is conserved across different Plasmodium species that have different types of variant gene families. In P. falciparum, where a large set of recombination events that occurred over time in cultured parasites has been mapped, we found a strong spatial association between these recombination events and putative G4-forming sequences. Finally, we searched Plasmodium genomes for the three classes of helicase that can unwind G4s: Plasmodium spp. have no identifiable homologue of the highly efficient G4 helicase PIF1, but they do encode two putative RecQ helicases and one homologue of the RAD3-family helicase FANCJ. Conclusions Our analyses, conducted at the whole-genome level in multiple species of Plasmodium, support the concept that G4s are likely to be involved in recombination and diversification of antigen-encoding gene families in this important protozoan pathogen. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3183-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam Stanton
- School of Computing and Mathematics, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST55BG, UK
| | - Lynne M Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST55BG, UK
| | - Gemma Graham
- School of Medicine, Keele University, Keele, Staffordshire, ST55BG, UK
| | - Catherine J Merrick
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST55BG, UK.
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39
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Abstract
Plasmodium falciparum malaria remains a devastating public health problem. Recent discoveries have shed light on the origin and evolution of Plasmodium parasites and their interactions with their vertebrate and mosquito hosts. P. falciparum malaria originated in Africa from a single horizontal transfer between an infected gorilla and a human, and became global as the result of human migration. Today, P. falciparum malaria is transmitted worldwide by more than 70 different anopheline mosquito species. Recent studies indicate that the mosquito immune system can be a barrier to malaria transmission and that the P. falciparum Pfs47 gene allows the parasite to evade mosquito immune detection. Here, we review the origin and globalization of P. falciparum and integrate this history with analysis of the biology, evolution, and dispersal of the main mosquito vectors. This new perspective broadens our understanding of P. falciparum population structure and the dispersal of important parasite genetic traits.
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Affiliation(s)
- Alvaro Molina-Cruz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
| | - Martine M Zilversmit
- Richard Guilder Graduate School and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
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40
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Holding T, Recker M. Maintenance of phenotypic diversity within a set of virulence encoding genes of the malaria parasite Plasmodium falciparum. J R Soc Interface 2016; 12:20150848. [PMID: 26674193 PMCID: PMC4707858 DOI: 10.1098/rsif.2015.0848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Infection by the human malaria parasite Plasmodium falciparum results in a broad spectrum of clinical outcomes, ranging from severe and potentially life-threatening malaria to asymptomatic carriage. In a process of naturally acquired immunity, individuals living in malaria-endemic regions build up a level of clinical protection, which attenuates infection severity in an exposure-dependent manner. Underlying this shift in the immunoepidemiology as well as the observed range in malaria pathogenesis is the var multigene family and the phenotypic diversity embedded within. The var gene-encoded surface proteins Plasmodium falciparum erythrocyte membrane protein 1 mediate variant-specific binding of infected red blood cells to a diverse set of host receptors that has been linked to specific disease manifestations, including cerebral and pregnancy-associated malaria. Here, we show that cross-reactive immune responses, which minimize the within-host benefit of each additionally expressed gene during infection, can cause selection for maximum phenotypic diversity at the genome level. We further show that differential functional constraints on protein diversification stably maintain uneven ratios between phenotypic groups, in line with empirical observation. Our results thus suggest that the maintenance of phenotypic diversity within P. falciparum is driven by an evolutionary trade-off that optimizes between within-host parasite fitness and between-host selection pressure.
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Affiliation(s)
- Thomas Holding
- Centre for Mathematics and the Environment, University of Exeter, Penryn Campus, Penryn TR10 9EZ, UK
| | - Mario Recker
- Centre for Mathematics and the Environment, University of Exeter, Penryn Campus, Penryn TR10 9EZ, UK
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41
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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] [What about the content of this article? (0)] [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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42
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Quintana MDP, Angeletti D, Moll K, Chen Q, Wahlgren M. Phagocytosis-inducing antibodies to Plasmodium falciparum upon immunization with a recombinant PfEMP1 NTS-DBL1α domain. Malar J 2016; 15:416. [PMID: 27531359 PMCID: PMC4987995 DOI: 10.1186/s12936-016-1459-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Individuals living in endemic areas gradually acquire natural immunity to clinical malaria, largely dependent on antibodies against parasite antigens. There are many studies indicating that the variant antigen PfEMP1 at the surface of the parasitized red blood cell (pRBC) is one of the major targets of the immune response. It is believed that antibodies against PfEMP1 confer protection by blocking sequestration (rosetting and cytoadherence), inducing antibody-dependent cellular-inhibitory effect and opsonizing pRBCs for phagocytosis. METHODS A recombinant NTS-DBL1α domain from a rosette-mediating PfEMP1 was expressed in Escherichia coli. The resulting protein was purified and used for immunization to generate polyclonal (goat) and monoclonal (mouse) antibodies. The antibodies' ability to opsonize and induce phagocytosis in vitro was tested and contrasted with the presence of opsonizing antibodies naturally acquired during Plasmodium falciparum infection. RESULTS All antibodies recognized the recombinant antigen and the surface of live pRBCs, however, their capacity to opsonize the pRBCs for phagocytosis varied. The monoclonal antibodies isotyped as IgG2b did not induce phagocytosis, while those isotyped as IgG2a were in general very effective, inducing phagocytosis with similar levels as those naturally acquired during P. falciparum infection. These monoclonal antibodies displayed different patterns, some of them showing a concentration-dependent activity while others showed a prozone-like effect. The goat polyclonal antibodies were not able to induce phagocytosis. CONCLUSION Immunization with an NTS-DBL1-α domain of PfEMP1 generates antibodies that not only have a biological role in rosette disruption but also effectively induce opsonization for phagocytosis of pRBCs with similar activity to naturally acquired antibodies from immune individuals living in a malaria endemic area. Some of the antibodies with high opsonizing activity were not able to disrupt rosettes, indicating that epitopes of the NTS-DBL1-α other than those involved in rosetting are exposed on the pRBC surface and are able to induce functional antibodies. The ability to induce phagocytosis largely depended on the antibody isotype and on the ability to recognize the surface of the pRBC regardless of the rosette-disrupting capacity.
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Affiliation(s)
- Maria Del Pilar Quintana
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,Escuela de Medicina y Ciencias de la Salud, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Davide Angeletti
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Kirsten Moll
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Qijun Chen
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,Key Laboratory of Zoonosis, Jilin University, Changchun, People's Republic of China.,Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Mats Wahlgren
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.
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Warimwe GM, Abdi AI, Muthui M, Fegan G, Musyoki JN, Marsh K, Bull PC. Serological Conservation of Parasite-Infected Erythrocytes Predicts Plasmodium falciparum Erythrocyte Membrane Protein 1 Gene Expression but Not Severity of Childhood Malaria. Infect Immun 2016; 84:1331-5. [PMID: 26883585 DOI: 10.1128/IAI.00772-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 02/08/2016] [Indexed: 11/27/2022] Open
Abstract
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), expressed on P. falciparum-infected erythrocytes, is a major family of clonally variant targets of naturally acquired immunity to malaria. Previous studies have demonstrated that in areas where malaria is endemic, antibodies to infected erythrocytes from children with severe malaria tend to be more seroprevalent than antibodies to infected erythrocytes from children with nonsevere malaria. These data have led to a working hypothesis that PfEMP1 variants associated with parasite virulence are relatively conserved in structure. However, the longevity of such serologically conserved variants in the parasite population is unknown. Here, using infected erythrocytes from recently sampled clinical P. falciparum samples, we measured serological conservation using pools of antibodies in sera that had been sampled 10 to 12 years earlier. The serological conservation of infected erythrocytes strongly correlated with the expression of specific PfEMP1 subsets previously found to be associated with severe malaria. However, we found no association between serological conservation per se and disease severity within these data. This contrasts with the simple hypothesis that P. falciparum isolates with a serologically conserved group of PfEMP1 variants cause severe malaria. The data are instead consistent with periodic turnover of the immunodominant epitopes of PfEMP1 associated with severe malaria.
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44
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Bachmann A, Petter M, Krumkamp R, Esen M, Held J, Scholz JA, Li T, Sim BK, Hoffman SL, Kremsner PG, Mordmüller B, Duffy MF, Tannich E. Mosquito Passage Dramatically Changes var Gene Expression in Controlled Human Plasmodium falciparum Infections. PLoS Pathog 2016; 12:e1005538. [PMID: 27070311 DOI: 10.1371/journal.ppat.1005538] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/10/2016] [Indexed: 11/19/2022] Open
Abstract
Virulence of the most deadly malaria parasite Plasmodium falciparum is linked to the variant surface antigen PfEMP1, which is encoded by about 60 var genes per parasite genome. Although the expression of particular variants has been associated with different clinical outcomes, little is known about var gene expression at the onset of infection. By analyzing controlled human malaria infections via quantitative real-time PCR, we show that parasite populations from 18 volunteers expressed virtually identical transcript patterns that were dominated by the subtelomeric var gene group B and, to a lesser extent, group A. Furthermore, major changes in composition and frequency of var gene transcripts were detected between the parental parasite culture that was used to infect mosquitoes and Plasmodia recovered from infected volunteers, suggesting that P. falciparum resets its var gene expression during mosquito passage and starts with the broad expression of a specific subset of var genes when entering the human blood phase.
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Kirkman LA, Deitsch KW. Recombination and Diversification of the Variant Antigen Encoding Genes in the Malaria Parasite Plasmodium falciparum. Microbiol Spectr 2014; 2. [PMID: 26104446 DOI: 10.1128/microbiolspec.MDNA3-0022-2014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The most severe form of human malaria is caused by the protozoan parasite Plasmodium falciparum. These parasites invade and replicate within the circulating red blood cells of infected individuals leading to numerous disease manifestations, including severe anemia, altered circulation, and tissue inflammation. Malaria parasites are also known for their ability to maintain a chronic infection through antigenic variation, the ability to systematically alter the antigens displayed on the surface of infected cells and thereby avoid clearance by the host's antibody response. The genome of P. falciparum includes several large, multicopy gene families that encode highly variable forms of the surface proteins that are the targets of host immunity. Alterations in expression of genes within these families are responsible for antigenic variation. This process requires the continuous generation of new antigenic variants within these gene families, and studies have shown that new variants arise through extensive recombination and gene conversion events between family members. Malaria parasites possess an unusual complement of DNA repair pathways, thus the study of recombination between variant antigen encoding genes provides a unique view into the evolution of mobile DNA in an organism distantly related to the more closely studied model eukaryotes.
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Abdi AI, Warimwe GM, Muthui MK, Kivisi CA, Kiragu EW, Fegan GW, Bull PC. Global selection of Plasmodium falciparum virulence antigen expression by host antibodies. Sci Rep 2016; 6:19882. [PMID: 26804201 DOI: 10.1038/srep19882] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 12/21/2015] [Indexed: 12/22/2022] Open
Abstract
Parasite proteins called PfEMP1 that are inserted on the surface of infected erythrocytes, play a key role in the severe pathology associated with infection by the Plasmodium falciparum malaria parasite. These proteins mediate binding of infected cells to the endothelial lining of blood vessels as a strategy to avoid clearance by the spleen and are major targets of naturally acquired immunity. PfEMP1 is encoded by a large multi-gene family called var. Mutually-exclusive transcriptional switching between var genes allows parasites to escape host antibodies. This study examined in detail the patterns of expression of var in a well-characterized sample of parasites from Kenyan Children. Instead of observing clear inverse relationships between the expression of broad sub-classes of PfEMP1, we found that expression of different PfEMP1 groups vary relatively independently. Parasite adaptation to host antibodies also appears to involve a general reduction in detectable var gene expression. We suggest that parasites switch both between different PfEMP1 variants and between high and low expression states. Such a strategy could provide a means of avoiding immunological detection and promoting survival under high levels of host immunity.
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Abstract
The Plasmodium falciparum erythrocyte membrane protein 1 antigens that are inserted onto the surface of P. falciparum infected erythrocytes play a key role both in the pathology of severe malaria and as targets of naturally acquired immunity. They might be considered unlikely vaccine targets because they are extremely diverse. However, several lines of evidence suggest that underneath this molecular diversity there are a restricted set of epitopes which may act as effective targets for a vaccine against severe malaria. Here we review some of the recent developments in this area of research, focusing on work that has assessed the potential of these molecules as possible vaccine targets.
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Abstract
Plasmodium falciparum is the protozoan parasite that causes most malaria-associated morbidity and mortality in humans with over 500,000 deaths annually. The disease symptoms are associated with repeated cycles of invasion and asexual multiplication inside red blood cells of the parasite. Partial, non-sterile immunity to P. falciparum malaria develops only after repeated infections and continuous exposure. The successful evasion of the human immune system relies on the large repertoire of antigenically diverse parasite proteins displayed on the red blood cell surface and on the merozoite membrane where they are exposed to the human immune system. Expression switching of these polymorphic proteins between asexual parasite generations provides an efficient mechanism to adapt to the changing environment in the host and to maintain chronic infection. This chapter discusses antigenic diversity and variation in the malaria parasite and our current understanding of the molecular mechanisms that direct the expression of these proteins.
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Affiliation(s)
- Michaela Petter
- Department of Medicine Royal Melbourne Hospital, Peter Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, VIC, 3010, Australia.
| | - Michael F Duffy
- Department of Medicine Royal Melbourne Hospital, Peter Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, VIC, 3010, Australia.
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Agrawal MR, Ozarkar AD, Gupta S, Deobagkar DN, Deobagkar DD. Comparative study of Plasmodium falciparum erythrocyte membrane protein 1-DBLα domain variants with respect to antigenic variations and docking interaction analysis with glycosaminoglycans. Mol Biosyst 2015; 10:2466-79. [PMID: 24995459 DOI: 10.1039/c4mb00274a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The variant surface antigen PfEMP1 (Plasmodium falciparum erythrocyte membrane protein 1) encoded by the polymorphic multi-copy var gene family plays an important role in parasite biology and the host-parasite interactions. Sequestration and antigenic variation is an essential component in the survival and pathogenesis of Plasmodium falciparum and contributes to chronic infection. The DBLα domain of PfEMP1 is a potential target for immuno-epidemiological studies and has been visualized as a vaccine candidate against severe malaria. Specific host receptors like heparin, heparan sulphate, blood group A and complement receptor 1 have been reported to bind the DBLα domain. Although heparin has been experimentally shown to disrupt the parasite-host interaction and effectively disrupt rosetting, the binding sites for the DBLα domain and the mechanism behind heparin-mediated rosette inhibition have not been elucidated. In this study, 3D structures and epitopes of the DBLα domain in 3D7 and in two Indian isolates have been predicted and compared. We have carried out docking studies on DBLα domains with human GAG receptors (heparin and heparan sulphate) to predict the strength of association between the protein-ligand interactions. The DBLα domain structures showed extensive diversity and polymorphism in their binding sites. The docking results indicate that heparin binds more effectively with high affinity as compared to heparan sulphate with some common interacting residues. These common residues can play an important role in rosetting and will aid in the designing of inhibitors specific to the interactions between DBLα and heparin or heparan sulphate would be important in malaria treatment. Thus it may lead to the development of novel interference strategies to block red blood cell invasion and provide protection against malaria.
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Affiliation(s)
- Megha R Agrawal
- Bioinformatics Centre & Department of Zoology, Center of Advanced Studies, University of Pune, Pune 411007, India.
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Subramani R, Quadt K, Jeppesen AE, Hempel C, Petersen JE, Hassenkam T, Hviid L, Barfod L. Plasmodium falciparum-infected erythrocyte knob density is linked to the PfEMP1 variant expressed. mBio 2015; 6:e01456-15. [PMID: 26443460 DOI: 10.1128/mBio.01456-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Members of the clonally variant Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family mediate adhesion of infected erythrocytes (IEs) to vascular receptors. PfEMP1 expression is normally confined to nanoscale knob protrusions on the IE surface membrane. To investigate the relationship between the densities of these IE surface knobs and the PfEMP1 variant expressed, we used specific antibody panning to generate three sublines of the P. falciparum clone IT4, which expresses the PfEMP1 variants IT4VAR04, IT4VAR32b, and IT4VAR60. The knob density in each subline was then determined by atomic force microscopy (AFM) and scanning electron microscopy (SEM) and compared to PfEMP1 and knob-associated histidine-rich protein (KAHRP) expression. Selection for uniform expression of IT4VAR04 produced little change in knob density, compared to unselected IEs. In contrast, selection for IT4VAR32b expression increased knob density approximately 3-fold, whereas IEs selected for IT4VAR60 expression were essentially knobless. When IT4VAR60+ IEs were subsequently selected to express IT4VAR04 or IT4VAR32b, they again displayed low and high knob densities, respectively. All sublines expressed KAHRP regardless of the PfEMP1 expressed. Our study documents for the first time that knob density is related to the PfEMP1 variant expressed. This may reflect topological requirements to ensure optimal adhesive properties of the IEs. Infections with Plasmodium falciparum malaria parasites are still responsible for many deaths, especially among children and pregnant women. New interventions are needed to reduce severe illness and deaths caused by this malaria parasite. Thus, a better understanding of the mechanisms behind the pathogenesis is essential. A main reason why Plasmodium falciparum malaria is more severe than disease caused by other malaria species is its ability to express variant antigens on the infected erythrocyte surface. These antigens are presented on membrane protrusions known as knobs. This study set out to investigate the interplay between different variant antigens on the surface of P. falciparum-infected erythrocytes and the density of the knobs on which the antigens are expressed. Such a direct analysis of this relationship has not been reported before but adds to the important understanding of the complexity of malaria antigen presentation.
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