1
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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] [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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2
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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] [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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3
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Childs LM, Larremore DB. Network Models for Malaria: Antigens, Dynamics, and Evolution Over Space and Time. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11512-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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4
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Bhandari S, Krishna S, Patel PP, Singh MP, Singh N, Sharma A, Bharti PK. Diversity and expression of Plasmodium falciparum var gene in severe and mild malaria cases from Central India. Int J Infect Dis 2020; 103:552-559. [PMID: 33326872 DOI: 10.1016/j.ijid.2020.12.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Plasmodium falciparum erythrocyte membrane protein is encoded by a highly variable multicopy var gene family known to play a key role in malaria pathogenicity. Therefore, we investigated sequence variation, expression profile and immune response of the Duffy binding-like domain (DBLα) region of the var gene. METHODS Blood samples were collected from patients with cerebral, severe and mild malaria in Chhattisgarh, India, a region with endemic malaria. Polymerase chain reaction amplicons were cloned and sequenced to determine sequence variation. The expression level was analyzed targeting the upstream region of var gene using the Delta-Delta-Ct method. Immunoglobulin G (IgG) level was determined against the 6 synthetic peptides of the DBLα region. RESULTS The study identified that group 1 and group 5 sequences (cysteine/position of limited variability (cys/PoLV) classification) along with cys2/cys4 and MFK*/REY motifs and short amino acid length were significantly associated with malaria severity. The specific PoLV (MFKS, LREA, PTNL) were restricted to cerebral malaria. The expression level of var group A was higher than var groups B and C, demonstrating its prognostic characteristic. All peptides showed high-quality IgG response, while VAR P5 appeared to be a good marker for severity. CONCLUSIONS The present study illustrates the presence of specific sequences of DBLα tags involved in severe malaria that could be targeted in future interventions for malaria control and elimination.
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Affiliation(s)
- Sneha Bhandari
- ICMR-National Institute of Research in Tribal Health, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India.
| | - Sri Krishna
- ICMR-National Institute of Research in Tribal Health, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India.
| | - Priyanka P Patel
- ICMR-National Institute of Research in Tribal Health, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India.
| | - Mrigendra P Singh
- ICMR-National Institute of Malaria Research, Field Unit, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India.
| | - Neeru Singh
- ICMR-National Institute of Research in Tribal Health, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India.
| | - Anjana Sharma
- Department of Post Graduate Studies and Research in Biological Sciences, Rani Durgavati Vishwavidyalaya, Jabalpur, Madhya Pradesh, India.
| | - Praveen K Bharti
- ICMR-National Institute of Research in Tribal Health, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India.
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5
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Mita-Mendoza NK, Magallon-Tejada A, Parmar P, Furtado R, Aldrich M, Saidi A, Taylor T, Smith J, Seydel K, Daily JP. Dimethyl fumarate reduces TNF and Plasmodium falciparum induced brain endothelium activation in vitro. Malar J 2020; 19:376. [PMID: 33087130 PMCID: PMC7579885 DOI: 10.1186/s12936-020-03447-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/16/2020] [Indexed: 11/10/2022] Open
Abstract
Background Cerebral malaria (CM) is associated with morbidity and mortality despite the use of potent anti-malarial agents. Brain endothelial cell activation and dysfunction from oxidative and inflammatory host responses and products released by Plasmodium falciparum-infected erythrocytes (IE), are likely the major contributors to the encephalopathy, seizures, and brain swelling that are associated with CM. The development of adjunctive therapy to reduce the pathological consequences of host response pathways could improve outcomes. A potentially protective role of the nuclear factor E2-related factor 2 (NRF2) pathway, which serves as a therapeutic target in brain microvascular diseases and central nervous system (CNS) inflammatory diseases such as multiple sclerosis was tested to protect endothelial cells in an in vitro culture system subjected to tumour necrosis factor (TNF) or infected red blood cell exposure. NRF2 is a transcription factor that mediates anti-oxidant and anti-inflammatory responses. Methods To accurately reflect clinically relevant parasite biology a unique panel of parasite isolates derived from patients with stringently defined CM was developed. The effect of TNF and these parasite lines on primary human brain microvascular endothelial cell (HBMVEC) activation in an in vitro co-culture model was tested. HBMVEC activation was measured by cellular release of IL6 and nuclear translocation of NFκB. The transcriptional and functional effects of dimethyl fumarate (DMF), an FDA approved drug which induces the NRF2 pathway, on host and parasite induced HBMVEC activation was characterized. In addition, the effect of DMF on parasite binding to TNF stimulated HBMVEC in a semi-static binding assay was examined. Results Transcriptional profiling demonstrates that DMF upregulates the NRF2-Mediated Oxidative Stress Response, ErbB4 Signaling Pathway, Peroxisome Proliferator-activated Receptor (PPAR) Signaling and downregulates iNOS Signaling and the Neuroinflammation Signaling Pathway on TNF activated HBMVEC. The parasite lines derived from eight paediatric CM patients demonstrated increased binding to TNF activated HBMVEC and varied in their binding and activation of HBMVEC. Overall DMF reduced both TNF and CM derived parasite activation of HBMVEC. Conclusions These findings provide evidence that targeting the NRF2 pathway in TNF and parasite activated HBMVEC mediates multiple protective pathways and may represent a novel adjunctive therapy to improve infection outcomes in CM.
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Affiliation(s)
- Neida K Mita-Mendoza
- Department of Microbiology & Immunology and Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ariel Magallon-Tejada
- Seattle Biomedical Research Institute, Seattle, WA, USA.,Department of Research in Parasitology, Gorgas Memorial Research Institute for Health Studies, Panama City, Panama
| | - Priyanka Parmar
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Raquel Furtado
- Department of Microbiology & Immunology and Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Margaret Aldrich
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alex Saidi
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre 3, Malawi
| | - Terrie Taylor
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre 3, Malawi.,Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Joe Smith
- Seattle Children's Research Institute, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - Karl Seydel
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre 3, Malawi.,Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Johanna P Daily
- Department of Microbiology & Immunology and Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, USA. .,Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
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6
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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] [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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7
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Otto TD, Assefa SA, Böhme U, Sanders MJ, Kwiatkowski D, Berriman M, Newbold C. Evolutionary analysis of the most polymorphic gene family in falciparum malaria. Wellcome Open Res 2019; 4:193. [PMID: 32055709 PMCID: PMC7001760 DOI: 10.12688/wellcomeopenres.15590.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
The var gene family of the human malaria parasite Plasmodium falciparum encode proteins that are crucial determinants of both pathogenesis and immune evasion and are highly polymorphic. Here we have assembled nearly complete var gene repertoires from 2398 field isolates and analysed a normalised set of 714 from across 12 countries. This therefore represents the first large scale attempt to catalogue the worldwide distribution of var gene sequences We confirm the extreme polymorphism of this gene family but also demonstrate an unexpected level of sequence sharing both within and between continents. We show that this is likely due to both the remnants of selective sweeps as well as a worrying degree of recent gene flow across continents with implications for the spread of drug resistance. We also address the evolution of the var repertoire with respect to the ancestral genes within the Laverania and show that diversity generated by recombination is concentrated in a number of hotspots. An analysis of the subdomain structure indicates that some existing definitions may need to be revised From the analysis of this data, we can now understand the way in which the family has evolved and how the diversity is continuously being generated. Finally, we demonstrate that because the genes are distributed across the genome, sequence sharing between genotypes acts as a useful population genetic marker.
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Affiliation(s)
- Thomas D. Otto
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
| | - Sammy A. Assefa
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ulrike Böhme
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Dominic Kwiatkowski
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Pf3k consortium
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Matt Berriman
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Chris Newbold
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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8
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Duffy PE. Immunity to Severe Malaria: PfEMP1 Tags Tell a Tale. Cell Host Microbe 2019; 26:571-573. [PMID: 31726024 PMCID: PMC11132668 DOI: 10.1016/j.chom.2019.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
PfEMP1 is the major surface antigen of P. falciparum-infected erythrocytes, mediates endothelial adhesion, and displays extreme sequence diversity that underpins antigenic variation. In this issue of Cell Host & Microbe, Tessema et al. (2019) find that antibodies in sera from a pediatric cohort that bind a discrete PfEMP1 subset associate with protection from severe malaria and predict future risk.
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Affiliation(s)
- Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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9
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Kivisi CA, Muthui M, Hunt M, Fegan G, Otto TD, Githinji G, Warimwe GM, Rance R, Marsh K, Bull PC, Abdi AI. Exploring Plasmodium falciparum Var Gene Expression to Assess Host Selection Pressure on Parasites During Infancy. Front Immunol 2019; 10:2328. [PMID: 31681266 PMCID: PMC6798654 DOI: 10.3389/fimmu.2019.02328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/16/2019] [Indexed: 11/13/2022] Open
Abstract
In sub-Saharan Africa, children below 5 years bear the greatest burden of severe malaria because they lack naturally acquired immunity that develops following repeated exposure to infections by Plasmodium falciparum. Antibodies to the surface of P. falciparum infected erythrocytes (IE) play an important role in this immunity. In children under the age of 6 months, relative protection from severe malaria is observed and this is thought to be partly due to trans-placental acquired protective maternal antibodies. However, the protective effect of maternal antibodies has not been fully established, especially the role of antibodies to variant surface antigens (VSA) expressed on IE. Here, we assessed the immune pressure on parasites infecting infants using markers associated with the acquisition of naturally acquired immunity to surface antigens. We hypothesized that, if maternal antibodies to VSA imposed a selection pressure on parasites, then the expression of a relatively conserved subset of var genes called group A var genes in infants should change with waning maternal antibodies. To test this, we compared their expression in parasites from children between 0 and 12 months and above 12 months of age. The transcript quantity and the proportional expression of group A var subgroup, including those containing domain cassette 13, were positively associated with age during the first year of life, which contrasts with above 12 months. This was accompanied by a decline in infected erythrocyte surface antibodies and an increase in parasitemia during this period. The observed increase in group A var gene expression with age in the first year of life, when the maternal antibodies are waning and before acquisition of naturally acquired antibodies with repeated exposure, is consistent with the idea that maternally acquired antibodies impose a selection pressure on parasites that infect infants and may play a role in protecting these infants against severe malaria.
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Affiliation(s)
- Cheryl A Kivisi
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya.,Department of Biological Sciences, Pwani University, Kilifi, Kenya
| | | | - Martin Hunt
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Greg Fegan
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - George M Warimwe
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Richard Rance
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
| | - Kevin Marsh
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Peter C Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Abdirahman I Abdi
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
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10
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Bachmann A, Bruske E, Krumkamp R, Turner L, Wichers JS, Petter M, Held J, Duffy MF, Sim BKL, Hoffman SL, Kremsner PG, Lell B, Lavstsen T, Frank M, Mordmüller B, Tannich E. Controlled human malaria infection with Plasmodium falciparum demonstrates impact of naturally acquired immunity on virulence gene expression. PLoS Pathog 2019; 15:e1007906. [PMID: 31295334 PMCID: PMC6650087 DOI: 10.1371/journal.ppat.1007906] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/23/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
The pathogenesis of Plasmodium falciparum malaria is linked to the variant surface antigen PfEMP1, which mediates tethering of infected erythrocytes to the host endothelium and is encoded by approximately 60 var genes per parasite genome. Repeated episodes of malaria infection result in the gradual acquisition of protective antibodies against PfEMP1 variants. The antibody repertoire is believed to provide a selective pressure driving the clonal expansion of parasites expressing unrecognized PfEMP1 variants, however, due to the lack of experimental in vivo models there is only limited experimental evidence in support of this concept. To get insight into the impact of naturally acquired immunity on the expressed var gene repertoire early during infection we performed controlled human malaria infections of 20 adult African volunteers with life-long malaria exposure using aseptic, purified, cryopreserved P. falciparum sporozoites (Sanaria PfSPZ Challenge) and correlated serological data with var gene expression patterns from ex vivo parasites. Among the 10 African volunteers who developed patent infections, individuals with low antibody levels showed a steep rise in parasitemia accompanied by broad activation of multiple, predominantly subtelomeric var genes, similar to what we previously observed in naïve volunteers. In contrast, individuals with intermediate antibody levels developed asymptomatic infections and the ex vivo parasite populations expressed only few var gene variants, indicative of clonal selection. Importantly, in contrast to parasites from naïve volunteers, expression of var genes coding for endothelial protein C receptor (EPCR)-binding PfEMP1 that are associated with severe childhood malaria was rarely detected in semi-immune adult African volunteers. Moreover, we followed var gene expression for up to six parasite replication cycles and demonstrated for the first time in vivo a shift in the dominant var gene variant. In conclusion, our data suggest that P. falciparum activates multiple subtelomeric var genes at the onset of blood stage infection facilitating rapid expansion of parasite clones which express PfEMP1 variants unrecognized by the host's immune system, thus promoting overall parasite survival in the face of host immunity.
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Affiliation(s)
- Anna Bachmann
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Germany
| | - Ellen Bruske
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Ralf Krumkamp
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Germany
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Louise Turner
- Centre for Medical Parasitology, University of Copenhagen, Copenhagen K, Denmark
| | - J. Stephan Wichers
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Michaela Petter
- Mikrobiologisches Institut–Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jana Held
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Michael F. Duffy
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | | | | | - Peter G. Kremsner
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Bertrand Lell
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
| | - Thomas Lavstsen
- Centre for Medical Parasitology, University of Copenhagen, Copenhagen K, Denmark
| | - Matthias Frank
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Benjamin Mordmüller
- Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Egbert Tannich
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Germany
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11
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Tuju J, Mackinnon MJ, Abdi AI, Karanja H, Musyoki JN, Warimwe GM, Gitau EN, Marsh K, Bull PC, Urban BC. Antigenic cartography of immune responses to Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1). PLoS Pathog 2019; 15:e1007870. [PMID: 31260501 PMCID: PMC6625739 DOI: 10.1371/journal.ppat.1007870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 07/12/2019] [Accepted: 05/24/2019] [Indexed: 12/15/2022] Open
Abstract
Naturally acquired clinical immunity to Plasmodium falciparum is partly mediated by antibodies directed at parasite-derived antigens expressed on the surface of red blood cells which mediate disease and are extremely diverse. Unlike children, adults recognize a broad range of variant surface antigens (VSAs) and are protected from severe disease. Though crucial to the design and feasibility of an effective malaria vaccine, it is not yet known whether immunity arises through cumulative exposure to each of many antigenic types, cross-reactivity between antigenic types, or some other mechanism. In this study, we measured plasma antibody responses of 36 children with symptomatic malaria to a diverse panel of 36 recombinant proteins comprising part of the DBLα domain (the 'DBLα-tag') of PfEMP1, a major class of VSAs. We found that although plasma antibody responses were highly specific to individual antigens, serological profiles of responses across antigens fell into one of just two distinct types. One type was found almost exclusively in children that succumbed to severe disease (19 out of 20) while the other occurred in all children with mild disease (16 out of 16). Moreover, children with severe malaria had serological profiles that were narrower in antigen specificity and shorter-lived than those in children with mild malaria. Borrowing a novel technique used in influenza-antigenic cartography-we mapped these dichotomous serological profiles to amino acid sequence variation within a small sub-region of the PfEMP1 DBLα domain. By applying our methodology on a larger scale, it should be possible to identify epitopes responsible for eliciting the protective version of serological profiles to PfEMP1 thereby accelerating development of a broadly effective anti-disease malaria vaccine.
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Affiliation(s)
- James Tuju
- KEMRI-Wellcome Trust Research Programme, Kenya
- Department of Chemistry and Biochemistry, Pwani University, Kilifi, Kenya
| | | | | | | | | | - George M. Warimwe
- KEMRI-Wellcome Trust Research Programme, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Evelyn N. Gitau
- African Population and Health Research Center, Nairobi, Kenya
| | - Kevin Marsh
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Britta C. Urban
- Liverpool School of Tropical Medicine, Department of Tropical Disease Biology, Pembroke Place, Liverpool, United Kingdom
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12
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Bayes-optimal estimation of overlap between populations of fixed size. PLoS Comput Biol 2019; 15:e1006898. [PMID: 30925165 PMCID: PMC6440621 DOI: 10.1371/journal.pcbi.1006898] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/22/2019] [Indexed: 11/19/2022] Open
Abstract
Measuring the overlap between two populations is, in principle, straightforward. Upon fully sampling both populations, the number of shared objects—species, taxonomical units, or gene variants, depending on the context—can be directly counted. In practice, however, only a fraction of each population’s objects are likely to be sampled due to stochastic data collection or sequencing techniques. Although methods exists for quantifying population overlap under subsampled conditions, their bias is well documented and the uncertainty of their estimates cannot be quantified. Here we derive and validate a method to rigorously estimate the population overlap from incomplete samples when the total number of objects, species, or genes in each population is known, a special case of the more general β-diversity problem that is particularly relevant in the ecology and genomic epidemiology of malaria. By solving a Bayesian inference problem, this method takes into account the rates of subsampling and produces unbiased and Bayes-optimal estimates of overlap. In addition, it provides a natural framework for computing the uncertainty of its estimates, and can be used prospectively in study planning by quantifying the tradeoff between sampling effort and uncertainty. Understanding when two populations are composed of similar species is important for ecologists, epidemiologists, and population geneticists, and in principle it is easy: just sample the two populations, compare the sets of species identified in each, and count how many appear in both populations. In practice, however, this is difficult because sampling methods typically produce only a random subset of the total population, leaving current population overlap estimates biased. Knowing only the number of shared members between two of these partial population samples, this paper shows how we can nevertheless estimate the true overlap between the full populations, when those full populations’ sizes are known. Using Bayesian statistics, we can also compute credible intervals to produce error bars. We show that using this unbiased approach has a dramatic impact on the conclusions one might draw from previously published studies in the malaria literature, which used simple but biased methods. Because the method in this paper quantifies the tradeoff between sampling effort and uncertainty, we also show how to compute the number of samples required to ensure high-confidence results, which may be useful for planning future studies or budgeting lab reagents and time.
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13
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Rougeron V, Tiedje KE, Chen DS, Rask TS, Gamboa D, Maestre A, Musset L, Legrand E, Noya O, Yalcindag E, Renaud F, Prugnolle F, Day KP. Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance. Ecol Evol 2017; 7:9376-9390. [PMID: 29187975 PMCID: PMC5696401 DOI: 10.1002/ece3.3425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/07/2017] [Accepted: 08/19/2017] [Indexed: 11/11/2022] Open
Abstract
Strong founder effects resulting from human migration out of Africa have led to geographic variation in single nucleotide polymorphisms (SNPs) and microsatellites (MS) of the malaria parasite, Plasmodium falciparum. This is particularly striking in South America where two major founder populations of P. falciparum have been identified that are presumed to have arisen from the transatlantic slave trade. Given the importance of the major variant surface antigen of the blood stages of P. falciparum as both a virulence factor and target of immunity, we decided to investigate the population genetics of the genes encoding “Plasmodium falciparum Erythrocyte Membrane Protein 1” (PfEMP1) among several countries in South America, in order to evaluate the transmission patterns of malaria in this continent. Deep sequencing of the DBLα domain of var genes from 128 P. falciparum isolates from five locations in South America was completed using a 454 high throughput sequencing protocol. Striking geographic variation in var DBLα sequences, similar to that seen for SNPs and MS markers, was observed. Colombia and French Guiana had distinct var DBLα sequences, whereas Peru and Venezuela showed an admixture. The importance of such geographic variation to herd immunity and malaria vaccination is discussed.
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Affiliation(s)
- Virginie Rougeron
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Kathryn E Tiedje
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
| | - Donald S Chen
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA
| | - Thomas S Rask
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt and Departamento de Ciencias Celulares y Moleculares Facultad de Ciencias y Filosofia Universidad Peruana Cayetano Heredia Lima Peru
| | - Amanda Maestre
- Grupo Salud y Comunidad Facultad de Medicina Universidad de Antioquía Medellín Colombia
| | - Lise Musset
- Parasitology UnitInstitut Pasteur de Guyane Cayenne Cedex French Guiana
| | - Eric Legrand
- Parasitology UnitInstitut Pasteur de Guyane Cayenne Cedex French Guiana.,Unit of Genetics and Genomics on Insect Vectors Institut Pasteur Paris France
| | - Oscar Noya
- Centro para Estudios Sobre Malaria Instituto de Altos Estudios en Salud "Dr. Arnoldo Gabaldón" Ministerio del Poder Popular para la Salud and Instituto de Medicina Tropical Universidad Central de Venezuela Caracas Venezuela
| | - Erhan Yalcindag
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - François Renaud
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Franck Prugnolle
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Karen P Day
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
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14
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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] [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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15
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Carlos BC, Fotoran WL, Menezes MJ, Cabral FJ, Bastos MF, Costa FT, Sousa-Neto JA, Ribolla PE, Wunderlich G, Ferreira MU. Expressed var gene repertoire and variant surface antigen diversity in a shrinking Plasmodium falciparum population. Exp Parasitol 2016; 170:90-99. [DOI: 10.1016/j.exppara.2016.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 09/01/2016] [Accepted: 09/20/2016] [Indexed: 10/21/2022]
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16
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Newman MEJ, Clauset A. Structure and inference in annotated networks. Nat Commun 2016; 7:11863. [PMID: 27306566 PMCID: PMC4912639 DOI: 10.1038/ncomms11863] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/05/2016] [Indexed: 02/02/2023] Open
Abstract
For many networks of scientific interest we know both the connections of the network and information about the network nodes, such as the age or gender of individuals in a social network. Here we demonstrate how this 'metadata' can be used to improve our understanding of network structure. We focus in particular on the problem of community detection in networks and develop a mathematically principled approach that combines a network and its metadata to detect communities more accurately than can be done with either alone. Crucially, the method does not assume that the metadata are correlated with the communities we are trying to find. Instead, the method learns whether a correlation exists and correctly uses or ignores the metadata depending on whether they contain useful information. We demonstrate our method on synthetic networks with known structure and on real-world networks, large and small, drawn from social, biological and technological domains.
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Affiliation(s)
- M. E. J. Newman
- Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109, USA
- Center for the Study of Complex Systems, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA
| | - Aaron Clauset
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA
- Department of Computer Science, University of Colorado, 430 UCB, Boulder, Colorado 80309, USA
- BioFrontiers Institute, University of Colorado, 596 UCB, Boulder, Colorado 80309, USA
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17
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Serological Conservation of Parasite-Infected Erythrocytes Predicts Plasmodium falciparum Erythrocyte Membrane Protein 1 Gene Expression but Not Severity of Childhood Malaria. Infect Immun 2016; 84:1331-1335. [PMID: 26883585 PMCID: PMC4862716 DOI: 10.1128/iai.00772-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [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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18
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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. MOLECULAR BIOSYSTEMS 2015; 10:2466-79. [PMID: 24995459 DOI: 10.1039/c4mb00274a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [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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19
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Larremore DB, Sundararaman SA, Liu W, Proto WR, Clauset A, Loy DE, Speede S, Plenderleith LJ, Sharp PM, Hahn BH, Rayner JC, Buckee CO. Ape parasite origins of human malaria virulence genes. Nat Commun 2015; 6:8368. [PMID: 26456841 PMCID: PMC4633637 DOI: 10.1038/ncomms9368] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 08/14/2015] [Indexed: 12/22/2022] Open
Abstract
Antigens encoded by the var gene family are major virulence factors of the human malaria parasite Plasmodium falciparum, exhibiting enormous intra- and interstrain diversity. Here we use network analysis to show that var architecture and mosaicism are conserved at multiple levels across the Laverania subgenus, based on var-like sequences from eight single-species and three multi-species Plasmodium infections of wild-living or sanctuary African apes. Using select whole-genome amplification, we also find evidence of multi-domain var structure and synteny in Plasmodium gaboni, one of the ape Laverania species most distantly related to P. falciparum, as well as a new class of Duffy-binding-like domains. These findings indicate that the modular genetic architecture and sequence diversity underlying var-mediated host-parasite interactions evolved before the radiation of the Laverania subgenus, long before the emergence of P. falciparum. Antigens encoded by var genes are major virulence factors of the human malaria parasite Plasmodium falciparum. Here, Larremore et al. identify var-like genes in distantly related Plasmodium species infecting African apes, indicating that these genes already existed in an ancestral ape parasite many millions of years ago.
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Affiliation(s)
- Daniel B Larremore
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, Massachusetts 02115, USA.,Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Sesh A Sundararaman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - William R Proto
- Sanger Institute Malaria Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Aaron Clauset
- Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA.,Santa Fe Institute, Santa Fe, New Mexico 87501, USA.,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, USA
| | - Dorothy E Loy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Sheri Speede
- Sanaga-Yong Chimpanzee Rescue Center, IDA-Africa, Portland, Oregon 97204, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Julian C Rayner
- Sanger Institute Malaria Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, Massachusetts 02115, USA.,Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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20
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Tessema SK, Monk SL, Schultz MB, Tavul L, Reeder JC, Siba PM, Mueller I, Barry AE. Phylogeography of var gene repertoires reveals fine-scale geospatial clustering of Plasmodium falciparum populations in a highly endemic area. Mol Ecol 2015; 24:484-97. [PMID: 25482097 DOI: 10.1111/mec.13033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 11/14/2014] [Accepted: 11/17/2014] [Indexed: 11/28/2022]
Abstract
Plasmodium falciparum malaria is a major global health problem that is being targeted for progressive elimination. Knowledge of local disease transmission patterns in endemic countries is critical to these elimination efforts. To investigate fine-scale patterns of malaria transmission, we have compared repertoires of rapidly evolving var genes in a highly endemic area. A total of 3680 high-quality DBLα-sequences were obtained from 68 P. falciparum isolates from ten villages spread over two distinct catchment areas on the north coast of Papua New Guinea (PNG). Modelling of the extent of var gene diversity in the two parasite populations predicts more than twice as many var gene alleles circulating within each catchment (Mugil = 906; Wosera = 1094) than previously recognized in PNG (Amele = 369). In addition, there were limited levels of var gene sharing between populations, consistent with local parasite population structure. Phylogeographic analyses demonstrate that while neutrally evolving microsatellite markers identified population structure only at the catchment level, var gene repertoires reveal further fine-scale geospatial clustering of parasite isolates. The clustering of parasite isolates by village in Mugil, but not in Wosera was consistent with the physical and cultural isolation of the human populations in the two catchments. The study highlights the microheterogeneity of P. falciparum transmission in highly endemic areas and demonstrates the potential of var genes as markers of local patterns of parasite population structure.
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Affiliation(s)
- Sofonias K Tessema
- Division of Infection and Immunity, Walter and Eliza Hall Institute, 3052, Melbourne, Vic., Australia; Department of Medical Biology, University of Melbourne, 3052, Melbourne, Vic., Australia
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21
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Claessens A, Hamilton WL, Kekre M, Otto TD, Faizullabhoy A, Rayner JC, Kwiatkowski D. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis. PLoS Genet 2014; 10:e1004812. [PMID: 25521112 PMCID: PMC4270465 DOI: 10.1371/journal.pgen.1004812] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/08/2014] [Indexed: 11/25/2022] Open
Abstract
The most polymorphic gene family in P. falciparum is the ∼60 var genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1) that are critical for pathogenesis and immune evasion in Plasmodium falciparum. How var gene sequence diversity is generated is not currently completely understood. To address this, we constructed large clone trees and performed whole genome sequence analysis to study the generation of novel var gene sequences in asexually replicating parasites. While single nucleotide polymorphisms (SNPs) were scattered across the genome, structural variants (deletions, duplications, translocations) were focused in and around var genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving var exon 1 revealed that the average nucleotide sequence identity of two recombining exons was only 63% (range: 52.7–72.4%) yet the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved. Var exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes in vitro per life cycle. The high rate of var exon 1 recombination indicates that millions of new antigenic structures could potentially be generated each day in a single infected individual. We propose a model whereby var gene sequence polymorphism is mainly generated during the asexual part of the life cycle. Malaria kills >600,000 people each year, with most deaths caused by Plasmodium falciparum. A family of proteins known as P. falciparum erythrocyte membrane protein 1, PfEMP1, is expressed on the surface of infected erythrocytes and plays an important role in pathogenesis. Each P. falciparum genome contains approximately 60 highly polymorphic var genes encoding the PfEMP1 proteins, and monoallelic expression with periodic switching results in immune evasion. Var gene polymorphism is thus critical to this survival strategy. We investigated how var gene diversity is generated by performing an in vitro evolution experiment, tracking var gene mutation in ‘real-time’ with whole genome sequencing. We found that genome structural variation is focused in and around var genes. These genetic rearrangements created new ‘chimeric’ var gene sequences during the mitotic part of the life cycle, and were consistent with processes of mitotic non-allelic homologous recombination. The recombinant var genes were always in frame and with conserved overall var gene architecture, and the recombination rate implies that many millions of rearranged var gene sequences are produced every 48-hour life cycle within infected individuals. In conclusion, we provide a detailed description of how new var gene sequences are continuously generated in the parasite genome, helping to explain long-term parasite survival within infected human hosts.
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Affiliation(s)
- Antoine Claessens
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail:
| | | | - Mihir Kekre
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Thomas D. Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Adnan Faizullabhoy
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Julian C. Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Dominic Kwiatkowski
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
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22
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Albrecht L, Angeletti D, Moll K, Blomqvist K, Valentini D, D'Alexandri FL, Maurer M, Wahlgren M. B-cell epitopes in NTS-DBL1α of PfEMP1 recognized by human antibodies in Rosetting Plasmodium falciparum. PLoS One 2014; 9:e113248. [PMID: 25438249 PMCID: PMC4249881 DOI: 10.1371/journal.pone.0113248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/21/2014] [Indexed: 11/20/2022] Open
Abstract
Plasmodium falciparum is the most lethal of the human malaria parasites. The virulence is associated with the capacity of the infected red blood cell (iRBC) to sequester inside the deep microvasculature where it may cause obstruction of the blood-flow when binding is excessive. Rosetting, the adherence of the iRBC to uninfected erythrocytes, has been found associated with severe malaria and found to be mediated by the NTS-DBL1α-domain of Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1). Here we show that the reactivity of plasma of Cameroonian children with the surface of the FCR3S1.2-iRBC correlated with the capacity to disrupt rosettes and with the antibody reactivity with a recombinant PfEMP1 (NTS-DBL1α of IT4var60) expressed by parasite FCR3S1.2. The plasma-reactivity in a microarray, consisting of 96 overlapping 15-mer long peptides covering the NTS-DBL1α domain from IT4var60 sequence, was compared with their capacity to disrupt rosettes and we identified five peptides where the reactivity were correlated. Three of the peptides were localized in subdomain-1 and 2. The other two peptide-sequences were localized in the NTS-domain and in subdomain-3. Further, principal component analysis and orthogonal partial least square analysis generated a model that supported these findings. In conclusion, human antibody reactivity with short linear-peptides of NTS-DBL1α of PfEMP1 suggests subdomains 1 and 2 to hold anti-rosetting epitopes recognized by anti-rosetting antibodies. The data suggest rosetting to be mediated by the variable areas of PfEMP1 but also to involve structurally relatively conserved areas of the molecule that may induce biologically active antibodies.
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Affiliation(s)
- Letusa Albrecht
- Department of Microbiology, Tumor- and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- * E-mail: (MW); (LA)
| | - 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
| | - Karin Blomqvist
- Department of Microbiology, Tumor- and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Davide Valentini
- Therapeutic Immunology (TIM), Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- CAST, Karolinska University Hospital, Huddinge, Sweden
| | | | - Markus Maurer
- Therapeutic Immunology (TIM), Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- CAST, Karolinska University Hospital, Huddinge, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumor- and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- * E-mail: (MW); (LA)
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23
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Warimwe GM, Fegan G, Kiragu EW, Musyoki JN, Macharia AW, Marsh K, Williams TN, Bull PC. An assessment of the impact of host polymorphisms on Plasmodium falciparum var gene expression patterns among Kenyan children. BMC Infect Dis 2014; 14:524. [PMID: 25267261 PMCID: PMC4262213 DOI: 10.1186/1471-2334-14-524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 09/24/2014] [Indexed: 11/16/2022] Open
Abstract
Background Host genotype accounts for a component of the variability in susceptibility to childhood Plasmodium falciparum malaria. However, despite numerous examples of host polymorphisms associated with tolerance or resistance to infection, direct evidence for an impact of host genetic polymorphisms on the in vivo parasite population is difficult to obtain. Parasite molecules whose expression is most likely to be associated with such adaptation are those that are directly involved in the host-parasite interaction. A prime candidate is the family of parasite var gene-encoded molecules on P. falciparum-infected erythrocytes, PfEMP1, which binds various host molecules and facilitates parasite sequestration in host tissues to avoid clearance by the spleen. Methods To assess the impact of host genotype on the infecting parasite population we used a published parasite var gene sequence dataset to compare var gene expression patterns between parasites from children with polymorphisms in molecules thought to interact with or modulate display of PfEMP1 on the infected erythrocyte surface: ABO blood group, haemoglobin S, alpha-thalassaemia, the T188G polymorphism of CD36 and the K29M polymorphism of ICAM1. Results Expression levels of ‘group A-like’ var genes, which encode a specific group of PfEMP1 variants previously associated with low host immunity and severe malaria, showed signs of elevation among children of blood group AB. No other host factor tested showed evidence for an association with var expression. Conclusions Our preliminary findings suggest that host ABO blood group may have a measurable impact on the infecting parasite population. This needs to be verified in larger studies. Electronic supplementary material The online version of this article (doi:10.1186/1471-2334-14-524) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- George M Warimwe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.
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Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nat Commun 2014; 5:4754. [PMID: 25203297 PMCID: PMC4166903 DOI: 10.1038/ncomms5754] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 07/18/2014] [Indexed: 01/19/2023] Open
Abstract
Plasmodium falciparum causes most human malaria deaths, having prehistorically evolved from parasites of African Great Apes. Here we explore the genomic basis of P. falciparum adaptation to human hosts by fully sequencing the genome of the closely related chimpanzee parasite species P. reichenowi, and obtaining partial sequence data from a more distantly related chimpanzee parasite (P. gaboni). The close relationship between P. reichenowi and P. falciparum is emphasized by almost complete conservation of genomic synteny, but against this strikingly conserved background we observe major differences at loci involved in erythrocyte invasion. The organization of most virulence-associated multigene families, including the hypervariable var genes, is broadly conserved, but P. falciparum has a smaller subset of rif and stevor genes whose products are expressed on the infected erythrocyte surface. Genome-wide analysis identifies other loci under recent positive selection, but a limited number of changes at the host–parasite interface may have mediated host switching. Plasmodium falciparum, known to cause malaria in humans, evolved from parasites of African Great Apes. Here, the authors compare the genome of the human parasite, P. falciparum, with those of two related chimpanzee parasites, P. reichenowi and P. gaboni, and provide insight into the genetic basis of P. falciparum adaptation to human hosts.
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Fratus ASB, Cabral FJ, Fotoran WL, Medeiros MM, Carlos BC, Martha RD, da Silva LHP, Lopes SCP, Costa FTM, Wunderlich G. Antibody recognition of Plasmodium falciparum infected red blood cells by symptomatic and asymptomatic individuals in the Brazilian Amazon. Mem Inst Oswaldo Cruz 2014; 109:598-601. [PMID: 25099336 PMCID: PMC4156453 DOI: 10.1590/0074-0276140027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 05/12/2014] [Indexed: 12/31/2022] Open
Abstract
In the Amazon Region, there is a virtual absence of severe malaria and few fatal cases of naturally occurring Plasmodium falciparum infections; this presents an intriguing and underexplored area of research. In addition to the rapid access of infected persons to effective treatment, one cause of this phenomenon might be the recognition of cytoadherent variant proteins on the infected red blood cell (IRBC) surface, including the var gene encoded P. falciparum erythrocyte membrane protein 1. In order to establish a link between cytoadherence, IRBC surface antibody recognition and the presence or absence of malaria symptoms, we phenotype-selected four Amazonian P. falciparum isolates and the laboratory strain 3D7 for their cytoadherence to CD36 and ICAM1 expressed on CHO cells. We then mapped the dominantly expressed var transcripts and tested whether antibodies from symptomatic or asymptomatic infections showed a differential recognition of the IRBC surface. As controls, the 3D7 lineages expressing severe disease-associated phenotypes were used. We showed that there was no profound difference between the frequency and intensity of antibody recognition of the IRBC-exposed P. falciparum proteins in symptomatic vs. asymptomatic infections. The 3D7 lineages, which expressed severe malaria-associated phenotypes, were strongly recognised by most, but not all plasmas, meaning that the recognition of these phenotypes is frequent in asymptomatic carriers, but is not necessarily a prerequisite to staying free of symptoms.
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Affiliation(s)
| | - Fernanda Janku Cabral
- Departamento de Parasitologia, Instituto de Ciências Biomédicas,
Universidade de São Paulo, São Paulo, SP, Brasil
| | - Wesley Luzetti Fotoran
- Departamento de Parasitologia, Instituto de Ciências Biomédicas,
Universidade de São Paulo, São Paulo, SP, Brasil
| | - Márcia Melo Medeiros
- Departamento de Parasitologia, Instituto de Ciências Biomédicas,
Universidade de São Paulo, São Paulo, SP, Brasil
| | - Bianca Cechetto Carlos
- Departamento de Parasitologia, Instituto de Ciências Biomédicas,
Universidade de São Paulo, São Paulo, SP, Brasil
| | | | | | - Stefanie Costa Pinto Lopes
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia,
Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Fabio Trindade Maranhão Costa
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia,
Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Gerhard Wunderlich
- Departamento de Parasitologia, Instituto de Ciências Biomédicas,
Universidade de São Paulo, São Paulo, SP, Brasil
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Chan JA, Fowkes FJI, Beeson JG. Surface antigens of Plasmodium falciparum-infected erythrocytes as immune targets and malaria vaccine candidates. Cell Mol Life Sci 2014; 71:3633-57. [PMID: 24691798 PMCID: PMC4160571 DOI: 10.1007/s00018-014-1614-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/04/2014] [Accepted: 03/17/2014] [Indexed: 12/19/2022]
Abstract
Understanding the targets and mechanisms of human immunity to malaria caused by Plasmodium falciparum is crucial for advancing effective vaccines and developing tools for measuring immunity and exposure in populations. Acquired immunity to malaria predominantly targets the blood stage of infection when merozoites of Plasmodium spp. infect erythrocytes and replicate within them. During the intra-erythrocytic development of P. falciparum, numerous parasite-derived antigens are expressed on the surface of infected erythrocytes (IEs). These antigens enable P. falciparum-IEs to adhere in the vasculature and accumulate in multiple organs, which is a key process in the pathogenesis of disease. IE surface antigens, often referred to as variant surface antigens, are important targets of acquired protective immunity and include PfEMP1, RIFIN, STEVOR and SURFIN. These antigens are highly polymorphic and encoded by multigene families, which generate substantial antigenic diversity to mediate immune evasion. The most important immune target appears to be PfEMP1, which is a major ligand for vascular adhesion and sequestration of IEs. Studies are beginning to identify specific variants of PfEMP1 linked to disease pathogenesis that may be suitable for vaccine development, but overcoming antigenic diversity in PfEMP1 remains a major challenge. Much less is known about other surface antigens, or antigens on the surface of gametocyte-IEs, the effector mechanisms that mediate immunity, and how immunity is acquired and maintained over time; these are important topics for future research.
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Rorick MM, Rask TS, Baskerville EB, Day KP, Pascual M. Homology blocks of Plasmodium falciparum var genes and clinically distinct forms of severe malaria in a local population. BMC Microbiol 2013; 13:244. [PMID: 24192078 PMCID: PMC3827005 DOI: 10.1186/1471-2180-13-244] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/26/2013] [Indexed: 11/25/2022] Open
Abstract
Background The primary target of the human immune response to the malaria parasite Plasmodium falciparum, P. falciparum erythrocyte membrane protein 1 (PfEMP1), is encoded by the members of the hyper-diverse var gene family. The parasite exhibits antigenic variation via mutually exclusive expression (switching) of the ~60 var genes within its genome. It is thought that different variants exhibit different host endothelial binding preferences that in turn result in different manifestations of disease. Results Var sequences comprise ancient sequence fragments, termed homology blocks (HBs), that recombine at exceedingly high rates. We use HBs to define distinct var types within a local population. We then reanalyze a dataset that contains clinical and var expression data to investigate whether the HBs allow for a description of sequence diversity corresponding to biological function, such that it improves our ability to predict disease phenotype from parasite genetics. We find that even a generic set of HBs, which are defined for a small number of non-local parasites: capture the majority of local sequence diversity; improve our ability to predict disease severity from parasite genetics; and reveal a previously hypothesized yet previously unobserved parasite genetic basis for two forms of severe disease. We find that the expression rates of some HBs correlate more strongly with severe disease phenotypes than the expression rates of classic var DBLα tag types, and principal components of HB expression rate profiles further improve genotype-phenotype models. More specifically, within the large Kenyan dataset that is the focus of this study, we observe that HB expression differs significantly for severe versus mild disease, and for rosetting versus impaired consciousness associated severe disease. The analysis of a second much smaller dataset from Mali suggests that these HB-phenotype associations are consistent across geographically distant populations, since we find evidence suggesting that the same HB-phenotype associations characterize this population as well. Conclusions The distinction between rosetting versus impaired consciousness associated var genes has not been described previously, and it could have important implications for monitoring, intervention and diagnosis. Moreover, our results have the potential to illuminate the molecular mechanisms underlying the complex spectrum of severe disease phenotypes associated with malaria—an important objective given that only about 1% of P. falciparum infections result in severe disease.
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Affiliation(s)
- Mary M Rorick
- Department of Ecology and Evolutionary Biology, University of Michigan, 2019 Kraus Nat, Sci, Bldg,, 830 North University Ave, Ann Arbor 48109-1048, Michigan, USA.
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Larremore DB, Clauset A, Buckee CO. A network approach to analyzing highly recombinant malaria parasite genes. PLoS Comput Biol 2013; 9:e1003268. [PMID: 24130474 PMCID: PMC3794903 DOI: 10.1371/journal.pcbi.1003268] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/23/2013] [Indexed: 11/18/2022] Open
Abstract
The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences. The human malaria parasite kills nearly 1 million people each year globally. Frequent genetic exchange between malaria parasites creates enormous genetic diversity that largely explains the lack of an effective vaccine for the disease. Traditional phylogenetic tools cannot accommodate this type of diversity, however, and rigorous analytical tools capable of making sense of gene sequences that recombine frequently are still lacking. Here, we use network techniques that have been developed by the physics and network science communities to analyze malaria parasite gene sequences, allowing us to automatically identify highly variable mosaic regions in sequence data and to derive the network of recombination events. We apply our method to seven fully-sequenced parasite genomes, and show that our method provides new insights into the complex evolutionary patterns of the parasite. Our results suggest that the structure of these sequences allows the parasite to rapidly diversify to evade immune responses while maintaining antigen structure and function.
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Affiliation(s)
- Daniel B. Larremore
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
| | - Aaron Clauset
- Department of Computer Science, University of Colorado, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Caroline O. Buckee
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Warimwe GM, Recker M, Kiragu EW, Buckee CO, Wambua J, Musyoki JN, Marsh K, Bull PC. Plasmodium falciparum var gene expression homogeneity as a marker of the host-parasite relationship under different levels of naturally acquired immunity to malaria. PLoS One 2013; 8:e70467. [PMID: 23922996 PMCID: PMC3726600 DOI: 10.1371/journal.pone.0070467] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 06/19/2013] [Indexed: 11/19/2022] Open
Abstract
Acquired immunity to Plasmodium falciparum infection causes a change from frequent, sometimes life-threatening, malaria in young children to asymptomatic, chronic infections in older children and adults. Little is known about how this transition occurs but antibodies to the extremely diverse PfEMP1 parasite antigens are thought to play a role. PfEMP1 is encoded by a family of 60 var genes that undergo clonal antigenic variation, potentially creating an antigenically heterogeneous infecting population of parasites within the host. Previous theoretical work suggests that antibodies to PfEMP1 may play a role in "orchestrating" their expression within infections leading to sequential, homogeneous expression of var genes, and prolonged infection chronicity. Here, using a cloning and sequencing approach we compare the var expression homogeneity (VEH) between isolates from children with asymptomatic and clinical infections. We show that asymptomatic infections have higher VEH than clinical infections and a broader host antibody response. We discuss this in relation to the potential role of host antibodies in promoting chronicity of infection and parasite survival through the low transmission season.
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Affiliation(s)
- George M. Warimwe
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Mario Recker
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Esther W. Kiragu
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Caroline O. Buckee
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Juliana Wambua
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Jennifer N. Musyoki
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kevin Marsh
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter C. Bull
- Pathogen, Vector and Human Biology Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Sulistyaningsih E, Fitri LE, Löscher T, Berens-Riha N. Diversity of the var gene family of Indonesian Plasmodium falciparum isolates. Malar J 2013; 12:80. [PMID: 23446319 PMCID: PMC3614516 DOI: 10.1186/1475-2875-12-80] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 02/19/2013] [Indexed: 11/30/2022] Open
Abstract
Background The large polymorphic protein PfEMP1 is encoded by the var gene family. PfEMP1 has been shown to play an important role as cytoadherence ligand on the surface of infected erythrocytes and thereby contributes to the distinct pathogenesis of malaria. The study explored the diversity of the DBL1α and DBL2β-C2 domains of the protein from Indonesian Plasmodium falciparum field isolates. Methods Samples of patients with severe and uncomplicated malaria from two different malaria-endemic areas in Indonesia were collected and DNA directly extracted. Dried blood on filter paper was prepared for RNA extraction. PCR amplicons were either cloned and subsequently sequenced or directly sequenced for analysis on nucleotide and amino acid level. Recently published as well as self-designed primers were used for amplification. Results Blood from eight patients was finally used for analysis. Seventy-one different sequences out of over 500 DBL1α sequenced clones were observed, resulting in an average of 8.9 different DBL1α sequences per isolate. The average DBL1α sequence similarity within isolates was similar to between isolates. Phylogenetic analysis demonstrated no clustering of sequences regarding strain or geographical origin. The DBL1α sequences were analysed by distribution of semi-conserved features (cysteine/PoLV1-4 grouping) and classified into six sequence groups. The DBL1α cys2 type was observed in all expressed sequences in vivo. Expression of certain DBL sequences implied potential involvement in the pathogenesis. As expected, the DBL2β-C2 domains showed high to moderate homology among each other. Conclusion The DBL1α domains of PfEMP1 from clinical Indonesian isolates showed high divergence among same isolates and some similarities with other Asia-Pacific strains. Further investigations of important var gene domains with a larger sample size are required to confirm with statistical significance observed associations with severe malaria in Indonesian samples.
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Affiliation(s)
- Erma Sulistyaningsih
- Department of Tropical Medicine and Infectious Diseases, University of Munich, Munich 80802, Germany.
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Blomqvist K, Albrecht L, Quintana MDP, Angeletti D, Joannin N, Chêne A, Moll K, Wahlgren M. A sequence in subdomain 2 of DBL1α of Plasmodium falciparum erythrocyte membrane protein 1 induces strain transcending antibodies. PLoS One 2013; 8:e52679. [PMID: 23335956 PMCID: PMC3546040 DOI: 10.1371/journal.pone.0052679] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Accepted: 11/19/2012] [Indexed: 11/18/2022] Open
Abstract
Immunity to severe malaria is the first level of immunity acquired to Plasmodium falciparum. Antibodies to the variant antigen PfEMP1 (P. falciparum erythrocyte membrane protein 1) present at the surface of the parasitized red blood cell (pRBC) confer protection by blocking microvascular sequestration. Here we have generated antibodies to peptide sequences of subdomain 2 of PfEMP1-DBL1α previously identified to be associated with severe or mild malaria. A set of sera generated to the amino acid sequence KLQTLTLHQVREYWWALNRKEVWKA, containing the motif ALNRKE, stained the live pRBC. 50% of parasites tested (7/14) were positive both in flow cytometry and immunofluorescence assays with live pRBCs including both laboratory strains and in vitro adapted clinical isolates. Antibodies that reacted selectively with the sequence REYWWALNRKEVWKA in a 15-mer peptide array of DBL1α-domains were also found to react with the pRBC surface. By utilizing a peptide array to map the binding properties of the elicited anti-DBL1α antibodies, the amino acids WxxNRx were found essential for antibody binding. Complementary experiments using 135 degenerate RDSM peptide sequences obtained from 93 Ugandan patient-isolates showed that antibody binding occurred when the amino acids WxLNRKE/D were present in the peptide. The data suggests that the ALNRKE sequence motif, associated with severe malaria, induces strain-transcending antibodies that react with the pRBC surface.
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Affiliation(s)
- Karin Blomqvist
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Letusa Albrecht
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - 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
| | - Nicolas Joannin
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Arnaud Chêne
- Biologie des interactions Hôte-Parasite, Institut Pasteur, Paris, France
| | - Kirsten Moll
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Artzy-Randrup Y, Rorick MM, Day K, Chen D, Dobson AP, Pascual M. Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum. eLife 2012; 1:e00093. [PMID: 23251784 PMCID: PMC3524794 DOI: 10.7554/elife.00093] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/04/2012] [Indexed: 11/21/2022] Open
Abstract
The coexistence of multiple independently circulating strains in pathogen populations that undergo sexual recombination is a central question of epidemiology with profound implications for control. An agent-based model is developed that extends earlier ‘strain theory’ by addressing the var gene family of Plasmodium falciparum. The model explicitly considers the extensive diversity of multi-copy genes that undergo antigenic variation via sequential, mutually exclusive expression. It tracks the dynamics of all unique var repertoires in a population of hosts, and shows that even under high levels of sexual recombination, strain competition mediated through cross-immunity structures the parasite population into a subset of coexisting dominant repertoires of var genes whose degree of antigenic overlap depends on transmission intensity. Empirical comparison of patterns of genetic variation at antigenic and neutral sites supports this role for immune selection in structuring parasite diversity. DOI:http://dx.doi.org/10.7554/eLife.00093.001 Malaria is an infectious disease that is estimated to kill more than half a million people every year, mostly young children in Africa. It is spread by mosquitos that are infected with Plasmodium parasites that attack red blood cells in the human body. Plasmodium falciparum, the species that is responsible for most of these deaths, causes malaria by entering red blood cells and releasing antigens that travel to the surface of the cells, where they change the adhesion properties. This causes the infected red blood cells to accumulate in small blood vessels, surface capillaries or the brain, which can have severe consequences for the person infected. P. falciparum is particularly dangerous because of its ability to vary the antigens displayed on the cell surface: this process, known as antigenic variation, helps to maintain infections for extended periods of time by allowing the antigens to stay one step ahead of the immune system (a process known as immune escape). The origins of antigenic variation lie in the fact that each P. falciparum genome has a repertoire of between 50 and 60 var genes that code for the variability of a major antigen that is responsible for immune escape in malaria. Molecular sequencing has shown that local parasite populations contain thousands of different types of var genes: hence, meiotic recombination in the mosquito can create a vast number of combinations of var repertoires. Artzy-Randrup et al. have developed a computational model of this highly diverse and complex system to address the following question: is a local pathogen population composed of largely random and ephemeral repertoires of these genes, or is it structured into independently circulating strains? Their model goes beyond previous models by including interactions within the local host population that arise as a result of indirect competition between different strains of the pathogen for available hosts: this competition is influenced by the history of infection and, therefore, by the patterns of immunity within the host population. Previous models included within-host processes but not these higher, local population-level interactions. The model simulates the dynamics of all the unique combinations of var genes in a population of hosts, and shows that even with high rates of reproduction, the parasite population self-organizes into a limited number of coexisting strains: the distinct var repertoires of these strains only weakly overlap, suggesting that the immune response of the host population has been partitioned into distinct niches. By investigating genetic variation at both antigenic sites and regions of the genome that do not code for antigens, Artzy-Randrup et al. suggest that immune selection—the selection imposed on var repertoires by the build up of specific immunity at the population level—plays a central role in structuring parasite diversity. The new model should lead to a better understanding of the epidemiology of Plasmodium and other pathogens that work in similar ways, including Trypanosoma brucei (sleeping sickness), Borellia burgdorferi (Lyme disease) and Giardia lamblia (gastroenteritis), and help with global efforts to eliminate malaria and other diseases. DOI:http://dx.doi.org/10.7554/eLife.00093.002
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Affiliation(s)
- Yael Artzy-Randrup
- Department of Ecology and Evolutionary Biology , Howard Hughes Medical Institute and the University of Michigan , Ann Arbor , United States
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Plasmodium falciparum erythrocyte membrane protein 1 domain cassettes 8 and 13 are associated with severe malaria in children. Proc Natl Acad Sci U S A 2012; 109:E1791-800. [PMID: 22619319 DOI: 10.1073/pnas.1120455109] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The clinical outcome of Plasmodium falciparum infections ranges from asymptomatic parasitemia to severe malaria syndromes associated with high mortality. The virulence of P. falciparum infections is associated with the type of P. falciparum erythrocyte membrane protein 1 (PfEMP1) expressed on the surface of infected erythrocytes to anchor these to the vascular lining. Although var2csa, the var gene encoding the PfEMP1 associated with placental malaria, was discovered in 2003, the identification of the var/PfEMP1 variants associated with severe malaria in children has remained elusive. To identify var/PfEMP1 variants associated with severe disease outcome, we compared var transcript levels in parasites from 88 children with severe malaria and 40 children admitted to the hospital with uncomplicated malaria. Transcript analysis was performed by RT-quantitative PCR using a set of 42 primer pairs amplifying var subtype-specific loci covering most var/PfEMP1 subtypes. In addition, we characterized the near-full-length sequence of the most prominently expressed var genes in three patients diagnosed with severe anemia and/or cerebral malaria. The combined analysis showed that severe malaria syndromes, including severe anemia and cerebral malaria, are associated with high transcript levels of PfEMP1 domain cassette 8-encoding var genes. Transcript levels of group A var genes, including genes encoding domain cassette 13, were also significantly higher in patients with severe syndromes compared with those with uncomplicated malaria. This study specifies the var/PfEMP1 types expressed in severe malaria in children, and thereby provides unique targets for future efforts to prevent and treat severe malaria infections.
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Buckee CO, Recker M. Evolution of the multi-domain structures of virulence genes in the human malaria parasite, Plasmodium falciparum. PLoS Comput Biol 2012; 8:e1002451. [PMID: 22511852 PMCID: PMC3325180 DOI: 10.1371/journal.pcbi.1002451] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 02/10/2012] [Indexed: 11/30/2022] Open
Abstract
The var gene family of Plasmodium falciparum encodes the immunodominant variant surface antigens PfEMP1. These highly polymorphic proteins are important virulence factors that mediate cytoadhesion to a variety of host tissues, causing sequestration of parasitized red blood cells in vital organs, including the brain or placenta. Acquisition of variant-specific antibodies correlates with protection against severe malarial infections; however, understanding the relationship between gene expression and infection outcome is complicated by the modular genetic architectures of var genes that encode varying numbers of antigenic domains with differential binding specificities. By analyzing the domain architectures of fully sequenced var gene repertoires we reveal a significant, non-random association between the number of domains comprising a var gene and their sequence conservation. As such, var genes can be grouped into those that are short and diverse and genes that are long and conserved, suggesting gene length as an important characteristic in the classification of var genes. We then use an evolutionary framework to demonstrate how the same evolutionary forces acting on the level of an individual gene may have also shaped the parasite's gene repertoire. The observed associations between sequence conservation, gene architecture and repertoire structure can thus be explained by a trade-off between optimizing within-host fitness and minimizing between-host immune selection pressure. Our results demonstrate how simple evolutionary mechanisms can explain var gene structuring on multiple levels and have important implications for understanding the multifaceted epidemiology of P. falciparum malaria. Plasmodium falciparum, the most severe of the human malarias, contains within its genome a family of ∼60 var genes which play an important role in disease pathology and maintenance of chronic infections. Var genes have a modular genetic architecture and encode varying numbers of binding domains with specific preferences to a range of host tissues. Given the availability of host receptors for binding and the immunogenic properties of each domain it is not clear why genes encode multiple domains at once and how these are structured within each parasite's antigenic repertoire. Here we investigate the domain architecture of these important virulence genes and highlight an evolutionary trade-off between maintaining within-host fitness and optimizing between-host transmission success as an important driver in structuring var genes and var gene repertoires alike.
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Affiliation(s)
- Caroline O. Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Mario Recker
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Jiang N, Meng L, Lu HJ, Kang W, Peng S, Pan WQ, Yin JG, Chen QJ. Analysis of var genes cloned from a Plasmodium falciparum isolate in China. ASIAN PAC J TROP MED 2012; 5:85-90. [PMID: 22221747 DOI: 10.1016/s1995-7645(12)60001-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 12/15/2011] [Accepted: 01/15/2012] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To analyse the var gene repertoire and characterise the chondroitin sulphate A (CSA)-binding activity of the Duffy-binding like (DBL) domains encoded by the var2csa gene of a Plasmodium falciparum (P. falciparum) isolate in Hainan Province, China. METHODS The sequences of var DBL1 regions were PCR-amplified, sequenced and the sequence characteristics was bioinformatically analysed. Recombinant proteins encoded by the var2csa genes were expressed and purified. The binding activities of the recombinant proteins to CSA receptor was detected by ELISA assays. RESULTS Fifty six unique DBL α sequences were obtained, and the sequences represented similar diversity to the var genes of the genome parasite 3D7. There are two var2csa genes in the P. falciparum isolated from Hainan Province. Unlike in other falciparum parasites such as HB3, the two var2csa genes are more diverged. The receptor-binding capacity of DBL-5ε and DBL-6ε domains of HN var2CSA was studied. CONCLUSIONS This work represented the diversity of var genes of a P. falciparum isolate in China.
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Affiliation(s)
- Ning Jiang
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
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Barry AE, Trieu A, Fowkes FJI, Pablo J, Kalantari-Dehaghi M, Jasinskas A, Tan X, Kayala MA, Tavul L, Siba PM, Day KP, Baldi P, Felgner PL, Doolan DL. The stability and complexity of antibody responses to the major surface antigen of Plasmodium falciparum are associated with age in a malaria endemic area. Mol Cell Proteomics 2011; 10:M111.008326. [PMID: 21825279 PMCID: PMC3226400 DOI: 10.1074/mcp.m111.008326] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Individuals that are exposed to malaria eventually develop immunity to the disease with one possible mechanism being the gradual acquisition of antibodies to the range of parasite variant surface antigens in their local area. Major antibody targets include the large and highly polymorphic Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family of proteins. Here, we use a protein microarray containing 123 recombinant PfEMP1-DBLα domains (VAR) from Papua New Guinea to seroprofile 38 nonimmune children (<4 years) and 29 hyperimmune adults (≥15 years) from the same local area. The overall magnitude, prevalence and breadth of antibody response to VAR was limited at <2 years and 2–2.9 years, peaked at 3–4 years and decreased for adults compared with the oldest children. An increasing proportion of individuals recognized large numbers of VAR proteins (>20) with age, consistent with the breadth of response stabilizing with age. In addition, the antibody response was limited in uninfected children compared with infected children but was similar in adults irrespective of infection status. Analysis of the variant-specific response confirmed that the antibody signature expands with age and infection. This also revealed that the antibody signatures of the youngest children overlapped substantially, suggesting that they are exposed to the same subset of PfEMP1 variants. VAR proteins were either seroprevalent from early in life, (<3 years), from later in childhood (≥3 years) or rarely recognized. Group 2 VAR proteins (Cys2/MFK-REY+) were serodominant in infants (<1-year-old) and all other sequence subgroups became more seroprevalent with age. The results confirm that the anti-PfEMP1-DBLα antibody responses increase in magnitude and prevalence with age and further demonstrate that they increase in stability and complexity. The protein microarray approach provides a unique platform to rapidly profile variant-specific antibodies to malaria and suggests novel insights into the acquisition of immunity to malaria.
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Affiliation(s)
- Alyssa E Barry
- Centre for Population Health, Burnet Institute, Melbourne, Victoria 3004, Australia.
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Zhang Q, Zhang Y, Huang Y, Xue X, Yan H, Sun X, Wang J, McCutchan TF, Pan W. From in vivo to in vitro: dynamic analysis of Plasmodium falciparum var gene expression patterns of patient isolates during adaptation to culture. PLoS One 2011; 6:e20591. [PMID: 21674009 PMCID: PMC3108956 DOI: 10.1371/journal.pone.0020591] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Accepted: 05/04/2011] [Indexed: 11/18/2022] Open
Abstract
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), encoded by the var gene family, plays a crucial role in disease virulence through its involvement in binding to various host cellular receptors during infection. Growing evidence suggests that differential expression of the various var subgroups may be involved in parasite virulence. To further explore this issue, we have collected isolates from symptomatic patients in south China-Myanmar border, and characterized their sequence diversity and transcription profiles over time of var gene family, and cytoadherence properties from the time of their initial collection and extending through a two month period of adaptation to culture. Initially, we established a highly diverse, DBLα (4 cysteines) subtype-enriched, but unique local repertoire of var-DBL1α sequences by cDNA cloning and sequencing. Next we observed a rapid transcriptional decline of upsA- and upsB-subtype var genes at ring stage through qRT-PCR assays, and a switching event from initial ICAM-I binding to the CD36-binding activity during the first week of adaptive cultivation in vitro. Moreover, predominant transcription of upsA var genes was observed to be correlated with those isolates that showed a higher parasitemia at the time of collection and the ICAM-1-binding phenotype in culture. Taken together, these data indicate that the initial stage of adaptive process in vitro significantly influences the transcription of virulence-related var subtypes and expression of PfEMP1 variants. Further, the specific upregulation of the upsA var genes is likely linked to the rapid propagation of the parasite during natural infection due to the A-type PfEMP1 variant-mediated growth advantages.
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Affiliation(s)
- Qingfeng Zhang
- Institute of Infectious Disease and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Yilong Zhang
- Institute of Infectious Disease and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Yufu Huang
- Department of Pathogen Biology, Second Military Medical University, Shanghai, China
| | - Xiangyang Xue
- Institute of Infectious Disease and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - He Yan
- Institute of Infectious Disease and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Xiaodong Sun
- Yunnan Institute of Parasitic Diseases, Puer, China
| | - Jian Wang
- Yunnan Institute of Parasitic Diseases, Puer, China
| | - Thomas F. McCutchan
- Department of Pathogen Biology, Second Military Medical University, Shanghai, China
| | - Weiqing Pan
- Institute of Infectious Disease and Vaccine Development, Tongji University School of Medicine, Shanghai, China
- Department of Pathogen Biology, Second Military Medical University, Shanghai, China
- * E-mail:
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Modelling malaria population structure and its implications for control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 673:112-26. [PMID: 20632533 DOI: 10.1007/978-1-4419-6064-1_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Mathematical models of malaria transmission have been used to inform the design of malaria control programs since the mid 20th century, and many of these models have provided useful insights into the complexity of the disease. Among developing countries, however and particularly in sub-Saharan Africa, malaria remains a major cause of morbidity and mortality. One of the main difficulties in controlling the most virulent human malaria parasite, Plasmodium falciparum, is its genetic diversity, which confounds attempts to design an effective vaccine. The population structure of P. falciparum remains poorly understood but plays a key role in determining epidemiological patterns of disease and the development of immunity. We discuss the seminal model of malaria transmission developed by Ross and MacDonald, and the modifications that have been made since to include more realism. We show that age profiles of disease and serological data support a theoretical model in which the parasite population is diverse and structured into several antigenic types and highlight the implications of this structure for controlling malaria. Lastly, we discuss the current sequence data on parasite antigen genes that are important for the aquisition of immunity, and the results of a new analysis of P. falciparum population structure at the genomic level.
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Tembo D, Montgomery J. Var gene expression and human Plasmodium pathogenesis. Future Microbiol 2010; 5:801-15. [PMID: 20441551 DOI: 10.2217/fmb.10.33] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Plasmodium falciparum is responsible for most of the morbidity and mortality associated with malaria and is unique in its ability to sequester in organ postcapillary venules. Specific host-parasite interactions mediate this phenomenon and the P. falciparum erythrocyte membrane protein 1 is the predominant ligand responsible for adhering to host endothelial receptors. This review focuses on the current knowledge regarding this protein family, evidence for its role in various pathogenic mechanisms and on insights that have been gained in this area from field studies.
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Affiliation(s)
- Dumizulu Tembo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre 3, Malawi
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Badaut C, Bertin G, Rustico T, Fievet N, Massougbodji A, Gaye A, Deloron P. Towards the rational design of a candidate vaccine against pregnancy associated malaria: conserved sequences of the DBL6epsilon domain of VAR2CSA. PLoS One 2010; 5:e11276. [PMID: 20585655 PMCID: PMC2890577 DOI: 10.1371/journal.pone.0011276] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 05/30/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Placental malaria is a disease linked to the sequestration of Plasmodium falciparum infected red blood cells (IRBC) in the placenta, leading to reduced materno-fetal exchanges and to local inflammation. One of the virulence factors of P. falciparum involved in cytoadherence to chondroitin sulfate A, its placental receptor, is the adhesive protein VAR2CSA. Its localisation on the surface of IRBC makes it accessible to the immune system. VAR2CSA contains six DBL domains. The DBL6epsilon domain is the most variable. High variability constitutes a means for the parasite to evade the host immune response. The DBL6epsilon domain could constitute a very attractive basis for a vaccine candidate but its reported variability necessitates, for antigenic characterisations, identifying and classifying commonalities across isolates. METHODOLOGY/PRINCIPAL FINDINGS Local alignment analysis of the DBL6epsilon domain had revealed that it is not as variable as previously described. Variability is concentrated in seven regions present on the surface of the DBL6epsilon domain. The main goal of our work is to classify and group variable sequences that will simplify further research to determine dominant epitopes. Firstly, variable sequences were grouped following their average percent pairwise identity (APPI). Groups comprising many variable sequences sharing low variability were found. Secondly, ELISA experiments following the IgG recognition of a recombinant DBL6epsilon domain, and of peptides mimicking its seven variable blocks, allowed to determine an APPI cut-off and to isolate groups represented by a single consensus sequence. CONCLUSIONS/SIGNIFICANCE A new sequence approach is used to compare variable regions in sequences that have extensive segmental gene relationship. Using this approach, the VAR2CSA DBL6 domain is composed of 7 variable blocks with limited polymorphism. Each variable block is composed of a limited number of consensus types. Based on peptide based ELISA, variable blocks with 85% or greater sequence identity are expected to be recognized equally well by antibody and can be considered the same consensus type. Therefore, the analysis of the antibody response against the classified small number of sequences should be helpful to determine epitopes.
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Affiliation(s)
- Cyril Badaut
- Mother and Child Faced with Tropical Infections Research Unit, Institut de Recherche pour le Développement, UMR216, Paris, France
- Université Paris Descartes, Paris, France
- * E-mail: (CB); (PD)
| | - Gwladys Bertin
- Mother and Child Faced with Tropical Infections Research Unit, Institut de Recherche pour le Développement, UMR216, Paris, France
- Université Paris Descartes, Paris, France
| | - Tatiana Rustico
- Mother and Child Faced with Tropical Infections Research Unit, Institut de Recherche pour le Développement, UMR216, Paris, France
| | - Nadine Fievet
- Mother and Child Faced with Tropical Infections Research Unit, Institut de Recherche pour le Développement, UMR216, Paris, France
| | - Achille Massougbodji
- Département de Zoologie et Génétique, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Alioune Gaye
- Centre de Santé Roi Baudoin de Guédiawaye, Dakar, Senegal
| | - Philippe Deloron
- Mother and Child Faced with Tropical Infections Research Unit, Institut de Recherche pour le Développement, UMR216, Paris, France
- Université Paris Descartes, Paris, France
- * E-mail: (CB); (PD)
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Albrecht L, Castiñeiras C, Carvalho BO, Ladeia-Andrade S, Santos da Silva N, Hoffmann EHE, dalla Martha RC, Costa FTM, Wunderlich G. The South American Plasmodium falciparum var gene repertoire is limited, highly shared and possibly lacks several antigenic types. Gene 2010; 453:37-44. [PMID: 20079817 DOI: 10.1016/j.gene.2010.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 01/05/2010] [Accepted: 01/06/2010] [Indexed: 11/16/2022]
Abstract
The Plasmodium falciparum var gene family encodes large variant antigens, which are important virulence factors, and also targets of the humoral host response. The frequently observed mild outcomes of falciparum malaria in many places of the Amazon area prompted us to ask whether a globally restricted variant (var) gene repertoire is present in currently circulating and older isolates of this area. By exhaustive analysis of var gene tags from 89 isolates and clones taken during many years from all over the Brazilian Amazon, we estimate that there are probably no more than 350-430 distinct sequence types, less than for any similar sized area studied so far. Detailed analysis of the var tags from genetically distinct clones obtained from single isolates revealed restricted and redundant repertoires suggesting either a low incidence of infective bites or restricted variant gene diversity in inoculated parasites. Additionally, we found a structuring of var gene repertoires observed as a higher pairwise typing sharing in isolates from the same microregion compared to isolates from different regions. Fine analysis of translated var tags revealed that certain Distinct Sequence Identifiers (DSIDs) were differently represented in Brazilian/South American isolates when compared to datasets from other continents. By global alignment of worldwide var DBLalpha sequences and sorting in groups with more than 76% identity, 125 clusters were formed and more than half of all genes were found in nine clusters with 50 or more sequences. While Brazilian/South American sequences were represented only in 64 groups, African sequences were found in the majority of clusters. DSID type 1 related sequences accumulated almost completely in one single cluster, indicating that limited recombination occurs in these specific var gene types. These data demonstrate the so far highest pairwise type sharing values for the var gene family in isolates from all over an entire subcontinent. The apparent lack of specific sequences types suggests that the P. falciparum transmission dynamics in the whole Amazon are probably different from any other endemic region studied and possibly interfere with the parasite's ability to efficiently diversify its variant gene repertoires.
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Affiliation(s)
- Letusa Albrecht
- Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, Brazil
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Plasmodium falciparum var gene expression is modified by host immunity. Proc Natl Acad Sci U S A 2009; 106:21801-6. [PMID: 20018734 DOI: 10.1073/pnas.0907590106] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a potentially important family of immune targets, which play a central role in the host-parasite interaction by binding to various host molecules. They are encoded by a diverse family of genes called var, of which there are approximately 60 copies in each parasite genome. In sub-Saharan Africa, although P. falciparum infection occurs throughout life, severe malarial disease tends to occur only in childhood. This could potentially be explained if (i) PfEMP1 variants differ in their capacity to support pathogenesis of severe malaria and (ii) this capacity is linked to the likelihood of each molecule being recognized and cleared by naturally acquired antibodies. Here, in a study of 217 Kenyan children with malaria, we show that expression of a group of var genes "cys2," containing a distinct pattern of cysteine residues, is associated with low host immunity. Expression of cys2 genes was associated with parasites from young children, those with severe malaria, and those with a poorly developed antibody response to parasite-infected erythrocyte surface antigens. Cys-2 var genes form a minor component of all genomic var repertoires analyzed to date. Therefore, the results are compatible with the hypothesis that the genomic var gene repertoire is organized such that PfEMP1 molecules that confer the most virulence to the parasite tend also to be those that are most susceptible to the development of host immunity. This may help the parasite to adapt effectively to the development of host antibodies through modification of the host-parasite relationship.
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Horata N, Kalambaheti T, Craig A, Khusmith S. Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria. Malar J 2009; 8:184. [PMID: 19650937 PMCID: PMC3224928 DOI: 10.1186/1475-2875-8-184] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 08/04/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rosetting and cytoadherence of Plasmodium falciparum-infected red blood cells have been associated with severity of malaria. ICAM-1 and CD36 are the main host cell receptors, while PfEMP1-DBLalpha is a major parasite ligand, which can contribute to rosette formation. This study is aimed at demonstrating whether the highly polymorphic PfEMP1-DBLalpha sequences occurring among Thai isolates causing severe and uncomplicated malaria are associated with their ability to form rosettes and reflected the clinical outcome of the patients. METHODS Two hundred and ninety five PfEMP1-DBLalpha sequences from Thai clinical isolates causing severe and uncomplicated malaria were evaluated by sequencing and direct comparison using the specific text string analysis functions in Microsoft Excel and Perl. The relationships between the PfEMP1-DBLalpha sequences were also analysed by network analysis. The binding abilities of parasitized red blood cells (PRBCs) to CD36, wild type ICAM-1, ICAM-1Kilifi and ICAM-1S22/A under static condition were included. RESULTS Two hundred and eighty one non-identical amino acid sequences were identified (< 95% sequence identity). When the distributions of semi-conserved features (PoLV1-4 and sequence group) within the rosetting domain PfEMP1-DBLalpha were observed, close similarity was found between isolates from the two disease groups. The sequence group 1 representing uncomplicated malaria was significantly different from the sequence group 3 representing the majority of severe malaria (p = 0.027). By using a simple non-phylogenetic approach to visualize the sharing of polymorphic blocks (position specific polymorphic block, PSPB) and cys/PoLV among DBLalpha sequences, the sequence group 1 was split from the other five sequence groups. The isolates belonging to sequence group 5 gave the highest mean rosetting rate (21.31%). However, within sequence group 2 and group 6, the isolates causing severe malaria had significantly higher rosetting rate than those causing uncomplicated malaria (p = 0.014, p = 0.007, respectively). CONCLUSION This is the first report of PfEMP1-DBLalpha analysis in clinical Thai isolates using semi-conserved features (cys/PoLV and PSPBs). The cys/PoLV group 5 gave the highest rosetting rate. PfEMP1-DBLalpha domains in Thai isolates are highly diverse, however, clinical isolates from severe and uncomplicated malaria shared common sequences.
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Affiliation(s)
- Natharinee Horata
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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An in vivo and in vitro model of Plasmodium falciparum rosetting and autoagglutination mediated by varO, a group A var gene encoding a frequent serotype. Infect Immun 2008; 76:5565-80. [PMID: 18809668 DOI: 10.1128/iai.00901-08] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the Saimiri sciureus monkey, erythrocytes infected with the varO antigenic variant of the Plasmodium falciparum Palo Alto 89F5 clone bind uninfected red blood cells (rosetting), form autoagglutinates, and have a high multiplication rate, three phenotypic characteristics that are associated with severe malaria in human patients. We report here that varO parasites express a var gene having the characteristics of group A var genes, and we show that the varO Duffy binding-like 1alpha(1) (DBL1alpha(1)) domain is implicated in the rosetting of both S. sciureus and human erythrocytes. The soluble varO N-terminal sequence (NTS)-DBL1alpha(1) recombinant domain, produced in a baculovirus-insect cell system, induced high titers of antibodies that reacted with varO-infected red blood cells and disrupted varO rosettes. varO parasites were culture adapted in vitro using human erythrocytes. They formed rosettes and autoagglutinates, and they had the same surface serotype and expressed the same varO gene as the monkey-propagated parasites. To develop an in vitro model with highly homogeneous varO parasites, rosette purification was combined with positive selection by panning with a varO NTS-DBL1alpha(1)-specific mouse monoclonal antibody. The single-variant, clonal parasites were used to analyze seroprevalence for varO at the village level in a setting where malaria is holoendemic (Dielmo, Senegal). We found 93.6% (95% confidence interval, 89.7 to 96.4%) seroprevalence for varO surface-reacting antibodies and 86.7% (95% confidence interval, 82.8 to 91.6%) seroprevalence for the recombinant NTS-DBL1alpha(1) domain, and virtually all permanent residents had seroconverted by the age of 5 years. These data imply that the varO model is a relevant in vivo and in vitro model for rosetting and autoagglutination that can be used for rational development of vaccine candidates and therapeutic strategies aimed at preventing malaria pathology.
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Bull PC, Buckee CO, Kyes S, Kortok MM, Thathy V, Guyah B, Stoute JA, Newbold CI, Marsh K. Plasmodium falciparum antigenic variation. Mapping mosaic var gene sequences onto a network of shared, highly polymorphic sequence blocks. Mol Microbiol 2008; 68:1519-34. [PMID: 18433451 PMCID: PMC2440560 DOI: 10.1111/j.1365-2958.2008.06248.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a potentially important family of immune targets, encoded by an extremely diverse gene family called var. Understanding of the genetic organization of var genes is hampered by sequence mosaicism that results from a long history of non-homologous recombination. Here we have used software designed to analyse social networks to visualize the relationships between large collections of short var sequences tags sampled from clinical parasite isolates. In this approach, two sequences are connected if they share one or more highly polymorphic sequence blocks. The results show that the majority of analysed sequences including several var-like sequences from the chimpanzee parasite Plasmodium reichenowi can be either directly or indirectly linked together in a single unbroken network. However, the network is highly structured and contains putative subgroups of recombining sequences. The major subgroup contains the previously described group A var genes, previously proposed to be genetically distinct. Another subgroup contains sequences found to be associated with rosetting, a parasite virulence phenotype. The mosaic structure of the sequences and their division into subgroups may reflect the conflicting problems of maximizing antigenic diversity and minimizing epitope sharing between variants while maintaining their host cell binding functions.
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Affiliation(s)
- Peter C Bull
- Kenya Medical Research Institute, Centre for Geographic Medicine Research, Coast, Kilifi, Kenya.
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Montgomery J, Mphande FA, Berriman M, Pain A, Rogerson SJ, Taylor TE, Molyneux ME, Craig A. Differential var gene expression in the organs of patients dying of falciparum malaria. Mol Microbiol 2007; 65:959-67. [PMID: 17617167 PMCID: PMC2170262 DOI: 10.1111/j.1365-2958.2007.05837.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sequestration of parasitized erythrocytes in the microcirculation of tissues is thought to be important in the pathogenesis of severe falciparum malaria. A major variant surface antigen, var/Plasmodium falciparum erythrocyte membrane protein 1, expressed on the surface of the infected erythrocyte, mediates cytoadherence to vascular endothelium. To address the question of tissue-specific accumulation of variant types, we used the unique resource generated by the clinicopathological study of fatal paediatric malaria in Blantyre, Malawi, to analyse var gene transcription in patients dying with falciparum malaria. Despite up to 102 different var genes being expressed by P. falciparum populations in a single host, only one to two of these genes were expressed at high levels in the brains and hearts of these patients. These major var types differed between organs. However, identical var types were expressed in the brains of multiple patients from a single malaria season. These results provide the first evidence of organ-specific accumulation of P. falciparum variant types and suggest that parasitized erythrocytes can exhibit preferential binding in the body, supporting the hypothesis of cytoadherence-linked pathogenesis.
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Affiliation(s)
- Jacqui Montgomery
- Malawi-Liverpool-Wellcome Programme of Clinical Tropical Research, College of Medicine, Blantyre, Malawi.
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