101
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Abdi AI, Hodgson SH, Muthui MK, Kivisi CA, Kamuyu G, Kimani D, Hoffman SL, Juma E, Ogutu B, Draper SJ, Osier F, Bejon P, Marsh K, Bull PC. Plasmodium falciparum malaria parasite var gene expression is modified by host antibodies: longitudinal evidence from controlled infections of Kenyan adults with varying natural exposure. BMC Infect Dis 2017; 17:585. [PMID: 28835215 PMCID: PMC5569527 DOI: 10.1186/s12879-017-2686-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 08/15/2017] [Indexed: 11/10/2022] Open
Abstract
Background The PfEMP1 family of Plasmodium falciparum antigens play a key role in pathogenesis of severe malaria through their insertion into the surface of parasite infected erythrocytes, and adhesion to host cells. Previous studies have suggested that parasites expressing PfEMP1 subclasses group A and DC8, associated with severe malaria, may have a growth advantage in immunologically naïve individuals. However, this idea has not been tested in longitudinal studies. Methods Here we assessed expression of the var genes encoding PfEMP1, in parasites sampled from volunteers with varying prior exposure to malaria, following experimental infection by sporozoites (PfSPZ). Using qPCR, we tested for associations between the expression of various var subgroups in surviving parasite populations from each volunteer and 1) the levels of participants’ antibodies to infected erythrocytes before challenge infection and 2) the apparent in vivo parasite multiplication rate. Results We show that 1) expression of var genes encoding for group A and DC8-like PfEMP1 were associated with low levels of antibodies to infected erythrocytes (αIE) before challenge, and 2) expression of a DC8-like CIDRα1.1 domain was associated with higher apparent parasite multiplication rate in a manner that was independent of levels of prior antibodies to infected erythrocytes. Conclusions This study provides insight into the role of antibodies to infected erythrocytes surface antigens in the development of naturally acquired immunity and may help explain why specific PfEMP1 variants may be associated with severe malaria. Trial registration Pan African Clinical Trial Registry: PACTR201211000433272. Date of registration: 10th October 2012.
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Affiliation(s)
- Abdirahman I Abdi
- KEMRI-Wellcome Trust Research Programme, CGMRC, P.O. Box 230-80108, Kilifi County, Kenya. .,Pwani University, P. O. Box 195-80108, Kilifi, Kenya.
| | | | - Michelle K Muthui
- KEMRI-Wellcome Trust Research Programme, CGMRC, P.O. Box 230-80108, Kilifi County, Kenya
| | - Cheryl A Kivisi
- KEMRI-Wellcome Trust Research Programme, CGMRC, P.O. Box 230-80108, Kilifi County, Kenya.,Pwani University, P. O. Box 195-80108, Kilifi, Kenya
| | - Gathoni Kamuyu
- KEMRI-Wellcome Trust Research Programme, CGMRC, P.O. Box 230-80108, Kilifi County, Kenya
| | - Domtila Kimani
- KEMRI-Wellcome Trust Research Programme, CGMRC, P.O. Box 230-80108, Kilifi County, Kenya
| | | | - Elizabeth Juma
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya.,Centre for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
| | - Bernhards Ogutu
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya.,Centre for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
| | | | - Faith Osier
- KEMRI-Wellcome Trust Research Programme, CGMRC, P.O. Box 230-80108, Kilifi County, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, CGMRC, P.O. Box 230-80108, Kilifi County, Kenya
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, CGMRC, P.O. Box 230-80108, Kilifi County, Kenya
| | - Peter C Bull
- Department of Pathology, University of Cambridge, 17 Tennis Court Road, Cambridge, CB2 1QP, UK.
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102
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Abstract
The human malaria parasite Plasmodium falciparum replicates within circulating red blood cells, where it is subjected to conditions that frequently cause DNA damage. The repair of DNA double-stranded breaks (DSBs) is thought to rely almost exclusively on homologous recombination (HR), due to a lack of efficient nonhomologous end joining. However, given that the parasite is haploid during this stage of its life cycle, the mechanisms involved in maintaining genome stability are poorly understood. Of particular interest are the subtelomeric regions of the chromosomes, which contain the majority of the multicopy variant antigen-encoding genes responsible for virulence and disease severity. Here, we show that parasites utilize a competitive balance between de novo telomere addition, also called “telomere healing,” and HR to stabilize chromosome ends. Products of both repair pathways were observed in response to DSBs that occurred spontaneously during routine in vitro culture or resulted from experimentally induced DSBs, demonstrating that both pathways are active in repairing DSBs within subtelomeric regions and that the pathway utilized was determined by the DNA sequences immediately surrounding the break. In combination, these two repair pathways enable parasites to efficiently maintain chromosome stability while also contributing to the generation of genetic diversity. Malaria is a major global health threat, causing approximately 430,000 deaths annually. This mosquito-transmitted disease is caused by Plasmodium parasites, with infection with the species Plasmodium falciparum being the most lethal. Mechanisms underlying DNA repair and maintenance of genome integrity in P. falciparum are not well understood and represent a gap in our understanding of how parasites survive the hostile environment of their vertebrate and insect hosts. Our work examines DNA repair in real time by using single-molecule real-time (SMRT) sequencing focused on the subtelomeric regions of the genome that harbor the multicopy gene families important for virulence and the maintenance of infection. We show that parasites utilize two competing molecular mechanisms to repair double-strand breaks, homologous recombination and de novo telomere addition, with the pathway used being determined by the surrounding DNA sequence. In combination, these two pathways balance the need to maintain genome stability with the selective advantage of generating antigenic diversity.
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103
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Hu W, Jiang ZD, Suo F, Zheng JX, He WZ, Du LL. A large gene family in fission yeast encodes spore killers that subvert Mendel's law. eLife 2017; 6:e26057. [PMID: 28631610 PMCID: PMC5478263 DOI: 10.7554/elife.26057] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/06/2017] [Indexed: 12/12/2022] Open
Abstract
Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them. Spores carrying one killer are protected from its killing effect but not that of the other killer. The killing and protecting activities can be uncoupled by mutation. The numbers and sequences of wtf genes vary considerably between S. pombe isolates, indicating rapid divergence. We propose that wtf genes contribute to the extensive intraspecific reproductive isolation in S. pombe, and represent ideal models for understanding how segregation-distorting elements act and evolve.
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Affiliation(s)
- Wen Hu
- National Institute of Biological Sciences, Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, China
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
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104
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Wahlgren M, Goel S, Akhouri RR. Variant surface antigens of Plasmodium falciparum and their roles in severe malaria. Nat Rev Microbiol 2017; 15:479-491. [DOI: 10.1038/nrmicro.2017.47] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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105
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Cerqueira GC, Cheeseman IH, Schaffner SF, Nair S, McDew-White M, Phyo AP, Ashley EA, Melnikov A, Rogov P, Birren BW, Nosten F, Anderson TJC, Neafsey DE. Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance. Genome Biol 2017; 18:78. [PMID: 28454557 PMCID: PMC5410087 DOI: 10.1186/s13059-017-1204-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/29/2017] [Indexed: 12/30/2022] Open
Abstract
Background Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutations in the kelch13 gene have been implicated in this resistance. We used longitudinal genomic surveillance to detect signals in kelch13 and other loci that contribute to artemisinin or partner drug resistance. We retrospectively sequenced the genomes of 194 P. falciparum isolates from five sites in Northwest Thailand, over the period of a rapid increase in the emergence of artemisinin resistance (2001–2014). Results We evaluate statistical metrics for temporal change in the frequency of individual SNPs, assuming that SNPs associated with resistance increase in frequency over this period. After Kelch13-C580Y, the strongest temporal change is seen at a SNP in phosphatidylinositol 4-kinase, which is involved in a pathway recently implicated in artemisinin resistance. Furthermore, other loci exhibit strong temporal signatures which warrant further investigation for involvement in artemisinin resistance evolution. Through genome-wide association analysis we identify a variant in a kelch domain-containing gene on chromosome 10 that may epistatically modulate artemisinin resistance. Conclusions This analysis demonstrates the potential of a longitudinal genomic surveillance approach to detect resistance-associated gene loci to improve our mechanistic understanding of how resistance develops. Evidence for additional genomic regions outside of the kelch13 locus associated with artemisinin-resistant parasites may yield new molecular markers for resistance surveillance, which may be useful in efforts to reduce the emergence or spread of artemisinin resistance in African parasite populations. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1204-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Ian H Cheeseman
- Texas Biomedical Research Institute, San Antonio, TX, 78245, USA
| | | | - Shalini Nair
- Texas Biomedical Research Institute, San Antonio, TX, 78245, USA
| | | | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol University, Mae Sot, Thailand
| | - Elizabeth A Ashley
- Shoklo Malaria Research Unit, Mahidol University, Mae Sot, Thailand.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Peter Rogov
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol University, Mae Sot, Thailand.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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106
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Tarique M, Ahmad M, Chauhan M, Tuteja R. Genome Wide In silico Analysis of the Mismatch Repair Components of Plasmodium falciparum and Their Comparison with Human Host. Front Microbiol 2017; 8:130. [PMID: 28232818 PMCID: PMC5298969 DOI: 10.3389/fmicb.2017.00130] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 01/18/2017] [Indexed: 12/28/2022] Open
Abstract
Malaria a major parasitic infection globally particularly in tropical and sub-tropical regions of the world is responsible for about 198 million cases and estimated deaths due to this disease are about 0.6 million. The emergence of drug resistance in the malaria parasite is alarming and it is necessary to understand its underlying cause and molecular mechanisms. It has been established that drug resistant malaria parasites have defective mismatch repair (MMR) therefore it is essential to study this pathway and its components in detail. Recently a number of non-synonymous Single Nucleotide Polymorphisms have been reported in genes involved in MMR pathways. PfMLH is an endonuclease essential to restore the MMR in drug resistant strains of Plasmodium falciparum. Considering all these facts about the role of MMR in emergence of drug resistant parasite, in this manuscript we report a genome wide analysis of the components of the MMR pathway such as MLH, Pms1, MSH2-1, MSH2-2, MSH6, and UvrD using in silico bioinformatics based approaches. The phylogenetic analysis revealed evolutionary closeness with the MMR components of various organisms. It is noteworthy that P. falciparum contains two homologs of MSH2, which are located on different chromosomes. The structural modeling of these components showed their similarity with the human/yeast MMR components. The docking studies reveal that PfUvrD and PfMLH interact with each other. The in silico identification of interacting partners of the major MMR components identified numerous P. falciparum specific proteins. In line with our previous studies the present study will also contribute significantly to understand the MMR pathway of malaria parasite.
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Affiliation(s)
- Mohammed Tarique
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Moaz Ahmad
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Manish Chauhan
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Renu Tuteja
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
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107
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Rutledge GG, Böhme U, Sanders M, Reid AJ, Cotton JA, Maiga-Ascofare O, Djimdé AA, Apinjoh TO, Amenga-Etego L, Manske M, Barnwell JW, Renaud F, Ollomo B, Prugnolle F, Anstey NM, Auburn S, Price RN, McCarthy JS, Kwiatkowski DP, Newbold CI, Berriman M, Otto TD. Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature 2017; 542:101-104. [PMID: 28117441 PMCID: PMC5326575 DOI: 10.1038/nature21038] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/04/2016] [Indexed: 01/12/2023]
Abstract
Elucidation of the evolutionary history and interrelatedness of Plasmodium species that infect humans has been hampered by a lack of genetic information for three human-infective species: P. malariae and two P. ovale species (P. o. curtisi and P. o. wallikeri). These species are prevalent across most regions in which malaria is endemic and are often undetectable by light microscopy, rendering their study in human populations difficult. The exact evolutionary relationship of these species to the other human-infective species has been contested. Using a new reference genome for P. malariae and a manually curated draft P. o. curtisi genome, we are now able to accurately place these species within the Plasmodium phylogeny. Sequencing of a P. malariae relative that infects chimpanzees reveals similar signatures of selection in the P. malariae lineage to another Plasmodium lineage shown to be capable of colonization of both human and chimpanzee hosts. Molecular dating suggests that these host adaptations occurred over similar evolutionary timescales. In addition to the core genome that is conserved between species, differences in gene content can be linked to their specific biology. The genome suggests that P. malariae expresses a family of heterodimeric proteins on its surface that have structural similarities to a protein crucial for invasion of red blood cells. The data presented here provide insight into the evolution of the Plasmodium genus as a whole.
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Affiliation(s)
- Gavin G Rutledge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Ulrike Böhme
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Adam J Reid
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - James A Cotton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Oumou Maiga-Ascofare
- Malaria Research and Training Center, University of Science, Techniques, and Technologies of Bamako, Bamako BP E.2528, Mali
- German Center for Infection Research, 20359 Hamburg, Germany
| | - Abdoulaye A Djimdé
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Malaria Research and Training Center, University of Science, Techniques, and Technologies of Bamako, Bamako BP E.2528, Mali
| | - Tobias O Apinjoh
- University of Buea, Post Office Box 63, Buea, South West Region, Republic of Cameroon
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Post Office Box 114, Navrongo, Upper East Region, Ghana
| | - Magnus Manske
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - John W Barnwell
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - François Renaud
- Laboratoire MIVEGEC (UM1-CNRS-IRD), 34394 Montpellier, France
| | - Benjamin Ollomo
- Centre International de Recherches Médicales de Franceville, BP 709 Franceville, Gabon
| | - Franck Prugnolle
- Laboratoire MIVEGEC (UM1-CNRS-IRD), 34394 Montpellier, France
- Centre International de Recherches Médicales de Franceville, BP 709 Franceville, Gabon
| | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0810, Australia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0810, Australia
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0810, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - James S McCarthy
- Clinical Tropical Medicine Laboratory, QIMR Berghofer Medical Research Institute, University of Queensland, Brisbane, Queensland 4006, Australia
| | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Chris I Newbold
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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108
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Claessens A, Affara M, Assefa SA, Kwiatkowski DP, Conway DJ. Culture adaptation of malaria parasites selects for convergent loss-of-function mutants. Sci Rep 2017; 7:41303. [PMID: 28117431 PMCID: PMC5259787 DOI: 10.1038/srep41303] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/19/2016] [Indexed: 12/30/2022] Open
Abstract
Cultured human pathogens may differ significantly from source populations. To investigate the genetic basis of laboratory adaptation in malaria parasites, clinical Plasmodium falciparum isolates were sampled from patients and cultured in vitro for up to three months. Genome sequence analysis was performed on multiple culture time point samples from six monoclonal isolates, and single nucleotide polymorphism (SNP) variants emerging over time were detected. Out of a total of five positively selected SNPs, four represented nonsense mutations resulting in stop codons, three of these in a single ApiAP2 transcription factor gene, and one in SRPK1. To survey further for nonsense mutants associated with culture, genome sequences of eleven long-term laboratory-adapted parasite strains were examined, revealing four independently acquired nonsense mutations in two other ApiAP2 genes, and five in Epac. No mutants of these genes exist in a large database of parasite sequences from uncultured clinical samples. This implicates putative master regulator genes in which multiple independent stop codon mutations have convergently led to culture adaptation, affecting most laboratory lines of P. falciparum. Understanding the adaptive processes should guide development of experimental models, which could include targeted gene disruption to adapt fastidious malaria parasite species to culture.
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Affiliation(s)
- Antoine Claessens
- London School of Hygiene and Tropical Medicine, London, UK
- Medical Research Council Unit The Gambia, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Muna Affara
- Medical Research Council Unit The Gambia, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
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109
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Ernst JD. Antigenic Variation and Immune Escape in the MTBC. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:171-190. [PMID: 29116635 DOI: 10.1007/978-3-319-64371-7_9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Microbes that infect other organisms encounter host immune responses, and must overcome or evade innate and adaptive immune responses to successfully establish infection. Highly successful microbial pathogens, including M. tuberculosis, are able to evade adaptive immune responses (mediated by antibodies and/or T lymphocytes) and thereby establish long-term chronic infection. One mechanism that diverse pathogens use to evade adaptive immunity is antigenic variation, in which structural variants emerge that alter recognition by established immune responses and allow those pathogens to persist and/or to infect previously-immune hosts. Despite the wide use of antigenic variation by diverse pathogens, this mechanism appears to be infrequent in M. tuberculosis, as indicated by findings that known and predicted human T cell epitopes in this organism are highly conserved, although there are exceptions. These findings have implications for diagnostic tests that are based on measuring host immune responses, and for vaccine design and development.
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Affiliation(s)
- Joel D Ernst
- Division of Infectious Diseases and Immunology, Departments of Medicine, Microbiology, and Pathology, New York University School of Medicine, Smilow Building, 9th floor, Rooms 901-907, 522 First Avenue, New York, NY, 10016, USA.
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110
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Bruske EI, Dimonte S, Enderes C, Tschan S, Flötenmeyer M, Koch I, Berger J, Kremsner P, Frank M. In Vitro Variant Surface Antigen Expression in Plasmodium falciparum Parasites from a Semi-Immune Individual Is Not Correlated with Var Gene Transcription. PLoS One 2016; 11:e0166135. [PMID: 27907004 PMCID: PMC5132323 DOI: 10.1371/journal.pone.0166135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/24/2016] [Indexed: 12/17/2022] Open
Abstract
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is considered to be the main variant surface antigen (VSA) of Plasmodium falciparum and is mainly localized on electron-dense knobs in the membrane of the infected erythrocyte. Switches in PfEMP1 expression provide the basis for antigenic variation and are thought to be critical for parasite persistence during chronic infections. Recently, strain transcending anti-PfEMP1 immunity has been shown to develop early in life, challenging the role of PfEMP1 in antigenic variation during chronic infections. In this work we investigate how P. falciparum achieves persistence during a chronic asymptomatic infection. The infected individual (MOA) was parasitemic for 42 days and multilocus var gene genotyping showed persistence of the same parasite population throughout the infection. Parasites from the beginning of the infection were adapted to tissue culture and cloned by limiting dilution. Flow cytometry using convalescent serum detected a variable surface recognition signal on isogenic clonal parasites. Quantitative real-time PCR with a field isolate specific var gene primer set showed that the surface recognition signal was not correlated with transcription of individual var genes. Strain transcending anti-PfEMP1 immunity of the convalescent serum was demonstrated with CD36 selected and PfEMP1 knock-down NF54 clones. In contrast, knock-down of PfEMP1 did not have an effect on the antibody recognition signal in MOA clones. Trypsinisation of the membrane surface proteins abolished the surface recognition signal and immune electron microscopy revealed that antibodies from the convalescent serum bound to membrane areas without knobs and with knobs. Together the data indicate that PfEMP1 is not the main variable surface antigen during a chronic infection and suggest a role for trypsin sensitive non-PfEMP1 VSAs for parasite persistence in chronic infections.
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Affiliation(s)
- Ellen Inga Bruske
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
| | - Sandra Dimonte
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
| | - Corinna Enderes
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
| | - Serena Tschan
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
| | | | - Iris Koch
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Jürgen Berger
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Peter Kremsner
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
- CERMEL (Centre de Recherche Médicale de Lambaréné), Lambaréné, Gabon
| | - Matthias Frank
- Institute of Tropical Medicine, University of Tuebingen, Tuebingen, Germany
- CERMEL (Centre de Recherche Médicale de Lambaréné), Lambaréné, Gabon
- * E-mail:
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111
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Cytoadhesion to gC1qR through Plasmodium falciparum Erythrocyte Membrane Protein 1 in Severe Malaria. PLoS Pathog 2016; 12:e1006011. [PMID: 27835682 PMCID: PMC5106025 DOI: 10.1371/journal.ppat.1006011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 10/19/2016] [Indexed: 11/19/2022] Open
Abstract
Cytoadhesion of Plasmodium falciparum infected erythrocytes to gC1qR has been associated with severe malaria, but the parasite ligand involved is currently unknown. To assess if binding to gC1qR is mediated through the P. falciparum erythrocyte membrane protein 1 (PfEMP1) family, we analyzed by static binding assays and qPCR the cytoadhesion and var gene transcriptional profile of 86 P. falciparum isolates from Mozambican children with severe and uncomplicated malaria, as well as of a P. falciparum 3D7 line selected for binding to gC1qR (Pf3D7gC1qR). Transcript levels of DC8 correlated positively with cytoadhesion to gC1qR (rho = 0.287, P = 0.007), were higher in isolates from children with severe anemia than with uncomplicated malaria, as well as in isolates from Europeans presenting a first episode of malaria (n = 21) than Mozambican adults (n = 25), and were associated with an increased IgG recognition of infected erythrocytes by flow cytometry. Pf3D7gC1qR overexpressed the DC8 type PFD0020c (5.3-fold transcript levels relative to Seryl-tRNA-synthetase gene) compared to the unselected line (0.001-fold). DBLβ12 from PFD0020c bound to gC1qR in ELISA-based binding assays and polyclonal antibodies against this domain were able to inhibit binding to gC1qR of Pf3D7gC1qR and four Mozambican P. falciparum isolates by 50%. Our results show that DC8-type PfEMP1s mediate binding to gC1qR through conserved surface epitopes in DBLβ12 domain which can be inhibited by strain-transcending functional antibodies. This study supports a key role for gC1qR in malaria-associated endovascular pathogenesis and suggests the feasibility of designing interventions against severe malaria targeting this specific interaction. Plasmodium falciparum sequesters in vital organs. This phenomenon mediated by cytoadhesion of infected-erythrocytes to host receptors in the microvasculature, contributes to the development of severe malaria. Although cytoadhesion to Endothelial Protein-C Receptor has a central role in severe malaria, other host receptors are also likely to be involved. Our results generated by the analysis of P. falciparum isolates from Mozambican patients and laboratory parasite lines indicate that a specific domain (DBLβ12) from DC8-type PfEMP1s can bind to the human receptor gC1qR, previously associated with severe malaria. Our findings revealed that antibodies against PfEMP1 could provide strain-transcending inhibition of gC1qR-binding. Overall, these results support a key role for the adhesion to gC1qR in malaria-associated endovascular pathogenesis and the feasibility of new interventions targeting this specific interaction.
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112
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Stanton A, Harris LM, Graham G, Merrick CJ. Recombination events among virulence genes in malaria parasites are associated with G-quadruplex-forming DNA motifs. BMC Genomics 2016; 17:859. [PMID: 27809775 PMCID: PMC5093961 DOI: 10.1186/s12864-016-3183-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/21/2016] [Indexed: 11/10/2022] Open
Abstract
Background Malaria parasites of the genus Plasmodium possess large hyper-variable families of antigen-encoding genes. These are often variantly-expressed and are major virulence factors for immune evasion and the maintenance of chronic infections. Recombination and diversification of these gene families occurs readily, and may be promoted by G-quadruplex (G4) DNA motifs within and close to the variant genes. G4s have been shown to cause replication fork stalling, DNA breakage and recombination in model systems, but these motifs remain largely unstudied in Plasmodium. Results We examined the nature and distribution of putative G4-forming sequences in multiple Plasmodium genomes, finding that their co-distribution with variant gene families is conserved across different Plasmodium species that have different types of variant gene families. In P. falciparum, where a large set of recombination events that occurred over time in cultured parasites has been mapped, we found a strong spatial association between these recombination events and putative G4-forming sequences. Finally, we searched Plasmodium genomes for the three classes of helicase that can unwind G4s: Plasmodium spp. have no identifiable homologue of the highly efficient G4 helicase PIF1, but they do encode two putative RecQ helicases and one homologue of the RAD3-family helicase FANCJ. Conclusions Our analyses, conducted at the whole-genome level in multiple species of Plasmodium, support the concept that G4s are likely to be involved in recombination and diversification of antigen-encoding gene families in this important protozoan pathogen. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3183-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam Stanton
- School of Computing and Mathematics, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST55BG, UK
| | - Lynne M Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST55BG, UK
| | - Gemma Graham
- School of Medicine, Keele University, Keele, Staffordshire, ST55BG, UK
| | - Catherine J Merrick
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST55BG, UK.
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113
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Volkman SK, Herman J, Lukens AK, Hartl DL. Genome-Wide Association Studies of Drug-Resistance Determinants. Trends Parasitol 2016; 33:214-230. [PMID: 28179098 DOI: 10.1016/j.pt.2016.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/26/2016] [Accepted: 10/06/2016] [Indexed: 02/07/2023]
Abstract
Population genetic strategies that leverage association, selection, and linkage have identified drug-resistant loci. However, challenges and limitations persist in identifying drug-resistance loci in malaria. In this review we discuss the genetic basis of drug resistance and the use of genome-wide association studies, complemented by selection and linkage studies, to identify and understand mechanisms of drug resistance and response. We also discuss the implications of nongenetic mechanisms of drug resistance recently reported in the literature, and present models of the interplay between nongenetic and genetic processes that contribute to the emergence of drug resistance. Throughout, we examine artemisinin resistance as an example to emphasize challenges in identifying phenotypes suitable for population genetic studies as well as complications due to multiple-factor drug resistance.
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Affiliation(s)
- Sarah K Volkman
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Disease, Boston, MA, USA; The Broad Institute of MIT and Harvard, Infectious Disease Initiative, Cambridge, MA, USA; Simmons College, School of Nursing and Health Science, Boston, MA, USA.
| | - Jonathan Herman
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Disease, Boston, MA, USA; Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Amanda K Lukens
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Disease, Boston, MA, USA; The Broad Institute of MIT and Harvard, Infectious Disease Initiative, Cambridge, MA, USA
| | - Daniel L Hartl
- The Broad Institute of MIT and Harvard, Infectious Disease Initiative, Cambridge, MA, USA; Harvard University, Organismic and Evolutionary Biology, Cambridge, MA, USA
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114
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Singh GP, Sharma A. South-East Asian strains of Plasmodium falciparum display higher ratio of non-synonymous to synonymous polymorphisms compared to African strains. F1000Res 2016; 5:1964. [PMID: 27853513 PMCID: PMC5089136 DOI: 10.12688/f1000research.9372.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/19/2016] [Indexed: 11/20/2022] Open
Abstract
Resistance to frontline anti-malarial drugs, including artemisinin, has repeatedly arisen in South-East Asia, but the reasons for this are not understood. Here we test whether evolutionary constraints on
Plasmodium falciparum strains from South-East Asia differ from African strains. We find a significantly higher ratio of non-synonymous to synonymous polymorphisms in
P. falciparum from South-East Asia compared to Africa, suggesting differences in the selective constraints on
P. falciparum genome in these geographical regions. Furthermore, South-East Asian strains showed a higher proportion of non-synonymous polymorphism at conserved positions, suggesting reduced negative selection. There was a lower rate of mixed infection by multiple genotypes in samples from South-East Asia compared to Africa. We propose that a lower mixed infection rate in South-East Asia reduces intra-host competition between the parasite clones, reducing the efficiency of natural selection. This might increase the probability of fixation of fitness-reducing mutations including drug resistant ones.
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Affiliation(s)
- Gajinder Pal Singh
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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115
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Anderson TJC, Nair S, McDew-White M, Cheeseman IH, Nkhoma S, Bilgic F, McGready R, Ashley E, Pyae Phyo A, White NJ, Nosten F. Population Parameters Underlying an Ongoing Soft Sweep in Southeast Asian Malaria Parasites. Mol Biol Evol 2016; 34:131-144. [PMID: 28025270 PMCID: PMC5216669 DOI: 10.1093/molbev/msw228] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Multiple kelch13 alleles conferring artemisinin resistance (ART-R) are currently spreading through Southeast Asian malaria parasite populations, providing a unique opportunity to observe an ongoing soft selective sweep, investigate why resistance alleles have evolved multiple times and determine fundamental population genetic parameters for Plasmodium. We sequenced kelch13 (n = 1,876), genotyped 75 flanking SNPs, and measured clearance rate (n = 3,552) in parasite infections from Western Thailand (2001–2014). We describe 32 independent coding mutations including common mutations outside the kelch13 propeller associated with significant reductions in clearance rate. Mutations were first observed in 2003 and rose to 90% by 2014, consistent with a selection coefficient of ∼0.079. ART-R allele diversity rose until 2012 and then dropped as one allele (C580Y) spread to high frequency. The frequency with which adaptive alleles arise is determined by the rate of mutation and the population size. Two factors drive this soft sweep: (1) multiple kelch13 amino-acid mutations confer resistance providing a large mutational target—we estimate the target is 87–163 bp. (2) The population mutation parameter (Θ = 2Neμ) can be estimated from the frequency distribution of ART-R alleles and is ∼5.69, suggesting that short term effective population size is 88 thousand to 1.2 million. This is 52–705 times greater than Ne estimated from fluctuation in allele frequencies, suggesting that we have previously underestimated the capacity for adaptive evolution in Plasmodium. Our central conclusions are that retrospective studies may underestimate the complexity of selective events and the Ne relevant for adaptation for malaria is considerably higher than previously estimated.
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Affiliation(s)
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Marina McDew-White
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell Nkhoma
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Fatma Bilgic
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Elizabeth Ashley
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Nicholas J White
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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116
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Holding T, Recker M. Maintenance of phenotypic diversity within a set of virulence encoding genes of the malaria parasite Plasmodium falciparum. J R Soc Interface 2016; 12:20150848. [PMID: 26674193 PMCID: PMC4707858 DOI: 10.1098/rsif.2015.0848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Infection by the human malaria parasite Plasmodium falciparum results in a broad spectrum of clinical outcomes, ranging from severe and potentially life-threatening malaria to asymptomatic carriage. In a process of naturally acquired immunity, individuals living in malaria-endemic regions build up a level of clinical protection, which attenuates infection severity in an exposure-dependent manner. Underlying this shift in the immunoepidemiology as well as the observed range in malaria pathogenesis is the var multigene family and the phenotypic diversity embedded within. The var gene-encoded surface proteins Plasmodium falciparum erythrocyte membrane protein 1 mediate variant-specific binding of infected red blood cells to a diverse set of host receptors that has been linked to specific disease manifestations, including cerebral and pregnancy-associated malaria. Here, we show that cross-reactive immune responses, which minimize the within-host benefit of each additionally expressed gene during infection, can cause selection for maximum phenotypic diversity at the genome level. We further show that differential functional constraints on protein diversification stably maintain uneven ratios between phenotypic groups, in line with empirical observation. Our results thus suggest that the maintenance of phenotypic diversity within P. falciparum is driven by an evolutionary trade-off that optimizes between within-host parasite fitness and between-host selection pressure.
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Affiliation(s)
- Thomas Holding
- Centre for Mathematics and the Environment, University of Exeter, Penryn Campus, Penryn TR10 9EZ, UK
| | - Mario Recker
- Centre for Mathematics and the Environment, University of Exeter, Penryn Campus, Penryn TR10 9EZ, UK
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117
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Miles A, Iqbal Z, Vauterin P, Pearson R, Campino S, Theron M, Gould K, Mead D, Drury E, O'Brien J, Ruano Rubio V, MacInnis B, Mwangi J, Samarakoon U, Ranford-Cartwright L, Ferdig M, Hayton K, Su XZ, Wellems T, Rayner J, McVean G, Kwiatkowski D. Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum. Genome Res 2016; 26:1288-99. [PMID: 27531718 PMCID: PMC5052046 DOI: 10.1101/gr.203711.115] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/28/2016] [Indexed: 12/14/2022]
Abstract
The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable and thus difficult to analyze using short-read sequencing technologies. Here, we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired.
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Affiliation(s)
- Alistair Miles
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Paul Vauterin
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Richard Pearson
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Susana Campino
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Michel Theron
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Kelda Gould
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Daniel Mead
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Eleanor Drury
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | | | | | - Bronwyn MacInnis
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Jonathan Mwangi
- Department of Biochemistry, Medical School, Mount Kenya University, 01000 Thika, Kenya; Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Upeka Samarakoon
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Lisa Ranford-Cartwright
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Michael Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Karen Hayton
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-9806, USA
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-9806, USA
| | - Thomas Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-9806, USA
| | - Julian Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom; Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
| | - Dominic Kwiatkowski
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
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118
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Vembar SS, Seetin M, Lambert C, Nattestad M, Schatz MC, Baybayan P, Scherf A, Smith ML. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Res 2016; 23:339-51. [PMID: 27345719 PMCID: PMC4991835 DOI: 10.1093/dnares/dsw022] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/10/2016] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging due to the skewed AT-richness [∼80.6% (A + T)] of its genome and the lack of technology to assemble highly polymorphic subtelomeric regions that contain clonally variant, multigene virulence families (Ex: var and rifin). To address this, we performed amplification-free, single molecule, real-time sequencing of P. falciparum genomic DNA and generated reads of average length 12 kb, with 50% of the reads between 15.5 and 50 kb in length. Next, using the Hierarchical Genome Assembly Process, we assembled the P. falciparum genome de novo and successfully compiled all 14 nuclear chromosomes telomere-to-telomere. We also accurately resolved centromeres [∼90–99% (A + T)] and subtelomeric regions and identified large insertions and duplications that add extra var and rifin genes to the genome, along with smaller structural variants such as homopolymer tract expansions. Overall, we show that amplification-free, long-read sequencing combined with de novo assembly overcomes major challenges inherent to studying the P. falciparum genome. Indeed, this technology may not only identify the polymorphic and repetitive subtelomeric sequences of parasite populations from endemic areas but may also evaluate structural variation linked to virulence, drug resistance and disease transmission.
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Affiliation(s)
- Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris 75015, France CNRS, ERL 9195, Paris 75015, France INSERM, Unit U1201, Paris 75015, France
| | | | | | | | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris 75015, France CNRS, ERL 9195, Paris 75015, France INSERM, Unit U1201, Paris 75015, France
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119
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McCulloch R, Navarro M. The protozoan nucleus. Mol Biochem Parasitol 2016; 209:76-87. [PMID: 27181562 DOI: 10.1016/j.molbiopara.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/16/2022]
Abstract
The nucleus is arguably the defining characteristic of eukaryotes, distinguishing their cell organisation from both bacteria and archaea. Though the evolutionary history of the nucleus remains the subject of debate, its emergence differs from several other eukaryotic organelles in that it appears not to have evolved through symbiosis, but by cell membrane elaboration from an archaeal ancestor. Evolution of the nucleus has been accompanied by elaboration of nuclear structures that are intimately linked with most aspects of nuclear genome function, including chromosome organisation, DNA maintenance, replication and segregation, and gene expression controls. Here we discuss the complexity of the nucleus and its substructures in protozoan eukaryotes, with a particular emphasis on divergent aspects in eukaryotic parasites, which shed light on nuclear function throughout eukaryotes and reveal specialisations that underpin pathogen biology.
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Affiliation(s)
- Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (CSIC), Avda. del Conocimiento s/n, 18100 Granada, Spain.
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120
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Lee AH, Fidock DA. Evidence of a Mild Mutator Phenotype in Cambodian Plasmodium falciparum Malaria Parasites. PLoS One 2016; 11:e0154166. [PMID: 27100094 PMCID: PMC4839739 DOI: 10.1371/journal.pone.0154166] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/09/2016] [Indexed: 12/22/2022] Open
Abstract
Malaria control efforts have been continuously stymied by drug-resistant strains of Plasmodium falciparum, which typically originate in Southeast Asia prior to spreading into high-transmission settings in Africa. One earlier proposed explanation for Southeast Asia being a hotbed of resistance has been the hypermutability or "Accelerated Resistance to Multiple Drugs" (ARMD) phenotype, whereby multidrug-resistant Southeast Asian parasites were reported to exhibit 1,000-fold higher rates of resistance to unrelated antimalarial agents when compared to drug-sensitive parasites. However, three recent studies do not recapitulate this hypermutability phenotype. Intriguingly, genome sequencing of recently derived multidrug-resistant Cambodian isolates has identified a high proportion of DNA repair gene mutations in multidrug-resistant parasites, suggesting their potential role in shaping local parasite evolution. By adapting fluctuation assays for use in P. falciparum, we have examined the in vitro mutation rates of five recent Cambodian isolates and three reference laboratory strains. For these studies we also generated a knockout parasite line lacking the DNA repair factor Exonuclease I. In these assays, parasites were typed for their ability to acquire resistance to KAE609, currently in advanced clinical trials, yielding 13 novel mutations in the Na+/H+-ATPase PfATP4, the primary resistance determinant. We observed no evidence of hypermutability. Instead, we found evidence of a mild mutator (up to a 3.4-fold increase in mutation rate) phenotype in two artemisinin-resistant Cambodian isolates, which carry DNA repair gene mutations. We observed that one such mutation in the Mismatch Repair protein Mlh1 contributes to the mild mutator phenotype when modeled in yeast (scmlh1-P157S). Compared to basal rates of mutation, a mild mutator phenotype may provide a greater overall benefit for parasites in Southeast Asia in terms of generating drug resistance without incurring detrimental fitness costs.
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Affiliation(s)
- Andrew H. Lee
- Department of Microbiology and Immunology, Columbia University, New York, New York, United States of America
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University, New York, New York, United States of America
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, United States of America
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121
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Campino S, Benavente ED, Assefa S, Thompson E, Drought LG, Taylor CJ, Gorvett Z, Carret CK, Flueck C, Ivens AC, Kwiatkowski DP, Alano P, Baker DA, Clark TG. Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines. Malar J 2016; 15:229. [PMID: 27098483 PMCID: PMC4839107 DOI: 10.1186/s12936-016-1254-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 03/30/2016] [Indexed: 11/10/2022] Open
Abstract
Background Transmission of the malaria parasite Plasmodium falciparum from humans to the mosquito vector requires differentiation of a sub-population of asexual forms replicating within red blood cells into non-dividing male and female gametocytes. The nature of the molecular mechanism underlying this key differentiation event required for malaria transmission is not fully understood. Methods Whole genome sequencing was used to examine the genomic diversity of the gametocyte non-producing 3D7-derived lines F12 and A4. These lines were used in the recent detection of the PF3D7_1222600 locus (encoding PfAP2-G), which acts as a genetic master switch that triggers gametocyte development. Results The evolutionary changes from the 3D7 parental strain through its derivatives F12 (culture-passage derived cloned line) and A4 (transgenic cloned line) were identified. The genetic differences including the formation of chimeric var genes are presented. Conclusion A genomics resource is provided for the further study of gametocytogenesis or other phenotypes using these parasite lines. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1254-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Samuel Assefa
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Eloise Thompson
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Laura G Drought
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Catherine J Taylor
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Zaria Gorvett
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Celine K Carret
- The European Molecular Biology Organization, Heidelberg, Germany
| | - Christian Flueck
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Al C Ivens
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Pietro Alano
- Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate, Istituto Superiore di Sanità, Rome, Italy
| | - David A Baker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
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122
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Good MF, Yanow SK. Cryptic epitope for antibodies should not be forgotten in vaccine design. Expert Rev Vaccines 2016; 15:675-6. [DOI: 10.1586/14760584.2016.1154791] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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123
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Gunawardena S, Karunaweera ND. Advances in genetics and genomics: use and limitations in achieving malaria elimination goals. Pathog Glob Health 2016; 109:123-41. [PMID: 25943157 DOI: 10.1179/2047773215y.0000000015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Success of the global research agenda towards eradication of malaria will depend on the development of new tools, including drugs, vaccines, insecticides and diagnostics. Genetic and genomic information now available for the malaria parasites, their mosquito vectors and human host, can be harnessed to both develop these tools and monitor their effectiveness. Here we review and provide specific examples of current technological advances and how these genetic and genomic tools have increased our knowledge of host, parasite and vector biology in relation to malaria elimination and in turn enhanced the potential to reach that goal. We then discuss limitations of these tools and future prospects for the successful achievement of global malaria elimination goals.
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Abstract
The current epidemic of artemisinin resistant Plasmodium falciparum in Southeast Asia is the result of a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of variations that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions. DOI:http://dx.doi.org/10.7554/eLife.08714.001 Malaria is an infectious disease caused by a microscopic parasite called Plasmodium, which is transferred between humans by mosquitos. One species of malaria parasite called Plasmodium falciparum can cause particularly severe and life-threatening forms of the disease. Currently, the most widely used treatment for P. falciparum infections is artemisinin combination therapy, a treatment that combines the drug artemisinin (or a closely related molecule) with another antimalarial drug. However, resistance to artemisinin has started to spread throughout Southeast Asia. Artemisinin resistance is caused by mutations in a parasite gene called kelch13, and researchers have identified over 20 different mutations in P. falciparum that confer artemisinin resistance. The diversity of mutations involved, and the fact that the same mutation can arise independently in different locations, make it difficult to track the spread of resistance using conventional molecular marker approaches. Here, Amato, Miotto et al. sequenced the entire genomes of more than 3,000 clinical samples of P. falciparum from Southeast Asia and Africa, collected as part of a global network of research groups called the MalariaGEN Plasmodium falciparum Community Project. Amato, Miotto et al. found that African parasites had independently acquired many of the same kelch13 mutations that are known to cause resistance to artemisinin in Southeast Asia. However the kelch13 mutations seen in Africa remained at low levels in the parasite population, and appeared to be under much less pressure for evolutionary selection than those found in Southeast Asia. These findings demonstrate that the emergence and spread of resistance to antimalarial drugs does not depend solely on the mutational process, but also on other factors that influence whether the mutations will spread in the population. Understanding how this is affected by different patterns of drug treatments and other environmental conditions will be important in developing more effective strategies for combating malaria. DOI:http://dx.doi.org/10.7554/eLife.08714.002
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125
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Gabryszewski SJ, Modchang C, Musset L, Chookajorn T, Fidock DA. Combinatorial Genetic Modeling of pfcrt-Mediated Drug Resistance Evolution in Plasmodium falciparum. Mol Biol Evol 2016; 33:1554-70. [PMID: 26908582 PMCID: PMC4868112 DOI: 10.1093/molbev/msw037] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The emergence of drug resistance continuously threatens global control of infectious diseases, including malaria caused by the protozoan parasite Plasmodium falciparum. A critical parasite determinant is the P. falciparum chloroquine resistance transporter (PfCRT), the primary mediator of chloroquine (CQ) resistance (CQR), and a pleiotropic modulator of susceptibility to several first-line artemisinin-based combination therapy partner drugs. Aside from the validated CQR molecular marker K76T, P. falciparum parasites have acquired at least three additional pfcrt mutations, whose contributions to resistance and fitness have been heretofore unclear. Focusing on the quadruple-mutant Ecuadorian PfCRT haplotype Ecu1110 (K76T/A220S/N326D/I356L), we genetically modified the pfcrt locus of isogenic, asexual blood stage P. falciparum parasites using zinc-finger nucleases, producing all possible combinations of intermediate pfcrt alleles. Our analysis included the related quintuple-mutant PfCRT haplotype 7G8 (Ecu1110 + C72S) that is widespread throughout South America and the Western Pacific. Drug susceptibilities and in vitro growth profiles of our combinatorial pfcrt-modified parasites were used to simulate the mutational trajectories accessible to parasites as they evolved CQR. Our results uncover unique contributions to parasite drug resistance and growth for mutations beyond K76T and predict critical roles for the CQ metabolite monodesethyl-CQ and the related quinoline-type drug amodiaquine in driving mutant pfcrt evolution. Modeling outputs further highlight the influence of parasite proliferation rates alongside gains in drug resistance in dictating successful trajectories. Our findings suggest that P. falciparum parasites have navigated constrained pfcrt adaptive landscapes by means of probabilistically rare mutational bursts that led to the infrequent emergence of pfcrt alleles in the field.
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Affiliation(s)
| | - Charin Modchang
- Department of Physics, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Lise Musset
- Laboratoire de Parasitologie, WHO Collaborating Center for Surveillance of Anti-Malarial Drug Resistance, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Thanat Chookajorn
- Genomics and Evolutionary Medicine Unit, Center of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY
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126
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Global selection of Plasmodium falciparum virulence antigen expression by host antibodies. Sci Rep 2016; 6:19882. [PMID: 26804201 PMCID: PMC4726288 DOI: 10.1038/srep19882] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 12/21/2015] [Indexed: 12/22/2022] Open
Abstract
Parasite proteins called PfEMP1 that are inserted on the surface of infected erythrocytes, play a key role in the severe pathology associated with infection by the Plasmodium falciparum malaria parasite. These proteins mediate binding of infected cells to the endothelial lining of blood vessels as a strategy to avoid clearance by the spleen and are major targets of naturally acquired immunity. PfEMP1 is encoded by a large multi-gene family called var. Mutually-exclusive transcriptional switching between var genes allows parasites to escape host antibodies. This study examined in detail the patterns of expression of var in a well-characterized sample of parasites from Kenyan Children. Instead of observing clear inverse relationships between the expression of broad sub-classes of PfEMP1, we found that expression of different PfEMP1 groups vary relatively independently. Parasite adaptation to host antibodies also appears to involve a general reduction in detectable var gene expression. We suggest that parasites switch both between different PfEMP1 variants and between high and low expression states. Such a strategy could provide a means of avoiding immunological detection and promoting survival under high levels of host immunity.
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127
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Abstract
The Plasmodium falciparum erythrocyte membrane protein 1 antigens that are inserted onto the surface of P. falciparum infected erythrocytes play a key role both in the pathology of severe malaria and as targets of naturally acquired immunity. They might be considered unlikely vaccine targets because they are extremely diverse. However, several lines of evidence suggest that underneath this molecular diversity there are a restricted set of epitopes which may act as effective targets for a vaccine against severe malaria. Here we review some of the recent developments in this area of research, focusing on work that has assessed the potential of these molecules as possible vaccine targets.
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128
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Wilson BA, Garud NR, Feder AF, Assaf ZJ, Pennings PS. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens. Mol Ecol 2016; 25:42-66. [PMID: 26578204 PMCID: PMC4943078 DOI: 10.1111/mec.13474] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/28/2015] [Accepted: 10/08/2015] [Indexed: 01/09/2023]
Abstract
Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance.
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Affiliation(s)
| | | | | | - Zoe J. Assaf
- Department of GeneticsStanford UniversityStanfordCA94305USA
| | - Pleuni S. Pennings
- Department of BiologySan Francisco State UniversityRoom 520Hensill Hall1600 Holloway AveSan FranciscoCA94132USA
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129
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Galatas B, Bassat Q, Mayor A. Malaria Parasites in the Asymptomatic: Looking for the Hay in the Haystack. Trends Parasitol 2015; 32:296-308. [PMID: 26708404 DOI: 10.1016/j.pt.2015.11.015] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/21/2015] [Accepted: 11/24/2015] [Indexed: 12/11/2022]
Abstract
With malaria elimination back on the international agenda, programs face the challenge of targeting all Plasmodium infections, not only symptomatic cases. As asymptomatic individuals are unlikely to seek treatment, they are missed by passive surveillance while remaining infectious to mosquitoes, thus acting as silent reservoirs of transmission. To estimate the risk of asymptomatic infections in various phases of malaria elimination, we need a deeper understanding of the underlying mechanisms favoring carriage over disease, which may involve both pathogen and host factors. Here we review our current knowledge on the determinants leading to Plasmodium falciparum symptomless infections. Understanding the host-pathogen interactions that are most likely to affect transitions between malaria disease states could guide the development of tools to tackle asymptomatic carriers in elimination settings.
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Affiliation(s)
- Beatriz Galatas
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Quique Bassat
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Alfredo Mayor
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.
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130
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Deroost K, Pham TT, Opdenakker G, Van den Steen PE. The immunological balance between host and parasite in malaria. FEMS Microbiol Rev 2015; 40:208-57. [PMID: 26657789 DOI: 10.1093/femsre/fuv046] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2015] [Indexed: 12/16/2022] Open
Abstract
Coevolution of humans and malaria parasites has generated an intricate balance between the immune system of the host and virulence factors of the parasite, equilibrating maximal parasite transmission with limited host damage. Focusing on the blood stage of the disease, we discuss how the balance between anti-parasite immunity versus immunomodulatory and evasion mechanisms of the parasite may result in parasite clearance or chronic infection without major symptoms, whereas imbalances characterized by excessive parasite growth, exaggerated immune reactions or a combination of both cause severe pathology and death, which is detrimental for both parasite and host. A thorough understanding of the immunological balance of malaria and its relation to other physiological balances in the body is of crucial importance for developing effective interventions to reduce malaria-related morbidity and to diminish fatal outcomes due to severe complications. Therefore, we discuss in this review the detailed mechanisms of anti-malarial immunity, parasite virulence factors including immune evasion mechanisms and pathogenesis. Furthermore, we propose a comprehensive classification of malaria complications according to the different types of imbalances.
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Affiliation(s)
- Katrien Deroost
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000 Leuven, Belgium The Francis Crick Institute, Mill Hill Laboratory, London, NW71AA, UK
| | - Thao-Thy Pham
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000 Leuven, Belgium
| | - Ghislain Opdenakker
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000 Leuven, Belgium
| | - Philippe E Van den Steen
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000 Leuven, Belgium
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131
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Abstract
Plasmodium falciparum is the protozoan parasite that causes most malaria-associated morbidity and mortality in humans with over 500,000 deaths annually. The disease symptoms are associated with repeated cycles of invasion and asexual multiplication inside red blood cells of the parasite. Partial, non-sterile immunity to P. falciparum malaria develops only after repeated infections and continuous exposure. The successful evasion of the human immune system relies on the large repertoire of antigenically diverse parasite proteins displayed on the red blood cell surface and on the merozoite membrane where they are exposed to the human immune system. Expression switching of these polymorphic proteins between asexual parasite generations provides an efficient mechanism to adapt to the changing environment in the host and to maintain chronic infection. This chapter discusses antigenic diversity and variation in the malaria parasite and our current understanding of the molecular mechanisms that direct the expression of these proteins.
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Affiliation(s)
- Michaela Petter
- Department of Medicine Royal Melbourne Hospital, Peter Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, VIC, 3010, Australia.
| | - Michael F Duffy
- Department of Medicine Royal Melbourne Hospital, Peter Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, VIC, 3010, Australia.
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132
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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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133
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Abstract
Since discovering PfEMP1 virulence proteins in Plasmodium falciparum, malariologists have struggled to reconcile their limitless sequence diversity with their binding to relatively few host receptors. In this issue of Cell Host & Microbe, Lau et al. (2015) explore how diverse PfEMP1s embrace EPCR, promoting parasite survival and killing African children.
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Affiliation(s)
- Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway, Room 3E-10A, Rockville, MD 20852, USA.
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134
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Childs LM, Buckee CO. Dissecting the determinants of malaria chronicity: why within-host models struggle to reproduce infection dynamics. J R Soc Interface 2015; 12:20141379. [PMID: 25673299 PMCID: PMC4345506 DOI: 10.1098/rsif.2014.1379] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The duration of infection is fundamental to the epidemiological behaviour of any infectious disease, but remains one of the most poorly understood aspects of malaria. In endemic areas, the malaria parasite Plasmodium falciparum can cause both acute, severe infections and asymptomatic, chronic infections through its interaction with the host immune system. Frequent superinfection and massive parasite genetic diversity make it extremely difficult to accurately measure the distribution of infection lengths, complicating the estimation of basic epidemiological parameters and the prediction of the impact of interventions. Mathematical models have qualitatively reproduced parasite dynamics early during infection, but reproducing long-lived chronic infections remains much more challenging. Here, we construct a model of infection dynamics to examine the consequences of common biological assumptions for the generation of chronicity and the impact of co-infection. We find that although a combination of host and parasite heterogeneities are capable of generating chronic infections, they do so only under restricted parameter choices. Furthermore, under biologically plausible assumptions, co-infection of parasite genotypes can alter the course of infection of both the resident and co-infecting strain in complex non-intuitive ways. We outline the most important puzzles for within-host models of malaria arising from our analysis, and their implications for malaria epidemiology and control.
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Affiliation(s)
- Lauren M Childs
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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135
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Real-Time Evolution of a Subtelomeric Gene Family in Candida albicans. Genetics 2015; 200:907-19. [PMID: 25956943 PMCID: PMC4512551 DOI: 10.1534/genetics.115.177451] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 05/05/2015] [Indexed: 01/02/2023] Open
Abstract
Subtelomeric regions of the genome are notable for high rates of sequence evolution and rapid gene turnover. Evidence of subtelomeric evolution has relied heavily on comparisons of historical evolutionary patterns to infer trends and frequencies of these events. Here, we describe evolution of the subtelomeric TLO gene family in Candida albicans during laboratory passaging for over 4000 generations. C. albicans is a commensal and opportunistic pathogen of humans and the TLO gene family encodes a subunit of the Mediator complex that regulates transcription and affects a range of virulence factors. We identified 16 distinct subtelomeric recombination events that altered the TLO repertoire. Ectopic recombination between subtelomeres on different chromosome ends occurred approximately once per 5000 generations and was often followed by loss of heterozygosity, resulting in the complete loss of one TLO gene sequence with expansion of another. In one case, recombination within TLO genes produced a novel TLO gene sequence. TLO copy number changes were biased, with some TLOs preferentially being copied to novel chromosome arms and other TLO genes being frequently lost. The majority of these nonreciprocal recombination events occurred either within the 3′ end of the TLO coding sequence or within a conserved 50-bp sequence element centromere-proximal to TLO coding sequence. Thus, subtelomeric recombination is a rapid mechanism of generating genotypic diversity through alterations in the number and sequence of related gene family members.
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136
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Kwiatkowski D. Malaria genomics: tracking a diverse and evolving parasite population. Int Health 2015; 7:82-4. [PMID: 25733556 PMCID: PMC4379983 DOI: 10.1093/inthealth/ihv007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 01/21/2015] [Accepted: 01/21/2015] [Indexed: 11/14/2022] Open
Abstract
Malaria parasites are continually evolving to evade the immune system and human attempts to control the disease. To eliminate malaria from regions where it is deeply entrenched we need ways of monitoring what is going on in the parasite population, detecting problematic changes as soon as they arise, and executing a prompt and effective response based on a deep understanding of this natural evolutionary process. Powerful new tools to address this problem are emerging from the fast-growing field of genomic epidemiology, driven by new sequencing technologies and computational methods that allow parasite genome variation to be studied in much greater detail and in many more samples than was previously considered possible. These new tools will provide a deep understanding of what is going on in the parasite population, generating actionable knowledge for strategic planning of control interventions, for monitoring their effects and steering them for greatest impact, and for raising the alert if things start to go wrong.
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Affiliation(s)
- Dominic Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA and Oxford University, Henry Wellcome Building for Molecular Physiology, Old Road Campus, Headington, Oxford, OX3 7BN, UK
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137
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Affiliation(s)
- David E. Arnot
- University of Edinburgh, School of Biological Sciences, Institute for Immunology and Infection Research, Edinburgh, United Kingdom
- * E-mail:
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