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Andradi-Brown C, Wichers-Misterek JS, von Thien H, Höppner YD, Scholz JAM, Hansson H, Filtenborg Hocke E, Gilberger TW, Duffy MF, Lavstsen T, Baum J, Otto TD, Cunnington AJ, Bachmann A. A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture. eLife 2024; 12:RP87726. [PMID: 38270586 PMCID: PMC10945709 DOI: 10.7554/elife.87726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
The pathogenesis of severe Plasmodium falciparum malaria involves cytoadhesive microvascular sequestration of infected erythrocytes, mediated by P. falciparum erythrocyte membrane protein 1 (PfEMP1). PfEMP1 variants are encoded by the highly polymorphic family of var genes, the sequences of which are largely unknown in clinical samples. Previously, we published new approaches for var gene profiling and classification of predicted binding phenotypes in clinical P. falciparum isolates (Wichers et al., 2021), which represented a major technical advance. Building on this, we report here a novel method for var gene assembly and multidimensional quantification from RNA-sequencing that outperforms the earlier approach of Wichers et al., 2021, on both laboratory and clinical isolates across a combination of metrics. Importantly, the tool can interrogate the var transcriptome in context with the rest of the transcriptome and can be applied to enhance our understanding of the role of var genes in malaria pathogenesis. We applied this new method to investigate changes in var gene expression through early transition of parasite isolates to in vitro culture, using paired sets of ex vivo samples from our previous study, cultured for up to three generations. In parallel, changes in non-polymorphic core gene expression were investigated. Modest but unpredictable var gene switching and convergence towards var2csa were observed in culture, along with differential expression of 19% of the core transcriptome between paired ex vivo and generation 1 samples. Our results cast doubt on the validity of the common practice of using short-term cultured parasites to make inferences about in vivo phenotype and behaviour.
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Affiliation(s)
- Clare Andradi-Brown
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Department of Life Sciences, Imperial College London, South KensingtonLondonUnited Kingdom
- Centre for Paediatrics and Child Health, Imperial College LondonLondonUnited Kingdom
| | - Jan Stephan Wichers-Misterek
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Heidrun von Thien
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Yannick D Höppner
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Judith AM Scholz
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
| | - Helle Hansson
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
- Department of Infectious Diseases, Copenhagen University HospitalCopenhagenDenmark
| | - Emma Filtenborg Hocke
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
- Department of Infectious Diseases, Copenhagen University HospitalCopenhagenDenmark
| | - Tim Wolf Gilberger
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Michael F Duffy
- Department of Microbiology and Immunology, University of MelbourneMelbourneAustralia
| | - Thomas Lavstsen
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
- Department of Infectious Diseases, Copenhagen University HospitalCopenhagenDenmark
| | - Jake Baum
- Department of Life Sciences, Imperial College London, South KensingtonLondonUnited Kingdom
- School of Biomedical Sciences, Faculty of Medicine & Health, UNSW, KensingtonSydneyUnited Kingdom
| | - Thomas D Otto
- School of Infection & Immunity, MVLS, University of GlasgowGlasgowUnited Kingdom
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Centre for Paediatrics and Child Health, Imperial College LondonLondonUnited Kingdom
| | - Anna Bachmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-StrasseHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-RiemsHamburgGermany
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Tan MH, Shim H, Chan YB, Day KP. Unravelling var complexity: Relationship between DBLα types and var genes in Plasmodium falciparum. FRONTIERS IN PARASITOLOGY 2023; 1. [PMID: 36998722 PMCID: PMC10060044 DOI: 10.3389/fpara.2022.1006341] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The enormous diversity and complexity of var genes that diversify rapidly by recombination has led to the exclusion of assembly of these genes from major genome initiatives (e.g., Pf6). A scalable solution in epidemiological surveillance of var genes is to use a small ‘tag’ region encoding the immunogenic DBLα domain as a marker to estimate var diversity. As var genes diversify by recombination, it is not clear the extent to which the same tag can appear in multiple var genes. This relationship between marker and gene has not been investigated in natural populations. Analyses of in vitro recombination within and between var genes have suggested that this relationship would not be exclusive. Using a dataset of publicly-available assembled var sequences, we test this hypothesis by studying DBLα-var relationships for four study sites in four countries: Pursat (Cambodia) and Mae Sot (Thailand), representing low malaria transmission, and Navrongo (Ghana) and Chikwawa (Malawi), representing high malaria transmission. In all study sites, DBLα-var relationships were shown to be predominantly 1-to-1, followed by a second largest proportion of 1-to-2 DBLα-var relationships. This finding indicates that DBLα tags can be used to estimate not just DBLα diversity but var gene diversity when applied in a local endemic area. Epidemiological applications of this result are discussed.
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Affiliation(s)
- Mun Hua Tan
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute, Melbourne, VIC, Australia
| | - Heejung Shim
- School of Mathematics and Statistics/Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Yao-ban Chan
- School of Mathematics and Statistics/Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Karen P. Day
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute, Melbourne, VIC, Australia
- CORRESPONDENCE Karen P. Day,
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Successful Profiling of Plasmodium falciparum var Gene Expression in Clinical Samples via a Custom Capture Array. mSystems 2021; 6:e0022621. [PMID: 34846163 PMCID: PMC8631312 DOI: 10.1128/msystems.00226-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
var genes encode Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) antigens. These highly diverse antigens are displayed on the surface of infected erythrocytes and play a critical role in immune evasion and sequestration of infected erythrocytes. Studies of var expression using non-leukocyte-depleted blood are challenging because of the predominance of host genetic material and lack of conserved var segments. Our goal was to enrich for parasite RNA, allowing de novo assembly of var genes and detection of expressed novel variants. We used two overall approaches: (i) enriching for total mRNA in the sequencing library preparations and (ii) enriching for parasite RNA with a custom capture array based on Roche’s SeqCap EZ enrichment system. The capture array was designed with probes based on the whole 3D7 reference genome and an additional >4,000 full-length var gene sequences from other P. falciparum strains. We tested each method on RNA samples from Malian children with severe or uncomplicated malaria infections. All reads mapping to the human genome were removed, the remaining reads were assembled de novo into transcripts, and from these, var-like transcripts were identified and annotated. The capture array produced the longest maximum length and largest numbers of var gene transcripts in each sample, particularly in samples with low parasitemia. Identifying the most-expressed var gene sequences in whole-blood clinical samples without the need for extensive processing or generating sample-specific reference genome data is critical for understanding the role of PfEMP1s in malaria pathogenesis. IMPORTANCE Malaria parasites display antigens on the surface of infected red blood cells in the human host that facilitate attachment to blood vessels, contributing to the severity of infection. These antigens are highly variable, allowing the parasite to evade the immune system. Identifying these expressed antigens is critical to understanding the development of severe malarial disease. However, clinical samples contain limited amounts of parasite genetic material, a challenge for sequencing efforts further compounded by the extreme diversity of the parasite surface antigens. We present a method that enriches for these antigen sequences in clinical samples using a custom capture array, requiring minimal processing in the field. While our results are focused on the malaria parasite Plasmodium falciparum, this approach has broad applicability to other highly diverse antigens from other parasites and pathogens such as those that cause giardiasis and leishmaniasis.
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Tessema SK, Hathaway NJ, Teyssier NB, Murphy M, Chen A, Aydemir O, Duarte EM, Simone W, Colborn J, Saute F, Crawford E, Aide P, Bailey JA, Greenhouse B. Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome. J Infect Dis 2020; 225:1227-1237. [PMID: 32840625 PMCID: PMC8974853 DOI: 10.1093/infdis/jiaa527] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/24/2020] [Indexed: 01/28/2023] Open
Abstract
Background Targeted next-generation sequencing offers the potential for consistent, deep coverage of information-rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited. Methods A bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, whole-genome sequencing data were generated for the same controls. Results Using publicly available genomes, 4465 high-diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median expected heterozygosity = 0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%), and sensitivity (90% for haplotypes with 5% within sample frequency in dried blood spots with 100 parasites/µL). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic single-nucleotide polymorphism barcodes. Conclusions The bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high-throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.
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Affiliation(s)
- Sofonias K Tessema
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Nicholas J Hathaway
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Noam B Teyssier
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Maxwell Murphy
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Anna Chen
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Elias M Duarte
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Wilson Simone
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - James Colborn
- Clinton Health Access Initiative, Maputo, Mozambique
| | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Bryan Greenhouse
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, California, United States
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Moser KA, Drábek EF, Dwivedi A, Stucke EM, Crabtree J, Dara A, Shah Z, Adams M, Li T, Rodrigues PT, Koren S, Phillippy AM, Munro JB, Ouattara A, Sparklin BC, Dunning Hotopp JC, Lyke KE, Sadzewicz L, Tallon LJ, Spring MD, Jongsakul K, Lon C, Saunders DL, Ferreira MU, Nyunt MM, Laufer MK, Travassos MA, Sauerwein RW, Takala-Harrison S, Fraser CM, Sim BKL, Hoffman SL, Plowe CV, Silva JC. Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential. Genome Med 2020; 12:6. [PMID: 31915075 PMCID: PMC6950926 DOI: 10.1186/s13073-019-0708-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plasmodium falciparum (Pf) whole-organism sporozoite vaccines have been shown to provide significant protection against controlled human malaria infection (CHMI) in clinical trials. Initial CHMI studies showed significantly higher durable protection against homologous than heterologous strains, suggesting the presence of strain-specific vaccine-induced protection. However, interpretation of these results and understanding of their relevance to vaccine efficacy have been hampered by the lack of knowledge on genetic differences between vaccine and CHMI strains, and how these strains are related to parasites in malaria endemic regions. METHODS Whole genome sequencing using long-read (Pacific Biosciences) and short-read (Illumina) sequencing platforms was conducted to generate de novo genome assemblies for the vaccine strain, NF54, and for strains used in heterologous CHMI (7G8 from Brazil, NF166.C8 from Guinea, and NF135.C10 from Cambodia). The assemblies were used to characterize sequences in each strain relative to the reference 3D7 (a clone of NF54) genome. Strains were compared to each other and to a collection of clinical isolates (sequenced as part of this study or from public repositories) from South America, sub-Saharan Africa, and Southeast Asia. RESULTS While few variants were detected between 3D7 and NF54, we identified tens of thousands of variants between NF54 and the three heterologous strains. These variants include SNPs, indels, and small structural variants that fall in regulatory and immunologically important regions, including transcription factors (such as PfAP2-L and PfAP2-G) and pre-erythrocytic antigens that may be key for sporozoite vaccine-induced protection. Additionally, these variants directly contributed to diversity in immunologically important regions of the genomes as detected through in silico CD8+ T cell epitope predictions. Of all heterologous strains, NF135.C10 had the highest number of unique predicted epitope sequences when compared to NF54. Comparison to global clinical isolates revealed that these four strains are representative of their geographic origin despite long-term culture adaptation; of note, NF135.C10 is from an admixed population, and not part of recently formed subpopulations resistant to artemisinin-based therapies present in the Greater Mekong Sub-region. CONCLUSIONS These results will assist in the interpretation of vaccine efficacy of whole-organism vaccines against homologous and heterologous CHMI.
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Affiliation(s)
- Kara A. Moser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Present address: Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, USA
| | - Elliott F. Drábek
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Emily M. Stucke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Antoine Dara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Zalak Shah
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Tao Li
- Sanaria, Inc., Rockville, MD 20850 USA
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - James B. Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Benjamin C. Sparklin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Kirsten E. Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Luke J. Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Michele D. Spring
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Krisada Jongsakul
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chanthap Lon
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - David L. Saunders
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Present address: Warfighter Expeditionary Medicine and Treatment, US Army Medical Material Development Activity, Frederick, USA
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Myaing M. Nyunt
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Present address: Duke Global Health Institute, Duke University, Durham, NC 27708 USA
| | - Miriam K. Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Mark A. Travassos
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Robert W. Sauerwein
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | | | | | - Christopher V. Plowe
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Present address: Duke Global Health Institute, Duke University, Durham, NC 27708 USA
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
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Otto TD, Assefa SA, Böhme U, Sanders MJ, Kwiatkowski D, Berriman M, Newbold C. Evolutionary analysis of the most polymorphic gene family in falciparum malaria. Wellcome Open Res 2019; 4:193. [PMID: 32055709 PMCID: PMC7001760 DOI: 10.12688/wellcomeopenres.15590.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
The var gene family of the human malaria parasite Plasmodium falciparum encode proteins that are crucial determinants of both pathogenesis and immune evasion and are highly polymorphic. Here we have assembled nearly complete var gene repertoires from 2398 field isolates and analysed a normalised set of 714 from across 12 countries. This therefore represents the first large scale attempt to catalogue the worldwide distribution of var gene sequences We confirm the extreme polymorphism of this gene family but also demonstrate an unexpected level of sequence sharing both within and between continents. We show that this is likely due to both the remnants of selective sweeps as well as a worrying degree of recent gene flow across continents with implications for the spread of drug resistance. We also address the evolution of the var repertoire with respect to the ancestral genes within the Laverania and show that diversity generated by recombination is concentrated in a number of hotspots. An analysis of the subdomain structure indicates that some existing definitions may need to be revised From the analysis of this data, we can now understand the way in which the family has evolved and how the diversity is continuously being generated. Finally, we demonstrate that because the genes are distributed across the genome, sequence sharing between genotypes acts as a useful population genetic marker.
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Affiliation(s)
- Thomas D. Otto
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
| | - Sammy A. Assefa
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ulrike Böhme
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Dominic Kwiatkowski
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Pf3k consortium
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Matt Berriman
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Chris Newbold
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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7
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Stucke EM, Niangaly A, Berry AA, Bailey JA, Coulibaly D, Ouattara A, Lyke KE, Laurens MB, Dara A, Adams M, Pablo J, Jasinskas A, Nakajima R, Zhou AE, Agrawal S, Friedman-Klabanoff DJ, Takala-Harrison S, Kouriba B, Kone AK, Rowe JA, Doumbo OK, Felgner PL, Thera MA, Plowe CV, Travassos MA. Serologic responses to the PfEMP1 DBL-CIDR head structure may be a better indicator of malaria exposure than those to the DBL-α tag. Malar J 2019; 18:273. [PMID: 31409360 PMCID: PMC6692945 DOI: 10.1186/s12936-019-2905-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/05/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) antigens play a critical role in host immune evasion. Serologic responses to these antigens have been associated with protection from clinical malaria, suggesting that antibodies to PfEMP1 antigens may contribute to natural immunity. The first N-terminal constitutive domain in a PfEMP1 is the Duffy binding-like alpha (DBL-α) domain, which contains a 300 to 400 base pair region unique to each particular protein (the DBL-α "tag"). This DBL-α tag has been used as a marker of PfEMP1 diversity and serologic responses in malaria-exposed populations. In this study, using sera from a malaria-endemic region, responses to DBL-α tags were compared to responses to the corresponding entire DBL-α domain (or "parent" domain) coupled with the succeeding cysteine-rich interdomain region (CIDR). METHODS A protein microarray populated with DBL-α tags, the parent DBL-CIDR head structures, and downstream PfEMP1 protein fragments was probed with sera from Malian children (aged 1 to 6 years) and adults from the control arms of apical membrane antigen 1 (AMA1) vaccine clinical trials before and during a malaria transmission season. Serological responses to the DBL-α tag and the DBL-CIDR head structure were measured and compared in children and adults, and throughout the season. RESULTS Malian serologic responses to a PfEMP1's DBL-α tag region did not correlate with seasonal malaria exposure, or with responses to the parent DBL-CIDR head structure in either children or adults. Parent DBL-CIDR head structures were better indicators of malaria exposure. CONCLUSIONS Larger PfEMP1 domains may be better indicators of malaria exposure than short, variable PfEMP1 fragments such as DBL-α tags. PfEMP1 head structures that include conserved sequences appear particularly well suited for study as serologic predictors of malaria exposure.
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Affiliation(s)
- Emily M Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Andrea A Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Drissa Coulibaly
- Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Amed Ouattara
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kirsten E Lyke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew B Laurens
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Antoine Dara
- Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Matthew Adams
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jozelyn Pablo
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, CA, USA
| | - Algis Jasinskas
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, CA, USA
| | - Rie Nakajima
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, CA, USA
| | - Albert E Zhou
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sonia Agrawal
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - DeAnna J Friedman-Klabanoff
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye K Kone
- Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - J Alexandra Rowe
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Philip L Felgner
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, CA, USA
| | - Mahamadou A Thera
- Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Mark A Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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Kamaliddin C, Rombaut D, Guillochon E, Royo J, Ezinmegnon S, Agbota G, Huguet S, Guemouri S, Peirera C, Coppée R, Broussard C, Alao JM, Aubouy A, Guillonneau F, Deloron P, Bertin GI. From genomic to LC-MS/MS evidence: Analysis of PfEMP1 in Benin malaria cases. PLoS One 2019; 14:e0218012. [PMID: 31251748 PMCID: PMC6599223 DOI: 10.1371/journal.pone.0218012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/23/2019] [Indexed: 11/18/2022] Open
Abstract
Background PfEMP1 is the major protein from parasitic origin involved in the pathophysiology of severe malaria, and PfEMP1 domain subtypes are associated with the infection outcome. In addition, PfEMP1 variability is endless and current publicly available protein repositories do not reflect the high diversity of the sequences of PfEMP1 proteins. The identification of PfEMP1 protein sequences expressed with samples remains challenging. The aim of our study is to identify the different PfEMP1 proteins variants expressed within patient samples, and therefore identify PfEMP1 proteins domains expressed by patients presenting uncomplicated malaria or severe malaria in malaria endemic setting in Cotonou, Benin. Methods We performed a multi-omic approach to decipher PfEMP1 expression at the patient’s level in different clinical settings. Using a combination of whole genome sequencing approach and RNA sequencing, we were able to identify new PfEMP1 sequences and created a new custom protein database. This database was used for protein identification in mass spectrometry analysis. Results The differential expression analysis of RNAsequencing data shows an increased expression of the var domains transcripts DBLα1.7, DBLα1.1, DBLα2 and DBLβ12 in samples from patients suffering from Cerebral Malaria compared to Uncomplicated Malaria. Our approach allowed us to attribute PfEMP1 sequences to each sample and identify new peptides associated to PfEMP1 proteins in mass spectrometry. Conclusion We highlighted the diversity of the PfEMP1 sequences from field sample compared to reference sequences repositories and confirmed the validity of our approach. These findings should contribute to further vaccine development strategies based on PfEMP1 proteins.
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Affiliation(s)
| | - David Rombaut
- 3p5 Proteomic Facility, Université de Paris, Paris, France
| | | | - Jade Royo
- UMR 152 – PHARMADEV, IRD, Paul Sabatier Toulouse III University, Toulouse, France
| | - Sem Ezinmegnon
- UMR 261 – MERIT, IRD, Université de Paris, Paris, France
- Centre pour la Recherche et l’Etude du paludisme associé à la grossesse et à l’enfance, Cotonou, Bénin
| | - Gino Agbota
- UMR 261 – MERIT, IRD, Université de Paris, Paris, France
- Centre pour la Recherche et l’Etude du paludisme associé à la grossesse et à l’enfance, Cotonou, Bénin
| | - Stéphanie Huguet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Saclay, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA Université Paris-Diderot, Sorbonne Paris-Cité, Gif sur Yvette, France
| | - Sayeh Guemouri
- UMR 261 – MERIT, IRD, Université de Paris, Paris, France
| | - Céline Peirera
- UMR 261 – MERIT, IRD, Université de Paris, Paris, France
| | - Romain Coppée
- UMR 261 – MERIT, IRD, Université de Paris, Paris, France
| | | | | | - Agnès Aubouy
- UMR 152 – PHARMADEV, IRD, Paul Sabatier Toulouse III University, Toulouse, France
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9
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Ruybal-Pesántez S, Tiedje KE, Tonkin-Hill G, Rask TS, Kamya MR, Greenhouse B, Dorsey G, Duffy MF, Day KP. Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda. Sci Rep 2017; 7:11810. [PMID: 28924231 PMCID: PMC5603532 DOI: 10.1038/s41598-017-11814-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/30/2017] [Indexed: 12/18/2022] Open
Abstract
Plasmodium falciparum causes a spectrum of malarial disease from asymptomatic to uncomplicated through to severe. Investigations of parasite virulence have associated the expression of distinct variants of the major surface antigen of the blood stages known as Pf EMP1 encoded by up to 60 var genes per genome. Looking at the population genomics of var genes in cases of uncomplicated malaria, we set out to determine if there was any evidence of a selective sweep of specific var genes or clonal epidemic structure related to the incidence of uncomplicated disease in children. By sequencing the conserved DBLα domain of var genes from six sentinel sites in Uganda we found that the parasites causing uncomplicated P. falciparum disease in children were highly diverse and that every child had a unique var DBLα repertoire. Despite extensive var DBLα diversity and minimal overlap between repertoires, specific DBLα types and groups were conserved at the population level across Uganda. This pattern was the same regardless of the geographic distance or malaria transmission intensity. These data lead us to propose that any parasite can cause uncomplicated malarial disease and that these diverse parasite repertoires are composed of both upsA and non-upsA var gene groups.
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Affiliation(s)
- Shazia Ruybal-Pesántez
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia.,Department of Microbiology, New York University, New York, USA
| | - Kathryn E Tiedje
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia.,Department of Microbiology, New York University, New York, USA
| | | | - Thomas S Rask
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia.,Department of Microbiology, New York University, New York, USA
| | - Moses R Kamya
- School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, USA
| | - Grant Dorsey
- Department of Medicine, University of California, San Francisco, USA
| | - Michael F Duffy
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | - Karen P Day
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia. .,Department of Microbiology, New York University, New York, USA.
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10
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Dara A, Travassos MA, Adams M, Schaffer DeRoo S, Drábek EF, Agrawal S, Laufer MK, Plowe CV, Silva JC. A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples. Malar J 2017; 16:343. [PMID: 28818101 PMCID: PMC5561619 DOI: 10.1186/s12936-017-1976-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 08/04/2017] [Indexed: 11/14/2022] Open
Abstract
Background VAR2CSA, a member of the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family, mediates the binding of P. falciparum-infected erythrocytes to chondroitin sulfate A, a surface-associated molecule expressed in placental cells, and plays a central role in the pathogenesis of placental malaria. VAR2CSA is a target of naturally acquired immunity and, as such, is a leading vaccine candidate against placental malaria. This protein is very polymorphic and technically challenging to sequence. Published var2csa sequences, mostly limited to specific domains, have been generated through the sequencing of cloned PCR amplicons using capillary electrophoresis, a method that is both time consuming and costly, and that performs poorly when applied to clinical samples that are commonly polyclonal. A next-generation sequencing platform, Pacific Biosciences (PacBio), offers an alternative approach to overcome these issues. Methods PCR primers were designed that target a 5 kb segment in the 5′ end of var2csa and the resulting amplicons were sequenced using PacBio sequencing. The primers were optimized using two laboratory strains and were validated on DNA from 43 clinical samples, extracted from dried blood spots on filter paper or from cryopreserved P. falciparum-infected erythrocytes. Sequence reads were assembled using the SMRT-analysis ConsensusTools module. Results Here, a PacBio sequencing-based approach for recovering a segment encoding the majority of VAR2CSA’s extracellular region is described; this segment includes the totality of the first four domains in the 5′ end of var2csa (~5 kb), from clinical malaria samples. The feasibility of the method is demonstrated, showing a high success rate from cryopreserved samples and more limited success from dried blood spots stored at room temperature, and characterized the genetic variation of the var2csa locus. Conclusions This method will facilitate a detailed analysis of var2csa genetic variation and can be adapted to sequence other hypervariable P. falciparum genes. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-1976-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antoine Dara
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark A Travassos
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew Adams
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sarah Schaffer DeRoo
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elliott F Drábek
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sonia Agrawal
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Miriam K Laufer
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Christopher V Plowe
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
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