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Ciubotariu II, Broyles BK, Xie S, Thimmapuram J, Mwenda MC, Mambwe B, Mulube C, Matoba J, Schue JL, Moss WJ, Bridges DJ, He Q, Carpi G. Diversity and selection analyses identify transmission-blocking antigens as the optimal vaccine candidates in Plasmodium falciparum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.11.24307175. [PMID: 38766239 PMCID: PMC11100930 DOI: 10.1101/2024.05.11.24307175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background A highly effective vaccine for malaria remains an elusive target, at least in part due to the under-appreciated natural parasite variation. This study aimed to investigate genetic and structural variation, and immune selection of leading malaria vaccine candidates across the Plasmodium falciparum's life cycle. Methods We analyzed 325 P. falciparum whole genome sequences from Zambia, in addition to 791 genomes from five other African countries available in the MalariaGEN Pf3k Rdatabase. Ten vaccine antigens spanning three life-history stages were examined for genetic and structural variations, using population genetics measures, haplotype network analysis, and 3D structure selection analysis. Findings Among the ten antigens analyzed, only three in the transmission-blocking vaccine category display P. falciparum 3D7 as the dominant haplotype. The antigens AMA1, CSP, MSP119 and CelTOS, are much more diverse than the other antigens, and their epitope regions are under moderate to strong balancing selection. In contrast, Rh5, a blood stage antigen, displays low diversity yet slightly stronger immune selection in the merozoite-blocking epitope region. Except for CelTOS, the transmission-blocking antigens Pfs25, Pfs48/45, Pfs230, Pfs47, and Pfs28 exhibit minimal diversity and no immune selection in epitopes that induce strain-transcending antibodies, suggesting potential effectiveness of 3D7-based vaccines in blocking transmission. Interpretations These findings offer valuable insights into the selection of optimal vaccine candidates against P. falciparum. Based on our results, we recommend prioritizing conserved merozoite antigens and transmission-blocking antigens. Combining these antigens in multi-stage approaches may be particularly promising for malaria vaccine development initiatives. Funding Purdue Department of Biological Sciences; Puskas Memorial Fellowship; National Institute of Allergy and Infectious Diseases (U19AI089680).
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Affiliation(s)
- Ilinca I. Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Bradley K. Broyles
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Mulenga C. Mwenda
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | | | - Jessica L. Schue
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - William J. Moss
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, Indiana, USA
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MacDonald NJ, Singh K, Reiter K, Nguyen V, Shimp R, Gittis AG, Chen B, Burkhardt M, Zhang B, Wang Z, Herrera R, Moler M, Lee DY, Orr-Gonzalez S, Herrod J, Lambert LE, Rausch KM, Muratova O, Jones DS, Wu Y, Jin AJ, Garboczi DN, Duffy PE, Narum DL. Structural and immunological differences in Plasmodium falciparum sexual stage transmission-blocking vaccines comprised of Pfs25-EPA nanoparticles. NPJ Vaccines 2023; 8:56. [PMID: 37061547 PMCID: PMC10105769 DOI: 10.1038/s41541-023-00655-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 03/29/2023] [Indexed: 04/17/2023] Open
Abstract
Development of a malaria vaccine that blocks transmission of different parasite stages to humans and mosquitoes is considered critical for elimination efforts. A vaccine using Pfs25, a protein on the surface of zygotes and ookinetes, is under investigation as a transmission-blocking vaccine (TBV) that would interrupt parasite passage from mosquitoes to humans. The most extensively studied Pfs25 TBVs use Pichia pastoris-produced recombinant forms of Pfs25, chemically conjugated to a recombinant carrier protein, ExoProtein A (EPA). The recombinant form of Pfs25 first used in humans was identified as Pfs25H, which contained a total of 14 heterologous amino acid residues located at the amino- and carboxyl-termini including a His6 affinity tag. A second recombinant Pfs25, identified as Pfs25M, was produced to remove the heterologous amino acid residues and conjugated to EPA (Pfs25M-EPA). Here, monomeric Pfs25M was characterized biochemically and biophysically for identity, purity, and integrity including protein structure to assess its comparability with Pfs25H. Although the biological activities of Pfs25H and Pfs25M, whether generated by monomeric forms or conjugated nanoparticles, appeared similar, fine-mapping studies with two transmission-blocking monoclonal antibodies detected structural and immunological differences. In addition, evaluation of antisera generated against conjugated Pfs25H or Pfs25M nanoparticles in nonhuman primates identified polyclonal IgG that recognized these structural differences.
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Affiliation(s)
- Nicholas J MacDonald
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Kavita Singh
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Karine Reiter
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Vu Nguyen
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Richard Shimp
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Apostolos G Gittis
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Beth Chen
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Martin Burkhardt
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Zhixiong Wang
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Raul Herrera
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Mackenzie Moler
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Duck-Yeon Lee
- National Heart, Lung, and Blood Institute, Bethesda, MD, 20814, USA
| | - Sachy Orr-Gonzalez
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Jessica Herrod
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Lynn E Lambert
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Kelly M Rausch
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Olga Muratova
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - David S Jones
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Yimin Wu
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Albert J Jin
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - David N Garboczi
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA
| | - David L Narum
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 29 Lincoln Drive, Bethesda, MD, 20892, USA.
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Ochwedo KO, Ariri FO, Otambo WO, Magomere EO, Debrah I, Onyango SA, Orondo PW, Atieli HE, Ogolla SO, Otieno ACA, Mukabana WR, Githeko AK, Lee MC, Yan G, Zhong D, Kazura JW. Rare Alleles and Signatures of Selection on the Immunodominant Domains of Pfs230 and Pfs48/45 in Malaria Parasites From Western Kenya. Front Genet 2022; 13:867906. [PMID: 35656326 PMCID: PMC9152164 DOI: 10.3389/fgene.2022.867906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023] Open
Abstract
Background: Malaria elimination and eradication efforts can be advanced by including transmission-blocking or reducing vaccines (TBVs) alongside existing interventions. Key transmission-blocking vaccine candidates, such as Pfs230 domain one and Pfs48/45 domain 3, should be genetically stable to avoid developing ineffective vaccines due to antigenic polymorphisms. We evaluated genetic polymorphism and temporal stability of Pfs230 domain one and Pfs48/45 domain three in Plasmodium falciparum parasites from western Kenya. Methods: Dry blood spots on filter paper were collected from febrile malaria patients reporting to community health facilities in endemic areas of Homa Bay and Kisumu Counties and an epidemic-prone area of Kisii County in 2018 and 2019. Plasmodium speciation was performed using eluted DNA and real-time PCR. Amplification of the target domains of the two Pfs genes was performed on P. falciparum positive samples. We sequenced Pfs230 domain one on 156 clinical isolates and Pfs48/45 domain three on 118 clinical isolates to infer the levels of genetic variability, signatures of selection, genetic diversity indices and perform other evolutionary analyses. Results: Pfs230 domain one had low nucleotide diversity (π = 0.15 × 10-2) with slight variation per study site. Six polymorphic sites with nonsynonymous mutations and eight haplotypes were discovered. I539T was a novel variant, whereas G605S was nearing fixation. Pfs48/45 domain three had a low π (0.063 × 10-2), high conservation index, and three segregating sites, resulting in nonsynonymous mutation and four haplotypes. Some loci of Pfs230 D1 were in positive or negative linkage disequilibrium, had negative or positive selection signatures, and others (1813, 1955) and (1813, 1983) had a history of recombination. Mutated loci pairs in Pfs48/45 domain three had negative linkage disequilibrium, and some had negative and positive Tajima's D values with no history of recombination events. Conclusion: The two transmission blocking vaccine candidates have low nucleotide diversity, a small number of zone-specific variants, high nucleotide conservation index, and high frequency of rare alleles. With the near fixation a polymorphic site and the proximity of mutated codons to antibody binding epitopes, it will be necessary to continue monitoring sequence modifications of these domains when designing TBVs that include Pfs230 and Pfs48/45 antigens.
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Affiliation(s)
- Kevin O. Ochwedo
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya,Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Fredrick O. Ariri
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Department of Zoology, School of Physical and Biological Sciences, Maseno University, Kisumu, Kenya
| | - Wilfred O. Otambo
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Department of Zoology, School of Physical and Biological Sciences, Maseno University, Kisumu, Kenya
| | - Edwin O. Magomere
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Department of Biochemistry, Egerton University, Nakuru, Kenya
| | - Isaiah Debrah
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,West Africa Centre for Cell Biology of Infectious Pathogen, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Shirley A. Onyango
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,School of Zoological Sciences, Kenyatta University, Nairobi, Kenya
| | - Pauline W. Orondo
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Harrysone E. Atieli
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Sidney O. Ogolla
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Antony C. A. Otieno
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Wolfgang R. Mukabana
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya,Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Andrew K. Githeko
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Ming-Chieh Lee
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States,*Correspondence: Daibin Zhong,
| | - James W. Kazura
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, United States
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