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Plata-Pineda SE, Cárdenas-Munévar LX, Castro-Cavadía CJ, Buitrago SP, Garzón-Ospina D. Evaluating the genetic diversity of the Plasmodium vivax siap2 locus: A promising candidate for an effective malaria vaccine? Acta Trop 2024; 251:107111. [PMID: 38151069 DOI: 10.1016/j.actatropica.2023.107111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/27/2023] [Accepted: 12/24/2023] [Indexed: 12/29/2023]
Abstract
Malaria is the deadliest parasitic disease in the world. Traditional control measures have become less effective; hence, there is a need to explore alternative strategies, such as antimalarial vaccines. However, designing an anti-Plasmodium vivax vaccine is considered a challenge due to the complex parasite biology and the antigens' high genetic diversity. Recently, the sporozoite invasion-associated protein 2 (SIAP2) has been suggested as a potential antigen to be considered in vaccine design due to its significance during hepatocyte invasion. However, its use may be limited by the incomplete understanding of gene/protein diversity. Here, the genetic diversity of pvsiap2 using P. vivax DNA samples from Colombia was assessed. Through PCR amplification and sequencing, we compared the Colombian sequences with available worldwide sequences, revealing that pvsiap2 displays low genetic diversity. Molecular evolutionary analyses showed that pvsiap2 appears to be influenced by directional selection. Moreover, the haplotypes found differ by a few mutational steps and several of them were shared between different geographical areas. On the other hand, several conserved regions within PvSIAP2 were predicted as potential B-cell or T-cell epitopes. Considering these characteristics and its role in hepatocyte invasion, the PvSIAP2 protein emerges as a promising antigen to be considered in a multi-antigen-multi-stage (multivalent) fully effective vaccine against P. vivax malaria.
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Affiliation(s)
- Sergio E Plata-Pineda
- School of Biological Sciences, Grupo de Estudios en Genética y Biología Molecular (GEBIMOL), Universidad Pedagógica y Tecnológica de Colombia - UPTC, Tunja, Boyacá, Colombia
| | - Laura X Cárdenas-Munévar
- School of Biological Sciences, Grupo de Estudios en Genética y Biología Molecular (GEBIMOL), Universidad Pedagógica y Tecnológica de Colombia - UPTC, Tunja, Boyacá, Colombia
| | - Carlos J Castro-Cavadía
- Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba (GIMBIC), School of Health Sciences, Universidad de Córdoba, Montería, Córdoba, Colombia
| | - Sindy P Buitrago
- School of Biological Sciences, Grupo de Estudios en Genética y Biología Molecular (GEBIMOL), Universidad Pedagógica y Tecnológica de Colombia - UPTC, Tunja, Boyacá, Colombia; Population Genetics And Molecular Evolution (PGAME), Fundación Scient, Tunja, Boyacá, Colombia
| | - Diego Garzón-Ospina
- School of Biological Sciences, Grupo de Estudios en Genética y Biología Molecular (GEBIMOL), Universidad Pedagógica y Tecnológica de Colombia - UPTC, Tunja, Boyacá, Colombia; Population Genetics And Molecular Evolution (PGAME), Fundación Scient, Tunja, Boyacá, Colombia.
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2
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Ahmed MA, Baruah P, Saif A, Han JH, Al-Zharani M, Wazid SW, Alkahtani S, Patgiri SJ, Al-Eissa MS, Quan FS. In Silico Analysis Reveals High Levels of Genetic Diversity of Plasmodium knowlesi Cell Traversal Protein for Ookinetes and Sporozoites ( PkCelTOS) in Clinical Samples. Trop Med Infect Dis 2023; 8:380. [PMID: 37624318 PMCID: PMC10458480 DOI: 10.3390/tropicalmed8080380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The cell-traversal protein for ookinetes and sporozoites (CelTOS), expressed on the surface of ookinetes and sporozoitesin Plasmodium species, is a promising malaria vaccine candidate. CelTOS is essential for parasite invasion into mosquito midgut and human hepatocytes, thereby contributing to malaria transmission and disease pathogenesis. This study explores the genetic diversity, polymorphisms, haplotypes, natural selection, phylogenetic analysis, and epitope prediction in the full-length Plasmodium knowlesi CelTOS gene in clinical samples from Sarawak, Malaysian Borneo, and long-term laboratory strains from Peninsular Malaysia and the Philippines. Our analysis revealed a high level of genetic variation in the PkCelTOS gene, with a nucleotide diversity of π ~ 0.021, which was skewed towards the 3' end of the gene. This level of diversity is double that observed in PfCelTOS and 20 times that observed in PvCelTOS from worldwide clinical samples. Tests of natural selection revealed evidence for positive selection within clinical samples. Phylogenetic analysis of the amino acid sequence of PkCelTOS revealed the presence of two distinct groups, although no geographical clustering was observed. Epitope prediction analysis identified two potential epitopes (96AQLKATA102 and 124TIKPPRIKED133) using the IEDB server and one epitope (125IKPPRIKED133) by Bcepred server on the C' terminal region of PkCelTOS protein. Both the servers predicted a common epitope region of nine amino acid length (IKPPRIKED) peptide, which can be studied in the future as a potential candidate for vaccine development. These findings shed light on the genetic diversity, polymorphism, haplotypes, and natural selection within PkCelTOS in clinical samples and provide insights about its future prospects as a potential candidate for P. knowlesi malaria vaccine development.
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Affiliation(s)
- Md Atique Ahmed
- ICMR-Regional Medical Research Centre, NE Region, Dibrugarh 786010, Assam, India (S.J.P.)
| | - Pratisthita Baruah
- ICMR-Regional Medical Research Centre, NE Region, Dibrugarh 786010, Assam, India (S.J.P.)
| | - Ahmed Saif
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, King Khalid University, Abha 61321, Saudi Arabia
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Mohammed Al-Zharani
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSU), Riyadh 11623, Saudi Arabia (M.S.A.-E.)
| | - Syeda Wasfeea Wazid
- Arogyo Society of Health, Welfare and Support (ASHWAS), Guwahati 785640, Assam, India;
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saurav J. Patgiri
- ICMR-Regional Medical Research Centre, NE Region, Dibrugarh 786010, Assam, India (S.J.P.)
| | - Mohammed S. Al-Eissa
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSU), Riyadh 11623, Saudi Arabia (M.S.A.-E.)
| | - Fu-Shi Quan
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, Core Research Institute (CRI), Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Medical Zoology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
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Habtamu K, Petros B, Yan G. Plasmodium vivax: the potential obstacles it presents to malaria elimination and eradication. Trop Dis Travel Med Vaccines 2022; 8:27. [PMID: 36522671 PMCID: PMC9753897 DOI: 10.1186/s40794-022-00185-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
Initiatives to eradicate malaria have a good impact on P. falciparum malaria worldwide. P. vivax, however, still presents significant difficulties. This is due to its unique biological traits, which, in comparison to P. falciparum, pose serious challenges for malaria elimination approaches. P. vivax's numerous distinctive characteristics and its ability to live for weeks to years in liver cells in its hypnozoite form, which may elude the human immune system and blood-stage therapy and offer protection during mosquito-free seasons. Many malaria patients are not fully treated because of contraindications to primaquine use in pregnant and nursing women and are still vulnerable to P. vivax relapses, although there are medications that could radical cure P. vivax. Additionally, due to CYP2D6's highly variable genetic polymorphism, the pharmacokinetics of primaquine may be impacted. Due to their inability to metabolize PQ, some CYP2D6 polymorphism alleles can cause patients to not respond to treatment. Tafenoquine offers a radical treatment in a single dose that overcomes the potentially serious problem of poor adherence to daily primaquine. Despite this benefit, hemolysis of the early erythrocytes continues in individuals with G6PD deficiency until all susceptible cells have been eliminated. Field techniques such as microscopy or rapid diagnostic tests (RDTs) miss the large number of submicroscopic and/or asymptomatic infections brought on by reticulocyte tropism and the low parasitemia levels that accompany it. Moreover, P. vivax gametocytes grow more quickly and are much more prevalent in the bloodstream. P. vivax populations also have a great deal of genetic variation throughout their genome, which ensures evolutionary fitness and boosts adaptation potential. Furthermore, P. vivax fully develops in the mosquito faster than P. falciparum. These characteristics contribute to parasite reservoirs in the human population and facilitate faster transmission. Overall, no genuine chance of eradication is predicted in the next few years unless new tools for lowering malaria transmission are developed (i.e., malaria elimination and eradication). The challenging characteristics of P. vivax that impede the elimination and eradication of malaria are thus discussed in this article.
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Affiliation(s)
- Kassahun Habtamu
- Department of Microbial, Cellular & Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Menelik II Medical & Health Science College, Addis Ababa, Ethiopia
| | - Beyene Petros
- Department of Microbial, Cellular & Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Guiyun Yan
- Program in Public Health, University of California at Irvine, Irvine, CA 92697 USA
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Semmeq A, Badawi M, Dziurla MA, Ouaskit S, Monari A. Nucleic Acids under Stress: Understanding and Simulating Nucleobase Fragmentation Pathways. Chempluschem 2021; 86:1426-1435. [PMID: 34637193 DOI: 10.1002/cplu.202100323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/24/2021] [Indexed: 11/10/2022]
Abstract
The effects of radiations on nucleic acids and their constituents is widely studied across several research fields using different experimental and theoretical protocols. While a large number of studies were performed in this context, many fundamental physical and chemical effects are still being investigated, particularly involving the effect of the biological environment. As an example, the interpretation of experimental nucleic acid bases mass spectra, and hence inferring their reactivity in complex environment still poses great challenge. This Minireview summarizes recent theoretical advancements aiming to predict and interpret the reactivity of nucleic acid bases. We focus not only on the understanding of the inherent fragmentation pathways of isolated nucleobases but also on the modeling of a realistic nano-environments highlighting the importance of molecular dynamics simulations and the non-innocent role of the environment and also the possibility to open novel fragmentation pathways.
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Affiliation(s)
| | - Michael Badawi
- Université de Lorraine and CNRS, UMR 7019 LPCT, 54000, Nancy, France
| | | | - Said Ouaskit
- Laboratoire de Physique de la Matière Condensée, Faculté de Sciences Ben M'sick, University Hassan II of Casablanca, Morocco
| | - Antonio Monari
- Université de Lorraine and CNRS, UMR 7019 LPCT, 54000, Nancy, France
- Université de Paris and CNRS, ITODYS, 75006, Paris, France
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Arévalo-Pinzón G, Garzón-Ospina D, Pulido FA, Bermúdez M, Forero-Rodríguez J, Rodríguez-Mesa XM, Reyes-Guarín LP, Suárez CF, Patarroyo MA. Plasmodium vivax Cell Traversal Protein for Ookinetes and Sporozoites (CelTOS) Functionally Restricted Regions Are Involved in Specific Host-Pathogen Interactions. Front Cell Infect Microbiol 2020; 10:119. [PMID: 32266169 PMCID: PMC7105572 DOI: 10.3389/fcimb.2020.00119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
Following the injection of Plasmodium sporozoites by a female Anopheles mosquito into the dermis, they become engaged on a long journey to hepatic tissue where they must migrate through different types of cell to become established in parasitophorous vacuoles in hepatocytes. Studies have shown that proteins such as cell traversal protein for Plasmodium ookinetes and sporozoites (CelTOS) play a crucial role in cell-traversal ability. Although CelTOS has been extensively studied in various species and included in pre-clinical assays it remains unknown which P. vivax CelTOS (PvCelTOS) regions are key in its interaction with traversed or target cells (Kupffer or hepatocytes) and what type of pressure, association and polymorphism these important regions could have to improve their candidacy as important vaccine antigens. This work has described producing a recombinant PvCelTOS which was recognized by ~30% P. vivax-infected individuals, thereby confirming its ability for inducing a natural immune response. PvCelTOS' genetic diversity in Colombia and its ability to interact with HeLa (traversal cell) and/or HepG2 cell (target cell) external membrane have been assessed. One region in the PvCelTOS amino-terminal region and another in its C-terminus were seen to be participating in host-pathogen interactions. These regions had important functional constraint signals (ω < 0.3 and several sites under negative selection) and were able to inhibit specific rPvCelTOS binding to HeLa cells. This led to suggesting that sequences between aa 41-60 (40833) and 141-160 (40838) represent promising candidates for an anti-P. vivax subunit-based vaccine.
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Affiliation(s)
- Gabriela Arévalo-Pinzón
- Receptor-Ligand Department, Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Diego Garzón-Ospina
- PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogota, Colombia
| | - Fredy A Pulido
- Receptor-Ligand Department, Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota, Colombia
| | - Maritza Bermúdez
- Receptor-Ligand Department, Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota, Colombia
| | - Johanna Forero-Rodríguez
- Molecular Biology and Immunology Department, Fundacion Instituto de Immunologia de Colombia (FIDIC), Bogota, Colombia
| | - Xandy M Rodríguez-Mesa
- Molecular Biology and Immunology Department, Fundacion Instituto de Immunologia de Colombia (FIDIC), Bogota, Colombia
| | - Leidy P Reyes-Guarín
- Molecular Biology and Immunology Department, Fundacion Instituto de Immunologia de Colombia (FIDIC), Bogota, Colombia
| | - Carlos F Suárez
- School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia.,Biomathematics Department, Fundacion Instituto de Immunologia de Colombia (FIDIC), Bogota, Colombia
| | - Manuel A Patarroyo
- School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia.,Molecular Biology and Immunology Department, Fundacion Instituto de Immunologia de Colombia (FIDIC), Bogota, Colombia
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Goodswen SJ, Kennedy PJ, Ellis JT. A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen. Front Genet 2018; 9:332. [PMID: 30177953 PMCID: PMC6109633 DOI: 10.3389/fgene.2018.00332] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/02/2018] [Indexed: 11/22/2022] Open
Abstract
Over the last two decades, various in silico approaches have been developed and refined that attempt to identify protein and/or peptide vaccines candidates from informative signals encoded in protein sequences of a target pathogen. As to date, no signal has been identified that clearly indicates a protein will effectively contribute to a protective immune response in a host. The premise for this study is that proteins under positive selection from the immune system are more likely suitable vaccine candidates than proteins exposed to other selection pressures. Furthermore, our expectation is that protein sequence regions encoding major histocompatibility complexes (MHC) binding peptides will contain consecutive positive selection sites. Using freely available data and bioinformatic tools, we present a high-throughput approach through a pipeline that predicts positive selection sites, protein subcellular locations, and sequence locations of medium to high T-Cell MHC class I binding peptides. Positive selection sites are estimated from a sequence alignment by comparing rates of synonymous (dS) and non-synonymous (dN) substitutions among protein coding sequences of orthologous genes in a phylogeny. The main pipeline output is a list of protein vaccine candidates predicted to be naturally exposed to the immune system and containing sites under positive selection. Candidates are ranked with respect to the number of consecutive sites located on protein sequence regions encoding MHCI-binding peptides. Results are constrained by the reliability of prediction programs and quality of input data. Protein sequences from Toxoplasma gondii ME49 strain (TGME49) were used as a case study. Surface antigen (SAG), dense granules (GRA), microneme (MIC), and rhoptry (ROP) proteins are considered worthy T. gondii candidates. Given 8263 TGME49 protein sequences processed anonymously, the top 10 predicted candidates were all worthy candidates. In particular, the top ten included ROP5 and ROP18, which are T. gondii virulence determinants. The chance of randomly selecting a ROP protein was 0.2% given 8263 sequences. We conclude that the approach described is a valuable addition to other in silico approaches to identify vaccines candidates worthy of laboratory validation and could be adapted for other apicomplexan parasite species (with appropriate data).
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Affiliation(s)
- Stephen J Goodswen
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Paul J Kennedy
- School of Software, Faculty of Engineering and Information Technology, Centre for Artificial Intelligence, University of Technology Sydney, Ultimo, NSW, Australia
| | - John T Ellis
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
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7
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Roth A, Adapa SR, Zhang M, Liao X, Saxena V, Goffe R, Li S, Ubalee R, Saggu GS, Pala ZR, Garg S, Davidson S, Jiang RHY, Adams JH. Unraveling the Plasmodium vivax sporozoite transcriptional journey from mosquito vector to human host. Sci Rep 2018; 8:12183. [PMID: 30111801 PMCID: PMC6093925 DOI: 10.1038/s41598-018-30713-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Malaria parasites transmitted by mosquito bite are remarkably efficient in establishing human infections. The infection process requires roughly 30 minutes and is highly complex as quiescent sporozoites injected with mosquito saliva must be rapidly activated in the skin, migrate through the body, and infect the liver. This process is poorly understood for Plasmodium vivax due to low infectivity in the in vitro models. To study this skin-to-liver-stage of malaria, we used quantitative bioassays coupled with transcriptomics to evaluate parasite changes linked with mammalian microenvironmental factors. Our in vitro phenotyping and RNA-seq analyses revealed key microenvironmental relationships with distinct biological functions. Most notable, preservation of sporozoite quiescence by exposure to insect-like factors coupled with strategic activation limits untimely activation of invasion-associated genes to dramatically increase hepatocyte invasion rates. We also report the first transcriptomic analysis of the P. vivax sporozoite interaction in salivary glands identifying 118 infection-related differentially-regulated Anopheles dirus genes. These results provide important new insights in malaria parasite biology and identify priority targets for antimalarial therapeutic interventions to block P. vivax infection.
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Affiliation(s)
- Alison Roth
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Min Zhang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Xiangyun Liao
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Vishal Saxena
- Molecular Parasitology and System Biology Lab, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Raaven Goffe
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Suzanne Li
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Ratawan Ubalee
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Gagandeep S Saggu
- Laboratory of Malaria and Vector Research, National Institute of Allergic and Infectious Diseases, National Institute of Health, Rockville, Maryland, USA
| | - Zarna R Pala
- Molecular Parasitology and System Biology Lab, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Shilpi Garg
- Molecular Parasitology and System Biology Lab, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Silas Davidson
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - John H Adams
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA.
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