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Oboh MA, Asmorom N, Falade C, Ojurongbe O, Thomas BN. High genetic and haplotype diversity in vaccine candidate Pfceltos but not Pfrh5 among malaria-infected children in Ibadan, Nigeria. PeerJ 2023; 11:e16519. [PMID: 38099304 PMCID: PMC10720411 DOI: 10.7717/peerj.16519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 11/03/2023] [Indexed: 12/17/2023] Open
Abstract
Malaria remains a global public health challenge. The disease has a great impact in sub-Saharan Africa among children under five years of age and pregnant women. Malaria control programs targeting the parasite and mosquitoes vectors with combinational therapy and insecticide-treated bednets are becoming obsolete due to the phenomenon of resistance, which is a challenge for reducing morbidity and mortality. Malaria vaccines would be effective alternative to the problem of parasite and insecticide resistance, but focal reports of polymorphisms in malaria candidate antigens have made it difficult to design an effective malaria vaccine. Therefore, studies geared towards elucidating the polymorphic pattern and how genes targeted for vaccine design evolve are imperative. We have carried out molecular and genetic analysis of two genes encoding vaccine candidates-the Plasmodium falciparum cell traversal ookinetes and sporozoites (Pfceltos) and P. falciparum reticulocyte binding protein 5 (Pfrh5) in parasite isolates from malaria-infected children in Ibadan, Nigeria to evaluate their genetic diversity, relatedness and pattern of molecular evolution. Pfceltos and Pfrh5 genes were amplified from P. falciparum positive samples. Amplified fragments were purified and sequenced using the chain termination method. Post-sequence edit of fragments and application of various population genetic analyses was done. We observed a higher number of segregating sites and haplotypes in the Pfceltos than in Pfrh5 gene, the former also presenting higher haplotype (0.942) and nucleotide diversity (θ = 0.01219 and π = 0.01148). In contrast, a lower haplotype (0.426) and nucleotide diversity (θ = 0.00125; π = 0.00095) was observed in the Pfrh5 gene. Neutrality tests do not show deviation from neutral expectations for Pfceltos, with the circulation of multiple low frequency haplotypes (Tajima's D = -0.21637; Fu and Li's D = -0.08164; Fu and Li's F = -0.14051). Strong linkage disequilibrium was observed between variable sites, in each of the genes studied. We postulate that the high diversity and circulation of multiple haplotypes has the potential of making a Pfceltos-subunit vaccine ineffective, while the low genetic diversity of Pfrh5 gene substantiates its evolutionary conservation and potential as a malaria vaccine candidate.
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Affiliation(s)
- Mary Aigbiremo Oboh
- Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States of America
| | - Naemy Asmorom
- Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States of America
| | - Catherine Falade
- Pharmacology and Therapeutics, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Olusola Ojurongbe
- Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomosho, Osun, Nigeria
- Centre for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomosho, Oyo, Nigeria
| | - Bolaji N. Thomas
- Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States of America
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Loskutov SI, Proshin SN, Ryabukhin DS. Evolutionary aspects of gastrointestinal tract microbiome-host interaction underlying gastrointestinal barrier integrity. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2022. [DOI: 10.15789/2220-7619-eao-1633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In the host sustenance and homeostasis, the microbiome is a key component in the functional system. Throughout ontogenetic development, microbiome including that of the gastrointestinal tract (GIT) is the vital factor that ensures not only host functioning, but also its interaction with environment. To uncover the mechanisms underlying GIT microbiome showing a decisive influence on host organism, a systematic approach is needed, because diverse microorganisms are predominantly localized in different parts of the GIT. Recently, a new interdisciplinary direction of science, nanobioinformatics that has been extensively developed considers gene networks as the major object of study representing a coordinated group of genes that functionally account for formation and phenotypic disclosure of various host traits. Here, an important place should be provided to the genetically determined level of the gastrointestinal tract microbiome, its interaction at the level of the host food systems. There have been increasing evidence indicating that the microbiome is directly involved in the pathogenesis of host diseases showing a multi-layered interaction with host metabolic and immune systems. At the same time, the microbial community is unevenly distributed throughout the gastrointestinal tract, and its different portions are variously active while interacting with the host immune system. The architecture of interaction between the microbiome and host cells is extremely complex, and the interaction of individual cells, at the same time, varies greatly. Bacteria colonizing the crypts of the small intestine regulate enterocyte proliferation by affecting DNA replication and gene expression, while bacteria at the tip of the intestinal villi mediate gene expression responsible for metabolism and immune response. Enterocytes and Paneth cells, in turn, regulate the vital activity of the community of microorganisms through the production of polysaccharides (carbohydrates) and antibacterial factors on their surface. Thus, the integrity of the gastrointestinal barrier (GIB) is maintained, which protects the body from infections and inflammation, while violation of its integrity leads to a number of diseases. It has been shown that depending on the dominance of certain types of bacteria the microbiome can maintain or disrupt GIB integrity. The structural and functional GIB integrity is important for body homeostasis. To date, at least 50 proteins have been characterized as being involved in the structural and functional integrability of tight junctions between gastrointestinal tract epithelial cells. The current review comprehensively discusses such issues and presents original research carried out at various facilities of translational biomedicine.
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Pringle JC, Wesolowski A, Berube S, Kobayashi T, Gebhardt ME, Mulenga M, Chaponda M, Bobanga T, Juliano JJ, Meshnick S, Moss WJ, Carpi G, Norris DE. High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo. Malar J 2019; 18:400. [PMID: 31801548 PMCID: PMC6894251 DOI: 10.1186/s12936-019-3023-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/21/2019] [Indexed: 01/25/2023] Open
Abstract
Background While the utility of parasite genotyping for malaria elimination has been extensively documented in low to moderate transmission settings, it has been less well-characterized in holoendemic regions. High malaria burden settings have received renewed attention acknowledging their critical role in malaria elimination. Defining the role for parasite genomics in driving these high burden settings towards elimination will enhance future control programme planning. Methods Amplicon deep sequencing was used to characterize parasite population genetic diversity at polymorphic Plasmodium falciparum loci, Pfama1 and Pfcsp, at two timepoints in June–July 2016 and January–March 2017 in a high transmission region along the international border between Luapula Province, Zambia and Haut-Katanga Province, the Democratic Republic of the Congo (DRC). Results High genetic diversity was observed across both seasons and in both countries. No evidence of population structure was observed between parasite populations on either side of the border, suggesting that this region may be one contiguous transmission zone. Despite a decline in parasite prevalence at the sampling locations in Haut-Katanga Province, no genetic signatures of a population bottleneck were detected, suggesting that larger declines in transmission may be required to reduce parasite genetic diversity. Analysing rare variants may be a suitable alternative approach for detecting epidemiologically important genetic signatures in highly diverse populations; however, the challenge is distinguishing true signals from potential artifacts introduced by small sample sizes. Conclusions Continuing to explore and document the utility of various parasite genotyping approaches for understanding malaria transmission in holoendemic settings will be valuable to future control and elimination programmes, empowering evidence-based selection of tools and methods to address pertinent questions, thus enabling more efficient resource allocation.
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Affiliation(s)
- Julia C Pringle
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Sophie Berube
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Tamaki Kobayashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Mary E Gebhardt
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | | | | | - Thierry Bobanga
- Université Protestante au Congo and University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Steven Meshnick
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - William J Moss
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Douglas E Norris
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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Ochola-Oyier LI, Wamae K, Omedo I, Ogola C, Matharu A, Musabyimana JP, Njogu FK, Marsh K. Few Plasmodium falciparum merozoite ligand and erythrocyte receptor pairs show evidence of balancing selection. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 69:235-245. [PMID: 30735814 PMCID: PMC6403450 DOI: 10.1016/j.meegid.2019.02.004] [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] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/16/2019] [Accepted: 02/04/2019] [Indexed: 01/06/2023]
Abstract
Erythrocyte surface proteins have been identified as receptors of Plasmodium falciparum merozoite proteins. The ligand-receptor interactions enable the parasite to invade human erythrocytes, initiating the clinical symptoms of malaria. These interactions are likely to have had an evolutionary impact on the genes that encode the ligand and receptor proteins. We used sequence data from Kilifi, Kenya to detect departures from neutrality in a paired analysis of P. falciparum merozoite ligands and their erythrocyte receptor genes from the same population. We genotyped parasite and human DNA obtained from 93 individuals with severe malaria. We examined six merozoite ligands EBA175, EBL1, EBA140, MSP1, Rh4 and Rh5, and their corresponding erythrocyte receptors, glycophorin (Gyp) A, GypB, GypC, band 3, complement receptor (CR) 1 and basigin, focusing on the regions involved in the ligand-receptor interactions. Positive Tajima's D values (>1) were observed only in the MSP1 C-terminal region and EBA175 region II, while negative values (<-1) were observed in EBL-1 region II, Rh4, basigin exons 3 and 5, CR1 exon 5, Gyp B exons 2, 3 and 4 and Gyp C exon 2. Additionally, ebl-1 region II and basigin exon 3 showed extreme negative values in all three tests, Tajima's D, Fu & Li D* and F*, ≤ - 2. A large majority of the erythrocyte receptor and merozoite genes have a negative Tajima's D even when compared with previously published whole genome data. Thus, highlighting EBA175 region II and MSP1-33, as outlier genes with a positive Tajima's D (>1). Both these genes contain multiple polymorphisms, which in the case of EBA175 may counteract receptor polymorphisms and/or evade host immune responses and in MSP1 the polymorphisms may primarily evade host immune responses.
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MESH Headings
- Alleles
- Child
- Child, Preschool
- Erythrocytes/metabolism
- Erythrocytes/parasitology
- Female
- Gene Frequency
- Host-Parasite Interactions
- Humans
- Infant
- Infant, Newborn
- Ligands
- Malaria, Falciparum/genetics
- Malaria, Falciparum/metabolism
- Malaria, Falciparum/parasitology
- Male
- Merozoites/metabolism
- Models, Molecular
- Plasmodium falciparum/classification
- Plasmodium falciparum/physiology
- Polymorphism, Genetic
- Protein Conformation
- Protozoan Proteins/genetics
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Structure-Activity Relationship
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Affiliation(s)
- Lynette Isabella Ochola-Oyier
- KEMRI-Wellcome Trust Collaborative Programme, P.O. Box 230, 80108 Kilifi, Kenya; Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya.
| | - Kevin Wamae
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Irene Omedo
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Christabel Ogola
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Abneel Matharu
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Jean Pierre Musabyimana
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Francis K Njogu
- KEMRI-Wellcome Trust Collaborative Programme, P.O. Box 230, 80108 Kilifi, Kenya
| | - Kevin Marsh
- KEMRI-Wellcome Trust Collaborative Programme, P.O. Box 230, 80108 Kilifi, Kenya
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Ararat-Sarria M, Patarroyo MA, Curtidor H. Parasite-Related Genetic and Epigenetic Aspects and Host Factors Influencing Plasmodium falciparum Invasion of Erythrocytes. Front Cell Infect Microbiol 2019; 8:454. [PMID: 30693273 PMCID: PMC6339890 DOI: 10.3389/fcimb.2018.00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/21/2018] [Indexed: 01/13/2023] Open
Abstract
Malaria, a disease caused by Plasmodium parasites, is widespread throughout tropical and sub-tropical regions worldwide; it mostly affects children and pregnant woman. Eradication has stalled despite effective prevention measures and medication being available for this disease; this has mainly been due to the parasite's resistance to medical treatment and the mosquito vector's resistance to insecticides. Tackling such resistance involves using renewed approaches and techniques for accruing a deep understanding of the parasite's biology, and developing new drugs and vaccines. Studying the parasite's invasion of erythrocytes should shed light on its ability to switch between invasion phenotypes related to the expression of gene sets encoding proteins acting as ligands during target cell invasion, thereby conferring mechanisms for evading a particular host's immune response and adapting to changes in target cell surface receptors. This review considers some factors influencing the expression of such phenotypes, such as Plasmodium's genetic, transcriptional and epigenetic characteristics, and explores some host-related aspects which could affect parasite phenotypes, aiming at integrating knowledge regarding this topic and the possible relationship between the parasite's biology and host factors playing a role in erythrocyte invasion.
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Affiliation(s)
- Monica Ararat-Sarria
- Receptor-Ligand Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Immunología de Colombia (FIDIC), Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Hernando Curtidor
- Receptor-Ligand Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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Abstract
Humoral immune responses against the malaria parasite are an important component of a protective immune response. Antibodies are often directed towards conformational epitopes, and the native structure of the antigenic region is usually critical for antibody recognition. We examined the structural features of various Plasmodium antigens that may impact on epitope location, by performing a comprehensive analysis of known and modelled structures from P. falciparum. Examining the location of known polymorphisms over all available structures, we observed a strong propensity for polymorphic residues to be exposed on the surface and to occur in particular secondary structure segments such as hydrogen-bonded turns. We also utilised established prediction algorithms for B-cell epitopes and MHC class II binding peptides, examining predicted epitopes in relation to known polymorphic sites within structured regions. Finally, we used the available structures to examine polymorphic hotspots and Tajima's D values using a spatial averaging approach. We identified a region of PfAMA1 involving both domains II and III under a high degree of balancing selection relative to the rest of the protein. In summary, we developed general methods for examining how sequence-based features relate to one another in three-dimensional space and applied these methods to key P. falciparum antigens.
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