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Joste V, Colard-Itté E, Guillochon É, Ariey F, Coppée R, Clain J, Houzé S. Genetic Profiling of Plasmodium ovale wallikeri Relapses With Microsatellite Markers and Whole-Genome Sequencing. J Infect Dis 2023; 228:1089-1098. [PMID: 37329228 DOI: 10.1093/infdis/jiad216] [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: 03/09/2023] [Revised: 05/14/2023] [Accepted: 06/15/2023] [Indexed: 06/18/2023] Open
Abstract
Like Plasmodium vivax, both Plasmodium ovale curtisi and Plasmodium ovale wallikeri have the ability to cause relapse in humans, defined as recurring asexual parasitemia originating from liver-dormant forms subsequent to a primary infection. Here, we investigated relapse patterns in P ovale wallikeri infections from a cohort of travelers who were exposed to the parasite in sub-Saharan Africa and then experienced relapses after their return to France. Using a novel set of 8 highly polymorphic microsatellite markers, we genotyped 15 P ovale wallikeri relapses. For most relapses, the paired primary and relapse infections were highly genetically related (with 12 being homologous), an observation that was confirmed by whole-genome sequencing for the 4 relapses we further studied. This is, to our knowledge, the first genetic evidence of relapses in P ovale spp.
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Affiliation(s)
- Valentin Joste
- Mère et enfant en milieu tropical, Institut Recherche pour le Développement, Université Paris Cité
- Centre National de Référence du Paludisme, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard
| | - Emma Colard-Itté
- Centre National de Référence du Paludisme, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard
| | - Émilie Guillochon
- Mère et enfant en milieu tropical, Institut Recherche pour le Développement, Université Paris Cité
| | - Frédéric Ariey
- Inserm U1016, Institut Cochin, Laboratoire de parasitologie-mycologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris Cité
| | - Romain Coppée
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, Paris, France
| | - Jérôme Clain
- Mère et enfant en milieu tropical, Institut Recherche pour le Développement, Université Paris Cité
- Centre National de Référence du Paludisme, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard
| | - Sandrine Houzé
- Mère et enfant en milieu tropical, Institut Recherche pour le Développement, Université Paris Cité
- Centre National de Référence du Paludisme, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard
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Kankinou SG, Yildiz M, Kocak A. Exploring potential Plasmodium kinase inhibitors: a combined docking, MD and QSAR studies. J Biomol Struct Dyn 2023:1-11. [PMID: 37599462 DOI: 10.1080/07391102.2023.2249111] [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: 02/03/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023]
Abstract
Malaria is a disease caused mostly by Plasmodium falciparum, affects millions of people each year. The kinases are validated targets for malaria infection. In this study, we investigate for real and hypothetical compounds that can inhibit cyclic guanosine monophosphate (CGMP)-dependent protein kinase using molecular docking via combined similarity analysis, molecular dynamics simulations, quantitative structure activity relationship (QSAR). Using Tanimoto similarity scores, ∼8.4 million compounds were screened. Compounds that have at least 70% similarity are used in further analysis. These compounds are assessed by means of docking, MMBPSA, MMGBSA and ANI_LIE. Based on consensus of different free energy methods and docking we revealed two potential inhibitors that can be useful for treatment of malaria. Apart from screening of real compounds, we have also selected the 10 most plausible hypothetical compounds by performing QSAR. By QSAR proposed pharmacophores, we generated over 247 hypothetical compounds and among them 19 molecules with lower QSAR predicted IC50 values and high docking scores were selected for further analysis. We selected the top 10 inhibitor candidates and performed MD simulations for free energy calculations like the protocol applied for real compounds. According to the free energy calculations, we suggest 2 real (C34H29F5N8O4S and C30H27F2N7O2S2, PubChem IDs: 140564801 and 89035196, respectively) and 2 hypothetical (C23H27FN6O2S, MOL3 and C23H25FN6O2S, MOL4) compounds that can be effective inhibitors against the protein kinase of Plasmodium falciparum.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Muslum Yildiz
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
| | - Abdulkadir Kocak
- Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
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Ren Z, Shi Q, Xu S, Xu J, Yin Y, Lin Z, Xu S, Ma X, Liu Y, Zhu G, He X, Lu J, Li Y, Zhang W, Liu J, Yang Y, Han ET, Cao J, Lu F. Elicitation of T-cell-derived IFN-γ-dependent immunity by highly conserved Plasmodium ovale curtisi Duffy binding protein domain region II (PocDBP-RII). Parasit Vectors 2023; 16:269. [PMID: 37553591 PMCID: PMC10410920 DOI: 10.1186/s13071-023-05897-9] [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] [Received: 05/24/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Infections with Plasmodium ovale are widely distributed but rarely investigated, and the resulting burden of disease has been underestimated. Plasmodium ovale curtisi Duffy binding protein domain region II (PocDBP-RII) is an essential ligand for reticulocyte recognition and host cell invasion by P. ovale curtisi. However, the genomic variation, antigenicity and immunogenicity of PocDBP-RII remain major knowledge gaps. METHODS A total of 93 P. ovale curtisi samples were collected from migrant workers who returned to China from 17 countries in Africa between 2012 and 2016. The genetic polymorphism, natural selection and copy number variation (CNV) were investigated by sequencing and real-time PCR. The antigenicity and immunogenicity of the recombinant PocDBP-RII (rPocDBP-RII) protein were further examined, and the humoral and cellular responses of immunized mice were assessed using protein microarrays and flow cytometry. RESULTS Efficiently expressed and purified rPocDBP-RII (39 kDa) was successfully used as an antigen for immunization in mice. The haplotype diversity (Hd) of PocDBP-RII gene was 0.105, and the nucleotide diversity index (π) was 0.00011. No increased copy number was found among the collected isolates of P. ovale curtisi. Furthermore, rPocDBP-RII induced persistent antigen-specific antibody production with a serum IgG antibody titer of 1: 16,000. IFN-γ-producing T cells, rather than IL-10-producing cells, were activated in response to the stimulation of rPocDBP-RII. Compared to PBS-immunized mice (negative control), there was a higher percentage of CD4+CD44highCD62L- T cells (effector memory T cells) and CD8+CD44highCD62L+ T cells (central memory T cells) in rPocDBP-RII‑immunized mice. CONCLUSIONS PocDBP-RII sequences were highly conserved in clinical isolates of P. ovale curtisi. rPocDBP-RII protein could mediate protective blood-stage immunity through IFN-γ-producing CD4+ and CD8+ T cells and memory T cells, in addition to inducing specific antibodies. Our results suggested that rPocDBP-RII protein has potential as a vaccine candidate to provide assessment and guidance for malaria control and elimination activities.
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Affiliation(s)
- Zhenyu Ren
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Qiyang Shi
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory On Parasite and Vector Control Technology, Jiangsu Provincial Medical Key Laboratory, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, People's Republic of China
| | - Simin Xu
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
- Changshu Second People's Hospital, Suzhou, 215500, Jiangsu, People's Republic of China
| | - Jiahui Xu
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Yi Yin
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Zhijie Lin
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Sui Xu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory On Parasite and Vector Control Technology, Jiangsu Provincial Medical Key Laboratory, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, People's Republic of China
| | - Xiaoqin Ma
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory On Parasite and Vector Control Technology, Jiangsu Provincial Medical Key Laboratory, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, People's Republic of China
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory On Parasite and Vector Control Technology, Jiangsu Provincial Medical Key Laboratory, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, People's Republic of China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory On Parasite and Vector Control Technology, Jiangsu Provincial Medical Key Laboratory, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, People's Republic of China
| | - Xinlong He
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jingyuan Lu
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Yinyue Li
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Wenwen Zhang
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jiali Liu
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Yun Yang
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory On Parasite and Vector Control Technology, Jiangsu Provincial Medical Key Laboratory, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, People's Republic of China.
| | - Feng Lu
- Department of Pathogenic Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China.
- Affiliated Hospital of Yangzhou University, Yangzhou, 225000, People's Republic of China.
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, School of Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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Development and Optimization of a Selective Whole-Genome Amplification To Study Plasmodium ovale Spp. Microbiol Spectr 2022; 10:e0072622. [PMID: 36098524 PMCID: PMC9602584 DOI: 10.1128/spectrum.00726-22] [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] [Indexed: 12/30/2022] Open
Abstract
Since 2010, the human-infecting malaria parasite Plasmodium ovale spp. has been divided into two genetically distinct species, P. ovale wallikeri and P. ovale curtisi. In recent years, application of whole-genome sequencing (WGS) to P. ovale spp. allowed to get a better understanding of its evolutionary history and discover some specific genetic patterns. Nevertheless, WGS data from P. ovale spp. are still scarce due to several drawbacks, including a high level of human DNA contamination in blood samples, infections with commonly low parasite density, and the lack of robust in vitro culture. Here, we developed two selective whole-genome amplification (sWGA) protocols that were tested on six P. ovale wallikeri and five P. ovale curtisi mono-infection clinical samples. Blood leukodepletion by a cellulose-based filtration was used as the gold standard for intraspecies comparative genomics with sWGA. We also demonstrated the importance of genomic DNA preincubation with the endonuclease McrBC to optimize P. ovale spp. sWGA. We obtained high-quality WGS data with more than 80% of the genome covered by ≥5 reads for each sample and identified more than 5,000 unique single-nucleotide polymorphisms (SNPs) per species. We also identified some amino acid changes in pocdhfr and powdhfr for which similar mutations in P. falciparum and P. vivax are associated with pyrimethamine or cycloguanil resistance. In conclusion, we developed two sWGA protocols for P. ovale spp. WGS that will help to design much-needed large-scale P. ovale spp. population studies. IMPORTANCE Plasmodium ovale spp. has the ability to cause relapse, defined as recurring asexual parasitemia originating from liver-dormant forms. Whole-genome sequencing (WGS) data are of importance to identify putative molecular markers associated with relapse or other virulence mechanisms. Due to low parasitemia encountered in P. ovale spp. infections and no in vitro culture available, WGS of P. ovale spp. is challenging. Blood leukodepletion by filtration has been used, but no technique exists yet to increase the quantity of parasite DNA over human DNA when starting from genomic DNA extracted from whole blood. Here, we demonstrated that selective whole-genome amplification (sWGA) is an easy-to-use protocol to obtain high-quality WGS data for both P. ovale spp. species from unprocessed blood samples. The new method will facilitate P. ovale spp. population genomic studies.
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