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Elsworth B, Ye S, Dass S, Tennessen JA, Sultana Q, Thommen BT, Paul AS, Kanjee U, Grüring C, Ferreira MU, Gubbels MJ, Zarringhalam K, Duraisingh MT. The essential genome of Plasmodium knowlesi reveals determinants of antimalarial susceptibility. Science 2025; 387:eadq6241. [PMID: 39913579 DOI: 10.1126/science.adq6241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 12/05/2024] [Indexed: 02/09/2025]
Abstract
Measures to combat the parasites that cause malaria have become compromised because of reliance on a small arsenal of drugs and emerging drug resistance. We conducted a transposon mutagenesis screen in the primate malaria parasite Plasmodium knowlesi, producing the most complete classification of gene essentiality in any Plasmodium spp. to date, with the resolution to define truncatable genes. We found conservation in the druggable genome between Plasmodium spp. and divergences in mitochondrial metabolism. Perturbation analyses with the frontline antimalarial artemisinin revealed modulators that both increase and decrease drug susceptibility. Our findings aid prioritization of drug and vaccine targets for the Plasmodium vivax clade and reveal mechanisms of resistance that can inform therapeutic development.
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Affiliation(s)
- Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Sida Ye
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Mathematics, University of Massachusetts Boston, Boston, MA, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Sheena Dass
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jacob A Tennessen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qudseen Sultana
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
- Department of Computer Science, University of Massachusetts Boston, Boston, MA, USA
| | - Basil T Thommen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Aditya S Paul
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christof Grüring
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal
| | | | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Oberstaller J, Xu S, Naskar D, Zhang M, Wang C, Gibbons J, Pires CV, Mayho M, Otto TD, Rayner JC, Adams JH. Supersaturation mutagenesis reveals adaptive rewiring of essential genes among malaria parasites. Science 2025; 387:eadq7347. [PMID: 39913589 DOI: 10.1126/science.adq7347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 12/05/2024] [Indexed: 03/27/2025]
Abstract
Malaria parasites are highly divergent from model eukaryotes. Large-scale genome engineering methods effective in model organisms are frequently inapplicable, and systematic studies of gene function are few. We generated more than 175,000 transposon insertions in the Plasmodium knowlesi genome, averaging an insertion every 138 base pairs, and used this "supersaturation" mutagenesis to score essentiality for 98% of genes. The density of mutations allowed mapping of putative essential domains within genes, providing a completely new level of genome annotation for any Plasmodium species. Although gene essentiality was largely conserved across P. knowlesi, Plasmodium falciparum, and rodent malaria model Plasmodium berghei, a large number of shared genes are differentially essential, revealing species-specific adaptations. Our results indicated that Plasmodium essential gene evolution was conditionally linked to adaptive rewiring of metabolic networks for different hosts.
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Affiliation(s)
- Jenna Oberstaller
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Shulin Xu
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Deboki Naskar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Min Zhang
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Chengqi Wang
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Justin Gibbons
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Camilla Valente Pires
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Matthew Mayho
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas D Otto
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Laboratory of Pathogens and Host Immunity, Centre National de la Recherche Scientifique, and Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - John H Adams
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Shi L, Gu R, Long J, Duan G, Yang H. Application of CRISPR-cas-based technology for the identification of tuberculosis, drug discovery and vaccine development. Mol Biol Rep 2024; 51:466. [PMID: 38551745 DOI: 10.1007/s11033-024-09424-6] [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: 10/08/2023] [Accepted: 03/06/2024] [Indexed: 04/02/2024]
Abstract
Tuberculosis (TB), which caused by Mycobacterium tuberculosis, is the leading cause of death from a single infectious agent and continues to be a major public health burden for the global community. Despite being the only globally licenced prophylactic vaccine, Bacillus Calmette-Guérin (BCG) has multiple deficiencies, and effective diagnostic and therapeutic options are limited. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is an adaptive immune system that is found in bacteria and has great potential for the development of novel antituberculosis drugs and vaccines. In addition, CRISPR-Cas is currently recognized as a prospective tool for the development of therapies for TB infection with potential diagnostic and therapeutic value, and CRISPR-Cas may become a viable tool for eliminating TB in the future. Herein, we systematically summarize the current applications of CRISPR-Cas-based technology for TB detection and its potential roles in drug discovery and vaccine development.
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Affiliation(s)
- Liqin Shi
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Ruiqi Gu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Jinzhao Long
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Guangcai Duan
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China.
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Sy Thau N, Nguyen TK, Truong NV, Chu TTH, Na SH, Moon RW, Lau YL, Nyunt MH, Park WS, Chun WJ, Lu F, Lee SK, Han JH, Han ET. Characterization of merozoite-specific thrombospondin-related anonymous protein (MTRAP) in Plasmodium vivax and P. knowlesi parasites. Front Cell Infect Microbiol 2024; 14:1354880. [PMID: 38465236 PMCID: PMC10920329 DOI: 10.3389/fcimb.2024.1354880] [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: 12/13/2023] [Accepted: 02/08/2024] [Indexed: 03/12/2024] Open
Abstract
Plasmodium vivax, the most widespread human malaria parasite, and P. knowlesi, an emerging Plasmodium that infects humans, are the phylogenetically closest malarial species that infect humans, which may induce cross-species reactivity across most co-endemic areas in Southeast Asia. The thrombospondin-related anonymous protein (TRAP) family is indispensable for motility and host cell invasion in the growth and development of Plasmodium parasites. The merozoite-specific TRAP (MTRAP), expressed in blood-stage merozoites, is supposed to be essential for human erythrocyte invasion. We aimed to characterize MTRAPs in blood-stage P. vivax and P. knowlesi parasites and ascertain their cross-species immunoreactivity. Recombinant P. vivax and P. knowlesi MTRAPs of full-length ectodomains were expressed in a mammalian expression system. The MTRAP-specific immunoglobulin G, obtained from immune animals, was used in an immunofluorescence assay for subcellular localization and invasion inhibitory activity in blood-stage parasites was determined. The cross-species humoral immune responses were analyzed in the sera of patients with P. vivax or P. knowlesi infections. The MTRAPs of P. vivax (PvMTRAP) and P. knowlesi (PkMTRAP) were localized on the rhoptry body of merozoites in blood-stage parasites. Both anti-PvMTRAP and anti-PkMTRAP antibodies inhibited erythrocyte invasion of blood-stage P. knowlesi parasites. The humoral immune response to PvMTRAP showed high immunogenicity, longevity, and cross-species immunoreactivity with P. knowlesi. MTRAPs are promising candidates for development of vaccines and therapeutics against vivax and knowlesi malaria.
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Affiliation(s)
- Nguyen Sy Thau
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon, Gangwon-do, Republic of Korea
| | - Tuyet-Kha Nguyen
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon, Gangwon-do, Republic of Korea
| | - Nguyen Van Truong
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon, Gangwon-do, Republic of Korea
| | - Thi-Thanh Hang Chu
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon, Gangwon-do, Republic of Korea
| | - Sung-Hun Na
- Department of Obstetrics and Gynecology, Kangwon National University School of Medicine, Chuncheon, Gangwon-d, Republic of Korea
| | - Robert W. Moon
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Won-Sun Park
- Department of Physiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Wan-Joo Chun
- Department of Pharmacology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Feng Lu
- Department of Pathogen Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Seong-Kyun Lee
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon, Gangwon-do, Republic of Korea
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon, Gangwon-do, Republic of Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon, Gangwon-do, Republic of Korea
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