Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum
Abstract In vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by ed...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-38774-1 |
| _version_ | 1797817943190405120 |
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| author | Krittikorn Kümpornsin Theerarat Kochakarn Tomas Yeo John Okombo Madeline R. Luth Johanna Hoshizaki Mukul Rawat Richard D. Pearson Kyra A. Schindler Sachel Mok Heekuk Park Anne-Catrin Uhlemann Gouranga P. Jana Bikash C. Maity Benoît Laleu Elodie Chenu James Duffy Sonia Moliner Cubel Virginia Franco Maria G. Gomez-Lorenzo Francisco Javier Gamo Elizabeth A. Winzeler David A. Fidock Thanat Chookajorn Marcus C. S. Lee |
| author_facet | Krittikorn Kümpornsin Theerarat Kochakarn Tomas Yeo John Okombo Madeline R. Luth Johanna Hoshizaki Mukul Rawat Richard D. Pearson Kyra A. Schindler Sachel Mok Heekuk Park Anne-Catrin Uhlemann Gouranga P. Jana Bikash C. Maity Benoît Laleu Elodie Chenu James Duffy Sonia Moliner Cubel Virginia Franco Maria G. Gomez-Lorenzo Francisco Javier Gamo Elizabeth A. Winzeler David A. Fidock Thanat Chookajorn Marcus C. S. Lee |
| author_sort | Krittikorn Kümpornsin |
| collection | DOAJ |
| description | Abstract In vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by editing catalytic residues of Plasmodium falciparum DNA polymerase δ. Mutation accumulation assays reveal a ~5–8 fold elevation in the mutation rate, with an increase of 13–28 fold in drug-pressured lines. Upon challenge with the spiroindolone PfATP4-inhibitor KAE609, high-level resistance is obtained more rapidly and at lower inocula than wild-type parasites. Selections also yield mutants with resistance to an “irresistible” compound, MMV665794 that failed to yield resistance with other strains. We validate mutations in a previously uncharacterised gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), as causal for resistance to MMV665794 and a panel of quinoxaline analogues. The increased genetic repertoire available to this “mutator” parasite can be leveraged to drive P. falciparum resistome discovery. |
| first_indexed | 2024-03-13T09:00:49Z |
| format | Article |
| id | doaj.art-cd0bb7acaa454eeba503bf34e9f1ecc8 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-13T09:00:49Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-cd0bb7acaa454eeba503bf34e9f1ecc82023-05-28T11:22:14ZengNature PortfolioNature Communications2041-17232023-05-0114111410.1038/s41467-023-38774-1Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparumKrittikorn Kümpornsin0Theerarat Kochakarn1Tomas Yeo2John Okombo3Madeline R. Luth4Johanna Hoshizaki5Mukul Rawat6Richard D. Pearson7Kyra A. Schindler8Sachel Mok9Heekuk Park10Anne-Catrin Uhlemann11Gouranga P. Jana12Bikash C. Maity13Benoît Laleu14Elodie Chenu15James Duffy16Sonia Moliner Cubel17Virginia Franco18Maria G. Gomez-Lorenzo19Francisco Javier Gamo20Elizabeth A. Winzeler21David A. Fidock22Thanat Chookajorn23Marcus C. S. Lee24Wellcome Sanger Institute, Wellcome Genome CampusThe Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå UniversityDepartment of Microbiology and Immunology, Columbia University Irving Medical CenterDepartment of Microbiology and Immunology, Columbia University Irving Medical CenterDepartment of Pediatrics, School of Medicine, University of California, San DiegoWellcome Sanger Institute, Wellcome Genome CampusWellcome Sanger Institute, Wellcome Genome CampusWellcome Sanger Institute, Wellcome Genome CampusDepartment of Microbiology and Immunology, Columbia University Irving Medical CenterDepartment of Microbiology and Immunology, Columbia University Irving Medical CenterDivision of Infectious Diseases, Department of Medicine, Columbia University Irving Medical CenterCenter for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical CenterTCG Lifesciences Private Limited, Salt-lake Electronics ComplexTCG Lifesciences Private Limited, Salt-lake Electronics ComplexMedicines for Malaria Venture, International Centre CointrinMedicines for Malaria Venture, International Centre CointrinMedicines for Malaria Venture, International Centre CointrinGlobal Health Medicines R&D, GlaxoSmithKline, Tres CantosGlobal Health Medicines R&D, GlaxoSmithKline, Tres CantosGlobal Health Medicines R&D, GlaxoSmithKline, Tres CantosGlobal Health Medicines R&D, GlaxoSmithKline, Tres CantosDepartment of Pediatrics, School of Medicine, University of California, San DiegoDepartment of Microbiology and Immunology, Columbia University Irving Medical CenterThe Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå UniversityWellcome Sanger Institute, Wellcome Genome CampusAbstract In vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by editing catalytic residues of Plasmodium falciparum DNA polymerase δ. Mutation accumulation assays reveal a ~5–8 fold elevation in the mutation rate, with an increase of 13–28 fold in drug-pressured lines. Upon challenge with the spiroindolone PfATP4-inhibitor KAE609, high-level resistance is obtained more rapidly and at lower inocula than wild-type parasites. Selections also yield mutants with resistance to an “irresistible” compound, MMV665794 that failed to yield resistance with other strains. We validate mutations in a previously uncharacterised gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), as causal for resistance to MMV665794 and a panel of quinoxaline analogues. The increased genetic repertoire available to this “mutator” parasite can be leveraged to drive P. falciparum resistome discovery.https://doi.org/10.1038/s41467-023-38774-1 |
| spellingShingle | Krittikorn Kümpornsin Theerarat Kochakarn Tomas Yeo John Okombo Madeline R. Luth Johanna Hoshizaki Mukul Rawat Richard D. Pearson Kyra A. Schindler Sachel Mok Heekuk Park Anne-Catrin Uhlemann Gouranga P. Jana Bikash C. Maity Benoît Laleu Elodie Chenu James Duffy Sonia Moliner Cubel Virginia Franco Maria G. Gomez-Lorenzo Francisco Javier Gamo Elizabeth A. Winzeler David A. Fidock Thanat Chookajorn Marcus C. S. Lee Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum Nature Communications |
| title | Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum |
| title_full | Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum |
| title_fullStr | Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum |
| title_full_unstemmed | Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum |
| title_short | Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum |
| title_sort | generation of a mutator parasite to drive resistome discovery in plasmodium falciparum |
| url | https://doi.org/10.1038/s41467-023-38774-1 |
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