Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum

Kumpornsin, K.; Kochakarn, T.; Yeo, T.; Luth, M.; Pearson, R. D.; Hoshizaki, J.; Schindler, K.; Mok, S.; Park, H.; Uhlemann, A.-C.; Cubel, S. M.; Franco, V.; Gomez-Lorenzo, M.; Gamo, F.-J.; Winzeler, E.; Fidock, D. A.; Chookajorn, T.; Lee, M. C.

doi:10.1101/2022.08.23.504974

bioRxiv · 10.1101/2022.08.23.504974

Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum

Kumpornsin, K.·Kochakarn, T.·Yeo, T.·Luth, M.·Pearson, R. D.·Hoshizaki, J.·Schindler, K.·Mok, S.·Park, H.·Uhlemann, A.-C.·Cubel, S. M.·Franco, V.·Gomez-Lorenzo, M.·Gamo, F.-J.·Winzeler, E.·Fidock, D. A.·Chookajorn, T.·Lee, M. C.

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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 {delta}. Mutation accumulation assays revealed a [~]5-8 fold elevation in the mutation rate, with an increase of 13-28 fold in drug-pressured lines. When challenged with KAE609, high-level resistance was obtained more rapidly and at lower inoculum than wild-type parasites. Selections were also successful with an "irresistible" compound, MMV665794 that failed to yield resistance with other strains. Mutations in a previously uncharacterized gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), were validated as causal for resistance to MMV665794 and an analog, MMV007224. The increased genetic repertoire available to this "mutator" parasite can be leveraged to drive P. falciparum resistome discovery.

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Kumpornsin, K., Kochakarn, T., Yeo, T., Luth, M., Pearson, R. D., Hoshizaki, J., Schindler, K., Mok, S., Park, H., Uhlemann, A.-C., Cubel, S. M., Franco, V., Gomez-Lorenzo, M., Gamo, F.-J., Winzeler, E., Fidock, D. A., Chookajorn, T., Lee, M. C.. 2022-08-23. Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum. https://doi.org/10.1101/2022.08.23.504974

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