A genomic and evolutionary approach reveals  non-genetic drug resistance in malaria.
BACKGROUND
Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated.


RESULTS
We previously described two mutations in the cytoplasmic prolyl-tRNA synthetase (cPRS) gene that confer resistance to halofuginone. We describe here the evolutionary trajectory of halofuginone resistance of two independent drug resistance selections in Plasmodium falciparum. Using this novel methodology, we discover an unexpected non-genetic drug resistance mechanism that P. falciparum utilizes before genetic modification of the cPRS. P. falciparum first upregulates its proline amino acid homeostasis in response to halofuginone pressure. We show that this non-genetic adaptation to halofuginone is not likely mediated by differential RNA expression and precedes mutation or amplification of the cPRS gene. By tracking the evolution of the two drug resistance selections with whole genome sequencing, we further demonstrate that the cPRS locus accounts for the majority of genetic adaptation to halofuginone in P. falciparum. We further validate that copy-number variations at the cPRS locus also contribute to halofuginone resistance.


CONCLUSIONS
We provide a three-step model for multi-locus evolution of halofuginone drug resistance in P. falciparum. Informed by genomic approaches, our results provide the first comprehensive view of the evolutionary trajectory malaria parasites take to achieve drug resistance. Our understanding of the multiple genetic and non-genetic mechanisms of drug resistance informs how we will design and pair future anti-malarials for clinical use.
Jonathan D
JD
Herman
Daniel P
DP
Rice
Ulf
U
Ribacke
Jacob
J
Silterra
Amy A
AA
Deik
Eli L
EL
Moss
Kate M
KM
Broadbent
Daniel E
DE
Neafsey
Michael M
MM
Desai
Clary B
CB
Clish
Ralph
R
Mazitschek
Dyann F
DF
Wirth
D005075:Biological Evolution; D004351:Drug Resistance; D023281:Genomics; D006801:Humans; D016778:Malaria, Falciparum / Q000188:drug therapy* / Q000235:genetics / Q000469:parasitology; D009154:Mutation; D010880:Piperidines / Q000627:therapeutic use; D010963:Plasmodium falciparum / Q000187:drug effects* / Q000235:genetics; D015800:Protozoan Proteins; D052999:Quinazolinones / Q000627:therapeutic use; D017422:Sequence Analysis, DNA
D010880:Piperidines; D015800:Protozoan Proteins; D052999:Quinazolinones; C010176:halofuginone