Biology subjects

Button-Simons, K.

Publications and source records attributed to Button-Simons, K..

4 recordsLinked to original sources

bioRxiv2020

The endosymbiotic origins of the apicoplast link fever-survival and artemisinin-resistance in the malaria parasite

BackgroundThe emergence and spread of Plasmodium falciparum parasites resistant to front-line antimalarial artemisinin-combination therapies (ACT) threatens to erase the considerable gains against the disease of the last decade. We developed a new large-scale phenotypic screening pipeline and used it to carry out the first large-scale forward-genetic phenotype screen in P. falciparum to identify genes that allow parasites to survive febrile temperatures. ResultsScreening identified more than 200 P. falciparum mutants with differential responses to increased temperature. These mutants were more likely to be sensitive to artemisinin derivatives as well as to heightened oxidative stress. Major processes critical for P. falciparum tolerance to febrile temperatures and artemisinin included highly essential, conserved pathways associated with protein-folding, heat-shock and proteasome-mediated degradation, and unexpectedly, isoprenoid biosynthesis, which originated from the ancestral genome of the parasites algal endosymbiont-derived plastid, the apicoplast. Apicoplast-targeted genes in general were up-regulated in response to heat shock, as were other Plasmodium genes with orthologs in plant and algal genomes. ConclusionsPlasmodium falciparum parasites appear to exploit their innate febrile-response mechanisms to mediate resistance to artemisinin. Both responses depend on endosymbiotic cynobacterium-related ancestral genes in the parasites genome, suggesting a link to the evolutionary origins of Plasmodium parasites in free-living ancestors.

genomics↗

bioRxiv2020

Bulk Segregant Approaches to Nutritional Genomics in Plasmodium falciparum

What genes determine growth and nutrient utilization in asexual blood-stage malaria parasites? Competition experiments between a lab-adapted African parasite (NF54), and a recently isolated Asian parasite (NHP4026) reveal contrasting outcomes in different media: NF54 outcompetes NHP4026 in media containing human serum, while NHP4026 outcompetes NF54 in media containing AlbuMAX, a lipid-rich bovine serum formulation. We conducted parasite genetic crosses and compared genome-wide allele frequency changes in progeny populations cultured in media containing serum or AlbuMAX: this bulk segregant analysis (BSA) reveals three quantitative trait loci (QTL) underlying differential growth. The strongest QTL (chromosome 13) contains EBA-140: competition experiments between EBA-140-knockout and isogenic wildtype parasites showed fitness reversals in the two media types, validating this locus as the causative gene. These results (i) demonstrate the effectiveness of BSA for dissecting fitness traits in Plasmodium falciparum, and (ii) reveal an intimate link between red blood cell invasion and nutrient composition of growth media.

genetics↗

bioRxiv2020

Cyclical Regression Covariates remove the major confounding effect of cyclical developmental gene expression with strain-specific drug response in the malaria parasite Plasmodium falciparum

BackgroundThe cyclical nature of parasite gene expression in the intraerythrocytic development cycle (IDC) in human blood confounds the accurate detection of specific transcriptional differences due to drug resistance in Plasmodium falciparum. Here, we propose the use of cyclical regression covariates to eliminate the major confounding of developmentally driven transcriptional changes with changes due to drug response. We show that elimination of this confounding can reduce both Type I and Type II errors, and demonstrate the effect of approach on real data. ResultsWe apply this method to two publicly available datasets, and demonstrate its ability to reduce the potential confounding of differences in expression due the species-specific intraerythrocytic development cycle from strain-specific differences in drug response. We show that the application of cyclical regression covariates has minimal impact on the pool of transcripts identified as significantly different in a dataset generated from single timepoint clinical blood samples with low variance for developmental stage and a profound impact on another clinical data set with more variance among the samples for developmental stage. ConclusionsCyclical regression covariates have immediate application to studies where in-vitro synchronization of all samples to the same developmental timepoint is not feasible, primarily parasite transcriptome sequencing direct from clinical blood samples, a widely used approach to frontline detection of emerging drug resistance.

genomics↗

bioRxiv2019

Genetic mapping of fitness determinants across the malaria parasite Plasmodium falciparum life cycle

Malaria is transmitted through female Anopheline mosquitoes where gamete fusion and meiosis occurs, and humans where parasites proliferate asexually. We describe a powerful approach to identify the genetic determinants of parasite fitness across both invertebrate and vertebrate life-cycle stages in human malaria parasite Plasmodium falciparum using bulk segregant analysis (BSA). We combined experimental genetic crosses using humanized mice, with selective whole genome amplification and BSA at multiple developmental stages in both mosquito and vertebrate host to examine parasite competition and identify genomic regions under selection. We generated crosses between artemisinin resistant (ART-R, kelch13-C580Y) and ART-sensitive (ART-S, kelch13-WT) parasite clones recently isolated from Southeast Asian patients. We then quantified genome-wide changes in allele frequency in the parasite progeny population from infected midgut and salivary glands of Anopheles stephensi mosquitoes, infected livers, emerging merozoites and aliquots of in vitro cultured progeny parasites at intervals over 30 days. Three striking results emerge: we observed (i) a strong skew (>80%) towards alleles from the ART-R parent in the mosquito stage, that dropped to [~]50% in the blood stage as selfed ART-R parasites were selected against; (ii) highly repeatable skews in allele frequencies across the genome in blood stage parasites; (iii) particularly strong selection (selection coefficient (s) [≤] 0.18/asexual cycle) against alleles from the ART-R parent at loci on chromosome 12 containing MRP2 and chromosome 14 containing ARPS10. This approach robustly identifies selected loci and has strong potential for identifying parasite genes that interact with the mosquito vector or compensatory loci involved in drug resistance.

evolutionary biology↗