Identification of Co-Existing Mutations and Gene Expression Trends Associated With K13-Mediated Artemisinin Resistance in Plasmodium falciparum

Abstract

Plasmodium falciparum infects millions and kills thousands of people annually the world over. With the emergence of artemisinin and/or multidrug resistant strains of the pathogen, it has become even more challenging to control and eliminate the disease. Multiomics studies of the parasite have started to provide a glimpse into the confounding genetics and mechanisms of artemisinin resistance and identified mutations in Kelch13 (K13) as a molecular marker of resistance. Over the years, thousands of genomes and transcriptomes of artemisinin-resistant/sensitive isolates have been documented, supplementing the search for new genes/pathways to target artemisinin-resistant isolates. This meta-analysis seeks to recap the genetic landscape and the transcriptional deregulation that demarcate artemisinin resistance in the field. To explore the genetic territory of artemisinin resistance, we use genomic single-nucleotide polymorphism (SNP) datasets from 2,517 isolates from 15 countries from the MalariaGEN Network (The Pf3K project, pilot data release 4, 2015) to dissect the prevalence, geographical distribution, and co-existing patterns of genetic markers associated with/enabling artemisinin resistance. We have identified several mutations which co-exist with the established markers of artemisinin resistance. Interestingly, K13-resistant parasites harbor α-ß hydrolase and putative HECT domain–containing protein genes with the maximum number of SNPs. We have also explored the multiple, publicly available transcriptomic datasets to identify genes from key biological pathways whose consistent deregulation may be contributing to the biology of resistant parasites. Surprisingly, glycolytic and pentose phosphate pathways were consistently downregulated in artemisinin-resistant parasites. Thus, this meta-analysis highlights the genetic and transcriptomic features of resistant parasites to propel further exploratory studies in the community to tackle artemisinin resistance.

Nutrient limitation mimics artemisinin tolerance in malaria

“…protein-protein interactions between P. falciparum and the red blood cell). Upregulation of exported proteins has been previously observed in both the artemisinin resistance transcriptome and as a response to nutrient limitation 36–38 . Translational regulation was also significantly upregulated in all three conditions in concordance with previous knowledge of the eIF2α-mediated response under nutrient stress ( Fig.…”

“…C ) Previous studies identified pathways associated with artemisinin tolerance. Vesicular trafficking: kelch13 28 , coronon 39 , Ap2μ 59 ; Autophagy: ATG18 29,31 ; Translational regulation: unfolded protein response 60 , proteasomal degradation (UBP1 59 ); Exported proteins 36,38 ; Invasion: GLURP and Phil1 40 ; Kinome: STK2, STK, CDPK 40 , Latency: grey text-unclear if distinct from nutrient-dependent latency or directly contributes to tolerance 25,61 .…”

Genomic analysis of Indian isolates of Plasmodium falciparum: Implications for drug resistance and virulence factors

“…To identify genes with high polymorphism in Indian isolates specifically, we conducted an analysis of single nucleotide polymorphisms (SNPs) to identify genes exhibiting high polymorphism. We partitioned the SNP dataset to identify mutations present in more than 75% of Indian isolates and less than 25% of other global isolates (adapted from a previous study by ( Rawat et al, 2022 )). From this analysis, we identified 1581 mutations that were specific to Indian isolates, spread across 922 genes ( Supplementary Table S2 ).…”

“…This indicates a possibility of PfKelch13 independent artemisinin resistance by a novel set of mutations. Since there are ample reports suggesting ACT resistance independent of PfKelch13 ( Das et al, 2021 ; Ghanchi et al, 2021 ; Nima et al, 2022 ), we looked into a list of mutations of genes that have a high association probability in ACT resistant samples ( Rawat et al, 2022 ). We then compared the list of genes having mutations in Indian isolates with that of genes defined to be co-existing in PfKelch13 mutated/artemisinin resistance isolates ( Rawat et al, 2022 ).…”

“…Furthermore, considering the sheer abundance of cellular targets for artemisinin in the cell, and the fitness cost associated with the PfKelch13 mutations, numerous “background mutant genes” may be required before resistance is manifest ( Hott et al, 2015 ; Nair et al, 2018 ). Recent reports also suggest the possibility of co-existing mutations in the background genome that assist resistant parasites in survival ( Miotto et al, 2015 ; Rawat et al, 2022 ; Ray et al, 2022 ) or can be independently responsible for artemisinin resistance ( Chakrabarti et al, 2019 ; Das et al, 2021 ; Mishra et al, 2016 ; Nima et al, 2022 ). Taken together, it suggests that though PfKelch13 is strongly associated with the artemisinin tolerance, there are possibly other genetic determinants associated with the decreased artemisinin tolerance in isolates from Africa and India.…”