Biology subjects

Ebel, E. R.

Publications and source records attributed to Ebel, E. R..

6 recordsLinked to original sources

bioRxiv2023

Expansion of GTP cyclohydrolase I copy number in malaria parasites resistant to a pyrimidine biosynthesis inhibitor

Increases in the copy number of large genomic regions, termed genome amplification, are an important adaptive strategy for malaria parasites. Numerous amplifications across the Plasmodium falciparum genome contribute directly to drug resistance or impact the fitness of this protozoan parasite. During the characterization of parasite lines with amplifications of the dihydroorotate dehydrogenase (DHODH) gene, we detected increased copies of an additional genomic region that encompassed 3 genes (~5 kb) including GTP cyclohydrolase I (GCH1 amplicon). While this gene is reported to increase the fitness of antifolate resistant parasites, GCH1 amplicons had not previously been implicated in any other antimalarial resistance context. Here, we further explored the association between GCH1 and DHODH copy number. Using long read sequencing and single read visualization, we directly observed a higher number of tandem GCH1 amplicons in parasites with increased DHODH copies (up to 9 amplicons) compared to parental parasites (3 amplicons). While all GCH1 amplicons shared a consistent structure, expansions arose in 2-unit steps (from 3 to 5 to 7, etc copies). Adaptive evolution of DHODH and GCH1 loci was further bolstered when we evaluated prior selection experiments; DHODH amplification was only successful in parasite lines with pre-existing GCH1 amplicons. These observations, combined with the direct connection between metabolic pathways that contain these enzymes, lead us to propose that the GCH1 locus is beneficial for the fitness of parasites exposed to DHODH inhibitors. This finding highlights the importance of studying variation within individual parasite genomes as well as biochemical connections of drug targets as novel antimalarials move towards clinical approval. Author SummaryMalaria is caused by a protozoan parasite that readily evolves resistance to drugs that are used to treat this deadly disease. Changes that arise in the parasite genome, including extra copies of important genes, directly contribute to this resistance or improve how well the resistant parasite competes. In this study, we identified that extra copies of one gene (GTP cyclohydrolase or GCH1) were more likely to be found in parasites with extra copies of another gene on a different chromosome (dihydroorotate dehydrogenase or DHODH). A method that allows us to view long pieces of DNA from individual genomes was especially important for this study; we were able to assess gene number, arrangement, and boundary sequences, which provided clues into how extra copies evolved. Additionally, by analyzing previous experiments, we identified that extra GCH1 copies improved resistance to drugs that target DHODH. The relationship between these two loci is supported by a direct connection between the folate and pyrimidine biosynthesis pathways that the parasite uses to make DNA. Since GCH1 amplicons are common in clinical parasites worldwide, this finding highlights the need to study metabolic connections to avoid resistance evolution.

genomics↗

bioRxiv2023

Antigenic diversity in malaria parasites is maintained on extrachromosomal DNA

Sequence variation among antigenic var genes enables Plasmodium falciparum malaria parasites to evade host immunity. Using long sequence reads from haploid clones from a mutation accumulation experiment, we detect var diversity inconsistent with simple chromosomal inheritance. We discover putatively circular DNA that is strongly enriched for var genes, which exist in multiple alleles per locus separated by recombination and indel events. Extrachromosomal DNA likely contributes to rapid antigenic diversification in P. falciparum.

genetics↗

bioRxiv2020

Malaria parasite fitness in healthy human red cells is driven by common host variation

The replication of Plasmodium falciparum parasites within red blood cells (RBCs) causes severe disease in humans, especially in Africa. The influence of host RBC variation on parasite replication is largely uncharted, aside from a handful of deleterious alleles like sickle cell. Here, we integrated analyses of exome sequencing, RBC phenotyping, and parasite fitness assays on blood from 122 individuals, most with African ancestry. In donors lacking alleles for hemoglobinopathies or G6PD deficiency, RBC phenotypes including size, deformability, and hydration status explained 21-38% of the variation in parasite growth rate. With the addition of non-pathogenic polymorphisms in 14 RBC proteins including SPTA1, PIEZO1, and ATP2B4, our model explained 73-82% of the variation in parasite growth rate. Interestingly, we observed little evidence for divergent selection on this variation between Africans and Europeans. These findings suggest a model in which widespread, non-pathogenic variation in a moderate number of genes strongly modulates P. falciparum fitness in RBCs.

genetics↗

bioRxiv2020

Shifts in antimalarial drug policy since 2006 have rapidly selected P. falciparum resistance alleles in Angola

BACKGROUNDPlasmodium falciparum resistance to chloroquine (CQ), the most widely used antimalarial drug, has historically posed a major threat to malaria control in Angola and throughout the world. Although Angola replaced CQ with artemisinin combination therapy (ACT) as a frontline treatment in 2006, malaria cases and deaths have recently been rising. CQ-resistance mutations may still be a contributing factor, given that (1) some also modulate resistance to ACT partner drugs and (2) ACT is not yet consistently implemented across Angola. It is important to continue monitoring all known resistance alleles in P. falciparum, but no studies have done so in Angola since 2012. METHODSWe sampled P. falciparum DNA from the blood of 50 hospital patients in Cabinda, Angola in 2018. Each infection was genotyped for 13 alleles in the genes crt, mdr1, dhps, dhfr, and kelch13, which collectively confer resistance to six common drugs. To analyze frequency trajectories over time, we also collated P. falciparum genotype data published from across Angola in the last two decades. RESULTSThe two most important alleles for CQ resistance, crt 72-76CVIET and mdr1 86Y, have both declined in frequency from respective highs of 98% in 1999 and 73% in 2003. However, the former remains at 71% frequency in this sample while the latter has dropped to just 7%. Of seven possible alleles for sulfadoxine-pyrimethamine (SP) resistance in dhps and dhfr, the average total number per isolate increased from 2.9 in 2004 to 4.4 in 2018. Finally, we detected no non-synonymous polymorphisms in kelch13, which is involved in artemisinin resistance in Southeast Asia. CONCLUSIONSChanges in drug policy in Angola since 2006 appear to have exerted strong selection on P. falciparum drug resistance alleles. Resistance to CQ is declining, but due to functional tradeoffs and novel selection at mdr1 loci, resistance to ACT partner drugs appears to be rising. More haplotype-based studies at mdr1 will be needed to understand the changing efficacy of multiple drugs. Finally, SP resistance has jumped rapidly since 2014, consistent with widespread use of intermittent SP treatment during pregnancy. These data can be used to support effective drug policy decisions in Angola.

evolutionary biology↗

bioRxiv2019

A common polymorphism in the druggable ion channel PIEZO1 is associated with protection from severe malaria

Malaria caused by the Apicomplexan parasite Plasmodium falciparum has served as a strong evolutionary force throughout human history, selecting for red blood cell polymorphisms that confer innate protection against severe disease. Recently, gain-of-function mutations in the mechanosensitive ion channel PIEZO1 were shown to ameliorate Plasmodium parasite growth, blood-brain barrier dysfunction, and mortality in a mouse model of malaria. In humans, the gain-of-function allele PIEZO1 E756del is highly prevalent and enriched in Africans, raising the possibility that it is under positive selection due to malaria. Here we used a case-control study design to test for an association between PIEZO1 E756del and malaria severity among children in Gabon. We found that the E756del variant is strongly associated with protection against severe malaria in heterozygotes, independent of the protection conferred by the sickle cell trait (hemoglobin AS). In vitro experiments using donor red blood cells failed to find an effect of E756del on parasite growth, suggesting this variant confers a mild channel defect and/or that its protective effect may be mediated by other tissue types in vivo. Nonetheless, we show that Yoda1, a small molecule agonist of PIEZO1, has potent antimalarial activity in both E756del and wild-type red blood cells. Our findings demonstrate that PIEZO1 is an important innate determinant of malaria susceptibility in humans and holds potential as druggable host target for malaria control.

microbiology↗

bioRxiv2016

Pervasive adaptation in Plasmodium-interacting proteins in mammals

The protozoan genus Plasmodium causes malaria in dozens of mammal species, including humans, non-human primates, rodents, and bats. In humans, Plasmodium infections have caused hundreds of millions of documented deaths, imposing strong selection on certain populations and driving the emergence of several resistance alleles. Over the deep timescale of mammalian evolution, however, little is known about host adaptation to Plasmodium. In this work, we expand the collection of known Plasmodium-interacting-proteins (PIPs) in mammalian hosts from ~10 to 410, by manually curating thousands of scientific abstracts. We use comparative tests of adaptation to show that PIPs have experienced >3 times more positive selection than similar mammalian proteins, consistent with Plasmodium as a major and long-standing selective pressure. PIP adaptation is strongly linked to gene expression in the blood, liver, and lung, all of which are clinically relevant tissues in Plasmodium infection. Interestingly, we find that PIPs with immune functions are especially enriched for additional interactions with viruses or bacteria, which together drive a 3.7-fold excess of adaptation. These pleiotropic interactions with unrelated pathogens, along with pressure from other Plasmodium-like Apicomplexan parasites, may help explain the PIP adaptation we observe in all clades of the mammalian tree. As a case study, we also show that alpha-spectrin, the major membrane component of mammalian red blood cells, has experienced accelerated adaptation in domains known to interact specifically with Plasmodium proteins. Similar interactions with Plasmodium-like parasites appear to have driven substantial adaptation in hundreds of host proteins throughout mammalian evolution.

evolutionary biology↗