Biology subjects

Carey, M. A.

Publications and source records attributed to Carey, M. A..

4 recordsLinked to original sources

bioRxiv2018

Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies

Malaria is a major global health problem, with the Plasmodium falciparum protozoan parasite causing the most severe form of the disease. Prevalence of drug-resistant P. falciparum highlights the need to understand the biology of resistance and to identify novel combination therapies that are effective against resistant parasites. Resistance has compromised the therapeutic use of many antimalarial drugs, including chloroquine, and limited our ability to treat malaria across the world. Fortunately, chloroquine resistance comes at a fitness cost to the parasite; this can be leveraged in developing combination therapies or to reinstate use of chloroquine. To understand biological changes induced by chloroquine treatment, we compared transcriptomics data from chloroquine-resistant parasites in the presence or absence of the drug. Using both linear models and a genome-scale metabolic network reconstruction of the parasite to interpret the expression data, we identified targetable pathways in resistant parasites. This study identified an increased importance of lipid synthesis, glutathione production/cycling, isoprenoids biosynthesis, and folate metabolism in response to chloroquine. We identified potential drug targets for chloroquine combination therapies. Significantly, our analysis suggests that the combination of chloroquine and sulfadoxine-pyrimethamine or fosmidomycin may be more effective against chloroquine-resistant parasites than either drug alone; further studies will explore the use of these drugs as chloroquine resistance blockers. Additional metabolic weaknesses were found in glutathione generation and lipid synthesis during chloroquine treatment. These processes could be targeted with novel inhibitors to reduce parasite growth and reduce the burden of malaria infections. Thus, we identified metabolic weaknesses of chloroquine-resistant parasites and propose targeted chloroquine combination therapies.

microbiology↗

bioRxiv2018

Metabolic mechanisms of interaction within a defined gut microbiota

Metabolic interactions among species are ubiquitous in nature, and the fitness costs and benefits they impose often reinforce and stabilize them over time. These interactions are of particular importance in the human gut, where they have functions ranging from enhancing digestion to preventing (or exacerbating) infections. The diversity and sheer number of species present lead to the potential for a multitude of metabolic interactions among species to occur. However, identifying the mechanism and consequences of metabolic interactions between even two species is incredibly challenging. Here, we develop, apply, and experimentally test a framework for identifying potential metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from the altered Schaedler flora (ASF), a defined murine microbiota. We then apply our novel framework, which we call the Constant Yield Expectation (ConYE) model, to dissect emergent metabolic behaviors that occur in co-culture. Using the ConYE model, we identify and interrogate an amino acid cross-feeding interaction that is likely to confer a growth benefit to one ASF strain (Clostridium sp. ASF356) in co-culture with another strain (Parabacteroides goldsteinii ASF519). We experimentally validate that the proposed interaction leads to a growth benefit for this strain via media supplementation experiments. Our results reveal the type and extent of emergent metabolic behavior in microbial communities and demonstrate how metabolomic data can be used to identify potential metabolic interactions between organisms such as gut microbes. Our in vitro characterization of the ASF strains and interactions between them also enhances our ability to interpret and design experiments that utilize ASF-colonized animals. We anticipate that this work will improve the tractability of studies utilizing mice colonized with the ASF. Here, we focus on growth-modulating interactions, but the framework we develop can be applied to generate specific hypotheses about mechanisms of interspecies interaction involved in any phenotype of interest within a microbial community.

microbiology↗

bioRxiv2017

Methods matter: Influential purification and analysis parameters for intracellular parasite metabolomics

Metabolomics is increasingly popular for the study of many pathogens. For the malaria parasite, Plasmodium falciparum, both targeted and untargeted metabolite detection has improved our understanding of pathogenesis, host-parasite interactions, and antimalarial drug treatment and resistance. However, purification and analysis procedures for performing metabolomics on intracellular pathogens have not been explored. Here, we investigate the impact of host contamination on the metabolome when preparing samples using standard methods. We purified in vitro grown ring stage intra-erythrocytic P. falciparum parasites for untargeted metabolomics studies; the small size of this developmental stage amplifies the challenges associated with metabolomics studies as the ratio between host and parasite biomass is maximized. Following metabolite identification and data preprocessing, we investigated whether host contributions could be corrected post hoc using various normalization approaches (including double stranded DNA, total protein, or parasite number). We conclude that normalization parameters have large effects on differential abundance analysis and recommend the thoughtful selection of these parameters. However, normalization does not remove the contribution from the parasites extracellular environment (culture media and host erythrocyte). In fact, we found that extra-parasite material is as influential on the metabolome as treatment with a potent antimalarial drug with known metabolic effects (artemisinin). Because of this influence, we could not detect significant changes associated with drug treatment. Instead, we identified metabolites predictive of host and media contamination that can be used to assess sample purification. Our findings provide a basis for development of improved experimental and analytical methods for future metabolomics studies of intracellular organisms.

microbiology↗

bioRxiv2017

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

BACKGROUNDMalaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing experimental knowledge and further understanding of these mechanisms.\n\nRESULTSHere, we developed a novel genome-scale metabolic network reconstruction, iPfal17, of the asexual blood-stage P. falciparum parasite to expand our understanding of metabolic changes that support resistance. We identified 11 metabolic tasks to evaluate iPfal17 performance. Flux balance analysis and simulation of gene knockouts and enzyme inhibition predict candidate drug targets unique to resistant parasites. Moreover, integration of clinical parasite transcriptomes into the iPfal17 reconstruction reveals patterns associated with antimalarial resistance. These results predict that artemisinin sensitive and resistant parasites differentially utilize scavenging and biosynthetic pathways for multiple essential metabolites including folate and polyamines, and others within the mitochondria. Our findings are consistent with experimental literature, while generating novel hypotheses about artemisinin resistance and parasite biology. We detect evidence that resistance parasites maintain greater metabolic flexibility, perhaps representing an incomplete transition to the metabolic state most appropriate for nutrient-rich blood.\n\nCONCLUSIONUsing this systems biology approach, we identify metabolic shifts that arise with or in support of the resistant phenotype. This perspective allows us to more productively analyze and interpret clinical expression data for the identification of candidate drug targets for the treatment of resistant parasites.

systems biology↗