The poorly understood fungus Pneumocystis jirovecii is an important cause of lethal pneumonia (PCP) in immunocompromised humans, especially those with AIDS. Research approaches and clinical management of P. jirovecii pneumonia have been significantly hindered by the lack of a culture system. Attempts to develop a continuous in vitro system using standard methods have failed. We will employ a new approach, metatranscriptomics, recently used to successfully direct the supplementation of medium for a previously uncultivable bacterium. This approach will be used for the first time on an uncultivable eukaryotic pathogen. The reduced cost for next generation sequencing (NGS) of mRNA and genomic DNA has revolutionized many aspects of research. We will use NGS of mRNA to identify enzymes and transporters that are highly expressed by growing Pneumocystis populations. The substrates and targets of these proteins will be tested in an established short term in vitro culture system in an iterative fashion until an optimized culture is identified that supports the continuous propagation of Pneumocystis spp. Our objectives are to: 1) Use RNA-seq to obtain the metatranscriptome of infected rat lungs, which includes P. carinii, rat lung, and accompanying microbiota, to identify metabolic gene signatures associated with P. carinii growth and decline; 2) Use approaches of systems biology and structural bioinformatics to determine genes, key players in Pneumocystis proliferation, their possible ligands, substrates and products, to select candidate supplements for testing in vitro; 3) Evaluate modified culture media in a short term in vitro culture assay using a high throughput iterative strategy to identify essential nutrients and their concentrations that support the continuous growth of P. carinii; 4) Validate the in vitro culture using P. murina (mouse derived) and P. jirovecii (human derived) to develop a universal supplementary regime for Pneumocystis growth. Success of this project will fundamentally change the clinical diagnosis of PCP by providing a test for viable Pneumocystis and will also propel clinical and basic research forward by allowing application of powerful molecular genetic tools such as transformation and site directed mutation; facilitate drug discovery; and allow testing, tracking and investigation of drug resistance

Public Health Relevance

Pneumocystis pneumonia (PCP) continues to be a global health problem even in the context of combined antiretroviral therapy (cART). Clinical management of PCP, including new therapeutics, and all aspects of research, have been hindered by the lack of a continuous culture system for these fungi. This proposal will identify essential nutrients using a novel strategy, metatranscriptomics, to define an optimal system to support Pneumocystis growth outside the lung, thereby facilitating research that will result in major advancements in diagnosis and treatment of this disease.

National Institute of Health (NIH)
National Heart, Lung, and Blood Institute (NHLBI)
Research Project (R01)
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Special Emphasis Panel (ZRG1)
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Caler, Elisabet V
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University of Cincinnati
Internal Medicine/Medicine
Schools of Medicine
United States
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Cox, Jeremy W; Ballweg, Richard A; Taft, Diana H et al. (2017) A fast and robust protocol for metataxonomic analysis using RNAseq data. Microbiome 5:7
Baker, Frazier N; Cushion, Melanie T; Porollo, Aleksey (2016) A Quantitative Model to Estimate Drug Resistance in Pathogens. J Fungi (Basel) 2:
Cushion, Melanie T; Collins, Margaret S; Sesterhenn, Thomas et al. (2016) Functional Characterization of Pneumocystis carinii Inositol Transporter 1. MBio 7:
Porollo, Aleksey; Sesterhenn, Thomas M; Collins, Margaret S et al. (2014) Comparative genomics of pneumocystis species suggests the absence of genes for myo-inositol synthesis and reliance on inositol transport and metabolism. MBio 5:e01834
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