Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi

Chagas disease is a neglected tropical disease and a leading cause of heart failure in Latin America caused by a protozoan called Trypanosoma cruzi. This parasite presents a complex multi-stage life cycle. Anti-Chagas drugs currently available are limited to benznidazole and nifurtimox, both with severe side effects. Thus, there is a need for alternative and more efficient drugs. Genome-scale metabolic models (GEMs) can accurately predict metabolic capabilities and aid in drug discovery in metabolic genes. This work developed an extended GEM, hereafter referred to as iIS312, of the published and validated T. cruzi core metabolism model. From iIS312, we then built three stage-specific models through transcriptomics data integration, and showed that epimastigotes present the most active metabolism among the stages (see S1–S4 GEMs). Stage-specific models predicted significant metabolic differences among stages, including variations in flux distribution in core metabolism. Moreover, the gene essentiality predictions suggest potential drug targets, among which some have been previously proven lethal, including glutamate dehydrogenase, glucokinase and hexokinase. To validate the models, we measured the activity of enzymes in the core metabolism of the parasite at different stages, and showed the results were consistent with model predictions. Our results represent a potential step forward towards the improvement of Chagas disease treatment. To our knowledge, these stage-specific models are the first GEMs built for the stages Amastigote and Trypomastigote. This work is also the first to present an in silico GEM comparison among different stages in the T. cruzi life cycle.
Author summary Chagas disease is a neglected tropical disease that affect millions of people. Chagas disease is caused by T. cruzi, a protozoan that can be transmitted through insect vectors. Currently, medications for chagas disease are limited and have severe side effects. T. cruzi presents a complex multi-stage life cycle including 3 stages, which poses additional challenges in drug development. In this study, we deepened the understanding of the metabolism of T. cruzi across its life cycle through integrating omics data with GEMs. We reconstructed an updated GEM of T.cruzi with additional subsystems using novel genome annotations—the number of gene included increased by ~50%. We then generated models for each stage using stage-specific transcriptomics data to model only genes that were expressed at each stage. Simulations of stage-specific models suggest remarkable differences in metabolism across stages of T. cruzi. Gene and pathway essentiality was also predicted to vary greatly across its multi-stage life cycle, some of which were confirmed by previous studies. Our models were verified with experimentally measured enzyme activity at each stage. In conclusion, our results revealed stage-specific differences in metabolism in T. cruz and provided valuable insight into drug discovery.