PhyloQuant approach provides insights into Trypanosoma cruzi evolution using a systems-wide mass spectrometry-based quantitative protein profile

• DOI: 10.1038/s42003-021-01762-6
• Publication Date: 2021-03-11T11:03:49Z
• Authors: Simon Ngao Mule; André Guilherme C...; Livia Rosa-Fernandes; Gilberto Santos d...; Carla Monadeli F....; Daniel Quina; Graziella E. Rosein; Marta Maria Geral...; Giuseppe Palmisano
• Keywords: Proteomics; 0301 basic medicine; 0303 health sciences; Proteome; QH301-705.5; Trypanosoma cruzi; Protozoan Proteins; Article; 3. Good health; Evolution, Molecular; 03 medical and health sciences; Gene Expression Regulation; Tandem Mass Spectrometry; Biology (General); Chromatography, High Pressure Liquid; Phylogeny

AbstractThe etiological agent of Chagas disease, Trypanosoma cruzi, is a complex of seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution requires understanding the parasite origin and population structure. In this study, we introduce the PhyloQuant approach to infer the evolutionary relationships between organisms based on differential mass spectrometry-based quantitative features. In particular, large scale quantitative bottom-up proteomics features (MS1, iBAQ and LFQ) were analyzed using maximum parsimony, showing a correlation between T. cruzi DTUs and closely related trypanosomes’ protein expression and sequence-based clustering. Character mapping enabled the identification of synapomorphies, herein the proteins and their respective expression profiles that differentiate T. cruzi DTUs and trypanosome species. The distance matrices based on phylogenetics and PhyloQuant clustering showed statistically significant correlation highlighting the complementarity between the two strategies. Moreover, PhyloQuant allows the identification of differentially regulated and strain/DTU/species-specific proteins, and has potential application in the identification of specific biomarkers and candidate therapeutic targets.