A framework to deduce the convoluted repertoire and epitope hierarchy of human T cell responses in visceral leishmaniasis: patient meets in silico.

Visceral leishmaniasis (VL) is one of the most severe parasitic infectious diseases with 0.4 million cases annually. There are currently no vaccines for VL, although there is evidence of acquired T cell-mediated immunity and resistance to reinfection. Indeed, VL vaccine development is severely hampered by the absence of a good animal model and the multitude of possible Leishmania antigens that remain uncharacterized because of the low-throughput screening methodologies currently applied. As such, there is a complete lack of insight in epitope reactivity, epitope dominance hierarchy and antigenic variation. In this project, we aim to unlock this status quo by implementing a patient-centered framework integrated with in silico epitope prediction tools and in vitro immunopeptidomics that can comprehensively deduce and confirm the Leishmania epitope hierarchy in patients. Additionally, we will phenotype and monitor the human Leishmania-specific T-cell response and repertoire during the complete course of infection using single-cell RNAseq, single-cell TCRseq and CITE-seq. These recent, state-of-the art tools allow unprecedented resolution by providing an exhaustive, timely and high-throughput immune profiling. We believe that this framework can be directly wheeled for diagnostic tools and to expedite vaccine development against Leishmania and serve as a proof of concept for similar complex eukaryotic pathogens.

Keywords:IMMUNO INFORMATICS, BIOINFORMATICS, DATA MINING

Disciplines:Bioinformatics of disease, Single-cell data analysis, Adaptive immunology, Vaccinology, Tropical medicine

Project type:Collaboration project