Characterization of the protein interaction network during T cell exhausting by multidimensional proteomics to develop new therapeutic approaches

T cells exposed to prolonged stimulation, such as during chronic infection or in the cancer microenvironment, become dysfunctional, a state referred to as exhaustion.

Checkpoint inhibitors can rejuvenate only PD-1Intermediate cells, whereas PD-1high cells are terminally exhausted and do not show any functional improvement, indicating heterogeneity in the exhausted T cell pool.

In this project, we will employ temperature and ion-based Proteome Integral Solubility Alteration coupled to expression proteomics (PISA-Express), methods developed during my Ph.D. and combine them with protein interaction techniques (Gordon lab, Emory University), to study the social architecture of proteins during T cell exhaustion.

In year 1, we will stimulate CD8+ T cells in vitro and in vivo in combination with six checkpoint inhibitors. Protein abundance and structural changes will be quantified in distinct subpopulations of exhausted T cells.

During year 2, the comprehensive protein interaction landscape of candidate proteins will be determined by AP-MS and TurboID.

In year 3, we will test interventions directed towards key pathways to determine if they revert the exhaustion phenotype. Additionally, our multidimensional proteomic data will be made publicly available as an interactive web interface.

Elucidating the protein interactions mediating T cell exhaustion will allow us to provide novel molecular information and accelerate the development of novel therapeutic approaches.