T cell, NKT, and NK cell immune response assessment in infectious diseases

The T cell Immunology and Vaccines (TIV) group of IrsiCaixa has extensive experience in characterizing the cellular cytotoxic immune response to infectious diseases, mainly mediated by T cells but also on NKT and NK cells. We have wide experience measuring T cell antigen-specific responses using ELISPOT and AIM-ICS flow cytometry (Classic and Spectral). Furthermore, we have been mapping T cell epitopes and measuring TCR avidity for over 20 years. During this time, we have been collaborating closely with the HIV immune database in Los Alamos, curating the optimally defined HIV epitope list. With the development of single-cell TCR sequencing, we have started to study the TCR repertoire to different infectious diseases at an unsurpassed detail, a necessary complement to HLA epitope studies to understand T cell immunity.

We have also developed immune profiling flow cytometry panels to characterize T and NK cell subpopulations, activation (using activation-induced markers), homing, cytokine production (by intracellular cytokine staining), and polarization. Recently, we have introduced the use of -omics (transcriptomics and epigenetics) to characterize T, NKT, and NK responses to specific antigens, and we are now using scRNA/TCRseq to relate them to disease evolution and pathogen control (Moraes-Cardoso et al. Lancet Microbe. 2024 Aug;5(8):100859; Duran-Castells et al. EBioMedicine. 2023 Sep;95:104732; Bailon et al Nat Med. 2022 Dec;28(12):2611-2621). We are also integrating the interaction of the T cell response with the microbiota combining metagenomic microbiota data with the -omics data.