Peptide Driven Identification of TCRs (PDI-TCR) reveals dynamics and phenotypes of CD4 T cells in tuberculosis [TCR-Seq]

We developed the Peptide-Driven Identification of TCRs (PDI-TCR), an approach that leverages antigen-specific peptide pools, bulk TCR sequencing, and statistical analyses to pinpoint antigen-specific TCRs. We discerned antigen-specific TCRs within a group of active tuberculosis (ATB) patients and individuals with a positive Interferon-γ release assay (IGRA+). We found Mtb-specific effectors to have an HLA-DR+ Th1* phenotype, and to be exclusive to active disease. Conversely, HLA-DR- Mtb-specific T cells appeared in Th1 cells in both ATB and IGRA+ cohorts. We also identified Cross-reactive T cells, that were abundant ex vivo regardless of disease state having a cytotoxic phenotype. PBMCs were stimulated with a Mtb-specific (MTB300) or a PT-specific (PT132) peptide pool and cultured for 14 days. Cells were harvested and their DNA was extracted for bulk survey TCR sequencing using the immunoseq platform. Simultaneously Ex vivo PBMCs from 4 ATB donors were subjected to CD4 isolation and deep TCR sequencing. *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. ***************************************************************