Immunity & infection
Understanding the antigen binding specificities of lymphocytes is key to the development of effective therapeutics for cancers and infectious diseases. Recent technological advancements have enabled the integration of simultaneous cell-surface protein, transcriptome, immune repertoire and antigen specificity measurements at single cell resolution, providing comprehensive, scalable, high-throughput characterization of immune cells.
Using the 10x Genomics Single Cell Immune Profiling Solution with Feature Barcoding technology along with oligo-conjugated antibodies and peptide-MHC (pMHC) Dextramer reagents, we performed multi-omic characterization of PBMCs from cytomegalovirus (CMV) seronegative and seropositive patients. Full length, paired TCRα/β sequences with specificity to known CMV antigens were identified in the seropositive donor, but not in the seronegative donor. A large Epstein Barr Virus (EBV) pMHC specific T cell expansion was identified in the CMV seronegative donor, suggesting an active EBV response. Moreover, the combination of transcriptomic and cell surface protein information resulted in an increase in resolution of cell type identification. This workflow allowed the identification of enriched amino acid motifs within the TCR sequences that contained novel and known CDR3 amino acid sequences specific to CMV.
We scaled this technology with 14 oligo-conjugated antibodies and 50 pMHC Dextramer reagents spanning different CMV, EBV, Influenza, HIV, and Cancer antigens and performed a comprehensive characterization of ~200,000 CD8+ T cells from four MHC-matched donors. In addition to identifying novel and known TCR–pMHC specificity, we also observed TCR alloreactivity. These technological advancements provide new biological insights that are critical for progress in the field.