Graduate Student Fred Hutch/Univ. of Washington/Seattle Children’s Cancer Consortium, United States
Introduction/Rationale: There is an urgent need for an effective HIV- vaccine, but the durability and clonal diversity of HIV vaccine-elicited T-cells are poorly understood.
Methods: To characterize the HIV-specific TCR repertoire elicited by vaccination, we developed a novel and high-throughput method for efficient TCR cataloging of rare antigen-specific T-cells. We applied this approach to generate HIV-ENV and GAG-specific TCR libraries using PBMC samples of healthy vaccinees. We also performed bulk TCR-sequencing on longitudinal samples.
Results: We identified 1680 unique ENV- and GAG-specific TCR-clonotypes and found the magnitude of responses correlated with intracellular cytokine staining (ICS) data on the same cohort, except for higher frequency of CD8 T-cell response to GAG, as measured by TCR sequencing than by ICS. Through detailed TCR repertoire analyses, we were able to delineate the major clonotypic and kinetic differences between ENV- and GAG-CD4 and CD8 T-cells in response to prime and boost. Specifically, we observed boosting expanded short-lived GAG-specific CD8 T-cell clonotypes that likely contributed to under sampling of the response by ICS. In an unbiased approached, we clustered clonotypes by the magnitude of their trajectories and identified 6099 additional vaccine-responsive TCRs. Three clusters displayed stable memory trajectories, and two clusters, which contains GAG-CD8 T-cell clones, resembled short-lived effectors. Lastly, our data was further validated when we observed concordance in cell-type and antigen for matched T-cell clones between our data and published HIV datasets.
Conclusion: We developed a new pipeline to identify antigen-specific TCRs from peripheral blood samples. To our knowledge, this dataset represents the largest HIV-specific TCR catalogue to date, which can be used for discovery and comparison in other HIV contexts. Our longitudinal data provides an in-depth characterization of the cellular immune response to HIV vaccination.
