UCLA

The adaptive immune system provides protection against disease and maintains memory of past exposures. Randomly rearranged antigen receptors can recognize virtually any pathogen. T cells recognize processed peptides that originate from protein fragments and are presented on major histocompatibility complex molecules. Human T cell receptor (TCR) function is mostly studied in the context of model antigens. TCRs against the majority of presented epitopes are not defined. Single cell sequencing allowed for paired TCRα/β sequencing at a scale not previously imaginable, which increased interest in identification of antigen specific TCRs.

Antigen specific TCR discovery efforts are challenging because of the repertoire diversity. Up to 10^19 possible TCRs can be randomly generated in the thymus. Antigen specific T cells can be selected by a range of techniques based on either physical staining of the TCR or selection of cells activated with specific antigen. Antigen specific T cell rarity and abundance of weakly reactive cells leads to selection of large numbers of false positive clones. The TCRα/β needs to be sequenced and genetically reconstructed in allogeneic T cells to confirm antigen recognition. The qualities of an antigen specific TCR include the ability to direct the killing of target cell lines, stimulating the production of multiple cytokines, and driving cell division. Such data can then be used to rank TCRs and identify highly functional clones. More sensitive and specific selection prior to sequencing can reduce the amount of labor involved when profiling TCRs.

This thesis work describes a new technology for sequencing antigen specific TCRs, which is used to study T cell responses against SARS-CoV-2. We developed a protocol that allows for TCR sequencing in cells that have been identified as functional based on cytokine production in response to stimulation with specific antigens. TCR engagement drives cytokine production which is one of the fundamental properties of a T cell. For this reason, intracellular cytokine staining is one of the most commonly used techniques to quantify antigen specific T cells. We then identified SARS-CoV-2 polymerase specific TCRs in unexposed human donors. Polymerase specific TCRs are able to recognize multiple human coronaviruses, indicating the potential to provide immunity regardless of the SARS-CoV-2 variant. Broadly reactive T cells provide heterosubtypic immunity against Influenza, another respiratory virus. Based on this work our laboratory, in collaboration with other laboratories at UCLA, is developing a novel COVID-19 vaccine strategy.

Our SARS-CoV-2 work illustrates the utility of studying single TCRs to discover immune responses, but another approach is to use TCRs directly as therapeutics. TCR engineered T cells are effective in the clinic and cure late-stage tumors. Projects described in this thesis are helping drive other efforts in our laboratory that are directed at identifying TCRs against novel prostate cancer antigens.