A high-throughput nanoparticle assay to characterize cancer neoepitope-specific T cells

PROJECT SUMMARYAs of early May 2020, there have been approximately 3.7 million confirmed cases of COVID-19 infectionworldwide, and approximately 260,000 deaths.1 A retrospective cohort study of patients from Wuhan, Chinademonstrated that although both survivors and non-survivors initially follow similar clinical courses, developingsepsis and acute respiratory distress syndrome (ARDS) at similar time points, non-survivors progress on tomulti-organ failure (MOF), secondary infection, and death.2 Additionally, pediatric cases have been shown tohave a much milder disease course than adults, and the reasons for this are not clear.3These differences inclinical courses could in part be explained by the patients' pre-existing T cell repertoire, phenotype, and HLA-specificity, which may influence downstream T cell phenotype and cytokine responses. Using in silicoapproaches, we identified multiple potential T cell epitopes which can be divided into 3 broad categories: 1)Epitopes with homology to the original SARS virus 2) Epitopes with homology to other viruses/bacteria 3)Epitopes with homology to self-antigens. We have developed aAPC constructs to interrogate both HLA class Iand HLA class II CD8+ and CD4+ T cell responses, respectively. As such, we will be able to obtain a broadunderstanding of the role these 3 different types of virus-specific epitopes play in the development of COVID-19 specific responses. A better understanding of how T cells contribute to progression of disease severity isespecially pertinent to patients who are on long-term immunosuppressive therapies because of malignancies,bone marrow transplant, or organ transplant. Patients with cancer were found to have higher probabilities ofhaving more severe disease and worse outcomes in China than both patients without cancer and cancersurvivors.4This proposal builds upon previously published work to screen patients for virus-specific T cellsusing only 100 L of whole blood, and with a turn-around time of less than 24 hours.5 In addition, we have alsodeveloped an enrichment and expansion (E+E) technology to rapidly expand virus and tumor-specific T cellswithin a 7 day time frame.6-12Combining these two approaches, we will identify clinically important T cellepitopes and demonstrate that functional T cells can be expanded to large numbers over a brief period-of-timein otherwise healthy donors and patients with cancer.