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

截至2020年5月初，全球约有370万例COVID-19确诊病例，约26万人死亡一项针对中国武汉患者的回顾性队列研究表明，尽管幸存者和非幸存者最初的临床病程相似，在相似的时间点出现败血症和急性呼吸窘迫综合征（ARDS），但非幸存者进展为多器官衰竭（MOF）、继发感染和死亡此外，儿科病例的病程比成人轻得多，其原因尚不清楚。这些临床过程的差异可以部分解释为患者先前存在的T细胞库、表型和hla特异性，这可能会影响下游T细胞表型和细胞因子反应。利用计算机方法，我们鉴定了多个潜在的T细胞表位，可分为3大类：1)与原始SARS病毒同源的表位；2)与其他病毒/细菌同源的表位；3)与自身抗原同源的表位。我们已经开发了aAPC结构来分别询问HLA I类和HLA II类CD8+和CD4+ T细胞反应。因此，我们将能够广泛了解这3种不同类型的病毒特异性表位在covid - 19特异性反应的发展中所起的作用。更好地了解T细胞如何促进疾病严重程度的进展，尤其与因恶性肿瘤、骨髓移植或器官移植而长期接受免疫抑制治疗的患者有关。研究发现，在中国，癌症患者比非癌症患者和癌症幸存者更有可能患上更严重的疾病，预后也更差。4 .这项建议建立在先前发表的工作的基础上，该工作仅使用100L的全血筛选患者的病毒特异性T细胞，并且周转时间不到24小时此外，我们还开发了一种富集和扩增（E+E）技术，可在7天内快速扩增病毒和肿瘤特异性T细胞。结合这两种方法，我们将确定临床上重要的T细胞表位，并证明功能性T细胞可以在短时间内在健康供体和癌症患者中大量扩增。

As of early May 2020, there have been approximately 3.7 million confirmed cases of COVID-19 infection worldwide, and approximately 260,000 deaths.1 A retrospective cohort study of patients from Wuhan, China demonstrated that although both survivors and non-survivors initially follow similar clinical courses, developing sepsis and acute respiratory distress syndrome (ARDS) at similar time points, non-survivors progress on to multi-organ failure (MOF), secondary infection, and death.2 Additionally, pediatric cases have been shown to have a much milder disease course than adults, and the reasons for this are not clear.3These differences in clinical courses could in part be explained by the patients’ pre-existing T cell repertoire, phenotype, and HLAspecificity, which may influence downstream T cell phenotype and cytokine responses. Using in silico approaches, 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 I and HLA class II CD8+ and CD4+ T cell responses, respectively. As such, we will be able to obtain a broad understanding of the role these 3 different types of virus-specific epitopes play in the development of COVID19 specific responses. A better understanding of how T cells contribute to progression of disease severity is especially 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 of having more severe disease and worse outcomes in China than both patients without cancer and cancer survivors.4This proposal builds upon previously published work to screen patients for virus-specific T cells using only 100 L of whole blood, and with a turn-around time of less than 24 hours.5 In addition, we have also developed an enrichment and expansion (E+E) technology to rapidly expand virus and tumor-specific T cells within a 7 day time frame.6–12Combining these two approaches, we will identify clinically important T cell epitopes and demonstrate that functional T cells can be expanded to large numbers over a brief period-of-time in otherwise healthy donors and patients with cancer.