Immune Responses To HIV And Other Pathogens

在这个项目中，我们使用下一代测序方法来测序抗原特异性B细胞和T细胞的适应性免疫受体。测序越来越多地在单细胞水平上进行，并与全转录组分析配对。我们在疫苗接种、自然感染和小鼠癌症模型的背景下这样做。目的是了解有效的抗原特异性适应性免疫反应的性质。我们已经实施了10x Genomics Chromium平台以及内部SMART-seq协议。我们已经成功地开发并实施了定制引物库制备方法，使得我们可以调整标准10 × 5免疫球蛋白和T细胞受体测序方案，以用于来自恒河猴和食蟹猴以及豚鼠的样品。此外，我们通过去除片段化步骤将文库制备的灵敏度提高了100倍。我们已经使用定制的缀合抗体实现了CITE-seq应用，以执行高参数细胞表面蛋白质组学。所有这些方法都已用于研究自然感染和接种疫苗后HIV、COVID-19、癌症和流感中抗原特异性T细胞和抗体应答的性质和演变。

In this project we use next generation sequencing approaches to sequence the adaptive immune receptors of antigen-specific B cells and T cells. The sequencing is increasingly at the single cell level and paired with whole transcriptome analysis. We do this in the context of vaccination, natural infection and mouse models of cancer. The aim is to understand the nature of effective antigen-specific adaptive immune responses. We have implemented the 10x Genomics Chromium platform as well as an in-house SMART-seq protocol. We have successfully developed and implemented a custom primer library prep approach so that we may adapt the standard 10x 5 immunoglobulin and T cell receptor sequencing protocol for use with samples from rhesus and cynomolgus macaques, and Guinea pigs. In addition, we have increased the sensitivity of the library prep by 100-fold by removing the fragmentation step. We have implemented CITE-seq applications using custom conjugated antibodies to perform high parameter cell surface proteomics. All of these approaches have been used to investigate the nature and evolution of antigen-specific T cell and antibody responses in HIV, COVID-19, cancer, and influenza in natural infection and after vaccination.