Whole Transcriptome and Mouse TCR sequencing characterize changes to the immune repertoire during cancer metastasis

The Reticker-Flynn Lab at Stanford is working to understand the process by which tumors evade the immune system and metastasize to invade the body.

In this experiment, we are interested in how T cell phenotypes and clonotypes in lymph nodes are altered upon cancer metastasis, with a focus on the role of regulatory T cells in the development of tolerance. We are examining whether metastasis to sites such as lymph nodes (LNs) affects TCR repertoire diversity and whether LN involvement drives TCR diversification or clonal expansion, in particular within T cell subsets. In addition, the paired TCR sequences will be used for downstream testing to determine tumor reactivity.

The dataset comprises 3 control samples from tumor naïve mice and 6 samples from tumor bearing mice, from a transplant model of lymph node (LN) metastasis (Reticker-Flynn, et al., Cell, 2022). Tumor-draining lymph nodes were dissociated and negative bead isolation was used to isolate T cells. The samples were then characterized using the Evercode Whole Transcriptome kit and the new Parse Mouse TCR assay.