Expression profiling by high throughput sequencing
Summary
Dendritic cells (DCs) are uniquely capable of transporting tumoral antigens to tumor-draining lymph nodes (tdLNs), and also interact with effector T cells within the tumors themselves, mediating both natural antitumor immunity and the response to checkpoint blockade immunotherapy. Using LIPSTIC (Labeling Immune Partnerships by SorTagging Intercellular Contacts)-based single-cell transcriptomics, we identify individual DCs capable of presenting antigen to CD4+ T cells in the tdLN as well as inside tumors. These represent only a fraction of all DCs present and display a distinctive activated phenotype that in the LN includes production of cytokine IL-27, required for efficient T cell priming and tumor rejection. Tumor progression results in loss of effective priming of naïve CD4+ T cells, downstream of transcriptional changes in DCs that are manifested already when they arrive at the tdLN, which can be rescued by CTLA4 checkpoint blockade.
Overall design
Proximity-dependent labeling and subsequent RNA sequencing (Plate-based scRNA-seq, 10x Genomics, and bulk RNA-seq) were used to analyze dendritic cells (DCs) from tumor-draining lymph nodes (tdLNs) and tumor microenvironments (TME) in mice. The dataset includes RNA profiles of DCs involved in tumor-specific CD4+ T cell interactions, captured via photoactivation and LIPSTIC labeling, under steady-state and checkpoint blockade conditions.
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