Bulk RNA-seq for B-cell specific checkpoint molecules regulating anti-tumor immunity

The role of B cells in anti-tumor immunity is still debated and accordingly, most therapies have focused on targeting T and NK cells to inhibit tumor growth1,2. Here, using high-throughput flow cytometry, bulk and single-cell RNA- and BCR-sequencing of B cells temporally during B16F10 melanoma growth, we identified a subset of B cells that expands specifically in the draining lymph node over time in tumor bearing-mice. The expanding B cell subset expresses the cell surface molecule T cell immunoglobulin and mucin domain 1 (TIM-1) and a unique transcriptional signature, including multiple co-inhibitory molecules such as PD-1, TIM-3, TIGIT and LAG-3. While conditional deletion of these co-inhibitory molecules on B cells had little or no effect on tumor burden, selective deletion of Havcr1 (the gene encoding TIM-1) in B cells both dramatically inhibited tumor growth and enhanced effector T cell responses. Loss of TIM-1 enhanced the type 1 interferon response in B cells, which augmented B cell activation and increased antigen presentation and co-stimulation, resulting in increased expansion of tumor-specific effector T cells. Our results demonstrate that manipulation of TIM-1-expressing B cells enables engagement of the second arm of adaptive immunity to promote anti-tumor immunity and inhibit tumor growth. Analysis of B cells derived from tumor, dLN, ndLN and spleen of B16F10-bearing wild-type mice (n=3)