A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma

A complete chart of the chromatin regulatory elements of immune cells in patients with cancer and their dynamic behavior is necessary to understand the developmental fates and guide therapeutic strategies. Here, we map the single-cell chromatin landscape of immune cells from blood, normal tumor-adjacent kidney tissue and malignant tissue from patients with early-stage clear cell renal cell carcinoma (ccRCC). We catalog the T cell states dictated by tissue-specific and developmental-stage-specific chromatin accessibility patterns, infer key chromatin regulators and observe rewiring of regulatory networks in the progression to dysfunction in CD8(+) T cells. Unexpectedly, among the transcription factors orchestrating the path to dysfunction, NF-kappa B is associated with a pro-apoptotic program in late stages of dysfunction in tumor-infiltrating CD8(+) T cells. Importantly, this epigenomic profiling stratified ccRCC patients based on a NF-kappa B-driven pro-apoptotic signature. This study provides a rich resource for understanding the functional states and regulatory dynamics of immune cells in ccRCC. Skokos and colleagues characterize human early-stage clear cell renal cell carcinoma with single-cell ATAC-seq and RNA-seq, identifying a spectrum of NF kappa B-promoted T cell dysfunction in the microenvironment and defining a pro-apoptotic signature.