Downregulation of KEAP1 in melanoma promotes resistance to immune checkpoint blockade [scBisulfite-seq]

Immune checkpoint blockade (ICB) has demonstrated efficacy in patients with melanoma, but many exhibit poor responses. Using single cell RNA sequencing of melanoma patient-derived circulating tumor cells (CTCs) and functional characterization using mouse melanoma models, we show that the KEAP1/NRF2 pathway modulates sensitivity to ICB, independently of tumorigenesis. The NRF2 negative regulator, KEAP1, shows intrinsic variation in expression, leading to tumor heterogeneity and subclonal resistance. Single cells from a culture of melanoma circulating tumor cells (MEL167, PMID: 33203734) were isolated by cell sorting. A total of 35 cells were used for matched bisulfite- and RNA-sequencing using a previously established protocol (PMID: 30498128 and PMID: 26902283).