154 Dissecting the keratinocyte lineage of basal cell carcinoma using single cell RNA sequencing

Abstract

It remains unclear whether basal cell carcinomas (BCCs) originate from the stem cells in the hair follicle bulge or inter-follicular epithelial (IFE) regions. To explore the lineage derivation of BCC tumors, we applied single-cell RNA sequencing to 56219 cells isolated from 4 BCCs and 2 normal skin samples, profiling tumor keratinocyte, immune, stromal, melanocyte and endothelial cell subpopulations. Pseudotime trajectories of keratinocyte and fibroblast clusters displayed a common origin of normal cells, then a bifurcation into two branches in BCCs. In particular, tumor keratinocyte clusters characterized by high levels of EPCAM also expressed high levels of human bulge markers (KRT15, LGR5, DKK3) and low levels of human IFE markers (CD34, KIT). In contrast, keratinocyte clusters with low EPCAM expression had low levels of human bulge markers and high levels of mouse IFE markers (GRHL3, OVOL1). Single-cell analyses also defined distinct tumor keratinocyte-stromal interaction patterns. Our findings support the hair follicle bulge stem cells as the lineage of origin for BCC and elucidate the tumor and microenvironment pathways that evolve during BCC development.