Single-nucleus RNA-seq analysis resolves chromatin and transcriptional features of fibrolamellar carcinoma

FLC is characterized by thick stroma, which has long suggested an important role of the tumor microenvironment. Over the past decade, several studies have revealed aberrant molecular markers and pathways in FLC.

However, an important limitation of these efforts is that they were conducted on bulk tumor samples. Consequently, the cell types that contribute to the different molecular features of FLC have remained unknown. In this study we primarily leverage single nucleus ATAC-seq to unveil cell-type specific signal for chromatin activity, microRNAs, super enhancers, and transcription factor networks (such as CREB1, AP-1 and ETV2) in FLC.