Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [bulk RNAseq]

Single-cell RNA sequencing (scRNA-seq) has proven to be an invaluable tool for the study of tumor evolution. However, interrogating regulatory epigenetic alterations during cancer progression at the resolution of single-cells has remained a major challenge due to the lack of sensitivity of current assays. Here, we developed the highly-sensitive single-nucleus CUT&RUN (snCUT&RUN) assay to profile histone modifications in primary, metastatic, and cisplatin-resistant head and neck squamous cell carcinoma (HNSCC) patient-derived cell lines. We find that the epigenome can employ diverse modes to contribute towards cancer progression. Notably, we demonstrate that gene expression changes during cancer progression are co-modulated by alterations in both copy number and chromatin activity to drive epigenetic rewiring of cell-states. Furthermore, intratumor epigenetic heterogeneity may predispose sub-clonal populations within the primary tumor to acquire malignant characteristics. In conclusion, snCUT&RUN serves as a valuable addition to existing toolkit of single-cell assays to dissect the function of the epigenome during cancer progression.