Single cell gene expression profile of patient-derived head and neck squamous carcinoma cells subjected to different treatments.

As other tumours, HNSCC are heterogenous, hence different cell populations within a given tumour may have different response towards treatment. Most of previous studies on HNSCC resistance towards treatment have been performed on “bulk” samples, which confound the influence of its heterogenous nature. In the recent years, single cell sequencing technologies have been developing rapidly and successfully applied to investigate numerous cancer response towards treatment. A recent scRNA-seq study on HNSCC cell lines confirmed the heterogenous response towards cetuximab. To further investigate both intrinsic and acquired resistance in HNSCC, we employed two primary cells modelling different responses towards selection with EGFR inhibitor, radiation, as well as a combination of EGFR inhibitor and radiation. These cell populations were studied using RAID technology, in which RNA and protein level were simultaneously quantified at a single cell resolution. Overall design: The treated cells were sorted into single cells and subjected to single cell sequencing.