Single-cell transcriptomic profiling for inferring tumor origin and mechanisms of therapeutic resistance

We performed single-cell RNA sequencing on three different tumors isolated from an HNSCC patient who had a mixed response to checkpoint inhibitor therapy. A total of 11,470 single cells were profiled after the removal of cells that did not pass QC: Tumor-1: NPSCC (PR; n=3818; HN19-1); Tumor-2: NPSCC lymph node (PR; n=2870; HN19-2); and Tumor-3: Laryngeal SCC (PD; n=4782; HN19-3). Overall design: To identify drivers of response and resistance in an HNSCC patient treated with checkpoint inhibitor therapy, two responding and one non-responding tumor (all isolated at the same time) were dissociated and profiled using a 10x Genomics Chromium single-cell VDJ NextGEM v1.1 kit