Xenium Spatial Transcriptomics of Head and Neck Single Cell Carcinoma

Recent work has shown that the spatial organization of immune responses is a critical determinant of anti-tumor immunity. Here, we profiled ten head and neck squamous cell carcinoma (HNSCC) patient tumors and one ameloblastoma tumor using Xenium V1 spatial transcriptomics. The 10X genomics human multi-tissue and cancer gene expression panel targeting 377 genes was used in combination with 100 custom Xenium probes targeting patient-specific CDR3 regions of T cell receptors (TCRs) in T cells, additoinal T cell specific genes, HPV oncoprotein genes, and tumor genes of interest. This enabled the detection of 477 transcripts within each tumor sample at a single-cell resolution. For seven of the ten HNSCC samples, different tissue sections run on different days were analyzed as technical replicates. Together, these findings introduce a scalable platform for spatial clonal T cell analysis and provide new insight into the spatial relationship of cells within the HNSCC tumor microenvironment. Ten fresh-frozen HNSCC tumors, five of which were HPV+, were used for analysis. Seven of the ten tumors were run in replicate on different slides on different days for a total of 17 HNSCC tumor sections analyzed via Xenium spatial transcriptomics. One ameloblastoma tumor was also analysised via Xenium spatial transcriptomics.