Multi-omic Single-Cell Analysis of Antigen-Presenting Compartment Reveals a Unique Functional Signature for Head and Neck Squamous Cell Carcinoma.

e15179 Background: Immune studies in head and neck squamous cell carcinoma (HNSCC) are lacking. Studies in the past decade have highlighted the biological significance and the distinct functional properties of immune cell subsets that are resident in non-lymphoid tissues. While tissue-resident memory T cells (TRM) have been well characterized, much less is known about the human myeloid compartment in HNSCC, which includes professional antigen-presenting cells (APCs) such as dendritic cells (DCs) and macrophages, both of which are critical for shaping the local T cell response. This is particularly relevant in the context of anti-tumor immune responses, which are currently a major focus for therapeutic intervention in HNSCC by either checkpoint inhibitory blockade or adoptive T cell therapy. Methods: A combination of multi-omic single cell RNA sequencing (sc-RNAseq) and 30-parameter fluorescent flow cytometry were used to define the APC compartment in 7 human head and neck squamous cell carcinoma (HNSCC) samples and 4 normal gingival tissue samples as references. Importantly, we performed parallel profiling of the adaptive and innate T cell compartment to elucidate the relationship between APCs and local TRM cells that have been designated as critical players for immune responses in solid tumor tissue. Results: Several novel myeloid phenotypes and an altered composition of the APC compartment in HNSCC relative to normal gingival tissues. APCs expressing pro-inflammatory cytokines such as IL-1b and IL-6 showed reduced abundance, while previously unknown APC subsets defined by the expression of a unique chemokine profile were found to infiltrate HNSCC tissue. Furthermore, our multi-omic approach allowed for profiling of the protein surface phenotype in these transcript-defined clusters, opening up avenues for future therapeutic targeting of tumor-specific antigen-presenting cells. Conclusions: A novel myeloid phenotype and APC compartment were observed in HNSCC when compared to normal gingival tissues. A multi-omic assay identified tumor-specific APCs that may represent future therapeutic targets.