Data from: Integrated single-cell and spatial analysis reveals context-dependent myeloid-T cell interactions in the response to immune checkpoint blockade in head and neck squamous cell carcinoma

Purpose: We conduct a systematic evaluation of cell-cell interactions
between tumor-infiltrating immune cells in patients with head and neck
cancer squamous cell carcinoma (HNSCC) who have been treated with immune
checkpoint blockade (ICB) using spatial and single-cell omics data.
Experimental Design: We employ complementary techniques from both Visium
spot-based spatial transcriptomics and CosMx SMI single-cell spatial
omics, utilizing a 64-plex protein panel and a 1000-gene RNA panel, which
includes 435 ligands and receptors. We conducted integrated bioinformatics
analyses to identify cellular neighborhoods of co-localizing cell types
and Ligand-Receptor interactions across different single-cell and spatial
data modalities. Results: With 522,399 single cells profiled for both RNA
and protein from 23 patients, along with spot-resolved spatial RNA-seq
data from 8 patients treated with ICB, and through bioinformatics analysis
of publicly available single-cell and bulk RNA-seq, we identified a
spatial and cell-type specific context dependency in the differences of
myeloid and T cell interactions between Responders and Non-Responders
samples. We further defined the cellular neighborhood and sources of
chemokine CXCL9/10-CXCR3 interactions, emphasizing the specificity of this
marker in Responders samples, an emerging target in ICB, as well as other
underappreciated markers and targets for ICB response in HNSCC, such as
CXCL16-CXCR6, CCL4/5-CCR5. Conclusions: We have provided a valuable
resource for analyzing spatial and cell-cell ligand-receptor interactions,
including the cellular and spatial contexts of ICB response markers. Our
data suggest that future mechanistic studies should consider this context
specificity when evaluating ICB response biomarkers and targets.