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 identif..., , , # 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

[https://doi.org/10.5061/dryad.n2z34tn7x](https://doi.org/10.5061/dryad.n2z34tn7x)

Protein and RNA CosMx TMA samples were generated using CosMx SMI by Nanostring Technologies Inc. (Bruker Spatial Biology), Seattle, WA, using a Human Universal Cell Characterization 1000-plex RNA panel, including cell typing markers and a list of 435 ligand-receptors ([https://nanostring.com/resources/cosmx-smi-universal-cell-characterization-panel-gene-list/](https://nanostring.com/resources/cosmx-smi-universal-cell-characterization-panel-gene-list/)) and Human Immune Oncology Protein Panel including 64 markers ([https://nanostring.com/products/cosmx-spatial-molecular-imager/cosmx-protein-assays/cosmx-human-immuno-oncology-protein-panel/](https://nanostring.com/products/cosmx-spatial-molecular-imager/cosmx-p..., The clinical sample collection and analyses were conducted in accordance with the Declaration of Helsinki and received institutional ethics approval from the University of Wisconsin-Madison (UW18144 with IRB#2018–1510, subproject number 2022-009), under a waiver of informed consent. Samples are de-identified by the clinical research team before data profiling and analysis. ,