Single-cell spatial transcriptomics uncovers niches that govern response to PD-1/PD-L1 blockade in cutaneous squamous cell carcinoma

Neoadjuvant PD-1/PD-L1 blockade demonstrates robust efficacy in cutaneous squamous cell carcinoma, yet a significant proportion of patients do not achieve a major pathological response for unclear reasons. Here, we characterize spatially resolved gene expression profiles before, during, and after treatment in cutaneous squamous cell carcinoma (cSCC) patients enrolled on two pivotal phase II clinical trials of neoadjuvant PD-1/PD-L1 blockade. Using single-cell RNA-based spatial molecular imaging, we profiled more than 56 million transcripts from over 250,000 cells across 27 patients. Traditional cell type clustering uncovered five broad cell types (keratinocytes, fibroblasts, B-lineage cells, myeloid cells, and a mixed dendritic/T/NK compartment). Genes associated with interferon signaling and metabolic pathways were significantly upregulated in responders, but bulk gene expression alone did not fully distinguish responders from non-responders. We then applied a spatial clustering approa..., , # Single-cell spatial transcriptomics uncovers niches that govern response to PD-1/PD-L1 blockade in cutaneous squamous cell carcinoma

Dataset DOI: [10.5061/dryad.s4mw6m9jh](10.5061/dryad.s4mw6m9jh)

## Description of the data and file structure

This repository contains a Seurat object (named “seurat_object”) generated from CosMx SMI using the manufacturer's 1000 plex panel. The object enables researchers to reproduce or extend the analyses performed in our study. All cell metadata has been de-identified according to our IRB-approved protocol, and no personally identifiable information (PII) is included. The data comes from 2 tissue microarrays of formalin fixed paraffin embedded tissue of human cutaneous SCC specimens taken before, during, or after immunotherapy. 

### Files and variables

#### Seurat_Object_cSCC.RDS

```
– A serialized R object in Seurat format, which includes:
– Filtered and normalized gene expression data.
– Cell-level metadata (excluding direct identifie..., All patient data used in this study were de-identified in accordance with institutional review board (IRB) requirements and relevant data privacy regulations (e.g., HIPAA). Specifically, the research team removed or replaced all direct and indirect identifiers, including names, dates of birth, addresses, and medical record numbers, with coded pseudonyms or aggregated values. No link to identifiable personal information was retained, ensuring that the data cannot be traced back to individual participants. All de-identified data were stored in secure, access-controlled repositories with strict oversight, and were only used for the purposes of this study.