Neoadjuvant pembrolizumab in locally advanced cutaneous squamous cell carcinoma: mIF analysis

Single-cell phenotype and spatial coordinate data derived from multiplex immunofluorescence (mIF) imaging of tumor specimens from a single-arm, phase II clinical trial of neoadjuvant pembrolizumab in patients with high-risk resectable cutaneous squamous cell carcinoma (cSCC) (NCT04808999). Pre-treatment core biopsies and post-treatment surgical specimens were profiled with two mIF antibody panels: Panel 1 (CD20, CD68, CD8, PD-1, panCK, PD-L1) and Panel 2 (CD163, CD68, MHCII, CD11c, panCK, PD-L1). Files include AnnData with cell typing results for pre and post treatment specimens with the corresponding UMAP results. We also include csv files cell types and registered coordinates for the two panels, these are the basis of the density analysis. AnnData with recurrent cellular neighborhood analysis from the registered images is included. Analysis code is available at https://github.com/Huang-AI4Medicine-Lab/cscc_mif_analysis.