Single-Cell Spatial Proteomics Analyses of Head and Neck Squamous Cell Carcinoma Reveal Tumor Heterogeneity and Immune Architectures Associated with Clinical Outcome

Data supporting the findings of the paper "Single-Cell Spatial Proteomics Analyses of Head and Neck Squamous Cell Carcinoma Reveal Tumor Heterogeneity and Immune Architectures Associated with Clinical Outcome." Files include output of multiplex immunohistochemistry computational image processing workflow for each tumor region and survival data for each patient. The code used to produce the results of this study is available at: https://github.com/kblise/HNSCC_mIHC_paper.

Notes about data files:

• clinicalData.csv = Contains progression free survival in 'dtr' (days to recurrence) column and therapy administered in 'tx' column for each patient.
• pt .csv files = Matrix of single cells (rows) and marker expression (columns). One file per tumor region (n=47). Other columns include:
  • class = Cell phenotype assigned via hierarchical gating strategy (see below for classes)
  • Location_Center_X and Location_Center_Y = Cartesian coordinates of cell center
  • PD1 = PD-1 expression; 1 = PD-1⁺, 0 = PD-1^-
  • PDL1 = PD-L1 expression; 1 = PD-L1⁺, 0 = PD-L1^-
  • KI67 = Ki-67 expression; 1 = Ki-67⁺, 0 = Ki-67^-

Classes, corresponding cell phenotype, and gating strategy used:

• A = CD8⁺ T Cell (CD45⁺ CD20^- CD3⁺ CD8⁺)
• B = CD4⁺ T Helper (CD45⁺ CD20^- CD3⁺ CD8^- FOXP3^-)
• C = B Cell (CD45⁺ CD20⁺)
• D = Macrophage (CD45⁺ CD20^- CD3^- CD66B^- CD68⁺)
• E = Other Immune (CD45⁺ CD20^- CD3^- CD66B^- CD68^- MHCII^-)
• F = Other Non-Immune (CD45^- PANCK^- αSMA^-)
• G = Noise
• H = Neoplastic Tumor (CD45^- PANCK⁺)
• J = Granulocyte (CD45⁺ CD20^- CD3^- CD66B⁺)
• K = CD4⁺ Regulatory T Cell (CD45⁺ CD20^- CD3⁺ CD8^- FOXP3⁺)
• N = αSMA⁺ Mesenchymal (CD45^- PANCK^- αSMA⁺)
• X = Dendritic Cell (CD45⁺ CD20^- CD3^- CD66B^- CD68^- MHCII⁺)