Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma

Data supporting the findings of the paper "Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma." 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 the following columns for each tumor region:
  • sample = tumor region ID
  • dtr = Progression free survival (days to recurrence)
  • tnm = TNM stage
  • anatomy = anatomic site of resection
  • tx = therapy administered
  • area = area in mm² of tissue region
• 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
  • Cellsp_PD1p = PD-1 expression; 1 = PD-1⁺, 0 = PD-1^-
  • Cellsp_PDL1p = PD-L1 expression; 1 = PD-L1⁺, 0 = PD-L1^-
  • Cellsp_KI67p = 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^- CD8^- FOXP3^-)
• F = Other Non-Immune (CD45^- PANCK^- αSMA^-) - excluded from analysis
• G = Noise - excluded from analysis
• 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 = Antigen Presenting Cell (CD45⁺ CD20^- CD3^- CD66B^- CD68^- MHCII⁺)