Additional file 1 of The immune microenvironment of HPV-positive and HPV-negative oropharyngeal squamous cell carcinoma: a multiparametric quantitative and spatial analysis unveils a rationale to target treatment-naïve tumors with immune checkpoint inhibitors

Additional file 1: Supplementary Table S1. Automatic definition of cell types by NanoString nSolver Software. Supplementary Table S2. Automatic definition of immune pathways by NanoString nSolver Software. Supplementary Fig. S1. Representative images of cell-to-cell distance analyses. (A) For mean distance between different cell subtypes, the nearest neighbors analysis was used. The mean distance between tumor cells (light blue dots) and the nearest CD8+ cells (red dots) is represented in the figure as an example. (B) The count within analysis was employed to calculate the percentage of reference cells, among the total number of reference cells, which are present within a 20 μm radius from at least one cell of a different phenotype. The percentage of tumor cells (light blue dots) within a 20 μm radius from a CD8+ T lymphocyte (red dots) is represented in the figure as an example. Original magnification X20. Supplementary Table S3. Differentially expressed genes (DEGs) between HPV-positive and HPV-negative (used as baseline) OPSCC patients. Supplementary Fig. S2. Differential expression of immune-related pathways and cell type genes in HPV-positive and HPV-negative OPSCC. Trend plots depicting differential expression of predefined (A) pathway genes and (B) gene expression-based cell types in HPV-positive and HPV-negative OPSCC. Supplementary Table S4. Correlation analysis between immune cell populations in HPV-positive and HPV-negative primary tumors and metastases. Supplementary Fig. S3. Immune cells in primary tumors and related metastases. Density (number of cells/mm2) of different immune cell populations in HPV-positive and HPV-negative primary tumors and metastases. Supplementary Fig. S4. The immune cell contexture of metastases correlates with patient outcome. (A-C) Kaplan-Meier survival curves for disease-free survival according to the immune cell composition of (A) the entire cohort (n = 39), (B) HPV-positive (n = 24) and (C) HPV-negative (n = 15) lymph node metastases. The median cut-off of each immune cell subset density was used to separate high and low infiltrated groups. Log-rank p values, hazard ratios (HR) and 95% confidence intervals (CI) are reported in each graph. Supplementary Fig. S5. The density of immune cells differs between females and males with HPV-positive lesions. Density (number of cells/mm2) of different immune cell populations in females and males with HPV-positive (A) primary tumors and (B) metastases.