Supplementary data from Characterization of the T-Cell Receptor Repertoire and Immune Microenvironment in Patients with Locoregionally Advanced Squamous Cell Carcinoma of the Head and Neck

<p>Supplementary Figure 1. TCR-β DI in HPV-positive patients (excluding smokers with {greater than or equal to}10packyear history) versus HPV-negative patients (excluding patients with <10pack-year history) (Mann-Whitney U-test, p=0.004). Supplementary Figure 2. Sum of percentages of top 10 CDR3 clonotypes in HPV-positive versus HPV-negative tumors (Mann-Whitney U-test, p=0.01). Supplementary Figure 3. RT-PCR results for CTLA4, PD-1, IDO1, PD-L1, PD-L2, CD206 and FOXP3/CD4 ratio in HPV-positive versus HPV-negative tumors (Mann-Whitney U-test). Supplementary Figure 4. TCR-β DI, recurrence-free survival and overall survival Kaplan-Meier curves. Supplementary Figure 5. TCR-β DI, T-stage, N-stage and tumor localization (Mann-Whitney U- test). Supplementary Figure 6. Significant correlations of GRZB and PRF1 with B7-H3, CD206, FOXP3 and CTLA4 using RT-PCR in tissues from 44 patients with locoregionally advanced SCCHN. Pearson''s correlation co-efficients and p-values are shown for each graph. Supplementary Figure 7. Significant correlations of CD4, CTLA4 and FOXP3 with TCR-β DI using RT-PCR and TCR sequencing in tissues from 43 patients with locoregionally advanced SCCHN. Pearson''s correlation co-efficients and p-values are shown for each graph. Supplementary Figure 8. HLA-A mRNA levels in HPV-positive versus HPV-negative patients (n=44) and association of HLA-A mRNA with TCR-β DI. HLA-A expression (logarithmic scale) was divided by median (T1-T2) and the TCR-β DI (logarithmic scale) was plotted against the HLA-A expression categories. Supplementary Table 1. Univariate and multivariate Cox-regression analysis of overall survival for immune markers and HPV status, tumor and nodal stage.</p>