Predicted Th2 Infiltrate is Associated with Outcome in HPV(-) Head and Neck Cancer.

Abstract

<h3>Purpose/Objective(s)</h3> We previously showed that immune infiltrate affects treatment response in Head/Neck Cancer (HNC) treated with radiation. Here, we evaluate the effect of predicted tumor infiltrating lymphocytes (TILs) on treatment failure following radiation. <h3>Materials/Methods</h3> Nintey-four human papillomavirus negative (HPV-) HNC patients in the TCGA treated with surgery and adjuvant radiation (PORT) comprised the discovery cohort. Pre-treatment tumors were analyzed using RNA-seq. These data were then used to predict tumor cell type abundance using xCell, which quantifies 64 immune, stroma, and tumor cell abundance from tissue RNA-seq data. Predicted TILs associated with overall survival (OS), distant metastasis (DM), and locoregional recurrence (LRR) in the discovery cohort were examined in a validation cohort of 102 HPV(-) HNC patients treated with surgery and PORT. All patients in the HPV(-) TCGA cohort with available mutation and gene expression data (n=403) were analyzed as were a separate 40 patient HPV(-) HNC cohort. Significant (MutSig) tumor mutations in cancer genes (OncoKB) were examined for association with predicted Th2 infiltrate. Gene expression significantly different between CD4+ T helper 2 (Th2) high and low tumors were analyzed using ingenuity pathway analysis (IPA) to identify pathways associated with predicted Th2 infiltrate. <h3>Results</h3> Several predicted TILs were associated with outcome, but only predicted Th2 infiltrate was significantly associated with higher rates of LRR in both the discovery (p=4e-3) and validation cohorts (p=9e-3). Predicted Th2 infiltrate was significantly increased in tumors harboring mutations in: CASP8, EP300, HRAS, HLA-A, and ZNF750. IPA using genes significantly (FDR 0.01) associated with predicted Th2 infiltrate identified activation of DDR-related pathways and repression of the tumor microenvironment (TME) pathway in tumors with high predicted Th2 infiltrate. Gene expression within each pathway was used to generate a pathway activation score with positive correlation between predicted Th2 and the BRCA1 in DDR pathway (Pearson R 0.73, p<2.2e-16) and negative correlation with the TME pathway (R= -0.45, p<2.2e-16). Similar patterns were seen in a separate 40 patient cohort, with predicted Th2 infiltrate correlated positively with the BRCA1 in DDR pathway (R=0.77, p=5.6e-9) and negatively with the TME pathway (R= -0.42, p=7.2e-3). <h3>Conclusion</h3> We identified predicted Th2 infiltrate associated with LRR in two homogeneously treated, HPV(-) HNC cohorts. We found that Th2 infiltrate was associated with mutations in genes known to be associated with both poor outcome and modulation of TILs. Finally, predicted Th2 was associated with increased activation of DNA damage response pathways and local repression of immune function in the TME. Thus, Th2 infiltrate may potentially mediate resistance to radiation in HPV(-) HNC.