Background: Immunotherapy confers clinical benefit in head and neck squamous cell carcinoma (HNSCC); however, only a fraction of patients respond. The non-T cell-inflamed tumor microenvironment is associated with lack of response, and tumor-intrinsic molecular signaling pathways may be critical drivers of immune exclusion. Therefore, understanding correlations between T-cell inflammation and mutated or activated oncogenic pathways may inform combination immunotherapy approaches.

Methods: RNAseq, somatic mutations, and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database for 484 HNSCC patients (88 HPV-positive, 396 HPV-negative). Gene expression was used to segregate tumors into non-T cell-inflamed, T cell-inflamed, or intermediate groups and genes more frequently mutated in non-T cell-inflamed versus inflamed (or vice versa) were identified. Differentially expressed genes (DEGs) between the two groups were detected by limma voom with precision weights. Pathway activation was identified by Ingenuity Pathway Analysis® (IPA). Association between molecular markers and patients’ overall survival (OS) was tested using Cox proportional-hazards regression models.

Results: 132 (27%) and 183 (38%) tumors were categorized into the non-T cell-inflamed and inflamed group, respectively, with the rest intermediate. Survival analysis revealed that among age, sex, tumor grade, and HPV status, age was the strongest prognostic factor (p=0.003), with older patients showing a decreased 5-year survival. The absence of a T cell-inflamed signature was significantly associated with poorer prognosis within patients ≤65 years of age (p=0.03, HR=1.18) and remained significant after adjusting for covariates such as HPV status. This association was not observed in older patients. Comparison of somatic mutational profiles between the non-T cell-inflamed and inflamed groups identified top mutated genes enriched (TP53, COL11A1, NSD1) and depleted (CASP8) in noninflamed relative to inflamed (FDR-corrected p<0.05). Comparing gene expression profiles of non-T cell-inflamed to inflamed patient groups identified 4092 DEGs (FDR-corrected p<0.05, fold change ≥1.5 or ≤-1.5). Utilizing these DEGs as downstream target molecules in IPA causal network analysis, activation of MYC, SOX2, NFE2L2, and CTNNB1 transcriptional programs correlated with the non-T cell-inflamed tumor microenvironment (z-score ≥2.0, p<0.05). Of note, NFE2L2 (nuclear factor erythroid-2-related factor 2; NRF2) has been described as a context-dependent regulator of innate immune responses and modulator of checkpoint inhibitor response in murine models.

Conclusions: A discrete list of oncogenes, some with known targeted therapies, associates with immune exclusion, suggesting rational immunotherapy combinations to overcome non-T cell-inflamed tumors in HNSCC.

Citation Format: Riyue Bao, Jason J. Luke. Molecular correlates of the non-T cell-inflamed tumor microenvironment in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; 2019 Apr 29-30; Austin, TX. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_2):Abstract nr B04.