Association of an APOBEC mutational signature, mutational load, and BRCAness with inflammation and PD-L1 expression in HNSCC.

Abstract

e14613 Background: Immune checkpoints are an emerging treatment target in head and neck squamous cell carcinoma (HNSCC). Expression of PD-L1 and an IFNG immune signature have been shown as biomarkers of response. In this study we analyzed mutational signatures to identify recurrent mutational patterns associated with inflammation. Methods: HNSCC mutation and gene expression data were downloaded (n = 496, TCGA). Inflamed tumors were identified through upregulation of a predefined 6-gene IFNG immune signature. Mutational load, base exchange motifs and a BRCAness signature were analyzed in inflamed and non-inflamed tumors. Results were validated in independent datasets of cervical, urothelial and lung cancer (TCGA). Results: Total mutational load did not correlate with tumor inflammation (r = -0.03, p = 0.5). An APOBEC-associated tCw (thymine – cytosine – adenine/thymine) mutational signature was significantly associated with inflammation (r = 0.26, p = 2.923e-09). The tCw signature was furthermore correlated with the expression of PD-L1 and other immune checkpoints (r = 0.19, p = 1.723e-05). The TCW mutational signature correlated with the expression of APOBEC3 genes. Expression of APOBEC3 genes also correlated with tumor inflammation (r = 0.62, p < 2.2e-16). As a second mutational signature, indels and an independent BRCAness signature were significantly enriched in non-inflamed tumors (p = 6.464e-14). Enrichment of an APOBEC mutational signature in inflamed tumors could be validated in cervical and urothelial carcinoma but not NSCLC. Conclusions: In HNSCC, overall mutational load is not associated with inflammation. BRCAness is significantly associated with immune-desertion whereas expression of APOBEC genes and an APOBEC mutational signature significantly correlates with the expression of PD-L1 and a T-cell inflamed signature. These findings suggest that a specific mutational pattern might serve as a biomarker for immune checkpoint inhibition in cancer.