Abstract B05: Tumor evolution and oxidative stress in recurrent human papillomavirus-mediated oropharyngeal squamous cell carcinoma
Authors: Faden Daniel , Harbison Richard A. , Zhang Qing , Delrow Jeffrey , Duvvuri Umamaheswar 
Published: September 2020

Abstract
Background: Human papillomavirus (HPV)-mediated head and neck squamous cell carcinomas (HPVmHNSCC) are more responsive to platinum-based concurrent chemoradiation treatment than non-HPVmHNSCC. Previously, our group demonstrated that recurrent HPVmHNSCC are genomically more characteristic of HPV-negative than non-recurrent HPVmHNSCC. Moreover, we observed a propensity for NFE2L2 hotspot mutations among HPVmHNSCC that recurred. Since NFE2L2 is a transcription factor regulating oxidative stress, we hypothesized that genes involved with the management of oxidative stress would be upregulated in recurrent HPVmHNSCC.
Methods: We performed whole-exome sequencing (WES) and RNA-Seq on matched primary and metachronous HPVmHNSCC from the Universities of Pittsburgh (UPitt) and Washington (UW). Somatic nucleotide (SNVs) and copy number variants (CNVs) were quantified. Clonal evolution analyses were performed. Differential expression and gene set enrichment (GSEA) were quantified.
Results: RNA-Seq was available for 10 tumor pairs and WES for 7/10. Consistent with prior WES data, KMT2D was the most frequently mutated gene. We found two unique NFE2L2 hotspot mutations in one paired set. The primary tumor had an NFE2L2H150Y mutation while the recurrent tumor had an NFE2L2E79K mutation. Metachronous tumors possessed significantly more deleterious somatic alterations in genes involved with regulation of oxidative stress and NFE2L2 networks compared to the primary tumors. Clonality analyses revealed a propensity for subclonal mutations in oxidative-stress related genes. RNA-Seq analysis revealed differential expression of genes involved in mitochondrial oxidative stress (MAP3K9) and oxidoreductase activity (CYP24A1, HEPHL1). Moreover, 6/8 enriched gene sets among the metachronous recurrent tumors by GSEA were involved with oxidative stress response, mitochondrial genes, and electron transport.
Conclusions: Here, using WES and RNA-Seq of pairs of primary and metachronous HPVmHNSCC we identified increased expression of and somatic alterations in oxidative stress regulatory pathways in recurrent HPVmHNSCC that appear to occur later in tumor evolution. One possible explanation for this is that treatment selects for tumor clones that can withstand the oxidative environment induced by chemoradiation. Ultimately, understanding the role of oxidative stress response under therapy may be critical to mitigating recurrence and treating recurrences with a favorable genomic profile.
Citation Format: Daniel Faden, Richard A. Harbison, Qing Zhang, Jeffrey Delrow, Umamaheswar Duvvuri. Tumor evolution and oxidative stress in recurrent human papillomavirus-mediated oropharyngeal 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 B05.