Abstract The Fanconi Anemia/BRCA DNA repair pathway plays a critical role in genomic stability and treatment response in head and neck squamous cell carcinoma (HNSCC). However, whether FA pathway gene expression changes with tumor stage in sporadic HNSCC is insufficiently understood. We examined stage-dependent expression patterns of 23 FA pathway genes in HPV-negative HNSCC. We analyzed mRNA expression data (RNA-seq Z-scores) from 415 HPV-negative HNSCC tumors in The Cancer Genome Atlas via cBioPortal. Twenty-three FA pathway genes were examined across core complex, ID2 complex, homologous recombination, nuclease, and associated components. Tumors were stratified by AJCC stage into early-stage (I/II, n=84) and late-stage (III/IV, n=292) groups, eliminating 39 unstaged patients. Lymph node staging data was available for 402 patients (96.9%), with late-stage tumors showing significantly higher rates of lymph node involvement compared to early-stage disease (67.1% vs 1.2% N+, p0.001). We performed differential expression analysis using two-sample t-tests with Benjamini-Hochberg FDR correction for multiple testing (α=0.05). Effect sizes were calculated using Cohen's d. Late-stage tumors demonstrated more aggressive clinical features with increased lymph node metastases. After FDR correction, only RAD51C showed significant differential expression (q=0.046), with higher expression in late-stage disease (mean±SD: 7.86±0.62 vs 7.65±0.51, log2 FC=-0.21, p=0.002, d=-0.37). Six additional genes showed nominal significance (p0.05) but did not survive FDR correction. Four genes were elevated in early-stage tumors: BRCA2 (log2 FC=0.33, p=0.006), ERCC4 (log2 FC=0.16, p=0.022), SLX4 (log2 FC=0.12, p=0.023), and BRIP1 (log2 FC=0.24, p=0.042). Two genes were elevated in late-stage tumors: FANCE (log2 FC=-0.20, p=0.009) and UBE2T (log2 FC=-0.21, p=0.025). All effect sizes were small (|d|=0.24-0.37). Most FA pathway genes in the RNA-seq dataset (16/23, 70%) showed no stage-dependent differences, including BRCA1, PALB2, RAD51, and most core complex members. RAD51C is uniquely upregulated in late-stage HPV-negative HNSCC after correction for multiple testing, distinguishing it from other FA pathway genes. This finding suggests that RAD51C could be a targetable weakness specifically in advanced HNSCC, which deserves further investigation for stage-directed therapies. Because the six additional genes which showed nominal significance did not survive FDR correction, this suggests that aside from RAD51C, the FA pathway appears to be preserved during HNSCC progression. For both Fanconi Anemia cancers and sporadic non-Fanconi HNSCC, the next step would be examining mutations in these genes to see how they affect function in stage-dependent pathophysiology. Citation Format: Olivia A. Swaim, Alexander Straughan, Beverly Wuertz, Frank Ondrey. Stage-dependent expression of Fanconi anemia pathway genes in HPV-negative head and neck squamous cell carcinoma abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1198.
Swaim et al. (Fri,) studied this question.