Associations of Intratumoral Alphapapillomavirus With Survival Outcomes and Tumorigenic Pathways in Esophageal Squamous Cell Carcinoma

Introduction: Oncogenic strains of human papillomavirus (HPV) play a significant role in the development of squamous cell carcinomas at multiple anatomical sites, including the oropharynx and anogenital tract. However, the impact of HPV on esophageal squamous cell carcinoma (ESCC) remains unclear. To enhance our understanding of the clinical and biological implications of HPV in ESCC, we conducted an integrated transcriptome analysis of Alphapapillomavirus, the viral genus containing the majority of known oncogenic HPV species. Methods: The study sample consisted of patients with primary ESCC from The Cancer Genome Atlas (TCGA). Using Alphapapillomavirus RNA and tumor messenger RNA sequencing data, we estimated intratumoral HPV abundance by calculating the average log2 transcripts per million (TPM) and quantified expression levels for 17,501 genes in ESCC tissue. Multivariate Cox proportional hazards models were used to estimate the relative hazard ratio for cancer-specific survival by comparing Alphapapillomavirus abundance above and below the median, adjusted for sex, age, pathologic tumor stage, and year of diagnosis (P< 0.05). Additionally, pathway analysis was performed by stratifying tumor gene expression based on Alphapapillomavirus TPM quartiles, using the first quartile as baseline comparison. Ingenuity Pathway Analysis (IPA) was used to identify biologically relevant tumor gene expression pathways associated with Alphapapillomavirus quartiles using activation z-scores and enrichment P< 0.05 (Table 1). Results: Our study included 95 patients with primary ESCC tumors from TCGA. Demographic and clinical characteristics are provided in Higher intratumoral Alphapapillomavirus levels were significantly associated with improved cancer-specific survival in ESCC (HR=0.67; P=0.02) after adjusting for age, sex, tumor stage, and year of diagnosis. Pathway analysis revealed differential activation of canonical pathways associated with Alphapapillomavirus abundance, including G protein-coupled receptor, S100 protein family, and pathogen-induced cytokine storm signaling pathways, which were significantly upregulated in ESCC tumors with lower Alphapapillomavirus levels (Figure 1). Conclusion: Our results suggest that increased intratumoral Alphapapillomavirus abundance is linked to improved survival in ESCC, potentially due to the downregulation of oncogenic pathways within the tumor microenvironment. Further investigation of intratumoral HPV level as a prognostic tool in patients with ESCC is warranted.Figure 1.: Heatmap of differentially activated pathways associated with intratumoral Alphapapillomavirus levels stratified by quartiles. The heatmap displays the pathway expression levels for each quartile of Alphapapillomavirus abundance, using the first quartile as baseline comparison. The color scale represents the fold-change in expression levels, with red indicating upregulation and blue indicating downregulation (P< 0.05 for all colored pathways). Table 1. - Demographic and clinical characteristics of study participants Parameter N (%) Sex Male 81 (85) Female 14 (15) Age < 65 72 (76) ≥65 23 (24) Race White 42 (44) African American 5 (5) Asian 45 (47) Unknown 3 (3) Ethnicity Non-Hispanic 64 (67) Hispanic 3 (3) Unknown 28 (29) Pathologic Tumor Stage T1 7 (7) T2 32 (34) T3 50 (53) T4 4 (4) Unknown 2 (2) Survival Status Living 63 (66) Deceased 32 (34)