GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE289nnn/GSE289363/primaryOK200OtherHomo sapiensOtherhttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE289363GEOGSEfalseIntratumoral spatiotemporal heterogeneity of HPV status in HPV-associated oropharyngeal squamous cell carcinoma with clinical recordHeterogeneity in HPV status within HPV-associated oropharyngeal squamous cell carcinoma (HPV-OPSCC) has gained attention, but the origin and relevance of HPV-absent cancer cells remain unclear. Among 83 OPSCCs, including 48 HPV-OPSCCs, seven showed spatial HPV heterogeneity. Using HPV-DNA in situ hybridization, histomorphology, immunohistochemistry, and spatial transcriptomics, we revealed that HPV-absent subsets differentiate from initial HPV-positive cells, forming distinct lineages. HPV-OPSCC was associated with p16 expression, with HPV-absent clones showing robust p16 expression and poorly differentiated histology. Despite these aggressive features, prognosis was comparable to HPV-homogeneous tumors, likely due to tumor microenvironment differences. HPV-absent clones exhibited increased interferon signaling, hypoxia signaling, and cytotoxic lymphocyte infiltration, indicating a loss of antiviral immune evasion. Conversely, HPV-positive clones were linked to FGFR3 ligand-receptor signaling. This study highlights the emergence, evolution, and microenvironmental impact of HPV-absent clones in HPV-OPSCC.2026/05/20GSE289363GSM8789932GSM8789933GSM878993424676289363Homo sapiens[41943047]