Transcriptomic Immune-related Signature Predictive of Chemoradiotherapy Response in Anal Squamous Cell Carcinoma

Anal squamous cell carcinoma (ASCC) is a rare malignancy associated with high-risk HPV, with rising incidence among younger adults. While immunotherapy has improved outcomes in metastatic ASCC, treatment for localized disease remains largely unchanged, with high recurrence rates. This study provides comprehensive exome and transcriptome profiling of 40 stage I-III non-metastatic ASCC patients treated with curative chemoradiotherapy (CRT) to identify predictors of treatment response and progression-free survival. Transcriptomic analysis revealed 350 differentially expressed genes between complete responders (CR) and non-complete responders (NCR) (p-value < 0.01; FC > 2). CR was associated with modulation of immune-related pathways, cytokine production, epidermis development, cell differentiation, and signaling pathways associated with TNFA/NFkB and epithelial to mesenchymal transition. Immune infiltrate analysis showed significant enrichment of CD8 + central memory T cells (p = 0.008) in CR cases, correlating with increased tertiary lymphoid structure and improved overall (p = 0.0026) and disease-free survival (p = 0.0098). Exome-seq identified alterations in novel and known cancer driver genes without association to CRT response, despite high tumor mutational burden (TMB) was significantly associated with shorter overall (p = 0.03) and disease-free survival (p = 0.027) compared with low TMB cases. These findings highlight the potential of incorporating gene expression signatures (e.g., FDCSP , ALDOB , ADGRB1 , SPINK7 ) alongside immune-related markers into clinical practice to enhance the prediction of treatment response and guide personalized therapies in ASCC. A robust and functionally active immune microenvironment—characterized by specific T and B cell populations and the presence of tertiary lymphoid structures—emerges as a hallmark of complete response and improved survival in ASCC patients undergoing chemoradiotherapy.