Longitudinal tumor microenvironment analysis to predict immunochemotherapy response in salivary duct carcinoma

Background: Salivary duct carcinoma (SDC) is a rare but highly aggressive malignancy. Although neoadjuvant cytotoxic chemotherapy followed by surgery is standard for locally advanced high-grade SDC, recent studies suggest potential benefit from immune checkpoint inhibitors (ICIs) in the perioperative setting. To characterize treatment-related tumor microenvironment (TME) features, we analyzed paired pre- and post-immunochemotherapy samples from a perioperative clinical trial (ONO-4538-X78). Method: A total of 42 tumor samples from 30 SDC patients were analyzed using whole-transcriptome sequencing (WTS). Samples were collected at diagnosis (T1) and at surgery (T2) after three cycles of immunochemotherapy. Patients with <10% residual viable tumor were classified as major pathologic responders (MPR). Samples were classified into T1 non-MPR (n=7), T1 MPR (n=15), T2 non-MPR (n=11), and T2 MPR (n=9), and TMEs were compared across time points and response groups. Result: To characterize TME differences, we inferred cell states for each response group. At baseline (T1), non-MPR tumors exhibited a pro-angiogenic TME driven by malignant epithelial cells, consistent with EMT and angiogenesis pathways. In contrast, T1 MPR tumors showed a more immune-infiltrated TME with interferon-related signaling. From the surgical samples (T2), direct comparison of MPR and non-MPR revealed distinct antitumor immune patterns, indicating robust T- and B-cell-mediated adaptive immunity in MPR, whereas non-MPR displayed chronic inflammatory signatures rather than effective antitumor responses. ssGSEA using core enrichment genes from T- and B-cell-related GOBP pathways confirmed significantly higher immune activation in the T2 MPR group compared with T2 non-MPR (p=0.001). Longitudinal comparison further highlighted divergent trajectories. In non-MPR tumors, T2 non-MPR tumors were inferred to retain malignant epithelial features with minimal immune cells; DEG analysis supported this with inflammatory responses at T2 and EMT programs at T1.Conversely, T2 MPR tumors were inferred to lose malignant epithelial signatures and show immune activation, consistent with T cell-mediated adaptive responses pathways, whereas T1 MPR displayed epithelial cell-cycle pathways. Conclusion: In this study, we found that MPR tumors exhibited a pre-existing interferon-activated tumor microenvironment at baseline, which transitioned into an adaptive immune response after immunochemotherapy. These findings suggest that an interferon-primed TME is a prerequisite for effective post-treatment immune activation and may serve as a predictive biomarker for immunochemotherapy responsiveness.