SAAL1: A novel biomarker for predicting and therapeutic target for overcoming immunotherapy resistance in esophageal squamous cell carcinoma

Background: Neoadjuvant chemoradiotherapy (nCRT) is the standard treatment for locally advanced esophageal squamous cell carcinoma (ESCC). Our previous NEOCRTEC1901 study demonstrated that adding a PD-1 inhibitor to nCRT significantly increases the pathological complete response (pCR) rate to 50%, positioning this combination as a potential new standard. However, responses to immunotherapy vary dramatically, highlighting an urgent need to elucidate tumor immune escape mechanisms and identify biomarkers and targets to improve efficacy. This study aims to identify and characterize key molecules influencing immunotherapy response in ESCC using a multi-omics approach. Mechanistically , through an integrated multi-omics screening encompassing transcriptomic, proteomic, survival, and protein-protein interaction data, we have, for the first time, identified the oncogene SAAL1 , which interacts with PD-L1, as a key negative regulator of immunotherapy in ESCC. Mechanistically, SAAL1 directly binds to PD-L1 protein and recruits the deubiquitinase USP5 to remove ubiquitin chains from PD-L1. This action inhibits PD-L1 degradation via the endoplasmic reticulum-associated degradation (ERAD)-proteasome pathway, thereby stabilizing PD-L1 protein levels. Single-cell RNA sequencing analysis further revealed that upregulated SAAL1 expression in tumor cells coincides with malignant evolutionary trajectories, and its high expression remodels cellular communication within the tumor immune microenvironment. Functionally , by stabilizing PD-L1, SAAL1 significantly enhances the binding capacity of PD-L1 on the tumor cell surface to PD-1, inhibits the cytotoxic function of CD8⁺ T cells, and drives the formation of an immunosuppressive tumor microenvironment (TME). This manifests as reduced infiltration of effector immune cells like CD8⁺ T cells, coupled with a pro-inflammatory state characterized by increased neutrophil infiltration, collectively shaping an "immune-desert" or "cold tumor" phenotype. In vitro and in vivo experiments showed that knocking down SAAL1 inhibited ESCC cell proliferation and clonogenicity, promoted the expression of anti-tumor immune factors, and significantly enhanced the tumor-killing efficacy of CD8⁺ T cells. Importantly, in animal models, the combination of SAAL1 knockdown with a PD-1 inhibitor demonstrated superior anti-tumor effects compared to PD-1 inhibitor monotherapy. Conclusion: Starting from clinical cohorts, this study identifies SAAL1 as a novel negative regulator and a potential prognostic biomarker for immunotherapy in ESCC. High SAAL1 expression indicates poor prognosis in both treatment-naïve and neoadjuvant immunotherapy-treated ESCC patients, and its predictive power surpasses that of the TNM and ypTNM staging. Its molecular mechanism involves promoting tumor immune escape by co-operating with USP5 to deubiquitinate and stabilize PD-L1 protein. These findings unveil the central role of the SAAL1-USP5-PD-L1 axis in ESCC immunosuppression and provide a novel combinatorial therapeutic strategy and target for overcoming immunotherapy resistance in ESCC.