GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE314nnn/GSE314906/primaryOK200TranscriptomicsHomo sapiensExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE314906GEOGSEfalseCX3CR1⁺ CD8⁺ Cytotoxic T Cells Drive Tumor Killing in Esophageal Squamous Cell Carcinoma During Neoadjuvant TherapyThe efficacy of immune checkpoint blockade (ICB) in esophageal squamous cell carcinoma (ESCC) remains highly variable, and the underlying mechanisms driving differential responses are poorly understood. Here, we performed single-cell RNA sequencing (scRNA-seq), T cell receptor (TCR) sequencing, and whole exome sequencing (WES) on 52 ESCC patients from a phase III neoadjuvant clinical trial to characterize the tumor microenvironment (TME) and its association with therapeutic outcomes. We identified a selective expansion of non-exhausted cytotoxic CD8⁺ T cells, particularly CX3CR1⁺ CD8⁺ T cells, in well responders, driven by the CX3CL1-CX3CR1 axis. These cells exhibited high cytotoxicity, clonal expansion, and tumor-killing potential, while exhausted T cell subsets, including CXCL13⁺ CD8⁺ T cells, were reduced in well responders. Pre-treatment tumor mutational profiles revealed that a high cancer cell fraction (CCF) mutation burden and neoantigen abundance were predictive of response, with immune editing reducing immunogenic mutations post-treatment. Additionally, tumor epithelial differentiation (Gp1/Gp2 subtypes) and stromal remodeling influenced treatment outcomes, with Gp2 tumors associated with immune suppression and resistance. Our findings provide new insights into the immune dynamics of ESCC, highlighting CX3CR1⁺ CD8⁺ T cells, the CX3CL1-CX3CR1 axis, and tumor differentiation as potential therapeutic targets to enhance ICB efficacy.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 sapiens