Multi-omics profiling reveals tumor microenvironment characteristics linked to immunotherapy response and prognosis in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) patients frequently develop resistance to immunotherapy, underscoring the need for novel predictive biomarkers and a deeper understanding of the underlying mechanisms. In this study, we integrated bulk and single-cell transcriptomic analyses across 31 datasets to elucidate the immune infiltration features distinguishing immunotherapy responders from non-responders. We identified elevated infiltration of ZNF683 + CD8 + T cells as a crucial subset enriched in responders, with ZNF683 expression serving as a robust indicator of immunotherapy responsiveness. By screening 296 algorithm combinations, a ZNF683 + CD8 + T cell-related Riskscore (ZNFRS) was constructed using the optimal StepCox[forward] + Ridge combination, which demonstrated superior prognostic capability for lung adenocarcinoma patients. High-ZNFRS tumors exhibited a “cold” tumor microenvironment (TME) characterized by reduced immune infiltration, immunotherapy resistance, and enhanced SPP1 signaling. In vivo experiments revealed that anti-SPP1 treatment suppressed tumor growth, restored CD8 + T cell effector function, inhibited M2-like macrophage polarization, and significantly enhanced the efficacy of anti-PD-1 therapy. Our findings highlight ZNF683 as a promising biomarker for immunotherapy response and establish the ZNFRS as a robust prognostic indicator. Furthermore, targeting the SPP1 pathway, identified as a key driver of immunosuppression in high-risk patients, represents a viable strategy to enhance anti-PD-1 therapy efficacy in NSCLC.