Immunosuppressive Tumor Microenvironment Signatures Predict Early Progression in NSCLC Patients Receiving Immune Checkpoint Inhibitors: A Transcriptomic and Immune Deconvolution Analysis of GSE135222

Background and Objectives: Early progression (PFS < 90 days) in NSCLC patients undergoing ICI treatment constitutes a significant clinical challenge. Although predictive biomarkers have been extensively investigated, specific transcriptomic and immune microenvironment characteristics contributing to early progression remain inadequately characterized. Materials and Methods: We analyzed RNA-seq data from 27 NSCLC patients receiving anti-PD-1/PD-L1 therapy (GSE135222). Patients were categorized as Early Progression (PFS < 90 days; n = 17) or Clinical Benefit (PFS ≥ 90 days; n = 10). GSEA was performed with Hallmark and C7 ImmuneSigDB gene sets. Immune cell deconvolution was performed using EPIC. An 87-gene immunosuppressive risk score was derived from TGF-β, WNT/β-catenin, and EMT pathway leading-edge genes. Results: GSEA identified 17 significantly enriched Hallmark pathways in early progressors, predominantly immunosuppressive (TGF-β, WNT/β-catenin) and oncogenic (MYC targets, E2F targets, G2M checkpoint) programs. C7 ImmuneSigDB analysis revealed 131 enriched immune signatures including CD8 T cell dysfunction, Treg activation, and M2 macrophage polarization. An 87-gene immunosuppressive risk score demonstrated a significant negative correlation with PFS (Spearman ρ = −0.516, p = 0.006) and a trend toward poorer survival outcomes (HR = 2.12, p = 0.093). Conclusions: In NSCLC patients receiving ICI, early disease progression is marked by simultaneous activation of TGF-β/WNT-mediated immunosuppressive pathways, oncogenic signaling, and CD8 T cell dysfunction. The 87-gene immunosuppressive risk score demonstrates a statistically significant negative correlation with PFS (Spearman ρ = −0.516, p = 0.006); however, given the small sample size (n = 27) and absence of external validation, these findings should be interpreted as exploratory and hypothesis-generating, warranting prospective validation in independent cohorts.