Single‐Cell and Bulk Transcriptomic Integration Reveals an Adverse SPP1 Inflammatory TAM State and INHBA as a Candidate Biomarker in Non‐Small Cell Lung Cancer Immunotherapy

Abstract

Background Biomarkers that capture the microenvironmental basis of response to neoadjuvant immunotherapy in non‐small cell lung cancer (NSCLC) remain limited. We integrated single‐cell and bulk transcriptomic data to identify response‐associated immune programs with patient‐level relevance. Methods Single‐cell RNA‐seq and clinical annotations from GSE207422 were used to construct an NSCLC tumor microenvironment atlas and refine myeloid and T cell states. UCell scoring, sample‐level summaries, pseudobulk differential analysis, Monocle2 trajectory inference, and targeted macrophage–T cell interaction analysis were applied. A posttreatment SPP1 inflammatory TAM‐derived NR‐TAM signature was projected to pretreatment bulk RNA‐seq from the same cohort. INHBA was evaluated in pretreatment bulk data, TCGA‐LUAD/TCGA‐LUSC, and lung cancer cell line assays. Results SPP1 inflammatory TAM was enriched in nonmajor pathologic response (NMPR) samples and co‐occurred with exhausted CD8 T cell abundance, malignant cell hypoxia, and EMT programs. The NR‐TAM signature was partially recapitulated in pretreatment bulk RNA‐seq, with higher scores in NMPR but substantial group overlap. Exploratory ROC analysis showed modest discrimination for NR‐TAM score (AUC = 0.60), INHBA (AUC = 0.64), and the combined model (AUC = 0.64; LOOCV AUC = 0.37). INHBA was higher in NMPR cases, correlated with residual tumor burden and selected TAM‐related genes, showed less favorable survival trends particularly in LUSC, and its knockdown reduced proliferation and migration in lung cancer cells. Conclusions An SPP1 inflammatory TAM program is associated with unfavorable pathologic response in NSCLC neoadjuvant immunotherapy. INHBA is a prioritized exploratory candidate within this program. Because the evidence is associative and predictive performance is modest, these markers require prospective validation before clinical use.