Early transcriptional divergence and spatial remodeling toward immune activation and evasion shape lung adenocarcinoma precancer evolution.

Tumor heterogeneity is a universal feature of cancer and may arise as early as precancer stages during lung adenocarcinoma evolution, yet the emergence of aggressive transcriptional programs remains incompletely understood. Here, we integrated spatial transcriptomics with single-cell RNA sequencing to characterize inter- and intratumoral heterogeneity across hyperplasia, adenoma, and invasive adenocarcinoma (IAC) in a genetically engineered mouse model (129S4/Sv KrasLSL-G12D/+). Disease progression was accompanied by coordinated remodeling of epithelial, stromal, and immune compartments, along with dynamic changes in proliferation, immune response, and metabolic pathways. Notably, lesions of the same histological stage exhibited substantial transcriptional heterogeneity. By quantifying dedifferentiation states, we identified a subset of adenomas that had already diverged toward highly proliferative and metabolically active programs despite lacking invasive features. These lesions were further marked by early chromosome 6 amplification, whose corresponding human ortholog signature recapitulated aggressive proliferation-associated programs in early-stage human lung adenocarcinoma. Spatial analyses further revealed pronounced intratumoral heterogeneity within IAC, with tumor core regions showing increased proliferation and metabolism but reduced immune signaling compared to peripheral regions. In addition, immune checkpoint gene expression in T cells was transiently elevated at the hyperplasia stage, suggesting early immune modulation prior to overt malignancy. Together, these findings indicate that aggressive transcriptional divergence can emerge early during lung adenocarcinoma evolution and that spatial organization critically shapes tumor and immune programs before and after invasion.