Real-time Evolutionary Landscape of the Bronchial Epithelium and Corresponding Dynamic Immune Cell Alterations in Lung Squamous Cell Carcinogenesis

The molecular mechanism by which tumor cells and the microenvironment evolve during lung squamous cell carcinoma (LUSC) carcinogenesis remains unclear, which greatly limits its early diagnosis and treatment effectiveness in patients. To replicate the pathogenic process and identify the determinants of cell evolution, a rat model was established with tobacco-derived chemical carcinogens. Here, we presented a series of single-cell transcriptome profiling from normal lung epithelium, hyperplasia, metaplasia, dysplasia, and squamous cell carcinoma in situ (CIS), to invasive squamous cell carcinoma (SCC). A large portion of canonical copy number variations (CNVs) were detected in the hyperplasia/metaplasia stages, and their frequency increased with lesion progression. Although epithelial cells in the bronchi are heterogeneous, they all exhibit three cell states during the evolution to malignant cells. Additionally, we revealed that immune sensing or response could occur at the earliest stage of cell transformation. With the persistent exposure to carcinogen, normal resident myeloid cell populations are gradually replaced by monocyte-derived macrophages and plasmacytoid dendritic cells, along with T-cell exhaustion. These findings depict an evolutionary trajectory of cancer and the immune microenvironment, emphasizing the need for CNV evaluation in early screening and immune-based therapy for some lesions at high risk of progressing to LUSC.