Single-nucleus multi-omics delineates distinct epigenetic programs associated with tumor progression in lung adenocarcinoma.

[BACKGROUND] Lung adenocarcinoma (LUAD), the most prevalent type of lung cancer, displays marked molecular and cellular heterogeneity driven by diverse oncogenic alterations. Many of these changes are thought to occur during the transformation of alveolar type 2 (AT2) cells, which function as stem-like progenitors and likely cells of origin for LUAD. To investigate the regulatory mechanisms underlying AT2 cell transformation and intratumoral heterogeneity, we performed single-nucleus RNA sequencing (snRNA-seq) and single-nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) as a multiome assay.

[RESULTS] Tumor specimens from two LUAD patients with TP53 mutations, one harboring a ROS1 fusion, were analyzed. snRNA-seq defined major cell populations and distinguished tumor cells from AT2 cells based on inferred copy number alterations. Integration with snATAC-seq data identified differentially accessible chromatin regions and their linked target genes through peak-to-gene associations. Trajectory inference indicated a gradual transition from AT2 to tumor cell states in one case, accompanied by transcription factor-driven epigenomic remodeling. In contrast, the ROS1 fusion case exhibited a breakpoint between SLC34A2 (exon 13) and ROS1 (exons 31-32), associated with PI3K/AKT/mTOR pathway activation and distinct gene activity profiles.

[CONCLUSIONS] These findings indicate patient-specific patterns of tumor evolution in LUAD, with one case showing a progressive AT2-to-tumor transition and another driven by ROS1 fusion-mediated oncogenic signaling. Together, they highlight how transcriptional and epigenetic programs diverge across tumor contexts, contributing to inter-patient heterogeneity in LUAD.