Subtype-specific RNA sequencing using micro-dissection revealed extracellular matrix alterations as key factors in lung adenocarcinoma invasion.

Background: Tumor invasion is a critical step in tumorigenesis and represents an important therapeutic target. However, the molecular mechanisms underlying the invasion process of lung adenocarcinoma (LUAD) remain poorly understood. In this study, we investigated the transcriptomic and epigenetic alterations occurring during LUAD invasion to elucidate the key biological processes. Methods: Frozen section of LUAD tumors, which contained both invasive and non-invasive subtypes, was selected as the study model. These subtypes were identified, micro-dissected, and separately processed for RNA sequencing (RNA-seq). Subsequent analysis identified differentially expressed genes (DEGs) and significantly enriched biological processes. Additionally, RNA-seq data from independent LUAD tissues were analyzed to screen for critical genes, and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) was conducted to explore potential regulatory mechanisms. Finally, survival analysis was performed using The Cancer Genome Atlas (TCGA) database to validate the clinical relevance of the identified genes. Results: Subtype-specific RNA-seq analysis revealed that alteration in the extracellular matrix (ECM) was a key hallmark of LUAD invasion, which was validated by transcriptomic changes in independent tissue samples. Furthermore, several of these ECM genes were significantly associated with LUAD prognosis. Based on these findings, we hypothesized that epigenetic alterations during LUAD progression may drive these ECM changes, and that subsequent remodeling of the immune microenvironment may also contribute to the invasive process. Conclusions: Our integrated analysis demonstrated that epigenetic and transcriptomic dysregulation-induced ECM alterations were critical for LUAD invasion. Specifically, key ECM genes, including