Abstract LB208: Chronic inflammation induces cell type-specific epigenetic and transcriptomic alterations to promote development of distinct NSCLC subtypes in a genetic driver-specific manner
Authors: Na Wang, Raksha Padaki, Ray-Whay Chiu Yen, Sara-Jayne Thursby, Leslie Cope, Malcolm Brock, Edward Gabrielson, Hariharan Easwaran, Stephen Baylin, Michelle Vaz
Journal: Cancer Research (2025)

Abstract Lung cancer remains the leading cause of cancer-related mortality worldwide, as well as non-small cell lung cancer (NSCLC), the major type of lung cancer. NSCLC arises from distinct lung progenitor cells and is driven by specific genetic mutations. The leading cause of NSCLC is cigarette smoking, which induces chronic inflammation in the lung. Chronic inflammation plays a pivotal role in driving lung cancer, contributing to pathogenesis through the induction of epigenetic and transcriptomic abnormalities, These, in turn, modulate the microenvironment to facilitate the emergence of immune evasive mechanisms to aid tumor development. However, specific molecular processes guiding lung tumorigenesis from the very earliest steps occurring in the stem cells through to initiation of different major NSCLC subtypes, especially in the context of chronic-smoking-induced inflammation, are little studied and not well defined. Here, we utilize lung organoids (LOs) exposed chronically to cigarette smoke condensate (CSC) to model these dynamics. We find that CSC progressively induces pro-tumorigenic shifts in stem cell phenotypes with earliest changes being abnormal epigenetic and transcriptomic events over a six-month time course. Genome wide DNA methylation analysis reveals that CSC methylated genes were associated with differentiation, cell fate commitment, calcium signaling and other tumorigenesis promoting pathways. Bulk RNA sequencing approaches identified distinct temporal changes in transcriptional signatures in CSC exposed organoids suggestive of evolution of an immune evasive and pro-tumorigenic phenotype. Gene set enrichment analysis revealed a downregulation of interferon signaling and upregulation of Myc targets and oxidative phosphorylation pathways in CSC treated organoids. At this point, cells from CSC-exposed LOs are able to modulate key immune cells that progressively develop a pro-tumorigenic phenotype. Significantly, at the 6-month time-point only CSC exposed organoids and not control LO’s, are sensitized to transformation and form tumors in vivo following independent introduction of two different leading NSCLC-associated genetic driver mutations. Further, tumors generated are representative of distinct NSCLC subtypes known to harbor genetic abnormalities in human NSCLC. Most importantly, single-cell RNA sequencing provided crucial insights into CSC-induced cell states that evolve from distinct lung progenitor populations to facilitate the emergence of these tumor subtypes. Altogether, our results demonstrate the ability of chronic inflammation to drive key cell type-specific transcriptomic and epigenetic changes and provide novel insights for the very early steps of how cigarette smoking alters different lung stem cells and initiate molecular events that support oncogenic potential of distinct genetic drivers to initiate leading types of NSCLC. These tumor-promoting cell states are especially relevant for future development of novel cancer interception and early therapy strategies for NSCLC. Citation Format: Na Wang, Raksha Padaki, Ray-Whay Chiu Yen, Sara-Jayne Thursby, Leslie Cope, Malcolm Brock, Edward Gabrielson, Hariharan Easwaran, Stephen Baylin, Michelle Vaz. Chronic inflammation induces cell type-specific epigenetic and transcriptomic alterations to promote development of distinct NSCLC subtypes in a genetic driver-specific manner [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB208.