Regulation of Alveolar Epithelial Cell States in Lung Regeneration and Cancer

Abstract

Alveolar epithelial cells adopt distinct cell states during tissue regeneration and disease. Following lung injury, alveolar type 2 (AT2) cells transiently enter intermediate transcriptional states that facilitate epithelial repair, whereas persistent activation of these programs is associated with chronic lung disease and lung adenocarcinoma (LUAD). However, the mechanisms regulating alveolar epithelial cell states remain incompletely understood. In this dissertation, I investigate the regulation of alveolar epithelial cell states across lung regeneration and cancer using organoid models, genetically engineered mouse models, and transcriptomic approaches. Using KRAS/p53 (KP)-driven tumor organoids, we identify two transcriptionally and functionally distinct early tumor cell states: an AT2-enriched SPC-high state and an EMT-associated, Hmga2-high state. We show that these two states display distinct tumorigenic capacity, niche dependence, and therapeutic vulnerability. I further identify the DNA- and RNA-binding protein Y-box binding protein 1 (YBX1) as a critical regulator of alveolar epithelial cell state and early-stage LUAD tumorigenesis. YBX1 is highly expressed in alveolar differentiation intermediate (ADI) cells during regeneration and in oncogenic KP-driven LUAD. Genetic perturbation studies in organoids reveal that YBX1 promotes transitional epithelial states, supports tumor initiation, sustains oncogenic signaling, and contributes to therapeutic resistance. Loss of YBX1 suppresses the ADI program and restores AT2 lineage identity in both wild-type alveolar organoids and KP tumor organoids, reduces tumor burden in vivo, and enhances sensitivity of KP tumor organoids to KRAS-targeted therapies. Together, these findings establish that functionally distinct epithelial cell states arise early in tumorigenesis and that regulation of alveolar epithelial cell state is a central mechanism linking lung regeneration and cancer and identify YBX1 as a potential therapeutic target in LUAD.