Abstract

Lineage plasticity in non-small cell lung cancer (NSCLC) drives resistance to tyrosine kinase inhibitor (TKI) therapies, yet the epigenetic drivers of this phenotypic transition remain poorly defined. Here, we identify loss of the histone methyltransferase KMT2D as a critical event that disrupts adenocarcinoma lineage fidelity and promotes squamous transition. KMT2D expression is markedly reduced in TKI-resistant NSCLC with squamous-like features, and its mutation correlates with elevated squamous lineage markers and poorer clinical outcomes. Mechanistically, KMT2D loss triggers global transcriptional and epigenomic reprogramming, upregulating squamous master regulators such as ΔNp63 and SOX2. CRISPR-based screening reveals that KMT2D-deficient tumors are preferentially dependent on AURKA to maintain squamous identity and cell proliferation. Notably, loss of KMT2D enhances AURKA stability and activity by disrupting its interaction with the E3 ligase FBXW7, resulting in reduced ubiquitination and prolonged AURKA signaling. Pharmacologic inhibition of AURKA abrogates squamous features and suppresses tumor growth in patient-derived organoids, xenografts, and orthotopic models, with KMT2D-deficient tumors exhibiting heightened sensitivity. These findings uncover that KMT2D alteration drives chromatin reprogramming that facilitates adeno-to-squamous transition and identifies AURKA as a lineage-specific vulnerability, providing a precision strategy to overcome TKI resistance. Statement of significance Our study identifies KMT2D loss as a key event of lineage switch that promotes adeno-to-squamous transition and TKI resistance in NSCLC. This epigenetic shift renders tumors dependent on AURKA, revealing a novel therapeutic target to counteract drug resistance and improve treatment outcomes.