Dosage amplification dictates oncogenic regulation by the NKX2-1 lineage factor in lung adenocarcinoma

Abstract

Amplified oncogene expression is a critical and widespread driver event in cancer, yet our understanding of how amplification-mediated elevated dosage mediates oncogenic regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage super-enhancer near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1, and activation or repression controls NKX2-1 expression. We find that NKX2-1 is a widespread dependency in LUAD cell lines, where NKX2-1 pioneers enhancer accessibility to drive a lineage addicted state in LUAD, and NKX2-1 confers persistence to EGFR inhibitors. Notably, we find that oncogenic NKX2-1 regulation requires expression above a minimum dosage threshold--NKX2-1 dosage below this threshold is insufficient for cell viability, enhancer remodeling, and TKI persistence. Our data suggest that copy-number amplification can be a gain-of-function alteration, wherein amplification elevates oncogene expression above a critical dosage required for oncogenic regulation and cancer cell survival. O_LSTHighlightsC_LSTO_LIThe most significant amplification event in LUAD targets a lineage super-enhancer that controls expression of the NKX2-1 lineage oncogene. C_LIO_LINKX2-1 is a dosage dependency in most NKX2-1(+) LUAD cell lines C_LIO_LINKX2-1 remodels lineage enhancer accessibility to drive a lineage addicted state and confer persistence to EGFR targeted therapy C_LIO_LINKX2-1 oncogenic regulation requires a minimum oncogenic dosage, which dictates NKX2-1 regulation of enhancer remodeling, TKI persistence, and cancer cell viability C_LI