Amplification and Dosage in the Oncogenic Regulation of the NKX2-1 Lineage Transcription Factor

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 and regulation. We find that NKX2-1 pioneers enhancer accessibility to drive a lineage addicted state in LUAD, and that NKX2-1 directly controls chromatin accessibility independent of subsequent transcription changes. Notably, we precisely map the effects of NKX2-1 dosage modulation upon both overexpression and knockdown, and identify distinct linear and non-linear effects of NKX2-1 dosage in distinct contexts. We find that NKX2-1 is a widespread dependency in LUAD cell lines, where NKX2-1 confers persistence to EGFR inhibitors, and that oncogenic effects of NKX2-1 expression are dose-dependent. 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.