Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma [ATAC-seq]

Amplification-mediated oncogene overexpression is a critical and widespread driver event in cancer, yet our understanding of how amplification and dosage mediate oncogene 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 controls NKX2-1 expression and regulation. We find that NKX2-1 directly controls enhancer accessibility to drive a lineage-addicted state in LUAD. We precisely map the effects of NKX2-1 dosage modulation upon both overexpression and knockdown and identify both linear and non-linear regulation by NKX2-1 dosage. We find that NKX2-1 is a widespread dependency in LUAD cell lines and that NKX2-1 confers persistence to EGFR inhibitors. Our data suggest a defining role for dosage in the oncogenic regulation of amplified NKX2-1 and that amplified NKX2-1 lineage addiction defines LUAD tumors. Overall design: Lung adenocarcinoma cancer cell lines (NCI-H441, NCI-H2087, NCI-H1975, PC9, NCI-H1975) were lentivirally infected with indicated constructs, selected, and harvested for ATAC-seq at day 7-10 post infection for constitutive overexpresison and knockdown experiments. NCI-H441 and PC9 cells were prepared in experimental batches, which are distinguished by "Set2". For degron experiments, LUAD cell lines (PC9, NCI-H1975) were lentivirally infected and selected as indicated, then treated for 2hr with 500nM dTagV-1 or dTagV-1NEG control then harvested for ATAC-seq.