Opposing lineage specifiers induce a pro-tumor hybrid-identity state in lung adenocarcinoma [ChIP-seq]

Lineage plasticity is critical for tumor progression and therapy resistance, but the molecular mechanisms underlying cell identity shifts in cancer remain poorly understood. In lung adenocarcinoma (LUAD), the loss of pulmonary lineage fidelity and acquisition of alternate identity programs converge on hybrid-identity (hybrid-ID) states which are postulated to be key intermediates in LUAD evolution and are characterized by the co-activation of developmentally incompatible identity programs within individual cells. Here, we uncover a previously unrecognized role for the gastrointestinal transcriptional regulator HNF4a in driving tumor growth and hybrid-ID states in LUAD. In LUAD cells expressing the lung lineage specifier NKX2-1, HNF4a induces a GI/liver-like state by directly binding and activating its canonical targets. HNF4a also disrupts NKX2-1 genomic localization and dampens pulmonary identity within hybrid-ID LUAD. We show that this hybrid-ID state is maintained by sustained by RAS/MEK signaling. Inhibition of the RAS/MEK signaling cascade augments NKX2-1 chromatin binding at pulmonary-specific genes and induces drug resistance-associated pulmonary signatures. Finally, we demonstrate that HNF4a depletion sensitizes LUAD cells to KRASG12D inhibition. Collectively, our data show that co-expression of opposing lineage specifiers is a novel mechanism of identity dysregulation in LUAD that influences both tumor progression and response to targeted therapy. Overall design: ChIP-seq was performed on murine 3154 organoids treated with EtOH or 4OHT to delete Hnf4a, human H1651 cells treated with dox (or vehicle) to overexpress HNF4a, murine 3311 cells treated with Trametinib (MEKi) (or vehicle), murine 1027B organoids treated with Trametinib (MEKi) (or vehicle), human H358 cells treated with Trametinib (MEKi) (or vehicle). Sequential ChIP-seq (ChIP-re-ChIP) was performed on murine 3311 cells for HNF4a and NKX2-1.