Abstract 5752: Enhancer amplification defines lineage addiction in human lung adenocarcinoma

Abstract

Abstract Lung cancer is the most common cause of death from cancer worldwide, and lung adenocarcinoma (LUAD) is the most common type of lung cancer. NKX2-1 (also known as TTF-1, TITF-1) is a lineage defining transcription factor for normal lung development. In LUAD, NKX2-1 is a highly specific and sensitive marker for both primary and metastatic LUADs, with 85-90% expressing NKX2-1. We and others identified that NKX2-1 as the most significantly amplified gene in LUAD, with 22.5% of primary LUADs exhibiting copy number gains. NKX2-1 is amplified as the earliest stages of LUAD development, and NKX2-1 amplification is a truncal event in multi-region LUAD evolution. Despite strong evidence for an oncogenic role for NKX2-1, little is known about the mechanisms of NKX2-1 activation, or how its oncogenic regulation drives LUAD. Here, we identify recurrent focal amplification targeting a super-enhancer (SE) of NKX2-1 as a driving event in LUAD. Using epigenomic data from LUAD cell lines and tumors, we identify this region as a alveolar lineage super-enhancer (NKX2-1 SE) that is specifically active in NKX2-1(+) LUAD cell lines and primary tumors. Notably, this region is co-amplified with NKX2-1 in 96-100% of NKX2-1-amplified samples, suggesting this region a critical component of the NKX2-1 amplicon. Using endogenous ChIP-seq and exogenous luciferase assays, we show the enhancer activity of the NKX2-1 SE is comprised of three constituent enhancers, and demonstrate that the key enhancer elements can activate transcription of the NKX2-1 promoter. Using CRISPR inhibition (CRISPRi) and CRISPR activation (CRISPRa) in LUAD cell lines expressing high or low levels of NKX2-1, we show that activity of the NKX2-1 SE defines endogenous NKX2-1 expression. Using RNA-seq, ChIP-seq, and ATAC-seq, we find that NKX2-1 controls the transcriptional and epigenomic landscape of lung adenocarcinoma. NKX2-1 knockdown activates an epithelial-mesenchymal transition (EMT) gene signature and downregulates an alveolar differentiation signature, including critical markers of LUAD differentiation, such as NAPSA, SFTPA1/2, and HOPX, at which NKX2-1 mediates lineage enhancer accessibility to regulate target gene expression. Global clustering of LUAD cell lines by RNA-seq or H3K27ac ChIP-seq identifies a distinct NKX2-1(+) cluster, and we find that NKX2-1 directly regulates the genes (57/97) and enhancers that distinguish this subpopulation. Using genome-wide shRNA and CRISPR screens, we identify a NKX2-1 dependency in NKX2-1(+) LUAD cell lines, and find that the majority of NKX2-1(+) LUAD cell lines (11/14) assayed are dependent on NKX2-1. Our data demonstrates that enhancer amplification is a hallmark of oncogenic NKX2-1 activation in LUAD, through which NKX2-1 drives a lineage addicted state and oncogenic cell proliferation. This suggests that NKX2-1 is a critical defining oncogene for LUAD, and that targeting of NKX2-1 or its enhancer may suppress LUAD. Citation Format: John Louis Pulice, Matthew Meyerson. Enhancer amplification defines lineage addiction in human lung adenocarcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5752.