Abstract 2231: Epigenomic profiling uncovers distinct enrichment patterns of PBX1 super-enhancer among lung adenocarcinoma
Authors: Mansell Douglas M. , Fridrich Maya , Jiang Feng , Chen Benjamin , Patel Ayushi , Li-Wang Tian , Powell Charles A. , Watanabe Hideo 
Published: April 2023

Small cell lung cancers and squamous cell cancers can be epigenetically subtyped (Kong R et al 2022, Sato T et al, 2019) with focus on super-enhancer (SE) signals within or adjacent to transcription factors (TF). We reasoned that specific epigenomic subsets in lung adenocarcinomas (LUAD) operate with similar cellular programming showing TF dependency for lineage commitment and survival. We hypothesize that these dependencies on lineage programming are associated with a specific epigenomic landscape. Therefore, we investigated enrichment of SEs across the spectrum of LUADs to identify potential regulators for lineage commitment and survival.

We obtained data for genome-wide H3K27ac enrichment by chromatin immunoprecipitation followed by sequencing (ChIP-seq) on a total of 53 LUAD cell lines. We performed unsupervised hierarchical clustering of signals on SEs at gene loci annotated with transcriptional regulation identified in two or more cell lines. To Uncover 3D contact information, we employed HiChIP, using antibody against SMC1, a cohesin complex, on NCI-H460. Three LUAD cell lines with distinct enhancer profiles were transfected with five enhancer segments of the SE at the PBX1 gene cloned into a Firefly luciferase plasmid. Lastly, four LUAD cell lines were treated with a PBX1 inhibitor, T417 for 72 hours in varying concentrations ranging from 20uM to 10nM and evaluated for sensitivity to the compound.

Clustering analysis identified LUADs with differential enhancer enrichment for TFs. Among those, we focused on the PBX1 gene locus in LUADs harboring SEs proximal to its promoter. SMC1 HiChIP analysis on NCI-H460 suggest all enhancer segments are within a local topologically-associated domain with the PBX1 promoter. Luciferase reporter assay demonstrate activity of enhancer segments within the PBX1 SE, unique to each cell line (NCI-H460, PC-9 and NCI-H1437), with enhancers e4 and e5 rendered the highest level of activity while e2 being the most active in PC-9. The effects of these enhancer segments are congruent to H3K27ac enrichment patterns. Treatment with T417 showed reduction in cell proliferation at an IC50 of 2.5 uM and 0.97 uM for NCI-H460 and PC-9, respectively, whereas T417 did not affect cell viability in NCI-H1792 and NCI-H125.

Data indicate a distinct subset of LUADs, enriched for the enhancer segments within the SE at the PBX1 gene locus, at which the HiChIP data displayed the enhancer segments lie within the same topologically-associated domain. The enhancer activity of enhancer segments correlated with H3K27ac enrichment pattern for each cell line, suggesting enrichment correlates with impact. Data with PBX1 T417 exposure suggests dependency of PBX1 in maintaining lineage state and survival for unique subsets of LUADs. Further investigation is needed to determine if T417 dependent inhibition is uniform to all PBX1 active LUADs and if other LUAD subsets are dependent on other TFs.

Citation Format: Douglas M. Mansell, Maya Fridrich, Feng Jiang, Benjamin Chen, Ayushi Patel, Tian Li-Wang, Charles A. Powell, Hideo Watanabe. Epigenomic profiling uncovers distinct enrichment patterns of PBX1 super-enhancer among 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 2231.