Differential gene expression analysis of Kat7 inhibitor-treated versus control-treated lung adenocarcinoma cells [bulk RNA-seq]

Epigenomic dysregulation is widespread in cancer. However, the specific epigenomic regulators and the processes they control to drive cancer phenotypes are poorly understood. We employed a novel, scalable and high-throughput in vivo method to perform iterative functional screens of >250 epigenomic regulators within autochthonous oncogenic KRAS-driven lung tumors. We identified many previously unappreciated epigenomic tumor-suppressor and tumor-dependency genes. We show that a specific HBO1 complex and MLL1 complex are robust tumor suppressors in lung cancer. Histone modifications generated by HBO1 complex are frequently reduced in human lung adenocarcinomas and is associated with worse clinical features. HBO1 and MLL1 complexes co-occupy shared genomic regions, impacting chromatin accessibility, expression of canonical tumor suppressor genes and lineage fidelity. The HBO1 complex is epistatic with the MLL1 complex and other tumor suppressor genes in lung adenocarcinoma development. Together, these results uncover the HBO1 and MLL1 complexes as critical functional modules in restraining lung adenocarcinoma development and provide a in vivo phenotypic roadmap of epigenomic regulators in lung tumorigenesis. Overall design: Murine KrasG12D; p53-/- lung adenocarcinoma cells were cultured in 6-well plates in DMEM supplemented with 10% FBS and 1% Pen/Strep. The cells were treated with either 1 µM WM3835 or 0.02% DMSO (vehicle control) for 5 consecutive days. Each technical replicate is a from an separate well. Total RNA was extracted for bulk RNA-sequencing.