Aberrant super-enhancer landscape reveals core transcriptional regulatory circuitry in lung adenocarcinoma

Te Zhang,Zeyu Zhang,Feng Jiang,Xuming Song,Gaochao Dong,Lin Xu,Qixing Mao,Wenjie Xia

doi:10.1038/s41389-020-00277-9

Abstract

Lung adenocarcinoma (LUAD) relies on dysregulated gene expression to sustain its infinite growth and progression. Emerging evidence indicates that aberrant transcriptional program results from core transcriptional regulatory circuitry (CRC) which is driven by super-enhancers (SEs). In this study, by integrating profiles of H3K27Ac chromatin immunoprecipitation sequencing (ChIP-seq) from normal adult lung and LUAD cell lines, we revealed that widespread alterations of the super-enhancer were presence during lung carcinogenesis. With SE-based modeling of regulatory circuits and assessments of transcription factor (TF) dependencies, we reconstructed an interconnected transcriptional regulation network formed by three master TFs, including ELF3, EHF, and TGIF1, all of which promoted each other’s expression that confirmed by ChIP-qPCR and western blot. Loss-of function assay revealed that each of them is essential for LUAD cells survival, invasion and metastasis. Meanwhile, the rescue assay also illustrated the transacting transcriptional regulatory circuitry. In addition, the mRNA levels of ELF3, EHF, and TGIF1 were differentially expressed in LUAD tumors and peritumoral tissue. IHC of serial sections revealed that high expressions of CRC (ELF3/EHF/TGIF1-High) were closely associated with high proliferative activity in tumor tissue and poor prognosis on patients with LUAD. Finally, we used small molecular inhibitors to perturb the transcriptional circuitry, also exhibited a prominent anti-cancer effect in vitro. Our findings reveal the mechanism of the transcriptional dysregulation and addiction of LUAD.

Highlights

Lung cancer is the leading cause of cancer-related death worldwide because of its high incidence and associated mortality[1]
A total of 1792 lung adenocarcinoma (LUAD)-acquired SE-associated genes were identified in the LUAD cells, of which 334 genes were commonly acquired in both cell lines (Fig. 1B)
In A549 cells, expression of ELF3, EHF, and TGIF1 decreased when small molecular inhibitors addition compared to DMSO addition (Fig. S3F). In both Transwell assay and Matrigel invasion assay, cell migratory, and invasive capabilities were decreased by inhibition of these key SE complex components (Fig. 5E), Histogram representing the number of invasive or immigrate cells per 200× field (Fig. 5F, G). These results revealed that targeted small molecular inhibitors could suppress LUAD cells malignant progression via perturbation of SE complex key components resulting in master transcription factor (TF) decreased and CRC structure destroyed

Summary

Introduction

Lung cancer is the leading cause of cancer-related death worldwide because of its high incidence and associated mortality[1]. Lung cancer has a substantial mortality rate and the incidence of lung cancer has been increasing gradually[2]. Lung cancer is divided into small cell lung cancer (SCLC) and non-SCLC (NSCLC). NSCLC accounts for over 80% of all lung carcinomas and continues to increase in incidence[3]. There are two main subtypes of NSCLC: lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), of which LUAD is the most common. With a 5year survival rate of only 10%, it remains of great importance to explore the underlying mechanisms of LUAD to develop more effective therapeutic interventions

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Results

Conclusion