1. A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks
- Author
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Yunjian Pan, Yizhou Peng, Yang Zhang, Chao Cheng, Hui Hong, Fei-Long Meng, Hsin-Yi Huang, Xingxin Yao, Xiuqi Gui, Muyu Kuang, Qiang Zheng, Zhen Shao, Xuxia Shen, Haojie Chen, Yihua Sun, Xiaoting Tao, Shiqi Tu, Hongbin Ji, and Chongze Yuan
- Subjects
Lung adenocarcinoma ,Epigenomics ,Core regulators ,Lung Neoplasms ,Transcription, Genetic ,QH301-705.5 ,Adenocarcinoma of Lung ,QH426-470 ,Biology ,Epigenesis, Genetic ,Histones ,Epigenome ,Genetics ,medicine ,Humans ,Gene Regulatory Networks ,Genes, Tumor Suppressor ,Epigenetics ,Biology (General) ,Lung cancer ,Enhancer ,Research ,Gene Expression Profiling ,Lysine ,Acetylation ,Oncogenes ,medicine.disease ,Prognosis ,Human genetics ,Gene Expression Regulation, Neoplastic ,Histone ,Super-enhancers ,Enhancer Elements, Genetic ,Treatment Outcome ,Cancer research ,biology.protein ,Adenocarcinoma ,Classification model ,Transcriptome - Abstract
BackgroundLung adenocarcinoma (LUAD) is a highly malignant and heterogeneous tumor that involves various oncogenic genetic alterations. Epigenetic processes play important roles in lung cancer development. However, the variation in enhancer and super-enhancer landscapes of LUAD patients remains largely unknown. To provide an in-depth understanding of the epigenomic heterogeneity of LUAD, we investigate the H3K27ac histone modification profiles of tumors and adjacent normal lung tissues from 42 LUAD patients and explore the role of epigenetic alterations in LUAD progression.ResultsA high intertumoral epigenetic heterogeneity is observed across the LUAD H3K27ac profiles. We quantitatively model the intertumoral variability of H3K27ac levels at proximal gene promoters and distal enhancers and propose a new epigenetic classification of LUAD patients. Our classification defines two LUAD subgroups which are highly related to histological subtypes. Group II patients have significantly worse prognosis than group I, which is further confirmed in the public TCGA-LUAD cohort. Differential RNA-seq analysis between group I and group II groups reveals that those genes upregulated in group II group tend to promote cell proliferation and induce cell de-differentiation. We construct the gene co-expression networks and identify group-specific core regulators. Most of these core regulators are linked with group-specific regulatory elements, such as super-enhancers. We further show that CLU is regulated by 3 group I-specific core regulators and works as a novel tumor suppressor in LUAD.ConclusionsOur study systematically characterizes the epigenetic alterations during LUAD progression and provides a new classification model that is helpful for predicting patient prognosis.
- Published
- 2021