Super-Enhancer-Associated Hub Genes In Chronic Myeloid Leukemia Identified Using Weighted Gene Co-Expression Network Analysis

Hongying Ma,1,2 Jian Qu,3 Jian Luo,1,2 Tingting Qi,3 Huanmiao Tan,4 Zhaohui Jiang,1 Haiwen Zhang,1 Qiang Qu1,2 1Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People’s Republic of China; 2Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People’s Republic of China; 3Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha 410078, Hunan, People’s Republic of China; 4College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, Hunan, People’s Republic of ChinaCorrespondence: Qiang QuDepartment of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People’s Republic of ChinaTel/Fax +86 731 84327460Email quqiang@csu.edu.cnPurpose: Super-enhancer (SE)-associated oncogenes extensively potentiate the uncontrolled proliferation capacity of cancer cells. In this study, we aimed to identify the SE-associated hub genes associated with the clinical characteristics of chronic myeloid leukemia (CML).Methods: Eigengenes from CML clinical modules were determined using weighted gene co-expression network analysis (WGCNA). Overlapping genes between eigengenes and SE-associated genes were used to construct protein–protein interaction (PPI) networks and annotate for pathway enrichment analysis. Expression patterns of the top-ranked SE-associated hub genes were further determined in CML patients and healthy controls via real-time PCR. After treatment of K562 cells with the BRD4 inhibitor, JQ1, for 24 hrs, mRNA and protein levels of SE-associated hub genes were evaluated using real-time PCR and Western blotting, respectively. H3K27ac, H3K4me1 and BRD4 ChIP-seq signal peaks were used to predict and identify SEs visualized by the Integrative Genomics Viewer.Results: The yellow module was significantly related to the status and pathological phase of CML. SE-associated hub candidate genes were mainly enriched in the cell cycle pathway. Based on the PPI networks of hub genes and the top rank of degree, five SE-associated genes were identified: specifically, BUB1, CENPO, KIF2C, ORC1, and RRM2. Elevated expression of these five genes was not only related to CML status and phase but also positively regulated by SE and suppressed by the BRD4 inhibitor, JQ1, in K562 cells. Strong signal peaks of H3K27ac, H3K4me1 and BRD4 ChIP-seq of the five genes were additionally observed close to the predicted SE regions.Conclusion: This is the first study to characterize SE-associated genes linked to clinical characteristics of CML via weighted gene co-expression network analysis. Our results support a novel mechanism involving aberrant expression of hub SE-associated genes in CML patients and K562 cells, and these genes will be potential new therapeutic targets for human leukemia.Keywords: chronic myeloid leukemia, WGCNA, super-enhancer, hub gene, eigengene