Etoposide-induced DNA damage affects multiple cellular pathways in addition to DNA damage response
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Fengxiang Wei1, Peng Hao2, Xiangzhong Zhang3, Haiyan Hu4, Dan Jiang5, Aihua Yin6, Lijuan Wen1,7, Lihong Zheng8, Jeffrey Zheru He9, Wenjuan Mei10,12, Hui Zeng11,12 and Damu Tang12
1The Genetics Laboratory, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, PR China
2Division of Nephrology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, PR China
3Department of Hematology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
4Department of Obstetrics and Gynecology, Shenzhen Maternal and Child Healthcare Hospital, Southern Medical University, Shenzhen, Guangdong, PR China
5Shenzhen Hua Da Clinical Laboratory Center Co., Ltd., Shenzhen, Guangdong, PR China
6Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, PR China
7Zunyi Medical University, Zunyi, Guizhou, PR China
8Department of Biogenetics, Qiqihar Medical University, Qiqihar, Heilongjiang, PR China
9Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
10Department of Nephrology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, PR China
11Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang City, Hebei, PR China
12Division of Nephrology, Department of Medicine, McMaster University, Hamilton, ON, Canada
Fengxiang Wei, email: [email protected]
Damu Tang, email: [email protected]
Keywords: etoposide; DNA damage response; gene expression; RNA sequencing
Received: October 14, 2017 Accepted: February 10, 2018 Epub: February 16, 2018 Published: May 08, 2018
DNA damage response (DDR) coordinates lesion repair and checkpoint activation. DDR is intimately connected with transcription. However, the relationship between DDR and transcription has not been clearly established. We report here RNA-sequencing analyses of MCF7 cells containing double-strand breaks induced by etoposide. While etoposide does not apparently cause global changes in mRNA abundance, it altered some gene expression. At the setting of fold alteration ≥ 2 and false discovery rate (FDR) ≤ 0.001, FDR < 0.05, or p < 0.05, etoposide upregulated 96, 268, or 860 genes and downregulated 41, 133, or 503 genes in MCF7 cells. Among these differentially expressed genes (DEGs), the processes of biogenesis, metabolism, cell motility, signal transduction, and others were affected; the pathways of Ras GTPase activity, RNA binding, cytokine-mediated signaling, kinase regulatory activity, protein binding, and translation were upregulated, and those pathways related to coated vesicle, calmodulin binding, and microtubule-based movement were downregulated. We further identified RABL6, RFTN2, FAS-AS1, and TCEB3CL as new DDR-affected genes in MCF7 and T47D cells. By metabolic labelling using 4-thiouridine, we observed dynamic alterations in the transcription of these genes in etoposide-treated MCF7 and T47D cells. During 0-2 hour etoposide treatment, RABL6 transcription was robustly increased at 0.5 and 1 hour in MCF7 cells and at 2 hours in T47D cells, while FAS-AS1 transcription was dramatically and steadily elevated in both cell lines. Taken together, we demonstrate dynamic alterations in transcription and that these changes affect multiple cellular processes in etoposide-induced DDR.
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