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Wang G, Jia Y, Ye Y, Kang E, Chen H, Wang J, He X. Identification of key methylation differentially expressed genes in posterior fossa ependymoma based on epigenomic and transcriptome analysis. J Transl Med 2021; 19:174. [PMID: 33902636 PMCID: PMC8077736 DOI: 10.1186/s12967-021-02834-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Background Posterior fossa ependymoma (EPN-PF) can be classified into Group A posterior fossa ependymoma (EPN-PFA) and Group B posterior fossa ependymoma (EPN-PFB) according to DNA CpG island methylation profile status and gene expression. EPN-PFA usually occurs in children younger than 5 years and has a poor prognosis. Methods Using epigenome and transcriptome microarray data, a multi-component weighted gene co-expression network analysis (WGCNA) was used to systematically identify the hub genes of EPN-PF. We downloaded two microarray datasets (GSE66354 and GSE114523) from the Gene Expression Omnibus (GEO) database. The Limma R package was used to identify differentially expressed genes (DEGs), and ChAMP R was used to analyze the differential methylation genes (DMGs) between EPN-PFA and EPN-PFB. GO and KEGG enrichment analyses were performed using the Metascape database. Results GO analysis showed that enriched genes were significantly enriched in the extracellular matrix organization, adaptive immune response, membrane raft, focal adhesion, NF-kappa B pathway, and axon guidance, as suggested by KEGG analysis. Through WGCNA, we found that MEblue had a significant correlation with EPN-PF (R = 0.69, P = 1 × 10–08) and selected the 180 hub genes in the blue module. By comparing the DEGs, DMGs, and hub genes in the co-expression network, we identified five hypermethylated, lower expressed genes in EPN-PFA (ATP4B, CCDC151, DMKN, SCN4B, and TUBA4B), and three of them were confirmed by IHC. Conclusion ssGSEA and GSVA analysis indicated that these five hub genes could lead to poor prognosis by inducing hypoxia, PI3K-Akt-mTOR, and TNFα-NFKB pathways. Further study of these dysmethylated hub genes in EPN-PF and the pathways they participate in may provides new ideas for EPN-PF treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02834-1.
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Affiliation(s)
- Guanyi Wang
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Yibin Jia
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Yuqin Ye
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China.,Department of Neurosurgery, PLA 163Rd Hospital (Second Affiliated Hospital of Hunan Normal University), Changsha, 410000, China
| | - Enming Kang
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Huijun Chen
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Jiayou Wang
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Xiaosheng He
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China.
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Pan Y, Wang X, He Y, Lin S, Zhu M, Li Y, Wang J, Wang J, Ma X, Xu J, Yang L, Yang G, Huang J, Lu Y, Sheng J. Tumor suppressor ATP4B serve as a promising biomarker for worsening of gastric atrophy and poor differentiation. Gastric Cancer 2021; 24:314-326. [PMID: 33111209 DOI: 10.1007/s10120-020-01128-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hydrogen/potassium ATPase β (ATP4B) is a proton pump acting an essential role in gastric acid secretion. This study aimed to investigate the diagnostic performance of ATP4B and its biological role in tumor progression in gastric cancer. METHODS The correlations between ATP4B expression level and clinicopathologic parameters, as well as the relevance of ATP4B expression with overall survival were assessed. The functional roles of ATP4B in gastric cancer were verified by gain- and loss-of-function cell models and tumor xenograft models. The possible downstream effects of ATP4B were analyzed by iTRAQ-based quantitative proteomics analysis. RESULTS A dramatic decrease in ATP4B was associated with malignant transformation in gastric mucosa lesions and correlated with poor differentiation. Restoration of ATP4B expression in gastric cancer cells significantly suppressed cell proliferation, cell viability, migration, invasion, tumorigenicity and induced apoptosis, whereas ATP4B silencing exerted the opposite effects. Mechanistically, we found a quality control on mitochondrial metabolism and functions in ATP4B-overexpression GC cells. CONCLUSIONS Our data suggest that decreasing ATP4B is an indicator for gastric mucosa malignant transformation and GC aggressive phenotype and it plays an inhibitory role in gastric cancer as a tumor suppressor via regulating mitochondrial metabolism and apoptosis pathway.
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Affiliation(s)
- Yuanming Pan
- Department of Gastroenterology, the 7th Medical Center of Chinese PLA General Hospital, No. 5 Nanmencang, Dongcheng District, Beijing, 100700, China.,Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Xin Wang
- Department of Gastroenterology, the 7th Medical Center of Chinese PLA General Hospital, No. 5 Nanmencang, Dongcheng District, Beijing, 100700, China
| | - Yuqi He
- Department of Gastroenterology, the 7th Medical Center of Chinese PLA General Hospital, No. 5 Nanmencang, Dongcheng District, Beijing, 100700, China.,The Second School of Clinical Medicine, Southern Medical University, 253 Middle Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Shuye Lin
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China.,College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, 3 Shangyuan Residence, Haidian District, Beijing, 100044, China
| | - Min Zhu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Yangjie Li
- Department of Gastroenterology, the 7th Medical Center of Chinese PLA General Hospital, No. 5 Nanmencang, Dongcheng District, Beijing, 100700, China.,The Second School of Clinical Medicine, Southern Medical University, 253 Middle Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao University, Qingdao, China.,Center for Regenerative Medicine, Institute for Translational Medicine, Qingdao University, Qingdao, China
| | - Jiheng Wang
- Department of Gastroenterology, the 7th Medical Center of Chinese PLA General Hospital, No. 5 Nanmencang, Dongcheng District, Beijing, 100700, China
| | - Xianzong Ma
- Department of Gastroenterology, the 7th Medical Center of Chinese PLA General Hospital, No. 5 Nanmencang, Dongcheng District, Beijing, 100700, China
| | - Junfeng Xu
- Department of Gastroenterology, the 7th Medical Center of Chinese PLA General Hospital, No. 5 Nanmencang, Dongcheng District, Beijing, 100700, China
| | - Lang Yang
- Department of Gastroenterology, the 7th Medical Center of Chinese PLA General Hospital, No. 5 Nanmencang, Dongcheng District, Beijing, 100700, China
| | - Guibin Yang
- Department of Gastroenterology, Aerospace Clinic Medical College of Peking University, No. 15 Yuanquan Road, Haidian District, Beijing, 100049, China
| | - Jiaqiang Huang
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, 3 Shangyuan Residence, Haidian District, Beijing, 100044, China. .,Cancer and Inflammation Program (CIP), Center for Cancer Research (CCR), National Cancer Institute (NCI), Frederick, MD, USA.
| | - Youyong Lu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China.
| | - Jianqiu Sheng
- Department of Gastroenterology, the 7th Medical Center of Chinese PLA General Hospital, No. 5 Nanmencang, Dongcheng District, Beijing, 100700, China.
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Cao D, Zhao D, Jia Z, Su T, Zhang Y, Wu Y, Wu M, Tsukamoto T, Oshima M, Jiang J, Cao X. Reactivation of Atp4a concomitant with intragenic DNA demethylation for cancer inhibition in a gastric cancer model. Life Sci 2019; 242:117214. [PMID: 31884095 DOI: 10.1016/j.lfs.2019.117214] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/15/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022]
Abstract
Accumulating evidence suggests that aberrant DNA methylation and gene silencing of tumor suppressors are pervasive in gastric malignancies, supporting reactivation of tumor suppressors through DNA demethylation as a potential therapeutic opportunity. Atp4a is an important tumor suppressor gene, encoding H+, K+-ATPase, and mediating gastric acid secretion in the stomach. Using transgenic gastric cancer model K19-Wnt1/C2mE (Gan) mice, by combining the transcriptome and MeDIP (methylated DNA immunoprecipitation) sequencing, together with qRT-PCR, we showed that Atp4a was expressed at low levels in tumor tissues and multiple GC cells, while both 5-aza-CdR and 18β-glycyrrhetinic acid (GRA) pharmacological treatment triggered Atp4a activation with downregulation of DNMT1. In addition, CpG island (CGI) search showed that the CpG rich region is absent in the promoter region but present in exons 9-14 of Atp4a. Methylation specific PCR (MSP) indicated that Atp4a was fully or partly methylated in multiple GC cells. Further MassArray suggested that the demethylation in the CpG site 75, 183, 196, 262-268 might be responsible for the reactivation of Atp4a. Our research identified that GRA, a bioactive component found in abundance in Radix Glycyrrhiza, reactivated Atp4a expression and inhibited gastric tumorigenesis as a potential demethylation agent.
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Affiliation(s)
- Donghui Cao
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Dan Zhao
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Zhifang Jia
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Tongrong Su
- Department of Gastric and Colorectal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yangyu Zhang
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yanhua Wu
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Menghui Wu
- Department of Gastric and Colorectal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Tetsuya Tsukamoto
- Department of Diagnostic Pathology I, School of Medicine, Fujita Health University, Toyoake 470-1192, Japan
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Jing Jiang
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Xueyuan Cao
- Department of Gastric and Colorectal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, China.
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Lin S, Lin B, Wang X, Pan Y, Xu Q, He JS, Gong W, Xing R, He Y, Guo L, Lu Y, Wang JM, Huang J. Silencing of ATP4B of ATPase H +/K + Transporting Beta Subunit by Intragenic Epigenetic Alteration in Human Gastric Cancer Cells. Oncol Res 2017; 25:317-329. [PMID: 28281974 PMCID: PMC7840950 DOI: 10.3727/096504016x14734735156265] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ATPase H+/K+ Transporting Beta Subunit (ATP4B) encodes the β subunit of the gastric H+, K+-ATPase, which controls gastric acid secretion and is therefore a target for acid reduction. Downregulation of ATP4B was recently observed in human gastric cancer (GC) without known mechanisms. In the present study, we demonstrated that ATP4B expression was decreased in human GC tissues and cell lines associated with DNA hypermethylation and histone hypoacetylation of histone H3 lysine 9 at its intragenic region close to the transcriptional start site. The expression of ATP4B was restored in GC cell lines by treatment with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5-AZA), or histone deacetylase inhibitor, trichostatin A (TSA), with further enhancement by combined treatment with both drugs. In contrast, 5-AZA had no effect on ATP4B expression in human hepatocellular carcinoma (HCC) and pancreatic cancer cell lines, in which ATP4B was silenced and accompanied by intragenic methylation. Chromatin immunoprecipitation (ChIP) showed that, in BGC823 GC cells, histone H3 lysine 9 acetylation (H3K9ac) was enhanced in the intragenic region of ATP4B upon TSA treatment, whereas 5-AZA showed a minimal effect. Additionally, ATP4B expression enhanced the inhibitory effects of chemotherapeutic mediation docetaxel on GC cell growth. Thus, as opposed to HCC and pancreatic cancer cells, the silencing of ATP4B in GC cells is attributable to the interplay between intragenic DNA methylation and histone acetylation of ATP4B, the restoration of which is associated with a favorable anticancer effect of docetaxel. These results have implications for targeting epigenetic alteration at the intragenic region of ATP4B in GC cells to benefit diagnosis and treatment of GC.
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Affiliation(s)
- Shuye Lin
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
- †Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Bonan Lin
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Xiaoyue Wang
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Yuanming Pan
- ‡Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, Beijing, P.R. China
| | - Qing Xu
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Jin-Shen He
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Wanghua Gong
- §Basic Research Program, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Rui Xing
- ‡Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, Beijing, P.R. China
| | - Yuqi He
- ¶Department of Gastroenterology, PLA Army General Hospital, Beijing, P.R. China
| | - Lihua Guo
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Youyong Lu
- ‡Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, Beijing, P.R. China
| | - Ji Ming Wang
- †Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jiaqiang Huang
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
- †Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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Juxtaposed genes in 7q21-22 amplicon contribute for two major gastric cancer sub-Types by mutual exclusive expression. Mol Carcinog 2016; 56:1239-1250. [DOI: 10.1002/mc.22586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/23/2016] [Accepted: 10/28/2016] [Indexed: 12/29/2022]
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