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Song C, Wang G, Liu M, Xu Z, Liang X, Ding K, Chen Y, Wang W, Lou W, Liu L. Identification of methylation driver genes for predicting the prognosis of pancreatic cancer patients based on whole-genome DNA methylation sequencing technology. Heliyon 2024; 10:e29914. [PMID: 38737285 PMCID: PMC11088258 DOI: 10.1016/j.heliyon.2024.e29914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024] Open
Abstract
This study was based on the use of whole-genome DNA methylation sequencing technology to identify DNA methylation biomarkers in tumor tissue that can predict the prognosis of patients with pancreatic cancer (PCa). TCGA database was used to download PCa-related DNA methylation and transcriptome atlas data. Methylation driver genes (MDGs) were obtained using the MethylMix package. Candidate genes in the MDGs were screened for prognostic relevance to PCa patients by univariate Cox analysis, and a prognostic risk score model was constructed based on the key MDGs. ROC curve analysis was performed to assess the accuracy of the prognostic risk score model. The effects of PIK3C2B knockdown on malignant phenotypes of PCa cells were investigated in vitro. A total of 2737 differentially expressed genes were identified, with 649 upregulated and 2088 downregulated, using 178 PCa samples and 171 normal samples. MethylMix was employed to identify 71 methylation-driven genes (47 hypermethylated and 24 hypomethylated) from 185 TCGA PCa samples. Cox regression analyses identified eight key MDGs (LEF1, ZIC3, VAV3, TBC1D4, FABP4, MAP3K5, PIK3C2B, IGF1R) associated with prognosis in PCa. Seven of them were hypermethylated, while PIK3C2B was hypomethylated. A prognostic risk prediction model was constructed based on the eight key MDGs, which was found to accurately predict the prognosis of PCa patients. In addition, the malignant phenotypes of PANC-1 cells were decreased after the knockdown of PIK3C2B. Therefore, the prognostic risk prediction model based on the eight key MDGs could accurately predict the prognosis of PCa patients.
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Affiliation(s)
- Chao Song
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200000, China
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital of Fudan University, Shanghai, 200000, China
- Department of General Surgery, Affiliated Zhongshan Hospital of Fudan University, Qingpu Branch, Shanghai, 200000, China
| | - Ganggang Wang
- Department of Hepatobiliary Surgery, Pudong Hospital, Fudan University, Shanghai, 200000, China
| | - Mengmeng Liu
- Department of Gastroenterology, Affiliated Zhongshan Hospital of Fudan University, Qingpu Branch, Shanghai, 200000, China
| | - Zijin Xu
- Department of General Surgery, Affiliated Zhongshan Hospital of Fudan University, Qingpu Branch, Shanghai, 200000, China
| | - Xin Liang
- CAS Key Laboratory of Nutrition, University of Chinese Academy of Sciences, Shanghai, 200000, China
| | - Kai Ding
- CAS Key Laboratory of Nutrition, University of Chinese Academy of Sciences, Shanghai, 200000, China
| | - Yu Chen
- CAS Key Laboratory of Nutrition, University of Chinese Academy of Sciences, Shanghai, 200000, China
| | - Wenquan Wang
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital of Fudan University, Shanghai, 200000, China
| | - Wenhui Lou
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital of Fudan University, Shanghai, 200000, China
| | - Liang Liu
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200000, China
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital of Fudan University, Shanghai, 200000, China
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Shi J, Qiao F, Ye M, Jiang T, Liu J, Zhang M, Xie G, Fok KL, Li X, Chen H. CSE1L/CAS regulates cell proliferation through CDK signalling in mouse spermatogenesis. Cell Prolif 2022; 55:e13334. [PMID: 36097754 PMCID: PMC9628239 DOI: 10.1111/cpr.13334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/09/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jianwu Shi
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Feng Qiao
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Mei Ye
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Ting Jiang
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Jianni Liu
- Medical Laboratory Department of Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Mengya Zhang
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Gangcai Xie
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Kin Lam Fok
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaofeng Li
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Hao Chen
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
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Ye M, Chen Y, Liu J, Tian J, Wang X, Fok KL, Shi J, Chen H. Interfering with CSE1L/CAS inhibits tumour growth via C3 in triple-negative breast cancer. Cell Prolif 2022; 55:e13226. [PMID: 35403306 PMCID: PMC9136492 DOI: 10.1111/cpr.13226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 12/14/2022] Open
Abstract
Triple‐negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. However, the treatment regimens for TNBC are limited. Chromosome segregation 1‐like (CSE1L), also called cellular apoptosis susceptibility protein (CAS), is highly expressed in breast cancer and plays a crucial role in the progression of various tumours. However, the involvement of CAS in TNBC remains elusive. In this study, we showed that the expression of CAS was higher in TNBC samples than in non‐TNBC samples in the Gene Expression Omnibus database. Knockdown of CAS inhibited MDA‐MB‐231 cell growth, migration and invasion. Further RNA‐seq analysis revealed that complement pathway activity was significantly elevated. Of note, complement component 3 (C3), the key molecule in the complement pathway, was significantly upregulated, and the expression of C3 was negatively correlated with that of CAS in breast cancer. Lower C3 expression was related to poor prognosis. Interestingly, the expression level of C3 was positively correlated with the infiltration of multiple immune cells. Taken together, our findings suggest that CAS participates in the development of TNBC through C3‐mediated immune cell suppression and might constitute a potential therapeutic target for TNBC.
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Affiliation(s)
- Mei Ye
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Yufei Chen
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Jianni Liu
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Jiawei Tian
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Xunda Wang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Kin Lam Fok
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jianwu Shi
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Hao Chen
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
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