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Heydari Z, Moeinvaziri F, Mirazimi SMA, Dashti F, Smirnova O, Shpichka A, Mirzaei H, Timashev P, Vosough M. Alteration in DNA methylation patterns: Epigenetic signatures in gastrointestinal cancers. Eur J Pharmacol 2024; 973:176563. [PMID: 38593929 DOI: 10.1016/j.ejphar.2024.176563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Abnormalities in epigenetic modifications can cause malignant transformations in cells, leading to cancers of the gastrointestinal (GI) tract, which accounts for 20% of all cancers worldwide. Among the epigenetic alterations, DNA hypomethylation is associated with genomic instability. In addition, CpG methylation and promoter hypermethylation have been recognized as biomarkers for different malignancies. In GI cancers, epigenetic alterations affect genes responsible for cell cycle control, DNA repair, apoptosis, and tumorigenic-specific signaling pathways. Understanding the pattern of alterations in DNA methylation in GI cancers could help scientists discover new molecular-based pharmaceutical treatments. This study highlights alterations in DNA methylation in GI cancers. Understanding epigenetic differences among GI cancers may improve targeted therapies and lead to the discovery of new diagnostic biomarkers.
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Affiliation(s)
- Zahra Heydari
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Farideh Moeinvaziri
- Department of Regenerative Medicine, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyed Mohammad Ali Mirazimi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Dashti
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Kashan University of Medical Sciences, Kashan, Iran
| | - Olga Smirnova
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Anastasia Shpichka
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Peter Timashev
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia; World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov University, Moscow, Russia; Chemistry Department, Lomonosov Moscow State University, Moscow, Russia.
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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Ruan S, Wang H, Zhang Z, Yan Q, Chen Y, Cui J, Huang S, Zhou Q, Zhang C, Hou B. Identification and validation of stemness-based and ferroptosis-related molecular clusters in pancreatic ductal adenocarcinoma. Transl Oncol 2024; 41:101877. [PMID: 38262107 PMCID: PMC10832490 DOI: 10.1016/j.tranon.2024.101877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/04/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with an extremely poor prognosis. Cancer stem cells (CSCs) are considered to be responsible for the poor survival, recurrence and therapy resistance of PDAC. Ferroptosis plays a crucial role in the sustain and survival of CSCs. Here, we employed a rigorous evaluation of multiple datasets to identify a novel stemness-based and ferroptosis-related genes (SFRGs) signature to access the potential prognostic application. This work we retrieved RNA-sequencing and clinical annotation data from the TCGA, ICGC, GTEx and GEO database, and acquired 26 stem cell gene sets and 259 ferroptosis genes from StemChecker database and FerrDb database, respectively. Based on consensus clustering and ssGSEA analysis, we identified two expression patterns of CSCs traits (C1 and C2). Then, WGCNA analysis was implemented to screen out hub module genes correlated with stemness. Furthermore, differential expression analysis, Pearson correlation analysis, and the Least absolute shrinkage and selection operator (LASSO) and Cox regression were performed to identify the SFRGs and to construct model. In addition, the differences in prognosis, tumor microenvironment (TME) components and therapy responses were evaluated between two risk groups. Finally, we verified the most influential marker ARNTL2 experimentally by western blot, qRT-PCR, sphere formation assay, mitoscreen assay, intracellular iron concentration determination and MDA determination assays. In conclusion, we developed a stemness-based and ferroptosis-related prognostic model, which could help predict overall survival for PDAC patients. Targeting ferroptosis may be a promising therapeutic strategy to inhibit PDAC progression by suppressing CSCs.
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Affiliation(s)
- Shiye Ruan
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Hailiang Wang
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; Department of Hepatobiliary Surgery, Weihai Central Hospital Affiliated to Qingdao University, Weihai 264400, China
| | - Zhongyan Zhang
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Qian Yan
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; School of Medicine South China University of Technology, Guangzhou 51000, China
| | - Yubin Chen
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; School of Medicine South China University of Technology, Guangzhou 51000, China
| | - Jinwei Cui
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; School of Medicine South China University of Technology, Guangzhou 51000, China
| | - Shanzhou Huang
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Qi Zhou
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China; Department of General Surgery, Hui Ya Hospital of The First Affiliated Hospital, Sun Yat-Sen University, Huizhou, Guangdong 516081, China.
| | - Chuanzhao Zhang
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China.
| | - Baohua Hou
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; School of Medicine South China University of Technology, Guangzhou 51000, China; Heyuan People's Hospital, Heyuan 517000, China.
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