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Yan X, Qi Y, Yao X, Zhou N, Ye X, Chen X. DNMT3L inhibits hepatocellular carcinoma progression through DNA methylation of CDO1: insights from big data to basic research. J Transl Med 2024; 22:128. [PMID: 38308276 PMCID: PMC10837993 DOI: 10.1186/s12967-024-04939-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/27/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND DNMT3L is a crucial DNA methylation regulatory factor, yet its function and mechanism in hepatocellular carcinoma (HCC) remain poorly understood. Bioinformatics-based big data analysis has increasingly gained significance in cancer research. Therefore, this study aims to elucidate the role of DNMT3L in HCC by integrating big data analysis with experimental validation. METHODS Dozens of HCC datasets were collected to analyze the expression of DNMT3L and its relationship with prognostic indicators, and were used for molecular regulatory relationship evaluation. The effects of DNMT3L on the malignant phenotypes of hepatoma cells were confirmed in vitro and in vivo. The regulatory mechanisms of DNMT3L were explored through MSP, western blot, and dual-luciferase assays. RESULTS DNMT3L was found to be downregulated in HCC tissues and associated with better prognosis. Overexpression of DNMT3L inhibits cell proliferation and metastasis. Additionally, CDO1 was identified as a target gene of DNMT3L and also exhibits anti-cancer effects. DNMT3L upregulates CDO1 expression by competitively inhibiting DNMT3A-mediated methylation of CDO1 promoter. CONCLUSIONS Our study revealed the role and epi-transcriptomic regulatory mechanism of DNMT3L in HCC, and underscored the essential role and applicability of big data analysis in elucidating complex biological processes.
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Affiliation(s)
- Xiaokai Yan
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China.
| | - Yao Qi
- Shanghai Molecular Medicine Engineering Technology Research Center, Shanghai, 201203, China
- Shanghai National Engineering Research Center of Biochip, Shanghai, 201203, China
| | - Xinyue Yao
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Nanjing Zhou
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xinxin Ye
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xing Chen
- Department of Hepatopancreatobiliary Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
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Wan S, Li KP, Wang CY, Yang JW, Chen SY, Wang HB, Li XR, Yang L. Immunologic Crosstalk of Endoplasmic Reticulum Stress Signaling in Bladder Cancer. Curr Cancer Drug Targets 2024; 24:701-719. [PMID: 38265406 DOI: 10.2174/0115680096272663231121100515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/19/2023] [Accepted: 11/02/2023] [Indexed: 01/25/2024]
Abstract
Bladder cancer (BC) is a common malignant tumor of the urinary system. While current approaches involving adjuvant chemotherapy, radiotherapy, and immunotherapy have shown significant progress in BC treatment, challenges, such as recurrence and drug resistance, persist, especially in the case of muscle-invasive bladder cancer (MIBC). It is mainly due to the lack of pre-existing immune response cells in the tumor immune microenvironment. Micro-environmental changes (such as hypoxia and under-nutrition) can cause the aggregation of unfolded and misfolded proteins in the lumen, which induces endoplasmic reticulum (ER) stress. ER stress and its downstream signaling pathways are closely related to immunogenicity and tumor drug resistance. ER stress plays a pivotal role in a spectrum of processes within immune cells and the progression of BC cells, encompassing cell proliferation, autophagy, apoptosis, and resistance to therapies. Recent studies have increasingly recognized the potential of natural compounds to exhibit anti-BC properties through ER stress induction. Still, the efficacy of these natural compounds remains less than that of immune checkpoint inhibitors (ICIs). Currently, the ER stress-mediated immunogenic cell death (ICD) pathway is more encouraging, which can enhance ICI responses by mediating immune stemness. This article provides an overview of the recent developments in understanding how ER stress influences tumor immunity and its implications for BC. Targeting this pathway may soon emerge as a compelling therapeutic strategy for BC.
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Affiliation(s)
- Shun Wan
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, 730000, PR China
- Gansu Province Clinical Research Center for Urology, Lanzhou, 730000, PR China
| | - Kun-Peng Li
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, 730000, PR China
- Gansu Province Clinical Research Center for Urology, Lanzhou, 730000, PR China
| | - Chen-Yang Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, 730000, PR China
- Gansu Province Clinical Research Center for Urology, Lanzhou730000, PR China
| | - Jian-Wei Yang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, 730000, PR China
| | - Si-Yu Chen
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, 730000, PR China
- Gansu Province Clinical Research Center for Urology, Lanzhou, 730000, PR China
| | - Hua-Bin Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, 730000, PR China
- Gansu Province Clinical Research Center for Urology, Lanzhou, 730000, PR China
| | - Xiao-Ran Li
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, 730000, PR China
- Gansu Province Clinical Research Center for Urology, Lanzhou, 730000, PR China
| | - Li Yang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, 730000, PR China
- Gansu Province Clinical Research Center for Urology, Lanzhou, 730000, PR China
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Guo H, Zhang S, Zhang B, Shang Y, Liu X, Wang M, Wang H, Fan Y, Tan K. Immunogenic landscape and risk score prediction based on unfolded protein response (UPR)-related molecular subtypes in hepatocellular carcinoma. Front Immunol 2023; 14:1202324. [PMID: 37457742 PMCID: PMC10348016 DOI: 10.3389/fimmu.2023.1202324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most common type of cancer and causes a significant number of cancer-related deaths worldwide. The molecular mechanisms underlying the development of HCC are complex, and the heterogeneity of HCC has led to a lack of effective prognostic indicators and drug targets for clinical treatment of HCC. Previous studies have indicated that the unfolded protein response (UPR), a fundamental pathway for maintaining endoplasmic reticulum homeostasis, is involved in the formation of malignant characteristics such as tumor cell invasiveness and treatment resistance. The aims of our study are to identify new prognostic indicators and provide drug treatment targets for HCC in clinical treatment based on UPR-related genes (URGs). Methods Gene expression profiles and clinical information were downloaded from the TCGA, ICGC and GEO databases. Consensus cluster analysis was performed to classify the molecular subtypes of URGs in HCC patients. Univariate Cox regression and machine learning LASSO algorithm were used to establish a risk prognosis model. Kaplan-Meier and ROC analyses were used to evaluate the clinical prognosis of URGs. TIMER and XCell algorithms were applied to analyze the relationships between URGs and immune cell infiltration. Real time-PCR was performed to analyze the effect of sorafenib on the expression levels of four URGs. Results Most URGs were upregulated in HCC samples. According to the expression pattern of URGs, HCC patients were divided into two independent clusters. Cluster 1 had a higher expression level, worse prognosis, and higher expression of immunosuppressive factors than cluster 2. Patients in cluster 1 were more prone to immune escape during immunotherapy, and were more sensitive to chemotherapeutic drugs. Four key UPR genes (ATF4, GOSR2, PDIA6 and SRPRB) were established in the prognostic model and HCC patients with high risk score had a worse clinical prognosis. Additionally, patients with high expression of four URGs are more sensitive to sorafenib. Moreover, ATF4 was upregulated, while GOSR2, PDIA6 and SRPRB were downregulated in sorafenib-treated HCC cells. Conclusion The UPR-related prognostic signature containing four URGs exhibits high potential application value and performs well in the evaluation of effects of chemotherapy/immunotherapy and clinical prognosis.
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Affiliation(s)
| | | | | | | | | | | | | | - Yumei Fan
- *Correspondence: Yumei Fan, ; Ke Tan,
| | - Ke Tan
- *Correspondence: Yumei Fan, ; Ke Tan,
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Wang J, Chen H, Deng Q, Chen Y, Wang Z, Yan Z, Wang Y, Tang H, Liang H, Jiang Y. High expression of RNF169 is associated with poor prognosis in pancreatic adenocarcinoma by regulating tumour immune infiltration. Front Genet 2023; 13:1022626. [PMID: 36685833 PMCID: PMC9849556 DOI: 10.3389/fgene.2022.1022626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Background: Pancreatic adenocarcinoma (PAAD) is a highly deadly and aggressive tumour with a poor prognosis. However, the prognostic value of RNF169 and its related mechanisms in PAAD have not been elucidated. In this study, we aimed to explore prognosis-related genes, especially RNF169 in PAAD and to identify novel potential prognostic predictors of PAAD. Methods: The GEPIA and UALCAN databases were used to investigate the expression and prognostic value of RNF169 in PAAD. The correlation between RNF169 expression and immune infiltration was determined by using TIMER and TISIDB. Correlation analysis with starBase was performed to identify a potential regulatory axis of lncRNA-miRNA-RNF169. Results: The data showed that the level of RNF169 mRNA expression in PAAD tissues was higher than that in normal tissues. High RNF169 expression was correlated with poor prognosis in PAAD. In addition, analysis with the TISIDB and TIMER databases revealed that RNF169 expression was positively correlated with tumour immune infiltration in PAAD. Correlation analysis suggested that the long non-coding RNA (lncRNA) AL049555.1 and the microRNA (miRNA) hsa-miR-324-5p were involved in the expression of RNF169, composing a potential regulatory axis to control the progression of PAAD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that RNF169 plays a role in PAAD through pathways such as TNF, Hippo, JAK-STAT and Toll-like receptor signaling. Conclusion: In summary, the upregulation of RNF169 expression mediated by ncRNAs might influence immune cell infiltration in the microenvironment; thus, it can be used as a prognostic biomarker and a potential therapeutic target in PAAD.
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Affiliation(s)
- Jieyan Wang
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Hanghang Chen
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qiong Deng
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Yeda Chen
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Zhu Wang
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Zhengzheng Yan
- Dongguan Key Laboratory of Respiratory and Critical Care Medicine, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Yinglin Wang
- Department of Pediatrics, The Second Hospital of Zhuzhou, Zhuzhou, Hunan, China
| | - Haoxuan Tang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hui Liang
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China,*Correspondence: Hui Liang, ; Yong Jiang,
| | - Yong Jiang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Dongguan Key Laboratory of Respiratory and Critical Care Medicine, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China,*Correspondence: Hui Liang, ; Yong Jiang,
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Construction and Validation of a UPR-Associated Gene Prognostic Model for Head and Neck Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8677309. [PMID: 35707371 PMCID: PMC9192238 DOI: 10.1155/2022/8677309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/12/2022] [Indexed: 11/27/2022]
Abstract
Our study is aimed at constructing and validating a UPR-associated gene signature to predict HNSCC prognosis. We obtained 544 samples of RNA sequencing data and clinical characteristics from TCGA database and randomly grouped the samples into training and testing cohorts (1 : 1 ratio). After identifying 14 UPR-associated genes with LASSO and univariate Cox regression analysis, HNSCC samples were categorized into low-risk (LR) and high-risk (HR) subgroups depending on the risk score. Our analyses indicated that low-risk patients had a much better prognosis in the training and testing cohorts. To predict the HNSCC prognosis with the 14 UPR-associated gene signatures, we incorporated the UPR gene risk score, N stage, M stage, and age into a nomogram model. We further explored the sensitivity to anticancer drugs by using the IC50 analysis in two subgroups from the Cancer Genome Project database. The outcomes showed that the AKT inhibitor III and sorafenib were sensitive anticancer drugs in HR and LR patients, respectively. The immune cell infiltration analysis and GSEA provided strong evidence for elucidating the molecular mechanisms of UPR-associated genes affecting HNSCC. In conclusion, the UPR-associated gene risk score, N stage, M stage, and age can serve as a robust model for predicting prognosis and can improve decision-making at the individual patient level.
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