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Chen KC, Dhar T, Chen CR, Chen ECY, Peng CC. Nicotinamide phosphoribosyltransferase modulates PD-L1 in bladder cancer and enhances immunotherapeutic sensitivity. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167106. [PMID: 38428685 DOI: 10.1016/j.bbadis.2024.167106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/11/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
Bladder cancer (BLCA) is one of the most prevalent malignancies worldwide with a high mortality rate and poor response to immunotherapy in patients expressing lower programmed death ligand 1 (PD-L1) levels. Nicotinamide phosphoribosyltransferase (NAMPT), a rate-limiting enzyme responsible for the biosynthesis of nicotinamide adenine dinucleotide (NAD+) from nicotinamide was reported to be overexpressed in various cancers; however, the role of NAMPT in BLCA is obscure. Immunohistochemistry of tissue microarrays, a real-time polymerase chain reaction, Western blotting, proliferation assay, NAD+ quantification, transwell-migration assay, and colony-formation assay were performed to measure NAMPT and PD-L1 expression levels in patients and the effect of NAMPT inhibition on T24 cells. Our study revealed that NAMPT expression was upregulated in BLCA patients with different grades and associated with poor T-cell infiltration. Notably, FK866-mediated NAMPT inhibition decreased cell viability by depleting NAD+, and reducing the migration ability and colony-formation ability of T24 cells. Interestingly, NAMPT negatively regulated PD-L1 under an interferon (IFN)-γ-mediated microenvironment. However, exogenous NAMPT activator has no effect on PD-L1. NAD+ supplementation also only increased PD-L1 in the absence of IFN-γ. Conclusively, NAMPT is crucial for BLCA tumorigenic properties, and it regulates expression of the PD-L1 immune checkpoint protein. NAMPT could be considered a target for modulating sensitivity to immunotherapy.
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Affiliation(s)
- Kuan-Chou Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Urology, Taipei Medical University Shuang-Ho Hospital, Zhong-He District, New Taipei City 23561, Taiwan; Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; TMU-Research Center of Urology and Kidney, Taipei Medical University, Taipei, 11031, Taiwan
| | - Trayee Dhar
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Chang-Rong Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Eugene Chang-Yu Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Chiung-Chi Peng
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
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Peng T, Xiong K, He Z, Cheng S, Chen S, Chen S, Yang Z, Xiang W, Ju L, Zhang Y, Qian K, Xiao Y, Wang G. Acyl-coenzyme A: cholesterol acyltransferase inhibitor avasimibe suppresses tumorigenesis and induces G1-phase cell-cycle arrest by activating PPARγ signaling pathway in bladder cancer. J Cancer 2024; 15:370-382. [PMID: 38169575 PMCID: PMC10758042 DOI: 10.7150/jca.83856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024] Open
Abstract
Reprogramming of energy metabolism is one of the most important characteristics of tumors. Bladder cancer (BLCA) cells contain higher levels of cholesterol content compared to normal cells, and acyl-coenzyme A (CoA): cholesterol acyltransferase-1 (ACAT1) plays a crucial role in the esterification of cholesterol. Avasimibe is a drug that has been used in the treatment of atherosclerosis, and it can effectively inhibit ACAT1. We observed that ACAT1 was significantly up-regulated in BLCA and positively correlated with tumor grade. By avasimibe administration, the proliferation and migration ability of BLCA cells were reduced, while the production of ROS was strongly increased, accompanied by the up-regulated expression of ROS metabolism-related proteins SOD2 and catalase. Furthermore, BLCA cell cycle was arrested at the G1 phase, accompanied by the downregulation of cell cycle-related proteins (CCNA1/2, CCND1, CDK2 and CDK4), while the PPARγ was found to be up-regulated at both transcriptional and protein levels after avasimibe treatment. Then we found that the PPARγ antagonist GW9662 could reverse the effect of avasimibe on the cell cycle. Moreover, xenograft and pulmonary metastasis models further demonstrated that avasimibe could inhibit tumor cell growth and metastasis in vivo. Taken together, our results for the first time revealed that avasimibe can inhibit BLCA progression and metastasis, and PPARγ signaling pathway may play a key role in regulation of cell cycle distribution induced by avasimibe.
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Affiliation(s)
- Tianchen Peng
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kangping Xiong
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhiwen He
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Songtao Cheng
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Siming Chen
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Song Chen
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhonghua Yang
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wan Xiang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lingao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resource Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yi Zhang
- Euler Technology, ZGC Life Sciences Park, Beijing, China
- Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, China
| | - Kaiyu Qian
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Xiao
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gang Wang
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resource Preservation Center of Hubei Province, Wuhan, China
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Li W, Xiong Y, Zhu J, Jin X, Meng J, He W. Establishing a prognostic model with ferroptosis-related long non-coding RNAs in bladder cancer. Transl Cancer Res 2023; 12:2023-2032. [PMID: 37701097 PMCID: PMC10493782 DOI: 10.21037/tcr-23-194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/21/2023] [Indexed: 09/14/2023]
Abstract
Background Ferroptosis is a distinct form of cell death that has the potential to supersede the drug resistance that is commonly observed with current chemotherapeutic agents. As a result, ferroptosis presents a new and innovative therapeutic pathway for cancer treatment. The current understanding regarding the expression of genes associated with ferroptosis in bladder cancer (BLCA) and their prognostic implications remains unclear. Consequently, this study aimed to examine the potential prognostic value of ferroptosis-associated long non-coding RNAs (lncRNAs) in BLCA. Methods The Cancer Genome Atlas (TCGA) was accessed to download RNA sequencing data and clinicopathological features of BLCA while accessing the FerrDb database to download ferroptosis-associated genes. The study calculated risk scores for ferroptosis-associated lncRNAs, and subsequently divided patients with BLCA into two groups, namely high- and low-risk, on the basis of the median risk score. Moreover, Kaplan-Meier (K-M) curves, Cox regression analysis, and column plots were utilized for evaluating the risk score prognostic value. Subsequently, the involvement of ferroptosis-associated mRNA, N6-methyladenosine (m6A) mRNA status, and immune responses was investigated for BLCA prognosis. Results Thirty-six lncRNAs were identified to be differently expressed and linked to the prognosis of BLCA. The findings from the K-M curve analysis indicated a significant association between a high-risk lncRNA profile and poor BLCA prognosis. The area under curve (AUC) value of the receiver operating characteristic (ROC) curve was 0.810. The risk assessment model exhibited superior performance in predicting prognosis for BLCA compared to conventional clinicopathological features. Conclusions Thirty-six lncRNAs were found to be linked to ferroptosis for the prognosis of patients with BLCA, and these results may provide new insights for treating BLCA.
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Affiliation(s)
- Weisheng Li
- Henan University of Chinese Medicine, Zhengzhou, China
- Department of Urology, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Yang Xiong
- Henan University of Chinese Medicine, Zhengzhou, China
- Department of Urology, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Junlei Zhu
- Henan University of Chinese Medicine, Zhengzhou, China
- Department of Urology, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiaoxiao Jin
- Department of Urology, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Jin Meng
- Department of Urology, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Wenqiang He
- Department of Urology, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
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Cheng J, Zhang S, Fan A, Li Y, Xu P, Huang J, He M, Wang H. An immune-related gene signature for the prognosis of human bladder cancer based on WGCNA. Comput Biol Med 2022; 151:106186. [PMID: 36335813 DOI: 10.1016/j.compbiomed.2022.106186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/30/2022] [Accepted: 10/08/2022] [Indexed: 12/27/2022]
Abstract
The innovation of immunotherapy was a milestone in the treatment of bladder cancer (BLCA). However, the treatment benefits varied by individual thus promoting the investigation of the biomarker of the patients. Unfortunately, there were not many effective predictive models, which were desired by clinicians, for BLCA that can predict the prognosis and benefit of immunotherapy. We constructed a three genes prognosis prediction model termed RiskScore based on the result of weighted correlation network analysis (WGCNA) from The Cancer Genome Atlas (TCGA) cohort (n = 406). We then validated the prediction accuracy with three validation cohort(GSE13507 (n = 165), GSE48075(n = 73), GSE32894(n = 224)). We compared the differences in gene expression, immune relate function, and immune infiltration between two groups divided by RiskScore. We further discovered the potential drug target and suitable compounds for high-risk groups. Our results suggested that the low-risk group may be more potential for immunotherapy for they have higher B cell infiltration, higher expression of immune checkpoints(PDCD1, CTLA4), and much more active immune-related pathways(B cell and T cell receptor signaling pathway). The RiskScore showed a well predictive accuracy for the prognosis of BLCA. After Spearman analysis, we found the suitable drug target and compounds for the patients in the high-risk group. The model we constructed is able to predict the prognosis of BLCA patients with ease and accuracy. PLK1 and gefitinib may be utilized for further treatment of BLCA patients.
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Affiliation(s)
- Jiangting Cheng
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sihong Zhang
- Department of Urology, Xuhui Hospital, Fudan University, Shanghai, China
| | - Aoyu Fan
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yaohui Li
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peirong Xu
- Department of Urology, Xuhui Hospital, Fudan University, Shanghai, China
| | - Jiaqi Huang
- Department of Urology, Minhang Hospital, Fudan University, Shanghai, China
| | - Minke He
- Department of Urology, Minhang Hospital, Fudan University, Shanghai, China
| | - Hang Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.
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Gao S, Shan L, Zhang M, Wang Y, Zhan X, Yin Y, Jiang Z, Tao X, Li X, Ye M, Liu Y. Inhibition of PP2A by LB100 sensitizes bladder cancer cells to chemotherapy by inducing p21 degradation. Cell Oncol 2022; 45:1203-1215. [PMID: 36136269 DOI: 10.1007/s13402-022-00710-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Bladder carcinoma (BLCA) is the most common urinary tract malignancy and exhibits a poor response to chemotherapy. Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase involved in a wide variety of regulatory cellular processes, including apoptosis and the DNA-damage response (DDR). LB100, a small molecule inhibitor of PP2A, has been shown to act as a chemo-sensitizer in multiple types of cancer. However, the anti-tumor effect and mode of action of LB100 in BLCA have yet to be identified. METHODS In vitro and in vivo experiments were performed to assess the anti-tumor effect of LB100 alone or in combination with gemcitabine. Mass spectrometry (MS)-based phosphoproteomics analysis was used to identify the downstream substrates of PP2A and to explore the mechanism underlying LB100-induced DNA damage and apoptosis. In addition, we established a chemo-resistant BLCA cell line (RT-112-R) by prolonged drug exposure and determined the effect of LB100 in enhancing genotoxicity in BLCA cell lines and xenograft mouse models. RESULTS We found that LB100 is sufficient to induce an anti-tumor response in BLCA cells by inducing DNA damage and apoptosis both in vitro and in vivo. Furthermore, we found that PP2A potentially dephosphorylates p-p21-ser130 to stabilize p21. Inhibition of PP2A by LB100 increased the level of p-p21-ser130, subsequently leading to a reduction in p21 level in a dose-dependent manner. In addition, we found that treatment of LB100 abrogated the G1/S cell cycle checkpoint, resulting in increased phosphorylation of γH2AX in BLCA cells. Moreover, LB100 enhanced genotoxicity in chemo-resistant BLCA cells by inducing DNA damage and apoptosis in vitro and in vivo. CONCLUSION Our findings indicate that PP2A may serve as a potential therapeutic target in BLCA through regulating p21 stability.
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Affiliation(s)
- Song Gao
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Liping Shan
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Mo Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Yan Wang
- (CAS) Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, China Academy of Sciences, Dalian, 116023, China
| | - Xi Zhan
- (CAS) Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, China Academy of Sciences, Dalian, 116023, China
| | - Yalei Yin
- (CAS) Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, China Academy of Sciences, Dalian, 116023, China
| | - Zhonghao Jiang
- Department of Hepatobiliary and Splenic Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xinyi Tao
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.,Innovative Research Center for Integrated Cancer Omics, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xinyu Li
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, 110004, China. .,Innovative Research Center for Integrated Cancer Omics, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
| | - Mingliang Ye
- (CAS) Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, China Academy of Sciences, Dalian, 116023, China.
| | - Yang Liu
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, 110004, China. .,Innovative Research Center for Integrated Cancer Omics, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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Cheng C, Wu X, Song W, Li D, Hao L, Li X, Zhang W, Li D. A reporting quality evaluation of the clinical practice guidelines for bladder cancer based on the RIGHT checklist. Transl Androl Urol 2022; 11:1586-1597. [PMID: 36507483 PMCID: PMC9732693 DOI: 10.21037/tau-22-712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background The Reporting Items for Practice Guidelines in Healthcare (RIGHT) checklist was developed to improve the reporting quality in clinical practice guidelines (CPGs). CPGs could provide the recommendations for key clinical issues with alternative care options and adherence to them could improve the outcomes. And, high reporting quality CPGs can assist health workers to incorporate the best evidence into the individual practice. There is no evaluation study on the reporting quality of CPGs in bladder cancer (BLCA). This study assessed the reporting quality of CPGs on BLCA and provided new insights for the development of CPGs in this disease. Methods We conducted a systematic search in multiple literature databases, including PubMed, Wanfang, China National Knowledge Infrastructure (CNKI) and China Biology Medicine (CBM) as well as the medical associations and websites of guideline development organizations. Relevant CPGs published between January 2017 and December 2021 were identified. Four trained investigators independently screened the extracted documents to include all eligible CPGs and evaluated whether the items in the RIGHT checklist were reported in each CPG. Subsequently, the reporting rate of each CPG and item, as well as the mean reporting rate of each domain in the RIGHT checklist was calculated. Results A total of 23 CPGs related to BLCA were finally included, of which, 22 guidelines were written in English and 1 was published in Chinese. The mean reporting rate of the included CPGs was approximately 65%. The reporting rates of the items in each RIGHT domain were 77% for basic information domain, 75% for recommendations domain, 72% for evidence domain, 69% for background domain, 43% for funding and declaration and management of interest domain, 35% for review and quality assurance domain, and 41% for other information domain. The reporting rate was determined as the mean value in Office Excel 2019. Conclusions The reporting quality of BLCA CPGs related to the domains of funding and declaration and management of interest domain, review and quality assurance domain, and other information domain is poor and warrants improvement in the future.
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Affiliation(s)
- Cheng Cheng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Xuan Wu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wenping Song
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China;,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Henan Cancer Hospital, Zhengzhou, China;,Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou, China
| | - Dongbei Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Lidan Hao
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Xiaojing Li
- Department of Pharmacy, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenzhou Zhang
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China;,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Henan Cancer Hospital, Zhengzhou, China;,Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou, China
| | - Ding Li
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China;,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Henan Cancer Hospital, Zhengzhou, China;,Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou, China
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Li D, Wu X, Fan X, Cheng C, Li D, Zhang W. Comprehensive analysis of cuproptosis-related lncRNAs in the prognosis and therapy response of patients with bladder cancer. Ann Transl Med 2022; 10:1232. [PMID: 36544685 PMCID: PMC9761144 DOI: 10.21037/atm-22-5294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022]
Abstract
Background Cuproptosis is the recently defined regulatory cell death (RCD) that plays essential roles in tumorigenesis and progression. Long noncoding RNAs (lncRNAs) regulate the gene expression through various means. However, the clinical value of cuproptosis-related lncRNAs in bladder cancer (BLCA) remains poorly described. Methods We downloaded the transcriptome sequencing data and clinical information from The Cancer Genome Atlas (TCGA) database. Univariate, multivariate, and lasso Cox regression analyses were performed to construct the prognostic risk signature, the predictive accuracy of which was validated in the subsequent independence and stratification analyses. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to explore the underlying molecular mechanisms involved in the signature to explore therapeutic vulnerabilities and potential targets in BLCA. Tumor mutational burden (TMB) and tumor immune dysfunction and exclusion (TIDE) were used to estimate the response to immune checkpoint inhibitors (ICIs). We further explored the potential new drug-target candidates based on the half maximal inhibitory concentration for this patient population. Results Fifteen cuproptosis-related lncRNAs significantly associated with survival were identified to construct the risk signature based on the normalized expression level and regression coefficient of each gene. The patients with BLCA and high-risk scores defined by the signature were associated with worse survival outcomes. The differentially expressed genes (DEGs) between the 2 risk groups had different biological activity. Furthermore, the patients in the low-risk group exhibited a higher TMB index and a lower TIDE score. The sensitivity of multiple antitumor drugs was negatively related to risk score, including AR-42, AS605240, FK866, TAK-715, and tubastatin A, while the sensitivity of some antitumor drugs, such as AMG-706, BX-795, and RO-3306, were positively correlated with risk score. Conclusions Our study established and verified a novel clinical risk signature with cuproptosis-related lncRNAs that may predict therapy response and prognosis with robust and stable accuracy in patients with BLCA and enhance the personalized management of this patient population.
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Affiliation(s)
- Ding Li
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China;,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Henan Cancer Hospital, Zhengzhou, China;,Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou, China
| | - Xuan Wu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Xinxin Fan
- Department of Hematology, Zhengzhou Third People’s Hospital, Zhengzhou, China
| | - Cheng Cheng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Dongbei Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Wenzhou Zhang
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China;,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Henan Cancer Hospital, Zhengzhou, China;,Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou, China
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Zhou Q, Chen Q, Chen X, Hao L. Bioinformatics analysis to screen DNA methylation-driven genes for prognosis of patients with bladder cancer. Transl Androl Urol 2021; 10:3604-3619. [PMID: 34733656 PMCID: PMC8511533 DOI: 10.21037/tau-21-326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
Background Bladder cancer (BLCA) is the most prevalent tumor affecting the urinary system, and has contributed to a rise in morbidity and mortality rates. Herein, we sought to identify the methylation-driven genes (MDGs)of BLCA in an effort to develop prognostic biomarkers suitable for the individualized assessment of patients with this particular cancer. Methods The Cancer Genome Atlas (TCGA) dataset was distributed into training set (n=272) and testing set(n=117). The ConsensusClusterPluspackage was used to identify BLCA subtypes. The ChAMP package was used to analyze differential methylation probe (DMP) and differential methylation region (DMR). The differentially expressed genes (DEGs) were detected using DESeq2. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were utilized to identify the pathways enriched of DEGs. Correlation analysis between 5’-C-phosphate-G-3’s (CpGs) and DEGs was employed to identify the MDGs. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) was used to build the protein-protein interaction (PPI) network of MDGs. Screening for BLCA prognosis-related MDGs and clinical features was conducted via the Cox regression model. A prognosis-related nomogram was developed and validated for prediction of the BLCA patients’ survival. Results We identified 2 BLCA clusters. Differential methylations at CpGs sites (dm-CpGs) were observed between cluster2 and cluster1, with 14,189 of them hypermethylated and 878 hypomethylated, predominantly in the CpG islands. In addition, a total 4,234 DEGs were identified between cluster2 and cluster1. The KEGG pathway and GO term enrichment analyses found that some DEGs were significantly enriched in multiple cancer-related pathways. A total of 33 MDGs were detected from correlation analysis between CpGs and DEGs. We selected BLCA-specific prognostic DMGs signatures for risk model development. The nomogram comprised a risk model to predict survival for BLCA patients. The efficiency of the prognostic prediction model was validated in the training and testing set. Conclusions This study discovered differential methylation patterns and MDGs in BLCA patients, which provided a bioinformatics basis for guiding BLCA early diagnosis and prognosis analyses.
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Affiliation(s)
- Qing Zhou
- Central Laboratory, People's Hospital of Baoan District, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qiuyan Chen
- Science and Education Department, Shenzhen Baoan Shiyan People's Hospital, Shenzhen, China
| | - Xi Chen
- Central Laboratory, People's Hospital of Baoan District, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lu Hao
- Science and Education Department, Shenzhen Baoan Shiyan People's Hospital, Shenzhen, China
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