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Zhang J, He J, Chen W, Chen G, Wang L, Liu Y, Wang Z, Yang M, Huang G, Yang Y, Ma W, Li Y. Single-cell RNA-binding protein pattern-mediated molecular subtypes depict the hallmarks of the tumor microenvironment in bladder urothelial carcinoma. ONCOLOGIE 2024; 26:657-669. [DOI: 10.1515/oncologie-2024-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Abstract
Objectives
Bladder carcinoma (BC) is a common malignancy of the urinary tract. As a new hallmark of cancer for drug therapy, RNA-binding proteins (RBPs) are key regulatory factors in alternative splicing events. This work is to uncover the relationship between BC and RBP in order to find drug targets in BC.
Methods
In this work, data from single-cell RNA-seq GSE1355337, PRJNA662018, and the TCGA-Bladder urothelial carcinoma (BLCA) cohorts are integrated to identify their relationships. A scoring system is constructed according to RBPs gene expression and patients’ survival. A network is constructed to analyze the alternative splicing events and RBP genes.
Results
A scoring system identified 321 RBPs significantly associated with the prognosis of patients. Subsequent typing of these RBP genes in two single-cell datasets demonstrated that most of the RBP genes had variable copy numbers. Three RBP clusters were identified. Using RBP genes as a signature in BC epithelial cells allows for differentiation between different grades of BC samples. The novel RBP genes-based subtype system reflects BC clinical staging. Notably, CellChat analysis revealed that the RBP genes-associated cell subtypes of T cells had extensive interactions with epithelial cells. Further analysis showed that the ligand-receptor pair MIF-CXCR4 mediated the communication between RBP-associated subtypes of BC epithelial cells and T cells.
Conclusions
Taken together, RBP genes are associated with BC progress and offer new indicators for precision medicine in BC.
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Affiliation(s)
- Jun Zhang
- Department of Urology Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Jiejie He
- Department of Surgical Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Wen Chen
- Wuhan Ruixing Biotechnology Co. Ltd. , Wuhan , Hubei Province , China
| | - Guojun Chen
- Department of Urology Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Liang Wang
- Department of Gastrointestinal Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Yuchan Liu
- Department of Gynecology and Obstetrics , Jingmen Central Hospital , Jingmen , Hubei Province , China
| | - Zhanjin Wang
- Medical College of Qinghai University , Xining , Qinghai Province , China
| | - Ming Yang
- Department of Medical Records and Statistic, Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Guoyi Huang
- Wuhan Ruixing Biotechnology Co. Ltd. , Wuhan , Hubei Province , China
| | - Yongli Yang
- Department of Gynecology , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Wei Ma
- Department of Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Yan Li
- Department of Gynecologic Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
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Savchenko E, Bunimovich-Mendrazitsky S. Investigation toward the economic feasibility of personalized medicine for healthcare service providers: the case of bladder cancer. Front Med (Lausanne) 2024; 11:1388685. [PMID: 38808135 PMCID: PMC11130437 DOI: 10.3389/fmed.2024.1388685] [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: 02/20/2024] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
In today's complex healthcare landscape, the pursuit of delivering optimal patient care while navigating intricate economic dynamics poses a significant challenge for healthcare service providers (HSPs). In this already complex dynamic, the emergence of clinically promising personalized medicine-based treatment aims to revolutionize medicine. While personalized medicine holds tremendous potential for enhancing therapeutic outcomes, its integration within resource-constrained HSPs presents formidable challenges. In this study, we investigate the economic feasibility of implementing personalized medicine. The central objective is to strike a balance between catering to individual patient needs and making economically viable decisions. Unlike conventional binary approaches to personalized treatment, we propose a more nuanced perspective by treating personalization as a spectrum. This approach allows for greater flexibility in decision-making and resource allocation. To this end, we propose a mathematical framework to investigate our proposal, focusing on Bladder Cancer (BC) as a case study. Our results show that while it is feasible to introduce personalized medicine, a highly efficient but highly expensive one would be short-lived relative to its less effective but cheaper alternative as the latter can be provided to a larger cohort of patients, optimizing the HSP's objective better.
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Liu XS, Liu ZY, Zeng DB, Hu J, Chen XL, Gu JL, Gao Y, Pei ZJ. Functional enrichment analysis reveals the involvement of DARS2 in multiple biological pathways and its potential as a therapeutic target in esophageal carcinoma. Aging (Albany NY) 2024; 16:3934-3954. [PMID: 38382106 PMCID: PMC10929822 DOI: 10.18632/aging.205569] [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: 10/06/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024]
Abstract
OBJECTIVE The enzyme Aspartyl tRNA synthetase 2 (DARS2) is a crucial enzyme in the mitochondrial tRNA synthesis pathway, playing a critical role in maintaining normal mitochondrial function and protein synthesis. However, the role of DARS2 in ESCA is unclear. MATERIALS AND METHODS Transcriptional data of pan-cancer and ESCA were downloaded from UCSC XENA, TCGA, and GEO databases to analyze the differential expression of DARS2 between tumor samples and normal samples, and its correlation with clinicopathological features of ESCA patients. R was used for GO, KEGG, and GSEA functional enrichment analysis of DARS2 co-expression and to analyze the connection of DARS2 with glycolysis and m6A-related genes. In vitro experiments were performed to assess the effects of interfering with DARS2 expression on ESCA cells. TarBase v.8, mirDIP, miRTarBase, ENCORI, and miRNet databases were used to analyze and construct a ceRNA network containing DARS2. RESULTS DARS2 was overexpressed in various types of tumors. In vitro experiments confirmed that interfering with DARS2 expression significantly affected the proliferation, migration, apoptosis, cell cycle, and glycolysis of ESCA cells. DARS2 may be involved in multiple biological pathways related to tumor development. Furthermore, correlation and differential analysis revealed that DARS2 may regulate ESCA m6A modification through its interaction with METTL3 and YTHDF1. A ceRNA network containing DARS2, DLEU2/has-miR-30a-5p/DARS2, was successfully predicted and constructed. CONCLUSIONS Our findings reveal the upregulation of DARS2 in ESCA and its association with clinical features, glycolysis pathway, m6A modification, and ceRNA network. These discoveries provide valuable insights into the molecular mechanisms underlying ESCA.
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Affiliation(s)
- Xu-Sheng Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Zi-Yue Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Dao-Bing Zeng
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jian Hu
- Department of Critical Care Medicine, Danjiangkou First Hospital, Danjiangkou 420381, Hubei, China
| | - Xuan-Long Chen
- Department of Medical Ultrasound, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jiao-Long Gu
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yan Gao
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
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XU YUANYUAN, CHEN XIAOKE. MicroRNA (let-7b-5p)-targeted DARS2 regulates lung adenocarcinoma growth by PI3K/AKT signaling pathway. Oncol Res 2024; 32:517-528. [PMID: 38361754 PMCID: PMC10865744 DOI: 10.32604/or.2023.030293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/09/2023] [Indexed: 02/17/2024] Open
Abstract
Background The aberrant intracellular expression of a mitochondrial aspartyl-tRNA synthetase 2 (DARS2) has been reported in human cancers. Nevertheless, its critical role and detailed mechanism in lung adenocarcinoma (LUAD) remain unexplored. Methods Initially, The Cancer Genome Atlas (TCGA)-based Gene Expression Profiling Interactive Analysis (GEPIA) database (http://gepia.cancer-pku.cn/) was used to analyze the prognostic relevance of DARS2 expression in LUAD. Further, cell counting kit (CCK)-8, immunostaining, and transwell invasion assays in LUAD cell lines in vitro, as well as DARS2 silence on LUAD by tumorigenicity experiments in vivo in nude mice, were performed. Besides, we analyzed the expression levels of p-PI3K (phosphorylated-Phosphotylinosital3 kinase), PI3K, AKT (Protein Kinase B), p-AKT (phosphorylated-Protein Kinase B), PCNA (proliferating cell nuclear antigen), cleaved-caspase 3, E-cadherin, and N-cadherin proteins using the Western blot analysis. Results LUAD tissues showed higher DARS2 expression compared to normal tissues. Upregulation of DARS2 could be related to Tumor-Node-Metastasis (TNM) stage, high lymph node metastasis, and inferior prognosis. DARS2 silence decreased the proliferation, migration, and invasion abilities of LUAD cells. In addition, the DARS2 downregulation decreased the PCNA and N-cadherin expression and increased cleaved-caspase 3 and E-cadherin expressions in LUAD cells, coupled with the inactivation of the PI3K/AKT signaling pathway. Moreover, DARS2 silence impaired the tumorigenicity of LUAD in vivo. Interestingly, let-7b-5p could recognize DARS2 through a complementary sequence. Mechanistically, the increased let-7b-5p expression attenuated the promo-oncogenic action of DARS2 during LUAD progression, which were inversely correlated to each other in the LUAD tissues. Conclusion In summary, let-7b-5p downregulated DARS2 expression, regulating the progression of LUAD cells by the PI3K/AKT signaling pathway.
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Affiliation(s)
- YUANYUAN XU
- Department of Oncology Surgery, Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - XIAOKE CHEN
- Department of Oncology Surgery, Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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Luo Q, Huang C, Chen M. Comprehensive analysis of N1-methylandenosine regulators and m1A-related mRNAs and lncRNAs as prognostic factors in bladder cancer. Gene 2023; 887:147735. [PMID: 37625558 DOI: 10.1016/j.gene.2023.147735] [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: 04/24/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Bladder cancer (BC) is a lethal malignancy and recurs frequently. m1A plays a vital role in maintaining the biological functions of non-coding RNAs. The Cancer Genome Atlas (TCGA) is a free website from where transcriptome data of BC were obtained. We chose m1A methylation regulators for this study. Six m1A methylation regulator genes have a higher expression in BC tissue compared to normal tissue. The aberrant expression of those m1A regulator genes was remarkably related to BC prognosis and clinicopathological features. First, m1A-related mRNAs and long noncoding RNAs (lncRNAs) were identified. Next, univariate Cox regression, least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox regression were performed to get the optimum RNAs for the development of prognostic signatures. Also, a nomogram with T status, lncRNA risk scores and mRNA risk scores was constructed. It revealed an adequate capacity to predict the overall survival of BC cases in the training set as well as in the testing set and in the total TCGA cohort. In conclusion, m1A methylation regulator genes played an important role in predicting the overall survival of BC patients. In addition, m1A-related lncRNAs and mRNAs illustrated underlying mechanisms of tumorigenesis and development of BC.
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Affiliation(s)
- Qizhan Luo
- Urology Department, The Central Hospital of Shaoyang, University of South China, China; Urology Department, Uniklinik, RWTH Aachen, Germany
| | - Chuyang Huang
- Urology Department, The Central Hospital of Shaoyang, University of South China, China
| | - Mingquan Chen
- Department of Geriatric Urology, Xiangya International Medical Center, Xiangya Hospital, Central South University, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China.
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Liu XS, Yuan LL, Gao Y, Ming X, Zhang YH, Zhang Y, Liu ZY, Yang Y, Pei ZJ. DARS2 overexpression is associated with PET/CT metabolic parameters and affects glycolytic activity in lung adenocarcinoma. J Transl Med 2023; 21:574. [PMID: 37626419 PMCID: PMC10463715 DOI: 10.1186/s12967-023-04454-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/19/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND This study investigated the correlation between the expression of DARS2 and metabolic parameters of 18F-FDG PET/CT, and explored the potential mechanisms of DARS2 affecting the proliferation and glycolysis of lung adenocarcinoma (LUAD) cells. METHODS This study used genomics and proteomics to analyze the difference in DARS2 expression between LUAD samples and control samples. An analysis of 62 patients with LUAD who underwent 18F-FDG PET/CT examinations before surgery was conducted retrospectively. The correlation between DARS2 expression and PET/CT metabolic parameters, including SUVmax, SUVmean, MTV, and TLG, was examined by Spearman correlation analysis. In addition, the molecular mechanism of interfering with DARS2 expression in inhibiting LUAD cell proliferation and glycolysis was analyzed through in vitro cell experiments. RESULTS DARS2 expression was significantly higher in LUAD samples than in control samples (p < 0.001). DARS2 has high specificity (98.4%) and sensitivity (95.2%) in the diagnosis of LUAD. DARS2 expression was positively correlated with SUVmax, SUVmean, and TLG (p < 0.001). At the same time, the sensitivity and specificity of SUVmax in predicting DARS2 overexpression in LUAD were 88.9% and 65.9%, respectively. In vitro cell experiments have shown that interfering with DARS2 expression can inhibit the proliferation and migration of LUAD cells, promote cell apoptosis, and inhibit the glycolytic activity of tumor cells by inhibiting the expression of glycolytic related genes SLC2A1, GPI, ALDOA, and PGAM1. CONCLUSIONS Overexpression of DARS2 is associated with metabolic parameters on 18F-FDG PET/CT, which can improve LUAD diagnosis accuracy. DARS2 may be a useful biomarker to diagnose, prognosis, and target treatment of LUAD patients.
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Affiliation(s)
- Xu-Sheng Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Ling-Ling Yuan
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Yan Gao
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Xing Ming
- Department of Infection Control, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Yao-Hua Zhang
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Yu Zhang
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Zi-Yue Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Yi Yang
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China.
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Novosad VO, Maltseva DV. The RNA-Binding Proteins OAS1, ZFP36L2, and DHX58 Are Involved in the Regulation of CD44 mRNA Splicing in Colorectal Cancer Cells. Bull Exp Biol Med 2023:10.1007/s10517-023-05826-x. [PMID: 37336810 DOI: 10.1007/s10517-023-05826-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Indexed: 06/21/2023]
Abstract
Regulation of alternative splicing is carried out by RNA-binding proteins. Each alternative splicing event is controlled by several RNA-binding proteins, which in combination create the distribution of alternative splicing products in a given cell type. Transmembrane protein CD44 plays an important role at various stages of the metastatic cascade and is considered as a promising molecule for the therapy of tumor diseases and the construction of prognostic classifiers. However, the functions of specific isoforms of this protein may differ significantly. In this work, we performed a bioinformatic search of RNA-binding proteins that can determine the expression of clinically significant isoforms 3 and 4 of CD44 protein. The analysis revealed five RNA-binding proteins, three of which (OAS1, ZFP36L2, and DHX58) are shown for the first time as potential regulators of the studied process.
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Affiliation(s)
- V O Novosad
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - D V Maltseva
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia.
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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Zhu W, Zhao R, Guan X, Wang X. The emerging roles and mechanism of N6-methyladenosine (m 6A) modifications in urologic tumours progression. Front Pharmacol 2023; 14:1192495. [PMID: 37284313 PMCID: PMC10239868 DOI: 10.3389/fphar.2023.1192495] [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: 03/23/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
Prostate cancer (PCa), bladder cancer (BC), and renal cell cancer (RCC) are the most common urologic tumours in males. N6-methyladenosine (m6A), adenosine N6 methylation, is the most prevalent RNA modification in mammals. Increasing evidence suggests that m6A plays a crucial role in cancer development. In this review, we comprehensively analyzed the influence of m6A methylation on Prostate cancer, bladder cancer, and renal cell cancer and the relationship between the expression of relevant regulatory factors and their development and occurrence, which provides new insights and approaches for the early clinical diagnosis and targeted therapy of urologic malignancies.
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Jin X, Zhang H, Sui Q, Li M, Liang J, Hu Z, Cheng Y, Zheng Y, Chen Z, Lin M, Wang H, Zhan C. Identification and validation of the mitochondrial function related hub genes by unsupervised machine learning and multi-omics analyses in lung adenocarcinoma. Heliyon 2022; 8:e11966. [PMID: 36506395 PMCID: PMC9732315 DOI: 10.1016/j.heliyon.2022.e11966] [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: 09/15/2022] [Revised: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Background The mitochondrion and its associated genes were heavily implicated in developing and therapy tumors as the primary cellular organelle in charge of metabolic reprogramming and ferroptosis. Our work focuses on discovering new potential targets while analyzing the multi-omics data of mitochondria-related genes in lung adenocarcinoma (LUAD). Methods The Cancer Genome Atlas (TCGA) database provided multi-omics data for LUAD patients. Based on the expression profile of the genes associated with mitochondria, the patients were grouped by the unsupervised clustering method. R was used to explore the differential expressed protein-code gene, miRNA, and lncRNA, as well as their enriched functions and ceRNA networks. Additionally, the discrepancy between immune infiltration and genetic variation was comprehensively characterized. Our clinical samples and in vitro experiments investigated the hub gene determined by LASSO and batch analysis. Results Two clusters are distinguished using unsupervised consensus clustering based on mitochondrial heterogeneity. The integrated analysis emphasized that patients in cluster B had a worse prognosis, higher mutation frequencies, and less immune cell infiltration. The hub genes DARS2 and COX5B are identified by further analysis using LASSO penalization. In vitro experiments indicated that DARS2 and COX5B knockdown inhibited tumor cell proliferation. The specimen of our hospital cohort conducted the immunohistochemistry analysis and validated that DARS2 and COX5B's expression was significantly higher in the tumor than in adjacent normal tissue and correlated to LUAD patients' prognosis. Conclusion Our observations implied that LUAD patients' tumors had distinct mitochondrial function heterogeneity with different clinical and molecular characteristics. DARS2 and COX5B might be critical genes involved in mitochondrial alterations and potential therapeutic targets.
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Affiliation(s)
- Xing Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Huan Zhang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Qihai Sui
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Ming Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Zhengyang Hu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Ye Cheng
- Institutes of Biomedical Sciences and Children's Hospital, Fudan University, Shanghai 201102, China
| | - Yuansheng Zheng
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Zhencong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Miao Lin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China,Corresponding author.
| | - Hao Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China,Corresponding author.
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China,Corresponding author.
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Zheng Q, Yang R, Ni X, Yang S, Xiong L, Yan D, Xia L, Yuan J, Wang J, Jiao P, Wu J, Hao Y, Wang J, Guo L, Jiang Z, Wang L, Chen Z, Liu X. Accurate Diagnosis and Survival Prediction of Bladder Cancer Using Deep Learning on Histological Slides. Cancers (Basel) 2022; 14:cancers14235807. [PMID: 36497289 PMCID: PMC9737237 DOI: 10.3390/cancers14235807] [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: 10/26/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
(1) Background: Early diagnosis and treatment are essential to reduce the mortality rate of bladder cancer (BLCA). We aimed to develop deep learning (DL)-based weakly supervised models for the diagnosis of BLCA and prediction of overall survival (OS) in muscle-invasive bladder cancer (MIBC) patients using whole slide digitized histological images (WSIs). (2) Methods: Diagnostic and prognostic models were developed using 926 WSIs of 412 BLCA patients from The Cancer Genome Atlas cohort. We collected 250 WSIs of 150 BLCA patients from the Renmin Hospital of Wuhan University cohort for external validation of the models. Two DL models were developed: a BLCA diagnostic model (named BlcaMIL) and an MIBC prognostic model (named MibcMLP). (3) Results: The BlcaMIL model identified BLCA with accuracy 0.987 in the external validation set, comparable to that of expert uropathologists and outperforming a junior pathologist. The C-index values for the MibcMLP model on the internal and external validation sets were 0.631 and 0.622, respectively. The risk score predicted by MibcMLP was a strong predictor independent of existing clinical or histopathologic indicators, as demonstrated by univariate Cox (HR = 2.390, p < 0.0001) and multivariate Cox (HR = 2.414, p < 0.0001) analyses. The interpretability of DL models can help in the analysis of critical regions associated with tumors to enrich the information obtained from WSIs. Furthermore, the expression of six genes (ANAPC7, MAPKAPK5, COX19, LINC01106, AL161431.1 and MYO16-AS1) was significantly associated with MibcMLP-predicted risk scores, revealing possible potential biological correlations. (4) Conclusions: Our study developed DL models for accurately diagnosing BLCA and predicting OS in MIBC patients, which will help promote the precise pathological diagnosis of BLCA and risk stratification of MIBC to improve clinical treatment decisions.
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Affiliation(s)
- Qingyuan Zheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Rui Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xinmiao Ni
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Song Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lin Xiong
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Dandan Yan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lingli Xia
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jingsong Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Panpan Jiao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jiejun Wu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yiqun Hao
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jianguo Wang
- Department of Hepatic-Biliary-Pancreatic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Liantao Guo
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhengyu Jiang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lei Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhiyuan Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Correspondence: (Z.C.); (X.L.)
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Correspondence: (Z.C.); (X.L.)
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Establishment and Validation of a Tumor Microenvironment Prognostic Model for Predicting Bladder Cancer Survival Status Based on Integrated Bioinformatics Analyses. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4351005. [PMID: 36225190 PMCID: PMC9550453 DOI: 10.1155/2022/4351005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/13/2022] [Indexed: 11/05/2022]
Abstract
This study was designed to analyze the characteristics of bladder cancer-related genes and establish a prognostic model of bladder cancer. The model passed an independent external validation set test. Differentially expressed genes (DEGs) related to bladder cancer were obtained from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and Genotype-Tissue Expression (GTEx) databases. WGCNA was used to fit the GSE188715, TCGA, and GTEx RNA-Seq data. Fusing the module genes with the high significance in tumor development extracted from WGCNA and DEGs screened from multiple databases. 709 common prognostic-related genes were obtained. The 709 genes were enriched in the Gene Ontology database. Univariate Cox and LASSO regression analyses were used to screen out 21 prognostic-related genes and further multivariate Cox regression established a bladder cancer prognostic model consisting of 8 genes. After the eight-gene prognostic model was established, the Human Protein Atlas (HPA) database, GEPIA 2, and quantitative real-time PCR (qRT-PCR) verified the differential expression of these genes. Gene Set Enrichment Analysis and immune infiltration analysis found biologically enrichment pathways and cellular immune infiltration related to this bladder cancer prognostic model. Then, we selected bladder cancer patients in the TCGA database to evaluate the predictive ability of the model on the training set and validation set. The overall survival status of the two TCGA patient groups in the training and the test sets was obtained by Kaplan–Meier survival analysis. Three-year survival rates in the training and test sets were 37.163% and 25.009% for the low-risk groups and 70.000% and 62.235% for the high-risk groups, respectively. Receiver operating characteristic curve (ROC) analysis showed that the areas under the curve (AUCs) for the training and test sets were above 0.7. In an external independent validation database GSE13507, Kaplan–Meier survival analysis showed that the three-year survival rates of the high-risk and the low-risk groups in this database were 56.719% and 76.734%, respectively. The AUCs of the ROC drawn in the external validation set were both above 0.65. Here, we constructed a prognostic model of bladder cancer based on data from the GEO, TCGA, and GTEx databases. This model has potential prognostic and clinical auxiliary diagnostic value.
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Górnicki T, Lambrinow J, Mrozowska M, Podhorska-Okołów M, Dzięgiel P, Grzegrzółka J. Role of RBMS3 Novel Potential Regulator of the EMT Phenomenon in Physiological and Pathological Processes. Int J Mol Sci 2022; 23:ijms231810875. [PMID: 36142783 PMCID: PMC9503485 DOI: 10.3390/ijms231810875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
RNA-binding protein 3 (RBMS3) plays a significant role in embryonic development and the pathogenesis of many diseases, especially cancer initiation and progression. The multiple roles of RBMS3 are conditioned by its numerous alternative expression products. It has been proven that the main form of RBMS3 influences the regulation of microRNA expression or stabilization. The absence of RBMS3 activates the Wnt/β-catenin pathway. The expression of c-Myc, another target of the Wnt/β-catenin pathway, is correlated with the RBMS3 expression. Numerous studies have focused solely on the interaction of RBMS3 with the epithelial-mesenchymal transition (EMT) protein machinery. EMT plays a vital role in cancer progression, in which RBMS3 is a new potential regulator. It is also significant that RBMS3 may act as a prognostic factor of overall survival (OS) in different types of cancer. This review presents the current state of knowledge about the role of RBMS3 in physiological and pathological processes, with particular emphasis on carcinogenesis. The molecular mechanisms underlying the role of RBMS3 are not fully understood; hence, a broader explanation and understanding is still needed.
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Affiliation(s)
- Tomasz Górnicki
- Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Jakub Lambrinow
- Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Monika Mrozowska
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | | | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Jędrzej Grzegrzółka
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
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Jiang Y, You J, Wu C, Kang Y, Chen F, Chen L, Wu W. High expression of DARS2 indicates poor prognosis in lung adenocarcinoma. J Clin Lab Anal 2022; 36:e24691. [PMID: 36085578 PMCID: PMC9550967 DOI: 10.1002/jcla.24691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 01/25/2023] Open
Abstract
Background DARS2 was overexpressed in multiple tumor types, but the biological role of DARS2 in lung adenocarcinoma (LUAD) have not been elucidated. Methods Firstly, the DARS2 expression in LUAD was explored using The Cancer Genome Atlas (TCGA). Then, qRT‐PCR and Western blot were performed to confirm DARS2 expression in LUAD. Next, Cox regression and Kaplan–Meier methods were utilized to evaluate whether DARS2 expression can affect the overall survival. The relationships between DARS2 expression and clinicopathological characteristics were investigated by TCGA database. Moreover, we utilized Gene Set Enrichment Analysis (GSEA) to detect DARS2‐related signaling pathways in LUAD. Finally, the special function of DARS2 in cell proliferation, invasion and apoptosis was assessed in vitro. Results The higher expression of DARS2 was found in LUAD compared to para‐carcinoma tissues and significantly related to tumor stage, T stage, and M stage. The survival analysis indicated that DARS2 overexpression was related to poor prognosis in LUAD. Multivariate analysis suggested that DARS2 expression was a prognostic indicator. GSEA revealed that DARS2 was primarily involved in cell cycle‐related pathways. In addition, upregulation of DARS2 facilitated LUAD cell proliferation, migration, invasion and inhabited apoptosis, DARS2 knockdown showed an opposite result. Conclusion DARS2 modulates the proliferation, invasion and apoptosis of LUAD cells, and sever as a promising therapeutic target for LUAD.
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Affiliation(s)
- Yingfeng Jiang
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Jianbin You
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Chuncai Wu
- Department of Clinical Laboratory, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Yanli Kang
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Falin Chen
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Liangyuan Chen
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Wenbing Wu
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
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Sarafidis M, Lambrou GI, Zoumpourlis V, Koutsouris D. An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer. Cancers (Basel) 2022; 14:cancers14143358. [PMID: 35884419 PMCID: PMC9319344 DOI: 10.3390/cancers14143358] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Bladder cancer is evidently a challenge as far as its prognosis and treatment are concerned. The investigation of potential biomarkers and therapeutic targets is indispensable and still in progress. Most studies attempt to identify differential signatures between distinct molecular tumor subtypes. Therefore, keeping in mind the heterogeneity of urinary bladder tumors, we attempted to identify a consensus gene-related signature between the common expression profile of bladder cancer and control samples. In the quest for substantive features, we were able to identify key hub genes, whose signatures could hold diagnostic, prognostic, or therapeutic significance, but, primarily, could contribute to a better understanding of urinary bladder cancer biology. Abstract Bladder cancer (BCa) is one of the most prevalent cancers worldwide and accounts for high morbidity and mortality. This study intended to elucidate potential key biomarkers related to the occurrence, development, and prognosis of BCa through an integrated bioinformatics analysis. In this context, a systematic meta-analysis, integrating 18 microarray gene expression datasets from the GEO repository into a merged meta-dataset, identified 815 robust differentially expressed genes (DEGs). The key hub genes resulted from DEG-based protein–protein interaction and weighted gene co-expression network analyses were screened for their differential expression in urine and blood plasma samples of BCa patients. Subsequently, they were tested for their prognostic value, and a three-gene signature model, including COL3A1, FOXM1, and PLK4, was built. In addition, they were tested for their predictive value regarding muscle-invasive BCa patients’ response to neoadjuvant chemotherapy. A six-gene signature model, including ANXA5, CD44, NCAM1, SPP1, CDCA8, and KIF14, was developed. In conclusion, this study identified nine key biomarker genes, namely ANXA5, CDT1, COL3A1, SPP1, VEGFA, CDCA8, HJURP, TOP2A, and COL6A1, which were differentially expressed in urine or blood of BCa patients, held a prognostic or predictive value, and were immunohistochemically validated. These biomarkers may be of significance as prognostic and therapeutic targets for BCa.
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Affiliation(s)
- Michail Sarafidis
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., 15780 Athens, Greece;
- Correspondence: ; Tel.: +30-210-772-2430
| | - George I. Lambrou
- Choremeio Research Laboratory, First Department of Pediatrics, National and Kapodistrian University of Athens, 8 Thivon & Levadeias Str., 11527 Athens, Greece;
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 8 Thivon & Levadeias Str., 11527 Athens, Greece
| | - Vassilis Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vas. Konstantinou Ave., 11635 Athens, Greece;
| | - Dimitrios Koutsouris
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., 15780 Athens, Greece;
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Roles and mechanisms of the m 6A reader YTHDC1 in biological processes and diseases. Cell Death Dis 2022; 8:237. [PMID: 35501308 PMCID: PMC9061745 DOI: 10.1038/s41420-022-01040-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022]
Abstract
N6-methyladenosine (m6A) is a key area in Epigenetics and has been increasingly focused these years. In the m6A process, readers recognize the m6A modification on mRNAs or noncoding RNAs and mediate different downstream events. Emerging studies have shown that YTHDC1, an important m6A reader, plays a key role in many biological functions and disease progression, especially cancers. Here we summarized the current mechanisms of YTHDC1 in biological functions and diseases and offered guidance for future researches to provide potential strategy for clinical diagnose and therapy.
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Xu C, Pei D, Liu Y, Yu Y, Guo J, Liu N, Kang Z. Identification of a Novel Tumor Microenvironment Prognostic Signature for Bladder Urothelial Carcinoma. Front Oncol 2022; 12:818860. [PMID: 35299749 PMCID: PMC8921452 DOI: 10.3389/fonc.2022.818860] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/26/2022] [Indexed: 12/24/2022] Open
Abstract
Background The tumor microenvironment (TME) regulates the proliferation and metastasis of solid tumors and the effectiveness of immunotherapy against them. We investigated the prognostic role of TME-related genes based on transcriptomic data of bladder urothelial carcinoma (BLCA) and formulated a prediction model of TME-related signatures. Methods Molecular subtypes were identified using the non-negative matrix factorization (NMF) algorithm based on TME-related genes from the TCGA database. TME-related genes with prognostic significance were screened with univariate Cox regression analysis and lasso regression. Nomogram was developed based on risk genes. Receiver operating characteristic (ROC) curve and decision curve analysis (DCA) were used for inner and outer validation of the model. Risk scores (RS) of patients were calculated and divided into high-risk group (HRG) and low-risk group (LRG) to compare the differences in clinical characteristics and PD-L1 treatment responsiveness between HRG and LRG. Results We identified two molecular subtypes (C1 and C2) according to the NMF algorithm. There were significant differences in overall survival (OS) (p<0.05), progression-free survival (PFS) (p<0.05), and immune cell infiltration between the two subtypes. A total of eight TME-associated genes (CABP4, ZNF432, BLOC1S3, CXCL11, ANO9, OAS1, FBN2, CEMIP) with independent prognostic significance were screened to build prognostic risk models. Age (p<0.001), grade (p<0.001), and RS (p<0.001) were independent predictors of survival in BLCA patients. The developed RS nomogram was able to predict the prognosis of BLCA patients at 1, 3, and 5 years more potentially than the models of other investigators according to ROC and DCA. RS showed significantly higher values (p = 0.047) in patients with stable disease (SD)/progressive disease (PD) compared to patients with complete response (CR)/partial response (PR). Conclusions We successfully clustered and constructed predictive models for TME-associated genes and helped guide immunotherapy strategies.
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Affiliation(s)
- Chaojie Xu
- Department of Urology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Dongchen Pei
- Department of Urology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yi Liu
- Department of Urology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yang Yu
- Department of Urology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Jinhua Guo
- Department of Urology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Nan Liu
- Department of Urology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Zhengjun Kang
- Department of Urology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
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Chen Q, Cai L, Liang J. Construction of prognosis model of bladder cancer based on transcriptome. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:79-86. [PMID: 35462469 PMCID: PMC9109759 DOI: 10.3724/zdxbyxb-2021-0368] [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: 11/29/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To screen for prognosis related genes in bladder cancer, and to establish prognosis model of bladder cancer. METHODS The clinical information and bladder tissue RNA sequencing data of 406 bladder cancer patients, and the bladder tissue RNA sequencing data of 28 healthy individuals were downloaded from The Cancer Genome Atlas (TCGA) database, Genotype-Tissue Expression (GTEx) database through the UCSC Xena platform. The weighted gene co-expression network analysis (WGCNA), univariate Cox regression, LASSO regression analysis and multivariate Cox regression analysis were used to screen the prognosis-related genes of bladder cancer and the prognostic model was established. The prognostic model was evaluated with receiver operator characteristic curve (ROC curve). RESULTS A total of 2308 differentially expressed genes related to bladder cancer were obtained from the analysis. Six gene modules were obtained by WGCNA, and 829 genes with significant effect on bladder cancer prognosis were screened out. Univariate Cox regression and LASSO regression analysis showed that 24 genes were related to the prognosis of bladder cancer patients. Multivariate Cox regression analysis revealed 9 genes as independent predictors in training set, namely ADCY9, MAFG_DT, EMP1, CAST, PCOLCE2, LTBP1, CSPG4, NXPH4, SLC1A6, which were used to establish the prognosis model of bladder cancer patients. The 3-year survival rates of the high-risk group and the low-risk group in the training set were 31.814% and 59.821%, respectively. The 3-year survival rates of the high-risk group and the low-risk group in the test set were 32.745% and 68.932%, respectively. The areas under the ROC curve of the model for predicting the prognosis of bladder cancer patients in both the training set and the test set were above 0.7. CONCLUSION The established model in this study has good predictive ability for the survival of bladder cancer patients.
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Affiliation(s)
- Qiu Chen
- 1. Yangzhou University Medical College, Yangzhou 225001, Jiangsu Province, China
| | - Liangliang Cai
- 1. Yangzhou University Medical College, Yangzhou 225001, Jiangsu Province, China
- 2. Institute of Translational Medicine, Yangzhou University, Yangzhou 225001, Jiangsu Province, China
- 3. Jiangsu Provincial Key Laboratory of Geriatric Disease Prevention and Control, Yangzhou 225001, Jiangsu Province, China
| | - Jingyan Liang
- 1. Yangzhou University Medical College, Yangzhou 225001, Jiangsu Province, China
- 2. Institute of Translational Medicine, Yangzhou University, Yangzhou 225001, Jiangsu Province, China
- 3. Jiangsu Provincial Key Laboratory of Geriatric Disease Prevention and Control, Yangzhou 225001, Jiangsu Province, China
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Huang QR, Li JW, Pan XB. A novel risk signature with 6 RNA binding proteins for prognosis prediction in patients with glioblastoma. Medicine (Baltimore) 2021; 100:e28065. [PMID: 35049227 PMCID: PMC9191310 DOI: 10.1097/md.0000000000028065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/10/2021] [Indexed: 11/26/2022] Open
Abstract
Recent studies suggested that RNA binding proteins (RBPs) were related to the tumorigenesis and progression of glioma. This study was conducted to identify prognostic RBPs of glioblastoma (GBM) and construct an RBP signature to predict the prognosis of GBM.Univariate Cox regression analysis was carried out to identify the RBPs associated with overall survival of GBM in the The Cancer Genome Atlas (TCGA), GSE16011, and Repository for Molecular Brain Neoplasia data (Rembrandt) datasets, respectively. Overlapping RBPs from the TCGA, GSE16011, and Rembrandt datasets were selected. The biological role of prognostic RBPs was assessed by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction analyses. Least absolute shrinkage and selection operator regression analysis and multivariate Cox regression analysis were used to construct an RBP-related risk signature. The prognostic value of RBP signature was measured by Kaplan-Meier method and time-dependent receiver operating characteristic curve. A nomogram based on independent prognostic factors was established to predict survival for GBM. The CGGA cohort was used as the validation cohort for external validation.This study identified 27 RBPs associated with the prognosis of GBM and constructed a 6-RPBs signature. Kaplan-Meier curves suggested that high-risk score was associated with a poor prognosis. Area under the curve of 1-, 3-, and 5-year overall survival was 0.618, 0.728, and 0.833 for TCGA cohort, 0.655, 0.909, and 0.911 for GSE16011 cohort, and 0.665, 0.792, and 0.781 for Rembrandt cohort, respectively. A nomogram with 4 parameters (age, chemotherapy, O6-methylguanine-DNA methyltransferase promoter status, and risk score) was constructed. The calibration curve showed that the nomogram prediction was in good agreement with the actual observation.The 6-RBPs signature could effectively predict the prognosis of GBM, and our findings supplemented the prognostic index of GBM to a certain extent.
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Affiliation(s)
- Qian-Rong Huang
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, P.R. China
| | - Jian-Wen Li
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, P.R. China
| | - Xin-Bin Pan
- Department of Radiation Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, P.R. China
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He Y, Wu Y, Liu Z, Li B, Jiang N, Xu P, Xu A. Identification of Signature Genes Associated With Invasiveness and the Construction of a Prognostic Model That Predicts the Overall Survival of Bladder Cancer. Front Genet 2021; 12:694777. [PMID: 34589112 PMCID: PMC8473900 DOI: 10.3389/fgene.2021.694777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Bladder cancer has become the tenth most diagnosed cancer worldwide. The prognosis has been shown to differ between non-muscle invasive bladder cancer (NMIBC) and muscle invasive bladder cancer (MIBC). We aimed to identify signature genes that are associated with the invasiveness and survival of bladder cancer and to identify potential treatments. Methods: We downloaded gene expression profiles of bladder cancer from the Gene Expression Omnibus database to identify differentially expressed genes and perform weighted gene co-expression network analysis. Functional enrichment was analyzed by GO and KEGG analyses. Hub genes were identified from the significant module. Another dataset was also acquired to verify the expression of hub genes. Univariate and multivariate Cox regression analyses were applied to the dataset downloaded from The Cancer Genome Atlas database. Risk scores were calculated and the effect was evaluated by Kaplan-Meier survival analysis. A nomogram was constructed and validated using training and testing samples, respectively. Analysis of the tumor immune microenvironment was conducted with the CIBERSORT algorithm. Results: In total, 1,245 differentially expressed genes (DEGs) were identified. A distinct module was identified that was significantly correlated to invasiveness. The genes within this module were found to be significantly associated with extracellular exosomes, GTPase activity, metabolic pathways, etc. Three hub genes (VSIG2, PPFIBP2, and DENND2D) were identified as biomarkers of invasiveness; two of these (PPFIBP2 and DENND2D) were closely associated with prognosis. The risk score was regarded as an independent prognostic factor. The nomogram was associated with acceptable accuracy for predicting 1- and 5-year overall survival. The infiltrating levels of resting NK cells, activated natural killer (NK) cells, CD8+ T cells, activated memory CD4+ T cells, and T follicular helper cells, were significantly higher in the group with lower risk scores. The group with higher risk scores showed predominant infiltration by regulatory T cells (Tregs). Conclusion: We successfully identified three signature genes related to invasiveness and constructed a nomogram of bladder cancer with acceptable performance. Differences suggested by risk scores between groups of patients showing diverse patterns of immune cell infiltration may be beneficial for selecting therapeutic approaches and predicting prognosis.
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Affiliation(s)
- Yang He
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yongxin Wu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhe Liu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Boping Li
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ning Jiang
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Xu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Abai Xu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Urology, The First People's Hospital of Kashgar Prefecture, Kashgar, China
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Over-activation of EFTUD2 correlates with tumor propagation and poor survival outcomes in hepatocellular carcinoma. Clin Transl Oncol 2021; 24:93-103. [PMID: 34282556 DOI: 10.1007/s12094-021-02673-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/18/2021] [Indexed: 01/10/2023]
Abstract
PURPOSE Elongation factor Tu GTP-binding domain containing 2 (EFTUD2) is an essential constituent of U5 small nuclear ribonucleoproteins (snRNPs) and plays a crucial role in spliceosome activation and cancer. The mechanism of EFTUD2 on carcinogenesis and development of liver cancer still need further study. METHODS Bioinformatic analysis was performed to find differential expressed genes and related pathways. Western blotting and quantitative PCR assays were used to verify the EFTUD2 expression in HCC cell lines and tumor tissues of liver cancer patients. Transfection of shRNAs in SKHEP1 and Huh7 cell lines was conducted to explore the mechanisms of EFTUD2 in HCC. CCK-8 method, colony formation, and cell cycle detection kit were used to detect the proliferation. A tumor model in nude mice was used to explore the role of EFTUD2 in liver cancer in vivo. RESULTS Based on the tumor tissues and para-tumor tissues in our HCC patients, we identified EFTUD2 as highly expressed in HCC tissues (P < 0.001). Bioinformatic analysis from the TCGA database also supported this biological phenomenon (P = 1.911e-17). Furtherly, the results of clinical specimens and TCGA data suggested that higher EFTUD2 expression levels correlated with high histologic grades, high pathological grades, and poor survival prognoses in HCC patients. And knockdown of EFTUD2 suppressed cell proliferation and colony formation in vitro. In vivo, knockdown of EFTUD2 constrained the tumor growing and expansion derived from SKHEP1 cells and induced a decrease in the tumor volume and tumor weight resected from nude mice. Furthermore, RNA sequencing based on EFTUD2 knockdown revealed that EFTUD2 affected target genes concerned with the cell cycle. Flow cytometric analyses in the SKHEP1 cell model revealed that knockdown significantly suppressed cell cycle course and caused cell cycle arrest in the G1 phase. CyclinD1 proteins were also inhibited by knocking down of EFTUD2. CONCLUSION EFTUD2 is markedly overexpressed in HCC tumor tissues. High EFTUD2 expression in HCC patients is associated with clinical features. Moreover, we confirmed that EFTUD2 shows a pivotal role in HCC cell proliferation and cell cycle course and could be a possible therapeutic avenue in HCC through disturbing EFTUD2.
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