scholarly journals An eight-mRNA signature predicts the prognosis of patients with bladder urothelial carcinoma

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7836 ◽  
Author(s):  
Rui Zhu ◽  
Xin Yang ◽  
Wenna Guo ◽  
Xin-Jian Xu ◽  
Liucun Zhu
Keyword(s):  
Bladder Cancer ◽  
Urothelial Carcinoma ◽  
Survival Time ◽  
Roc Curve ◽  
Cox Regression ◽  
Prognostic Biomarker ◽  
Prognostic Biomarkers ◽  
Kaplan Meier ◽  
Bladder Urothelial Carcinoma ◽  
Significant Difference

Background Bladder cancer is one of the most common cancers, and its histopathological type is mainly bladder urothelial carcinoma, accounting for about 90%. The prognostic biomarkers of bladder cancer are classified into clinical features biomarkers and molecular biomarkers. Nevertheless, due to the existence of individual specificity, patients with similar pathological characteristics still have great differences in the risk of disease recurrence. Therefore, it is often inaccurate to predict the survival status of patients based on clinical characteristic biomarkers, and a prognostic molecular biomarker that can grade the risk of bladder cancer patients is needed. Methods A total of three bladder urothelial carcinoma datasets were used in this study from the Cancer Genome Atlas database and Gene Expression Omnibus database. In order to avoid overfitting, all samples were randomly divided into one training set and three validation sets, which were used to construct and test the prognostic biomarker model of bladder urothelial carcinoma. Univariate and multivariate Cox regression were used to screen candidate mRNAs and construct prognostic biomarkers model. Kaplan–Meier survival analysis and the receiver operating characteristic (ROC) curve were used to evaluate the predictive performance of the model. Results A prognostic biomarker model of bladder urothelial carcinoma combining with eight mRNA was constructed. Kaplan–Meier analyses indicated that a significant difference in the survival time of patients between the high-risk and the low-risk group. The area under the ROC curve were 0.632 (95% confidence interval (CI) [0.541–0.723]), 0.693 (95% CI [0.601–0.784]) and 0.686 (95% CI [0.540–0.831]) when the model was used to predict the patient’s survival time in three validation datasets. The model showed high accuracy and applicability.

Prognostic value of hypoxia gene expression in bladder cancer patients.

2020 ◽  
Vol 38 (6_suppl) ◽  
pp. 548-548
Author(s):  
Hyun Chang ◽  
Seung-Hyun Lee ◽  
Taeryool Koo ◽  
Moon Ho Kim ◽  
Soo-Yoon Sung
Keyword(s):  
Bladder Cancer ◽  
Urothelial Carcinoma ◽  
Cancer Patients ◽  
Prognostic Value ◽  
Cox Regression ◽  
Gene Signature ◽  
Survival Curves ◽  
Kaplan Meier ◽  
Bladder Urothelial Carcinoma

548 Background: The prognostic value of hypoxia in bladder cancer remains unknown. We aimed to evaluate the potential role of hypoxia gene signature as prognostic factors in bladder cancer patients. Methods: We investigated the hypoxia gene signature and clinicopathologic features of The Cancer Genome Atlas (TCGA) bladder urothelial carcinoma (n = 408) using the Kaplan-Meier survival curves and multivariate Cox regression analyses. The clinicopathologic data and the processed data of hypoxia gene signature were obtained from TCGA Bladder urothelial carcinoma database. Results: Hypoxia gene signature score was significantly associated with overall survival (OS) and progression-free survival (PFS). Higher score resulted in shorter OS and PFS in Kaplan-Meier survival curves with Log-rank test ( P < 0.01 and P <0.05, respectively). In multivariate analysis containing clinical prognostic variables, higher hypoxia gene signature score predicted poor OS (adjusted HR= 1.58, 95% CI 1.15 - 2.19; P <0.01). Conclusions: Hypoxia gene signature was an independent prognostic factor in bladder cancer. Prospective studies are needed to evaluate the prognostic role of hypoxia in bladder cancer patients.

scholarly journals An RNA-sequencing-based transcriptome for a significantly prognostic novel driver signature identification in bladder urothelial carcinoma

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9422
Author(s):  
Danqi Liu ◽  
Boting Zhou ◽  
Rangru Liu
Keyword(s):  
Overall Survival ◽  
Bladder Cancer ◽  
Regression Analysis ◽  
Urothelial Carcinoma ◽  
Cox Regression ◽  
Protein Coding ◽  
Cox Regression Analysis ◽  
Protein Coding Genes ◽  
Bladder Urothelial Carcinoma ◽  
Rna Signature

Bladder cancer (BC) is the ninth most common malignancy worldwide. Bladder urothelial carcinoma (BLCA) constitutes more than 90% of bladder cancer (BC). The five-year survival rate is 5–70%, and patients with BLCA have a poor clinical outcome. The identification of novel clinical molecular markers in BLCA is still urgent to allow for predicting clinical outcomes. This study aimed to identify a novel signature integrating the three-dimension transcriptome of protein coding genes, long non-coding RNAs, microRNAs that is related to the overall survival of patients with BLCA, contributing to earlier prediction and effective treatment selection, as well as to the verification of the established model in the subtypes identified. Gene expression profiling and the clinical information of 400 patients diagnosed with BLCA were retrieved from The Cancer Genome Atlas (TCGA) database. A univariate Cox regression analysis, robust likelihood-based survival modelling analysis and random forests for survival regression and classification algorithms were used to identify the critical biomarkers. A multivariate Cox regression analysis was utilized to construct a risk score formula with a maximum area under the curve (AUC = 0.7669 in the training set). The significant signature could classify patients into high-risk and low-risk groups with significant differences in overall survival time. Similar results were confirmed in the test set (AUC = 0.645) and in the entire set (AUC = 0.710). The multivariate Cox regression analysis indicated that the five-RNA signature was an independent predictive factor for patients with BLCA. Non-negative matrix factorization and a similarity network fusion algorithm were applied for identifying three molecular subtypes. The signature could separate patients in every subtype into high- and low- groups with a distinct difference. Gene set variation analysis of protein-coding genes associated with the five prognostic RNAs demonstrated that the co-expressed protein-coding genes were involved in the pathways and biological process of tumourigenesis. The five-RNA signature could serve as to some degree a reliable independent signature for predicting outcome in patients with BLCA.

scholarly journals TSHZ3 is A Prognostic Biomarker with Immune Infiltration in Stomach Adenocarcinoma and Bladder Urothelial Carcinoma

2020 ◽  
Author(s):  
Xi Zhang ◽  
Ming Wang ◽  
Han-qi Lu ◽  
Qiu-xing He ◽  
Yan-ting You ◽  
...  
Keyword(s):  
Urothelial Carcinoma ◽  
Prognostic Biomarker ◽  
Th2 Cells ◽  
Poor Overall Survival ◽  
Clinical Prognosis ◽  
Immune Infiltration ◽  
Normal Tissues ◽  
Kaplan Meier ◽  
Bladder Urothelial Carcinoma ◽  
Stomach Adenocarcinoma

Abstract Background: This study aimed to investigate the expressions of Teashirt zinc finger homeobox 3 (TSHZ3) in different cancer types and identify the cancers of which prognosis can be predicted by TSHZ3 expression. Furthermore, we aimed to explore the correlations between tumor-infiltrating immune cells (TIICs) and TSHZ3 expression in these cancers.Methods: TSHZ3 expression was analyzed by the Oncomine database and Gene Expression Profiling Interactive Analysis (GEPIA). We examined the influence of TSHZ3 on the clinical prognosis with Kaplan-Meier plotter and TIMER (Tumor Immune Estimation Resource). The correlations between tumor immune infiltrates and TSHZ3 expressions were investigated with TIMER and validated by GEPIA.Results: TSHZ3 expressions were significantly higher in stomach adenocarcinoma (STAD) and bladder urothelial carcinoma (BLCA) when compared to normal tissues. Survival analysis results showed that high TSHZ3 expression was correlated with poor overall survival (OS) in STAD and BLCA. The infiltrations of pro-tumorigenic TIICs (M2 macrophages, monocytes, B cells and pDCs) were positively correlated with TSHZ3 expression in STAD and BLCA. Besides, the infiltration of other pro-tumorigenic TIICs (tumor-associated macrophages (TAMs), Th2 cells and Tregs) and expression of T cell exhaustion markers (PD-1 and TIM-3) were positively correlated with TSHZ3 expression in STAD.Conclusions: TSHZ3 expression was up-regulated in STAD and BLCA. High TSHZ3 expression predicted poor prognosis of patients with STAD or BLCA. In addition, TSHZ3 expression potentially contributes to the increased infiltrations of pro-tumorigenic TIICs. TSHZ3 can be used as a prognostic biomarker for predicting prognosis and immune infiltration in STAD and BLCA.

The Significance of Squamous Histology on Clinical Outcomes and PD-L1 Expression in Bladder Cancer

2021 ◽  
pp. 106689692110272
Author(s):  
Jennifer B. Gordetsky ◽  
Kathleen W. Montgomery ◽  
Giovanna A. Giannico ◽  
Soroush Rais-Bahrami ◽  
Prabin Thapa ◽  
...  
Keyword(s):  
Risk Factors ◽  
Bladder Cancer ◽  
Urothelial Carcinoma ◽  
Clinical Outcomes ◽  
Cox Regression ◽  
Squamous Differentiation ◽  
Clinicopathologic Characteristics ◽  
Cancer Specific Survival ◽  
Kaplan Meier ◽  
Never Smokers

Objectives. To compare the clinicopathologic characteristics of urothelial carcinoma (UC), urothelial carcinoma with squamous differentiation (UCSD), and squamous cell carcinoma (SCC) of the bladder, which have been suggested to differ in terms of risk factors, immunophenotype, and prognosis. Methods. We evaluated the clinicopathologic features of radical cystectomy specimens between 1980 and 2015 with a diagnosis of SCC, UCSD, and UC. PD-L1 immunohistochemistry (clinically available clones 22C3, SP142, and SP263) was performed on SCC and UCSD. Multivariate Cox regression was used to identify prognostic factors. Kaplan–Meier curves were plotted to assess cancer-specific survival (CSS). Results. Of the 1478 cases, there were 1126 UC (76%), 217 UCSD (15%), and 135 SCC (9%). Bladder cancer was more common in men than women (80% vs 20%, P < .0001). However, a higher proportion of SCC and UCSD occurred in women (SCC-36%, UCSD-22%, UC-18%). Women were significantly more likely to be never smokers in all 3 cohorts (UC: 45% vs 16%, UCSD: 44% vs 12%, SCC: 40% vs 18%, P < .0001). Patients with SCC and UCSD were at a higher pathologic stage (>pT2) at the time of cystectomy (UCSD-74%, SCC 71%, UC-44%, P < .0001) and had worse CSS compared to patients with UC ( P = 0.006). SCC had higher PD-L1 scores (all clones) than UCSD ( P < .0001). PD-L1 22C3 ( P = .02, HR: 0.36) and SP142 scores ( P = .046, HR: 0.27) predicted CSS on Kaplan–Meier analysis for SCC cases. Conclusions. UC, UCSD, and SCC are associated with different risk factors, gender distributions, and clinical outcomes. PD-L1 is expressed in SCC and UCSD, suggesting some patients may benefit from targeted therapy.

scholarly journals WISP1 and miR-29c-3p are novel prognostic biomarkers and therapeutic targets for bladder cancer

2021 ◽  
Author(s):  
Lihua Zhang ◽  
Zhuo Wang ◽  
Hongyi Zhou ◽  
Ming Zhu ◽  
Leilei Zhu ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Cell Lines ◽  
Tumor Size ◽  
In Silico ◽  
Cox Regression ◽  
Therapeutic Targets ◽  
Prognostic Biomarkers ◽  
Aberrant Expression ◽  
Cox Regression Analysis ◽  
Kaplan Meier

Abstract Background: Aberrant expression of WISP1 is associated with carcinogenesis; however, the expression and prognostic values of WISP1 in bladder cancer (BC) remain elusive. Therefore, the present study aimed to investigate the WISP1 expression in BC and explore the possible mechanisms and clinical value of WISP1 in BC. Methods: The in silico analysis based on oncomine and Kaplan-Meier Plotter databases were to reveal WISP1 expression and prognosis in BC. Besides, qRT-PCR, immunohistochemistry (IHC) and western blot assays were used to detect WISP1 expression both in BC tissues and BC cell lines. TargetScan database was used to predict miRNAs that putatively regulate the expression of WISP1. COX regression and the Kaplan-Meier method were applied to evaluate the prognostic value of WISP1 and miRNAs in BC.Results: WISP1 was up-regulated in BC and associated with poor survival in patients with BC through in silico analysis. Besides, WISP1 expression was identified to be up-regulated both in BC tissues and cell lines. We identified 13 miRNAs that putatively regulate the expression of WISP1. Of these miRNAs, only miR-29c-3p was found to be significantly negatively correlated with WISP1 in BC tissues. The correlation of in situ expressions of WISP1 and miR-29c-3p by immunohistochemistry (IHC) and clinical characteristics revealed that WISP1 was significantly associated with tumor size and hsa-miR-23b-3p expression, and miR-29c-3p was associated with tumor size, M stage, and WISP1 expression. Multivariate Cox regression analysis indicated that TNM stage and WISP1 expression were predictors of unfavorable prognosis, while hsa-miR-29c-3p was a predictor of favorable prognosis in patients with BC. Conclusions: Collectively, the findings indicated that WISP1 and miR-29c-3p might serve as novel prognostic biomarkers and potential therapeutic targets for BC.

Cisplatin versus carboplatin-based chemotherapy in inoperable or recurrent urothelial carcinoma: A retrospective analysis

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 14558-14558
Author(s):  
A. Bamias ◽  
E. Kastritis ◽  
G. Bozas ◽  
V. Koutsoukou ◽  
N. Antoniou ◽  
...  
Keyword(s):  
Urothelial Carcinoma ◽  
Combination Chemotherapy ◽  
Cox Regression ◽  
Distant Metastases ◽  
First Line ◽  
Cox Regression Analysis ◽  
The Poor ◽  
Kaplan Meier ◽  
Significant Difference ◽  
Poor Tolerance

14558 Background: Cisplatin-based chemotherapy represents the standard for patients with inoperable or recurrent urothelial carcinoma. Carboplatin-based chemotherapy is reserved for not-fit-for-cisplatin patients. Recent data suggest that carboplatin-based chemotherapy may be effective in fit-for-cisplatin patients. We examined the differences in the outcome according to the compound used as first-line treatment. Methods: We selected patients who received first-line combination chemotherapy based on cisplatin or carboplatin. The major end point was survival. Survival curves were estimated with the Kaplan-Meier method, while cox regression analysis was used for multivariate models. Results: 445 patients, treated with cisplatin (330) or carboplatin (115)-based chemotherapy were included in this analysis. After a median follow-up of 52 months, there was no significant difference in survival between the two treatment groups (Table). Subgroup analyses according to PS, distant metastases, Hb, weight loss, showed that the use of cisplatin was independently associated with improved survival only in the PS 2,3 subgroup (see Table). When patients were stratified according to the Bajorin prognostic criteria (PS 0,1 vs. 2,3 and/or distant metastases yes vs. no; J Clin Oncol 1999, 17: 3173), again cisplatin-based chemotherapy was associated with a trend towards improved outcome only in the worst prognostic group (Table). Conclusions: Carboplatin-based chemotherapy may be equally effective to cisplatin-based treatment in patients with inoperable or recurrent urothelial cancer and no or one adverse factors. Cisplatin-based treatment may be beneficial in patients with poor prognosis. Nevertheless, the clinical relevance of this superiority is limited due to the poor outcome and the poor tolerance of cisplatin-based combination chemotherapy in this group of patients. (see Table) Median survival (95% CI) after first-line chemotherapy for advanced urothelial carcinoma. [Table: see text] No significant financial relationships to disclose.

scholarly journals Predicting the difference in treatment response and survival time of lung adenocarcinoma patients based on a prognostic risk model of glycolysis-related genes

2021 ◽  
Author(s):  
Rongchang Zhao ◽  
Dan Ding ◽  
Yan Ding ◽  
Rongbo Han ◽  
Xiujuan Wang ◽  
...  
Keyword(s):  
High Risk ◽  
Lung Adenocarcinoma ◽  
Survival Time ◽  
Risk Score ◽  
Roc Curve ◽  
Cox Regression ◽  
Risk Group ◽  
Risk Groups ◽  
Low Risk ◽  
Significant Difference

Abstract Background Multiple factors affect the survival time of patients with lung adenocarcinoma (LUAD). Specifically, the therapeutic effect of medicines and the disease recurrence probability differs among patients with the same stage of LUAD. Thus, effective prognostic predictors need to be identified. Methods Based on the tumor mutation burden (TMB) data obtained by TCGA, LUAD was divided into high and low groups, and the differentially expressed glycolysis-related genes between the two groups were screened out. Cox regression was used to obtain a prognostic model. A receiver operating characteristic (ROC) curve and calibration curve were generated to evaluate the nomogram that was constructed based on clinicopathological characteristics and the risk score. Two datasets (GSE68465 and GSE11969) from Gene Expression Omnibus (GEO) were used to verify the prognostic performance of the gene. Furthermore, differences in immune cell distribution, immune-related molecules and drug susceptibility were assessed for their relationship with the risk score. Results We confirmed a 5-gene signature (FKBP4, HMMR, B4GALT1, ERO1L, ENO1) capable of dividing patients into two risk groups. There was a significant difference in overall survival (OS) times between the high-risk group and the low-risk group (P = 1.085e-4), with the low-risk group having a better survival outcome. Through multivariate Cox analysis, the risk score was confirmed to be an independent prognostic factor (HR = 1.289, 95% CI = 1.202-1.383, P < 0.001), and the ROC curve and nomogram exhibited accurate prediction performance. Validation of the data obtained in the GEO database yielded similar results. Additionally, there were significant differences in cisplatin, paclitaxel, gemcitabine, docetaxel, gefitiniband erlotinib sensitivity between the low-risk and high-risk groups. Conclusions Our results reveal that glycolysis-related gene are feasible predictors of LUAD patient survival and response to therapeutics.

scholarly journals Cohort study of the overall survival of patients with pancreatic cancer in a hospital of specialties of Quito-Ecuador in the period 2007–2017

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Andrés Moreno Roca ◽  
Luciana Armijos Acurio ◽  
Ruth Jimbo Sotomayor ◽  
Carlos Céspedes Rivadeneira ◽  
Carlos Rosero Reyes ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Cohort Study ◽  
Survival Time ◽  
Univariate Analysis ◽  
Rank Test ◽  
Kaplan Meier ◽  
Significant Difference ◽  
Icd 10 ◽  
The Difference ◽  
Clinical Records

Abstract Objectives Pancreatic cancers in most patients in Ecuador are diagnosed at an advanced stage of the disease, which is associated with lower survival. To determine the characteristics and global survival of pancreatic cancer patients in a social security hospital in Ecuador between 2007 and 2017. Methods A retrospective cohort study and a survival analysis were performed using all the available data in the electronic clinical records of patients with a diagnosis of pancreatic cancer in a Hospital of Specialties of Quito-Ecuador between 2007 and 2017. The included patients were those coded according to the ICD 10 between C25.0 and C25.9. Our univariate analysis calculated frequencies, measures of central tendency and dispersion. Through the Kaplan-Meier method we estimated the median time of survival and analyzed the difference in survival time among the different categories of our included variables. These differences were shown through the log rank test. Results A total of 357 patients diagnosed with pancreatic cancer between 2007 and 2017 were included in the study. More than two-thirds (69.9%) of the patients were diagnosed in late stages of the disease. The median survival time for all patients was of 4 months (P25: 2, P75: 8). Conclusions The statistically significant difference of survival time between types of treatment is the most relevant finding in this study, when comparing to all other types of treatments.

scholarly journals Comprehensive analysis of genomic mutation signature and tumor mutation burden for prognosis of intrahepatic cholangiocarcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rui Zhang ◽  
Qi Li ◽  
Jialu Fu ◽  
Zhechuan Jin ◽  
Jingbo Su ◽  
...  
Keyword(s):  
Intrahepatic Cholangiocarcinoma ◽  
Cox Regression ◽  
Tnm Stage ◽  
Gene Set Enrichment Analysis ◽  
Functional Enrichment ◽  
Tumor Mutation Burden ◽  
Kaplan Meier ◽  
Mutation Burden ◽  
Significant Difference ◽  
Genomic Mutation

Abstract Background Intrahepatic cholangiocarcinoma (iCCA) is a highly lethal malignancy of the biliary tract. Analysis of somatic mutational profiling can reveal new prognostic markers and actionable treatment targets. In this study, we explored the utility of genomic mutation signature and tumor mutation burden (TMB) in predicting prognosis in iCCA patients. Methods Whole-exome sequencing and corresponding clinical data were collected from the ICGC portal and cBioPortal database to detect the prognostic mutated genes and determine TMB values. To identify the hub prognostic mutant signature, we used Cox regression and Lasso feature selection. Mutation-related signature (MRS) was constructed using multivariate Cox regression. The predictive performances of MRS and TMB were assessed using Kaplan–Meier (KM) analysis and receiver operating characteristic (ROC). We performed a functional enrichment pathway analysis using gene set enrichment analysis (GSEA) for mutated genes. Based on the MRS, TMB, and the TNM stage, a nomogram was constructed to visualize prognosis in iCCA patients. Results The mutation landscape illustrated distributions of mutation frequencies and types in iCCA, and generated a list of most frequently mutated genes (such as Tp53, KRAS, ARID1A, and IDH1). Thirty-two mutated genes associated with overall survival (OS) were identified in iCCA patients. We obtained a six-gene signature using the Lasso and Cox method. AUCs for the MRS in the prediction of 1-, 3-, and 5-year OS were 0.759, 0.732, and 0.728, respectively. Kaplan–Meier analysis showed a significant difference in prognosis for patients with iCCA having a high and low MRS score (P < 0.001). GSEA was used to show that several signaling pathways, including MAPK, PI3K-AKT, and proteoglycan, were involved in cancer. Conversely, survival analysis indicated that TMB was significantly associated with prognosis. GSEA indicated that samples with high MRS or TMB also showed an upregulated expression of pathways involved in tumor signaling and the immune response. Finally, the predictive nomogram (that included MRS, TMB, and the TNM stage) demonstrated satisfactory performance in predicting survival in patients with iCCA. Conclusions Mutation-related signature and TMB were associated with prognosis in patients with iCCA. Our study provides a valuable prognostic predictor for determining outcomes in patients with iCCA.

scholarly journals EPDR1 is related to stages and metastasize in bladder cancer and can be used as a prognostic biomarker

BMC Urology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yue Yang ◽  
Hanchao Zhang ◽  
Zhengdao Liu ◽  
Faliang Zhao ◽  
Guobiao Liang
Keyword(s):  
Bladder Cancer ◽  
T Cells ◽  
Prognostic Biomarker ◽  
Transmembrane Protein ◽  
Tumor Stage ◽  
Receptor Interaction ◽  
Advanced Tumor Stage ◽  
Normal Bladder ◽  
Advanced Tumor ◽  
Significant Difference

AbstractBackgroundBladder cancer (BLCA) is a malignant urothelial carcinoma and has a high mortality rate. EPDR1 (ependymin related 1) is a type II transmembrane protein and related to calcium-dependent cell adhesion.MethodsWe explored the potential oncogenic roles of EPDR1 in BLCA basing on the multiple public datasets.ResultsWe found that EPDR1 expression had a significant difference in BLCA and adjacent normal bladder tissues, and the level of EPDR1was up-regulated with advanced tumor stage and metastasis in BLCA. Meanwhile, the high expression group of EPDR1 had a shorter OS compared to the low or medium expression-group. Furthermore, EPDR1 expression was associated with tumor-infiltrating immune cells (TIICs), including NK cells, CD8 + T cells, CD4 + T cells, Macrophages cells, and so on. Moreover, EPDR1 also involved in several signaling pathways as well as PI3K/AKT pathway, Cytokine receptor interaction, and apoptosis.ConclusionEPDR1 can be used as a novel prognostic biomarker as well as an effective target for diagnosis and treatment in BLCA.

Sign in / Sign up

Export Citation Format

Share Document