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https://www.readbyqxmd.com/read/28324890/regulation-of-itga3-by-the-dual-stranded-microrna-199-family-as-a-potential-prognostic-marker-in-bladder-cancer
#1
Takashi Sakaguchi, Hirofumi Yoshino, Masaya Yonemori, Kazutaka Miyamoto, Satoshi Sugita, Ryosuke Matsushita, Toshihiko Itesako, Shuichi Tatarano, Masayuki Nakagawa, Hideki Enokida
BACKGROUND: Based on the microRNA (miRNA) signature of bladder cancer (BC) by deep sequencing, we recently found that several double-stranded mature miRNAs derived from the same pre-miRNAs were sufficiently expressed and acted as tumour suppressors by regulating common target genes in BC. Our deep-sequencing signature of BC showed that all miR-199 family members (miR-199a-3p/-5p and miR-199b-3p/-5p) were also downregulated. We hypothesised that these miRNAs may function as tumour suppressors by regulating common target genes...
March 21, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28321693/age-at-diagnosis-obesity-smoking-and-molecular-subtypes-in-muscle-invasive-bladder-cancer
#2
Xuezheng Sun, Katherine A Hoadley, William Y Kim, Helena Furberg, Andrew F Olshan, Melissa A Troester
BACKGROUND: Heterogeneity of muscle-invasive bladder cancer (MIBC) has been characterized using whole-genome mRNA expression data, showing distinct molecular and clinicopathological characteristics by subtypes. However, associations between risk factors and molecular subtypes have not been reported. METHODS: Four previously published schemes were used to categorize molecular subtypes in 372 MIBC patients from the Cancer Genome Atlas (TCGA). Data on gene expression (RNA-seq), demographic, and clinicopathological characteristics were retrieved through TCGA data portal...
March 20, 2017: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/28319171/a-reported-20-gene-expression-signature-to-predict-lymph-node-positive-disease-at-radical-cystectomy-for-muscle-invasive-bladder-cancer-is-clinically-not-applicable
#3
Kim E M van Kessel, Harmen J G van de Werken, Irene Lurkin, Angelique C J Ziel-van der Made, Ellen C Zwarthoff, Joost L Boormans
BACKGROUND: Neoadjuvant chemotherapy (NAC) for muscle-invasive bladder cancer (MIBC) provides a small but significant survival benefit. Nevertheless, controversies on applying NAC remain because the limited benefit must be weight against chemotherapy-related toxicity and the delay of definitive local treatment. Therefore, there is a clear clinical need for tools to guide treatment decisions on NAC in MIBC. Here, we aimed to validate a previously reported 20-gene expression signature that predicted lymph node-positive disease at radical cystectomy in clinically node-negative MIBC patients, which would be a justification for upfront chemotherapy...
2017: PloS One
https://www.readbyqxmd.com/read/28291637/is-the-cancer-genome-atlas-tcga-bladder-cancer-cohort-representative-of-invasive-bladder-cancer
#4
Roland Seiler, Peter C Black, George Thalmann, Arnulf Stenzl, Tilman Todenhöfer
PURPOSE: The Cancer Genome Atlas (TCGA) Research Consortium has conducted a comprehensive molecular characterization of invasive bladder cancer (BCa). This open-access dataset has become the critical reference for studying biomarkers and mechanisms of disease in BCa. In order for this data to be considered representative, and to allow comparisons of markers between cohorts, clinicopathologic characteristics of this cohort need to conform to those established for this disease state. The aim of this study was to critically evaluate clinicopathologic characteristics and outcomes of the TCGA BCa cohort in comparison with published cystectomy series...
March 10, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28207521/quantitative-assessment-of-the-relationship-between-rassf1a-gene-promoter-methylation-and-bladder-cancer-prisma
#5
Leyun Zhan, Bingyi Zhang, Yaojun Tan, Chengliang Yang, Chenhong Huang, Qiongya Wu, Yulin Zhang, Xiaobo Chen, Mi Zhou, Aihua Shu
BACKGROUND: Methylation of the Ras-association domain family 1 isoform A (RASSF1A) gene promoter region is thought to participate in the initiation and development of many different cancers. However, in bladder cancer the role of RASSF1A methylation was unclear. To evaluate the relationship between RASSF1A methylation and bladder cancer, a quantitative assessment of an independent meta-analysis was performed. In addition, a DNA methylation microarray database from the cancer genome atlas (TCGA) project was used to validate the results of the meta-analysis...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28167242/epigenome-wide-dna-methylation-profiling-identifies-differential-methylation-biomarkers-in-high-grade-bladder-cancer
#6
Ekaterina Olkhov-Mitsel, Andrea J Savio, Ken J Kron, Vaijayanti V Pethe, Thomas Hermanns, Neil E Fleshner, Bas W van Rhijn, Theodorus H van der Kwast, Alexandre R Zlotta, Bharati Bapat
Epigenetic changes, including CpG island hypermethylation, occur frequently in bladder cancer (BC) and may be exploited for BC detection and distinction between high-grade (HG) and low-grade (LG) disease. Genome-wide methylation analysis was performed using Agilent Human CpG Island Microarrays to determine epigenetic differences between LG and HG cases. Pathway enrichment analysis and functional annotation determined that the most frequently methylated pathways in HG BC were enriched for anterior/posterior pattern specification, embryonic skeletal system development, neuron fate commitment, DNA binding, and transcription factor activity...
April 2017: Translational Oncology
https://www.readbyqxmd.com/read/28060759/a-potential-prognostic-lncrna-signature-for-predicting-survival-in-patients-with-bladder-urothelial-carcinoma
#7
Zhenyu Bao, Weitao Zhang, Dong Dong
Increasing evidence has highlighted the critical roles of long non-coding RNA (lncRNA) in cancer development and progression. However, the prognostic power of expression-based lncRNA signature for predicting overall survival in patients with Bladder Urothelial Carcinoma (BLCA) has not been investigated. Here, we performed a comprehensive analysis for lncRNA expression profiles and corresponding clinical information of 234 BLCA patients from The Cancer Genome Atlas (TCGA). We established a set of four-lncRNAs that were significantly associated with BLCA patients' survival...
February 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28039401/smoking-correlates-with-increased-cytoskeletal-protein-related-coding-region-mutations-in-the-lung-and-head-and-neck-datasets-of-the-cancer-genome-atlas
#8
John M Yavorski, George Blanck
Cancer from smoking tobacco is considered dependent on mutagens, but significant molecular aspects of smoking-specific, cancer development remain unknown. We defined sets of coding regions for oncoproteins, tumor suppressor proteins, and cytoskeletal-related proteins that were compared between nonsmokers and smokers, for mutation occurrences, in the lung adenocarcinoma (LUAD), head and neck squamous carcinoma (HNSC), bladder carcinoma (BLCA), and pancreatic adenocarcinoma ( PAAD) datasets from the cancer genome atlas (TCGA)...
December 2016: Physiological Reports
https://www.readbyqxmd.com/read/27966459/the-transcription-levels-and-prognostic-values-of-seven-proteasome-alpha-subunits-in-human-cancers
#9
Yunhai Li, Jing Huang, Jiazheng Sun, Shili Xiang, Dejuan Yang, Xuedong Ying, Mengqi Lu, Hongzhong Li, Guosheng Ren
Proteasome alpha subunits (PSMAs) have been shown to participate in the malignant progression of human cancers. However, the expression patterns and prognostic values of individual PSMAs remain elusive in most cancers. In the present study, we investigated the mRNA expression levels of seven PSMAs in different kinds of cancers using Oncomine and The Cancer Genome Atlas (TCGA) databases. The prognostic significance of PSMAs was also determined by Kaplan-Meier Plotter and PrognScan databases. Combined with Oncomine and TCGA, the mRNA expression levels of PSMA1-7 were significantly upregulated in breast, lung, gastric, bladder and head and neck cancer compared with normal tissues...
December 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27924948/foxa1-gata3-and-ppar%C3%A9-cooperate-to-drive-luminal-subtype-in-bladder-cancer-a-molecular-analysis-of-established-human-cell-lines
#10
Joshua I Warrick, Vonn Walter, Hironobu Yamashita, Eunah Chung, Lauren Shuman, Vasty Osei Amponsa, Zongyu Zheng, Wilson Chan, Tiffany L Whitcomb, Feng Yue, Tejaswi Iyyanki, Yuka I Kawasawa, Matthew Kaag, Wansong Guo, Jay D Raman, Joo-Seop Park, David J DeGraff
Discrete bladder cancer molecular subtypes exhibit differential clinical aggressiveness and therapeutic response, which may have significant implications for identifying novel treatments for this common malignancy. However, research is hindered by the lack of suitable models to study each subtype. To address this limitation, we classified bladder cancer cell lines into molecular subtypes using publically available data in the Cancer Cell Line Encyclopedia (CCLE), guided by genomic characterization of bladder cancer by The Cancer Genome Atlas (TCGA)...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27863388/comprehensive-analysis-of-aberrantly-expressed-profiles-of-lncrnas-and-mirnas-with-associated-cerna-network-in-muscle-invasive-bladder-cancer
#11
Hanbo Wang, Leilei Niu, Shaobo Jiang, Jing Zhai, Ping Wang, Feng Kong, Xunbo Jin
Although initially thought to be transcriptional noise, long noncoding RNAs (lncRNAs) are gaining increased attention in human cancers as its diversity function. At present, lncRNAs are regarded as the main part of competing endogenous RNA (ceRNA) network due to its regulation on protein-coding gene expression by acting as miRNA sponges. However, functional roles of lncRNA-mediated ceRNAs in muscle-invasive bladder cancer remain unclear. To clarify relevant potential mechanisms, here we comprehensively compared the expression profiles of mRNAs, lncRNAs and miRNAs between 322 muscle-invasive bladder cancer tissues and 19 non-tumor bladder tissues, based on the Cancer Genome Atlas (TCGA)...
November 15, 2016: Oncotarget
https://www.readbyqxmd.com/read/27845906/specific-micro-rna-expression-patterns-distinguish-the-basal-and-luminal-subtypes-of-muscle-invasive-bladder-cancer
#12
Andrea E Ochoa, Woonyoung Choi, Xiaoping Su, Arlene Siefker-Radtke, Bogdan Czerniak, Colin Dinney, David J McConkey
The roles of non-coding RNAs in controlling clinical and biological heterogeneity in bladder cancer remain unclear. We used TCGA's published dataset (n = 405 tumors) as a discovery cohort and created a new validation cohort to define the miRNA expression patterns in the basal and luminal molecular subtypes of muscle-invasive bladder cancer (MIBC). We identified 63 miRNAs by PAM, which optimally identified basal and luminal tumors. The targets of the top luminal miRNAs were activators of EMT (ZEB1, ZEB2) and basal subtype transcription (IL-6, EGFR, STAT3), whereas the targets of the top basal miRNAs were involved in adipogenesis pathways and luminal breast cancer (ERBB2, ERBB3)...
November 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27836246/emerging-role-of-immunotherapy-in-urothelial-carcinoma-immunobiology-biomarkers
#13
REVIEW
Randy F Sweis, Matthew D Galsky
Urothelial bladder cancer is one of the first cancers recognized to be immunogenic since 40 years ago when the use of bacillus Calmette-Guerin was shown to prevent recurrence. Since that time, our knowledge of immune biology of cancer has expanded tremendously, and patients with bladder cancer finally have new active immunotherapeutic drugs on the horizon. Anti-programmed cell death-1 (PD-1)/programmed cell death ligand-1 (PD-L1) therapy has shown impressively durable responses in urothelial bladder cancer (UBC), but the reported response rates warrant improvement...
December 2016: Urologic Oncology
https://www.readbyqxmd.com/read/27818121/evidence-for-apobec3b-mrna-and-protein-expression-in-oral-squamous-cell-carcinomas
#14
Galinos Fanourakis, Konstantinos Tosios, Nikolaos Papanikolaou, Ioulia Chatzistamou, Marios Xydous, Sofia Tseleni-Balafouta, Alexandra Sklavounou, Gerassimos E Voutsinas, Heleni Vastardis
It has been demonstrated that APOBEC3B possesses cytidine deaminase activity, which is likely to result in C-to-T signature mutations. Increased expression of the APOBEC3B gene has been shown to correlate with higher incidence of such mutations in various cancer types, such as breast, bladder, lung, and head and neck carcinomas. In the current study, we used in silico methods, immunohistochemistry and qRT-PCR to detect the presence of APOBEC3B signature mutations and examine the levels and patterns of APOBEC3B expression in oral squamous cell carcinomas (OSCCs)...
December 2016: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/27804056/smoking-status-usual-adult-occupation-and-risk-of-recurrent-urothelial-bladder-carcinoma-data-from-the-cancer-genome-atlas-tcga-project
#15
Amber N Wilcox, Debra T Silverman, Melissa C Friesen, Sarah J Locke, Daniel E Russ, Noorie Hyun, Joanne S Colt, Jonine D Figueroa, Nathaniel Rothman, Lee E Moore, Stella Koutros
PURPOSE: Tobacco smoking and occupational exposures are the leading risk factors for developing urothelial bladder carcinoma (UBC), yet little is known about the contribution of these two factors to risk of UBC recurrence. We evaluated whether smoking status and usual adult occupation are associated with time to UBC recurrence for 406 patients with muscle-invasive bladder cancer submitted to The Cancer Genome Atlas (TCGA) project. METHODS: Kaplan-Meier and Cox proportional hazard methods were used to assess the association between smoking status, employment in a high-risk occupation for bladder cancer, occupational diesel exhaust exposure, and 2010 Standard Occupational Classification group and time to UBC recurrence...
December 2016: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/27695045/tumor-specific-epigenetic-silencing-of-corticotropin-releasing-hormone-binding-protein-in-renal-cell-carcinoma-association-of-hypermethylation-and-metastasis
#16
Hossein Tezval, Natalia Dubrowinskaja, Inga Peters, Christel Reese, Katrin Serth, Faranaz Atschekzei, Jörg Hennenlotter, Arnulf Stenzl, Markus A Kuczyk, Jürgen Serth
The relevance of Corticotropin Releasing Hormone (CRH)-system in human malignancies is a question of growing interest. Here we investigated hypermethylation and epigenetic silencing of the CRH-Binding Protein (CRHBP) gene in clear cell renal cell cancer (ccRCC). Relative methylation of the CRHBP CpG island (CGI) was determined in 17 tumor cell lines as well as 86 ccRCC samples and 66 paired normal tissues using pyrosequencing and quantitative methylation specific PCR of bisulfite converted DNA. Results were statistically compared with relative mRNA expression levels of CRHBP and clinicopathological parameters of patients...
2016: PloS One
https://www.readbyqxmd.com/read/27669755/fibroblast-growth-factor-receptor-fgfr-alterations-in-squamous-differentiated-bladder-cancer-a-putative-therapeutic-target-for-a-small-subgroup
#17
Philipp H Baldia, Angela Maurer, Timon Heide, Michael Rose, Robert Stoehr, Arndt Hartmann, Sarah V Williams, Margaret A Knowles, Ruth Knuechel, Nadine T Gaisa
Although drugable fibroblast growth factor receptor (FGFR) alterations in squamous cell carcinomas (SCC) of various entities are well known, little is known about FGFR modifications in squamous differentiated bladder cancer. Therefore, our study evaluated FGFR1-3 alterations as a putative therapeutic target in this subgroup. We analyzed 73 squamous differentiated bladder cancers (n = 10 pT2, n = 55 pT3, n = 8 pT4) for FGFR1-3 protein expression, FGFR1-3 copy number variations, FGFR3 chromosomal rearrangements (fluorescence in situ hybridization (FISH)) and FGFR3 mutations (SNapShot analysis)...
September 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/27649287/ephrin-b2-overexpression-predicts-for-poor-prognosis-and-response-to-therapy-in-solid-tumors
#18
Ayman Oweida, Shilpa Bhatia, Kellen Hirsch, Dylan Calame, Anastacia Griego, Steve Keysar, Todd Pitts, Jaspreet Sharma, Gail Eckhardt, Antonio Jimeno, Xiao Jing Wang, Gill Parkash, Joseph Califano, Sana D Karam
Ephrin B2 is variably expressed on tumor cells and its blockade has been shown to inhibit angiogenesis in animal models of pancreatic, colorectal, lung and head, and neck squamous cell carcinomas. However, the implications of ephrinB2 expression in cancer patients have remained elusive. In this study, we analyzed the cancer genome atlas (TCGA) for ephrinB2 expression. We report significant correlations between EFNB2 expression, overall survival and disease-free survival in head and neck squamous cell carcinoma (HNSCC, n = 519), pancreatic adenocarcinoma (n = 186), and bladder urothelial carcinoma (n = 410)...
March 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/27612592/meta-analysis-of-the-luminal-and-basal-subtypes-of-bladder-cancer-and-the-identification-of-signature-immunohistochemical-markers-for-clinical-use
#19
Vipulkumar Dadhania, Miao Zhang, Li Zhang, Jolanta Bondaruk, Tadeusz Majewski, Arlene Siefker-Radtke, Charles C Guo, Colin Dinney, David E Cogdell, Shizhen Zhang, Sangkyou Lee, June G Lee, John N Weinstein, Keith Baggerly, David McConkey, Bogdan Czerniak
BACKGROUND: It has been suggested that bladder cancer can be divided into two molecular subtypes referred to as luminal and basal with distinct clinical behaviors and sensitivities to chemotherapy. We aimed to validate these subtypes in several clinical cohorts and identify signature immunohistochemical markers that would permit simple and cost-effective classification of the disease in primary care centers. METHODS: We analyzed genomic expression profiles of bladder cancer in three cohorts of fresh frozen tumor samples: MD Anderson (n=132), Lund (n=308), and The Cancer Genome Atlas (TCGA) (n=408) to validate the expression signatures of luminal and basal subtypes and relate them to clinical follow-up data...
October 2016: EBioMedicine
https://www.readbyqxmd.com/read/27381624/the-doppelg%C3%A3-nger-effect-hidden-duplicates-in-databases-of-transcriptome-profiles
#20
Levi Waldron, Markus Riester, Marcel Ramos, Giovanni Parmigiani, Michael Birrer
Whole-genome analysis of cancer specimens is commonplace, and investigators frequently share or re-use specimens in later studies. Duplicate expression profiles in public databases will impact re-analysis if left undetected, a so-called "doppelgänger" effect. We propose a method that should be routine practice to accurately match duplicate cancer transcriptomes when nucleotide-level sequence data are unavailable, even for samples profiled by different microarray technologies or by both microarray and RNA sequencing...
November 2016: Journal of the National Cancer Institute
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