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https://www.readbyqxmd.com/read/29151929/identification-of-circular-rna-signature-in-bladder-cancer
#1
Xiao Yang, Wenbo Yuan, Jun Tao, Peng Li, Chengdi Yang, Xiaheng Deng, Xiaolei Zhang, Jingyuan Tang, Jie Han, Jingzi Wang, Pengchao Li, Qiang Lu, Min Gu
Circular RNA (circRNA) comprises a class of endogenous species of RNA consisting of a circular loop that is crucial for genetic and epigenetic regulation. The significance of circRNA in bladder cancer (BCa) remains to be investigated. Here we performed genome‑wide circRNA analysis of 5 paired tumour and adjacent normal tissue samples from BCa patients via next generation sequencing (NGS) technology. Next we confirmed NGS data in a separate set of 32 paired BCa samples using quantitative real-time reverse transcription polymerase chain reaction...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/29141603/detect-i-detect-ii-a-study-protocol-for-a-prospective-multicentre-observational-study-to-validate-the-uromark-assay-for-the-detection-of-bladder-cancer-from-urinary-cells
#2
Wei Shen Tan, Andrew Feber, Liqin Dong, Rachael Sarpong, Sheida Rezaee, Simon Rodney, Pramit Khetrapal, Patricia de Winter, Frelyn Ocampo, Rumana Jalil, Norman R Williams, Chris Brew-Graves, John D Kelly
BACKGROUND: Haematuria is a common finding in general practice which requires visual inspection of the bladder by cystoscopy as well as upper tract imaging. In addition, patients with non-muscle invasive bladder cancer (NMIBC) often require surveillance cystoscopy as often as three monthly depending on disease risk. However, cystoscopy is an invasive procedure which is uncomfortable, requires hospital attendance and is associated with a risk of urinary tract infection. We have developed the UroMark assay, which can detect 150 methylation specific alteration specific to bladder cancer using DNA from urinary sediment cells...
November 15, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29121415/efficacy-and-safety-of-trametinib-in-japanese-patients-with-advanced-biliary-tract-cancers-refractory-to-gemcitabine
#3
Masafumi Ikeda, Tatsuya Ioka, Akira Fukutomi, Chigusa Morizane, Akiyoshi Kasuga, Hideaki Takahashi, Akiko Todaka, Takuji Okusaka, Caretha L Creasy, Shelby Gorman, Daniel J Felitsky, Mikiro Kobayashi, Fanghong Zhang, Junji Furuse
Gemcitabine-based therapy remains the mainstay of treatment for patients with biliary tract cancers (BTCs) with no second-line treatment(s) established yet. Aberrant activation of MAPK pathway in patients with BTC indicates its importance in BTC. Trametinib is a potent, highly selective, allosteric non-competitive inhibitor of MEK1/MEK2. In this Phase IIa open-label, single-arm study, we investigated efficacy and safety of trametinib in Japanese patients with advanced BTC refractory to gemcitabine-based therapy...
November 9, 2017: Cancer Science
https://www.readbyqxmd.com/read/29119511/a-method-for-cross-species-visualization-and-analysis-of-rna-sequence-data
#4
Stephen A Ramsey
In this methods article, I describe a computational workflow for cross-species visualization and comparison of mRNA-seq transcriptome profiling data. The workflow is based on gene set variation analysis (GSVA) and is illustrated using commands in the R programming language. I provide a complete step-by-step procedure for the workflow using mRNA-seq data sets from dog and human bladder cancer as an example.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29119388/potentialities-of-microrna-diagnosis-in-patients-with-bladder-cancer
#5
P V Shegay, A A Zhavoronkov, N M Gaifullin, N V Vorob'ev, B Ya Alekseev, S V Popov, A V Garazha, A A Buzdin, A D Kaprin
Despite promising vista of the use of microRNA in molecular diagnosis of bladder cancer, there are few data on their expression profiles, which impedes assessment of diagnostic value of these marker molecules. In this study, suppression subtractive hybridization, on-chip hybridization, and high-throughput deep sequencing focused on profiling microRNA and assessing the diagnostic value of revealed marker molecules.
November 9, 2017: Bulletin of Experimental Biology and Medicine
https://www.readbyqxmd.com/read/29107929/viral-sequences-in-human-cancer
#6
Paul G Cantalupo, Joshua P Katz, James M Pipas
We have developed a virus detection and discovery computational pipeline, Pickaxe, and applied it to NGS databases provided by The Cancer Genome Atlas (TCGA). We analyzed a collection of whole genome (WGS), exome (WXS), and RNA (RNA-Seq) sequencing libraries from 3052 participants across 22 different cancers. NGS data from nearly all tumor and normal tissues examined contained contaminating viral sequences. Intensive computational and manual efforts are required to remove these artifacts. We found that several different types of cancers harbored Herpesviruses including EBV, CMV, HHV1, HHV2, HHV6 and HHV7...
November 3, 2017: Virology
https://www.readbyqxmd.com/read/29067547/low-levels-of-psma-expression-limit-the-utility-of-18-f-dcfpyl-pet-ct-for-imaging-urothelial-carcinoma
#7
Scott P Campbell, Alexander S Baras, Mark W Ball, Max Kates, Noah M Hahn, Trinity J Bivalacqua, Michael H Johnson, Martin G Pomper, Mohamad E Allaf, Steven P Rowe, Michael A Gorin
OBJECTIVE: To explore the clinical utility of PSMA-targeted (18)F-DCFPyL PET/CT in patients with metastatic urothelial carcinoma. METHODS: Three patients with metastatic urothelial carcinoma were imaged with (18)F-DCFPyL PET/CT. All lesions with perceptible radiotracer uptake above background were considered positive. Maximum standardized uptake values were recorded for each detected lesion and findings on (18)F-DCFPyL PET/CT were compared to those on conventional imaging studies...
October 24, 2017: Annals of Nuclear Medicine
https://www.readbyqxmd.com/read/29061046/visual-label-free-telomerase-activity-monitor-via-enzymatic-etching-of-gold-nanorods
#8
Haitang Yang, Anran Liu, Min Wei, Yuanjian Liu, Bingjing Lv, Wei Wei, Yuanjian Zhang, Songqin Liu
Early diagnosis and life-long surveillance are clinically important to improve the long-term survival of cancer patients. Telomerase activity is a valuable biomarker for cancer diagnosis, but its measurement often used complex label procedures. Herein, we designed a novel, simple, visual and label-free method for telomerase detection by using enzymatic etching of gold nanorods (GNRs). First, repeating (TTAGGG)x sequences were extented on telomerase substrate (TS) primer. It formed G-quadruplex under the help of Hemin and K(+)...
November 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29047227/telomerase-reverse-transcriptase-tert-promoter-mutations-are-rare-in-urachal-cancer
#9
Sebastian Thiem, Thomas Herold, Ulrich Krafft, Felix Bremmer, Yuri Tolkach, Attila M Szász, Joerg Kriegsmann, Nadine T Gaisa, Christian Niedworok, Tibor Szarvas, Henning Reis
High rates of telomerase reverse transcriptase (TERT) promoter mutations have recently been described in urothelial carcinoma (UC). Unlike UC in the bladder, adenocarcinomas account for the majority of urachal cancer (UrC) cases. As data in UrC is unclear, we analyzed TERT promoter mutations in a large cohort of UrC for its differential diagnostic, clinicopathological and prognostic significance. UrC cases from six academic centers were analyzed for c.-146C>T (C250T) and c.-124C>T (C228T) TERT promoter mutations by PCR and Sanger sequencing...
October 19, 2017: Pathology International
https://www.readbyqxmd.com/read/29023722/prevalence-and-clonality-of-synchronous-primary-carcinomas-in-the-bladder-and-prostate
#10
Ying Jing, Ruiyun Zhang, Pengfei Ma, Mei-Chun Cai, Guanglei Zhuang, Haige Chen
Incidental prostate adenocarcinoma (IPCa) has been frequently discovered during postoperative histopathological evaluation of radical cystoprostatectomy specimens in patients with bladder cancer (BCa). However, there is currently no conclusive study addressing the clinical significance of IPCa and the clonal relatedness of IPCa and BCa. Here, we performed a retrospective single-center review of 919 BCa cases and an additional meta-analysis including a total of 19,868 individuals who underwent radical cystectomy for bladder cancer...
October 11, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28987698/diagnostic-performance-of-mri-for-prediction-of-muscle-invasiveness-of-bladder-cancer-a-systematic-review-and-meta-analysis
#11
Sungmin Woo, Chong Hyun Suh, Sang Youn Kim, Jeong Yeon Cho, Seung Hyup Kim
PURPOSE: To review the diagnostic performance of ≥1.5-T MRI for local staging of bladder cancer. METHODS: MEDLINE and EMBASE were searched up to February 21, 2017. We included diagnostic accuracy studies published since 2000 that used ≥1.5-T MRI for local staging (≥T2 [muscle-invasive]) in patients with bladder cancer, using pathology as the reference standard. The methodological quality was assessed using Quality Assessment of Diagnostic Accuracy Studies-2...
October 2017: European Journal of Radiology
https://www.readbyqxmd.com/read/28977858/identification-of-hmex-3a-and-its-effect-on-human-bladder-cancer-cell-proliferation
#12
Ying Huang, Chao Fang, Jing-Wen Shi, Yu Wen, Da Liu
In this study, hMex-3A was selected from TCGA database as a research object to observe the effects of small interfering RNA (siRNA) targeting hMex-3A on the biological activities of human bladder cancer and explore its mechanism for the first time. In this study, there were 2 groups including negative control group and hMex-3A-siRNA-transfected cells group for 5637 and T24 cell lines, respectively. After bladder cancer cells were transfected with the interference RNA sequence, proliferation of transfected cells were assessed by Celigo Cell Counting, and apoptosis were detected by flow cytometry...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28976501/bladder-cancer-drug-sequencing-in-metastatic-disease
#13
Clemens Thoma
No abstract text is available yet for this article.
November 2017: Nature Reviews. Urology
https://www.readbyqxmd.com/read/28976369/regression-and-statistical-shape-model-based-substitute-ct-generation-for-mri-alone-external-beam-radiation-therapy-from-standard-clinical-mri-sequences
#14
Soumya Ghose, Peter B Greer, Jidi Sun, Peter Pichler, David Rivest-Henault, Jhimli Mitra, Haylea Richardson, Chris Wratten, Jarad Martin, Jameen Arm, Leah Best, Jason A Dowling
In MR only radiation therapy planning, generation of the tissue specific HU map directly from the MRI may improve radiation therapy planning. The aim of the work is to generate and validate substitute CT (sCT) scans generated from standard T2 weighted MR pelvic scans in prostate radiation therapy dose planning. A Siemens Skyra 3T MRI scanner with laser bridge, flat couch and pelvic coil mounts was used to scan 39 patients scheduled for external beam radiation therapy for localized prostate cancer. For sCT generation a whole pelvis MRI was acquired...
October 4, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28974397/comprehensive-genomic-sequencing-of-urothelial-tumors-identifies-rare-smarcb1-ini-1-deficient-carcinomas-of-the-urinary%C3%A2-system
#15
Sumati Gupta, Daniel Albertson, David Gaston, Marta E Heilbrun, Neeraj Agarwal, Ken Boucher, Timothy J Parnell, Ting Liu, Alicia Morgans, Russell Madison, Kyle Gowen, Vincent A Miller, Jeffrey S Ross, Siraj M Ali, Sherri Z Millis
PURPOSE: Tumor genomic profiling helps direct therapy for advanced urothelial carcinoma (UC). In the course of clinical care, we encountered a patient with a complete loss of SMARCB1 (switch/sucrose nonfermentable-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1), which encodes INI-1 (integrase interactor 1), as the sole detected driver of their urinary tract tumor. Our objective was the identification and genomic characterization of urinary tract neoplasia with complete SMARCB1 loss...
September 7, 2017: Clinical Genitourinary Cancer
https://www.readbyqxmd.com/read/28970362/functional-impact-of-chromatin-remodeling-gene-mutations-and-predictive-signature-for-therapeutic-response-in-bladder-cancer
#16
Jason E Duex, Kalin E Swain, Garrett M Dancik, Richard D Paucek, Charles Owens, Mair E A Churchill, Dan Theodorescu
Urothelial carcinoma accounts for most the of bladder cancer cases. Using next-generation sequencing (NGS) technologies we found that a significant percentage (83%) of tumors had mutations in chromatin remodeling genes. Here, we examined the functional relevance of mutations in two chromatin remodeling genes, EP300 and its paralog, CREBBP, which are mutated in almost a third of patients. Interestingly, almost half of missense mutations cluster in the histone-acetyltransferase (HAT) domain of EP300/CREBBP. This domain catalyzes the transfer of an acetyl group to target molecules such as histones, thereby regulating chromatin dynamics...
October 2, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28958829/monitoring-treatment-response-and-metastatic-relapse-in-advanced-bladder-cancer-by-liquid-biopsy-analysis
#17
Karin Birkenkamp-Demtröder, Emil Christensen, Iver Nordentoft, Michael Knudsen, Ann Taber, Søren Høyer, Philippe Lamy, Mads Agerbæk, Jørgen Bjerggaard Jensen, Lars Dyrskjøt
Of the patients undergoing radical cystectomy, 20-80% experience relapse. Minimally invasive methods for early detection of metastatic relapse after cystectomy and for monitoring ongoing therapy are urgently needed to improve individualised follow-up and treatment. Therefore, we evaluated the use of circulating tumour DNA (ctDNA) in plasma and urine to detect metastatic relapse after cystectomy and measure treatment efficacy. We exome sequenced tumour and germline DNA from patients with muscle-invasive bladder cancer and monitored ctDNA in 370 liquid biopsies throughout the disease courses by 84 personalised digital droplet polymerase chain reaction assays targeting 61 genes...
September 25, 2017: European Urology
https://www.readbyqxmd.com/read/28927152/expression-levels-of-fgfr3-as-a-prognostic-marker-for-the-progression-of-primary-pt1-bladder-cancer-and-its-association-with-mutation-status
#18
Ho Won Kang, Ye-Hwan Kim, Pildu Jeong, Cheol Park, Won Tae Kim, Dong Hee Ryu, Eun-Jong Cha, Yun-Sok Ha, Tae-Hwan Kim, Tae Gyun Kwon, Sung-Kwon Moon, Yung Hyun Choi, Seok-Joong Yun, Wun-Jae Kim
The present study examined the utility of fibroblast growth factor receptor 3 (FGFR3) mutation status and gene expression as a prognostic marker in primary pT1 bladder cancer (BC). A total of 120 patients with primary pT1 BC were enrolled. FGFR3 mutation status was determined by direct sequencing and FGFR3 mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis. The results were compared with the clinicopathological parameters, and the prognostic value of FGFR3 was evaluated by Kaplan-Meier analysis and a multivariate Cox regression test...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28917596/response-rate-to-chemotherapy-after-immune-checkpoint-inhibition-in-metastatic-urothelial-cancer
#19
Bernadett Szabados, Nick van Dijk, Yen Zhi Tang, Michiel S van der Heijden, Akhila Wimalasingham, Alfonso Gomez de Liano, Simon Chowdhury, Simon Hughes, Sarah Rudman, Mark Linch, Thomas Powles
Immune checkpoint inhibitors (ICIs) are active in metastatic urothelial carcinoma (MUC). They have joined chemotherapy (CT) as a standard of care. Here, we investigate the activity of CT after progression on ICIs. Two cohorts of sequential patients with MUC were described (n=28). Cohort A received first-line ICIs followed by CT after progression. Cohort B received CT after failure of first-line platinum-based CT followed by ICIs. Response rate (RR) to CT was assessed using Response Evaluation Criteria in Solid Tumors (RECIST v1...
September 13, 2017: European Urology
https://www.readbyqxmd.com/read/28916750/comprehensive-multiregional-analysis-of-molecular-heterogeneity-in-bladder-cancer
#20
Mathilde Borg Houlberg Thomsen, Iver Nordentoft, Philippe Lamy, Søren Vang, Line Reinert, Christophe Kamungu Mapendano, Søren Høyer, Torben F Ørntoft, Jørgen Bjerggaard Jensen, Lars Dyrskjøt
Genetic alterations identified in adjacent normal appearing tissue in bladder cancer patients are indicative of a field disease. Here we assessed normal urothelium transformation and intra-tumour heterogeneity (ITH) in four patients with bladder cancer. Exome sequencing identified private acquired mutations in a lymph node metastasis and local recurrences. Deep re-sequencing revealed presence of at least three and four subclones in two patients with multifocal disease, while no demarcation of subclones was identified in the two patients with unifocal disease...
September 15, 2017: Scientific Reports
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