keyword
MENU ▼
Read by QxMD icon Read
search

Tcga prostate

keyword
https://www.readbyqxmd.com/read/29295717/cribriform-and-intraductal-prostate-cancer-are-associated-with-increased-genomic-instability-and-distinct-genomic-alterations
#1
René Böttcher, Charlotte F Kweldam, Julie Livingstone, Emilie Lalonde, Takafumi N Yamaguchi, Vincent Huang, Fouad Yousif, Michael Fraser, Robert G Bristow, Theodorus van der Kwast, Paul C Boutros, Guido Jenster, Geert J L H van Leenders
BACKGROUND: Invasive cribriform and intraductal carcinoma (CR/IDC) is associated with adverse outcome of prostate cancer patients. The aim of this study was to determine the molecular aberrations associated with CR/IDC in primary prostate cancer, focusing on genomic instability and somatic copy number alterations (CNA). METHODS: Whole-slide images of The Cancer Genome Atlas Project (TCGA, N = 260) and the Canadian Prostate Cancer Genome Network (CPC-GENE, N = 199) radical prostatectomy datasets were reviewed for Gleason score (GS) and presence of CR/IDC...
January 2, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29245927/a-bioinformatics-to-clinic-sequential-approach-to-analysis-of-prostate-cancer-biomarkers-using-tcga-datasets-and-clinical-samples-a-new-method-for-precision-oncology
#2
Hidekazu Yoshie, Anna S Sedukhina, Kimino Minagawa, Keiko Oda, Shigeko Ohnuma, Nobuyuki Yanagisawa, Ichiro Maeda, Masayuki Takagi, Hiroya Kudo, Ryuto Nakazawa, Hideo Sasaki, Toshio Kumai, Tatsuya Chikaraishi, Ko Sato
Biomarker-driven cancer therapy has met with significant clinical success. Identification of a biomarker implicated in a malignant phenotype and linked to poor clinical outcome is required if we are to develop these types of therapies. A subset of prostate adenocarcinoma (PACa) cases are treatment-resistant, making them an attractive target for such an approach. To identify target molecules implicated in shorter survival of patients with PACa, we established a bioinformatics-to-clinic sequential analysis approach, beginning with 2-step in silico analysis of a TCGA dataset for localized PACa...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29233929/single-cell-rna-seq-reveals-a-subpopulation-of-prostate-cancer-cells-with-enhanced-cell-cycle-related-transcription-and-attenuated-androgen-response
#3
Aaron M Horning, Yao Wang, Che-Kuang Lin, Anna D Louie, Rohit R Jadhav, Chia-Nung Hung, Chiou-Miin Wang, Chun-Lin Lin, Nameer B Kirma, Michael A Liss, Addanki P Kumar, LuZhe Sun, Zhijie Liu, Wei-Ting Chao, Qianben Wang, Victor X Jin, Chun-Liang Chen, Tim H-M Huang
Increasing evidence suggests the presence of minor cell subpopulations in prostate cancer that are androgen independent and poised for selection as dominant clones after androgen-deprivation therapy. In this study, we investigated this phenomenon by stratifying cell subpopulations based on transcriptome profiling of 144 single LNCaP prostate cancer cells treated or untreated with androgen after cell cycle synchronization. Model-based clustering of 397 differentially expressed genes identified eight potential subpopulations of LNCaP cells, revealing a previously unappreciable level of cellular heterogeneity to androgen stimulation...
December 12, 2017: Cancer Research
https://www.readbyqxmd.com/read/29212506/chromosome-9p-copy-number-gains-involving-pd-l1-are-associated-with-a-specific-proliferation-and-immune-modulating-gene-expression-program-active-across-major-cancer-types
#4
Jan Budczies, Carsten Denkert, Balázs Győrffy, Peter Schirmacher, Albrecht Stenzinger
BACKGROUND: Inhibition of the PD-L1/PD-1 immune checkpoint axis represents one of the most promising approaches of immunotherapy for various cancer types. However, immune checkpoint inhibition is successful only in subpopulations of patients emphasizing the need for powerful biomarkers that adequately reflect the complex interaction between the tumor and the immune system. Recently, recurrent copy number gains (CNG) in chromosome 9p involving PD-L1 were detected in many cancer types including lung cancer, melanoma, bladder cancer, head and neck cancer, cervical cancer, soft tissue sarcoma, prostate cancer, gastric cancer, ovarian cancer, and triple-negative breast cancer...
December 6, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29207133/potential-role-of-microrna%C3%A2-223%C3%A2-3p-in-the-tumorigenesis-of-hepatocellular-carcinoma-a-comprehensive-study-based-on-data-mining-and-bioinformatics
#5
Rui Zhang, Li-Jie Zhang, Mei-Ling Yang, Lan-Shan Huang, Gang Chen, Zhen-Bo Feng
The aims of the present study were to examine the potential role of microRNA‑233‑3p (miR)‑223‑3p in the tumorigenesis of hepatocellular carcinoma (HCC), and to investigate its diagnostic accuracy and potential molecular mechanisms. The expression data of miR‑223‑3p in HCC were obtained from the Gene Expression Omnibus (GEO). Data for the precursor miR‑223 were obtained from The Cancer Genome Atlas (TCGA). The diagnostic role of miR‑223‑3p was identified by the receiver operating curve (ROC), and the diagnostic value of miR‑223‑3p in HCC was calculated from qualified reports in the literature...
November 27, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29206234/markers-of-epithelial-to-mesenchymal-transition-reflect-tumor-biology-according-to-patient-age-and-gleason-score-in-prostate-cancer
#6
Dorota Jędroszka, Magdalena Orzechowska, Raneem Hamouz, Karolina Górniak, Andrzej K Bednarek
INTRODUCTION: Prostate carcinoma (PRAD) is one of the most frequently diagnosed malignancies amongst men worldwide. It is well-known that androgen receptor (AR) plays a pivotal role in a vast majority of prostate tumors. However, recent evidence emerged stating that estrogen receptors (ERs) may also contribute to prostate tumor development. Moreover, progression and aggressiveness of prostate cancer may be associated with differential expression genes of epithelial-to-mesenchymal transition (EMT)...
2017: PloS One
https://www.readbyqxmd.com/read/29196733/regulation-of-hmgb3-by-antitumor-mir-205-5p-inhibits-cancer-cell-aggressiveness-and-is-involved-in-prostate-cancer-pathogenesis
#7
Yasutaka Yamada, Rika Nishikawa, Mayuko Kato, Atsushi Okato, Takayuki Arai, Satoko Kojima, Kazuto Yamazaki, Yukio Naya, Tomohiko Ichikawa, Naohiko Seki
Our recent determination of a microRNA (miRNA) expression signature in prostate cancer (PCa) revealed that miR-205-5p was significantly reduced in PCa tissues and that it acted as an antitumor miRNA. The aim of this study was to identify oncogenic genes and pathways in PCa cells that were regulated by antitumor miR-205-5p. Genome-wide gene expression analyses and in silico miRNA database searches showed that 37 genes were putative targets of miR-205-5p regulation. Among those genes, elevated expression levels of seven in particular (HMGB3, SPARC, MKI67, CENPF, CDK1, RHOU, and POLR2D) were associated with a shorter disease-free survival in a large number of patients in the The Cancer Genome Atlas (TCGA) database...
December 1, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29187560/multi-omics-approach-reveals-distinct-differences-in-left-and-right-sided-colon-cancer
#8
Wangxiong Hu, Yanmei Yang, Xiaofen Li, Minran Huang, Fei Xu, Weiting Ge, Suzhan Zhang, Shu Zheng
Increasing evidence suggests that left-sided colon cancer (LCC) and right-sided colon cancer (RCC) are emerging as two different colorectal cancer (CRC) types with distinct clinical characteristics. However, the discrepancy in the underlying molecular event between these types of cancer has not been thoroughly elucidated to date and warrants comprehensive investigation. To this end, an integrated data set from The Cancer Genome Atlas (TCGA) was used to compare and contrast LCC and RCC, covering mutation, DNA methylation, gene expression, and miRNA...
November 29, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29186328/meta-analytic-principal-component-analysis-in-integrative-omics-application
#9
SungHwan Kim, Dongwan Kang, Zhiguang Huo, Yongseok Park, George C Tseng
Motivation: With the prevalent usage of microarray and massively parallel sequencing, numerous high-throughput omics datasets have become available in the public domain. Integrating abundant information among omics datasets is critical to elucidate biological mechanisms. Due to the high-dimensional nature of the data, methods such as principal component analysis (PCA) have been widely applied, aiming at effective dimension reduction and exploratory visualization. Results: In this paper, we combine multiple omics datasets of identical or similar biological hypothesis and introduce two variations of meta-analytic framework of PCA, namely MetaPCA...
November 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29151113/cpne1-is-a-useful-prognostic-marker-and-is-associated-with-tnf-receptor-associated-factor-2-traf2-expression-in-prostate-cancer
#10
Jiabei Liang, Jian Zhang, Jun Ruan, Yuanyuan Mi, Qiang Hu, Zhirong Wang, Bingbing Wei
BACKGROUND CPNE1 plays a vital role in regulating cell differentiation. The clinical and biological values of CPNE1 in prostate cancer are still unclear. The aim of this study was to investigate the clinicopathological value of CPNE1 and the association of CPNE1 with TRAF2 expression in patients with prostate cancer. MATERIAL AND METHODS CPNE1 expression in prostate cancer was analyzed using Gene Expression Omnibus (GEO) databases. The Cancer Genome Atlas (TCGA) dataset was used to investigate the association of CPNE1 expression with TRAF2 expression in prostate cancer...
November 19, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29141691/involvement-of-aberrantly-activated-hotair-ezh2-mir-193a-feedback-loop-in-progression-of-prostate-cancer
#11
Zhixin Ling, Xiaoyan Wang, Tao Tao, Lei Zhang, Han Guan, Zonghao You, Kai Lu, Guangyuan Zhang, Shuqiu Chen, Jianping Wu, Jinke Qian, Hui Liu, Bin Xu, Ming Chen
BACKGROUND: Though androgen deprivation therapy is the standard treatment for prostate cancer (PCa), most patients would inevitably progress to castration-resistant prostate cancer (CRPC) which is the main cause of PCa death. Therefore, the identification of novel molecular mechanism regulating cancer progression and achievement of new insight into target therapy would be necessary for improving the benefits of PCa patients. This study aims to study the function and regulatory mechanism of HOTAIR/EZH2/miR-193a feedback loop in PCa progression...
November 15, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29137428/pten-loss-is-associated-with-prostate-cancer-recurrence-and-alterations-in-tumor-dna-methylation-profiles
#12
Milan S Geybels, Min Fang, Jonathan L Wright, Xiaoyu Qu, Marina Bibikova, Brandy Klotzle, Jian-Bing Fan, Ziding Feng, Elaine A Ostrander, Peter S Nelson, Janet L Stanford
Background: Prostate cancer (PCa) with loss of the tumor suppressor gene PTEN has an unfavorable prognosis. DNA methylation profiles associated with PTEN loss may provide further insights into the mechanisms underlying these more aggressive, clinically relevant tumors. Methods: The cohort included patients with clinically localized PCa. Samples taken from the primary tumor were used to determine PTEN genomic deletions using FISH, and to analyze epigenome-wide DNA methylation profiles...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29073199/reduced-expression-of-iqgap2-and-higher-expression-of-iqgap3-correlates-with-poor-prognosis-in-cancers
#13
Dinesh Kumar, Md Khurshidul Hassan, Niharika Pattnaik, Nachiketa Mohapatra, Manjusha Dixit
IQGAPs is a family of proteins which comprises three members, in humans. The expression pattern and role of IQGAP1 has been well established in many cancers, whereas those of IQGAP2 and IQGAP3, have mostly remained unexplored. We used available large datasets, to explore the pan-cancer status of these two genes in-silico. Here we have analysed their mRNA expression and correlation with survivability in eight different cancers, including lung, breast, gastric, brain, colorectal, prostate, liver and kidney cancers and, their subtypes...
2017: PloS One
https://www.readbyqxmd.com/read/29021619/pan-cancer-analysis-of-bi-allelic-alterations-in-homologous-recombination-dna-repair-genes
#14
Nadeem Riaz, Pedro Blecua, Raymond S Lim, Ronglai Shen, Daniel S Higginson, Nils Weinhold, Larry Norton, Britta Weigelt, Simon N Powell, Jorge S Reis-Filho
BRCA1 and BRCA2 are involved in homologous recombination (HR) DNA repair and are germ-line cancer pre-disposition genes that result in a syndrome of hereditary breast and ovarian cancer (HBOC). Whether germ-line or somatic alterations in these genes or other members of the HR pathway and if mono- or bi-allelic alterations of HR-related genes have a phenotypic impact on other cancers remains to be fully elucidated. Here, we perform a pan-cancer analysis of The Cancer Genome Atlas (TCGA) data set and observe that bi-allelic pathogenic alterations in homologous recombination (HR) DNA repair-related genes are prevalent across many malignancies...
October 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28938548/promoter-dna-methylation-analysis-reveals-a-combined-diagnosis-of-cpg-based-biomarker-for-prostate-cancer
#15
Yuanyuan Tang, Shusuan Jiang, Yinmin Gu, Weidong Li, Zengnan Mo, Yuanjie Huang, Tianyu Li, Yanling Hu
BACKGROUND: Prostate cancer (PCa) is the most common tumor in elderly men. However, the specificity and sensitivity of serum prostate-specific antigen levels in PCa diagnosis are controversial. This study aims to reveal a novel diagnosis biomarker in PCa. MATERIALS AND METHODS: The differential methylated CpG sites between 423 primary PCa and 39 adjacent samples from The Cancer Genome Atlas (TCGA) on Illumina HumanMethylation 450 platform were analyzed. The diagnostic methylation markers were mined using the Prediction Analysis of Microarrays package in Bioconductor...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28923030/the-eef1a2-gene-expression-as-risk-predictor-in-localized-prostate-cancer
#16
Thomas Stefan Worst, Frank Waldbillig, Abdallah Abdelhadi, Cleo-Aron Weis, Maria Gottschalt, Annette Steidler, Jost von Hardenberg, Maurice Stephan Michel, Philipp Erben
BACKGROUND: Besides clinical stage and Gleason score, risk-stratification of prostate cancer in the pretherapeutic setting mainly relies on the serum PSA level. Yet, this is associated with many uncertainties. With regard to therapy decision-making, additional markers are needed to allow an exact risk prediction. Eukaryotic translation elongation factor 1 alpha 2 (EEF1A2) was previously suggested as driver of tumor progression and potential biomarker. In the present study its functional and prognostic relevance in prostate cancer was investigated...
September 18, 2017: BMC Urology
https://www.readbyqxmd.com/read/28912897/genomic-analysis-of-tumor-microenvironment-immune-types-across-14-solid-cancer-types-immunotherapeutic-implications
#17
Yu-Pei Chen, Yu Zhang, Jia-Wei Lv, Ying-Qin Li, Ya-Qin Wang, Qing-Mei He, Xiao-Jing Yang, Ying Sun, Yan-Ping Mao, Jing-Ping Yun, Na Liu, Jun Ma
We performed a comprehensive immuno-genomic analysis of tumor microenvironment immune types (TMITs), which is classified into four groups based on PD-L1+CD8A or PD-L1+cytolytic activity (CYT) expression, across a broad spectrum of solid tumors in order to help identify patients who will benefit from anti- PD-1/PD-L1 therapy. The mRNA sequencing data from The Cancer Genome Atlas (TCGA) of 14 solid cancer types representing 6,685 tumor samples was analyzed. TMIT was classified only for those tumor types that both PD-L1 and CD8A/CYT could prefict mutation and/or neoantigen number...
2017: Theranostics
https://www.readbyqxmd.com/read/28910345/circulating-mrnas-and-mirnas-as-candidate-markers-for-the-diagnosis-and-prognosis-of-prostate-cancer
#18
MULTICENTER STUDY
Marilesia Ferreira de Souza, Hellen Kuasne, Mateus de Camargo Barros-Filho, Heloísa Lizotti Cilião, Fabio Albuquerque Marchi, Paulo Emilio Fuganti, Alexandre Rossi Paschoal, Silvia Regina Rogatto, Ilce Mara de Syllos Cólus
Circulating nucleic acids are found in free form in body fluids and may serve as minimally invasive tools for cancer diagnosis and prognosis. Only a few studies have investigated the potential application of circulating mRNAs and microRNAs (miRNAs) in prostate cancer (PCa). The Cancer Genome Atlas (TCGA) database was used for an in silico analysis to identify circulating mRNA and miRNA as potential markers of PCa. A total of 2,267 genes and 49 miRNAs were differentially expressed between normal and tumor samples...
2017: PloS One
https://www.readbyqxmd.com/read/28870994/conditional-deletion-of-ell2-induces-murine-prostate-intraepithelial-neoplasia
#19
Laura E Pascal, Khalid Z Masoodi, June Liu, Xiaonan Qiu, Qiong Song, Yujuan Wang, Yachen Zang, Tiejun Yang, Yao Wang, Lora H Rigatti, Uma Chandran, Leandro M Colli, Ricardo Z N Vencio, Yi Lu, Jian Zhang, Zhou Wang
Elongation factor, RNA polymerase II, 2 (ELL2) is an RNA Pol II elongation factor with functional properties similar to ELL that can interact with the prostate tumor suppressor EAF2. In the prostate, ELL2 is an androgen response gene that is upregulated in benign prostatic hyperplasia (BPH). We recently showed that ELL2 loss could enhance prostate cancer cell proliferation and migration, and that ELL2 gene expression was downregulated in high Gleason score prostate cancer specimens. Here, prostate-specific deletion of ELL2 in a mouse model revealed a potential role for ELL2 as a prostate tumor suppressor in vivoEll2-knockout mice exhibited prostatic defects including increased epithelial proliferation, vascularity and PIN lesions similar to the previously determined prostate phenotype in Eaf2-knockout mice...
November 2017: Journal of Endocrinology
https://www.readbyqxmd.com/read/28855498/traf2-is-a-valuable-prognostic-biomarker-in-patients-with-prostate-cancer
#20
Bingbing Wei, Jiabei Liang, Jimeng Hu, Yuanyuan Mi, Jun Ruan, Jian Zhang, Zhirong Wang, Qiang Hu, Haowen Jiang, Qiang Ding
BACKGROUND TRAF2 exerts important functions in regulating the development and progression of cancer. The aim of this study is to investigate whether TRAF2 is a valuable prognostic biomarker and to determine if it regulates TRAIL-induced apoptosis in prostate cancer. MATERIAL AND METHODS Microarray gene expression data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to determine TRAF2 expression in prostate cancer. TRAF2 expression in prostate cancer was further investigated by immunohistochemistry assay...
August 31, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
keyword
keyword
71087
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"