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https://www.readbyqxmd.com/read/27926792/the-transcription-factor-pparalpha-is-overexpressed-and-is-associated-with-a-favourable-prognosis-in-idh-wildtype-primary-glioblastoma
#1
H R Haynes, P White, K M Hares, J Redondo, K C Kemp, W G B Singleton, C L Killick-Cole, J R Stevens, K Garadi, S Guglani, A Wilkins, K M Kurian
AIMS: PPARα agonists are in current clinical use as hypolipidaemic agents and show significant antineoplastic effects in human glioblastoma models. To date however, the expression of PPARα in large-scale glioblastoma data sets has not been examined. We aimed to investigate the expression of the transcription factor PPARα in primary glioblastoma, the relationship between PPARα expression and patients' clinicopathological features and other molecular markers associated with gliomagenesis...
December 7, 2016: Histopathology
https://www.readbyqxmd.com/read/27926518/higher-programmed-cell-death-1-ligand-1-pd-l1-mrna-level-in-clear-cell-renal-cell-carcinomas-is-associated-with-a-favorable-outcome-due-to-the-active-immune-responses-in-tumor-tissues
#2
Xiang-Hui Ning, Yan-Qing Gong, Shi-Ming He, Teng Li, Jiang-Yi Wang, Shuang-He Peng, Jin-Chao Chen, Jia-Yuan Liu, Nie-Nie Qi, Ying-Lu Guo, Kan Gong
Renal cell carcinoma is one of the most common urological tumors. The role of programmed cell death 1 ligand 1 (PD-L1) in renal cell carcinomas in predicting outcome of the patients is yet unclear. We analyzed the clinical and RNA-seq data of 522 kidney clear cell cancer, 259 kidney papillary cell carcinoma and 66 kidney chromophobe patients from The Cancer Genome Atlas (TCGA) database. In kidney clear cell cancer patients with high PD-L1 mRNA level and low PD-L1 mRNA level in tumors, the median overall survival periods were 45...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27926484/high-lncrna-h19-expression-as-prognostic-indicator-data-mining-in-female-cancers-and-polling-analysis-in-non-female-cancers
#3
Li Peng, Xiao-Qing Yuan, Zhao-Yang Liu, Wen-Ling Li, Chao-Yang Zhang, Ya-Qin Zhang, Xi Pan, Jun Chen, Yue-Hui Li, Guan-Cheng Li
Upregulation of lncRNA H19 expression is associated with an unfavorable prognosis in some cancers. However, the prognostic value of H19 in female-specific cancers has remained uncharacterized. In this study, the prognostic power of high H19 expression in female cancer patients from the TCGA datasets was analyzed using Kaplan-Meier survival curves and Cox's proportional hazard modeling. In addition, in a meta-analysis of non-female cancer patients from TCGA datasets and 12 independent studies, hazard ratios (HRs) with 95% confidence interval (CI) for overall survival (OS) and disease-free survival (DFS)/relapse-free survival (RFS)/metastasis-free survival (MFS)/progression-free survival (PFS) were pooled to assess the prognostic value of high H19 expression...
December 1, 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
#4
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/27923592/developments-in-targeted-therapy-in-melanoma
#5
REVIEW
V C Amann, E Ramelyte, S Thurneysen, R Pitocco, N Bentele-Jaberg, S M Goldinger, R Dummer, J Mangana
Melanomas are disease entities driven in part by the mitogen activated protein kinase (MAPK) pathway. The TCGA network recently defined four genetic subtypes based on the most prevalent significantly mutated genes, including mutant BRAF, mutant RAS (N/H/K), mutant NF1, and Triple wild-type melanoma (harboring none of the aforementioned mutations, but instead includes KIT, GNA and GNAQ mutations). The successful development of kinase inhibitors marked a milestone in the treatment of metastatic melanoma. Combination treatment with a BRAF- and MEK-inhibitor is the current standard of care for inoperable stage IIIC/IV BRAF-mutated melanoma...
November 5, 2016: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/27923049/expression-of-lncrnas-in-low-grade-gliomas-and-glioblastoma-multiforme-an-in-silico-analysis
#6
Brian J Reon, Jordan Anaya, Ying Zhang, James Mandell, Benjamin Purow, Roger Abounader, Anindya Dutta
BACKGROUND: Each year, over 16,000 patients die from malignant brain cancer in the US. Long noncoding RNAs (lncRNAs) have recently been shown to play critical roles in regulating neurogenesis and brain tumor progression. To better understand the role of lncRNAs in brain cancer, we performed a global analysis to identify and characterize all annotated and novel lncRNAs in both grade II and III gliomas as well as grade IV glioblastomas (glioblastoma multiforme [GBM]). METHODS AND FINDINGS: We determined the expression of all lncRNAs in over 650 brain cancer and 70 normal brain tissue RNA sequencing datasets from The Cancer Genome Atlas (TCGA) and other publicly available datasets...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27923043/clonal-evolutionary-analysis-during-her2-blockade-in-her2-positive-inflammatory-breast-cancer-a-phase-ii-open-label-clinical-trial-of-afatinib-vinorelbine
#7
Gerald Goh, Ramona Schmid, Kelly Guiver, Wichit Arpornwirat, Imjai Chitapanarux, Vinod Ganju, Seock-Ah Im, Sung-Bae Kim, Arunee Dechaphunkul, Jedzada Maneechavakajorn, Neil Spector, Thomas Yau, Mehdi Afrit, Slim Ben Ahmed, Stephen R Johnston, Neil Gibson, Martina Uttenreuther-Fischer, Javier Herrero, Charles Swanton
BACKGROUND: Inflammatory breast cancer (IBC) is a rare, aggressive form of breast cancer associated with HER2 amplification, with high risk of metastasis and an estimated median survival of 2.9 y. We performed an open-label, single-arm phase II clinical trial (ClinicalTrials.gov NCT01325428) to investigate the efficacy and safety of afatinib, an irreversible ErbB family inhibitor, alone and in combination with vinorelbine in patients with HER2-positive IBC. This trial included prospectively planned exome analysis before and after afatinib monotherapy...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27911271/immunoglobulin-superfamily-genes-are-novel-prognostic-biomarkers-for-breast-cancer
#8
Yue Li, Maoni Guo, Zhenkun Fu, Peng Wang, Yan Zhang, Yue Gao, Ming Yue, Shangwei Ning, Dianjun Li
Breast cancer progression is associated with dysregulated expression of the immunoglobulin superfamily (IgSF) genes that are involved in cell-cell recognition, binding and adhesion. Despite widespread evidence that many IgSF genes could serve as effective biomarkers, this potential has not been realized because the studies have focused mostly on individual genes and not the entire network. To gain a global perspective of the IgSF-related biomarkers, we constructed an IgSF-directed neighbor network (IDNN) and an IgSF-directed driver network (IDDN) by integrating multiple levels of data, including IgSF genes, breast cancer driver genes, protein-protein interaction (PPI) networks and gene expression profiling data...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27910065/pathology-of-endometrial-carcinoma
#9
Sigurd F Lax
On a clinicopathological and molecular level, two distinctive types of endometrial carcinoma, type I and type II, can be distinguished. Endometrioid carcinoma, the typical type I carcinoma, seems to develop through an estrogen-driven "adenoma carcinoma" pathway from atypical endometrial hyperplasia/endometrioid intraepithelial neoplasia (AEH/EIN). It is associated with elevated serum estrogen and high body mass index and expresses estrogen and progesterone receptors. They are mostly low grade and show a favorable prognosis...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#10
Etienne De Braekeleer, Jean-Loup Huret, Hossain Mossafa, Philippe Dessen
The main databases devoted stricto sensu to cancer cytogenetics are the "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer" ( http://cgap.nci.nih.gov/Chromosomes/Mitelman ), the "Atlas of Genetics and Cytogenetics in Oncology and Haematology" ( http://atlasgeneticsoncology.org ), and COSMIC ( http://cancer.sanger.ac.uk/cosmic ).However, being a complex multistep process, cancer cytogenetics are broadened to "cytogenomics," with complementary resources on: general databases (nucleic acid and protein sequences databases; cartography browsers: GenBank, RefSeq, UCSC, Ensembl, UniProtKB, and Entrez Gene), cancer genomic portals associated with recent international integrated programs, such as TCGA or ICGC, other fusion genes databases, array CGH databases, copy number variation databases, and mutation databases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909050/notch-pathway-is-activated-via-genetic-and-epigenetic-alterations-and-is-a-therapeutic-target-in-clear-cell-renal-cancer
#11
Tushar D Bhagat, Yiyu Zou, Shizeng Huang, Jihwan Park, Matthew B Palmer, Caroline Hu, Wejuan Li, Niraj Shenoy, Orsolya Giricz, Gaurav Choudhary, Yiting Yu, Yi-An Ko, Maria C Izquierdo, Ae Seo Deok Park, Nishanth Vallumsetla, Remi Laurence, Robert Lopez, Masako Suzuki, James Pullman, Justin Kaner, Benjamin Gartrell, A Ari Hakimi, John M Greally, Bharvin Patel, Karim Benhadji, Kith Pradhan, Amit Verma, Katalin Susztak
Clear cell renal cell carcinoma (CCRCC) is an incurable malignancy in advanced stages and needs newer therapeutic targets. Transcriptomic analysis of CCRCCs and matched microdissected renal tubular controls revealed overexpression of NOTCH ligands and receptors in tumor tissues. Examination of the TCGA RNA-seq dataset also revealed widespread activation of NOTCH pathway in a large cohort of CCRCC samples. Samples with NOTCH pathway activation were also clinically distinct and were associated with better overall survival...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27908706/highly-expressed-nrsn2-is-related-to-malignant-phenotype-in-ovarian-cancer
#12
Wenbin Tang, Aimin Ren, Hongyang Xiao, Huizhen Sun, Bin Li
Neurensin-2 (NRSN2) is a 24KD protein, which is reported located in the membrane, while its biological functions remain unknown, not to mention in the field of tumor biology. In current study, we aimed to analyze the functions of NRSN2 in ovarian cancer. We screened TCGA database and surprisingly found that its copy number and mRNA level are gained and heightened respectively in parts of serous ovarian cancer patients. In current study, both loss- and gain- function assays found that NRSN2 is associated with the malignant phenotype in ovarian cancer cells, because NRSN2 plays a remarkable role in anchorage-independent colony formation, subcutaneous tumor formation, cell invasion, and chemoresistance...
November 28, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27905892/mir-491-regulates-glioma-cells-proliferation-by-targeting-trim28-in-vitro
#13
Zengxin Qi, Shengyong Cai, Jiajun Cai, Lingchao Chen, Yu Yao, Liang Chen, Ying Mao
BACKGROUND: MicroRNAs are significantly involved in tumorigenesis and progression of glioma. However, the critical part they play in glioma have not been fully elaborated. miR-491 and Tripartite motif containing 28 (TRIM28) are reported to aberrantly express in glioblastoma multiforme (GBM). Here, we detected miR-491 and TRIM28 expression and function in glioma cells. METHODS: We analyzed miR-491 expressions in 20 primary human GBM tissues and 6 control brain tissues by qRT-PCR assays and searched for The Cancer Genome Atlas (TCGA) database...
December 1, 2016: BMC Neurology
https://www.readbyqxmd.com/read/27904773/upregulation-of-fam83d-promotes-malignant-phenotypes-of-lung-adenocarcinoma-by-regulating-cell-cycle
#14
Run Shi, Jing Sun, Qi Sun, Quanli Zhang, Wenjie Xia, Gaochao Dong, Anpeng Wang, Feng Jiang, Lin Xu
The family with sequence similarity 83, member D (FAM83D) gene is upregulated in hepatocellular carcinoma and ovarian cancer, and its overexpression has been reported to positively correlate with tumor progression. However, the clinical significance and biological function of FAM83D in lung adenocarcinoma has not been investigated. We determined the expression profile and clinical significance of FAM83D using The Cancer Genome Atlas (TCGA) and immunohistochemistry (IHC) analysis. Considerable upregulation of FAM83D was observed in LUAD tissues compared with adjacent normal tissues, and its overexpression was significantly associated with more advanced clinicopathological characteristics...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27903974/lncrnas-are-altered-in-lung-squamous-cell-carcinoma-and-lung-adenocarcinoma
#15
Bing Liu, Yifei Chen, Jiong Yang
Long non-coding RNAs (lncRNAs) have been implicated in pathogenesis of various cancers, including lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD). We used cBioPortal to analyze lncRNA alteration frequencies and their ability to predict overall survival (OS) using 504 LUSC and 522 LUAD samples from The Cancer Genome Atlas (TCGA) database. In LUSC, 624 lncRNAs had alteration rates > 1% and 64 > 10%. In LUAD 625 lncRNAs had alteration rates > 1% and 36 > 10%. Among those, 620 lncRNAs had alteration frequencies > 1% in both LUSC and LUAD, while 22 were LUSC-specific and 23 were LUAD-specific...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27903973/association-of-a-cytarabine-chemosensitivity-related-gene-expression-signature-with-survival-in-cytogenetically-normal-acute-myeloid-leukemia
#16
Han Yan, Lu Wen, Dan Tan, Pan Xie, Feng-Mei Pang, Hong-Hao Zhou, Wei Zhang, Zhao-Qian Liu, Jie Tang, Xi Li, Xiao-Ping Chen
The prognosis of cytogenetically normal acute myeloid leukemia (CN-AML) varies greatly among patients. Achievement of complete remission (CR) after chemotherapy is indispensable for a better prognosis. To develop a gene signature predicting overall survival (OS) in CN-AML, we performed data mining procedure based on whole genome expression data of both blood cancer cell lines and AML patients from open access database. A gene expression signature including 42 probes was derived. These probes were significantly associated with both cytarabine half maximal inhibitory concentration values in blood cancer cell lines and OS in CN-AML patients...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27903500/primary-resistance-to-pd-1-blockade-mediated-by-jak%C3%A2-mutations
#17
Daniel Sanghoon Shin, Jesse M Zaretsky, Helena Escuin-Ordinas, Angel Garcia-Diaz, Siwen Hu-Lieskovan, Anusha Kalbasi, Catherine S Grasso, Willy Hugo, Salemiz Sandoval, Davis Y Torrejon, Nicolaos Palaskas, Gabriel Abril Rodriguez, Giulia Parisi, Ariel Azhdam, Bartosz Chmielowski, Grace Cherry, Elizabeth Seja, Beata Berent-Maoz, I Peter Shintaku, Dung Thi Le, Drew M Pardoll, Luis A Diaz, Paul C Tumeh, Thomas G Graeber, Roger S Lo, Begoña Comin-Anduix, Antoni Ribas
Loss of function mutations in JAK½ can lead to acquired resistance to anti-programmed death protein 1 (PD-1) therapy. We reasoned they may also be involved in primary resistance to anti-PD-1 therapy. JAK½ inactivating mutations were noted in tumor biopsies of 1 of 23 patients with melanoma and in 1 of 16 patients with mismatch repair deficient colon cancer treated with PD-1 blockade. Both cases had a high mutational load but did not respond to anti-PD-1 therapy. Two out of 48 human melanoma cell lines had JAK½ mutations, which led to lack of PD-L1 expression upon interferon gamma exposure mediated by inability to signal through the interferon gamma receptor pathway...
November 30, 2016: Cancer Discovery
https://www.readbyqxmd.com/read/27903243/analysis-of-rna-expression-of-normal-and-cancer-tissues-reveals-high-correlation-of-cop9-gene-expression-with-respiratory-chain-complex-components
#18
Christina A Wicker, Tadahide Izumi
BACKGROUND: The COP9 signalosome, composed of eight subunits, is implicated in cancer genetics with its deneddylase activity to modulate cellular concentration of oncogenic proteins such as IkB and TGFβ. However, its function in the normal cell physiology remains elusive. Primarily focusing on gene expression data of the normal tissues of the head and neck, the cancer genome atlas (TCGA) database was used to identify groups of genes that were expressed synergistically with the COP9 genes, particularly with the COPS5 (CSN5), which possesses the catalytic activity of COP9...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27902969/rac1-gtp-ase-signals-wnt-beta-catenin-pathway-mediated-integrin-directed-metastasis-associated-tumor-cell-phenotypes-in-triple-negative-breast-cancers
#19
Pradip De, Jennifer H Carlson, Tyler Jepperson, Scooter Willis, Brian Leyland-Jones, Nandini Dey
The acquisition of integrin-directed metastasis-associated (ID-MA) phenotypes by Triple-Negative Breast Cancer (TNBC) cells is caused by an upregulation of the Wnt-beta-catenin pathway (WP). We reported that WP is one of the salient genetic features of TNBC. RAC-GTPases, small G-proteins which transduce signals from cell surface proteins including integrins, have been implicated in tumorigenesis and metastasis by their role in essential cellular functions like motility. The collective percentage of alteration(s) in RAC1 in ER+ve BC was lower as compared to ER-ve BC (35% vs 57%) (brca/tcga/pub2015)...
November 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27900679/bioinformatic-profiling-identifies-a-glucose-related-risk-signature-for-the-malignancy-of-glioma-and-the-survival-of-patients
#20
Shihong Zhao, Jinquan Cai, Jianlong Li, Guiqiu Bao, Di Li, Yongli Li, Xiuwei Zhai, Chuanlu Jiang, Lihua Fan
The aim of this study is to investigate the glucose metabolic status and its prognostic value in glioma. The Chinese Glioma Genome Atlas (CGGA), The Cancer Genome Atlas (TCGA), and GSE16011 datasets were used to develop the glucose-related signature. A cohort of 305 glioma samples with whole genome microarray expression data from the Chinese Glioma Genome Atlas database was included for discovery. TCGA and GSE16011 datasets were used for validation. Gene Set Enrichment Analysis (GSEA) and Cytoscape were used to explore the bioinformatic implication...
November 29, 2016: Molecular Neurobiology
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