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The cancer genome atlas

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https://www.readbyqxmd.com/read/29679906/microrna-876-5p-inhibits-epithelial-mesenchymal-transition-and-metastasis-of-hepatocellular-carcinoma-by-targeting-bcl6-corepressor-like-1
#1
Qiuran Xu, Qiaojuan Zhu, Zhenyu Zhou, Yufeng Wang, Xin Liu, Guozhi Yin, Xiangmin Tong, Kangsheng Tu
Our previous study has reported that BCL6 corepressor like 1 (BCORL1) plays an oncogenic role in hepatocellular carcinoma (HCC) via promoting epithelial-mesenchymal transition (EMT) and tumor metastasis. However, the regulation of BCORL1 mediated by microRNAs (miRNAs) remains poorly known. The analysis of our clinical samples indicated that BCORL1 expression was markedly higher in HCC tissues than that in tumor-adjacent normal tissues. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets revealed that high BCORL1 expression associated with high tumor grade, advanced tumor stage and poor survival of HCC patients...
April 18, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29678899/zfas1-functions-as-an-oncogenic-long-noncoding-rna-in-bladder-cancer
#2
Haifan Yang, Ge Li, Bo Cheng, Rui Jiang
Long non-coding RNA ZFAS1 has been suggested to function as an oncogenic role in the tumorigenesis of human malignant tumors. However, the expression status and biological function of ZFAS1 in bladder cancer is still unknown. Thus, the purpose of this study is to explore the clinical value of ZFAS1 in bladder cancer patient, and the biological function of ZFAS1 in bladder cancer cell. In the present study, we found ZFAS1 expression was increased in bladder cancer tissues compared with paired adjacent normal tissues through analyzing the Cancer Genome Atlas database...
April 20, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29678742/a-six-gene-based-prognostic-signature-for-hepatocellular-carcinoma-overall-survival-prediction
#3
Zhenglu Wang, Dahong Teng, Yan Li, Zhandong Hu, Lei Liu, Hong Zheng
AIMS: The purpose of this study was to propose a pipeline to identify prognostic signature for HCC overall survival (OS) prediction based on HCC gene expression datasets from The Cancer Genome Atlas (TCGA). RESULTS: Differential expression analysis identified 3573 genes aberrantly expressed (DEGs) in HCC samples. Univariate cox regression analysis obtained 1605 and 1067 HCC OS and relapse free survival (RFS) related genes, which are abbreviated as OS-Gene and RFS-Gene respectively...
April 17, 2018: Life Sciences
https://www.readbyqxmd.com/read/29676997/mining-tcga-database-for-genes-of-prognostic-value-in-glioblastoma-microenvironment
#4
Di Jia, Shenglan Li, Dali Li, Haipeng Xue, Dan Yang, Ying Liu
Glioblastoma (GBM) is one of the most deadly brain tumors. The convenient access to The Cancer Genome Atlas (TCGA) database allows for large-scale global gene expression profiling and database mining for potential correlation between genes and overall survival of a variety of malignancies including GBM. Previous reports have shown that tumor microenvironment cells and the extent of infiltrating immune and stromal cells in tumors contribute significantly to prognosis. Immune scores and stromal scores calculated based on the ESTIMATE algorithm could facilitate the quantification of the immune and stromal components in a tumor...
April 16, 2018: Aging
https://www.readbyqxmd.com/read/29673952/expression-of-c19mc-mirnas-in-hcc-associates-with-stem-cell-features-and-the-cancer-testis-genes-signature
#5
Claudia Augello, Federico Colombo, Andrea Terrasi, Elena Trombetta, Marco Maggioni, Laura Porretti, Giorgio Rossi, Silvana Guerneri, Rosamaria Silipigni, Silvano Bosari, Valentina Vaira
BACKGROUND: Intratumor heterogeneity of hepatocellular carcinoma (HCC) and, among HCC cell subsets, the cancer stem cell population (hCSC), is responsible for therapeutic resistance and disease relapse. AIMS: To characterize hCSC-enriched HCCs at the molecular level. METHODS: Side population (SP) was used to identify the hCSCs in multiple tumor sampling from different patients and primary HCCs cultures. FACS was used to immunoprofile cultures...
March 30, 2018: Digestive and Liver Disease
https://www.readbyqxmd.com/read/29673323/indel-detection-from-dna-and-rna-sequencing-data-with-transindel
#6
Rendong Yang, Jamie L Van Etten, Scott M Dehm
BACKGROUND: Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indels from splicing events in RNA-seq data. RESULTS: Here, we developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29672926/insights-into-the-etiology-associated-gene-regulatory-networks-in-hepatocellular-carcinoma-from-the-cancer-genome-atlas
#7
Veerabrahma Pratap Seshachalam, Karthik Sekar, Kam M Hui
BACKGROUND AND AIM: Hepatitis B virus, hepatitis C virus, alcoholic consumption and non-alcoholic fatty liver are the major known risk factors for Hepatocellular carcinoma (HCC). There have been very few studies comparing the underlying biological mechanisms associated with the different etiologies of HCC. In this study, we hypothesized the existence of different regulatory networks associated with different liver disease etiologies involved in hepatocarcinogenesis. METHODS: Using upstream regulatory analysis tool in ingenuity pathway analysis software, URs were predicted using differential expressed genes for HCC to facilitate the interrogation of global gene regulation...
April 19, 2018: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/29670856/cdkn2a-copy-number-loss-is-an-independent-prognostic-factor-in-hpv-negative-head-and-neck-squamous-cell-carcinoma
#8
William S Chen, Ranjit S Bindra, Allen Mo, Thomas Hayman, Zain Husain, Joseph N Contessa, Stephen G Gaffney, Jeffrey P Townsend, James B Yu
Background: HPV infection is associated with high p16 expression and good prognosis in head and neck squamous cell carcinomas (HNSCCs). Analysis of CDKN2A, the gene encoding p16, may further elucidate the association between p16 expression and prognosis. We sought to determine whether CDKN2A copy number loss was associated with poor survival in HPV-negative HNSCCs. Methods: The Cancer Genome Atlas HNSCC clinical and genomic data were obtained and integrated. Patients <80 years old with a primary tumor in the oral cavity, oropharynx, hypopharynx, or larynx were included...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29669750/current-challenges-and-opportunities-in-treating-glioblastoma
#9
Andrea Shergalis, Armand Bankhead, Urarika Luesakul, Nongnuj Muangsin, Nouri Neamati
Glioblastoma multiforme (GBM), the most common and aggressive primary brain tumor, has a high mortality rate despite extensive efforts to develop new treatments. GBM exhibits both intra- and intertumor heterogeneity, lending to resistance and eventual tumor recurrence. Large-scale genomic and proteomic analysis of GBM tumors has uncovered potential drug targets. Effective and "druggable" targets must be validated to embark on a robust medicinal chemistry campaign culminating in the discovery of clinical candidates...
July 2018: Pharmacological Reviews
https://www.readbyqxmd.com/read/29669324/clinical-significance-of-mir-210-and-its-prospective-signaling-pathways-in-non-small-cell-lung-cancer-evidence-from-gene-expression-omnibus-and-the-cancer-genome-atlas-data-mining-with-2763-samples-and-validation-via-real-time-quantitative-pcr
#10
Rong-Quan He, Wei-Luan Cen, Jie-Mei Cen, Wei-Ning Cen, Jia-Yi Li, Mei-Wei Li, Ting-Qing Gan, Xiao-Hua Hu, Gang Chen
BACKGROUND/AIMS: Since the function of microRNA (miR)-210 in non-small cell lung cancer (NSCLC) remains unclear, we aimed to explore the clinical significance of miR-210 in NSCLC. METHODS: NSCLC-related data from 1673 samples on Gene Expression Omnibus and 1090 samples on The Cancer Genome Atlas were obtained and analyzed. The expression level of miR-210 was validated via real-time quantitative PCR analysis with 125 paired clinical samples. A meta-analysis was performed to generate a comprehensive understanding of miR-210 expression and its clinical significance in NSCLC...
April 13, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29668835/methylmix-2-0-an-r-package-for-identifying-dna-methylation-genes
#11
Pierre-Louis Cedoz, Marcos Prunello, Kevin Brennan, Olivier Gevaert
Summary: DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a major mechanism of gene expression deregulation in a wide range of diseases. At the same time, high-throughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. We developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes...
April 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29668342/sequencing-the-next-generation-of-glioblastomas
#12
Ivana Jovčevska
The most aggressive brain malignancy, glioblastoma, accounts for 60-70% of all gliomas and is uniformly fatal. According to the molecular signature, glioblastoma is divided into four subtypes (proneural, neural, classical, and mesenchymal), each with its own genetic background. The Cancer Genome Atlas project provides information about the most common genetic changes in glioblastoma. They involve mutations in TP53, TERT, and PTEN, and amplifications in EFGR, PDGFRA, CDK4, CDK6, MDM2, and MDM4. Recently, epigenetics was used to demonstrate the oncogenic roles of miR-124, miR-137, and miR-128...
April 18, 2018: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29667778/dna-methylation-biomarkers-for-the-occurrence-of-lung-adenocarcinoma-from-tcga-data-mining
#13
Xiao-Feng Zhu, Bi-Sheng Zhu, Fei-Ma Wu, Hai-Bo Hu
The development of lung cancer is a combination of multifactor, multistage, and multiple genetic alterations processes. DNA methylation is an important factor. Currently, the study on the genome-scale epigenetic modification for studying the pathogenesis of lung cancer is still lacking. Here, we aimed to identify the epigenetic modifications of lung cancer, thus to provide scientific basis for the personalized medicine, and research of classification screening for lung adenocarcinoma patients. The DNA methylation data, and the corresponding clinical information of lung adenocarcinoma samples were extracted from the Cancer Genome Atlas (TCGA) database...
April 18, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29667299/usp4-expression-independently-predicts-favorable-survival-in-lung-adenocarcinoma
#14
Ming Zhong, Qi Jiang, Ronghui Jin
Ubiquitin specific protease 4 (USP4) is a member of the USPs family, which catalyzes the cleavage of ubiquitin from a series of protein substrates, thereby modulating a number of cellular signaling pathways. In this study, we aimed to explore the expression profile of USP4 in lung adenocarcinoma (LUAD) using large patient cohorts in the Cancer Genome Atlas and the International Cancer Genome Consortium and to investigate its prognostic value and the possible mechanisms of its dysregulation. Results showed that USP4 was significantly downregulated in LUAD tissues (N = 514) compared with the normal controls (N = 59)...
April 17, 2018: IUBMB Life
https://www.readbyqxmd.com/read/29666643/rna-seq-reveals-the-overexpression-of-igsf9-in-endometrial-cancer
#15
Zonggao Shi, Chunyan Li, Laura Tarwater, Jun Li, Yang Li, William Kaliney, Darshan S Chandrashekar, M Sharon Stack
We performed RNA-seq on an Illumina platform for 7 patients with endometrioid endometrial carcinoma for which both tumor tissue and adjacent noncancer tissue were available. A total of 66 genes were differentially expressed with significance level at adjusted p value < 0.01. Using the gene functional classification tool in the NIH DAVID bioinformatics resource, 5 genes were found to be the only enriched group out of that list of genes. The gene IGSF9 was chosen for further characterization with immunohistochemical staining of a larger cohort of human endometrioid carcinoma tissues...
2018: Journal of Oncology
https://www.readbyqxmd.com/read/29666445/p52-expression-enhances-lung-cancer-progression
#16
Jamie A Saxon, Hui Yu, Vasiliy V Polosukhin, Georgios T Stathopoulos, Linda A Gleaves, Allyson G McLoed, Pierre P Massion, Fiona E Yull, Zhongming Zhao, Timothy S Blackwell
While many studies have demonstrated that canonical NF-κB signaling is a central pathway in lung tumorigenesis, the role of non-canonical NF-κB signaling in lung cancer remains undefined. We observed frequent nuclear accumulation of the non-canonical NF-κB component p100/p52 in human lung adenocarcinoma. To investigate the impact of non-canonical NF-κB signaling on lung carcinogenesis, we employed transgenic mice with doxycycline-inducible expression of p52 in airway epithelial cells. p52 over-expression led to increased tumor number and progression after injection of the carcinogen urethane...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29666306/truncation-and-motif-based-pan-cancer-analysis-reveals-tumor-suppressing-kinases
#17
Andrew M Hudson, Natalie L Stephenson, Cynthia Li, Eleanor Trotter, Adam J Fletcher, Gitta Katona, Patrycja Bieniasz-Krzywiec, Matthew Howell, Chris Wirth, Simon Furney, Crispin J Miller, John Brognard
A major challenge in cancer genomics is identifying "driver" mutations from the many neutral "passenger" mutations within a given tumor. To identify driver mutations that would otherwise be lost within mutational noise, we filtered genomic data by motifs that are critical for kinase activity. In the first step of our screen, we used data from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas to identify kinases with truncation mutations occurring within or before the kinase domain...
April 17, 2018: Science Signaling
https://www.readbyqxmd.com/read/29666142/tumor-xenograft-modeling-identifies-tcf4-itf2-loss-associated-with-breast-cancer-chemoresistance
#18
Gorka Ruiz de Garibay, Francesca Mateo, Agostina Stradella, Rafael Valdés-Mas, Luis Palomero, Jordi Serra-Musach, Diana A Puente, Ander Díaz-Navarro, Gardenia Vargas-Parra, Eva Tornero, Idoia Morilla, Lourdes Farré, María Martinez-Iniesta, Carmen Herranz, Emmet McCormack, August Vidal, Anna Petit, Teresa Soler, Conxi Lázaro, Xose S Puente, Alberto Villanueva, Miguel Angel Pujana
Understanding the mechanisms of cancer therapeutic resistance is fundamental to improving cancer care. There is clear benefit from chemotherapy in different breast cancer settings; however, knowledge of the mutations and genes that mediate resistance is incomplete. In this study, by modeling chemoresistance in patient-derived xenografts (PDXs), we show that adaptation to therapy is genetically complex and identify loss of transcription factor 4 (TCF4) associated with this process. A triple-negative BRCA1 -mutated PDX was used to study the genetics of chemoresistance...
April 13, 2018: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/29666058/early-detection-sequencing-assays-prove-highly-specific
#19
(no author information available yet)
Ultrasensitive DNA-sequencing methods proved more than 99% specific, according to initial findings from GRAIL's Circulating Cell-Free Genome Atlas Study. The data, presented at the American Association for Cancer Research Annual Meeting 2018, demonstrate the feasibility of designing a blood test for early cancer detection.
April 17, 2018: Cancer Discovery
https://www.readbyqxmd.com/read/29665859/morphology-and-genomic-hallmarks-of-breast-tumours-developed-by-atm-deleterious-variant-carriers
#20
Anne-Laure Renault, Noura Mebirouk, Laetitia Fuhrmann, Guillaume Bataillon, Eve Cavaciuti, Dorothée Le Gal, Elodie Girard, Tatiana Popova, Philippe La Rosa, Juana Beauvallet, Séverine Eon-Marchais, Marie-Gabrielle Dondon, Catherine Dubois d'Enghien, Anthony Laugé, Walid Chemlali, Virginie Raynal, Martine Labbé, Ivan Bièche, Sylvain Baulande, Jacques-Olivier Bay, Pascaline Berthet, Olivier Caron, Bruno Buecher, Laurence Faivre, Marc Fresnay, Marion Gauthier-Villars, Paul Gesta, Nicolas Janin, Sophie Lejeune, Christine Maugard, Sébastien Moutton, Laurence Venat-Bouvet, Hélène Zattara, Jean-Pierre Fricker, Laurence Gladieff, Isabelle Coupier, Georgia Chenevix-Trench, Janet Hall, Anne Vincent-Salomon, Dominique Stoppa-Lyonnet, Nadine Andrieu, Fabienne Lesueur
BACKGROUND: The ataxia telangiectasia mutated (ATM) gene is a moderate-risk breast cancer susceptibility gene; germline loss-of-function variants are found in up to 3% of hereditary breast and ovarian cancer (HBOC) families who undergo genetic testing. So far, no clear histopathological and molecular features of breast tumours occurring in ATM deleterious variant carriers have been described, but identification of an ATM-associated tumour signature may help in patient management. METHODS: To characterise hallmarks of ATM-associated tumours, we performed systematic pathology review of tumours from 21 participants from ataxia-telangiectasia families and 18 participants from HBOC families, as well as copy number profiling on a subset of 23 tumours...
April 17, 2018: Breast Cancer Research: BCR
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