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https://www.readbyqxmd.com/read/28634282/genomic-alterations-in-fatal-forms-of-non-anaplastic-thyroid-cancer-identification-of-med12-and-rbm10-as-novel-thyroid-cancer-genes-associated-with-tumor-virulence
#1
Tihana Ibrahimpasic, Bin Xu, Iñigo Landa, Snjezana Dogan, Sumit Middha, Venkatraman Seshan, Shyamprasad Deraje Vasudeva, Diane Carlson, Jocelyn Migliacci, Jeffrey A Knauf, Brian R Untch, Michael F Berger, Luc Gt Morris, R Michael Tuttle, Timothy A Chan, James A Fagin, Ronald Ghossein, Ian Ganly
Purpose. Patients with anaplastic thyroid cancer have a very high death rate. In contrast, deaths from non-anaplastic thyroid cancer are much less common. The genetic alterations in fatal non-anaplastic thyroid cancers have not been reported. <p>Experimental Design. We performed next-generation sequencing of 410 cancer genes from 57 fatal non-anaplastic thyroid primary cancers. Results were compared to The Cancer Genome Atlas study (TCGA study) of papillary thyroid cancers (PTC) and to the genomic changes reported in anaplastic thyroid cancer (ATC)...
June 20, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28631555/grik3-a-novel-oncogenic-protein-related-to-tumor-tnm-stage-lymph-node-metastasis-and-poor-prognosis-of-gc
#2
Baocheng Gong, Yuan Li, Zhenguo Cheng, Pengliang Wang, Lei Luo, Hanwei Huang, Shijie Duan, Funan Liu
Glutamate receptor, ionotropic, kainate 3 (GRIK3), as a member of the glutamate kainate receptor family, mainly participated in neuroactive ligand receptor interaction pathway. Other members of GRIK family were previously reported to regulate cellular migration, transformation, and proliferation in tumor. However, the mechanism of GRIK3 in tumor is still unclear. Therefore, the purpose of our study was to reveal the expression and clinical significance of GRIK3 in gastric cancer (GC). First, we performed the expression analysis and survival analysis of GRIK3 using The Cancer Genome Atlas (TCGA) database, and the results showed that the GRIK3 expressed differentially between gastric cancer tissues and the adjacent normal tissues and that higher expression of GRIK3 was associated with poor survival outcomes...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28631396/pttg3p-promotes-gastric-tumour-cell-proliferation-and-invasion-and-is-an-indicator-of-poor-prognosis
#3
Weiwei Weng, Shujuan Ni, Yiqin Wang, Midie Xu, Qiongyan Zhang, Yusi Yang, Yong Wu, Qinghua Xu, Peng Qi, Cong Tan, Dan Huang, Ping Wei, Zhaohui Huang, Yuqing Ma, Wei Zhang, Weiqi Sheng, Xiang Du
Pseudogenes play a crucial role in cancer progression. However, the role of pituitary tumour-transforming 3, pseudogene (PTTG3P) in gastric cancer (GC) remains unknown. Here, we showed that PTTG3P expression was abnormally up-regulated in GC tissues compared with that in normal tissues both in our 198 cases of clinical samples and the cohort from The Cancer Genome Atlas (TCGA) database. High PTTG3P expression was correlated with increased tumour size and enhanced tumour invasiveness and served as an independent negative prognostic predictor...
June 19, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28630682/overexpressed-prame-is-a-potential-immunotherapy-target-in-sarcoma-subtypes
#4
Jason Roszik, Wei-Lien Wang, John A Livingston, Christina L Roland, Vinod Ravi, Cassian Yee, Patrick Hwu, Andrew Futreal, Alexander J Lazar, Shreyaskumar R Patel, Anthony P Conley
BACKGROUND: PRAME (preferentially expressed antigen in melanoma), a member of the cancer-testis antigen family, has been shown to have increased expression in solid tumors, including sarcoma, and PRAME-specific therapies are currently in development for other cancers such as melanoma. METHODS: To map the landscape of PRAME expression in sarcoma, we used publicly available data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE) projects and determined which sarcoma subtypes and subsets are associated with increased PRAME expression...
2017: Clinical Sarcoma Research
https://www.readbyqxmd.com/read/28628113/microrna-20a-mediated-loss-of-autophagy-contributes-to-breast-tumorigenesis-by-promoting-genomic-damage-and-instability
#5
L Liu, J He, X Wei, G Wan, Y Lao, W Xu, Z Li, H Hu, Z Hu, X Luo, J Wu, W Xie, Y Zhang, N Xu
Gene expression analysis of The Cancer Genome Atlas (TCGA) breast cancer data set show that miR-20a is upregulated in human breast cancer, especially in triple-negative subtype. Gene Set Enrichment Analysis suggests that miR-20a expression negatively correlates with the autophagy/lysosome pathway. We report here that miR-20a inhibits the basal and nutrient starvation-induced autophagic flux and lysosomal proteolytic activity, increases intracellular reactive oxygen species levels and DNA damage response by targeting several key regulators of autophagy, including BECN1, ATG16L1 and SQSTM1...
June 19, 2017: Oncogene
https://www.readbyqxmd.com/read/28627585/role-of-metadherin-in-estrogen-regulated-gene-expression
#6
Yujun Li, Jesus Gonzalez Bosquet, Shujie Yang, Kristina W Thiel, Yuping Zhang, Haitao Liu, Kimberly K Leslie, Xiangbing Meng
The disruption of estrogen signaling is widely associated with the development of breast, endometrial and ovarian cancers. As a multifunctional mediator of carcinogenesis, metadherin (MTDH)/astrocyte elevated gene-1 (AEG-1) overexpression has been associated with numerous types of cancer, with reported roles in tumor initiation, proliferation, invasion, metastasis and chemoresistance. At the molecular level, MTDH has been shown to interact with proteins that drive tumorigenesis, including nuclear factor-κB (NF-κB), promyelocytic leukaemia zinc finger (PLZF), BRCA2- and CDKN1A (p21Cip1/Waf-1/mda-6)-interacting protein α (BCCIPα) and staphylococcal nuclease and tudor domain containing 1 (SND1)...
June 13, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28627406/multi-omics-facilitated-variable-selection-in-cox-regression-model-for-cancer-prognosis-prediction
#7
Cong Liu, Xujun Wang, Georgi Z Genchev, Hui Lu
Motivation New developments in high-throughput genomic technologies have enabled the measurement of diverse types of omics biomarkers in a cost-efficient and clinically-feasible manner. Developing computational methods and tools for analysis and translation of such genomic data into clinically-relevant information is an ongoing and active area of investigation. For example, several studies have utilized an unsupervised learning framework to cluster patients by integrating omics data. Despite such recent advances, predicting cancer prognosis using integrated omics biomarkers remains a challenge...
June 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28626070/potential-susceptibility-loci-identified-for-renal-cell-carcinoma-by-targeting-obesity-related-genes
#8
Xiang Shu, Mark P Purdue, Yuanqing Ye, Huakang Tu, Christopher G Wood, Nizar M Tannir, Zhaoming Wang, Demetrius Albanes, Susan M Gapstur, Victoria L Stevens, Nathaniel Rothman, Stephen J Chanock, Xifeng Wu
BACKGROUND: Obesity is an established risk factor for renal cell carcinoma (RCC). Although genome-wide association studies (GWAS) of RCC have identified several susceptibility loci, additional variants might be missed due to the highly conservative selection. METHODS: We conducted a multiphase study utilizing three independent genome-wide scans at MD Anderson Cancer Center (MDA RCC GWAS and MDA RCC OncoArray) and National Cancer Institute (NCI RCC GWAS), which consisted of a total of 3,530 cases and 5,714 controls, to investigate genetic variations in obesity-related genes and RCC risk...
June 16, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28624807/regulation-of-actin-binding-protein-anln-by-antitumor-mir-217-inhibits-cancer-cell-aggressiveness-in-pancreatic-ductal-adenocarcinoma
#9
Tetsuya Idichi, Naohiko Seki, Hiroshi Kurahara, Keiichi Yonemori, Yusaku Osako, Takayuki Arai, Atsushi Okato, Yoshiaki Kita, Takaaki Arigami, Yuko Mataki, Yuko Kijima, Kosei Maemura, Shoji Natsugoe
Analysis of our microRNA (miRNA) expression signature of pancreatic ductal adenocarcinoma (PDAC) revealed that microRNA-217 (miR-217) was significantly reduced in cancer tissues. The aim of this study was to investigate the antitumor roles of miR-217 in PDAC cells and to identify miR-217-mediated molecular pathways involved in PDAC aggressiveness. The expression levels of miR-217 were significantly reduced in PDAC clinical specimens. Ectopic expression of miR-217 significantly suppressed cancer cell migration and invasion...
May 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28617833/clinical-performance-validation-of-pitx2-dna-methylation-as-prognostic-biomarker-in-patients-with-head-and-neck-squamous-cell-carcinoma
#10
Verena Sailer, Heidrun Gevensleben, Joern Dietrich, Diane Goltz, Glen Kristiansen, Friedrich Bootz, Dimo Dietrich
BACKGROUND: Despite advances in combined modality therapy, outcomes in head and neck squamous cell cancer (HNSCC) remain dismal with five-year overall survival rates of less than 50%. Prognostic biomarkers are urgently needed to identify patients with a high risk of death after initial curative treatment. Methylation status of the paired-like homeodomain transcription factor 2 (PITX2) has recently emerged as a powerful prognostic biomarker in various cancers. In the present study, the clinical performance of PITX2 methylation was validated in a HNSCC cohort by means of an independent analytical platform (Infinium HumanMethylation450 BeadChip, Illumina, Inc...
2017: PloS One
https://www.readbyqxmd.com/read/28617548/bioinformatic-analysis-of-prognostic-value-of-arap3-in-breast-cancer-and-the-associated-signaling-pathways
#11
J-J Han, B-R Du, C-H Zhang
OBJECTIVE: In this study, we tried to pool previous annotated genomic data to assess the association between ARAP3 expression and metastatic relapse (MR) risk in patients with breast cancer. Moreover, we also investigated the signaling pathways in which ARAP3 might be involved in breast cancer. MATERIALS AND METHODS: The raw microarray data (GDS5666) that compared gene transcriptional profiles of 4T1 derived lung-aggressive explant and primary tumor explant were reanalyzed to identify the dysregulated genes...
May 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28615526/identifying-prognostic-signature-in-ovarian-cancer-using-dirgenerank
#12
Jian-Yong Wang, Ling-Ling Chen, Xiong-Hui Zhou
Identifying the prognostic genes in cancer is essential not only for the treatment of cancer patients, but also for drug discovery. However, it's still a big challenge to select the prognostic genes that can distinguish the risk of cancer patients across various data sets because of tumor heterogeneity. In this situation, the selected genes whose expression levels are statistically related to prognostic risks may be passengers. In this paper, based on gene expression data and prognostic data of ovarian cancer patients, we used conditional mutual information to construct gene dependency network in which the nodes (genes) with more out-degrees have more chances to be the modulators of cancer prognosis...
May 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28615518/estrogen-activated-mdm2-disrupts-mammary-tissue-architecture-through-a-p53-independent-pathway
#13
Nandini Kundu, Angelika Brekman, Jun Yeob Kim, Gu Xiao, Chong Gao, Jill Bargonetti
The Cancer Genome Atlas (TCGA) data indicate that high MDM2 expression correlates with all subtypes of breast cancer. Overexpression of MDM2 drives breast oncogenesis in the presence of wild-type or mutant p53 (mtp53). Importantly, estrogen-receptor positive (ER+) breast cancers overexpress MDM2 and estrogen mediates this expression. We previously demonstrated that this estrogen-MDM2 axis activates the proliferation of breast cancer cell lines T47D (mtp53 L194F) and MCF7 (wild-type p53) in a manner independent of increased degradation of wild-type p53 (ie, p53-independently)...
May 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28615508/integrative-bioinformatics-analysis-identifies-robo1-as-a-potential-therapeutic-target-modified-by-mir-218-in-hepatocellular-carcinoma
#14
Junqing Wang, Yunyun Zhou, Xiaochun Fei, Xunhua Chen, Rui Chen, Zhenggang Zhu, Yongjun Chen
Patients diagnosed with advanced hepatocellular carcinoma (HCC) presented poor prognosis and short survival time. Althouth accumulating contribution of continuous research has gradually revealed complex tumorigenesis mechanism of HCC with numerous and jumbled biomarkers, those specific ones for HCC diagnose and therapeutic treatment are required illustration. Multiple genes over-expressed in HCC specimens with at least 1.5 fold change were cohorted, compared with the non-cancerous tissues through integrative bioinformatics analysis from Gene Expression Omnibus (GEO) datasets GSE14520 and GSE6764, including 445 and 45 cases of samples spearatly, along with intensive exploration on the Cancer Genome Altas (TCGA) dataset of liver cancer...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28612496/rin1-promotes-renal-cell-carcinoma-malignancy-by-activating-egfr-signalling-through-rab25
#15
Zi-Hao Feng, Yong Fang, Liang-Yun Zhao, Jun Lu, Yong-Qian Wang, Zhen-Hua Chen, Yong Huang, Jin-Huan Wei, Yan-Ping Liang, Jun-Jie Cen, Yi-Hui Pan, Bing Liao, Wei Chen, Jun-Hang Luo
We previously identified the important role of RIN1 expression in the prognosis of clear cell renal cell carcinoma (ccRCC). The role of RIN1 in ccRCC malignancy and underlying molecular mechanisms remain unclear. Here we report that ccRCC cells and tissues expressed more RIN1 than normal controls. Gain- and loss-of-function studies demonstrated that RIN1 enhanced ccRCC cell growth, migration and invasion abilities in vitro and promoted tumor growth and metastasis in vivo. Mechanistic studies revealed that RIN1 has an activating effect on EGFR signalling in ccRCC...
June 14, 2017: Cancer Science
https://www.readbyqxmd.com/read/28611308/an-oral-keratinocyte-life-cycle-model-identifies-novel-host-genome-regulation-by-human-papillomavirus-16-relevant-to-hpv-positive-head-and-neck-cancer
#16
Michael R Evans, Claire D James, Oonagh Loughran, Tara J Nulton, Xu Wang, Molly L Bristol, Brad Windle, Iain M Morgan
Many aspects of the HPV life cycle have been characterized in cervical cell lines (W12, CIN612) and in HPV immortalized primary foreskin keratinocytes. There is now an epidemic of HPV positive oropharyngeal cancers (HPV16 is responsible for 80-90% of these); therefore increased understanding of the HPV16 life cycle in oral keratinocytes is a priority. To date there have been limited reports characterizing the HPV16 life cycle in oral keratinocytes. Using TERT immortalized "normal" oral keratinocytes (NOKs) we generated clonal cell lines maintaining the HPV16 genome as an episome, NOKs+HPV16...
June 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28611305/kdm4a-as-a-prognostic-marker-of-oral-squamous-cell-carcinoma-evidence-from-tissue-microarray-studies-in-a-multicenter-cohort
#17
Xin Jin, Hao Xu, Xingyu Wu, Taiwen Li, Jing Li, Yu Zhou, Hongxia Dan, Lu Jiang, Xin Zeng, Ping Ji, Qianming Chen
PURPOSE: Previous studies have identified histone demethylase KDM4A to be a key epigenetic priming factor for the invasive squamous cell carcinoma growth and metastasis. The purpose of this study was to examine KDM4A as an independent prognostic marker in oral squamous cell carcinoma, using multicenter tissue microarrays. RESULTS: The expression of KDM4A was significantly correlated with lymph node metastasis and TNM stage. KDM4A overexpression was associated with poor overall survival, and it was found to be a statistically significant independent predictor of all-cause mortality...
May 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28608921/whole-exome-sequencing-reveals-critical-genes-underlying-metastasis-in-esophageal-squamous-cell-carcinoma
#18
Wei Dai, Josephine Mun Yee Ko, Sheyne Sta Ana Choi, Zhouyou Yu, Luwen Ning, Hong Zheng, Vinod Gopalan, Kin Tak Chan, Nikki Pui-Yue Lee, Kwok Wah Chan, Simon Ying-Kit Law, Alfred King-Yin Lam, Maria Li Lung
Esophageal squamous cell carcinoma (ESCC) is one of the most lethal cancers due to a high frequency of metastasis. However, little is known about the genomic landscape of metastatic ESCC. To identify the genetic alterations that underlie ESCC metastasis, whole-exome sequencing (WES) was performed for 41 primary tumors and 15 lymph nodes (LNs) with metastatic ESCC. Eleven cases included matched primary tumors, synchronous LN metastases and non-neoplastic mucosa. Approximately 50-76% of the mutations identified in primary tumors appeared in the synchronous LN metastases...
June 13, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28608251/rna-processing-as-an-alternative-route-to-attack-glioblastoma
#19
REVIEW
Fabiana Marcelino Meliso, Christopher G Hubert, Pedro A Favoretto Galante, Luiz O Penalva
Genomic analyses have become an important tool to identify new avenues for therapy. This is especially true for cancer types with extremely poor outcomes, since our lack of effective therapies offers no tangible clinical starting point to build upon. The highly malignant brain tumor glioblastoma (GBM) exemplifies such a refractory cancer, with only 15 month average patient survival. Analyses of several hundred GBM samples compiled by the TCGA (The Cancer Genome Atlas) have produced an extensive transcriptomic map, identified prevalent chromosomal alterations, and defined important driver mutations...
June 12, 2017: Human Genetics
https://www.readbyqxmd.com/read/28606921/overexpression-of-rcc2-enhances-cell-motility-and-promotes-tumor-metastasis-in-lung-adenocarcinoma-by-inducing-epithelial-mesenchymal-transition
#20
Bo Pang, Nan Wu, Rongwei Guan, Lin Pang, Xinlei Li, Su Li, Liudi Tang, Ying Guo, Jialei Chen, Donglin Sun, Haiming Sun, Jialin Dai, Jing Bai, Guohua Ji, Peng Liu, An Liu, Qiushi Wang, Sheng Xiao, Songbin Fu, Yan Jin
Investigate the role of regulator of chromosome condensation 2 (RCC2) on lung adenocarcinoma (LUAD) metastasis.<br /><br />Experimental Design: Clinical specimens were used to assess the impact of RCC2 on LUAD metastasis. Mouse models, cytobiology and molecular biology assays were performed to elucidate the function and underlying mechanisms of RCC2 in LUAD.<br /><br />Results: RCC2 expression was frequently increased in LUADs (88/122, 72.13%). It was confirmed by analysis of a larger cohort of TCGA RNA-seq data containing 488 LUADs and 58 normal lung tissues (P<0...
June 12, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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