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https://www.readbyqxmd.com/read/28742845/evaluation-of-k-ras-and-p53-expression-in-pancreatic-adenocarcinoma-using-the-cancer-genome-atlas
#1
Liming Lu, Jingchun Zeng
Genetic alterations in K-ras and p53 are thought to be critical in pancreatic cancer development and progression. However, K-ras and p53 expression in pancreatic adenocarcinoma have not been systematically examined in The Cancer Genome Atlas (TCGA) Data Portal. Information regarding K-ras and p53 alterations, mRNA expression data, and protein/protein phosphorylation abundance was retrieved from The Cancer Genome Atlas (TCGA) databases, and analyses were performed by the cBioPortal for Cancer Genomics. The mutual exclusivity analysis showed that events in K-ras and p53 were likely to co-occur in pancreatic adenocarcinoma (Log odds ratio = 1...
2017: PloS One
https://www.readbyqxmd.com/read/28742699/understanding-and-resetting-radiation-sensitivity-in-rectal-cancer
#2
Katherine A Kelley, Rebecca A Ruhl, Shushan R Rana, Elizabeth Dewey, Cristina Espinosa, Charles R Thomas, Robert G Martindale, Sudarshan Anand, Vassiliki L Tsikitis
OBJECTIVE: The aim of the study was to explore specific microRNAs (miRs) in rectal cancer that would predict response to radiation and identify target pathways that may be exploited for neoadjuvant therapies. SUMMARY BACKGROUND DATA: Chemoradiotherapy (CRT) response is a predictor of survival in rectal cancer. Studies have demonstrated changes in RNA expression correlate with chemoradiation sensitivity across cancers. METHODS: Forty-five rectal cancer patients, partial responders (PR = 18), nonresponders (NR = 13), and complete responders (CR = 14) to CRT, as defined by a tumor regression score, were examined...
July 24, 2017: Annals of Surgery
https://www.readbyqxmd.com/read/28742206/bioinformatics-analysis-of-rna-seq-data-revealed-critical-genes-in-colon-adenocarcinoma
#3
W-D Xi, Y-J Liu, X-B Sun, J Shan, L Yi, T-T Zhang
OBJECTIVE: RNA-seq data of colon adenocarcinoma (COAD) were analyzed with bioinformatics tools to discover critical genes in the disease. Relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. MATERIALS AND METHODS: RNA-seq data of COAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. False positive discovery (FDR) < 0.05 and |log2 (fold change)|>1 were set as the cut-offs to screen out differentially expressed genes (DEGs)...
July 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28740578/clinical-performance-of-e2fs-1-3-in-kidney-clear-cell-renal-cancer-evidence-from-bioinformatics-analysis
#4
Bin Liang, Jianying Zhao, Xuan Wang
Extensive research on the E2F transcription factor family has led to numerous insights that E2Fs were involved not only in proliferation and tumorigenesis but also in apoptosis and differentiation. In the present study, we analyzed the differential expression of E2Fs1-3 genes, and also evaluated the impact of E2Fs 1-3 genes expression on clinical outcome from the Cancer Genome Atlas (TCGA) database. The results showed that E2F1, E2F2 and E2F3 expression was increased in KIRC tissues than matched normal tissues (E2F1, P < 0...
May 2017: Genes & Cancer
https://www.readbyqxmd.com/read/28740507/mir-195-inhibits-tumor-growth-and-metastasis-in-papillary-thyroid-carcinoma-cell-lines-by-targeting-ccnd1-and-fgf2
#5
Yali Yin, Shubin Hong, Shuang Yu, Yanrui Huang, Shuwei Chen, Yujie Liu, Quan Zhang, Yanbing Li, Haipeng Xiao
BACKGROUND: MicroRNA (miRNA) dysregulation was commonly seen in papillary thyroid carcinoma (PTC), and miR-195 was verified to be downregulated in PTC by the large data set analysis from The Cancer Genome Atlas (TCGA). Our study aimed to explore the biological functions and the underlying molecular mechanisms of miR-195 in PTC. METHODS: The relative expression of miR-195 and its target genes were assessed by quantitative RT-PCR assay in 38 pairs of PTC and the adjacent thyroid tissues...
2017: International Journal of Endocrinology
https://www.readbyqxmd.com/read/28739740/global-analysis-of-mirna-mrna-interaction-network-in-breast-cancer-with-brain-metastasis
#6
Zhixin Li, Zhiqiang Peng, Siyu Gu, Junfang Zheng, Duiping Feng, Qiong Qin, Junqi He
BACKGROUND: MicroRNAs (miRNAs) have been linked to a number of cancer types including breast cancer. The rate of brain metastases is 10-30% in patients with advanced breast cancer which is associated with poor prognosis. The potential application of miRNAs in the diagnostics and therapeutics of breast cancer with brain metastasis is an area of intense interest. In an initial effort to systematically address the differential expression of miRNAs and mRNAs in primary breast cancer which may provide clues for early detection of brain metastasis, we analyzed the consequent changes in global patterns of gene expression in Gene Expression Omnibus (GEO) data set obtained by microarray from patients with in situ carcinoma and patients with brain metastasis...
August 2017: Anticancer Research
https://www.readbyqxmd.com/read/28739731/identification-of-novel-proteins-interacting-with-vascular-endothelial-growth-inhibitor-174-in-renal-cell-carcinoma
#7
Qiang Zhao, Duoer Kun, Baoan Hong, Xiaohu Deng, Sheng Guo, Xingxing Tang, Yong Yang, Kan Gong, Qing Li, Lin Ye, Wen G Jiang, Ning Zhang
BACKGROUND/AIM: Vascular endothelial growth inhibitor (VEGI) is a multipotential cytokine that plays a role in regulating immunity, anti-angiogenesis, and inhibiting tumor growth. However, the proteins that interact with it are still unknown. In the present study, we examined the proteins that interact with VEGI174 and their expression in renal cell carcinoma (RCC). MATERIALS AND METHODS: The proteins that interact with VEGI174 were identified using western blot, pull-down assay, and mass spectrometry...
August 2017: Anticancer Research
https://www.readbyqxmd.com/read/28738804/oncogenic-long-noncoding-rna-landscape-in-breast-cancer
#8
Shouping Xu, Dejia Kong, Qianlin Chen, Yanyan Ping, Da Pang
BACKGROUND: Few long noncoding RNAs (lncRNAs) that act as oncogenic genes in breast cancer have been identified. METHODS: Oncogenic lncRNAs associated with tumourigenesis and worse survival outcomes were examined and validated in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), respectively. Then, the potential biological functions and expression regulation of these lncRNAs were studied via bioinformatics and genome data analysis. Moreover, progressive breast cancer subtype-specific lncRNAs were investigated via high-throughput sequencing in our cohort and TCGA validation...
July 24, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28734892/correlation-between-rna-seq-and-microarrays-results-using-tcga-data
#9
Li Chen, Fenghao Sun, Xiaodong Yang, Yulin Jin, Mengkun Shi, Lin Wang, Yu Shi, Cheng Zhan, Qun Wang
RNA sequencing (RNA-Seq) and microarray are two of the most commonly used high-throughput technologies for transcriptome profiling; however, they both have their own inherent strengths and limitations. This research aims to analyze the correlation between microarrays and RNA-Seq detection of transcripts in the same tissue sample to explore the reproducibility between the techniques. Using data of RNA-Seq v2 and three different microarrays provided by The Cancer Genome Atlas, 11,120 genes of 111 lung squamous cell carcinoma samples were simultaneously detected by the four methods...
July 19, 2017: Gene
https://www.readbyqxmd.com/read/28734015/different-mir-21-3p-isoforms-and-their-different-features-in-colorectal-cancer
#10
Weijuan Jiao, Xueqin Leng, Qun Zhou, Yayun Wu, Lina Sun, Yan Tan, Hengli Ni, Xiaoqiang Dong, Tong Shen, Yao Liu, Jianming Li
MiR-21, the only miRNA found to be overexpressed in any type of solid tumor, its guide stand, miR-21-5p, has been studied a lot in colorectal cancer (CRC), however, few researchers focused on its passenger strand, miR-21-3p. In this study, based on The Cancer Genome Atlas (TCGA) data, we found that there were more variety and quantity of miR-21-3p isoforms in microsatellite instability (MSI)-type CRC. We further examined the role of miR-21-3p by in vitro and in vivo studies. MiR-21-3p may be an oncogene in CRC by promoting cellular mobility through epithelial-mesenchymal transition (EMT)...
July 22, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28733453/a-novel-functional-splice-variant-of-akt3-defined-by-analysis-of-alternative-splice-expression-in-hpv-positive-oropharyngeal-cancers
#11
Theresa Guo, Akihiro Sakai, Bahman Afsari, Michael Considine, Ludmila Danilova, Alexander V Favorov, Srinivasan Yegnasubramanian, Dylan Z Kelley, Emily Flam, Patrick K Ha, Zubair Khan, Sarah J Wheelan, J Silvio Gutkind, Elana J Fertig, Daria A Gaykalova, Joseph Califano
The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples...
July 21, 2017: Cancer Research
https://www.readbyqxmd.com/read/28732212/ualcan-a-portal-for-facilitating-tumor-subgroup-gene-expression-and-survival-analyses
#12
Darshan S Chandrashekar, Bhuwan Bashel, Sai Akshaya Hodigere Balasubramanya, Chad J Creighton, Israel Ponce-Rodriguez, Balabhadrapatruni V S K Chakravarthi, Sooryanarayana Varambally
Genomics data from The Cancer Genome Atlas (TCGA) project has led to the comprehensive molecular characterization of multiple cancer types. The large sample numbers in TCGA offer an excellent opportunity to address questions associated with tumo heterogeneity. Exploration of the data by cancer researchers and clinicians is imperative to unearth novel therapeutic/diagnostic biomarkers. Various computational tools have been developed to aid researchers in carrying out specific TCGA data analyses; however there is need for resources to facilitate the study of gene expression variations and survival associations across tumors...
July 18, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28731158/the-long-non-coding-rna-snhg3-functions-as-a-competing-endogenous-rna-to-promote-malignant-development-of-colorectal-cancer
#13
Weizhen Huang, Yunming Tian, Shaoting Dong, Yinlian Cha, Jun Li, Xiaohong Guo, Xia Yuan
Accumulating evidence has revealed that aberrantly expressed long non-coding transcripts are involved in the development and progression of colorectal cancer (CRC). Small nucleolar RNA host gene 3 (SNHG3) is a newly identified lncRNA, and little is known about its clinical significance and biological functions in the development of CRC. In the present study, we found that the expression of SNHG3 was significantly upregulated in CRC, and upregulation of SNHG3 predicted poor prognosis for patients with CRC as determined through analysis of the data obtained from TCGA database...
July 18, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28729955/identification-of-four-prognostic-lncrnas-for-survival-prediction-of-patients-with-hepatocellular-carcinoma
#14
Zhonghao Wang, Qian Wu, Shu Feng, Yanhua Zhao, Chuanmin Tao
BACKGROUND: As the fifth most common cancer worldwide, Hepatocellular carcinoma (HCC) is also the third most common cause of cancer-related death in China. Several lncRNAs have been demonstrated to be associated with occurrence and prognosis of HCC. However, identification of prognostic lncRNA signature for HCC with expression profiling data has not been conducted yet. METHODS: With the reuse of public available TCGA data, expression profiles of lncRNA for 371 patients with HCC were obtained and analyzed to find the independent prognostic lncRNA...
2017: PeerJ
https://www.readbyqxmd.com/read/28723667/resistance-to-ctla-4-checkpoint-inhibition-reversed-through-selective-elimination-of-granulocytic-myeloid-cells
#15
Paul E Clavijo, Ellen C Moore, Jianhong Chen, Ruth J Davis, Jay Friedman, Young Kim, Carter Van Waes, Zhong Chen, Clint T Allen
PURPOSE: Local immunosuppression remains a critical problem that limits clinically meaningful response to checkpoint inhibition in patients with head and neck cancer. Here, we assessed the impact of MDSC elimination on responses to CTLA-4 checkpoint inhibition. EXPERIMENTAL DESIGN: Murine syngeneic carcinoma immune infiltrates were characterized by flow cytometry. Granulocytic MDSCs (gMDSCs) were depleted and T-lymphocyte antigen-specific responses were measured...
June 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28719033/identification-of-driver-copy-number-alterations-in-diverse-cancer-types-and-application-in-drug-repositioning
#16
Wenbin Zhou, Zhangxiang Zhao, Ruiping Wang, Yue Han, Chengyu Wang, Fan Yang, Ya Han, Haihai Liang, Lishuang Qi, Chenguang Wang, Zheng Guo, Yunyan Gu
Results from numerous studies suggest an important role for somatic copy number alterations (SCNAs) in cancer progression. Our work aimed to identify the drivers (oncogenes or tumor suppressor genes) that reside in recurrently aberrant genomic regions, including a large number of genes or non-coding genes, which remain a challenge for decoding the SCNAs involved in carcinogenesis. Here, we propose a new approach to comprehensively identify drivers, using 8740 cancer samples involving 18 cancer types from The Cancer Genome Atlas (TCGA)...
July 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28718916/the-genetic-landscape-of-endometrial-clear-cell-carcinomas
#17
Deborah F DeLair, Kathleen A Burke, Pier Selenica, Raymond S Lim, Sasinya N Scott, Sumit Middha, Abhinita S Mohanty, Donavan T Cheng, Michael F Berger, Robert A Soslow, Britta Weigelt
Clear cell carcinoma of the endometrium is a rare type of endometrial cancer generally associated with an aggressive clinical behavior. Here we sought to define the repertoire of somatic genetic alterations in endometrial clear cell carcinomas (ECCs) and whether ECCs could be classified into the molecular subtypes described for endometrial endometrioid and serous carcinomas. We performed a rigorous histopathological review, immunohistochemical analysis and massively parallel sequencing targeting 300 cancer-related genes of 32 pure ECCs...
July 18, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28717245/development-and-validation-of-a-three-gene-prognostic-signature-for-patients-with-hepatocellular-carcinoma
#18
Binghua Li, Wendu Feng, Ouyang Luo, Tiancheng Xu, Yajuan Cao, Hongyan Wu, Decai Yu, Yitao Ding
Hepatocellular carcinoma (HCC) is the leading cause of cancer-related death worldwide, because recurrence often occurs in most HCC patients undergoing hepatectomy. It is necessary to identify patients with high risk for recurrence and adopt effective therapies. An obstacle to monitor patients at high risk for poor prognosis has been the lack of useful predictive biomarkers. Fortunately, recent progress in system biology allows to screen the biomarkers for HCC prognosis in a high-throughput manner. In this study, we performed systematic Kaplan-Meier survival analysis of the whole mRNA transcriptomics based on the Cancer Genome Atlas project (TCGA) and developed a three-gene prognostic signature composing of three genes UPB1, SOCS2 and RTN3...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717230/activin-signaling-is-an-essential-component-of-the-tgf-%C3%AE-induced-pro-metastatic-phenotype-in-colorectal-cancer
#19
Jonas J Staudacher, Jessica Bauer, Arundhati Jana, Jun Tian, Timothy Carroll, Georgina Mancinelli, Özkan Özden, Nancy Krett, Grace Guzman, David Kerr, Paul Grippo, Barbara Jung
Advanced colorectal cancer (CRC) remains a critical health care challenge worldwide. Various TGF-β superfamily members are important in colorectal cancer metastasis, but their signaling effects and predictive value have only been assessed in isolation. Here, we examine cross-regulation and combined functions of the two most prominent TGF-β superfamily members activin and TGF-β in advanced colorectal cancer. In two clinical cohorts we observed by immune-based assay that combined serum and tissue activin and TGF-β ligand levels predicts outcome in CRC patients and is superior to single ligand assessment...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717182/widespread-alternative-exon-usage-in-clinically-distinct-subtypes-of-invasive-ductal-carcinoma
#20
Sunniva Stordal Bjørklund, Anshuman Panda, Surendra Kumar, Michael Seiler, Doug Robinson, Jinesh Gheeya, Ming Yao, Grethe I Grenaker Alnæs, Deborah Toppmeyer, Margit Riis, Bjørn Naume, Anne-Lise Børresen-Dale, Vessela N Kristensen, Shridar Ganesan, Gyan Bhanot
Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort...
July 17, 2017: Scientific Reports
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