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https://www.readbyqxmd.com/read/29790898/ezh2-induces-the-expression-of-mir-1301-as-a-negative-feedback-control-mechanism-in-triple-negative-breast-cancer
#1
Qiuju Wu, Zekun Chen, Guihua Zhang, Wenhui Zhou, You Peng, Rong Liu, Ceshi Chen, Jing Feng
Breast cancer is one of the most common malignancies in women. ERα, PR, and HER2 triple negative breast cancer (TNBC) is the current research focus because of the lack of effective targeted therapies. In our study, lentivirus systems were used to overexpress EZH2 and miR-1301 in TNBC cell lines. Western blot analysis and RT-qPCR were used to detect the protein and microRNA levels. The TCGA and Kaplan Meier plotter databases were used to analyze the EZH2 and miR-1301 expression levels in breast cancer. The effect of miR-1301 overexpression on cell proliferation, migration and colony formation were determined by using the sulforhodamine B (SRB) assay, wound healing assay and colony formation assay, respectively...
May 22, 2018: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/29790169/met-in-gastric-cancer-with-liver-metastasis-the-relationship-between-met-amplification-and-met-overexpression-in-primary-stomach-tumors-and-liver-metastasis
#2
Han S Kim, Hong J Chon, Hyunki Kim, Su-Jin Shin, Volker Wacheck, Aaron M Gruver, Jong S Kim, Sun Y Rha, Hyun C Chung
BACKGROUND AND OBJECTIVES: Although MET amplification/overexpression was observed in a subset of gastric cancer (GC) patients, the relationship between MET amplification/overexpression in primary GC and liver metastasis was unclear. METHODS: GC samples and matched liver metastases (N = 47) were analyzed by fluorescence/silver in-situ hybridization (FISH/SISH) and by immunohistochemistry for MET amplification and MET expression, respectively. MET-copy number (CN) and Met expression data from The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD, N = 356) were also analyzed...
May 22, 2018: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29785121/association-between-angiogenesis-and-cytotoxic-signatures-in-the-tumor-microenvironment-of-gastric-cancer
#3
Yi Feng, Ying Dai, Zhihua Gong, Jia-Nan Cheng, Longhui Zhang, Chengdu Sun, Xianghua Zeng, Qingzhu Jia, Bo Zhu
Background: A suppressive immune microenvironment and pathological angiogenesis are hallmarks of gastric cancer. Theoretically, immune checkpoint inhibitors (ICIs) stimulate pre-primed neoantigen-specific T cells, and antiangiogenic agents then facilitate their infiltration into the tumor niche by promoting vascular normalization. Currently, the interconnections of these two phenotypes and their relevance to the tumor microenvironment (TME) have not been fully characterized in gastric cancer...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29785036/a-novel-microrna-signature-predicts-survival-in-liver-hepatocellular-carcinoma-after-hepatectomy
#4
Qiang Fu, Fan Yang, Tengxiao Xiang, Guoli Huai, Xingxing Yang, Liang Wei, Hongji Yang, Shaoping Deng
Liver hepatocellular carcinoma (LIHC) is the most common type of primary liver cancer. In the current study, genome-wide miRNA-Seq and mRNA profiles in 318 LIHC patients derived from The Cancer Genome Atlas (TCGA) were analysed to identify miRNA-based signatures for LIHC prognosis with survival analysis and a semi-supervised principal components (SPC) method. A seven-miRNA signature was confirmed for overall survival (OS) prediction by comparing miRNA profiles in paired primary tumour and solid tumour normal tissues...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784449/a-radiosensitivity-gene-signature-and-pd-l1-predict-the-clinical-outcomes-of-patients-with-lower-grade-glioma-in-tcga
#5
Bum-Sup Jang, In Ah Kim
PURPOSE: Identifying predictive factors for the clinical outcome of patients with lower grade gliomas following radiotherapy could help optimize patient treatments. Here, we investigate the predictive efficacy of both a previously identified "31-gene signature" and programmed death ligand-1 (PD-L1) expression. MATERIAL AND METHODS: We identified 511 patients with lower grade glioma (Grade 2 and 3) in The Cancer Genome Atlas dataset and divided them into two clusters: radiosensitive (RS) and radioresistant (RR)...
May 18, 2018: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
https://www.readbyqxmd.com/read/29781781/gene-expression-microarray-analysis-reveals-prognostic-markers-of-survival-in-high-grade-astrocytomas
#6
Jun Yang, Ziming Hou, Changjiang Wang, Hao Wang, Hongbing Zhang
OBJECTIVE: High grade astrocytoma (HGA) as an aggressive brain tumor, is always correlated with poor prognosis. In this paper, we aimed to explore the genetic prognostic biomarkers for HGA. METHODS: The genome-wide expression profile of 26 brain tumor samples obtained from 26 patients with HGA was downloaded from Gene Expression Omnibus. The risk genes for prognosis of HGA were identified and verified by the data in TCGA database. Protein-protein interaction (PPI) network of risk factor genes was constructed and significant module was screened...
May 21, 2018: Neurological Research
https://www.readbyqxmd.com/read/29781401/screening-of-prognostic-risk-micrornas-for-acute-myeloid-leukemia
#7
Hai-Yan Gao, Wei Wang, Xin-Guo Luo, Yong-Fang Jiang, Xin He, Ping Xu, Xi Chen, Xiao-Yun Li
OBJECTIVES: This study aimed to investigate the risk miRNAs (microRNAs) for AML (acute myeloid leukemia) prognosis and related regulatory mechanisms. METHODS: MiRNA and gene expression data, as well as clinical data of 176 patients were first downloaded from TCGA. Then miRNAs and genes significantly affecting the survival time based on KM survival curve were identified using Log Rank test. Next, COX proportional-hazard regression analysis was performed to screen the risk miRNAs (P-value < 0...
May 19, 2018: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/29781053/expression-of-nox-family-genes-and-their-clinical-significance-in-colorectal-cancer
#8
Sang Yeon Cho, Ju Seok Kim, Hyuk Soo Eun, Sun Hyung Kang, Eaum Seok Lee, Seok Hyun Kim, Jae Kyu Sung, Byung Seok Lee, Hyun Yong Jeong, Hee Seok Moon
BACKGROUND: The NADPH oxidase (NOX) family is overexpressed in many cancers and is associated with cancer cell proliferation and metastasis; however, little is known about the role of the NOX family in colorectal cancer (CRC). AIMS: To identify the expression of the NOX family in CRC and to investigate the relationship between the expression of NOXs with the prognosis of the patients. METHODS: In the TCGA data portal, mRNA expression data were obtained from 41 normal samples and 458 CRC samples to analyze mRNA expression and gene alteration...
May 21, 2018: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/29780284/up-regulation-of-ctd-2547g23-4-in-hepatocellular-carcinoma-tissues-and-its-prospective-molecular-regulatory-mechanism-a-novel-qrt-pcr-and-bioinformatics-analysis-study
#9
Dong-Yue Wen, Peng Lin, Hai-Wei Liang, Xia Yang, Hai-Yuan Li, Yun He, Hong Yang, Gang Chen
Background: Dysregulated expression of long non-coding RNAs (lncRNAs) has been reported in the pathogenesis and progression of multiple cancers, including hepatocellular carcinoma (HCC). LncRNA CTD-2547G23.4 is a novel lncRNA, and its role in HCC is still unknown. Here, we aimed to clarify the expression pattern and clinical value of CTD-2547G23.4 and to investigate the prospective regulatory mechanism via bioinformatics analysis in HCC. Methods: To identify differentially expressed lncRNAs in HCC, we downloaded RNA-Seq data for HCC and adjacent non-tumour tissues via The Cancer Genome Atlas (TCGA)...
2018: Cancer Cell International
https://www.readbyqxmd.com/read/29778426/germline-cytoskeletal-and-extra-cellular-matrix-related-single-nucleotide-variations-associated-with-distinct-cancer-survival-rates
#10
Shayan Falasiri, Tasnif Rahman, Yaping N Tu, Timothy J Fawcett, George Blanck
BACKGROUND: Human mutagenesis has a large stochastic component. Thus, large coding regions, especially cytoskeletal and extra-cellular matrix protein (CECMP) coding regions are particularly vulnerable to mutations. Recent results have verified a high level of somatic mutations in the CECMP coding regions in the cancer genome atlas (TCGA), and a relatively common occurrence of germline, deleterious mutations in the TCGA breast cancer dataset. METHODS: The objective of this study was to determine the correlations of CECMP coding region, germline nucleotide variations with both overall survival (OS) and disease-free survival (DFS)...
May 17, 2018: Gene
https://www.readbyqxmd.com/read/29776954/role-of-elevated-phip-copy-number-as-a-prognostic-and-progression-marker-for-cutaneous-melanoma
#11
Vladimir Bezrookove, Mehdi Nosrati, James R Miller, David de Semir, Altaf A Dar, Elham Vosoughi, Edith Vaquero, Antje Sucker, Alexander J Lazar, Jeffrey E Gershenwald, Michael A Davies, Dirk Schadendorf, Mohammed Kashani-Sabet
PURPOSE: Previous studies have indicated an important role for pleckstrin homology domain-interacting protein (PHIP) as a marker and mediator of melanoma metastasis. Here we aimed to confirm the role of PHIP copy number in successive stages of melanoma progression. EXPERIMENTAL DESIGN: PHIP copy number was examined using fluorescence in situ hybridization (FISH) in three independent cohorts by recording the percentage of cells harboring &gt; 3 copies of PHIP...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29776953/the-landscape-of-actionable-genomic-alterations-in-cell-free-circulating-tumor-dna-from-21-807-advanced-cancer-patients
#12
Oliver A Zill, Kimberly C Banks, Stephen R Fairclough, Stefanie Mortimer, James V Vowles, Reza Mokhtari, David R Gandara, Philip C Mack, Justin I Odegaard, Rebecca J Nagy, Arthur M Baca, Helmy Eltoukhy, Darya I Chudova, Richard B Lanman, AmirAli Talasaz
PURPOSE: Cell-free DNA (cfDNA) sequencing provides a non-invasive method for obtaining actionable genomic information to guide personalized cancer treatment, but the presence of multiple alterations in circulation related to treatment and tumor heterogeneity complicate the interpretation of the observed variants. Experimental Design: We describe the somatic mutation landscape of 70 cancer genes from cfDNA deep-sequencing analysis of 21,807 patients with treated, late-stage cancers across &gt;50 cancer types...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29775610/monocarboxylate-transporters-in-breast-cancer-and-adipose-tissue-are-novel-biomarkers-and-potential-therapeutic-targets
#13
Zhiyu Li, Qi Wu, Si Sun, Juan Wu, Juanjuan Li, Yimin Zhang, Changhua Wang, Jingping Yuan, Shengrong Sun
Monocarboxylate transporters (MCTs) are transmembrane proteins that control the lactate metabolism and associated with poor prognosis in solid tumors including breast cancer (BC). This study aimed to evaluate the clinical and prognostic value of MCTs used by immunohistochemistry and quantum dots-based fluorescent imaging technique in BC and surrounding stroma with emphasis on the interaction between tumour and stroma. Moreover, the data from The Cancer Genome Atlas (TCGA) was analyzed to evaluate the association between MCTs mRNA expression and prognosis of breast cancer patients...
May 15, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29774872/a-signature-based-on-survival-related-genes-identifies-high-risk-glioblastomas-harboring-immunosuppressive-and-aggressive-ecm-characteristics
#14
Di Chen, Dikang Chen, Dongqing Cao, Jian Hu, Yu Yao
To seek survival-related genes in glioblastoma and establish a survival-gene signature for predicting prognoses of glioblastoma using public databases.
 Methods: Three independent glioma databases (GEO GSE53733, CGGA, TCGA) with whole genome expression data were included for analysis. Survival-related genes were obtained by comparing the long-term (>36 months) and short-term (<12 months) survivors in the database GSE53733. CGGA was used as the training set to develop the signature and TCGA was used as the validation set...
April 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/29774870/radiomics-in-gliomas-a-promising-assistance-for-glioma-clinical-research
#15
Yueshuang Leng, Xiaoyi Wang, Weihua Liao, Ya Cao
Gliomas are the most common brain primary tumors worldwide, which is the earliest sequenced cancer gene in the Cancer Genome Atlas (TCGA) project. The World Health Organization Classification Update of Central Nervous System (CNS) Tumors 2016 highlights that glioma is the first tumor classified based on both of the molecular markers and histology. Radiomics is an extraction approach for high-throughput data which collects the quantitative image information appearing. Combined imaging data with genomics and proteomics, radiomics show promising prediction for cancer diagnosis, treatment, and prognosis...
April 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/29774579/integrative-epigenetic-analysis-reveals-therapeutic-targets-to-the-dna-methyltransferase-inhibitor-sgi-110-in-hepatocellular-carcinoma
#16
Minmin Liu, Lian Zhang, Hongtao Li, Toshinori Hinoue, Wanding Zhou, Hitoshi Ohtani, Anthony El-Khoueiry, John Daniels, Casey O'Connell, Tanya B Dorff, Qianjin Lu, Daniel J Weisenberger, Gangning Liang
There is an urgent need for developing more effective therapies for hepatocellular carcinoma (HCC) because of its aggressiveness. Guadecitabine (SGI-110) is a second-generation DNA methyltransferase inhibitor (DNMTi) currently in clinical trials for HCC and shows greater stability and performance over first generation DNMTis. In order to identify potential therapeutic targets of SGI-110 for clinical trials, HCC cell lines (SNU398, HepG2 and SNU475) were used to evaluate effects of transient SGI-110 treatment by an integrative analysis of DNA methylation, nucleosome accessibility, gene expression profiles and its clinical relevance by comparisons to TCGA HCC clinical data...
May 18, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29774095/a-long-non-coding-rna-signature-for-predicting-survival-in-patients-with-colorectal-cancer
#17
Yi-Lin Wang, Jun Shao, Xiaohong Wu, Tong Li, Ming Xu, Debing Shi
Dysregulation of long non-coding RNA (lncRNA) plays important roles in cancer development and progression. In this work, we attempted to develop a lncRNA signature to improve prognosis prediction of colorectal cancer. A comprehensive analysis for the lncRNA expression and corresponding clinical information of 344 colorectal patients has been performed based on the data from The Cancer Genome Atlas (TCGA). We randomly divided TCGA data into a training set ( n = 172) and a testing set ( n = 172). A four-lncRNA signature has been established which was significantly associated with the overall survival of colorectal cancer patients...
April 24, 2018: Oncotarget
https://www.readbyqxmd.com/read/29773494/plin3-is-up-regulated-and-correlates-with-poor-prognosis-in-clear-cell-renal-cell-carcinoma
#18
Keshan Wang, HaiLong Ruan, ZhengShuai Song, Qi Cao, Lin Bao, Di Liu, TianBo Xu, HaiBing Xiao, Cheng Wang, Gong Cheng, JunWei Tong, XianGui Meng, HongMei Yang, Ke Chen, XiaoPing Zhang
BACKGROUND: PLIN3, one of the members of the perilipin family, has been reported to be involved in the formation and accumulation of lipid droplets. However, the expression levels and diagnostic and prognostic value of PLIN3 in renal cell carcinoma (RCC) remain unclear. METHODS: Bioinformatic analysis was used to assess the levels of PLIN3 and the correlation between PLIN3 levels and clinicopathological parameters in renal cancer. The expression levels of PLIN3 were determined in human RCC tissues and cell lines by western blot, immunofluorescence and immunohistochemistry assays...
May 14, 2018: Urologic Oncology
https://www.readbyqxmd.com/read/29772079/detection-of-multiple-perturbations-in-multi-omics-biological-networks
#19
Paula J Griffin, Yuqing Zhang, William Evan Johnson, Eric D Kolaczyk
Cellular mechanism-of-action is of fundamental concern in many biological studies. It is of particular interest for identifying the cause of disease and learning the way in which treatments act against disease. However, pinpointing such mechanisms is difficult, due to the fact that small perturbations to the cell can have wide-ranging downstream effects. Given a snapshot of cellular activity, it can be challenging to tell where a disturbance originated. The presence of an ever-greater variety of high-throughput biological data offers an opportunity to examine cellular behavior from multiple angles, but also presents the statistical challenge of how to effectively analyze data from multiple sources...
May 17, 2018: Biometrics
https://www.readbyqxmd.com/read/29771422/has-mir-196a-2-is-up-regulated-and-acts-as-an-independent-unfavorable-prognostic-factor-in-thyroid-carcinoma
#20
Y-T Fu, D-Q Zhang, L Zhou, S-J Li, H Sun, X-L Liu, H-B Zheng
OBJECTIVE: To identify the role of hsa-miR-196a-2 in thyroid cancer by bioinformatics analysis. MATERIALS AND METHODS: The expression profiles of thyroid cancer was download from TCGA. The dysregulated microRNAs were obtained by edger R package. Then, the prognostic data were analyzed by K-M plot. The difference between different groups was analyzed by the t-test. At last, the biological processes of has-miR-196a-2 were obtained with GSEA. RESULTS: In this study, we found that has-miR-196a-2 was upregulated in thyroid carcinoma by analyzing the TCGA database, which was inversely proportional to the prognosis of patients with thyroid carcinoma...
May 2018: European Review for Medical and Pharmacological Sciences
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