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https://www.readbyqxmd.com/read/29776954/role-of-elevated-phip-copy-number-as-a-prognostic-and-progression-marker-for-cutaneous-melanoma
#1
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 > 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
#2
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 >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
#3
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/29774870/radiomics-in-gliomas-a-promising-assistance-for-glioma-clinical-research
#4
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/29774095/a-long-non-coding-rna-signature-for-predicting-survival-in-patients-with-colorectal-cancer
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/29770915/cytolytic-activity-score-to-assess-anticancer-immunity-in-colorectal-cancer
#9
Sumana Narayanan, Tsutomu Kawaguchi, Li Yan, Xuan Peng, Qianya Qi, Kazuaki Takabe
BACKGROUND: Elevated tumor-infiltrating lymphocytes (TILs) within the tumor microenvironment is a known positive prognostic factor in colorectal cancer (CRC). We hypothesized that since cytotoxic T cells release cytolytic proteins such as perforin (PRF1) and pro-apoptotic granzymes (GZMA) to attack cancer cells, a cytolytic activity score (CYT) would be a useful tool to assess anticancer immunity. METHODS: Genomic expression data were obtained from 456 patients from The Cancer Genome Atlas (TCGA)...
May 16, 2018: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/29770536/combination-of-ifitm1-knockdown-and-radiotherapy-inhibits-the-growth-of-oral-cancer
#10
Jie Yang, Lei Li, Yan Xi, Ruimei Sun, Hu Wang, Yanxin Ren, Liufang Zhao, Xiaoli Wang, Xiaojiang Li
This research aimed to analyze the effect of IFITM1 on the radioresistance of oral neoplasm. IFITM1 emerged using multi-group heat map from GSE9716 analysis of GEO database as the relevant radioresistance gene. IFITM1 was screened by TCGA database before its expression was analyzed. IFITM1 expression was quantified by qRT-PCR and immunohistochemistry in 19 paired oral neoplasm cases. The effects of time and dose of radiation on IFITM1 expression level in CAL27 and TSCC1 cell lines was tested via qRT-PCR. Oral neoplasm cells were transfected with siRNA after radiotherapy to disturb IFITM1 expression...
May 16, 2018: Cancer Science
https://www.readbyqxmd.com/read/29769742/modified-citrus-pectin-inhibited-bladder-tumor-growth-through-downregulation-of-galectin-3
#11
Tian Fang, Dan-Dan Liu, He-Ming Ning, Dan Liu, Jing-Ya Sun, Xiao-Jing Huang, Yu Dong, Mei-Yu Geng, Shi-Feng Yun, Jun Yan, Rui-Min Huang
Modified citrus pectin (MCP) is a carbohydrate enriched complex, which has been implicated in cancer treatment and prevention. However, the effects of MCP on urinary bladder cancer (UBC) are unknown. In this study, MCP was first tested in T24 and J82 human UBC cells and showed the inhibition of cell viability by the sulforhodamine B (SRB) assay. The MCP-treated UBC cells exhibited G2 /M phase arrest with the decrease of Cyclin B1 and phosphorylated Cdc2. Caspase-3 was also activated, leading to the cleavage of Caspase-3 and PARP...
May 16, 2018: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/29769662/novel-internal-regulators-and-candidate-mirnas-within-mir-379-mir-656-mirna-cluster-can-alter-cellular-phenotype-of-human-glioblastoma
#12
Subhashree Nayak, Meghali Aich, Anupam Kumar, Suman Sengupta, Prajakta Bajad, Parashar Dhapola, Deepanjan Paul, Kiran Narta, Suvendu Purkrait, Bharati Mehani, Ashish Suri, Debojyoti Chakraborty, Arijit Mukhopadhyay, Chitra Sarkar
Clustered miRNAs can affect functioning of downstream pathways due to possible coordinated function. We observed 78-88% of the miR-379/miR-656 cluster (C14MC) miRNAs were downregulated in three sub-types of diffuse gliomas, which was also corroborated with analysis from The Cancer Genome Atlas (TCGA) datasets. The miRNA expression levels decreased with increasing tumor grade, indicating this downregulation as an early event in gliomagenesis. Higher expression of the C14MC miRNAs significantly improved glioblastioma prognosis (Pearson's r = 0...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769535/systematic-pan-cancer-analysis-of-somatic-allele-frequency
#13
Liam Spurr, Muzi Li, Nawaf Alomran, Qianqian Zhang, Paula Restrepo, Mercedeh Movassagh, Chris Trenkov, Nerissa Tunnessen, Tatiyana Apanasovich, Keith A Crandall, Nathan Edwards, Anelia Horvath
Imbalanced expression of somatic alleles in cancer can suggest functional and selective features, and can therefore indicate possible driving potential of the underlying genetic variants. To explore the correlation between allele frequency of somatic variants and total gene expression of their harboring gene, we used the unique data set of matched tumor and normal RNA and DNA sequencing data of 5523 distinct single nucleotide variants in 381 individuals across 10 cancer types obtained from The Cancer Genome Atlas (TCGA)...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769534/a-five-microrna-signature-for-survival-prognosis-in-pancreatic-adenocarcinoma-based-on-tcga-data
#14
Xiu-Hui Shi, Xu Li, Hang Zhang, Rui-Zhi He, Yan Zhao, Min Zhou, Shu-Tao Pan, Chun-Le Zhao, Ye-Chen Feng, Min Wang, Xing-Jun Guo, Ren-Yi Qin
Novel biomarkers for pancreatic adenocarcinoma are urgently needed because of its poor prognosis. Here, by using The Cancer Genome Atlas (TCGA) RNA-seq data, we evaluated the prognostic values of the differentially expressed miRNAs and constructed a five-miRNA signature that could effectively predict patient overall survival (OS). The Kaplan-Meier overall survival curves of two groups based on the five miRNAs were notably different, showing overall survival in 10.2% and 47.8% at five years for patients in high-risk and low-risk groups, respectively...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29768063/overexpression-of-hoxc10-promotes-glioblastoma-cell-progression-to-a-poor-prognosis-via-the-pi3k-akt-signaling-pathway
#15
Yong Guan, Yajie He, Shaoping Lv, Xiaoqun Hou, Luo Li, Jianjun Song
OBJECTIVE: The HOX gene is expressed in neoplasias occurred in multiple tissues, such as the colon, lung, and breast. However, the effects of the HOX gene on glioblastoma (GBM) remain poorly understood. We examined HOXC10 expression in GBM tissues and cells, analyzed its effect on GBM prognosis, and finally assessed its possible underlying mechanisms in this study. METHODS: HOXC10 expression levels and its prognostic effects on GBM tissues were analyzed based on The Cancer Genome Atlas (TCGA) and ONCOMINE database...
May 16, 2018: Journal of Drug Targeting
https://www.readbyqxmd.com/read/29767233/potential-role-of-cyclin-f-mrna-expression-in-the-survival-of-skin-melanoma-patients-comprehensive-analysis-of-the-pathways-altered-due-to-cyclin-f-upregulation
#16
Maciej Gagat, Adrian Krajewski, Dariusz Grzanka, Alina Grzanka
Cyclin F is a part of the Skp, Cullin, F-box containing ligase complex. The activity of cyclin F includes cell cycle control, centrosome duplication and response to DNA damage. The cyclin F expression pattern is very similar to cyclin A, but cyclin F is an orphan cyclin without its cyclin-dependent kinase partner. There is little evidence concerning the role of cyclin F in cancer. In the present study, for the first time, we present analysis from The Cancer Genome Atlas (TCGA) data in the context of expression of cyclin F mRNA in melanoma patients...
May 16, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29767230/competing-endogenous-rna-regulatory-network-in-papillary-thyroid-carcinoma
#17
Shouhua Chen, Xiaobin Fan, He Gu, Lili Zhang, Wenhua Zhao
The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA‑sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE‑miRNAs), long non‑coding RNAs (DE‑lncRNAs) and genes (DEGs). Subsequently, lncRNA‑miRNA, miRNA‑gene (that is, miRNA‑mRNA) and gene‑gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA‑mRNA network were identified by topological analysis and recursive feature elimination analysis...
May 11, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29766637/subtype-specific-clinical-and-prognostic-relevance-of-tumor-expressed-f5-and-regulatory-f5-variants-in-breast-cancer-the-cocav-study
#18
Mari Tinholt, Øystein Garred, Elin Borgen, Elsa Beraki, Ellen Schlichting, Vessela Kristensen, Kristine Kleivi Sahlberg, Nina Iversen
BACKGROUND: Tumor expression of certain coagulation factors have been linked to cancer progression. Single nucleotide polymorphisms (SNPs) in F5 (encoding the FV protein) have been found associated with breast cancer, however, the role of coagulation factor V (FV) in cancer pathogenesis remains undiscovered. OBJECTIVES: We aimed to investigate the clinical significance of FV and the regulatory role of F5 gene variants in breast cancer. PATIENTS/METHODS: A Scandinavian 503-sample breast cancer cohort and three public breast cancer data sets (GOBO, TCGA, and KM plotter) were used to determine associations between F5 gene expression (tumor-specific), circulating FV, F5 SNPs, clinical characteristics, and breast cancer survival...
May 16, 2018: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/29766219/association-study-of-genetic-variants-in-estrogen-metabolic-pathway-genes-and-colorectal-cancer-risk-and-survival
#19
Shuwei Li, Lisheng Xie, Mulong Du, Kaili Xu, Lingjun Zhu, Haiyan Chu, Jinfei Chen, Meilin Wang, Zhengdong Zhang, Dongying Gu
Although studies have investigated the association of genetic variants and the abnormal expression of estrogen-related genes with colorectal cancer risk, the evidence remains inconsistent. We clarified the relationship of genetic variants in estrogen metabolic pathway genes with colorectal cancer risk and survival. A case-control study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in ten candidate genes with colorectal cancer risk in a Chinese population. A logistic regression model and Cox regression model were used to calculate SNP effects on colorectal cancer susceptibility and survival, respectively...
May 16, 2018: Archives of Toxicology
https://www.readbyqxmd.com/read/29764807/predicting-the-presence-of-oral-squamous-cell-carcinoma-using-commonly-dysregulated-microrna-in-oral-swirls
#20
Tami Yap, Kendrick Koo, Lesley Cheng, Laura J Vella, Andrew F Hill, Eric C Reynolds, Alf L Nastri, Nicola Cirillo, Christine A Seers, Michael McCullough
Oral swirls are a noninvasive, rapidly collected source of salivary microRNA potentially useful in the early detection of disease states, particularly oral squamous cell carcinoma (OSCC). The aim of this study was to predict the presence of oral squamous cell carcinoma using a panel of OSCC-related dysregulated microRNA found in oral swirls, identified jointly in data from formalin-fixed paraffin embedded (FFPE) and fresh frozen specimens. Next generation sequencing (NGS) was used to determine microRNA fold changes in FFPE OSCC specimens relative to histologically normal epithelium...
May 15, 2018: Cancer Prevention Research
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