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https://www.readbyqxmd.com/read/29332336/downregulation-of-guanine-nucleotide-binding-protein-beta-1-gnb1-is-associated-with-worsened-prognosis-of-clearcell-renal-cell-carcinoma-and-is-related-to-vegf-signaling-pathway
#1
C Chen, H Chi, L Min, Z Junhua
PURPOSE: Clear-cell renal cell carcinoma (ccRCC) is characterized by genetic abnormalities, while the role of Guanine Nucleotide-Binding Protein Beta 1 (GNB1) in ccRCC has not been studied. We thus aimed to evaluate the expression and prognostic value of GNB1 in ccRCC. METHODS: A two-stage study (exploration and validation) was conducted using in silico and immunohistochemical (IHC) scoring of ccRCC samples from our institute, to evaluate the association between GNB1 expression and clinicopathological parameters of ccRCC patients...
November 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29330617/characterizing-genomic-differences-of-human-cancer-stratified-by-the-tp53-mutation-status
#2
Mengyao Wang, Chao Yang, Xiuqing Zhang, Xiangchun Li
The key roles of the TP53 mutation in cancer have been well established. TP53 is the most frequently mutated gene, and its inactivation is widespread among human cancer types. However, the landscape of genomic alterations in human cancers stratified by the TP53 mutation has not yet been described. We obtained somatic mutation and copy number change data of 6551 regular-mutated samples from the Cancer Genome Atlas (TCGA) and compared significantly mutated genes (SMGs), copy number alterations, mutational signatures and mutational strand asymmetries between cancer samples with and without the TP53 mutation...
January 12, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29330370/a-rna-sequencing-approach-for-the-identification-of-novel-long-non-coding-rna-biomarkers-in-colorectal-cancer
#3
Atsushi Yamada, Pingjian Yu, Wei Lin, Yoshinaga Okugawa, C Richard Boland, Ajay Goel
Long non-coding RNAs (lncRNAs) have been implicated in human pathology, however, their role in colorectal carcinogenesis have not been fully elucidated. In the current study, whole-transcriptome analysis was performed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. Up-regulation of four lncRNAs, hereby named colorectal cancer associated lncRNA (CRCAL)-1 [AC021218...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330309/poverty-a-risk-factor-overlooked-a-cross-sectional-cohort-study-comparing-poverty-rate-and-cardiovascular-disease-outcomes-in-the-state-of-florida
#4
Bashar Al-Turk, Ciel Harris, Grant Nelson, Carmen Smotherman, Carlos Palacio, Jeff House
The purpose of this study is to examine the relationship between poverty rate and heart disease in our state. A cross-sectional data analysis was performed using figures provided by the Center for Disease Control's Interactive Atlas of Heart Disease and Stroke Tables. Spearman's correlations and simple regressions were used to determine if there was a relationship between poverty and cardiovascular hospitalization rate and cardiovascular death rate. There was a positive monotonic correlation between poverty rate and cardiovascular hospitalization rate (Rho=0...
January 12, 2018: Journal of Investigative Medicine: the Official Publication of the American Federation for Clinical Research
https://www.readbyqxmd.com/read/29330288/epigenetically-regulated-chromosome-14q32-mirna-cluster-induces-metastasis-and-predicts-poor-prognosis-in-lung-adenocarcinoma-patients
#5
Margarita Gonzalez-Vallinas, Manuel Rodriguez-Paredes, Marco Albrecht, Carsten Sticht, Damian Stichel, Julian Gutekunst, Adriana Pitea, Steffen Sass, Francisco J Sánchez-Rivera, Justo L Bermejo, Jennifer Schmitt, Carolina De La Torre, Arne Warth, Fabian Theis, Nikola Mueller, Norbert Gretz, Thomas Muley, Michael Meister, Darjus F Tschaharganeh, Peter Schirmacher, Franziska Matthäus, Kai Breuhahn
Most lung cancer deaths are related to metastases, which indicates the necessity of detecting and inhibiting tumor cell dissemination. Here, we aimed to identify microRNAs (miRNAs) involved in metastasis of lung adenocarcinoma as prognostic biomarkers and therapeutic targets. To that end, lymph node metastasis-associated miRNAs were identified in The Cancer Genome Atlas (TCGA) lung adenocarcinoma patient cohort (sequencing data; n=449) and subsequently validated by RT-qPCR in an independent clinical cohort (n=108)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330282/population-dependent-intron-retention-and-dna-methylation-in-breast-cancer
#6
Dongwook Kim, Manu Shivakumar, Seonggyun Han, Michael S Sinclair, Youngji Lee, Yonglan Zheng, Olufunmilayo I Olopade, Dokyoon Kim, Younghee Lee
Regulation of gene expression by DNA methylation in gene promoter regions is well-studied; however, the effects of methylation in the gene body (exons and introns) on gene expression are comparatively understudied. Recently, hyper-methylation has been implicated in the inclusion of alternatively spliced exons; moreover, exon recognition can be enhanced by recruiting the methyl-CpG-binding protein (MeCP2) to hyper-methylated sites. This study examines if methylation status of an intron is correlated with how frequently the intron is retained during splicing using DNA methylation and RNA sequencing (RNA-seq) data from breast cancer tissue specimens in The Cancer Genome Atlas (TCGA)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330202/high-risk-tp53-mutations-are-associated-with-extra-nodal-extension-ene-in-oral-cavity-squamous-cell-carcinoma-oscc
#7
Vlad C Sandulache, Chieko Michikawa, Pranav Kataria, Frederico O Gleber-Netto, Diana Bell, Sanchit Trivedi, Xiayu Rao, Jing Wang, Mei Zhao, Samar A Jasser, Jeffrey N Myers, Curtis R Pickering
PURPOSE:   Development of extra-nodal extension (ENE) has been associated with poor survival in patients with oral cavity squamous cell carcinoma (OSCC). Here we sought to confirm the role of ENE as a poor prognostic factor, and identify genomic and epigenetic markers of ENE in order to develop a predictive model and improve treatment selection. EXPERIMENTAL DESIGN: An institutional cohort (University of Texas MD Anderson Cancer Center) was utilized to confirm the impact of ENE on clinical outcomes and evaluate the genomic signature of primary and ENE containing tissue...
January 12, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29329368/discovering-personalized-driver-mutation-profiles-of-single-samples-in-cancer-by-network-control-strategy
#8
Wei-Feng Guo, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qian-Qian Shi, Lei Zhang, Ying Tang, Tao Zeng, Luonan Chen
Motivation: It is a challenging task to discover personalized driver genes that provide crucial information on disease risk and drug sensitivity for individual patients. However, few methods have been proposed to identify the personalized-sample driver genes from the cancer omics data due to the lack of samples for each individual. To circumvent this problem, here we present a novel single-sample controller strategy (SCS) to identify personalized driver mutation profiles from network controllability perspective...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29328510/a-multidimensional-assessment-of-the-burden-of-psoriasis-results-from-a-multinational-dermatologist-and-patient-survey
#9
C E M Griffiths, S J Jo, L Naldi, R Romiti, E Guevara-Sangines, T Howe, G Pietri, I Gilloteau, C Richardson, H Tian, M Augustin
BACKGROUND: Psoriasis is a chronic, immune-mediated disease, characterised by symptoms that include itching and skin pain and is often associated with comorbidities. Patients have a substantial detriment to quality of life (QoL) and work productivity with associated cost burden. OBJECTIVE: To investigate the incremental burden of comorbidities, itch, and affected body areas among systemic eligible patients with psoriasis, using a multinational survey of dermatologists and their psoriasis patients...
January 12, 2018: British Journal of Dermatology
https://www.readbyqxmd.com/read/29328463/construction-and-investigation-of-lncrna-associated-cerna-regulatory-network-in-papillary-thyroid-cancer
#10
Yangjing Zhao, Hui Wang, Chengjiang Wu, Meina Yan, Haojie Wu, Jingzhe Wang, Xinxin Yang, Qixiang Shao
Increasing evidence has experimentally proved the competitive endogenous RNA (ceRNA) hypothesis that long non-coding RNA (lncRNA) can affect the expression of RNA targets by competitively combining microRNA (miRNA) via miRNA response elements. However, an extensive ceRNA network of thyroid carcinoma in a large cohort has not been evaluated. We analyzed the RNAseq and miRNAseq data of 348 cases of primary papillary thyroid cancer (PTC) patients with clinical information downloaded from The Cancer Genome Atlas (TCGA) project to search for potential biomarkers or therapeutic targets...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29328377/feature-genes-in-metastatic-breast-cancer-identified-by-metade-and-svm-classifier-methods
#11
Youlin Tuo, Ning An, Ming Zhang
The aim of the present study was to investigate the feature genes in metastatic breast cancer samples. A total of 5 expression profiles of metastatic breast cancer samples were downloaded from the Gene Expression Omnibus database, which were then analyzed using the MetaQC and MetaDE packages in R language. The feature genes between metastasis and non‑metastasis samples were screened under the threshold of P<0.05. Based on the protein‑protein interactions (PPIs) in the Biological General Repository for Interaction Datasets, Human Protein Reference Database and Biomolecular Interaction Network Database, the PPI network of the feature genes was constructed...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328363/support-vector-machine-classifier-for-prediction-of-the-metastasis-of-colorectal-cancer
#12
Jiajun Zhi, Jiwei Sun, Zhongchuan Wang, Wenjun Ding
Colorectal cancer (CRC) is one of the most common cancers and a major cause of mortality. The present study aimed to identify potential biomarkers for CRC metastasis and uncover the mechanisms underlying the etiology of the disease. The five datasets GSE68468, GSE62321, GSE22834, GSE14297 and GSE6988 were utilized in the study, all of which contained metastatic and non-metastatic CRC samples. Among them, three datasets were integrated via meta-analysis to identify the differentially expressed genes (DEGs) between the two types of samples...
January 2, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29328002/dexamethasone-mediated-oncogenicity-in-vitro-and-in-an-animal-model-of-glioblastoma
#13
Markus M Luedi, Sanjay K Singh, Jennifer C Mosley, Islam S A Hassan, Masumeh Hatami, Joy Gumin, Lukas Andereggen, Erik P Sulman, Frederick F Lang, Frank Stueber, Gregory N Fuller, Rivka R Colen, Pascal O Zinn
OBJECTIVE Dexamethasone, a known regulator of mesenchymal programming in glioblastoma (GBM), is routinely used to manage edema in GBM patients. Dexamethasone also activates the expression of genes, such as CEBPB, in GBM stem cells (GSCs). However, the drug's impact on invasion, proliferation, and angiogenesis in GBM remains unclear. To determine whether dexamethasone induces invasion, proliferation, and angiogenesis in GBM, the authors investigated the drug's impact in vitro, in vivo, and in clinical information derived from The Cancer Genome Atlas (TCGA) cohort...
January 12, 2018: Journal of Neurosurgery
https://www.readbyqxmd.com/read/29327560/-research-progress-on-reatment-of-unstable-atlas-fracture-with-single-segment-fixation-by-transoral-approach
#14
REVIEW
Li-Ran Wang, Liu-Jun Zhao, Wei-Hu Ma
As a common type of fracture in cervical, atlas fracture is frequently unstable due to its special anatomical structure. In a previous treatment, external fixation was likely to bring low bony union rate and long-term neck pain, while occipito-cervical fusion and atlantoaxial fusion sacrifice range of motion in cervical spine. Reduction and single section fixation of atlas by anterior lateral mass screws through the transoral approach were reported by some scholars, and the retrospective study demonstrated the high healing rate, reservation of cervical ROM and less bleeding...
January 25, 2017: Zhongguo Gu Shang, China Journal of Orthopaedics and Traumatology
https://www.readbyqxmd.com/read/29327492/a-five-gene-signature-may-predict-sunitinib-sensitivity-and-serve-as-prognostic-biomarkers-for-renal-cell-carcinoma
#15
Yuan-Lei Chen, Guang-Ju Ge, Chao Qi, Huan Wang, Huai-Lan Wang, Li-Yang Li, Gong-Hui Li, Li-Qun Xia
Sunitinib resistance is, nowadays, the major challenge for advanced renal cell carcinoma patients. Illuminating the potential mechanisms and exploring effective strategies to overcome sunitinib resistance are highly desired. We constructed a reliable gene signature which may function as biomarkers for prediction of sunitinib sensitivity and clinical prognosis. The gene expression profiles were obtained from The Cancer Genome Atlas database. By performing GEO2R analysis, numerous differentially expressed genes (DEGs) were found to be associated with sunitinib resistance...
January 12, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29326478/publisher-correction-transcriptome-dynamics-revealed-by-a-gene-expression-atlas-of-the-early-arabidopsis-embryo
#16
Joakim Palovaara, Shunsuke Saiga, Jos R Wendrich, Nicole van 't Wout Hofland, J Paul van Schayck, Friederike Hater, Sumanth Mutte, Jouke Sjollema, Mark Boekschoten, Guido J Hooiveld, Dolf Weijers
In the version of this Resource originally published, the author information was incorrect. Jos R. Wendrich should have had a present address: Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052 Ghent, Belgium. Mark Boekschoten and Guido J. Hooiveld should have been affiliated to the Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE Wageningen, The Netherlands. In addition, the version of Supplementary Table 5 originally published with this Resource was not the intended final version and included inaccurate citations to the display items of the Resource, and the file format and extension did not match...
January 11, 2018: Nature Plants
https://www.readbyqxmd.com/read/29326043/upregulation-of-cdca5-promotes-gastric-cancer-malignant-progression-via-influencing-cyclin-e1
#17
Zhengyuan Zhang, Mingyang Shen, Guangrong Zhou
The cell division cycle associated 5(CDCA5) was reported to be associated with progression of several human cancers, however, its clinical significance and biological role still remain unknown in gastric cancer(GC). By analyzing The Cancer Genome Atlas(TCGA), we found CDCA5 was significantly upregulated in GC tissues compared to adjacent normal tissues. Tissue microarray(TMA) indicated upregulation of CDCA5 was significantly correlated with more advanced clinicopathological features, and acts as an independent risk factor for worse overall survival(OS) in GC patients...
January 8, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29326036/exploring-young-mothers-experiences-with-postpartum-contraception-in-ottawa-results-from-a-multi-methods-qualitative-study
#18
Elyse Fortier, Angel M Foster
OBJECTIVES: Postpartum contraception plays a significant role in reducing subsequent pregnancy. However, young mothers in Ottawa, the capital of Canada, face various barriers when trying to access contraception after delivery. Through this project we aimed to explore these barriers and understand the decision-making processes of young mothers surrounding postpartum contraception. STUDY DESIGN: We conducted 10 semi-structured in-depth interviews with young mothers living in Ottawa who had experienced a subsequent pregnancy within 24 months of their first childbirth...
January 8, 2018: Contraception
https://www.readbyqxmd.com/read/29325780/longitudinal-atlas-for-normative-human-brain-development-and-aging-over-the-lifespan-using-quantitative-susceptibility-mapping
#19
Yuyao Zhang, Hongjiang Wei, Matthew J Cronin, Naying He, Fuhua Yan, Chunlei Liu
Longitudinal brain atlases play an important role in the study of human brain development and cognition. Existing atlases are mainly based on anatomical features derived from T1-and T2-weighted MRI. A 4D developmental quantitative susceptibility mapping (QSM) atlas may facilitate the estimation of age-related iron changes in deep gray matter nuclei and myelin changes in white matter. To this end, group-wise co-registered QSM templates were generated over various age intervals from age 1-83 years old. Registration was achieved by combining both T1-weighted and QSM images...
January 8, 2018: NeuroImage
https://www.readbyqxmd.com/read/29325579/the-return-of-the-iberian-lynx-to-portugal-local-voices
#20
Margarida Lopes-Fernandes, Clara Espírito-Santo, Amélia Frazão-Moreira
BACKGROUND: Ethnographic research can help to establish dialog between conservationists and local people in reintroduction areas. Considering that predator reintroductions may cause local resistance, we assessed attitudes of different key actor profiles to the return of the Iberian lynx (Lynx pardinus) to Portugal before reintroduction started in 2015. We aimed to characterize a social context from an ethnoecological perspective, including factors such as local knowledge, perceptions, emotions, and opinions...
January 11, 2018: Journal of Ethnobiology and Ethnomedicine
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