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https://www.readbyqxmd.com/read/28537924/genetic-defects-of-the-irf1-mediated-major-histocompatibility-complex-class-i-antigen-presentation-pathway-occur-prevalently-in-the-jak2-gene-in-non-small-cell-lung-cancer
#1
Tao Shen, Zhengming Chen, Zhizhuang Joe Zhao, Jie Wu
Recognition of major histocompatibility complex (MHC) class I antigens on tumor cells by cytotoxic T cells is involved in T cell-mediated tumor immune surveillance and immune checkpoint therapy. The interferon-γ (IFNγ)-IRF1 signaling pathway regulates MHC class I antigen presentation. To examine genetic defects of the IFNγ-IRF1 pathway in non-small cell lung cancer (NSCLC), we analyzed The Cancer Genome Atlas (TCGA) lung adenocarcinoma (LuAd) and lung squamous cell carcinoma (LuSc) data. Loss-of-function (LOF) genetic alterations of the IFNγ-IRF1 pathway genes (IFNGR1, IFNGR2, JAK1, JAK2, STAT1, IRF1) were found in 64 (6...
May 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28535188/molecular-heterogeneity-at-the-network-level-high-dimensional-testing-clustering-and-a-tcga-case-study
#2
Nicolas Städler, Frank Dondelinger, Steven M Hill, Rehan Akbani, Yiling Lu, Gordon B Mills, Sach Mukherjee
Motivation: Molecular pathways and networks play a key role in basic and disease biology. An emerging notion is that networks encoding patterns of molecular interplay may themselves differ between contexts, such as cell type, tissue or disease (sub)type. However, while statistical testing of differences in mean expression levels has been extensively studied, testing of network differences remains challenging. Furthermore, since network differences could provide important and biologically interpretable information to identify molecular subgroups, there is a need to consider the unsupervised task of learning subgroups and networks that define them...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28535016/nherf1-inhibits-proliferation-of-triple-negative-breast-cancer-cells-by-suppressing-gper-signaling
#3
Yan Wang, Zhiqiang Peng, Ran Meng, Tao Tao, Qiqi Wang, Chunjuan Zhao, Hua Liu, Ran Song, Junfang Zheng, Qiong Qin, Junqi He
G protein-coupled estrogen receptor (GPER) signaling is activated in triple-negative breast cancer (TNBC); however, the detailed mechanisms of its regulation remain unclear. The present study aimed to elucidate the molecular mechanisms involved in GPER activation in TNBC. In MDA-MB-231 cells, a TNBC cell line, NHERF1 interaction with GPER was verified by co-immunoprecipitation and immunofluorescent staining assays. Overexpression of NHERF1 in MDA-MB-231 cells inhibited GPER-mediated proliferation and phosphorylation of ERK1/2 and Akt...
May 18, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28534507/cecr1-mediated-cross-talk-between-macrophages-and-vascular-mural-cells-promotes-neovascularization-in-malignant-glioma
#4
C Zhu, I Chrifi, D Mustafa, M van der Weiden, P J M Leenen, D J Duncker, J M Kros, C Cheng
Glioblastomas (glioblastoma multiforme, GBM) are most malignant brain tumors characterized by profound vascularization. The activation of macrophages strongly contributes to tumor angiogenesis during GBM development. Previously, we showed that extracellular adenosine deaminase protein Cat Eye Syndrome Critical Region Protein 1 (CECR1) is highly expressed by M2-like macrophages in GBM where it defines macrophage M2 polarization and contributes to tumor expansion. In this study, the effect of CECR1 in macrophages on tumor angiogenesis was investigated...
May 22, 2017: Oncogene
https://www.readbyqxmd.com/read/28533502/clinical-value-and-prospective-pathway-signaling-of-microrna-375-in-lung-adenocarcinoma-a-study-based-on-the-cancer-genome-atlas-tcga-gene-expression-omnibus-geo-and-bioinformatics-analysis
#5
Ting-Qing Gan, Wen-Jie Chen, Hui Qin, Su-Ning Huang, Li-Hua Yang, Ye-Ying Fang, Lin-Jiang Pan, Zu-Yun Li, Gang Chen
BACKGROUND Lung adenocarcinoma (LUAD) is the most frequent lung cancer. MicroRNAs (miRNAs) are believed to have fundamental roles in tumorigenesis of LUAD. Although miRNAs are broadly recognized in LUAD, the role of microRNA-375 in LUAD is still not fully elucidated. MATERIAL AND METHODS We evaluated the significance of miR-375 expression in LUAD by using analysis of a public dataset from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database and a literature review. Furthermore, we investigated the biological function of miR-375 by gene ontology enrichment and target prediction analysis...
May 23, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28533487/autophagy-related-gene-expression-is-an-independent-prognostic-indicator-of-glioma
#6
Huixue Zhang, Xiaoyan Lu, Ning Wang, Jianjian Wang, Yuze Cao, Tianfeng Wang, Xueling Zhou, Yang Jiao, Lei Yang, Xiaokun Wang, Lin Cong, Jianlong Li, Jie Li, He-Ping Ma, Yonghui Pan, Shangwei Ning, Lihua Wang
In this study, we identified 74 differentially expressed autophagy-related genes in glioma patients. Analysis using a Cox proportional hazard regression model showed that MAPK8IP1 and SH3GLB1, two autophagy-related genes, were associated with the prognostic signature for glioma. Glioma patients from the CGGA batches 1 and 2, GSE4412 and TCGA datasets could be divided into high- and low-risk groups with different survival times based on levels of MAPK8IP1 and SH3GLB1 expression. The autophagy-related signature was an independent predictor of survival outcomes in glioma patients...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28532995/histological-subtypes-of-hepatocellular-carcinoma-are-related-to-gene-mutations-and-molecular-tumour-classification
#7
Julien Calderaro, Gabrielle Couchy, Sandrine Imbeaud, Giuliana Amaddeo, Eric Letouzé, Jean-Frédéric Blanc, Christophe Laurent, Yacine Hajji, Daniel Azoulay, Paulette Bioulac-Sage, Jean-Charles Nault, Jessica Zucman-Rossi
BACKGROUND AND AIMS: Our increasing understanding of hepatocellular carcinoma (HCC) biology holds promise for personalized care, however its translation into clinical practice requires a precise knowledge of its relationship to tumour phenotype. METHODS: We aimed at investigating molecular-phenotypic correlations in a large series of HCC. To this purpose, 343 surgically resected HCC were investigated by pathological review, immunohistochemistry, gene expression profiling and sequencing...
May 19, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28532857/high-stathmin-expression-is-a-marker-for-poor-clinical-outcome-in-endometrial-cancer-an-nrg-oncology-group-gynecologic-oncology-group-study
#8
Henry D Reyes, Jeffrey Miecznikowski, Jesus Gonzalez-Bosquet, Eric J Devor, Yuping Zhang, Kristina W Thiel, Megan I Samuelson, Megan McDonald, Jean-Marie Stephan, Parviz Hanjani, Saketh Guntupalli, Krishnansu S Tewari, Floor Backes, Nilsa Ramirez, Gini F Fleming, Virginia Filiaci, Michael J Birrer, Kimberly K Leslie
OBJECTIVE: Gynecologic Oncology Group (GOG) 177 demonstrated that addition of paclitaxel to a backbone of adriamycin/cisplatin improves overall survival (OS) and progression-free survival (PFS) for patients with advanced or recurrent endometrial cancer. Using patient specimens from GOG-177, our objective was to identify potential mechanisms underlying the improved clinical response to taxanes. Stathmin (STMN1) is a recognized poor prognostic marker in endometrial cancer that functions as a microtubule depolymerizing protein, allowing cells to transit rapidly through mitosis...
May 19, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28532485/multidimensional-scaling-of-diffuse-gliomas-application-to-the-2016-world-health-organization-classification-system-with-prognostically-relevant-molecular-subtype-discovery
#9
Patrick J Cimino, Michael Zager, Lisa McFerrin, Hans-Georg Wirsching, Hamid Bolouri, Bettina Hentschel, Andreas von Deimling, David Jones, Guido Reifenberger, Michael Weller, Eric C Holland
Recent updating of the World Health Organization (WHO) classification of central nervous system (CNS) tumors in 2016 demonstrates the first organized effort to restructure brain tumor classification by incorporating histomorphologic features with recurrent molecular alterations. Revised CNS tumor diagnostic criteria also attempt to reduce interobserver variability of histological interpretation and provide more accurate stratification related to clinical outcome. As an example, diffuse gliomas (WHO grades II-IV) are now molecularly stratified based upon isocitrate dehydrogenase 1 or 2 (IDH) mutational status, with gliomas of WHO grades II and III being substratified according to 1p/19q codeletion status...
May 22, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/28531337/correlation-of-immune-phenotype-with-idh-mutation-in-diffuse-glioma
#10
Anna Sophie Berghoff, Barbara Kiesel, Georg Widhalm, Dorothee Wilhelm, Orsolya Rajky, Sebastian Kurscheid, Philip Kresl, Adelheid Wöhrer, Christine Marosi, Monika E Hegi, Matthias Preusser
Background: Tumor infiltrating lymphocytes (TILs) and programmed death ligand 1 (PD-L1) are targets of immune checkpoint inhibitors. Methods: Forty-three World Health Organization (WHO) grade II/III gliomas (39 IDH-mutant [mut], 4 IDH-wildtype [wt]) and 14 IDH-mut glioblastomas (GBM) were analyzed for TIL (CD3+; PD1+) infiltration and PD-L1 expression. Results were compared with the data of a previously published series of 117 IDH-wt glioblastomas. PD-L1 gene expression levels were evaluated in 677 diffuse gliomas grades II-IV from The Cancer Genome Atlas (TCGA) database...
May 20, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28531253/gender-related-prognostic-value-and-genomic-pattern-of-intra-tumor-heterogeneity-ith-in-colorectal-cancer
#11
Jieyun Zhang, Shican Yan, Xiyu Liu, Lu Gan, Zhenhua Wu, Yiwei Gong, Mingzhu Huang, Xiaowei Zhang, Weijian Guo
Intra-tumor heterogeneity (ITH) is crucial in tumorigenesis and resistance to target therapy. Here, we used mutant-allele tumor heterogeneity (MATH) to measure ITH based on next-generation sequencing data and high MATH was proven as an independent risk prognostic factor in male CRC patients in both a training set of 284 colorectal cancer (CRC) patients with from The Cancer Genome Atlas (TCGA) and a validating set of 187 CRC patients from International Cancer Genome Consortium (ICGC). Further, the genomic pattern according to MATH demonstrated that mutation rates of TP53, IRF5 and KRAS were independently associated with MATH, and the latter two were only significant in male patients...
May 20, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28528452/tumor-suppressor-protein-p53-exerts-negative-transcriptional-regulation-on-human-sodium-iodide-symporter-gene-expression-in-breast-cancer
#12
Madhura G Kelkar, Bhushan Thakur, Abhishek Derle, Sushmita Chatterjee, Pritha Ray, Abhijit De
PURPOSE: Aberrant expression of human sodium iodide symporter (NIS) in breast cancer (BC) is well documented but the transcription factors (TF) regulating its aberrant expression is poorly known. We identify the presence of three p53 binding sites on the human NIS promoter sequence by conducting genome-wide TF analysis, and further investigate their regulatory role. METHODS: The differences in transcription and translation were measured by real-time PCR, luciferase reporter assay, site-directed mutagenesis, in vivo optical imaging, and chromatin immunoprecipitation...
May 20, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28527107/an-immune-related-six-lncrna-signature-to-improve-prognosis-prediction-of-glioblastoma-multiforme
#13
Meng Zhou, Zhaoyue Zhang, Hengqiang Zhao, Siqi Bao, Liang Cheng, Jie Sun
Recent studies have demonstrated the utility and superiority of long non-coding RNAs (lncRNAs) as novel biomarkers for cancer diagnosis, prognosis, and therapy. In the present study, the prognostic value of lncRNAs in glioblastoma multiforme was systematically investigated by performing a genome-wide analysis of lncRNA expression profiles in 419 glioblastoma patients from The Cancer Genome Atlas (TCGA) project. Using survival analysis and Cox regression model, we identified a set of six lncRNAs (AC005013.5, UBE2R2-AS1, ENTPD1-AS1, RP11-89C21...
May 19, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28525377/dna-methylation-mediated-silencing-of-microrna-874-is-a-promising-diagnosis-and-prognostic-marker-in-breast-cancer
#14
Lei Zhang, Da-Li Yan, Fan Yang, Dan-Dan Wang, Xiu Chen, Jian-Zhong Wu, Jin-Hai Tang, Wen-Jie Xia
MicroRNA-874 (miR-874) is downregulated in several human cancers and has been suggested to be a tumor suppressor gene. However, the molecular mechanism of miR-874 downregulation in breast cancer has not been well elucidated. Here we aimed to study the aberrant hyper-methylation of CpG sites with the utility of miR-874 downreregulation in breast cancer and evaluate the clinical function of miR-874 as a prognostic marker. The miR-874 expressions in cells and tissues of two breast cancer lines were measured by real-time PCR...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28523575/znf281-promotes-growth-and-invasion-of-pancreatic-cancer-cells-by-activating-wnt-%C3%AE-catenin-signaling
#15
Yu Qian, Jingyi Li, Suhua Xia
BACKGROUND: Zinc finger protein 281 (ZNF281) has been identified to be involved in embryonic stem cell differentiation and tissue development. Also, ZNF281 was found in various types of cancers. However, its biological functions and clinical significance in pancreatic cancer remain elusive. AIMS: To explore the role of ZNF281 in pancreatic cancer cells proliferation and invasion. METHODS: ZNF281 expression was examined in public database Oncomine and cBioPortal...
May 18, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28522860/involvement-of-fak-erk2-signaling-pathway-in-ckap2-induced-proliferation-and-motility-in-cervical-carcinoma-cell-lines
#16
Qi-Sang Guo, Yu Song, Ke-Qin Hua, Shu-Jun Gao
Cervical carcinoma is the fourth most common cause of death in woman, caused by human papillomavirus (HPV) infections and arising from the cervix. Cytoskeleton-associated protein 2 (CKAP2), also known as tumor-associated microtubule-associated protein, has been linked to tumorigenic effects. In the present study, we screened CKAP2 as a new candidate gene which promotes development of cervical carcinoma, in two independent datasets (TCGA and GSE27678). Results showed that CKAP2 expression was significantly up-regulated in cervical cancerous tissues compared with normal counterparts...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522612/genomevip-a-cloud-platform-for-genomic-variant-discovery-and-interpretation
#17
Robert J Mashl, Adam D Scott, Kuan-Lin Huang, Matthew A Wyczalkowski, Christopher J Yoon, Beifang Niu, Erin DeNardo, Venkata D Yellapantula, Robert E Handsaker, Ken Chen, Daniel C Koboldt, Kai Ye, David Fenyö, Benjamin Raphael, Michael C Wendl, Li Ding
Identifying genomic variants is a fundamental first step towards the understanding of the role of inherited and acquired variations in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional 'download and analyze' paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28522603/smad4-loss-is-associated-with-cetuximab-resistance-and-induction-of-mapk-jnk-activation-in-head-and-neck-cancer-cells
#18
Hiroyuki Ozawa, Ruchira Ranaweera, Evgeny Izumchenko, Eugene Makarev, Alex Zhavoronkov, Elana J Fertig, Jason D Howard, Ana Markovic, Atul Bedi, Rajani Ravi, Jimena Perez, Quynh-Thu Le, Christina S Kong, Richard C K Jordan, Hao Wang, Hyunseok Kang, Harry Quon, David Sidransky, Christine H Chung
Purpose: We previously demonstrated an association between decreased SMAD4 expression and cetuximab resistance in head and neck squamous cell carcinoma (HNSCC). The purpose of this study was to further elucidate the clinical relevance of SMAD4 loss in HNSCC. Experimental Design: SMAD4 expression was assessed by immunohistochemistry in 130 newly diagnosed and 43 recurrent HNSCC patients. Correlative statistical analysis with clinicopathological data was also performed. OncoFinder, a bioinformatics tool, was used to analyze molecular signaling in TCGA tumors with low or high SMAD4 mRNA levels...
May 18, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28520848/pattern-fusion-analysis-by-adaptive-alignment-of-multiple-heterogeneous-omics-data
#19
Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng, Juan Liu, Luonan Chen
Motivation: Integrating different omics profiles is a challenging task, which provides a comprehensive way to understand complex diseases in a multi-view manner. One key for such an integration is to extract intrinsic patterns in concordance with data structures, so as to discover consistent information across various data types even with noise pollution. Thus, we proposed a novel framework called "pattern fusion analysis" (PFA), which performs automated information alignment and bias correction, to fuse local sample-patterns (e...
May 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28520777/network-based-stratification-of-major-cancers-by-integrating-somatic-mutation-and-gene-expression-data
#20
Zongzhen He, Junying Zhang, Xiguo Yuan, Zhaowen Liu, Baobao Liu, Shouheng Tuo, Yajun Liu
The stratification of cancer into subtypes that are significantly associated with clinical outcomes is beneficial for targeted prognosis and treatment. In this study, we integrated somatic mutation and gene expression data to identify clusters of patients. In contrast to previous studies, we constructed cancer-type-specific significant co-expression networks (SCNs) rather than using a fixed gene network across all cancers, such as the network-based stratification (NBS) method, which ignores cancer heterogeneity...
2017: PloS One
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