keyword
MENU ▼
Read by QxMD icon Read
search

Integrated cancer network

keyword
https://www.readbyqxmd.com/read/28211524/epigenetic-and-genetic-dissections-of-uv-induced-global-gene-dysregulation-in-skin-cells-through-multi-omics-analyses
#1
Yao Shen, Milda Stanislauskas, Gen Li, Deyou Zheng, Liang Liu
To elucidate the complex molecular mechanisms underlying the adverse effects UV radiation (UVR) on skin homeostasis, we performed multi-omics studies to characterize UV-induced genetic and epigenetic changes. Human keratinocytes from a single donor treated with or without UVR were analyzed by RNA-seq, exome-seq, and H3K27ac ChIP-seq at 4 h and 72 h following UVR. Compared to the relatively moderate mutagenic effects of UVR, acute UV exposure induced substantial epigenomic and transcriptomic alterations, illuminating a previously underappreciated role of epigenomic and transcriptomic instability in skin pathogenesis...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28208522/re-integrative-analyses-reveal-a-long-noncoding-rna-mediated-sponge-regulatory-network-in-prostate-cancer
#2
Anthony Atala
No abstract text is available yet for this article.
March 2017: Journal of Urology
https://www.readbyqxmd.com/read/28205554/the-oncoppi-network-of-cancer-focused-protein-protein-interactions-to-inform-biological-insights-and-therapeutic-strategies
#3
Zenggang Li, Andrei A Ivanov, Rina Su, Valentina Gonzalez-Pecchi, Qi Qi, Songlin Liu, Philip Webber, Elizabeth McMillan, Lauren Rusnak, Cau Pham, Xiaoqian Chen, Xiulei Mo, Brian Revennaugh, Wei Zhou, Adam Marcus, Sahar Harati, Xiang Chen, Margaret A Johns, Michael A White, Carlos Moreno, Lee A D Cooper, Yuhong Du, Fadlo R Khuri, Haian Fu
As genomics advances reveal the cancer gene landscape, a daunting task is to understand how these genes contribute to dysregulated oncogenic pathways. Integration of cancer genes into networks offers opportunities to reveal protein-protein interactions (PPIs) with functional and therapeutic significance. Here, we report the generation of a cancer-focused PPI network, termed OncoPPi, and identification of >260 cancer-associated PPIs not in other large-scale interactomes. PPI hubs reveal new regulatory mechanisms for cancer genes like MYC, STK11, RASSF1 and CDK4...
February 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28204826/pathway-deviation-based-biomarker-and-multi-effect-target-identification-in-asbestos-related-squamous-cell-carcinoma-of-the-lung
#4
Jiang Du, Lin Zhang
Asbestos-related lung carcinoma is one of the most devastating occupational cancers, and effective techniques for early diagnosis are still lacking. In the present study, a systematic approach was applied to detect a potential biomarker for asbestos-related lung cancer (ARLC); in particular asbestos-related squamous cell carcinoma (ARLC-SCC). Microarray data (GSE23822) were retrieved from the Gene Expression Omnibus database, including 26 ARLC-SCCs and 30 non-asbestos-related squamous cell lung carcinomas (NARLC-SCCs)...
February 6, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28202516/modeling-the-genetic-regulation-of-cancer-metabolism-interplay-between-glycolysis-and-oxidative-phosphorylation
#5
Linglin Yu, Mingyang Lu, Dongya Jia, Jianpeng Ma, Eshel Ben-Jacob, Herbert Levine, Benny A Kaipparettu, Jose' N Onuchic
Abnormal metabolism is a hallmark of cancer, yet its regulation remains poorly understood. Cancer cells were considered to utilize primarily glycolysis for ATP production, referred to as the Warburg effect. However, recent evidence suggests that oxidative phosphorylation (OXPHOS) plays a crucial role during cancer progression. Here we utilized a systems biology approach to decipher the regulatory principle of glycolysis and OXPHOS. Integrating information from literature, we constructed a regulatory network of genes and metabolites from which we extracted a core circuit containing HIF-1, AMPK, and ROS...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28187708/incorporating-prior-biological-knowledge-for-network-based-differential-gene-expression-analysis-using-differentially-weighted-graphical-lasso
#6
Yiming Zuo, Yi Cui, Guoqiang Yu, Ruijiang Li, Habtom W Ressom
BACKGROUND: Conventional differential gene expression analysis by methods such as student's t-test, SAM, and Empirical Bayes often searches for statistically significant genes without considering the interactions among them. Network-based approaches provide a natural way to study these interactions and to investigate the rewiring interactions in disease versus control groups. In this paper, we apply weighted graphical LASSO (wgLASSO) algorithm to integrate a data-driven network model with prior biological knowledge (i...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187513/collaboration-to-accelerate-proteogenomics-cancer-care-the-department-of-veterans-affairs-department-of-defense-and-the-national-cancer-institute-s-applied-proteogenomics-organizational-and-learning-apollo-network
#7
L D Fiore, H Rodriguez, C D Shriver
The ability to interrogate cancer at the proteogenomic level has the potential to transform oncology care from trial-and-error treatment strategies based on the anatomy and genomic profiling of tumors to one that is precisely based on the tumor's molecular profile. The next step in the evolution of precision oncology is developing proteogenomic approaches that make no exclusive assumptions a priori as to the molecular level of the patient's disease. The DoD, VA, and NCI responded to the Cancer Moonshot initiative by linking each agency's unique capabilities in clinical and basic science, computing, and high-throughput sequencing...
February 10, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28186503/a-novel-dlx3-pkc-integrated-signaling-network-drives-keratinocyte-differentiation
#8
Elisabetta Palazzo, Meghan D Kellett, Christophe Cataisson, Paul W Bible, Shreya Bhattacharya, Hong-Wei Sun, Anna C Gormley, Stuart H Yuspa, Maria I Morasso
Epidermal homeostasis relies on a well-defined transcriptional control of keratinocyte proliferation and differentiation, which is critical to prevent skin diseases such as atopic dermatitis, psoriasis or cancer. We have recently shown that the homeobox transcription factor DLX3 and the tumor suppressor p53 co-regulate cell cycle-related signaling and that this mechanism is functionally involved in cutaneous squamous cell carcinoma development. Here we show that DLX3 expression and its downstream signaling depend on protein kinase C α (PKCα) activity in skin...
February 10, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28185575/integration-of-metabolomics-lipidomics-and-clinical-data-using-a-machine-learning-method
#9
Animesh Acharjee, Zsuzsanna Ament, James A West, Elizabeth Stanley, Julian L Griffin
BACKGROUND: The recent pandemic of obesity and the metabolic syndrome (MetS) has led to the realisation that new drug targets are needed to either reduce obesity or the subsequent pathophysiological consequences associated with excess weight gain. Certain nuclear hormone receptors (NRs) play a pivotal role in lipid and carbohydrate metabolism and have been highlighted as potential treatments for obesity. This realisation started a search for NR agonists in order to understand and successfully treat MetS and associated conditions such as insulin resistance, dyslipidaemia, hypertension, hypertriglyceridemia, obesity and cardiovascular disease...
November 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28180060/gprc6a-jack-of-all-metabolism-or-master-of-none
#10
REVIEW
Min Pi, Satoru Kenneth Nishimoto, L Darryl Quarles
BACKGROUND: GPRC6A, a widely expressed G-protein coupled receptor, is proposed to be a master regulator of complex endocrine networks and metabolic processes. GPRC6A is activated by multiple ligands, including osteocalcin (Ocn), testosterone (T), basic amino acids, and various cations. SCOPE OF REVIEW: We review the controversy surrounding GPRC6A functions. In mice, GPRC6A is proposed to integrate metabolic functions through the coordinated secretion of hormones, including insulin, GLP-1, T, and IL-6, and direct effects of this receptor to control glucose and fat metabolism in the liver, skeletal muscle, and fat...
February 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/28168356/identifying-survival-associated-modules-from-the-dysregulated-triplet-network-in-glioblastoma-multiforme
#11
Jia-Bin Wang, Feng-Hua Liu, Jian-Hang Chen, Hai-Tao Ge, Lu-Yan Mu, Hong-Bo Bao, Zhi-Guo Lin
BACKGROUND: Long noncoding RNAs (lncRNAs) can act as competitive endogenous RNAs (ceRNAs) to compete with mRNAs for binding miroRNAs (miRNAs). The dysregulated triplets, composed by mRNAs, lncRNAs, and miRNAs, contributed to the development and progression of diseases, such as cancer. However, the roles played by triplet biomarkers are not fully understand in glioblastoma multiforme (GBM) patient survival. OBJECTIVES: Here, we constructed a differential triplet interaction network (TriNet) between GBM and normal tissues and identified GBM survival related triplets...
February 6, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28167779/integrity-of-the-human-centromere-dna-repeats-is-protected-by-cenp-a-cenp-c-and-cenp-t
#12
Simona Giunta, Hironori Funabiki
Centromeres are highly specialized chromatin domains that enable chromosome segregation and orchestrate faithful cell division. Human centromeres are composed of tandem arrays of α-satellite DNA, which spans up to several megabases. Little is known about the mechanisms that maintain integrity of the long arrays of α-satellite DNA repeats. Here, we monitored centromeric repeat stability in human cells using chromosome-orientation fluorescent in situ hybridization (CO-FISH). This assay detected aberrant centromeric CO-FISH patterns consistent with sister chromatid exchange at the frequency of 5% in primary tissue culture cells, whereas higher levels were seen in several cancer cell lines and during replicative senescence...
February 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28166200/upregulation-of-marcks-in-kidney-cancer-and-its-potential-as-a-therapeutic-target
#13
C-H Chen, L W R Fong, E Yu, R Wu, J F Trott, R H Weiss
Targeted therapeutics, such as those abrogating hypoxia inducible factor (HIF)/vascular endothelial growth factor signaling, are initially effective against kidney cancer (or renal cell carcinoma, RCC); however, drug resistance frequently occurs via subsequent activation of alternative pathways. Through genome-scale integrated analysis of the HIF-α network, we identified the major protein kinase C substrate MARCKS (myristoylated alanine-rich C kinase substrate) as a potential target molecule for kidney cancer...
February 6, 2017: Oncogene
https://www.readbyqxmd.com/read/28162975/comprehensive-molecular-characterization-of-pheochromocytoma-and-paraganglioma
#14
Lauren Fishbein, Ignaty Leshchiner, Vonn Walter, Ludmila Danilova, A Gordon Robertson, Amy R Johnson, Tara M Lichtenberg, Bradley A Murray, Hans K Ghayee, Tobias Else, Shiyun Ling, Stuart R Jefferys, Aguirre A de Cubas, Brandon Wenz, Esther Korpershoek, Antonio L Amelio, Liza Makowski, W Kimryn Rathmell, Anne-Paule Gimenez-Roqueplo, Thomas J Giordano, Sylvia L Asa, Arthur S Tischler, Karel Pacak, Katherine L Nathanson, Matthew D Wilkerson
We report a comprehensive molecular characterization of pheochromocytomas and paragangliomas (PCCs/PGLs), a rare tumor type. Multi-platform integration revealed that PCCs/PGLs are driven by diverse alterations affecting multiple genes and pathways. Pathogenic germline mutations occurred in eight PCC/PGL susceptibility genes. We identified CSDE1 as a somatically mutated driver gene, complementing four known drivers (HRAS, RET, EPAS1, and NF1). We also discovered fusion genes in PCCs/PGLs, involving MAML3, BRAF, NGFR, and NF1...
February 2, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28159918/protein-drug-target-activation-homogeneity-in-the-face-of-intra-tumor-heterogeneity-implications-for-precision-medicine
#15
Erika Maria Parasido, Alessandra Silvestri, Vincenzo Canzonieri, Claudio Belluco, Maria Grazia Diodoro, Massimo Milione, Flavia Melotti, Ruggero De Maria, Lance Liotta, Emanuel F Petricoin, Mariaelena Pierobon
INTRODUCTION: Recent studies indicated tumors may be comprised of heterogeneous molecular subtypes and incongruent molecular portraits may emerge if different areas of the tumor are sampled. This study explored the impact of intra-tumoral heterogeneity in terms of activation/phosphorylation of FDA approved drug targets and downstream kinase substrates. MATERIAL AND METHODS: Two independent sets of liver metastases from colorectal cancer were used to evaluate protein kinase-driven signaling networks within different areas using laser capture microdissection and reverse phase protein array...
December 15, 2016: Oncotarget
https://www.readbyqxmd.com/read/28155675/gene-microrna-network-module-analysis-for-ovarian-cancer
#16
Shuqin Zhang, Michael K Ng
BACKGROUND: MicroRNAs (miRNAs) are involved in many biological processes by regulating post-transcriptional gene expression. The alterations of the regulatory pathways can cause different diseases including cancer. Although many works have been done to study the gene-miRNA regulatory network, the intertwined relationship is far from being fully understood. The objective of this study is to integrate both gene expression data and miRNA data so as to explore the complex relationships among them...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155638/a-network-based-pathway-expanding-approach-for-pathway-analysis
#17
Qiaosheng Zhang, Jie Li, Haozhe Xie, Hanqing Xue, Yadong Wang
BACKGROUND: Pathway analysis combining multiple types of high-throughput data, such as genomics and proteomics, has become the first choice to gain insights into the pathogenesis of complex diseases. Currently, several pathway analysis methods have been developed to study complex diseases. However, these methods did not take into account the interaction between internal and external genes of the pathway and between pathways. Hence, these approaches still face some challenges. Here, we propose a network-based pathway-expanding approach that takes the topological structures of biological networks into account...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28155630/lndriver-identifying-driver-genes-by-integrating-mutation-and-expression-data-based-on-gene-gene-interaction-network
#18
Pi-Jing Wei, Di Zhang, Junfeng Xia, Chun-Hou Zheng
BACKGROUND: Cancer is a complex disease which is characterized by the accumulation of genetic alterations during the patient's lifetime. With the development of the next-generation sequencing technology, multiple omics data, such as cancer genomic, epigenomic and transcriptomic data etc., can be measured from each individual. Correspondingly, one of the key challenges is to pinpoint functional driver mutations or pathways, which contributes to tumorigenesis, from millions of functional neutral passenger mutations...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28155194/regulatory-network-analysis-of-epstein-barr-virus-identifies-functional-modules-and-hub-genes-involved-in-infectious-mononucleosis
#19
Mansour Poorebrahim, Ali Salarian, Saeideh Najafi, Mohammad Foad Abazari, Maryam Nouri Aleagha, Mohammad Nasr Dadras, Seyed Mohammad Jazayeri, Atousa Ataei, Vahdat Poortahmasebi
Epstein-Barr virus (EBV) is the most common cause of infectious mononucleosis (IM) and establishes lifetime infection associated with a variety of cancers and autoimmune diseases. The aim of this study was to develop an integrative gene regulatory network (GRN) approach and overlying gene expression data to identify the representative subnetworks for IM and EBV latent infection (LI). After identifying differentially expressed genes (DEGs) in both IM and LI gene expression profiles, functional annotations were applied using gene ontology (GO) and BiNGO tools, and construction of GRNs, topological analysis and identification of modules were carried out using several plugins of Cytoscape...
February 2, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28154515/metabolic-pathways-associated-with-kimchi-a-traditional-korean-food-based-on-in-silico-modeling-of-published-data
#20
Ga Hee Shin, Byeong-Chul Kang, Dai Ja Jang
Kimchi is a traditional Korean food prepared by fermenting vegetables, such as Chinese cabbage and radishes, which are seasoned with various ingredients, including red pepper powder, garlic, ginger, green onion, fermented seafood (Jeotgal), and salt. The various unique microorganisms and bioactive components in kimchi show antioxidant activity and have been associated with an enhanced immune response, as well as anti-cancer and anti-diabetic effects. Red pepper inhibits decay due to microorganisms and prevents food from spoiling...
December 2016: Genomics & Informatics
keyword
keyword
61594
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"