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https://www.readbyqxmd.com/read/28092656/influence-of-node-abundance-on-signaling-network-state-and-dynamics-analyzed-by-mass-cytometry
#1
Xiao-Kang Lun, Vito R T Zanotelli, James D Wade, Denis Schapiro, Marco Tognetti, Nadine Dobberstein, Bernd Bodenmiller
Signaling networks are key regulators of cellular function. Although the concentrations of signaling proteins are perturbed in disease states, such as cancer, and are modulated by drug therapies, our understanding of how such changes shape the properties of signaling networks is limited. Here we couple mass-cytometry-based single-cell analysis with overexpression of tagged signaling proteins to study the dependence of signaling relationships and dynamics on protein node abundance. Focusing on the epidermal growth factor receptor (EGFR) signaling network in HEK293T cells, we analyze 20 signaling proteins during a 1-h EGF stimulation time course using a panel of 35 antibodies...
January 16, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28092569/discovery-of-micrornas-and-transcription-factors-co-regulatory-modules-by-integrating-multiple-types-of-genomic-data
#2
Jiawei Luo, Gen Xiang, Chu Pan
It is well known that regulators known as microRNA (miRNA) and transcription factor (TF) have been found to play an important role in gene regulation. However, there are few researches of collaborative regulatory (co-regulatory) mechanism between miRNA and TF on system level (function level). Meanwhile, recent advances in high-throughput genomic technologies have enabled researchers to collect diverse large-scale genomic data, which can be used to study the co-regulatory mechanism between miRNA and TF. In this paper, we propose a novel method called SNCoNMF (Sparse Network regularized non-negative matrix factorization for Co-regulatory modules identification) which adopts multiple non-negative matrix factorization framework to identify co-regulatory modules including miRNAs, TFs and genes...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28090777/biodegradable-neuro-compatible-peptide-hydrogel-promotes-neurite-outgrowth-shows-significant-neuroprotection-and-delivers-anti-alzheimer-drug
#3
Anindyasundar Adak, Gaurav Das, Surajit Barman, Saswat Mohapatra, Debmalya Bhunia, Batakrishna Jana, Surajit Ghosh
A novel neuro-compatible peptide based hydrogel has been designed and developed, which contains microtubule stabilizing and neuroprotective short peptide. This hydrogel shows strong three dimensional cross-linked fibrillary networks, which can capture water molecules. Interestingly, this hydrogel serves as excellent biocompatible soft-material for 2D and 3D (neuro-sphere) neuron cell culture and provides stability of key cytoskeleton filaments such as microtubule and actin. Remarkably, it was observed that this hydrogel slowly enzymatically degrades and releases neuroprotective peptide, which promotes neurite outgrowth of neuron cell as well as exhibits excellent neuroprotection against anti-NGF induced toxicity in neuron cells...
January 16, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28090518/clinical-characteristics-and-molecular-pathology-of-skull-ectopic-thyroid-cancer
#4
Longxing Cao, Zhongyong Wang, Jiawei Ma, Jinsheng Chen, Haojiang Zhu, Xiaohua Zhou, Qing Zhu, Jun Dong, Qing Lan, Qiang Huang
Thyroid cancer is very common, but skull ectopic thyroid cancer has not been reported in 50 years of literatures in foreign countries. There are only four cases of the skull ectopic thyroid cancer reported in more than 30 years of domestic literature including the cases in this report. This paper aims to investigate the clinical characteristics and possible molecular mechanisms of this rare disease. Five keywords of "thyroid gland", "ectopic thyroid", "thyroid cancer", "ectopic thyroid cancer" and "metastatic thyroid cancer" were included and 50 years of literatures in the PubMed-MEDLINE and Wanfang database were reviewed...
December 2016: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28089917/micrornas-and-dicer1-are-regulated-by-1-25-dihydroxyvitamin-d-in-prostate-stroma
#5
Shweta Dambal, Angeline A Giangreco, Andres M Acosta, Andrew Fairchild, Zachary Richards, Ryan Deaton, Dennis Wagner, Reinhold Vieth, Peter H Gann, Andre Kajdacsy-Balla, Theodorus Van der Kwast, Larisa Nonn
Vitamin D deficiency increases the risk of lethal prostate adenocarcinomas (PCa) and the majority of older men are deficient. Although PCa arises from the epithelium, the surrounding stroma has hormonal regulatory control over the epithelium and contributes to carcinogenesis. Herein, we describe regulation of microRNAs (miRs) by the active hormone dihydroxyvitamin D (1,25(OH)2D) in human prostate stroma. 1,25(OH)2D binds the vitamin D receptor (VDR) transcription factor to regulate gene expression, including miRs, which have emerged as potent regulators of protein expression...
January 12, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28088579/the-microrna-449-family-inhibits-tgf-%C3%AE-mediated-liver-cancer-cell-migration-by-targeting-sox4
#6
Maria Sandbothe, Reena Buurman, Nicole Reich, Luisa Greiwe, Beate Vajen, Engin Gürlevik, Vera Schäffer, Marlies Eilers, Florian Kühnel, Alejandro Vaquero, Thomas Longerich, Stephanie Roessler, Peter Schirmacher, Michael P Manns, Thomas Illig, Brigitte Schlegelberger, Britta Skawran
BACKGROUND & AIMS: Modulation of microRNA expression is considered for treatment of hepatocellular carcinoma (HCC). Therefore, we characterized the epigenetically regulated microRNA-449 family (miR-449a, miR-449b, miR-449c) with regards to its functional effects and target genes in HCC. METHODS: After transfection of miR-449a, miR-449b, and/or miR-449c, tumor-relevant functional effects were analyzed using in vitro assays and a xenograft mouse model. Binding specificities, target genes, and regulated pathways of each microRNA were identified by microarray analyses...
January 11, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28088176/ttca-an-r-package-for-the-identification-of-differentially-expressed-genes-in-time-course-microarray-data
#7
Marco Albrecht, Damian Stichel, Benedikt Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn, Franziska Matthäus
BACKGROUND: The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements...
January 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28087714/dlg5-connects-cell-polarity-and-hippo-signaling-protein-networks-by-linking-par-1-with-mst1-2
#8
Julian Kwan, Anna Sczaniecka, Emad Heidary Arash, Liem Nguyen, Chia-Chun Chen, Srdjana Ratkovic, Olga Klezovitch, Liliana Attisano, Helen McNeill, Andrew Emili, Valeri Vasioukhin
Disruption of apical-basal polarity is implicated in developmental disorders and cancer; however, the mechanisms connecting cell polarity proteins with intracellular signaling pathways are largely unknown. We determined previously that membrane-associated guanylate kinase (MAGUK) protein discs large homolog 5 (DLG5) functions in cell polarity and regulates cellular proliferation and differentiation via undefined mechanisms. We report here that DLG5 functions as an evolutionarily conserved scaffold and negative regulator of Hippo signaling, which controls organ size through the modulation of cell proliferation and differentiation...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087642/stxbp4-drives-tumor-growth-and-is-associated-with-poor-prognosis-through-pdgf-receptor-signaling-in-lung-squamous-cell-carcinoma
#9
Yukihiro Otaka, Susumu Rokudai, Kyoichi Kaira, Michiru Fujieda, Ikuko Horikoshi, Reika Kawabata, Shinji Yoshiyama, Takehiko Yokobori, Yoichi Ohtaki, Kimihiro Shimizu, Tetsunari Oyama, Jun'ichi Tamura, Carol Prives, Masahiko Nishiyama
PURPOSE: Expression of the ΔN isoform of p63 (ΔNp63) is a diagnostic marker highly specific for lung squamous cell carcinoma (SCC). We previously found that Syntaxin Binding Protein 4 (STXBP4) regulates ΔNp63 ubiquitination, suggesting that STXBP4 may also be a SCC biomarker. To address this issue, we investigated the role of STXBP4 expression in SCC biology and the impact of STXBP4 expression on SCC prognosis. EXPERIMENTAL DESIGN: We carried out a clinicopathological analysis of STXBP4 expression in 87 lung SCC patients...
January 13, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28087598/bayesian-network-inference-modeling-identifies-trib1-as-a-novel-regulator-of-cell-cycle-progression-and-survival-in-cancer-cells
#10
Rina Gendelman, Heming Xing, Olga K Mirzoeva, Preeti Sarde, Christina Curtis, Heidi Feiler, Paul McDonagh, Joe W Gray, Iya Khalil, W Michael Korn
Molecular networks governing cellular responses to targeted therapies are complex dynamic systems with non-intuitive behaviors. Here we applied a novel computational strategy to infer probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell cycle arrest caused by inhibition of MEK1/2. Through simulation of reverse-engineered Bayesian network modeling, we generated predictions of G1-S transition...
January 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28087132/practice-patterns-of-thoracic-radiotherapy-for-extensive-stage-small-cell-lung-cancer-survey-of-us-academic-thoracic-radiation-oncologists
#11
Carl M Post, Vivek Verma, Timur Mitin, Charles B Simone
PURPOSE: Despite the recent CREST trial demonstrating a survival benefit to thoracic radiotherapy (TRT) for patients with extensive-stage small-cell lung cancer (ES-SCLC) with response to chemotherapy, as well as endorsement by current National Comprehensive Cancer Network guidelines, TRT may not be uniformly delivered in clinical practice across all circumstances. METHODS AND MATERIALS: We surveyed US academic thoracic radiation oncologists regarding their practice patterns for TRT and assessed conditions in which withholding TRT could be warranted...
December 22, 2016: Clinical Lung Cancer
https://www.readbyqxmd.com/read/28081052/identification-of-key-transcription-factors-associated-with-lung-squamous-cell-carcinoma
#12
Feng Zhang, Xia Chen, Ke Wei, Daoming Liu, Xiaodong Xu, Xing Zhang, Hong Shi
BACKGROUND Lung squamous cell carcinoma (lung SCC) is a common type of lung cancer, but its mechanism of pathogenesis is unclear. The aim of this study was to identify key transcription factors in lung SCC and elucidate its mechanism. MATERIAL AND METHODS Six published microarray datasets of lung SCC were downloaded from Gene Expression Omnibus (GEO) for integrated bioinformatics analysis. Significance analysis of microarrays was used to identify differentially expressed genes (DEGs) between lung SCC and normal controls...
January 12, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28080182/multi-professional-perspectives-on-adolescent-and-young-adult-oncology-across-europe-an-e-delphi-survey
#13
Simon A Pini, Faith Gibson, Lorna A Fern, Sue J Morgan, Robert S Phillips, Dan P Stark
The aims of this article are to describe the ongoing development of adolescent and young adult (AYA) cancer services within the European Union (EU), and to develop consensus on key areas within the field. This survey used an e-Delphi design. An initial survey was distributed via email to professionals working in Europe. A snowball sampling technique was used to promote distribution. Consensus was sought over three rounds from October 2012 to April 2015. Consensus was defined as >80% agreement ("agree" or "strongly agree")...
January 12, 2017: Journal of Adolescent and Young Adult Oncology
https://www.readbyqxmd.com/read/28079887/drp-1-is-required-for-bh3-mimetic-mediated-mitochondrial-fragmentation-and-apoptosis
#14
Mateus Milani, Dominic P Byrne, Georgia Greaves, Michael Butterworth, Gerald M Cohen, Patrick A Eyers, Shankar Varadarajan
The concept of using BH3 mimetics as anticancer agents has been substantiated by the efficacy of selective drugs, such as Navitoclax and Venetoclax, in treating BCL-2-dependent haematological malignancies. However, most solid tumours depend on MCL-1 for survival, which is highly amplified in multiple cancers and a major factor determining chemoresistance. Most MCL-1 inhibitors that have been generated so far, while demonstrating early promise in vitro, fail to exhibit specificity and potency in a cellular context...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28079819/efficacy-and-toxicity-of-different-concurrent-chemoradiotherapy-regimens-in-the-treatment-of-advanced-cervical-cancer-a-network-meta-analysis
#15
Zhan-Zhao Fu, Kun Li, Yong Peng, Yue Zheng, Li-Yan Cao, Yun-Jie Zhang, Yong-Mei Sun
OBJECTIVE: The aim of this study was to compare the efficacy and toxicity of different concurrent chemoradiotherapy (CCRT) regimens in the treatment of advanced cervical cancer (CC) by adopting a network meta-analysis. METHODS: We searched PubMed and Cochrane Library from the inception of these databases to September 2016, and all cohort studies (CSs) related to different CCRT regimens in the treatment of CC were included. A network analysis was adopted to compare the combination of direct and indirect evidence, to analyze the odds ratio (OR), and to draw a surface under the cumulative ranking curve of the efficacy and toxicity of different CCRT regimens for CC...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28079805/toxicities-of-different-first-line-chemotherapy-regimens-in-the-treatment-of-advanced-ovarian-cancer-a-network-meta-analysis
#16
Chang-Ping Qu, Gui-Xia Sun, Shao-Qin Yang, Jun Tian, Jin-Ge Si, Yi-Feng Wang
BACKGROUND: Ovarian cancer (OC) is the 5th leading cause of cancer-related deaths around the world, and several chemotherapy regimens have been applied in the treatment of OC. We aim to compare toxicities of different chemotherapy regimens in the treatment of advanced ovarian cancer (AOC) using network meta-analysis. METHODS: Literature research in Cochrane Library, PubMed, and EMBASE was performed up to November 2015. Eligible randomized controlled trials (RCTs) of different chemotherapy regimens were included...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28079775/association-of-hospital-volume-with-racial-and-ethnic-disparities-in-locally-advanced-cervical-cancer-treatment
#17
Shitanshu Uppal, Christina Chapman, Ryan J Spencer, Shruti Jolly, Kate Maturen, J Alejandro Rauh-Hain, Marcela G delCarmen, Laurel W Rice
OBJECTIVE: To evaluate racial-ethnic disparities in guideline-based care in locally advanced cervical cancer and their relationship to hospital case volume. METHODS: Using the National Cancer Database, we performed a retrospective cohort study of women diagnosed between 2004 and 2012 with locally advanced squamous or adenocarcinoma of the cervix undergoing definitive primary radiation therapy. The primary outcome was the race-ethnicity-based rates of adherence to the National Comprehensive Cancer Network guideline-based care...
January 9, 2017: Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28079712/a-comprehensive-review-of-genomics-and-noncoding-rna-in-gliomas
#18
Ahmed Hassan, Jennifer Mosley, Sanjay Singh, Pascal Olivier Zinn
Glioblastoma (GBM) is the most malignant primary adult brain tumor. In spite of our greater understanding of the biology of GBMs, clinical outcome of GBM patients remains poor, as their median survival with best available treatment is 12 to 18 months. Recent efforts of The Cancer Genome Atlas (TCGA) have subgrouped patients into 4 molecular/transcriptional subgroups: proneural, neural, classical, and mesenchymal. Continuing efforts are underway to provide a comprehensive map of the heterogeneous makeup of GBM to include noncoding transcripts, genetic mutations, and their associations to clinical outcome...
January 11, 2017: Topics in Magnetic Resonance Imaging: TMRI
https://www.readbyqxmd.com/read/28078775/comparison-of-three-surgical-approaches-for-staging-lymphadenectomy-in-high-risk-endometrial-cancer
#19
Katherine J Pulman, Ebernella S Dason, Lauren Philp, Marcus Q Bernardini, Sarah E Ferguson, Stéphane Laframboise, Eshetu G Atenafu, Taymaa May
OBJECTIVE: To compare laparotomy, laparoscopy, and robotic surgical approaches to lymphadenectomy for high-risk endometrial cancer staging. METHODS: A retrospective cohort study enrolled patients who underwent surgery for pathologic high-risk endometrial carcinoma at the University Health Network, Toronto, Canada, between January 1, 2005 and December 31, 2013. The primary outcome, the median number of nodes retrieved, was compared based on surgical technique. The secondary outcome was the detection of metastatic nodes...
December 7, 2016: International Journal of Gynaecology and Obstetrics
https://www.readbyqxmd.com/read/28078605/transcriptional-regulatory-network-analysis-for-gastric-cancer-based-on-mrna-microarray
#20
Yan Wang
We aimed to screen the differential expressed genes (DEGs) and transcriptional factors (TFs) related to gastric cancer. GSE19826 microarray data downloaded from Gene Expression Omnibus was used to identify the differentially expressed genes (DEGs) and PPI network of DEGs were constructed by the Retrieval of Interacting Genes database. Pathway enrichment analysis of DEGs were performed by Gene Set Enrichment Analysis. Then, the transcriptional regulatory network was constructed based on TRANSFAC database. Finally, regulatory impact factor (RIF) of TF was calculated...
January 11, 2017: Pathology Oncology Research: POR
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