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https://www.readbyqxmd.com/read/28098893/systematic-analysis-of-microarray-datasets-to-identify-parkinson-s-disease%C3%A2-associated-pathways-and-genes
#1
Yinling Feng, Xuefeng Wang
In order to investigate commonly disturbed genes and pathways in various brain regions of patients with Parkinson's disease (PD), microarray datasets from previous studies were collected and systematically analyzed. Different normalization methods were applied to microarray datasets from different platforms. A strategy combining gene co‑expression networks and clinical information was adopted, using weighted gene co‑expression network analysis (WGCNA) to screen for commonly disturbed genes in different brain regions of patients with PD...
January 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28098823/integrative-mirna-gene-expression-analysis-enables-refinement-of-associated-biology-and-prediction-of-response-to-cetuximab-in-head-and-neck-squamous-cell-cancer
#2
Loris De Cecco, Marco Giannoccaro, Edoardo Marchesi, Paolo Bossi, Federica Favales, Laura D Locati, Lisa Licitra, Silvana Pilotti, Silvana Canevari
This paper documents the process by which we, through gene and miRNA expression profiling of the same samples of head and neck squamous cell carcinomas (HNSCC) and an integrative miRNA-mRNA expression analysis, were able to identify candidate biomarkers of progression-free survival (PFS) in patients treated with cetuximab-based approaches. Through sparse partial least square-discriminant analysis (sPLS-DA) and supervised analysis, 36 miRNAs were identified in two components that clearly separated long- and short-PFS patients...
January 14, 2017: Genes
https://www.readbyqxmd.com/read/28092569/discovery-of-micrornas-and-transcription-factors-co-regulatory-modules-by-integrating-multiple-types-of-genomic-data
#3
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/28081052/identification-of-key-transcription-factors-associated-with-lung-squamous-cell-carcinoma
#4
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/28076842/systemically-identifying-and-prioritizing-risk-lncrnas-through-integration-of-pan-cancer-phenotype-associations
#5
Chaohan Xu, Rui Qi, Yanyan Ping, Jie Li, Hongying Zhao, Li Wang, Michael Yifei Du, Yun Xiao, Xia Li
LncRNAs have emerged as a major class of regulatory molecules involved in normal cellular physiology and disease, our knowledge of lncRNAs is very limited and it has become a major research challenge in discovering novel disease-related lncRNAs in cancers. Based on the assumption that diverse diseases with similar phenotype associations show similar molecular mechanisms, we presented a pan-cancer network-based prioritization approach to systematically identify disease-specific risk lncRNAs by integrating disease phenotype associations...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28076436/correction-a-network-based-data-integration-approach-to-support-drug-repurposing-and-multi-target-therapies-in-triple-negative-breast-cancer
#6
Francesca Vitali, Laurie D Cohen, Andrea Demartini, Angela Amato, Vincenzo Eterno, Alberto Zambelli, Riccardo Bellazzi
[This corrects the article DOI: 10.1371/journal.pone.0162407.].
2017: PloS One
https://www.readbyqxmd.com/read/28075450/integrated-analysis-of-differentially-expressed-genes-and-pathways-in-triple%C3%A2-negative-breast-cancer
#7
Cancan Peng, Wenli Ma, Wei Xia, Wenling Zheng
Triple‑negative breast cancer (TNBC) is a heterogeneous disease characterized by an aggressive phenotype and reduced survival. The aim of the present study was to investigate the molecular mechanisms involved in the carcinogenesis of TNBC and to identify novel target molecules for therapy. The differentially expressed genes (DEGs) in TNBC and normal adjacent tissue were assessed by analyzing the GSE41970 microarray data using Qlucore Omics Explorer, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes...
January 4, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28073935/brain-structure-and-function-associated-with-younger-adults-in-growth-hormone-receptor-deficient-humans
#8
Kaoru Nashiro, Jaime Guevara-Aguirre, Meredith N Braskie, George W Hafzalla, Rico Velasco, Priya Balasubramian, Min Wei, Paul M Thompson, Mara Mather, Marvin D Nelson, Alexandra Guevara, Enrique Teran, Valter D Longo
: Growth hormone receptor deficiency (GHRD) results in short stature, enhanced insulin sensitivity, and low circulating levels of insulin and insulin-like growth factor 1 (IGF-1). Previous studies in mice and humans suggested that GHRD has protective effects against age-related diseases, including cancer and diabetes. Whereas GHRD mice show improved age-dependent cognitive performance, the effect of GHRD on human cognition remains unknown. Using magnetic resonance imaging (MRI), we compared brain structure, function, and connectivity between 13 people with GHRD and 12 unaffected relatives...
January 10, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28071670/benzyl-isothiocyanate-potentiates-p53-signaling-and-antitumor-effects-against-breast-cancer-through-activation-of-p53-lkb1-and-p73-lkb1-axes
#9
Bei Xie, Arumugam Nagalingam, Panjamurthy Kuppusamy, Nethaji Muniraj, Peter Langford, Balázs Győrffy, Neeraj K Saxena, Dipali Sharma
Functional reactivation of p53 pathway, although arduous, can potentially provide a broad-based strategy for cancer therapy owing to frequent p53 inactivation in human cancer. Using a phosphoprotein-screening array, we found that Benzyl Isothiocynate, (BITC) increases p53 phosphorylation in breast cancer cells and reveal an important role of ERK and PRAS40/MDM2 in BITC-mediated p53 activation. We show that BITC rescues and activates p53-signaling network and inhibits growth of p53-mutant cells. Mechanistically, BITC induces p73 expression in p53-mutant cells, disrupts the interaction of p73 and mutant-p53, thereby releasing p73 from sequestration and allowing it to be transcriptionally active...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070575/network-pharmacology-based-virtual-screening-of-natural-products-from-clerodendrum-species-for-identification-of-novel-anti-cancer-therapeutics
#10
Barbi Gogoi, Dhrubajyoti Gogoi, Yumnam Silla, Bibhuti Bhushan Kakoti, Brijmohan Singh Bhau
Plant-derived natural products (NPs) play a vital role in the discovery of new drug molecules and these are used for development of novel therapeutic drugs for a specific disease target. Literature review suggests that natural products possess strong inhibitory efficacy against various types of cancer cells. Clerodendrum indicum and Clerodendrum serratum are reported to have anticancer activity; therefore a study was carried out to identify selective anticancer agents from these plants species. In this report, we employed a docking weighted network pharmacological approach to understand the multi-therapeutics potentiality of C...
January 10, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28067293/drug-response-prediction-as-a-link-prediction-problem
#11
Zachary Stanfield, Mustafa Coşkun, Mehmet Koyutürk
Drug response prediction is a well-studied problem in which the molecular profile of a given sample is used to predict the effect of a given drug on that sample. Effective solutions to this problem hold the key for precision medicine. In cancer research, genomic data from cell lines are often utilized as features to develop machine learning models predictive of drug response. Molecular networks provide a functional context for the integration of genomic features, thereby resulting in robust and reproducible predictive models...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28056600/the-use-of-teledermoscopy-in-the-accurate-identification-of-cancerous-skin-lesions-in-the-adult-population-a-systematic-review
#12
Amy F Bruce, Jennifer A Mallow, Laurie A Theeke
Background The use of teledermoscopy in the diagnostic management of pre-cancerous and cancerous skin lesions involves digital dermoscopic images transmitted over telecommunication networks via email or web applications. Teledermoscopy may improve the accuracy in clinical diagnoses of melanoma skin cancer if integrated into electronic medical records and made available to rural communities, potentially leading to decreased morbidity and mortality. Objective and method The purpose of this paper is to present a systematic review of evidence on the use of teledermoscopy to improve the accuracy of skin lesion identification in adult populations...
January 1, 2017: Journal of Telemedicine and Telecare
https://www.readbyqxmd.com/read/28055219/integrating-molecular-networking-and-biological-assays-to-target-the-isolation-of-a-cytotoxic-cyclic-octapeptide-samoamide-a-from-an-american-samoan-marine-cyanobacterium
#13
C Benjamin Naman, Ramandeep Rattan, Svetlana E Nikoulina, John Lee, Bailey W Miller, Nathan A Moss, Lorene Armstrong, Paul D Boudreau, Hosana M Debonsi, Frederick A Valeriote, Pieter C Dorrestein, William H Gerwick
Integrating LC-MS/MS molecular networking and bioassay-guided fractionation enabled the targeted isolation of a new and bioactive cyclic octapeptide, samoamide A (1), from a sample of cf. Symploca sp. collected in American Samoa. The structure of 1 was established by detailed 1D and 2D NMR experiments, HRESIMS data, and chemical degradation/chromatographic (e.g., Marfey's analysis) studies. Pure compound 1 was shown to have in vitro cytotoxic activity against several human cancer cell lines in both traditional cell culture and zone inhibition bioassays...
January 5, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28052061/integrated-genomic-characterization-of-oesophageal-carcinoma
#14
(no author information available yet)
Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas...
January 4, 2017: Nature
https://www.readbyqxmd.com/read/28051121/global-prioritizing-disease-candidate-lncrnas-via-a-multi-level-composite-network
#15
Qianlan Yao, Leilei Wu, Jia Li, Li Guang Yang, Yidi Sun, Zhen Li, Sheng He, Fangyoumin Feng, Hong Li, Yixue Li
LncRNAs play pivotal roles in many important biological processes, but research on the functions of lncRNAs in human disease is still in its infancy. Therefore, it is urgent to prioritize lncRNAs that are potentially associated with diseases. In this work, we developed a novel algorithm, LncPriCNet, that uses a multi-level composite network to prioritize candidate lncRNAs associated with diseases. By integrating genes, lncRNAs, phenotypes and their associations, LncPriCNet achieves an overall performance superior to that of previous methods, with high AUC values of up to 0...
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28048701/su-f-t-237-the-imaging-and-radiation-oncology-core-iroc-cooperatives-activities-supporting-the-nci-s-national-clinical-trial-network
#16
D Followill, J Galvin, J Michalski, M Rosen, T FitzGerald, M Knopp
PURPOSE: The Imaging and Radiation Oncology Core (IROC) Cooperative has been active for the past two years supporting the National Clinical Trial Network and the details of that support are reported. METHODS: There are six QA centers (Houston, Ohio, Philadelphia-RT, Philadelphia-DI, Rhode Island, St. Louis) providing an integrated RT and DI quality control program in support of the NCI's clinical trials. The QA Center's efforts are focused on assuring high quality data for clinical trials designed to improve the clinical outcomes for cancer patients worldwide...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047826/we-ab-207b-02-a-bayesian-network-approach-for-joint-prediction-of-tumor-control-and-radiation-pneumonitis-rp-in-non-small-cell-lung-cancer-nsclc
#17
Y Luo, D McShan, M Matuszak, S Hobson, S Jolly, R Ten Haken, I El Naqa
PURPOSE: NSCLC radiotherapy treatment is a trade-off between controlling the tumor while limiting radiation-induced toxicities. Here we identify hierarchical biophysical relationships that could simultaneously influence both local control (LC) and RP by using an integrated Bayesian Networks (BN) approach. METHODS: We studied 79 NSCLC patients treated on prospective protocol with 56 cases of LC and 21 events of RP. Beyond dosimetric information, each patient had 193 features including 12 clinical factors, 60 circulating blood cytokines before and during radiotherapy, 62 microRNAs, and 59 single-nucleotide polymorphisms (SNPs)...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28042992/are-rapidly-growing-cancers-more-lethal
#18
Hans-Olov Adami, Peter Csermely, Daniel V Veres, Louise Emilsson, Magnus Løberg, Michael Bretthauer, Mette Kalager
The view, that rapidly growing tumours are more likely than slow-growing tumours to metastasize and become lethal, has remained almost axiomatic for decades. Unaware of any solid evidence supporting this view, we undertook an exhaustive system-level analysis of intra- and intercellular signalling networks. This analysis indicated that rapid growth and metastasis are often different outcomes of complex integrated molecular events. Evidence from humans can be derived chiefly from screening interventions because interval cancers that surface clinically shortly after a negative screening test are, on average, more rapidly growing than cancers not detected by screening...
December 30, 2016: European Journal of Cancer
https://www.readbyqxmd.com/read/28036274/comprehensive-tissue-specific-gene-set-enrichment-analysis-and-transcription-factor-analysis-of-breast-cancer-by-integrating-14-gene-expression-datasets
#19
Wen-Xing Li, Kan He, Ling Tang, Shao-Xing Dai, Gong-Hua Li, Wen-Wen Lv, Yi-Cheng Guo, San-Qi An, Guo-Ying Wu, Dahai Liu, Jing-Fei Huang
Breast cancer is the most commonly diagnosed malignancy in women. Several key genes and pathways have been proven to correlate with breast cancer pathology. This study sought to explore the differences in key transcription factors (TFs), transcriptional regulation networks and dysregulated pathways in different tissues in breast cancer. We employed 14 breast cancer datasets from NCBI-GEO and performed an integrated analysis in three different tissues including breast, blood and saliva. The results showed that there were eight genes (CEBPD, EGR1, EGR2, EGR3, FOS, FOSB, ID1 and NFIL3) down-regulated in breast tissue but up-regulated in blood tissue...
December 27, 2016: Oncotarget
https://www.readbyqxmd.com/read/28035989/neuroblastoma-a-paradigm-for-big-data-science-in-pediatric-oncology
#20
REVIEW
Brittany M Salazar, Emily A Balczewski, Choong Yong Ung, Shizhen Zhu
Pediatric cancers rarely exhibit recurrent mutational events when compared to most adult cancers. This poses a challenge in understanding how cancers initiate, progress, and metastasize in early childhood. Also, due to limited detected driver mutations, it is difficult to benchmark key genes for drug development. In this review, we use neuroblastoma, a pediatric solid tumor of neural crest origin, as a paradigm for exploring "big data" applications in pediatric oncology. Computational strategies derived from big data science-network- and machine learning-based modeling and drug repositioning-hold the promise of shedding new light on the molecular mechanisms driving neuroblastoma pathogenesis and identifying potential therapeutics to combat this devastating disease...
December 27, 2016: International Journal of Molecular Sciences
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