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https://www.readbyqxmd.com/read/28713952/exploration-of-the-sequential-gene-changes-in-epithelial-ovarian-cancer-induced-by-carboplatin-via-microarray-analysis
#1
Shuqing Wei, Jianwu Liu, Yuxia Shi, Xi Zhang, Yongming Yang, Qingzhen Song
The purpose of the current study was to explore the carboplatin‑induced sequential changes in gene expression and screen out key genes, which were associated with effects of carboplatin on epithelial ovarian cancer (EOC). The microarray dataset GSE13525 was downloaded from the Gene Expression Omnibus database, including 6 EOC cell samples separately treated with carboplatin at 24, 30 and 36 h (case group), and 6 samples treated with phosphate‑buffered saline at the same time points (control group). A total of 3 sets of differentially expressed genes (DEGs) were respectively identified in case samples at 24, 30 and 36 h compared with the control group via the Limma package, and separately recorded as DEG‑24, DEG‑30 and DEG‑36...
July 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713815/bioinformatic-prediction-of-possible-targets-and-mechanisms-of-action-of-the-green-tea-compound-epigallocatechin-3-gallate-against-breast-cancer
#2
Xinqiang Song, Mu Zhang, Lei Chen, Qingsong Lin
Epigallocatechin-3-gallate (EGCG), a bioactive compound in green tea, is the most abundant and biologically active catechin, and it exerts multiple effects in humans through mechanisms that remain to be clarified. The present study used bioinformatics to identify possible mechanisms by which EGCG reduces risk of breast cancer. Possible human protein targets of EGCG were identified in the PubChem database, possible human gene targets were identified in the NCBI database, and then both sets of targets were analyzed using Ingenuity Pathway Analysis to predict molecular networks affected by EGCG in breast cancer...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28711912/identification-of-two-novel-biomarkers-of-rectal-carcinoma-progression-and-prognosis-via-co-expression-network-analysis
#3
Min Sun, Taojiao Sun, Zhongshi He, Bin Xiong
mRNA expression profiles provide important insights on a diversity of biological processes involved in rectal carcinoma (RC). Our aim was to comprehensively map complex interactions between the mRNA expression patterns and the clinical traits of RC. We employed the integrated analysis of five microarray datasets and The Cancer Genome Atlas rectal adenocarcinoma database to identify 2118 consensual differentially expressed genes (DEGs) in RC and adjacent normal tissue samples, and then applied weighted gene co-expression network analysis to parse DEGs and eight clinical traits in 66 eligible RC samples...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28711281/cancergd-a-resource-for-identifying-and-interpreting-genetic-dependencies-in-cancer
#4
Stephen Bridgett, James Campbell, Christopher J Lord, Colm J Ryan
Genes whose function is selectively essential in the presence of cancer-associated genetic aberrations represent promising targets for the development of precision therapeutics. Here, we present CancerGD, a resource that integrates genotypic profiling with large-scale loss-of-function genetic screens in tumor cell lines to identify such genetic dependencies. CancerGD provides tools for searching, visualizing, and interpreting these genetic dependencies through the integration of functional interaction networks...
July 11, 2017: Cell Systems
https://www.readbyqxmd.com/read/28710010/local-network-component-analysis-for-quantifying-transcription-factor-activities
#5
Qianqian Shi, Chuanchao Zhang, Weifeng Guo, Tao Zeng, Lina Lu, Zhonglin Jiang, Ziming Wang, Juan Liu, Luonan Chen
Transcription factors (TFs) could regulate physiological transitions or determine stable phenotypic diversity. The accurate estimation on TF regulatory signals or functional activities is of great significance to guide biological experiments or elucidate molecular mechanisms, but still remains challenging. Traditional methods identify TF regulatory signals at the population level, which masks heterogeneous regulation mechanisms in individuals or subgroups, thus resulting in inaccurate analyses. Here, we propose a novel computational framework, namely Local Network Component Analysis (LNCA), to exploit data heterogeneity and automatically quantify accurate transcription factor activity (TFA) in practical terms, through integrating the partitioned expression sets (i...
July 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28704211/how-to-emerge-from-the-conservatism-in-clinical-research-methodology
#6
Nuria Kotecki, Nicolas Penel, Ahmad Awada
PURPOSE OF REVIEW: Despite recent changes in clinical research methodology, many challenges remain in drug development methodology. RECENT FINDINGS: Advances in molecular biology and cancer treatments have changed the clinical research landscape. Thus, we moved from empirical clinical oncology to molecular and immunological therapeutic approaches. Along with this move, adapted dose-limiting toxicities definitions, endpoints, and dose escalation methods have been proposed...
July 12, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/28700989/doritool-a-bioinformatics-integrative-tool-for-post-association-functional-annotation
#7
Isabel Martín-Antoniano, Lola Alonso, Miguel Madrid, Evangelina López de Maturana, Núria Malats
The emergence of high-throughput data in biology has increased the need for functional in silico analysis and prompted the development of integrative bioinformatics tools to facilitate the obtainment of biologically meaningful data. In this paper, we present DoriTool, a comprehensive, easy, and friendly pipeline integrating biological data from different functional tools. The tool was designed with the aim to maximize reproducibility and reduce the working time of the researchers, especially of those with limited bioinformatics skills, and to help them with the interpretation of the results...
July 13, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28699531/identification-of-antineoplastic-targets-with-systems-approaches-using-resveratrol-as-an-in-depth-case-study
#8
Nivedita Singh, Sherry Freiesleben, Shailendra K Gupta, Yogeshwer Shukla, Olaf Wolkenhauer
The identification and validation of novel drug-target combinations are key steps in the drug discovery processes. Cancer is a complex disease that involves several genetic and environmental factors. High-throughput omics technologies are now widely available, however the integration of multi-omics data to identify viable anticancer drug-target combinations that allow for a better clinical outcome when considering the efficacy-toxicity spectrum, is challenging. In this review, we provide an overview of systems approaches that can help integrate a broad spectrum of technologies and data...
July 10, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28698868/diagnostic-microrna-biomarker-discovery-for-non-small-cell-lung-cancer-adenocarcinoma-by-integrative-bioinformatics-analysis
#9
Yang Shao, Bin Liang, Fei Long, Shu-Juan Jiang
Lung cancer is the leading cause of cancer death and its incidence is ranked high in men and women worldwide. Non-small-cell lung cancer (NSCLC) adenocarcinoma is one of the most frequent histological subtypes of lung cancer. The aberration profile and the molecular mechanism driving its progression are the key for precision therapy of lung cancer, while the screening of biomarkers is essential to the precision early diagnosis and treatment of the cancer. In this work, we applied a bioinformatics method to analyze the dysregulated interaction network of microRNA-mRNA in NSCLC, based on both the gene expression data and the microRNA-gene regulation network...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28694066/disease-gene-classification-with-metagraph-representations
#10
Sezin Ata Kircali, Yuan Fang, Min Wu, Xiao-Li Li, Xiaokui Xiao
Protein-protein interaction (PPI) networks play an important role in studying the functional roles of proteins, including their association with diseases. However, protein interaction networks are not sufficient without the support of additional biological knowledge for proteins such as their molecular functions and biological processes. To complement and enrich PPI networks, we propose to exploit biological properties of individual proteins. More specifically, we integrate keywords describing protein properties into the PPI network, and construct a novel PPI-Keywords (PPIK) network consisting of both proteins and keywords as two different types of nodes...
July 7, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28693226/screening-of-potentially-crucial-genes-and-regulatory-factors-involved-in-epithelial-ovarian-cancer-using-microarray-analysis
#11
Can Shi, Zhenyu Zhang
The present study aimed to screen potential genes implicated in epithelial ovarian cancer (EOC) and to further understand the molecular pathogenesis of EOC. In order to do this, datasets GSE14407 (containing 12 human ovarian cancer epithelia samples and 12 normal epithelia samples) and GSE29220 (containing 11 salivary transcriptomes from ovarian cancer patients with serous papillary adenocarcinoma and 11 matched controls) were obtained from the Gene Expression Omnibus. Differentially expressed genes (DEGs) within these datasets were screened using the Linear Models for Microarray Data package, and potential gene functions were predicted by functional and pathway enrichment analyses...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28691371/approaches-to-identify-kinase-dependencies-in-cancer-signalling-networks
#12
REVIEW
Maria Dermit, Arran Dokal, Pedro R Cutillas
Cells integrate extracellular signals into appropriate responses through a complex network of biochemical reactions driven by the activity of protein and lipid kinases, among other proteins. In order to understand this complexity, new approaches, both experimental and computational, have recently been developed with the aim to identify regulatory kinases and infer their activation status in the context of their signalling network. Here, we review such approaches with particular focus on those based on phosphoproteomics...
July 10, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28687755/the-integrated-pathway-of-tgf%C3%AE-snail-with-tnf%C3%AE-nf%C3%AE%C2%BAb-may-facilitate-the-tumor-stroma-interaction-in-the-emt-process-and-colorectal-cancer-prognosis
#13
Hui Li, Anjing Zhong, Si Li, Xianwen Meng, Xue Wang, Fangying Xu, Maode Lai
Substantial evidence has shown that epithelial-mesenchymal transition (EMT) plays critical roles in colorectal cancer (CRC) development and prognosis. To uncover the pivotal regulators that function in the cooperative interactions between cancer cells and their microenvironment and consequently affect the EMT process, we carried out a systematic analysis and evaluated prognosis in CRC specimens. Tumor buds and their surrounding stroma were captured using laser microdissection. We used gene expression profiling, bioinformatics analysis and regulatory network construction for molecular selection...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28683215/monitoring-lung-cancer-screening-utilization-and-outcomes-in-four-cancer-research-network-sites
#14
Michael K Gould, Lori C Sakoda, Debra P Ritzwoller, Michael J Simoff, Christine M Neslund-Dudas, Lawrence H Kushi, Lisa Carter-Harris, Heather Spencer Feigelson, George Minowada, V Paul Doria-Rose
RATIONALE: Lung cancer screening registries can monitor screening outcomes and improve quality of care. OBJECTIVES: To describe nascent lung cancer screening programs and share efficient data collection approaches for mandatory registry reporting in four integrated health care systems of the NCI-funded Cancer Research Network. METHODS: We documented the distinctive characteristics of lung cancer screening programs, provided examples of strategies to facilitate data collection, and described early challenges and possible solutions...
July 6, 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/28681694/uchl5-expression-associates-with-improved-survival-in-lymph-node-positive-rectal-cancer
#15
Leena Arpalahti, Jaana Hagström, Harri Mustonen, Mikael Lundin, Caj Haglund, Carina I Holmberg
Colorectal cancer is among the three most common cancer types for both genders, with a rising global incidence. To date, prognostic evaluation is difficult and largely dependent on early detection and successful surgery. UCHL5/Uch37 is an integral part of the protein homeostasis network as one of the three deubiquitinating enzymes associated with the 26S proteasome. Here, we have investigated in colorectal cancer the possible association of UCHL5 tumor expression and patient survival. UCHL5 tumor expression was evaluated by immunohistochemistry in 779 surgically treated colorectal cancer patients from Helsinki University Hospital, Finland, with assessment of clinicopathological parameters and the effect of UCHL5 expression on patient survival...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28678827/identifying-novel-genes-and-biological-processes-relevant-to-the-development-of-cancer-therapy-induced-mucositis-an-informative-gene-network-analysis
#16
Cielito C Reyes-Gibby, Stephanie C Melkonian, Jian Wang, Robert K Yu, Samuel A Shelburne, Charles Lu, Gary Brandon Gunn, Mark S Chambers, Ehab Y Hanna, Sai-Ching J Yeung, Sanjay Shete
Mucositis is a complex, dose-limiting toxicity of chemotherapy or radiotherapy that leads to painful mouth ulcers, difficulty eating or swallowing, gastrointestinal distress, and reduced quality of life for patients with cancer. Mucositis is most common for those undergoing high-dose chemotherapy and hematopoietic stem cell transplantation and for those being treated for malignancies of the head and neck. Treatment and management of mucositis remain challenging. It is expected that multiple genes are involved in the formation, severity, and persistence of mucositis...
2017: PloS One
https://www.readbyqxmd.com/read/28671190/compensatory-metabolic-networks-in-pancreatic-cancers-upon-perturbation-of-glutamine-metabolism
#17
Douglas E Biancur, Joao A Paulo, Beata Małachowska, Maria Quiles Del Rey, Cristovão M Sousa, Xiaoxu Wang, Albert S W Sohn, Gerald C Chu, Steven P Gygi, J Wade Harper, Wojciech Fendler, Joseph D Mancias, Alec C Kimmelman
Pancreatic ductal adenocarcinoma is a notoriously difficult-to-treat cancer and patients are in need of novel therapies. We have shown previously that these tumours have altered metabolic requirements, making them highly reliant on a number of adaptations including a non-canonical glutamine (Gln) metabolic pathway and that inhibition of downstream components of Gln metabolism leads to a decrease in tumour growth. Here we test whether recently developed inhibitors of glutaminase (GLS), which mediates an early step in Gln metabolism, represent a viable therapeutic strategy...
July 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28670954/predictors-of-patient-satisfaction-in-pediatric-oncology
#18
Josh Davis, James F Burrows, Bertha Ben Khallouq, Paul Rosen
OBJECTIVE: To understand key drivers of patient satisfaction in pediatric hematology/oncology. METHODS: The "top-box" scores of patient satisfaction surveys from 4 pediatric hematology/oncology practices were collected from 2012 to 2014 at an integrated Children's Health Network. One item, "Likelihood of recommending practice," was used as the surrogate for overall patient satisfaction, and all other items were correlated to this item. RESULTS: A total of 1244 satisfaction surveys were included in this analysis...
June 1, 2017: Journal of Pediatric Oncology Nursing: Official Journal of the Association of Pediatric Oncology Nurses
https://www.readbyqxmd.com/read/28669006/an-investigation-of-unmet-socio-economic-needs-among-arab-american-breast-cancer-patients-compared-with-other-immigrant-and-migrant-patients
#19
Claudia Ayash, Rosario Costas-Muñiz, Dalal Badreddine, Julia Ramirez, Francesca Gany
Although Arabs are a growing population in the United States, they are a hidden minority when compared to larger, more studied groups like Latinos and Caribbean immigrants of African descent (CIAD). There is limited research pertaining to patients' unmet socioeconomic and supportive care needs when undergoing breast cancer treatment, particularly among immigrants and migrants. This is a comparative study of a nested cohort of 36 Arabs, 145 Latinos and 128 CIAD breast cancer patients participating in the Integrated Cancer Care Access Network and their areas of needed assistance...
July 1, 2017: Journal of Community Health
https://www.readbyqxmd.com/read/28664150/coexpression-and-expression-quantitative-trait-loci-analyses-of-the-angiogenesis-gene-gene-interaction-network-in-prostate-cancer
#20
Hui-Yi Lin, Chia-Ho Cheng, Dung-Tsa Chen, Y Ann Chen, Jong Y Park
BACKGROUND: Prostate cancer (PCa) shows a substantial clinical heterogeneity. The existing risk classification for PCa prognosis based on clinical factors is not sufficient. Although some biomarkers for PCa aggressiveness have been identified, their underlying functional mechanisms are still unclear. We previously reported a gene-gene interaction network associated with PCa aggressiveness based on single nucleotide polymorphism (SNP)-SNP interactions in the angiogenesis pathway. The goal of this study is to investigate potential functional evidence of the involvement of the genes in this gene-gene interaction network...
October 2016: Translational Cancer Research
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