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https://www.readbyqxmd.com/read/29776332/telnet-a-database-for-human-and-yeast-genes-involved-in-telomere-maintenance
#1
Delia M Braun, Inn Chung, Nick Kepper, Katharina I Deeg, Karsten Rippe
BACKGROUND: The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway. The different telomere maintenance (TM) mechanisms appear to involve hundreds of proteins but their telomere repeat length related activities are only partly understood...
May 18, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29770165/targeting-oxidatively-induced-dna-damage-response-in-cancer-opportunities-for-novel-cancer-therapies
#2
REVIEW
Pierpaola Davalli, Gaetano Marverti, Angela Lauriola, Domenico D'Arca
Cancer is a death cause in economically developed countries that results growing also in developing countries. Improved outcome through targeted interventions faces the scarce selectivity of the therapies and the development of resistance to them that compromise the therapeutic effects. Genomic instability is a typical cancer hallmark due to DNA damage by genetic mutations, reactive oxygen and nitrogen species, ionizing radiation, and chemotherapeutic agents. DNA lesions can induce and/or support various diseases, including cancer...
2018: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/29765546/proteomic-screening-identifies-the-zonula-occludens-protein-zo-1-as-a-new-partner-for-adam12-in-invadopodia-like-structures
#3
Bassil Dekky, Michael Ruff, Dominique Bonnier, Vincent Legagneux, Nathalie Théret
The epithelial mesenchymal transition (EMT) is a key process for cancer cell invasion and migration. This complex program whereby epithelial tumor cells loose polarity and acquire mesenchymal phenotype is driven by the regulation of cell-cell adhesion and cell-substrate interactions. We recently described the association of ADAM12 with EMT and we now use immunoprecipitation and proteomic approaches to identify interacting partners for ADAM12 during EMT. We identify twenty proteins that are involved in molecular mechanisms associated with adhesion/invasion processes...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29765536/predicting-hepatocellular-carcinoma-through-cross-talk-genes-identified-by-risk-pathways
#4
Lei Liu, Lin Pang, Yunfeng Wang, Ming Hu, Zhuo Shao, Diwei Huo, Denan Zhang, Hongbo Xie, Jingbo Yang, Qiuqi Liu, Xiujie Chen
Hepatocellular carcinoma (HCC) is the most frequent type of liver cancer with poor survival rate and high mortality. Despite efforts on the mechanism of HCC, new molecular markers are needed for exact diagnosis, evaluation and treatment. Here, we combined transcriptome of HCC with networks and pathways to identify reliable molecular markers. Through integrating 249 differentially expressed genes with syncretic protein interaction networks, we constructed a HCC-specific network, from which we further extracted 480 pivotal genes...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29764514/integrative-analysis-of-gene-expression-profiles-reveals-specific-signaling-pathways-associated-with-pancreatic-duct-adenocarcinoma
#5
Jun Li, Wenle Tan, Linna Peng, Jialiang Zhang, Xudong Huang, Qionghua Cui, Jian Zheng, Wen Tan, Chen Wu, Dongxin Lin
BACKGROUND: Pancreatic duct adenocarcinoma (PDAC) remains a major health problem because conventional cancer treatments are relatively ineffective against it. Microarray studies have linked many genes to pancreatic cancer, but the available data have not been extensively mined for potential insights into PDAC. This study attempted to identify PDAC-associated genes and signaling pathways based on six microarray-based profiles of gene expression in pancreatic cancer deposited in the gene expression omnibus database...
April 27, 2018: Cancer communications
https://www.readbyqxmd.com/read/29764446/comprehensive-and-integrative-analysis-identifies-microrna-106-as-a-novel-non-invasive-biomarker-for-detection-of-gastric-cancer
#6
Qiliang Peng, Yi Shen, Kaisu Lin, Li Zou, Yuntian Shen, Yaqun Zhu
BACKGROUND: Recently, accumulating evidences have revealed that microRNA-106 (miR-106) may serve as a non-invasive and cost-effective biomarker in gastric cancer (GC) detection. However, inconsistent results have prevented its application to clinical practice. METHODS: As a result of this, a comprehensive meta-analysis was conducted to evaluate the diagnostic performance of miR-106 alone and miR-106-related combination markers for GC detection. Meanwhile, an integrative bioinformatics analysis was performed to explore the function of miR-106 at the systems biology level...
May 15, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29758295/systematic-bioinformatic-approaches-reveal-novel-gene-expression-signatures-associated-with-acquired-resistance-to-egfr-targeted-therapy-in-lung-cancer
#7
Marjan Mojtabavi Naeini, Manoochehr Tavassoli, Kamran Ghaedi
OBJECTIVES: Human non-small cell lung cancer (NSCLC) that harbors activating mutations in epidermal growth factor receptor (EGFR) initially responds to treatment with EGFR tyrosine kinase inhibitors (TKIs) such as gefitinib and erlotinib but eventually tumor cells acquire resistance. To date, several gene expression profiles have been reported in TKIs-resistant EGFR-mutant NSCLC. The objective of this study is to identify robust gene expression signatures, biological processes, and promising overcoming targets for TKIs-resistant EGFR-mutant NSCLC...
May 11, 2018: Gene
https://www.readbyqxmd.com/read/29756349/integrating-the-dna-damage-and-protein-stress-responses-during-cancer-development-and-treatment
#8
REVIEW
Vassilis G Gorgoulis, Dafni-Eleftheria Pefani, Ioannis S Pateras, Ioannis P Trougakos
Cells have developed during evolution a wide spectrum of stress response modules to assure homeostasis. The genome and proteome damage response pathways constitute the pillars of this interwoven "defensive" network. Consequently, the deregulation of these pathways correlates with aging and various pathophysiological states, including cancer. In the present review we highlight: i) the structure of the genome and proteome damage response pathways, ii) their functional crosstalk and, iii) the conditions under which they predispose to cancer...
May 13, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29753129/applications-of-rna-indexes-for-precision-oncology-in-breast-cancer
#9
REVIEW
Liming Ma, Zirui Liang, Hui Zhou, Lianghu Qu
Precision oncology aims to offer the most appropriate treatments to cancer patients mainly based on their individual genetic information. Genomics has provided numerous valuable data on driver mutations and risk loci; however, it remains a formidable challenge to transform these data into therapeutic agents. Transcriptomics describes the multifarious expression patterns of both mRNAs and non-coding RNAs (ncRNAs), which facilitates the deciphering of genomic codes. In this review, we take breast cancer as an example to demonstrate the applications of these rich RNA resources in precision medicine exploration...
May 9, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29750305/alterations-in-mrna-profiles-of-trastuzumab%C3%A2-resistant-her%C3%A2-2%C3%A2-positive-breast-cancer
#10
Bin Zhao, Yang Zhao, Yan Sun, Haitao Niu, Long Sheng, Dongfang Huang, Li Li
Breast cancer is one of the most common malignancies in women. Neoadjuvant trastuzumab therapy improves the prognosis of certain Her‑2‑positive breast cancer patients, however around two‑thirds of patients with Her‑2‑positive breast cancer do not benefit from Her‑2‑targeted therapy. To investigate the key mechanisms in trastuzumab resistance, potential biomarkers for neoadjuvant trastuzumab sensitivity were investigated using the gene expression omnibus (GEO) database for mRNA microarray data of Her‑2‑positive breast cancer patients who received neoadjuvant trastuzumab therapy...
May 7, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29749503/a-gene-interaction-network%C3%A2-based-method-to-measure-the-common-and-heterogeneous-mechanisms-of-gynecological-cancer
#11
Mingyuan Wang, Liping Li, Jinglan Liu, Jinjin Wang
Gynecological malignancies are a leading cause of mortality in the female population. The present study intended to identify the association between three severe types of gynecological cancer, specifically ovarian cancer, cervical cancer and endometrial cancer, and to identify the connective driver genes, microRNAs (miRNAs) and biological processes associated with these types of gynecological cancer. In the present study, individual driver genes for each type of cancer were identified using integrated analysis of multiple microarray data...
May 3, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29749474/pgc1%C3%AE-promotes-cisplatin-resistance-in-human-ovarian-carcinoma-cells-through-upregulation-of-mitochondrial-biogenesis
#12
Luyan Shen, Boyang Sun, Jiyao Sheng, Sihang Yu, Yanqing Li, Huadan Xu, Jing Su, Liankun Sun
The induction of lesions in nuclear and mitochondrial DNA by cisplatin is only a small component of its cytostatic/cytotoxic activity. The signaling pathway network in the nucleus and cytoplasm may contribute to chemotherapeutic resistance. Peroxisome proliferator-activated receptor-coactivator 1α (PGC1α)-mediated mitochondrial biogenesis regulates mitochondrial structural and the functional adaptive response against chemotherapeutic stress, and may be a therapeutic target. However, this regulatory network is complex and depends upon tumor types and environments, which require further investigation...
May 9, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29748206/deep-learning-convolutional-neural-networks-accurately-classify-genetic-mutations-in-gliomas
#13
P Chang, J Grinband, B D Weinberg, M Bardis, M Khy, G Cadena, M-Y Su, S Cha, C G Filippi, D Bota, P Baldi, L M Poisson, R Jain, D Chow
BACKGROUND AND PURPOSE: The World Health Organization has recently placed new emphasis on the integration of genetic information for gliomas. While tissue sampling remains the criterion standard, noninvasive imaging techniques may provide complimentary insight into clinically relevant genetic mutations. Our aim was to train a convolutional neural network to independently predict underlying molecular genetic mutation status in gliomas with high accuracy and identify the most predictive imaging features for each mutation...
May 10, 2018: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/29747501/multi-proteomic-and-transcriptomic-analysis-of-oncogenic-%C3%AE-catenin-molecular-networks
#14
Rob M Ewing, Jing Song, Giridharan Gokulrangan, Sheldon Bai, Emily Bowler, Rachel Bolton, Paul Skipp, Yihua Wang, Zhenghe Wang
Dys-regulation of Wnt signalling is a frequent occurrence in many different cancers. Oncogenic mutations of CTNNB1/β-catenin, the key nuclear effector of canonical Wnt signalling, lead to accumulation and stabilization of β-catenin protein with diverse effects in cancer cells. Although the transcriptional response to Wnt/β-catenin signaling activation has been widely studied, an integrated understanding of the effects of oncogenic β-catenin on molecular networks is lacking. We used Affinity-Purification Mass-Spectrometry (AP-MS), label-free LC-MS/MS and RNA-Seq to compare protein-protein interactions, protein expression and gene-expression in colorectal cancer cells expressing mutant/oncogenic or wild-type β-catenin...
May 10, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29745839/multi-target-drug-repositioning-by-bipartite-block-wise-sparse-multi-task-learning
#15
Limin Li, Xiao He, Karsten Borgwardt
BACKGROUND: Finding potential drug targets is a crucial step in drug discovery and development. Recently, resources such as the Library of Integrated Network-Based Cellular Signatures (LINCS) L1000 database provide gene expression profiles induced by various chemical and genetic perturbations and thereby make it possible to analyze the relationship between compounds and gene targets at a genome-wide scale. Current approaches for comparing the expression profiles are based on pairwise connectivity mapping analysis...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745833/differential-networking-meta-analysis-of-gastric-cancer-across-asian-and-american-racial-groups
#16
Wentao Dai, Quanxue Li, Bing-Ya Liu, Yi-Xue Li, Yuan-Yuan Li
BACKGROUND: Gastric Carcinoma is one of the most lethal cancer around the world, and is also the most common cancers in Eastern Asia. A lot of differentially expressed genes have been detected as being associated with Gastric Carcinoma (GC) progression, however, little is known about the underlying dysfunctional regulation mechanisms. To address this problem, we previously developed a differential networking approach that is characterized by involving differential coexpression analysis (DCEA), stage-specific gene regulatory network (GRN) modelling and differential regulation networking (DRN) analysis...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29744300/gene-expression-profiles-and-pathway-enrichment-analysis-of-human-osteosarcoma-cells-exposed-to-sorafenib
#17
Zhehao Dai, Haoyu Tang, Yue Pan, Junquan Chen, Yongping Li, Jun Zhu
Sorafenib is an inhibitor of a variety of tyrosine kinase receptors used to treat various cancers including hepatocellular, renal cell and thyroid carcinoma. It has been shown to change various targets associated with osteosarcoma, but the detailed mechanism remains unclear. In order to identify key genes, enriched pathways and important modules during the exposure of human osteosarcoma cells to sorafenib, data for gene expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155) were downloaded from the GEO database...
May 2018: FEBS Open Bio
https://www.readbyqxmd.com/read/29742928/an-integrated-study-on-the-antitumor-effect-and-mechanism-of-triphala-against-gynecological-cancers-based-on-network-pharmacological-prediction-and-in-vitro-experimental-validation
#18
Yuhang Zhao, Min Wang, Jokyab Tsering, Hanluo Li, Simin Li, Yuepeng Li, Yinghua Liu, Xianda Hu
OBJECTIVES: Triphala is a herbal medicine that has been widely used for treating a variety of ailments. This study aims to systematically analyze the antitumor effects of Triphala on gynecological cancers. METHODS: The antineoplastic activities of Triphala on gynecological cancers were analyzed using network pharmacology-based strategies. Afterward, the human ovarian cancer cell line SK-OV-3, cervical cancer cell line HeLa, and endometrial cancer cell line HEC-1-B were selected for experimetal valification...
May 1, 2018: Integrative Cancer Therapies
https://www.readbyqxmd.com/read/29739919/identification-of-core-genes-and-key-pathways-via-integrated-analysis-of-gene-expression-and-dna-methylation-profiles-in-bladder-cancer
#19
Yongzhen Zhang, Liang Fang, Yuanwei Zang, Zhonghua Xu
BACKGROUND Bladder cancer (BC) is the most common urological malignant tumor. In BC, aberrant DNA methylation is believed to be associated with carcinogenesis. Therefore, the identification of key genes and pathways could help determine the potential molecular mechanisms of BC development. MATERIAL AND METHODS Microarray data on gene expression and gene methylation were downloaded from the Gene Expression Omnibus (GEO) database. Abnormal methylated/expressed genes were analyzed by GEO2R and statistical software R...
May 9, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29739052/mechanism-comparison-of-gemcitabine-and-dasatinib-resistant-pancreatic-cancer-by-integrating-mrna-and-mirna-expression-profiles
#20
Zongjing Chen, Liang Zhao, Keqing Shi, Bicheng Chen
BACKGROUND: Pancreatic cancer is one of the most lethal cancers with limited treatment options. Gemcitabine has been the standard drug for patients with advanced pancreatic cancer. Dasatinib is a competitive inhibitor of Src kinase, which has shown promise in treatment of pancreatic cancer. Several studies have revealed the drug resistant mechanism of gemcitabine or dasatinib in human cancers; however, few reports focused on the different mechanisms of gemcitabine and dasatinib resistance in pancreatic cancer...
May 1, 2018: Clinical Laboratory
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