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Tissue specific gene network

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https://www.readbyqxmd.com/read/28088579/the-microrna-449-family-inhibits-tgf-%C3%AE-mediated-liver-cancer-cell-migration-by-targeting-sox4
#1
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/28087776/seed-plant-specific-gene-lineages-involved-in-carpel-development
#2
Kai C Pfannebecker, Matthias Lange, Oliver Rupp, Annette Becker
Evolutionary innovations are important drivers of speciation and some are the defining characters of entire phyla. One such major innovation is the carpel, the unifying character and most complex plant organ, composed of many clearly distinct tissue types to ensure reproductive success. The origin of the carpel is unknown, but many components of the gene regulatory network (GRN) governing carpel development and their genetic interactions are known from the core eudicot Arabidopsis thaliana To unravel the evolution of the carpel GRN and to discriminate between "early" and "late" steps in carpel evolution we calculated thorough phylogeny reconstructions based on sequenced genomes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087637/retinoic-acid-receptor-regulation-of-epimorphic-and-homeostatic-regeneration-in-the-axolotl
#3
Matthew Nguyen, Pankhuri Singhal, Judith Piet, Sandra J Shefelbine, Malcolm Maden, S Randal Voss, James R Monaghan
Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we target specific retinoic acid receptors (RARs) to either PD duplicate (RA treatment or RARγ agonist) or truncate (RARβ antagonist) regenerating limbs...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28087487/bioprinting-for-vascular-and-vascularized-tissue-biofabrication
#4
REVIEW
Pallab Datta, Bugra Ayan, Ibrahim T Ozbolat
: Bioprinting is a promising technology to fabricate design-specific tissue constructs due to its ability to create complex, heterocellular structures with anatomical precision. Bioprinting enables the deposition of various biologics including growth factors, cells, genes, neo-tissues and extra-cellular matrix-like hydrogels. Benefits of bioprinting have started to make a mark in the fields of tissue engineering, regenerative medicine and pharmaceutics. Specifically, in the field of tissue engineering, the creation of vascularized tissue constructs has remained a principal challenge till date...
January 10, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28076377/comparative-analysis-of-vertebrate-diurnal-circadian-transcriptomes
#5
Greg Boyle, Kerstin Richter, Henry D Priest, David Traver, Todd C Mockler, Jeffrey T Chang, Steve A Kay, Ghislain Breton
From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge regarding its connection to help regulate diurnal physiology...
2017: PloS One
https://www.readbyqxmd.com/read/28074264/nacl-stress-induces-cssams-gene-expression-in-cucumis-sativus-by-mediating-the-binding-of-csgt-3b-to-the-gt-1-element-within-the-cssams-promoter
#6
Li-Wei Wang, Mei-Wen He, Shi-Rong Guo, Min Zhong, Sheng Shu, Jin Sun
The CsSAMs promoter is a salt-stress-inducible promoter containing three GT-1 elements that are sufficient for the salt-stress response. The transcription factor CsGT-3b was found to bind to the GT-1 element. The S-adenosyl-L-methionine synthase (SAMs) gene is among the functional genes induced during environmental stress. However, little is known about the regulatory mechanism and upstream regulators of this salt-inducible gene in cucumber plants. Thus, it is necessary to understand the characteristics of the SAMs gene by analyzing its promoter and transcription factors...
January 10, 2017: Planta
https://www.readbyqxmd.com/read/28057848/a-pipeline-for-drug-target-identification-and-validation
#7
Eusebio Manchado, Chun-Hao Huang, Nilgun Tasdemir, Darjus F Tschaharganeh, John E Wilkinson, Scott W Lowe
Rapid and affordable tumor profiling has led to an explosion of genomic data that is facilitating the development of new cancer therapies. The potential of therapeutic strategies aimed at inactivating the oncogenic lesions that contribute to the aberrant survival and proliferation of tumor cells has yielded remarkable success in some malignancies such as BRAF-mutant melanoma and BCR-ABL expressing chronic myeloid leukemia. However, the direct inhibition of several well-established oncoproteins in some of these cancers is not possible or produces only transient benefits...
January 5, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28052653/how-can-we-treat-cancer-disease-not-cancer-cells
#8
Kyu-Won Kim, Su-Jae Lee, Woo-Young Kim, Ji Hae Seo, Ho-Young Lee
Since molecular biology studies began, researches in biological science have centered on proteins and genes at molecular level of a single cell. Cancer research has also focused on various functions of proteins and genes that distinguish cancer cells from normal cells. Accordingly, most contemporary anticancer drugs have been developed to target abnormal characteristics of cancer cells. Despite the great advances in the development of anticancer drugs, vast majority of patients with advanced cancer have shown grim prognosis and high rate of relapse...
January 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28047421/mo-de-207b-03-improved-cancer-classification-using-patient-specific-biological-pathway-information-via-gene-expression-data
#9
M Young, D Craft
PURPOSE: To develop an efficient, pathway-based classification system using network biology statistics to assist in patient-specific response predictions to radiation and drug therapies across multiple cancer types. METHODS: We developed PICS (Pathway Informed Classification System), a novel two-step cancer classification algorithm. In PICS, a matrix m of mRNA expression values for a patient cohort is collapsed into a matrix p of biological pathways. The entries of p, which we term pathway scores, are obtained from either principal component analysis (PCA), normal tissue centroid (NTC), or gene expression deviation (GED)...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28045567/disruption-of-the-gaa-gene-in-zebrafish-fails-to-generate-the-phenotype-of-classical-pompe-disease
#10
Jing Wu, Yi Yang, Chengjun Sun, Shaoyang Sun, Qiang Li, Yuxiao Yao, Fei Fei, Lingeng Lu, Zhuo Chang, Wenting Zhang, Xu Wang, Feihong Luo
The underlying pathogenic lesions of glycogen storage disease type II (GSD II) and the diversity of this disease among different species are still under exploration. Thus, we created an acid alpha-glucosidase (gaa) gene-mutated zebrafish model of GSD II and examined the sequential pathogenic changes. gaa mRNA and protein expression, enzymatic activity, and lysosomal glycogen accumulation were assessed, and the phenotypic changes were compared between wild-type (WT) and gaa-mutated zebrafish. The presence of a Δ13 frameshift mutation in the gaa gene was confirmed at both the DNA and transcribed mRNA levels by Sanger sequencing...
January 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28042869/genome-wide-screen-of-mirnas-and-targeting-mrnas-reveals-the-negatively-regulatory-effect-of-mir-130b-3p-on-pten-by-pi3k-and-integrin-%C3%AE-1-signaling-pathways-in-bladder-carcinoma
#11
Mengxin Lv, Zhenyu Zhong, Hong Chi, Mengge Huang, Rong Jiang, Junxia Chen
miRNAs have emerged as promising markers for tumors. However, the underlying mechanism of specific miRNAs in bladder cancer (BC) remains largely unknown. Here, a comprehensive miRNA/mRNA expression profile was executed by microarray assay for four pairs of bladder carcinoma and para-carcinoma tissues from patients with grade 2 (G2) T2. A total of 99 miRNAs and 4416 mRNAs were discovered to be significantly differentially expressed in BC tissues compared with controls. Five microRNAs and two mRNAs were validated by qRT-PCR in 30 pairs of samples, including G1-G3/T1-T4...
December 31, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28036392/a-differentiation-transcription-factor-establishes-muscle-specific-proteostasis-in-caenorhabditis-elegans
#12
Yael Bar-Lavan, Netta Shemesh, Shiran Dror, Rivka Ofir, Esti Yeger-Lotem, Anat Ben-Zvi
Safeguarding the proteome is central to the health of the cell. In multi-cellular organisms, the composition of the proteome, and by extension, protein-folding requirements, varies between cells. In agreement, chaperone network composition differs between tissues. Here, we ask how chaperone expression is regulated in a cell type-specific manner and whether cellular differentiation affects chaperone expression. Our bioinformatics analyses show that the myogenic transcription factor HLH-1 (MyoD) can bind to the promoters of chaperone genes expressed or required for the folding of muscle proteins...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/28036280/pan-organ-transcriptome-variation-across-21-cancer-types
#13
Wangxiong Hu, Yanmei Yang, Xiaofen Li, Shu Zheng
It is widely accepted that some messenger RNAs are evolutionarily conserved across species, both in sequence and tissue-expression specificity. To date, however, little effort has been made to exploit the transcriptome divergence between cancer and adjacent normal tissue at the pan-organ level. In this work, a transcriptome sequencing dataset from 675 normal-tumor pairs, representing 21 solid organs in The Cancer Genome Atlas, is used to evaluate expression evolution. The results show that in most cancer types, gene expression divergence and organ-specificity are reduced in cancer tissue compared to adjacent normal tissue...
December 27, 2016: Oncotarget
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
#14
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/28030800/the-role-of-mir-17-92-in-the-miregulatory-landscape-of-ewing-sarcoma
#15
Raphaela Schwentner, David Herrero-Martin, Maximilian O Kauer, Cornelia N Mutz, Anna M Katschnig, Grzegorz Sienski, Javier Alonso, Dave Nt Aryee, Heinrich Kovar
MicroRNAs serve to fine-tune gene expression and play an important regulatory role in tissue specific gene networks. The identification and validation of miRNA target genes in a tissue still poses a significant problem since the presence of a seed sequence in the 3'UTR of an mRNA and its expression modulation upon ectopic expression of the miRNA do not reliably predict regulation under physiological conditions. The chimeric oncoprotein EWS-FLI1 is the driving pathogenic force in Ewing sarcoma. MiR-17-92, one of the most potent oncogenic miRNAs, was recently reported to be among the top EWS-FLI1 activated miRNAs...
December 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/28028006/identification-and-analysis-of-the-human-sex-biased-genes
#16
Sisi Guo, Yuan Zhou, Pan Zeng, Guoheng Xu, Guoqing Wang, Qinghua Cui
Tremendous differences between human sexes are universally observed. Therefore, identifying and analyzing the sex-biased genes are becoming basically important for uncovering the mystery of sex differences and personalized medicine. Here, we presented a computational method to identify sex-biased genes from public gene expression databases. We obtained 1407 female-biased genes (FGs) and 1096 male-biased genes (MGs) across 14 different tissues. Bioinformatics analysis revealed that compared with MGs, FGs have higher evolutionary rate, higher single-nucleotide polymorphism density, less homologous gene numbers and smaller phyletic age...
December 27, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28018056/onecut-transcription-factors-in-development-and-disease
#17
Peter A Kropp, Maureen Gannon
Developmental processes are remarkably well conserved among species, and among the most highly conserved developmental regulators are transcription factor families. The Onecut transcription factor family consists of three members known for their single "cut" DNA-binding domain and an aberrant homeodomain. The three members of the Onecut family are highly conserved from Drosophila to humans and have significant roles in regulating the development of diverse tissues derived from the ectoderm or endoderm, where they activate a number of gene families...
2016: Trends in Developmental Biology
https://www.readbyqxmd.com/read/28008225/identifying-cell-type-specific-transcription-factors-by-integrating-chip-seq-and-eqtl-data-application-to-monocyte-gene-regulation
#18
Mudra Choudhury, Stephen A Ramsey
We describe a novel computational approach to identify transcription factors (TFs) that are candidate regulators in a human cell type of interest. Our approach involves integrating cell type-specific expression quantitative trait locus (eQTL) data and TF data from chromatin immunoprecipitation-to-tag-sequencing (ChIP-seq) experiments in cell lines. To test the method, we used eQTL data from human monocytes in order to screen for TFs. Using a list of known monocyte-regulating TFs, we tested the hypothesis that the binding sites of cell type-specific TF regulators would be concentrated in the vicinity of monocyte eQTLs...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/28007888/stable-binding-of-the-conserved-transcription-factor-grainy-head-to-its-target-genes-throughout-drosophila-melanogaster-development
#19
Markus Nevil, Eliana R Bondra, Katharine N Schulz, Tommy Kaplan, Melissa M Harrison
It has been suggested that transcription factor binding is temporally dynamic and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head is conserved from fungi to humans and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head gene, provide an excellent system to study this conserved factor...
December 22, 2016: Genetics
https://www.readbyqxmd.com/read/28005004/functional-evolution-of-a-morphogenetic-gradient
#20
Chun Wai Kwan, Jackie Gavin-Smyth, Edwin L Ferguson, Urs Schmidt-Ott
Bone Morphogenetic Proteins (BMPs) pattern the dorsal-ventral axis of bilaterian embryos; however, their roles in the evolution of body plan are largely unknown. We examined their functional evolution in fly embryos. BMP signaling specifies two extraembryonic tissues, the serosa and amnion, in basal-branching flies such as Megaselia abdita, but only one, the amnioserosa, in Drosophila melanogaster. The BMP signaling dynamics are similar in both species until the beginning of gastrulation, when BMP signaling broadens and intensifies at the edge of the germ rudiment in Megaselia, while remaining static in Drosophila...
December 22, 2016: ELife
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