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https://www.readbyqxmd.com/read/27460729/bioinformatic-analysis-of-rna-seq-data-unveiled-critical-genes-in-rectal-adenocarcinoma
#1
Z-G Zuo, X-F Zhang, X-Z Ye, Z-H Zhou, X-B Wu, S-C Ni, H-Y Song
OBJECTIVE: RNA-seq data of rectal adenocarcinoma (READ) were analyzed with bioinformatics tools to unveil potential biomarkers in the disease. MATERIALS AND METHODS: RNA-seq data of READ were downloaded from The Cancer Genome Atlas (TCGA) database. Differential analysis was performed with package edgeR. False discovery rate (FDR) < 0.05 and |log2 (fold change)|>1 were set as cut-off values to screen out differentially expressed genes (DEGs). Gene coexpression network was constructed with package Ebcoexpress...
July 2016: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/27217777/screening-of-biomarkers-for-prediction-of-response-to-and-prognosis-after-chemotherapy-for-breast-cancers
#2
Feng Bing, Yu Zhao
OBJECTIVE: To screen the biomarkers having the ability to predict prognosis after chemotherapy for breast cancers. METHODS: Three microarray data of breast cancer patients undergoing chemotherapy were collected from Gene Expression Omnibus database. After preprocessing, data in GSE41112 were analyzed using significance analysis of microarrays to screen the differentially expressed genes (DEGs). The DEGs were further analyzed by Differentially Coexpressed Genes and Links to construct a function module, the prognosis efficacy of which was verified by the other two datasets (GSE22226 and GSE58644) using Kaplan-Meier plots...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/26999808/inhibition-of-pancreatic-acinar-mitochondrial-thiamin-pyrophosphate-uptake-by-the-cigarette-smoke-component-4-methylnitrosamino-1-3-pyridyl-1-butanone
#3
Padmanabhan Srinivasan, Edwin C Thrower, Fred S Gorelick, Hamid M Said
Thiamin is essential for normal metabolism in pancreatic acinar cells (PAC) and is obtained from their microenvironment through specific plasma-membrane transporters, converted to thiamin pyrophosphate (TPP) in the cytoplasm, followed by uptake of TPP by mitochondria through the mitochondrial TPP (MTPP) transporter (MTPPT; product of SLC25A19 gene). TPP is essential for normal mitochondrial function. We examined the effect of long-term/chronic exposure of PAC in vitro (pancreatic acinar 266-6 cells) and in vivo (wild-type or transgenic mice carrying the SLC25A19 promoter) of the cigarette smoke toxin, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), on the MTPP uptake process...
May 15, 2016: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/26921499/atr-chk1-e2f3-signaling-transactivates-human-ribonucleotide-reductase-small-subunit-m2-for-dna-repair-induced-by-the-chemical-carcinogen-mnng
#4
Chaoju Gong, Hong Liu, Rui Song, Tingting Zhong, Meng Lou, Tingyang Wang, Hongyan Qi, Jing Shen, Lijun Zhu, Jimin Shao
BACKGROUND: N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), an alkylating agent and an environmental carcinogen, causes DNA lesions and even carcinomas. DNA damage responses induced by MNNG activate various DNA repair genes and related signaling pathways. The present study aimed to investigate the regulatory mechanisms of human RR small subunit M2 (hRRM2) in response to MNNG. RESULTS: In this study, we demonstrated that the RRM2 gene was transactivated by MNNG exposure more strongly than the other small subunit, p53R2...
April 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/26894282/noncoding-rnas-emerging-regulators-in-root-endosymbioses
#5
REVIEW
Christine Lelandais-Brière, Jérémy Moreau, Caroline Hartmann, Martin Crespi
Endosymbiosis interactions allow plants to grow in nutrient-deficient soil environments. The arbuscular mycorrhizal (AM) symbiosis is an ancestral interaction between land plants and fungi, whereas nitrogen-fixing symbioses are highly specific for certain plants, notably major crop legumes. The signaling pathways triggered by specific lipochitooligosaccharide molecules involved in these interactions have common components that also overlap with plant root development. These pathways include receptor-like kinases, transcription factors (TFs), and various intermediate signaling effectors, including noncoding (nc)RNAs...
March 2016: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/26832790/targeting-the-nuclear-import-receptor-kpn%C3%AE-1-as-an-anticancer-therapeutic
#6
Pauline J van der Watt, Alicia Chi, Tamara Stelma, Catherine Stowell, Erin Strydom, Sarah Carden, Liselotte Angus, Kate Hadley, Dirk Lang, Wei Wei, Michael J Birrer, John O Trent, Virna D Leaner
Karyopherin beta 1 (Kpnβ1) is a nuclear transport receptor that imports cargoes into the nucleus. Recently, elevated Kpnβ1 expression was found in certain cancers and Kpnβ1 silencing with siRNA was shown to induce cancer cell death. This study aimed to identify novel small molecule inhibitors of Kpnβ1, and determine their anticancer activity. An in silico screen identified molecules that potentially bind Kpnβ1 and Inhibitor of Nuclear Import-43, INI-43 (3-(1H-benzimidazol-2-yl)-1-(3-dimethylaminopropyl)pyrrolo[5,4-b]quinoxalin-2-amine) was investigated further as it interfered with the nuclear localization of Kpnβ1 and known Kpnβ1 cargoes NFAT, NFκB, AP-1, and NFY and inhibited the proliferation of cancer cells of different tissue origins...
April 2016: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/26559525/profiling-of-discrete-gynecological-cancers-reveals-novel-transcriptional-modules-and-common-features-shared-by-other-cancer-types-and-embryonic-stem-cells
#7
Kalliopi I Pappa, Alexander Polyzos, Jasmine Jacob-Hirsch, Ninette Amariglio, George D Vlachos, Dimitrios Loutradis, Nicholas P Anagnou
Studies on individual types of gynecological cancers (GCs), utilizing novel expression technologies, have revealed specific pathogenetic patterns and gene markers for cervical (CC), endometrial (EC) and vulvar cancer (VC). Although the clinical phenotypes of the three types of gynecological cancers are discrete, the fact they originate from a common embryological origin, has led to the hypothesis that they might share common features reflecting regression to early embryogenesis. To address this question, we performed a comprehensive comparative analysis of their profiles...
2015: PloS One
https://www.readbyqxmd.com/read/26280983/nanofiber-yarn-hydrogel-core-shell-scaffolds-mimicking-native-skeletal-muscle-tissue-for-guiding-3d-myoblast-alignment-elongation-and-differentiation
#8
Ling Wang, Yaobin Wu, Baolin Guo, Peter X Ma
Designing scaffolds that can mimic native skeletal muscle tissue and induce 3D cellular alignment and elongated myotube formation remains an ongoing challenge for skeletal muscle tissue engineering. Herein, we present a simple technique to generate core-shell composite scaffolds for mimicking native skeletal muscle structure, which comprise the aligned nanofiber yarn (NFY) core and the photocurable hydrogel shell. The aligned NFYs are prepared by the hybrid composition including poly(caprolactone), silk fibroin, and polyaniline via a developed dry-wet electrospinning method...
September 22, 2015: ACS Nano
https://www.readbyqxmd.com/read/26162987/functional-interplay-of-sp-family-members-and-nuclear-factor-y-is-essential-for-transcriptional-activation-of-the-human-calreticulin-gene
#9
Julian A Schardt, Manuela Keller, Katja Seipel, Thomas Pabst
Calreticulin (CALR) is a highly conserved, multifunctional protein involved in a variety of cellular processes including the maintenance of intracellular calcium homeostasis, proper protein folding, differentiation and immunogenic cell death. More recently, a crucial role for CALR in the pathogenesis of certain hematologic malignancies was discovered: in clinical subgroups of acute myeloid leukemia, CALR overexpression mediates a block in differentiation, while somatic mutations have been found in the majority of patients with myeloproliferative neoplasms with nonmutated Janus kinase 2 gene (JAK2) or thrombopoietin receptor gene (MPL)...
September 2015: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/26158455/regulation-of-stearoyl-coenzyme-a-desaturase-1-gene-promoter-in-bovine-mammary-cells
#10
O di Martino, A Troiano, L Addi, A Guarino, S Calabrò, R Tudisco, N Murru, M I Cutrignelli, F Infascelli, V Calabrò
Stearoyl-Coenzyme A desaturase 1 (SCD1) belongs to the fatty acid family of desaturases. In lactating ruminants, the SCD1 protein is highly expressed in the mammary gland and is relevant for the fatty acid composition of milk and dairy products. Bovine mammary epithelial cells (BME-UV1), cultured in vitro, have been proposed as a model to reproduce the biology of the mammary gland. The present study was designed to investigate the responsiveness of bovine SCD1 promoter to serum, insulin, oleic acid, and NFY transcription factor in BME-UV1 cells...
2015: Animal Biotechnology
https://www.readbyqxmd.com/read/26039627/e2f1-mediated-induction-of-nfyb-attenuates-apoptosis-via-joint-regulation-of-a-pro-survival-transcriptional-program
#11
Xiaolei Jiang, Joseph Roy Nevins, Igor Shats, Jen-Tsan Chi
The E2F1 transcription factor regulates cell proliferation and apoptosis through the control of a considerable variety of target genes. Previous work has detailed the role of other transcription factors in mediating the specificity of E2F function. Here we identify the NF-YB transcription factor as a novel direct E2F1 target. Genome-wide expression analysis of the effects of NFYB knockdown on E2F1-mediated transcription identified a large group of genes that are co-regulated by E2F1 and NFYB. We also provide evidence that knockdown of NFYB enhances E2F1-induced apoptosis, suggesting a pro-survival function of the NFYB/E2F1 joint transcriptional program...
2015: PloS One
https://www.readbyqxmd.com/read/25818641/the-expression-profile-analysis-of-nkx2-5-knock-out-embryonic-mice-to-explore-the-pathogenesis-of-congenital-heart-disease
#12
Jian Li, Yinyin Cao, Yao Wu, Weicheng Chen, Yuan Yuan, Xiaojing Ma, Guoying Huang
BACKGROUND: Mutation of NKX2-5 could lead to the development of congenital heart disease (CHD) which is a common inherited disease. This study aimed to investigate the pathogenesis of CHD in NKX2-5 knock-out embryonic mice. METHODS: The expression profile in the NKX2-5 knock-out embryonic mice (GSE528) was downloaded from Gene Expression Omnibus. The heart tissues from the null/heterozygous embryonic day 12.5 mice were compared with wild-type mice to identify differentially expressed genes (DEGs), and then DEGs corresponding to the transcriptional factors were filtered out based on the information in the TRANSFAC database...
December 2015: Journal of Cardiology
https://www.readbyqxmd.com/read/25655569/the-sre-motif-in-the-human-pnpla3-promoter-97-to-88%C3%A2-bp-mediates-transactivational-effects-of-srebp-1c
#13
Hua Liang, Jing Xu, Fen Xu, Hongxia Liu, Ding Yuan, Shuhua Yuan, Mengyin Cai, Jinhua Yan, Jianping Weng
Patatin-like phospholipase domain containing 3 (PNPLA3) is a non-secreted protein primarily expressed in liver and adipose tissue. Recently, numerous genetic studies have shown that PNPLA3 is a major susceptibility gene for nonalcoholic fatty liver disease (NAFLD). However, the mechanism involved in transcriptional regulation of the PNPLA3 gene remains unknown. We performed a detailed analysis of the human PNPLA3 gene promoter and identified two novel cis-acting elements (SRE and NFY binding motifs) located at -97/-88 and -26/-22 bp, respectively...
September 2015: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/25366989/genomic-mapping-of-the-mhc-transactivator-ciita-using-an-integrated-chip-seq-and-genetical-genomics-approach
#14
Daniel Wong, Wanseon Lee, Peter Humburg, Seiko Makino, Evelyn Lau, Vivek Naranbhai, Benjamin P Fairfax, Kenneth Chan, Katharine Plant, Julian C Knight
BACKGROUND: The master transactivator CIITA is essential to the regulation of Major Histocompatibility Complex (MHC)class II genes and an effective immune response. CIITA is known to modulate a small number of non-MHC genes involved in antigen presentation such as CD74 and B2M but its broader genome-wide function and relationship with underlying genetic diversity has not been resolved. RESULTS: We report the first genome-wide ChIP-seq map for CIITA and complement this by mapping inter-individual variation in CIITA expression as a quantitative trait...
2014: Genome Biology
https://www.readbyqxmd.com/read/25234828/ultraviolet-irradiation-represses-tgf-%C3%AE-type-ii-receptor-transcription-through-a-38-bp-sequence-in-the-proximal-promoter-in-human-skin-fibroblasts
#15
Tianyuan He, Taihao Quan, Gary J Fisher
Transforming growth factor-β (TGF-β) is a major regulator of collagen gene expression in human skin fibroblasts. Cellular responses to TGF-β are mediated primarily through its cell surface type I (TβRI) and type II (TβRII) receptors. Ultraviolet (UV) irradiation impairs TGF-β signalling largely due to reduced TβRII gene expression, thereby decreasing type I procollagen synthesis, in human skin fibroblasts. UV irradiation does not alter either TβRII mRNA or protein stability, indicating that UV reduction in TβRII expression likely results from transcriptional or translational repression...
October 2014: Experimental Dermatology
https://www.readbyqxmd.com/read/25118625/bioinformatics-analysis-of-biomarkers-and-transcriptional-factor-motifs-in-down-syndrome
#16
X D Kong, N Liu, X J Xu
In this study, biomarkers and transcriptional factor motifs were identified in order to investigate the etiology and phenotypic severity of Down syndrome. GSE 1281, GSE 1611, and GSE 5390 were downloaded from the gene expression ominibus (GEO). A robust multiarray analysis (RMA) algorithm was applied to detect differentially expressed genes (DEGs). In order to screen for biological pathways and to interrogate the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, the database for annotation, visualization, and integrated discovery (DAVID) was used to carry out a gene ontology (GO) function enrichment for DEGs...
October 2014: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/25058159/iregulon-from-a-gene-list-to-a-gene-regulatory-network-using-large-motif-and-track-collections
#17
Rekin's Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval Sanchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean-Christophe Marine, Stein Aerts
Identifying master regulators of biological processes and mapping their downstream gene networks are key challenges in systems biology. We developed a computational method, called iRegulon, to reverse-engineer the transcriptional regulatory network underlying a co-expressed gene set using cis-regulatory sequence analysis. iRegulon implements a genome-wide ranking-and-recovery approach to detect enriched transcription factor motifs and their optimal sets of direct targets. We increase the accuracy of network inference by using very large motif collections of up to ten thousand position weight matrices collected from various species, and linking these to candidate human TFs via a motif2TF procedure...
July 2014: PLoS Computational Biology
https://www.readbyqxmd.com/read/24886974/transcription-factors-involved-in-prostate-gland-adaptation-to-androgen-deprivation
#18
Rafaela Rosa-Ribeiro, Umar Nishan, Ramon Oliveira Vidal, Guilherme Oliveira Barbosa, Leonardo Oliveira Reis, Carlos Lenz Cesar, Hernandes F Carvalho
Androgens regulate prostate physiology, and exert their effects through the androgen receptor. We hypothesized that androgen deprivation needs additional transcription factors to orchestrate the changes taking place in the gland after castration and for the adaptation of the epithelial cells to the androgen-deprived environment, ultimately contributing to the origin of castration-resistant prostate cancer. This study was undertaken to identify transcription factors that regulate gene expression after androgen deprivation by castration (Cas)...
2014: PloS One
https://www.readbyqxmd.com/read/24714687/monocyte-to-macrophage-differentiation-goes-along-with-modulation-of-the-plasmalogen-pattern-through-transcriptional-regulation
#19
Stefan Wallner, Margot Grandl, Tatiana Konovalova, Alexander Sigrüner, Thomas Kopf, Markus Peer, Evelyn Orsó, Gerhard Liebisch, Gerd Schmitz
BACKGROUND: Dysregulation of monocyte-macrophage differentiation is a hallmark of vascular and metabolic diseases and associated with persistent low grade inflammation. Plasmalogens represent ether lipids that play a role in diabesity and previous data show diminished plasmalogen levels in obese subjects. We therefore analyzed transcriptomic and lipidomic changes during monocyte-macrophage differentiation in vitro using a bioinformatic approach. METHODS: Elutriated monocytes from 13 healthy donors were differentiated in vitro to macrophages using rhM-CSF under serum-free conditions...
2014: PloS One
https://www.readbyqxmd.com/read/23908595/a-novel-pten-mutant-p53-c-myc-bcl-xl-axis-mediates-context-dependent-oncogenic-effects-of-pten-with-implications-for-cancer-prognosis-and-therapy
#20
Xiaoping Huang, Ying Zhang, Yaqiong Tang, Napoleon Butler, Jungeun Kim, Fadila Guessous, David Schiff, James Mandell, Roger Abounader
Phosphatase and tensin homolog located on chromosome 10 (PTEN) is one of the most frequently mutated tumor suppressors in human cancer including in glioblastoma. Here, we show that PTEN exerts unconventional oncogenic effects in glioblastoma through a novel PTEN/mutant p53/c-Myc/Bcl-XL molecular and functional axis. Using a wide array of molecular, genetic, and functional approaches, we demonstrate that PTEN enhances a transcriptional complex containing gain-of-function mutant p53, CBP, and NFY in human glioblastoma cells and tumor tissues...
August 2013: Neoplasia: An International Journal for Oncology Research
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