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https://www.readbyqxmd.com/read/28102867/a-systems-approach-for-the-elucidation-of-crucial-genes-and-network-constituents-of-cervical-intraepithelial-neoplasia-1-cin1
#1
Shikha Suman, Ashutosh Mishra, Anurag Kulshrestha
Cervical intra-epithelial neoplasia 1 (CIN1) is a pre-cancerous cervical cancer condition characterized by changes in the squamous cells of the cervix. Early detection may facilitate treatment as CIN1 may increase the risk of developing cervical cancer. An extensive system level analysis has been carried out to detect crucial network components of CIN1. Differential expression analysis was performed to identify genes that are differentially expressed in CIN1 in comparison to normal cells. Gene Ontology (GO) and pathway enrichment analyses of DEGs were followed by the construction of a protein-protein interaction (PPI) network...
January 19, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28102354/a-signature-of-renal-stress-resistance-induced-by-short-term-dietary-restriction-fasting-and-protein-restriction
#2
F Jongbloed, T C Saat, M Verweij, C Payan-Gomez, J H J Hoeijmakers, S van den Engel, C T van Oostrom, G Ambagtsheer, S Imholz, J L A Pennings, H van Steeg, J N M IJzermans, M E T Dollé, R W F de Bruin
During kidney transplantation, ischemia-reperfusion injury (IRI) induces oxidative stress. Short-term preoperative 30% dietary restriction (DR) and 3-day fasting protect against renal IRI. We investigated the contribution of macronutrients to this protection on both phenotypical and transcriptional levels. Male C57BL/6 mice were fed control food ad libitum, underwent two weeks of 30%DR, 3-day fasting, or received a protein-, carbohydrate- or fat-free diet for various periods of time. After completion of each diet, renal gene expression was investigated using microarrays...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102325/viral-micrornas-target-a-gene-network-inhibit-stat-activation-and-suppress-interferon-responses
#3
Dhivya Ramalingam, Joseph M Ziegelbauer
Kaposi's sarcoma-associated herpesvirus (KSHV) encodes 12 pre-microRNAs during latency that are processed to yield ~25 mature microRNAs (miRNAs). We were interested in identifying cellular networks that were targeted by KSHV-miRNAs and employed network building strategies using validated KSHV miRNA targets. Here, we report the identification of a gene network centering on the transcription factor- signal transducer and activator of transcription 3 (STAT3) that is targeted by KSHV miRNAs. KSHV miRNAs suppressed STAT3 and STAT5 activation and inhibited STAT3-dependent reporter activation upon IL6-treatment...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102292/integrated-molecular-analysis-reveals-complex-interactions-between-genomic-and-epigenomic-alterations-in-esophageal-adenocarcinomas
#4
DunFa Peng, Yan Guo, Heidi Chen, Shilin Zhao, Kay Washington, TianLing Hu, Yu Shyr, Wael El-Rifai
The incidence of esophageal adenocarcinoma (EAC) is rapidly rising in the United States and Western countries. In this study, we carried out an integrative molecular analysis to identify interactions between genomic and epigenomic alterations in regulating gene expression networks in EAC. We detected significant alterations in DNA copy numbers (CN), gene expression levels, and DNA methylation profiles. The integrative analysis demonstrated that altered expression of 1,755 genes was associated with changes in CN or methylation...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101863/lessons-from-animal-models-of-cytoplasmic-intermediate-filament-proteins
#5
Jamal-Eddine Bouameur, Thomas M Magin
Cytoplasmic intermediate filaments (IFs) represent a major cytoskeletal network contributing to cell shape, adhesion and migration as well as to tissue resilience and renewal in numerous bilaterians, including mammals. The observation that IFs are dispensable in cultured mammalian cells, but cause tissue-specific, life-threatening disorders, has pushed the need to investigate their function in vivo. In keeping with human disease, the deletion or mutation of murine IF genes resulted in highly specific pathologies...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101583/integrated-analysis-of-microrna-and-transcription-factor-reveals-important-regulators-and-regulatory-motifs-in-adult-b-cell-acute-lymphoblastic-leukemia
#6
Xiao-Cong Lin, Xin-Guang Liu, Yu-Ming Zhang, Ning Li, Zhi-Gang Yang, Wei-Yu Fu, Liu-Bo Lan, Hai-Tao Zhang, Yong Dai
B-cell acute lymphoblastic leukemia (B‑ALL) is an aggressive hematological malignancy and a leading cause of cancer-related mortality in children and young adults. The molecular mechanisms involved in the regulation of its gene expression has yet to be fully elucidated. In the present study, we performed large scale expression profiling of microRNA (miRNA) and transcription factor (TF) by Illumina deep‑sequencing and TF array technology, respectively, and identified 291 differentially expressed miRNAs and 201 differentially expressed TFs in adult B‑ALL samples relative to their controls...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28101578/a-22q11-2-amplification-in-the-region-encoding-microrna-650-correlates-with-the-epithelial-to-mesenchymal-transition-in-breast-cancer-primary-cultures-of-mexican-patients
#7
M Lango-Chavarría, G K Chimal-Ramírez, M E Ruiz-Tachiquín, N A Espinoza-Sánchez, M C Suárez-Arriaga, E M Fuentes-Pananá
Breast cancer ranks first in incidence and mortality in working age women. Cancer initiation and progression relies on accumulation of genetic and epigenetic aberrations that alter cellular processes, among them, epithelial to mesenchymal transition (EMT) denotes particularly aggressive neoplasias given its capacity to invade and metastasize. Several microRNAs (miRNA) have been found able to regulate gene expression at the core of EMT. In this study, the Affymetrix CytoScan HD array was used to analyze three different primary tumor cell isolates from Mexican breast cancer patients...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28101576/multiple-effects-of-ellagic-acid-on-human-colorectal-carcinoma-cells-identified-by-gene-expression-profile-analysis
#8
Jinlu Zhao, Guodong Li, Wanlan Bo, Yuhui Zhou, Shuwei Dang, Jiufeng Wei, Xinglong Li, Ming Liu
Colorectal carcinoma (CRC) is the third most commonly diagnosed cancer in the world. Phytochemicals have become a research hotspot in recent years as cancer prevention and treatment agents due to their low toxicity and limited side-effects. Ellagic acid (EA), a natural phenolic constituent, displays various biological activities, including anticancer effects. However, the detailed anticancer mechanisms of EA remain unclear. In the present study, we found that EA inhibited the growth of HCT-116 colon cancer cells...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28101231/the-biological-significance-of-methylome-differences-in-human-papilloma-virus-associated-head-and-neck-cancer
#9
Maria J Worsham, Kang Mei Chen, Indrani Datta, Josena K Stephen, Dhananjay Chitale, Alexandra Gothard, George Divine
In recent years, studies have suggested that promoter methylation in human papilloma virus (HPV) positive head and neck squamous cell carcinoma (HNSCC) has a mechanistic role and has the potential to improve patient survival. The present study aimed to replicate key molecular findings from previous analyses of the methylomes of HPV positive and HPV negative HNSCC in an independent cohort, to assess the reliability of differentially methylated markers in HPV-associated tumors. HPV was measured using real-time quantitative PCR and the biological significance of methylation differences was assessed by Ingenuity Pathway Analysis (IPA)...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28101207/structure-function-analysis-of-dna-helicase-helq-a-new-diagnostic-marker-in-ovarian-cancer
#10
Ya-Ping Li, Jun-Juan Yang, Hui Xu, En-Yu Guo, Yan Yu
It has been previously reported that a deficiency of the helicase, POLQ-like (HELQ) gene increases the risk of ovarian cancer. The present study aimed to explore the structure-function association of HELQ and discuss the effect of molecular structure on the occurrence of tumors. ExPASy tools were employed to analyze the physicochemical properties and secondary structure of the genes. PHYRE2 Protein Fold Recognition Server was used to construct the three-dimensional model and find the ligand-binding sites of HELQ...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28101157/functional-analysis-of-keratinocyte-and-fibroblast-gene-expression-in-skin-and-keloid-scar-tissue-based-on-deviation-analysis-of-dynamic-capabilities
#11
Mingming Li, Lei Wu
The aim of the present study was to select key genes that are associated with fibroblasts and keratinocytes during keloid scar progression and development. The gene expression profile of GSE44270, which includes 32 samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in case samples compared with control samples were screened using the Limma R package followed by hierarchical clustering analysis. Protein-protein interaction (PPI) networks of the total selected DEGs were constructed using Cytoscape...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28100489/tale-induced-bhlh-transcription-factors-that-activate-a-pectate-lyase-contribute-to-water-soaking-in-bacterial-spot-of-tomato
#12
Allison R Schwartz, Robert Morbitzer, Thomas Lahaye, Brian J Staskawicz
AvrHah1 [avirulence (avr) gene homologous to avrBs3 and hax2, no. 1] is a transcription activator-like (TAL) effector (TALE) in Xanthomonas gardneri that induces water-soaked disease lesions on fruits and leaves during bacterial spot of tomato. We observe that water from outside the leaf is drawn into the apoplast in X. gardneri-infected, but not X. gardneriΔavrHah1 (XgΔavrHah1)-infected, plants, conferring a dark, water-soaked appearance. The pull of water can facilitate entry of additional bacterial cells into the apoplast...
January 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28100450/a-2-oxoglutarate-dependent-dioxygenase-mediates-the-biosynthesis-of-glucoraphasatin-in-radish
#13
Tomohiro Kakizaki, Hiroyasu Kitashiba, Zhongwei Zou, Feng Li, Nobuko Fukino, Takayoshi Ohara, Takeshi Nishio, Masahiko Ishida
Glucosinolates (GSLs) are secondary metabolites whose degradation products confer intrinsic flavors and aromas to Brassicaceae vegetables. Several structures of GSLs are known in the Brassicaceae, and the biosynthetic pathway and regulatory networks have been elucidated in Arabidopsis thaliana. GSLs are precursors of chemical defense substances against herbivorous pests. Specific GSLs can act as feeding blockers or stimulants, depending on the pest species. Natural selection has led to diversity in the GSL compositions even within individual species...
January 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28100246/genetic-effect-of-interleukin-1-beta-c-511t-polymorphism-on-the-structural-covariance-network-and-white-matter-integrity-in-alzheimer-s-disease
#14
Chi-Wei Huang, Shih-Wei Hsu, Shih-Jen Tsai, Nai-Ching Chen, Mu-En Liu, Chen-Chang Lee, Shu-Hua Huang, Weng-Neng Chang, Ya-Ting Chang, Wan-Chen Tsai, Chiung-Chih Chang
BACKGROUND: Inflammatory processes play a pivotal role in the degenerative process of Alzheimer's disease. In humans, a biallelic (C/T) polymorphism in the promoter region (position-511) (rs16944) of the interleukin-1 beta gene has been significantly associated with differences in the secretory capacity of interleukin-1 beta. In this study, we investigated whether this functional polymorphism mediates the brain networks in patients with Alzheimer's disease. METHODS: We enrolled a total of 135 patients with Alzheimer's disease (65 males, 70 females), and investigated their gray matter structural covariance networks using 3D T1 magnetic resonance imaging and their white matter macro-structural integrities using fractional anisotropy...
January 18, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28100172/integrated-genomics-based-mapping-reveals-the-genetics-underlying-maize-flavonoid-biosynthesis
#15
Min Jin, Xuehai Zhang, Mingchao Zhao, Min Deng, Yuanhao Du, Yang Zhou, Shouchuang Wang, Takayuki Tohge, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman, Jianbing Yan, Weiwei Wen
BACKGROUND: Flavonoids constitute a diverse class of secondary metabolites which exhibit potent bioactivities for human health and have been indicated to play an important role in plant development and defense. However, accumulation and variation of flavonoid content in diverse maize lines and the genes responsible for their biosynthesis in this important crop remain largely unknown. In this study, we combine genetic mapping, metabolite profiling and gene regulatory network analysis to further enhance understanding of the maize flavonoid pathway...
January 18, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28100166/smite-an-r-bioconductor-package-that-identifies-network-modules-by-integrating-genomic-and-epigenomic-information
#16
N Ari Wijetunga, Andrew D Johnston, Ryo Maekawa, Fabien Delahaye, Netha Ulahannan, Kami Kim, John M Greally
BACKGROUND: The molecular assays that test gene expression, transcriptional, and epigenetic regulation are increasingly diverse and numerous. The information generated by each type of assay individually gives an insight into the state of the cells tested. What should be possible is to add the information derived from separate, complementary assays to gain higher-confidence insights into cellular states. At present, the analysis of multi-dimensional, massive genome-wide data requires an initial pruning step to create manageable subsets of observations that are then used for integration, which decreases the sizes of the intersecting data sets and the potential for biological insights...
January 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28099997/on-joint-estimation-of-gaussian-graphical-models-for-spatial-and-temporal-data
#17
Zhixiang Lin, Tao Wang, Can Yang, Hongyu Zhao
In this article, we first propose a Bayesian neighborhood selection method to estimate Gaussian Graphical Models (GGMs). We show the graph selection consistency of this method in the sense that the posterior probability of the true model converges to one. When there are multiple groups of data available, instead of estimating the networks independently for each group, joint estimation of the networks may utilize the shared information among groups and lead to improved estimation for each individual network...
January 18, 2017: Biometrics
https://www.readbyqxmd.com/read/28099904/tianfoshen-oral-liquid-a-cfda-approved-clinical-traditional-chinese-medicine-normalizes-major-cellular-pathways-disordered-during-colorectal-carcinogenesis
#18
Siliang Wang, Hengbin Wang, Yin Lu
Colorectal cancer remains the third leading cause of cancer death worldwide, suggesting exploration of novel therapeutic avenues may be useful. In this study, therefore, we determined whether Tianfoshen oral liquid, a Chinese traditional medicine that has been used to treat non-small cell lung cancer, would be therapeutically beneficial for colorectal cancer patients. Our data show that Tianfoshen oral liquid effectively inhibits growth of colorectal cancer cells both in vitro and in vivo. We further employed a comprehensive strategy that included chemoinformatics, bioinformatics and network biology methods to unravel novel insights into the active compounds of Tianfoshen oral liquid and to identify the common therapeutic targets and processes for colorectal cancer treatment...
January 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28099903/talin-1-interaction-network-promotes-hepatocellular-carcinoma-progression
#19
Peng Chen, Xiaohu Zheng, Yonggang Zhou, Yechuan Xu, Lixin Zhu, Yeben Qian
Talin-1 is a known oncogene-associated protein. In this study, we set out to determine its role and mechanisms in hepatocellular carcinoma (HCC) progression. We found Talin-1 to be highly expressed in HCC cells relative to non-cancer liver epithelial cells and to promote tumor growth and metastasis. We used Whole Human Genome Oligo Microarray analysis with HCC cells and HCC cells in which Talin-1 was knocked down using shRNA to identify transcripts regulated by Talin-1. Of the 40,000 tested genes, 3099 were differentially expressed after Talin-1 knockdown; expression of 1924 genes was increased, while expression of 2175 was decreased...
January 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28099866/effector-regulatory-t-cell-differentiation-and-immune-homeostasis-depend-on-the-transcription-factor-myb
#20
Sheila Dias, Angela D'Amico, Erika Cretney, Yang Liao, Julie Tellier, Christine Bruggeman, Francisca F Almeida, Jamie Leahy, Gabrielle T Belz, Gordon K Smyth, Wei Shi, Stephen L Nutt
FoxP3-expressing regulatory T (Treg) cells are essential for maintaining immune homeostasis. Activated Treg cells undergo further differentiation into an effector state that highly expresses genes critical for Treg cell function, although how this process is coordinated on a transcriptional level is poorly understood. Here, we demonstrate that mice lacking the transcription factor Myb in Treg cells succumbed to a multi-organ inflammatory disease. Myb was specifically expressed in, and required for the differentiation of, thymus-derived effector Treg cells...
January 17, 2017: Immunity
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