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https://www.readbyqxmd.com/read/29351917/a-novel-method-for-rapid-molecular-subgrouping-of-medulloblastoma
#1
Soledad Gómez, Alícia Garrido-Garcia, Laura Garcia-Gerique, Isadora Lemos, Mariona Suñol, Carmen de Torres, Marta Kulis, Sara Perez-Jaume, Angel M Carcaboso, Betty Luu, Mark W Kieran, Nada Jabado, Alexey Kozlenkov, Stella Dracheva, Vijay Ramaswamy, Volker Hovestadt, Pascal Johann, David T W Jones, Stefan M Pfister, Andrés Morales La Madrid, Ofelia Cruz, Michael D Taylor, Jose I Martín-Subero, Jaume Mora, Cinzia Lavarino
PURPOSE: The classification of medulloblastoma into WNT, SHH, Group 3 and Group 4 subgroups has become of critical importance for patient risk-stratification and subgroup-tailored clinical trials. Here, we aimed to develop a simplified, clinically applicable classification approach that can be implemented in the majority of centers treating patients with medulloblastoma. EXPERIMENTAL DESIGN: We analyzed 1,577 samples comprising previously published DNA methylation microarray data (913 medulloblastomas, 457 non-medulloblastoma tumors, 85 normal tissues), and 122 frozen and formalin-fixed paraffin-embedded medulloblastoma samples...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29351810/identify-down-syndrome-transcriptome-associations-using-integrative-analysis-of-microarray-database-and-correlation-interaction-network
#2
Min Chen, Jiayan Wang, Yingjun Luo, Kailing Huang, Xiaoshun Shi, Yanhui Liu, Jin Li, Zhengfei Lai, Shuya Xue, Haimei Gao, Allen Chen, Dunjin Chen
BACKGROUND: Long non-coding RNAs (lncRNAs) have previously been emerged as key players in a series of biological processes. Dysregulation of lncRNA is correlated to human diseases including neurological disorders. Here, we developed a multi-step bioinformatics analysis to study the functions of a particular Down syndrome-associated gene DSCR9 including the lncRNAs. The method is named correlation-interaction-network (COIN), based on which a pipeline is implemented. Co-expression gene network analysis and biological network analysis results are presented...
January 19, 2018: Human Genomics
https://www.readbyqxmd.com/read/29349517/a-novel-genomic-signature-predicting-fdg-uptake-in-diverse-metastatic-tumors
#3
Aurora Crespo-Jara, Maria Carmen Redal-Peña, Elena Maria Martinez-Navarro, Manuel Sureda, Francisco Jose Fernandez-Morejon, Francisco J Garcia-Cases, Ramon Gonzalez Manzano, Antonio Brugarolas
BACKGROUND: Building a universal genomic signature predicting the intensity of FDG uptake in diverse metastatic tumors may allow us to understand better the biological processes underlying this phenomenon and their requirements of glucose uptake. METHODS: A balanced training set (n = 71) of metastatic tumors including some of the most frequent histologies, with matched PET/CT quantification measurements and whole human genome gene expression microarrays, was used to build the signature...
January 18, 2018: EJNMMI Research
https://www.readbyqxmd.com/read/29348876/genome-wide-transcriptional-profiling-identifies-potential-signatures-in-discriminating-active-tuberculosis-from-latent-infection
#4
Liping Pan, Na Wei, Hongyan Jia, Mengqiu Gao, Xiaoyou Chen, Rongrong Wei, Qi Sun, Shuxiang Gu, Boping Du, Aiying Xing, Zongde Zhang
To better understand the host immune response involved in the progression from latent tuberculosis infection (LTBI) to active tuberculosis (TB) and identify the potential signatures for discriminating TB from LTBI, we performed a genome-wide transcriptional profile of Mycobacterium tuberculosis (M.TB)-specific antigens-stimulated peripheral blood mononuclear cells (PBMCs) from patients with TB, LTBI individuals and healthy controls (HCs). A total of 209 and 234 differentially expressed genes were detected in TB vs...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348872/gene-expression-profiling-reveals-u1-snrna-regulates-cancer-gene-expression
#5
Zhi Cheng, Yu Sun, Xiaoran Niu, Yingchun Shang, Jishou Ruan, Ze Chen, Shan Gao, Tao Zhang
U1 small nuclear RNA (U1 snRNA), as one of the most abundant ncRNAs in human cells, plays an important role in splicing of pre-mRNAs. Compared to previous studies which have focused on the primary function of U1 snRNA and the neurodegenerative diseases caused by abnormalities of U1 snRNA, this study is to investigate how U1 snRNA over-expression affects the expression of mammal genes on a genome-wide scale. By comparing the gene expression profiles of U1 snRNA over-expressed cells with those of their controls using microarray experiments, 916 genes or loci were identified significantly Differentially Expressed (DE)...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348851/comprehensive-analysis-of-mrna-lncrna-co-expression-profile-revealing-crucial-role-of-imprinted-gene-cluster-dlk1-meg3-in-chordoma
#6
Hao Chen, Kai Zhang, Jian Lu, Guizhong Wu, Huilin Yang, Kangwu Chen
Chordoma is a rare bone tumor with high recurrence rate, but the mechanism of its development is unclear. Long non-coding RNAs(lncRNAs) are recently revealed to be regulators in a variety of biological processed by targeting on mRNA transcription. Their expression profile and function in chordoma have not been investigated yet. In this study, we firstly performed the comprehensive analysis of the lncRNA and coding genes expression analysis with three chordoma samples and three fetal nucleus pulposus tissues...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348839/differences-in-the-expression-of-long-noncoding-rnas-at-different-time-points-in-the-ptsd-like-syndrome-rat-hippocampus
#7
Qingzhen Liu, Qing Ji, Jian Liu, Lidong Zhang
The aim of this study was to characterize the expression profiles at different time points in the PTSD-like syndrome rat hippocampus and perform analyses. PTSD rat models were made as reported by Rau, and we collected the hippocampus at different time points. The lncRNAs at different time points were compared by microarray and listed. We used quantitative real-time PCR to confirm the lncRNA profiling expression data. Bioinformatics analysis was performed on EU056364_P1. Compare with control, a total of 948 lncRNAs and 2514 mRNAs were found (fold-change > 2...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348821/glycan-microarray-reveal-induced-iggs-repertoire-shift-against-a-dietary-carbohydrate-in-response-to-rabbit-anti-human-thymocyte-therapy
#8
Ron Amon, Shani Leviatan Ben-Arye, Limor Engler, Hai Yu, Noha Lim, Ludmilla Le Berre, Kristina M Harris, Mario R Ehlers, Stephen E Gitelman, Xi Chen, Jean-Paul Soulillou, Vered Padler-Karavani
Humans have circulating antibodies against diverse glycans containing N-glycolylneuraminic acid (Neu5Gc) due to function-loss mutation of the CMAH gene. This xenogenic non-human carbohydrate is abundant in red meat, xenografts and biotherapeutics. Low levels of diet-derived Neu5Gc is also present on normal human endothelial cells, and together with anti-Neu5Gc antibodies could potentially mediate "xenosialitis" chronic-inflammation. Rabbit anti-human thymocyte globulin (ATG) is a drug containing polyclonal IgG glycoproteins commonly used as an immunosuppressant in human transplantation and autoimmune diseases...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348435/macrophage-sensing-of-single-walled-carbon-nanotubes-via-toll-like-receptors
#9
Sourav P Mukherjee, Olesja Bondarenko, Pekka Kohonen, Fernando T Andón, Táňa Brzicová, Isabel Gessner, Sanjay Mathur, Massimo Bottini, Paolo Calligari, Lorenzo Stella, Elena Kisin, Anna Shvedova, Reija Autio, Heli Salminen-Mankonen, Riitta Lahesmaa, Bengt Fadeel
Carbon-based nanomaterials including carbon nanotubes (CNTs) have been shown to trigger inflammation. However, how these materials are 'sensed' by immune cells is not known. Here we compared the effects of two carbon-based nanomaterials, single-walled CNTs (SWCNTs) and graphene oxide (GO), on primary human monocyte-derived macrophages. Genome-wide transcriptomics assessment was performed at sub-cytotoxic doses. Pathway analysis of the microarray data revealed pronounced effects on chemokine-encoding genes in macrophages exposed to SWCNTs, but not in response to GO, and these results were validated by multiplex array-based cytokine and chemokine profiling...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348067/physiological-response-and-transcription-profiling-analysis-reveals-the-role-of-h2s-in-alleviating-excess-nitrate-stress-tolerance-in-tomato-roots
#10
Zhaolai Guo, Yuanlin Liang, Jinping Yan, En Yang, Kunzhi Li, Huini Xu
Soil secondary salinization caused by excess nitrate addition is one of the major obstacles in greenhouse vegetable production. Excess nitrate inhibited the growth of tomato plants, while application of 100 μM H2S donor NaHS efficiently increased the plant height, fresh and dry weight of shoot and root, root length, endogenous H2S contents and L-cysteine desulfhydrases activities. NaHS altered the oxidative status of nitrate-stressed plants as inferred by changes in reactive oxygen species (ROS) accumulation and lipid peroxidation accompanied by regulation of the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX)...
January 11, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29346685/metabolic-flux-engineering-of-cembratrien-ol-production-in-both-the-glandular-trichome-and-leaf-mesophyll-in-nicotiana-tabacum
#11
Hongying Zhang, Songtao Zhang, Yongxia Yang, Hongfang Jia, Hong Cui
Cembratrien-ol synthase (CBTS) catalyses the first step in cembranoid biosynthesis, producing cembratrien-ols in plant trichomes. In our previous study, microarray transcriptomes between leaves with trichomes and leaves without trichomes showed that a NtCBTS2 gene was expressed exclusively and abundantly in trichomes. Here, two NtCBTS2 isogenes (NtCBTS2a and NtCBTS2b), derived from a diploid genome donor, N. sylvestris, were identified from N. tabacum. Both genes were expressed primarily in trichomes, with relatively decreased transcription in flowers and stems, faint expression in roots, and no expression was detected in leaves lacking trichomes...
January 15, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29346010/identification-and-correction-of-additive-and-multiplicative-spatial-biases-in-experimental-high-throughput-screening
#12
Bogdan Mazoure, Iurie Caraus, Robert Nadon, Vladimir Makarenkov
Data generated by high-throughput screening (HTS) technologies are prone to spatial bias. Traditionally, bias correction methods used in HTS assume either a simple additive or, more recently, a simple multiplicative spatial bias model. These models do not, however, always provide an accurate correction of measurements in wells located at the intersection of rows and columns affected by spatial bias. The measurements in these wells depend on the nature of interaction between the involved biases. Here, we propose two novel additive and two novel multiplicative spatial bias models accounting for different types of bias interactions...
January 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29345255/pure-mechanistic-analysis-of-additive-neuroprotective-effects-between-baicalin-and-jasminoidin-in-ischemic-stroke-mice
#13
Peng-Qian Wang, Qiong Liu, Wen-Juan Xu, Ya-Nan Yu, Ying-Ying Zhang, Bing Li, Jun Liu, Zhong Wang
Both baicalin (BA) and jasminoidin (JA) are active ingredients in Chinese herb medicine Scutellaria baicalensis and Fructus gardeniae, respectively. They have been shown to exert additive neuroprotective action in ischemic stroke models. In this study we used transcriptome analysis to explore the pure therapeutic mechanisms of BA, JA and their combination (BJ) contributing to phenotype variation and reversal of pathological processes. Mice with middle cerebral artery obstruction were treated with BA, JA, their combination (BJ), or concha margaritifera (CM)...
January 18, 2018: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/29344893/profiling-tumor-infiltrating-immune-cells-with-cibersort
#14
Binbin Chen, Michael S Khodadoust, Chih Long Liu, Aaron M Newman, Ash A Alizadeh
Tumor infiltrating leukocytes (TILs) are an integral component of the tumor microenvironment and have been found to correlate with prognosis and response to therapy. Methods to enumerate immune subsets such as immunohistochemistry or flow cytometry suffer from limitations in phenotypic markers and can be challenging to practically implement and standardize. An alternative approach is to acquire aggregative high dimensional data from cellular mixtures and to subsequently infer the cellular components computationally...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344885/microrna-networks-in-breast-cancer-cells
#15
Andliena Tahiri, Miriam R Aure, Vessela N Kristensen
A variety of molecular techniques can be used in order to unravel the molecular composition of cells. In particular, the microarray technology has been used to identify novel biomarkers that may be useful in the diagnosis, prognosis, or treatment of cancer. The microarray technology is ideal for biomarker discovery as it allows for the screening of a large number of molecules at once. In this review, we focus on microRNAs (miRNAs) which are key molecules in cells and regulate gene expression post-transcriptionally...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344864/laser-capture-microdissection-in-traumatic-brain-injury-research-obtaining-hippocampal-subregions-and-pools-of-injured-neurons-for-genomic-analyses
#16
Deborah R Boone, Harris A Weisz, Stacy L Sell, Helen L Hellmich
The methods presented here are based on our laboratory's 15 years of experience using laser capture microdissection to obtain samples for the study of gene expression after traumatic brain injury (TBI) using a well-established rat model of experimental TBI. Here, we describe how to use the ArcturusXT laser capture microdissection system to capture swaths of specific regions of the rat hippocampus as well as specific neuronal populations defined by Fluoro-Jade C staining. Staining with Fluoro-Jade C identifies a neuron that is in the process of degeneration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344859/laser-capture-microdissection-and-isolation-of-high-quality-rna-from-frozen-endometrial-tissue
#17
Michele Cummings, Georgia Mappa, Nicolas M Orsi
Laser capture microdissection (LCM) allows expression profiling of specific cell populations within tissues. However, isolation of high-quality RNA from laser capture microdissected frozen tissue is beset by problems arising from intrinsic tissue RNase activity. Herein, we describe an optimized staining/LCM/RNA extraction protocol developed for the isolation of epithelial RNA from frozen tissue sections using human endometrial cancer as a model tissue. This method combines excellent, reproducible visualization of tissue morphology with the isolation of high-integrity RNA suitable for downstream applications such as expression microarray analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344642/microarray-analysis-reveals-tmub1-as-a-cell-cycle-associated-protein-in-rat-hepatocytes
#18
Hangwei Fu, Jianhua Xu, Jian Chen, Guangyao Li, Xiaobiao Zhao, Ping Chen
Transmembrane and ubiquitin-like domain containing protein 1 (Tmub1), formerly known as hepatocyte odd protein shuttling (HOPS) has been recognized as a ubiquitously expressed shuttling protein that moves between the nucleus and cytoplasm in hepatocytes. Tmub1 is involved in liver regeneration and functions as a bridging protein in tumor cell proliferation. To investigate the transcriptional profile and potential biological processes affected by Tmub1 expression in normal rat hepatocytes, microarray and bioinformatics experiments were used to identify 127 mRNAs differentially expressed between Tmub1‑overexpression, Tmub1‑knockdown and normal BRL‑3A cells (fold‑change ≥2...
January 17, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29344429/pathway-analysis-of-gene-expression-of-e14-versus-e18-fetal-fibroblasts
#19
Michael S Hu, Mimi R Borrelli, Michael Januszyk, Anna Luan, Samir Malhotra, Graham G Walmsley, Wan Xing Hong, Ruth Tevlin, Geoffrey C Gurtner, Michael T Longaker, Hermann P Lorenz
Objective: Fetuses early in gestation heal skin wounds without forming scars. The biological mechanisms behind this process are largely unknown. Fibroblasts, however, are cells known to be intimately involved in wound healing and scar formation. We examined fibroblasts in different stages of development to characterize differences in gene expression that may result in the switch from regenerative wound repair to repair with scarring. Approach: Fibroblasts were isolated and cultured from the back skin of BALB/c wild-type mouse fetuses at embryonic day (E)14 and E18 (n = 10)...
January 1, 2018: Advances in Wound Care
https://www.readbyqxmd.com/read/29344304/atherosclerosis-is-exacerbated-by-chitinase-3-like-1-in-amyloid-precursor-protein-transgenic-mice
#20
Yu Yeon Jung, Ki Cheon Kim, Mi Hee Park, Youngsik Seo, Heonyong Park, Min Hee Park, Jun Chang, Dae Youn Hwang, Sang Bae Han, Sanghyeon Kim, Dong Ju Son, Jin Tae Hong
Although the important role of amyloid precursor protein (APP) in vascular diseases associated with Alzheimer's disease (AD) has been demonstrated, the underlying molecular mechanisms and physiological consequences are unclear. We aimed to evaluate vascular inflammation and atherosclerosis in Swedish mutant of human APP transgenic (APPsw-Tg) and ApoE-/-/APPsw-Tg mice. We also aimed to explore the mechanisms underlying any changes observed in these mice compared with non-Tg controls. Methods: The transgenic and non-Tg mouse strains were subjected to partial ligation of the left carotid artery to induce atherosclerotic changes, which were measured using histological approaches, immunohistochemistry, quantitative polymerase chain reaction, and gene expression microarrays...
2018: Theranostics
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