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Differentially Expressed LncRNAs Might be Controlling Signaling Pathways by Establishing Interactions with mRNAs and MicroRNAs in Pediatric Astrocytoma

ABSTRACT: In this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The Affymetrix HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively. A total of seven astrocytic tumors and two control tissues were collected during the period of 2012–2014: four low-grade Ast (three pilocytic Ast (PAst) and one diffuse Ast (DAst)) and four high-grade Ast (four glioblastoma multiforme (GBM)).RNA was extracted from tissue samples using TRIzol (Ambion life technologies, Thermo Scientific Inc.) following the methodology described by Hongbao et al. 2008 and with certain modifications described by Vujovic et al. 2013. For expression analysis, Human Transcriptome Array 2.0 (HTA) (Santa Clara, CA, USA) was employed. in this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively.

ORGANISM(S): Homo sapiens

SUBMITTER: Ruth Ruiz-Esparza

PROVIDER: E-GEOD-72269 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Differentially Expressed LncRNAs Might be Controlling Signaling Pathways by Establishing Interactions with mRNAs and MicroRNAs in Pediatric Astrocytoma

Project description:In this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The Affymetrix HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively.

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Transcriptional profiling by array in rat of age-dependent gene expression in sensorimotor cortex following spinal cord injury

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The effect of Nebulin-Deficiency on Skeletal Muscle

Project description:Nebulin is a giant filamentous protein that is coextensive with the actin filaments of the skeletal muscle sarcomere. Nebulin mutations are the main cause of nemaline myopathy (NEM), with typical NEM adult patients having low expression of nebulin, yet the roles of nebulin in adult muscle remain poorly understood. To establish nebulin’s functional roles in adult muscle we performed studies on a novel conditional nebulin KO (Neb cKO) mouse model in which nebulin deletion was driven by the muscle creatine kinase (MCK) promotor. Neb cKO mice are born with high nebulin levels in their skeletal muscle but within weeks after birth nebulin expression rapidly falls to barely detectable levels Surprisingly, a large fraction of the mice survives to adulthood with low nebulin levels (<5% of control), contain nemaline rods, and undergo fiber-type switching towards oxidative types. These microarrays investigate the changes in gene expression when nebulin is deficient. Two skeletal muscle groups were studied: Quadriceps (which is markedly smaller in the Neb cKO mice relative to control) and Soleus (which is not significantly smaller in the Neb cKO relative to control). Six biological replicates for each muscle group were selected; all are age-matched males.

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RelA Nuclear factor-kappaB (NF-kB) Subunit binding Loci in Promoter Regions of PHM1-31 Myometrial Smooth Muscle Cells (expression)

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Expression Data from Memory P14 Tg CD8 T cells after either saline mock-infection, Pichinde Virus Infection (bystander infection) or Pichinde Virus infection with daily treatment with anti-CD122 (clone TM-b1)

Project description:Exposure to inflammatory cytokines driven by bystander cytokines can have profound effects on the function of memory CD8 T cells. Here we transferred a 1-5X10^4 of P14 TCR-tg T cells (specific for gp33-41 of LCMV) on day -1 followed by infection with 2X10^5 PFU of LCMV Armstrong ip to generate memory P14 populations. Mice were rested for >50 days before further challenge. Mice containing memory P14 populations were either mock-infected with saline, infected with 2X10^6 Pichinde Virus ip (no cross-reactivity wtih LCMV gp33-41) or infected with 2X10^6 Pichinde Virus ip together with daily injections of 200 micrograms of anti-CD122 antibody (clone TM-b1). On day 4 following indicated treatments P14s were flow sorted and RNA was extracted from 1X10^6 cells using an RNeasy kit (Qiagen). Each group had 3 biological replicates. Transcriptomes were compared by DAVID analysis (p<0.01, Fold-Change > 1.5) 3 biological replicates per group. Groups included P14 from mock-infected mice, P14 from Pichinde virus infected mice and P14 from Pichinde virus and anti-cd122 treated mice.

2015-09-01 | E-GEOD-69791 | biostudies-arrayexpress

Proteomics Indicates Lactate Dehydrogenase is Prognostic in Acetaminophen-induced Acute Liver Failure Patients and Reveals a Role for LKB1-AMPK Signaling

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2022-08-12 | PXD029576 | Pride

Circulating Y-RNAs, a predicted function mainly in controlling the Immune System, Cell Signaling, and DNA Replication in Pediatric Patients with Pilocytic and Diffuse Astrocytoma

Project description:Y-RNAs are small noncoding RNAs firstly identified in patients suffering the Sjögren’s syndrome and lupus erythematosus, having different predicted cellular functions. Y-RNAs are very abundant ncRNAs present in serum and only a few is known respect their molecular roles. The aim of the study was to determine the circulating Y-RNAs expression from blood serum of pediatric patients with pilocytic or diffuse astrocytoma. Y-RNAs expression was determined by means of the HTA 2.0 arrays. In addition, a bioinformatic approximation of the possible biological functions of Y-RNAs was determined with the “Random Forest” (RF) and “Vector Support Machine” (VSM) algorithms. Results. Data showed a differential expression of RNY-3, RNY-4, and RNY-5 in pediatric patients with astrocytoma, relative to the control. Meanwhile, RNY-1 was shown to be upregulated in the Diffuse condition versus the Pilocytic. The bioinformatic analysis showed that RNY-4 and RNY-5 had the highest scores of interaction with Claudin, Toll-like receptors, and Hyaluronidase-1. In addition, the Y-RNAs loop domain by itself had the highest score of interaction with B cell receptor CD22 (RNY-3) and Toll-like receptor 7 and 3 (RNY-4). Conclusions. Our results showed, for the first time a differential expression of circulating Y-RNAs in pediatric astrocytoma, allowing to distinguish pediatric subjects without cancer from patients with pediatric diffuse or pilocytic astrocytoma and their potential involvement in regulating diverse biological processes, such as immune activation-suppression, cell signaling, selective transcription, and cell proliferation through activation of DNA replication.

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2014-12-11 | E-GEOD-64045 | biostudies-arrayexpress

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