Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

38 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Impact of VSVd51-GFP on the expression profile of normal and cancer-associated fibroblasts isolated from the same lung carcinoma patient

ABSTRACT: To investigate the impact of the tumor microenvironment on fibroblast succeptibility to oncolytic virus infection, we treated normal and cancer-associatted fibrboblasts isolated from the same lung carcinoma patient with the oncolytic virus VSVd51. Birefly, 1E6 cells of both types were seeded in a 6 well dish to allow adherence overnight. The following day, cells were treated with VSV?51 at an MOI=0.01 or left untreated. Eighteen hours following treatment, total RNA was extracted using an RNAeasykit (Qiagen Inc., Valencia, CA) according to the manufactureM-^Rs protocol and triplicate samples were pooled prior to hybridization. Sample quality was verified on abioanalyzer (Agilent Technologies), processed and hybridized to a GeneChip Human Gene 1.0 ST Array according to manufacturer instructions

ORGANISM(S): Homo sapiens

SUBMITTER: Cory Batenchuk

PROVIDER: E-MTAB-2359 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Eftimie2019-Macrophages Plasticity

Project description:This paper describes the complex interactions between two extreme types of macrophages (M1 and M2 cells), effector T cells and an oncolytic Vesicular Stomatitis Virus (VSV), on the growth/elimination of B16F10 melanoma. The mathematics model descirbes, in terms of VSV and macrophages levels, two different types of immune responses which could ensure tumour control and eventual elimination. It shows that both innate and adaptive anti-tumour immune responses, as well as the oncolytic virus, could be very important in delaying tumour relapse and eventually eliminating the tumour. Overall this study supports the use mathematical modelling to increase our understanding of the complex immune interaction following oncolytic virotherapies. However, the complexity of the model combined with a lack of sufficient data for model parametrisation has an impact on the possibility of making quantitative predictions. The Model was created using COPASI version 4.24 (Build 197)

2024-09-02 | BIOMD0000000806 | BioModels

Comparative proteomics for identifying specific alterations within interferon response pathways in human glioblastoma multiforme and osteosarcoma cells

Project description:An acquisition of increased sensitivity of cancer cells to viruses is a common outcome of malignant progression that justifies the development of oncolytic viruses as anticancer therapeutics. Studying molecular changes that underlie the sensitivity to viruses would help to identify cases where oncolytic virus therapy would be most effective. We quantified changes in protein abundances in glioblastoma multiforme (GBM) and osteosarcoma cell lines that differ in the ability to induce resistance to vesicular stomatitis virus (VSV) infection in response to type I interferon (IFN) treatment. In IFN-treated samples we observed an up-regulation of protein products of some IFN-regulated genes (IRGs). In total, the proteome analysis revealed up to 20% more proteins encoded by IRGs in the glioblastoma cell line, which develops resistance to VSV infection after pre-treatment with IFN. In both cell lines protein-protein interaction and signaling pathway analyses have revealed a significant stimulation of processes related to type I IFN signaling and defense responses to viruses. The study has shown that the up-regulation of IRG proteins induced by the IFNα treatment of GBM cells can be detected at the proteome level. Similar analyses could be applied for revealing functional alterations within the antiviral mechanisms in glioblastoma samples, accompanying by acquisition of sensitivity to oncolytic viruses.

2022-06-09 | PXD022868 | Pride

VIGOR canine osteosarcoma tumor, cell line and skin samples

Project description:VSV-IFNβ-NIS is a recombinant oncolytic vesicular stomatitis virus (VSV) that is being evaluated clinically for the treatment of advanced malignancies. As with other cancer immunotherapies, identifying biomarkers of response will be critical to the clinical advancement of this treatment approach. . RNAseq analysis showed that virtually all the long-term responders had increased expression of a CD8 T-cell anchored immune gene cluster. We conclude that neoadjuvant VSV-IFNβ-NIS has an excellent safety profile and may provide a survival benefit for dogs with osteosarcoma whose tumors are permissive for immune infiltration.

2023-10-01 | GSE240033 | GEO

Nucleosome map of the IMR90 fibroblast cell line

Project description:We produced a map of nucleosome positions in IMR90 by sequencing the ends of MNase-digested chromatin fragments. IMR90 cells were grown in culture, about 1E6 cells were isolated and digested using micrococcal nuclease (MNase). Mononucleosomes were gel-selected and fragment ends were sequenced using the Illumina GAIIx sequencing platform.

2011-04-01 | E-GEOD-21823 | biostudies-arrayexpress

MAP3K7 and CHD1 are novel mediators of resistance to oncolytic vesicular stomatitis virus in PC3 prostate cancer cells

Project description:A key principle of oncolytic viral therapy is that many cancers develop defects in their antiviral responses, making them more susceptible to virus infection. However, some cancers display resistance to viral infection. Many of these resistant cancers constitutively express interferon-stimulated genes (ISGs). The goal of these experiments was to determine the role of two tumor suppressor genes, MAP3K7 and CHD1, in viral resistance and ISG expression in PC3 prostate cancer cells resistant to oncolytic vesicular stomatitis virus (VSV). MAP3K7 and CHD1 are often co-deleted in aggressive prostate cancers. Silencing expression of MAP3K7 and CHD1 in PC3 cells increased susceptibility to M protein mutant M51R-VSV as shown by increased expression of viral genes, increased yield of progeny virus, and reduction of tumor growth in nude mice. Silencing MAP3K7 alone had a greater effect on virus susceptibility than silencing CHD1. Silencing MAP3K7 and CHD1 decreased constitutive expression of ISG mRNAs and proteins, whereas silencing MAP3K7 alone decreased expression of ISG proteins, but actually increased expression of ISG mRNAs. These results suggest a role for the protein product of MAP3K7, transforming growth factor β-activated kinase 1 (TAK1), in regulating translation of ISG mRNAs and a role of CHD1 in maintaining the transcription of ISGs.

2021-02-24 | GSE145937 | GEO

RNA-seq of detecting the effect of CDK4&6 inhibitor Abemaciclib and VSV-M51 in glioma

Project description:The RNA-seq data provided evidence that CDK4&6 inhibitor Abemaciclib and VSV-M51 increase the oncolytic effect in glioma

2022-06-01 | GSE166914 | GEO

High throughput characterization of human glioblastoma multiforme cell response to Type 1 interferons

Project description:Oncolytic virus therapy is a promising direction for cancer treatment. Numerous oncolytic viruses are under development or examined in clinical trials, there are examples of FDA approved virus vaccines. Although evident progress exists, oncolytic viruses still suffer low efficiency and the mechanisms of their action remain poorly understood. Defects in antiviral mechanisms that include type I interferon (IFN) signaling, contribute to sensitivity of malignant cells to oncolytic viruses, however, this sensitivity significantly differs for different malignant cells. In this project, we present a collection of representative transcriptomics and proteomics data for primary glioblastoma multiforme (GBM) cell cultures with established sensitivity to type I IFNs and the comprehensive characterization of GBM responses at both protein and RNA levels. Analysis demonstrated that GBM cells can respond to treatment by extreme upregulation of IFN-induced genes that is very similar to classic response in normal human cells. GBM cultures can significantly differ from each other by a value of transcriptome and proteome changes that are well correlated with sensitivity tests. In our data, upregulation of IFIT1/2/3, OAS1/2/3/L, MX1/2 among the others, was a reproducible marker for the developed resistance of GBM cells to vesicular stomatitis virus (VSV).

2021-12-29 | GSE163949 | GEO

Model based Rational Design of an Oncolytic Virus with Improved Therapeutic Potential

Project description:Oncolytic viruses are complex biological agents that interact at multiple levels with both tumor and normal tissues. Anti-viral pathways induced by interferon are known to play a critical role in determining tumor cell sensitivity and normal cell resistance to infection with oncolytic viruses. Here we pursue a synthetic biology approach to identify methods that enhance anti-tumor activity of oncolytic viruses through suppression of IFN signaling. Based on the mathematical analysis of multiple strategies, we hypothesize that a positive feedback loop, established by virus-mediated expression of a soluble interferon-binding decoy receptor, increases tumor cytotoxicity without compromising normal cells. Oncolytic rhabodviruses engineered to express a secreted interferon antagonist have improved oncolytic potential in cellular cancer models, and display improved therapeutic potential in tumor-bearing mice. Our results demonstrate the potential of this methodology in evaluating potential caveats of viral immune evasion strategies and improving the design of oncolytic viruses. The following series of microarray experiments was utilized to assess the impact of cloning an IFN decoy receptor isolated from vaccinia virus termed B19R on the transcriptional response against an IFN sensitive maraba virus strain termed MG1. RNA extraction was performed 24h post infection in 786-0 cells. Duplicate samples were pooled, and hybridized on Affymetrix human gene 1.0 ST arrays according to manufacturer instructions. Data analysis was performed using AltAnalyze. Briefly, probeset filtering implemented a DABG threshold of 70 & pV<0.05 and utilized exclusively constitutively expressed exons to assess levels of gene expression.

2013-06-01 | E-MTAB-1636 | biostudies-arrayexpress

Expression data from mouse peritoneal macrophages

Project description:Biologic functions involved in innate immune response of macrophages rely on the precise regulation of kinds of immune molecular. In the virus infection procession, the macrophages are activated following a tightly controlled genetic programme where specific sets of genes are up-regulated or down-regulated. We used microarrays to detail the global programme of gene expression underlying VSV infection and identified distinct classes of up-regulated and down-regulated genes during this process. Mouse peritoneal macrophages were selected with/without VSV infection for 8 hours for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain expression profiles. We selected macrophages according to VSV infection at two time-points: uninfected macrophage(control) and VSV infected for 8 hour macrophages(VSV).

2012-07-23 | E-GEOD-39620 | biostudies-arrayexpress

Prospective, open, single-arm clinical study of novel oncolytic virus against CTC micrometastasis of lung cancer, colorectal cancer and other malignant tumors

Project description:Interventions: Lung Cancer group:Novel Oncolytic Virus;Colorectal Cancer group:Novel Oncolytic Virus Primary outcome(s): objective response rate;overall survival;Quality of life;Safety;disease control rate;disease-free survival Study Design: Single arm

| 2725682 | ecrin-mdr-crc

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data