Intergenic Disease-associated Regions are Abundant in Novel Regulatory Transcripts
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Qiagen, Illumina HiSeq 2000, TruSeq Stranded mRNA Sample Preparation Kit (Illumina)
ORGANISM(S): Homo sapiens
SUBMITTER: Michael Clark
PROVIDER: E-MTAB-4519 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:Using affinity purification for the detection of RNA-binding proteins in tapasin 3'UTR
2025-05-06 | PXD045056 | Pride
Project description:The recent success of monoclonal antibody checkpoint inhibitor therapies that enhance the ability of CD8+ T cells to detect cancer-related antigenic peptides has refocused the need to fully understand the repertoire of peptides being presented to the immune system. Whilst the peptide ligandome presented by cell surface HLA class I molecules on cancer cells has been studied extensively, the ligandome of extracellular vesicles remains poorly defined. Here we report the HLA class I ligandome of both cell surface and extracellular vesicles from eight breast cancer cell lines (MCF7, MDA-MB-231, MDA-MB-361, MDA-MB-415, MDA-MB-453, HCC 1806, HCC 1395, and HCC 1954), and additionally the melanoma cell line ESTDAB-056 and the multiple myeloma line RPMI 8226. Utilising HLA class I immunoisolation and mass spectrometry we detected a total of 6574 peptides from the cell surface and 2461 peptides from the extracellular vesicles of the cell lines studied. Within the extracellular vesicle HLA class I ligandome we identified 150 peptides derived from tumour associated antigenic proteins, of which 19 peptides have been shown to elicit T cell responses in previous studies. Our data thus confirms for the first time the presence of clinically relevant tumour-associated antigenic peptides in the HLA class I ligandome present on EV.
2022-04-01 | PXD025345 | Pride
Project description:Unluckily, FFPE archival methods lead to partial RNA degradation, limiting the amount of derivable information. This study aims to evaluate if the DASL gene expression assay, designed to generate reproducible data from degraded RNAs, is a reliable method to apply on RNA from FFPE tissues. In order to do that, we analyzed 20 FFPE breast cancer samples and 20 FF (Fresh Frozen) matched samples with the Illumina Whole Genome DASL platform for a genome-wide expression profiling.
2011-09-05 | E-TABM-1081 | biostudies-arrayexpress
Project description:We previously identified the induction of growth arrest with phenotypic characteristics of senescence in melanoma cell lines sensitive to diterpene esters, indicating a therapeutic potential. Here we compared the cytostatic effects of two diterpene esters namely TPA (12-O-tetradecanoylphorbol-13-acetate) and PEP008 (20-O-acetyl-ingenol-3-angelate) in sensitive and resistant cell lines derived from melanoma, breast cancer and colon cancer. We showed the diterpene esters to induce senescence-like growth arrest in the sensitive cells at 100-1000 ng/ml. Use of the pan-PKC inhibitor bisindolylmaleimide-l demonstrated that activation of PKC was required for growth arrest. Full genome expression profiling revealed that pivotal genes involved in DNA synthesis and cell cycle control were down-regulated by treatment in all three sensitive solid tumor models. At the protein level, prolonged down-regulation of E2F-1 and proliferating cell nuclear antigen (PCNA), sustained expression of p21WAF1/CIP1 and dephosphorylation of retinoblastoma (Rb) occurred in the sensitive cells. Although activation of extracellular signal-related kinase (ERK) 1/2 by the diterpene esters occurred in both sensitive and resistant cell lines, the HRASLS3 type II tumor suppressor, which appears to have a role in MAPK pathway suppression, was constitutively elevated in the resistant cell lines compared to their sensitive counterparts. Together, these results demonstrate the ability of the PKC activating drugs TPA and PEP008 to induce growth arrest with characteristics of senescence in solid tumor cell lines derived from a variety of tissue types through a similar mechanism. PKC-activating diterpene esters may therefore have therapeutic potential in a range of solid tumors. Experiment Overall Design: We analyzed the transcriptional profiles of the diterpene ester sensitive cell lines MCF7, COLO-205 and SK-MEL-5 following treatment with PEP008 using full genome expression profiling (Affymetrix, U133 Plus 2.0). Cells were treated for 24 h and 24 h plus 72 h recovery with 1000 ng/ml of the drug, before harvesting RNA for analysis. From the cell growth assays, all three cell lines demonstrated permanent growth arrest with diterpene ester treatments at the 1000 ng/ml dose. Mock controls were treated with solvent alone for 24 h. SK-MEL-5 cells were also treated with 1000 ng/ml TPA for 24 h.
2008-06-16 | E-GEOD-8742 | biostudies-arrayexpress
Project description:Proteomic methods for disease state characterization and biomarker discovery have traditionally utilized quantitative mass spectrometry methods to identify proteins with altered expression levels in disease states. Here we report on the large-scale use of protein folding stability measurements to characterize different subtypes of breast cancer using the Stable Isotope Labeling with Amino Acids in Cell Culture and Stability of Proteins from Rates of Oxidation (SILAC-SPROX) technique. Protein folding stability differences were studied in a comparison of two luminal breast cancer subtypes, luminal-A and -B (i.e., MCF-7 and BT-474 cells, respectively), and in a comparison of a luminal-A and basal subtype of the disease (i.e., MCF-7 and MDA-MB-468 cells, respectively). The 242 and 445 protein hits identified with altered stabilities in these comparative analyses, included a large fraction with no significant expression level changes. This suggests thermodynamic stability measurements create a new avenue for protein biomarker discovery. A number of the identified protein hits are known from other biochemical studies to play a role in tumorigenesis and cancer progression. This not only substantiates the biological significance of the protein hits identified using the SILAC-SPROX approach, but it also helps elucidate the molecular basis for their dysregulation and/or dysfunction in cancer.
2017-07-10 | PXD006703 | Pride
Project description:In order to identify new targets for basal-like breast cancers, we performed RNA-Seq of 10 breast cancer cell lines. Basal-like cell lines (MDAMB231, MDAMB436, HCC1937, SUM149, SUM1315 and MCF10A) were compared to luminal cell lines (MCF7 and T47D). Moreover we could also study BRCA1 influence on transcriptome of basal-like breast cancer. 4 of our cell lines are indeed BRCA1 mutated (MDAMB436, HCC1937, SUM149 and SUM1315) and we also developed 2 cell lines that come from the BRCA1 mutated SUM1315 cell line stably transfected with empty LXSN plasmid (SUM1315-LXSN) or with a BRCA1 coding plasmid (SUM1315-BRCA1).
2017-02-14 | E-MTAB-5465 | biostudies-arrayexpress
Project description:In order to identify new targets for basal-like breast cancers, we performed Methyl-Seq of 10 breast cancer cell lines. Basal-like cell lines (MDAMB231, MDAMB436, HCC1937, SUM149, SUM1315 and MCF10A) were compared to luminal cell lines (MCF7 and T47D). Moreover we could also study BRCA1 influence on methylome of basal-like breast cancer. 4 of our cell lines are indeed BRCA1 mutated (MDAMB436, HCC1937, SUM149 and SUM1315) and we also developed 2 cell lines that come from the BRCA1 mutated SUM1315 cell line stably transfected with empty LXSN plasmid (SUM1315-LXSN) or with a BRCA1 coding plasmid (SUM1315-BRCA1).
2017-02-14 | E-MTAB-5468 | biostudies-arrayexpress
Project description:Circular-RNAs are an emerging group of regulatory molecules involved in the control of numerous cellular processes and may play a role in the growth and diffusion of various types of tumors. In the present study, we define the expression of 15 selected circular-RNAs, which may be involved in the process of epithelial-to-mesenchymal-transition, using a panel of 18 breast cancer cell-lines recapitulating the heterogeneity of the tumor and consisting of three distinct groups according to the mesenchymal/epithelial phenotype. The circular RNA deriving from the DOCK1 gene (hsa_circ_0020397) is characterized by the most interesting expression profile, as it is undetectable in triple-negative mesenchymal cell-lines, while it is easily measurable in epithelial cell-lines independent of their positivity to estrogen receptor or the HER2 membrane receptor. Whole-genome RNA-sequencing experiments performed on the triple-negative/mesenchymal MDA-MB-231 and MDA-MB-157 cell-lines engineered to over-express hsa_circ_0020397 demonstrate that the circular-RNA controls the expression of 110 common genes. Pathway analysis of these genes indicate that over-expression of the circular-RNA differentiates the two mesenchymal cell-lines along the epithelial pathway and increase cell-to-cell adhesion. This is accompanied by a growth inhibitory effect and a reduction in the random/directional motility of the two cell-lines. The up-regulated AGR2, ENPP1 and PPP1R9A genes as well as the down-regulated APOE, AQP3, CD99L2 and IGFBP4 genes show an opposite regulation by circDOCK1 silencing in CAMA1 luminal cells.
2022-06-15 | E-MTAB-10819 | biostudies-arrayexpress
Project description:Nucleosome positioning in a 2.3 Mb region of human chromosome 12 (chr12: 6,140,000-8,460,000) containing GAPDH and NANOG loci in human IMR90 fibroblasts (hFibs) and fibroblast-derived human induced pluripotent stem cell (hiPSCs).
2022-06-30 | E-MTAB-10074 | biostudies-arrayexpress
Project description:Clinical approaches to treat advanced melanoma include immune therapies, whose benefits depend on tumor-reactive T-cells to infiltrate metastases. However, most tumors lack significant immune infiltration prior to therapy, and some immune therapies are hindered by a persistent lack of immune cell infiltration. CXCL10 has been implicated as a critical chemokine supporting T-cell migration into tumors; thus agents that induce CXCL10 in tumors may improve patient responses to systemic immune therapy. We find that melanoma cells treated with TLR2/6 agonists (MALP-2 or FSL-1) and interferon-gamma (IFNgamma) upregulate CXCL10 production, when compared to IFNgamma treatment alone or no treatment. Gene profiling of melanoma cells lines treated with TLR2/6 agonists and IFNgamma demonstrate that a selective profile of genes are induced which may be favorable for promoting immune cell infiltration of tumors. TLR2 and TLR6 are widely expressed on human melanoma cells, and treatment of melanoma cells with TLR2/6 agonists and IFNgamma does not hinder melanoma cell apoptosis or promote proliferation. Furthermore, melanoma cells from surgically resected patient tumors upregulate CXCL10 production after treatment with TLR2/6 agonists and IFNgamma when compared to treatment with either agent alone. Collectively, these data identify TLR2/6 agonists and IFNgamma as a novel target for promoting CXCL10 production directly from melanoma cells. Samples from four human melanoma cell lines, VMM1 (n=6), DM13 (n=6), DM93 (n=6) and VMM39 (n=6), were treated with media alone, MALP-2 (TLR2/6 agonist), FSL-1 (TLR2/6 agonist), IFNgamma alone, MALP-2 and IFNgamma, or FSL-1 and IFNgamma.
2015-11-22 | E-GEOD-64506 | biostudies-arrayexpress