Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human cell lines from 9 different cancer tissue (NCI-60) (U133 platform)

ABSTRACT: Comparison between cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel Experiment Overall Design: cell lines from 9 different cancer tissue of origin types

ORGANISM(S): Homo sapiens

SUBMITTER: Uma Shankavaram

PROVIDER: E-GEOD-5720 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study.

Shankavaram Uma T UT Reinhold William C WC Nishizuka Satoshi S Major Sylvia S Morita Daisaku D Chary Krishna K KK Reimers Mark A MA Scherf Uwe U Kahn Ari A Dolginow Douglas D Cossman Jeffrey J Kaldjian Eric P EP Scudiero Dominic A DA Petricoin Emanuel E Liotta Lance L Lee Jae K JK Weinstein John N JN

Molecular cancer therapeutics 20070305 3

To evaluate the utility of transcript profiling for prediction of protein expression levels, we compared profiles across the NCI-60 cancer cell panel, which represents nine tissues of origin. For that analysis, we present here two new NCI-60 transcript profile data sets (A based on Affymetrix HG-U95 and HG-U133A chips; Affymetrix, Santa Clara, CA) and one new protein profile data set (based on reverse-phase protein lysate arrays). The data sets are available online at http://discover.nci.nih.gov ...[more]

PMID: 17339364

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Project description:Uveal melanoma is a poor prognosis cancer with an imperative need for new treatment options. Ergolide, a sesquiterpene lactone isolated from the flowers of Inula species (a medicinal herb), exerts anti-cancer properties. The objective of this study was to 1) evaluate whether ergolide reduced metastatic uveal melanoma (MUM) cell survival/viability in vitro and in vivo; and 2) to understand the molecular mechanism of ergolide action. Ergolide treatment resulted in significant dose-dependent reduction (48.5 to 99.9%; p < 0.0001) in OMM2.5 cell survival in vitro and of normalized primary zebrafish xenograft fluorescence (56%; p< 0.0001) in vivo, compared to vehicle controls. Proteome profiling of ergolide treated OMM2.5 cells, identified 5023 proteins in total with 52 and 55 proteins significantly altered at 4 hours and 24 hours, respectively (p value <0.05; fold-change >1.2). Immunoblot analysis of heme oxygenase 1 (HMOX1), growth/differentiation factor 15 (GDF15) and macrophage migration inhibitory factor (MIF) corroborated the proteomics data. MIF was distinctly downregulated following ergolide treatment. Proteomics of EVs isolated from OMM2.5 cells treated with ergolide detected 2931 total proteins, 2679 of which are recognized as EV proteins based on the Vesiclepedia compendium. 252 additional putative novel EV proteins were also identified. Within the differentially expressed proteins, the proteasomal pathway was primarily altered. Interestingly, BRCA2 and CDKN1A Interacting Protein (BCCIP) and Chitinase Domain Containing 1 (CHID1), were the only proteins significantly differentially expressed by ergolide in both the OMM2.5 cell and EV isolates and they displayed inverse differential expression in the cells versus the EVs. In the TCGA database, no significant correlations occurred between BCCIP and CHID1 transcript levels and overall survival or disease-free survival in UM patients. Ergolide is a novel candidate that shows promise as an anti-proliferative agent for UM/MUM cells. Proteomic profiling of OMM2.5 cell lysates and EVs identified candidate pathways elucidating the action of ergolide and putative biomarkers of UM, that require further examination.

Dataset Information

Transcription profiling of human cell lines from 9 different cancer tissue (NCI-60) (U133 platform)

Publications

Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study.

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