Gene expression profiling of 13 primary and established human ovarian cancer cell lines
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE63553 | GEO | 2014/11/22
SECONDARY ACCESSION(S): PRJNA268193
REPOSITORIES: GEO
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Project description:Gene expression analysis was also performed on 13 primary and established human ovarian cancer cell lines (A2008, OAW42, OVCAR2, OVCAR3, OVCAR4, OVCAR5, OVCAR8, OVCAR10, OV7M, OV95, PE01, PE04, SKOV3) using Affymetrix Human Gene 1.0 ST Arrays The study focused on ovarian cancer chemokine expressions
2014-11-22 | E-GEOD-63553 | biostudies-arrayexpress
Project description:Analysis of a panel of 41 human ovarian cancer cell lines for the study of ovarian cancer biology, drug response and drug sensitivity. Ovarian cancer cell lines were either obtained from the American Type Culture Collection (ATCC, Manassas, VA) (CAOV3, OV90, OVCAR3, SKOV3, TOV112D), the European Collection of Cell Cultures, Salisbury, England (A2780CP, A2780S); Kyoto University, Kyoto, Japan (CHI, CHIcisR, M41, M41CSR, Tyknu, and TyknuCisR), or were kind gifts from Dr. Patricia Kruk, Department of Pathology, College of Medicine, University of South Florida, Tampa, FL; and Susan Murphy, PhD, Dept of OBGYN/Division of GYN Oncology, Duke University, Durham, NC (A2008, C13, CAOV2, FUOV1, HeyA8, IGR-OV1, IMCC3, IMCC5, MCAS, OV2008, OVCA420, OVCA429, OVCA432, OVCA433, OVCAR4, OVCAR5, OVCAR8, Dov13, BG1, Ovary1847, OVCAR10, OVCAR2, SK-OV-4). Cell lines were maintained in RPMI-1640 (Invitrogen; Carlsbad, California) supplemented with 10% fetal bovine serum (Fisher Scientific; Pittsburg, PN), 1% sodium pyruvate, 1% penicillin/streptomycin (Cellgro; Manassas, VA), and 1% nonessential amino acids (HyClone; Hudson, New Hampshire). Mycoplasma testing was performed every six months following manufacturer’s protocol (Lonza, Rockland ME).
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Project description:Genetic and epigenetic changes contribute to intratumor heterogeneity and chemotherapy resistance in several tumor types. LncRNAs have been implicated, directly or indirectly, in the epigenetic regulation of gene expression. We investigated lncRNAs that potentially mediate carboplatin-resistance of cell subpopulations, influencing the progression of ovarian cancer (OC). Four carboplatin-sensitive OC cell lines (IGROV1, OVCAR3, OVCAR4, and OVCAR5), their derivative resistant cells, and two inherently carboplatin-resistant cell lines (OVCAR8 and Ovc316) were subjected to RNA-sequencing and global DNA methylation analysis. Integrative and cross-validation analyses were performed using external (The Cancer Genome Atlas, TCGA dataset, n=111 OC samples) and internal datasets (n=39 OC samples) to identify lncRNA candidates. A total of 4,255 differentially expressed genes (DEGs) and 14,529 differentially methylated CpG positions (DMPs) were identified comparing sensitive and resistant OC cell lines. The comparison of DEGs between OC cell lines and TCGA-OC dataset revealed 570 genes, including 50 lncRNAs, associated with carboplatin resistance. Eleven lncRNAs showed DMPs, including the SNHG12. Knockdown of SNHG12 in Ovc316 and OVCAR8 cells increased their sensitivity to carboplatin. The results suggest that the lncRNA SNHG12 contributes to carboplatin resistance in OC and is a potential therapeutic target. We demonstrated that SNHG12 is functionally related to epigenetic mechanisms.
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2017-03-31 | GSE97226 | GEO
Project description:Expression profiles of aggressive versus non-aggressive ovarian, breast, melanoma, and prostate cancer cell lines Expression profiles of aggressive versus non-aggressive ovarian, breast, melanoma, and prostate cancer cell lines was determined. 231MFP, C8161, SKOV3, DU145, and PC3 are aggressive and MCF7, MUM2C, OVCAR3, and LNCaP are non-aggressive cancer cells. We are not comparing across all of the cell lines--just between C8161 and MUM2C, SKOV3 and OVCAR3, 231MFP and MCF7, and LNCaP/DU145/PC3. Therefore the normalization strategies used are different. We have not used the same normalization strategy
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Project description:Molecular communication between cancer cells and its stromal microenvironment is a key factor for cancer progression. Alongside classic secretory pathways, it has recently been proposed that small membranous vesicles are alternative mediators of intercellular communication. Exosomes carry an effector-rich proteome with the ability to modulate various functional properties of the recipient cell. In this study, exosomes isolated from four epithelial ovarian cancer cell lines (OVCAR3, OVCAR433, OVCAR5 and SKOV3) were characterized using mass spectrometry-based proteomics. Using an optimized workflow consisting of efficient exosome solubilization and the latest generation of proteomic instrumentation, we demonstrate improved detection depth. Systematic comparison of our cancer cell line exosome proteome against public data (ExoCarta) and the recently published NCI 60 proteome revealed enrichment of functional categories related to signaling biology and biomarker discovery.
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