Transcription profiling by array of human primary pancreatic cancer cells and cancer associated fibroblasts co-cultured to study the cross talk between these cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
DISEASE(S): adenocarcinoma
SUBMITTER: Marie Larsson
PROVIDER: E-MEXP-2826 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Effect of Dasatinib on primary cancer-associated fibroblasts from lung cancer specimens.
2011-01-12 | E-MEXP-2546 | biostudies-arrayexpress
Project description:SCC12 cells were seeded ontop of organotypic gels with HN-CAF (head and neck carcinoma associated fibroblasts). Differential gene expression was analysed between cancer cells not exposed to CAFs or non-invading cancer cells exposed to CAFs. Squamous cell cancer organotypics were constructed by embedding CAFs in collagen Matrigel matrix with SCC 12cells added on top. Gene expression was compared between non-invaded cancer cells and cancer cells not expoesd to CAFs.
2013-03-23 | E-GEOD-36776 | biostudies-arrayexpress
Project description:Epithelial-to-mesenchymal transition (EMT) and cancer stem cells play relevant roles in metastasis and drug resistance in castration-resistant PCa. Conditioned-media from Cancer-Associated Fibroblasts from two patients with aggressive PCa induce EMT, reversible DNA methylation and transcriptional variations in androgen independent PC3, but not in androgen dependent LN-CaP cells. Focal CpG islands hyper-methylation associated to transcriptional repression of epithelial markers occurs together with widespread hypo-methylation, including promoters of EMT and stemness regulating genes resulting in their transcriptional activation. Remarkably, DNA methylation and transcription patterns are entirely reverted upon exposure to serum-free medium (mesenchymal-to-epithelial transition). DNMT3A is required for de novo methylation and silencing of CDH1 and GRHL2, the ZEB1 direct repressor, while its knock-down prevents EMT entry. These unprecedented results highlight that CAF-released factors induce reversible DNA methylation patterns required for transcriptional variations essential for EMT and stemness in androgen independent PCa cells, suggesting that similar plasticity might occur in tumour microenvironment.
2017-03-09 | E-MTAB-4752 | biostudies-arrayexpress
Project description:The cyclin D1 oncogene encodes the regulatory subunit of a holoenzyme that phosphorylates and inactivates the Rb protein and promotes progression through G1 to S phase of the cell cycle. Several prostate cancer cell lines and a subset of primary prostate cancer samples have increased cyclin D1 protein expression. However, the relationship between cyclin D1 expression and prostate tumor progression has yet to be clearly characterized. This study examined the effects of manipulating cyclin D1 expression in either human prostatic epithelial or stromal cells using a tissue recombination model. The data showed that overexpression of cyclin D1 in the initiated BPH-1 cell line increased cell proliferation rate, but did not elicit tumorigenicity in vivo. However, overexpression of cyclin D1 in Normal Prostate Fibroblasts (NPF) that were subsequently recombined with BPH-1 did induce malignant transformation of the epithelial cells. The present study also showed that recombination of BPH-1 + cyclin D1 overexpressing fibroblasts (NPF cyclin D1) resulted in permanent malignant transformation of epithelial cells (BPH-1 NPF-cyclin D1 cells) similar to that seen with Carcinoma Associated Fibroblasts (CAFs). Microarray analysis showed that the expression profiles between CAFs and NPF cyclin D1 cells were highly concordant including cyclin D1 upregulation. These data indicated that the tumor-promoting activity of cyclin D1 may be tissue-specific. Keywords: cyclin D1; stromal-epithelial interactions; prostate cancer; cDNA microarray NPF cyclin D1 cells were generated from NPFs, which were isolated from two different patient samples; CAFs were isolated from two different patient samples as well. RNA was isolated from NPFs, CAFs, and NPF cyclin D1 cells using total RNA isolation kit (Qiagen). Custom spotted cDNA microarrays were constructed as previously described (True, L., Coleman, I., Hawley, S., Huang, C. Y., Gifford, D., Coleman, R., Beer, T. M., Gelmann, E., Datta, M., Mostaghel, E., Knudsen, B., Lange, P., Vessella, R., Lin, D., Hood, L., and Nelson, P. S. A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A, 103: 10991-10996, 2006) using a non-redundant set of 6,700 prostate-derived cDNA clones identified from the Prostate Expression Data Base (PEDB), a public sequence repository of expressed sequence tag data derived from human prostate cDNA libraries. Total RNA was amplified through one round of linear amplification using the MessageAmp aRNA kit (Ambion, Austin, TX). Sample quality and quantification was assessed by agarose gel electrophoresis and absorbance at A260. Cy3 and Cy5 labeled cDNA probes were made from 4 M-BM-5g of amplified RNA. Two NPF cyclin D1 and two CAF samples (labeled with Cy3) were hybridized head-to-head with an NPF control sample labeled with Cy5. Probes were hybridized competitively to microarrays under a coverslip for 16 h at 63M-BM-0C. Fluorescent array images were collected for both Cy3 and Cy5 by using a GenePix 4000B fluorescent scanner, and image intensity data were gridded and extracted using GenePix Pro 4.1 software. Differences in gene expression between NPF cyclin D1/NPF and CAF/NPF groups were determined using a two-sample t-test with Significance Analysis of Microarrays (SAM) software (http://www-stat.stanford.edu/_tibs/SAM/) with a False Discovery Rate (FDR) of M-bM-^IM-$ 10% considered significant (Tusher, PNAS, 2001). Similarities in gene expression between NPF cyclin D1/NPF and CAF/NPF groups were determined using a one-sample t-test in SAM with an FDR of M-bM-^IM-$ 0.1% considered significant. These results were reduced to unique genes by eliminating all but the highest scoring clones for each gene. A Pearson correlation coefficient was calculated in Excel to assess the strength of the linear relationship between NPF cyclin D1/NPF and CAF/NPF average log2 ratios.
2007-08-31 | E-GEOD-6936 | biostudies-arrayexpress
Project description:HBEC-5i (human brain endothelial cells) grown to confluence in 6-well tissue culture plates. Cocultures were either left unstimulated or incubated overnight with recombinant TNF?. HBEC were then washed in PBS and incubated with PLT (platelets), pRBC (P.falciparum-parasited red blood cells) or NRBC (normal red blood cells) according to the experimental conditions. Then HBEC were washed three times with PBS, and were harvested at 0 and 5h coculture. Each experimental condition was realized in triplicate.
2009-01-15 | E-MEXP-1989 | biostudies-arrayexpress
Project description:A pilot program for monitoring proficiency in microarray facilities using three replicates of two different RNA sources. Participating laboratories prepared and hybridized targets from the six RNA samples using their own protocols. The entire process was repeated three times over a nine-month period and included approximately fifteen distinct laboratories in each testing round.
2008-09-12 | E-MEXP-1568 | biostudies-arrayexpress
Project description:Culture of proB cells with IL7 in the presence or absence of CpG
2010-02-27 | E-MEXP-2595 | biostudies-arrayexpress
Project description:The relationships between cancer cells and the microenvironment play a critical role in cancer growth and development. The bone stroma consists of mesenchymal stem cells (MSCs) and mature osteoblasts that promote cancer growth. Yet it is not completely understood what are the molecular processes guiding cancer cells progression to the bone. In this study, a co-culture assay and subsequent gene profiling arrays were used to compare the gene expression profile of a pre-osteoblastic cell line (MBA-15) with that of a mammary adenocarcinoma (DA3) cells. Following co-culture, cells were separated by magnetic beads based on the expression of CD326 antigen. RNA was purified and hybridized on gene expression array. The gene expression pattern changes were followed by qRT-PCR. We demonstrate that co-cultured DA3 cells express elevated levels of genes that regulate growth and responses to both hormonal stimulus and wounding, as well as reduced expression of genes related to lipid metabolism. Also, co-cultured pre-osteoblastic cells showed reduced expression of cell-junction genes. The study presents a simplified model system, composed of pre-osteoblastic and mammary cancer cells, that potentially mimics the molecular interactions in the tumor microenvironment which contribute to tumor-progression. Gene expression was studied in 2 mouse cell lines: MBA-15, a pre-osteoblastic stromal cell line, and DA3, a mammary adenocarcinomal cell line. The interaction between these 2 cell lines was also analysed by gene expression. The experiment was performed in duplicates (see Date in the Sample characteristics field).
2014-11-23 | E-GEOD-34529 | biostudies-arrayexpress
Project description:PDR mutants , strain YYA100 (pdr1?::KanMx6, pdr3?::His3Mx6) from Mol Biol Cell. 2007 December; 18(12): 49324944, was grown to OD 1-1.5 in YEPD and hybridyzed to an expression array in one channel with a wild-type strain reference RNA on the other channel
2009-06-17 | E-MEXP-2150 | biostudies-arrayexpress
Project description:Gene expression profiling in human gastric cancer cells after 5-aza-2'-deoxycytidine (5-Aza-CdR) and 4-phenylbutyric acid (PBA) treatment was analyzed to investigate what genes are controlled by these chromatin modifying drug
2008-10-09 | E-MEXP-1821 | biostudies-arrayexpress