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Heterogeneity of gene expression in stromal fibroblasts of human breast carcinomas and normal breast

ABSTRACT: Twenty-one genes (27 probe sets) were up-regulated in CAF, as compared with NF. Known functions of these genes relate to paracrine or intracellular signaling, transcriptional regulation, extracellular matrix and cell adhesion/migration. Ten genes (14 probe sets) were down-regulated in CAF, including the pluripotency transcription factor KLF4. Quantitative RT–PCR analysis of 10 genes validated the array results. Immunohistochemical staining for three gene products confirmed stromal expression in terms of location and relative quantity. Surprisingly, the variability of gene expression was slightly higher in NF than in CAF, suggesting inter-individual heterogeneity of normal stroma.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20086 | GEO | 2010/01/29

SECONDARY ACCESSION(S): PRJNA124285

REPOSITORIES: GEO

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Heterogeneity of gene expression in stromal fibroblasts of human breast carcinomas and normal breast

Project description:Twenty-one genes (27 probe sets) were up-regulated in CAF, as compared with NF. Known functions of these genes relate to paracrine or intracellular signaling, transcriptional regulation, extracellular matrix and cell adhesion/migration. Ten genes (14 probe sets) were down-regulated in CAF, including the pluripotency transcription factor KLF4. Quantitative RTÃ¢Â?Â?PCR analysis of 10 genes validated the array results. Immunohistochemical staining for three gene products confirmed stromal expression in terms of location and relative quantity. Surprisingly, the variability of gene expression was slightly higher in NF than in CAF, suggesting inter-individual heterogeneity of normal stroma. Paired CAF and NF were isolated from six primary human breast carcinoma specimens. RNA was extracted from low-passage cultures of CAF and NF and analyzed with Affymetrix Human Genome U133 Plus 2.0 arrays. The array data were examined with an empirical Bayes model and filtered according to the posterior probability of equivalent expression and fold difference in expression.

2010-02-21 | E-GEOD-20086 | biostudies-arrayexpress

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Project description:Analysis of differentially expressed genes in CAF associated with PDAC vs NF Total RNA obtained from PDAC CAF and NF samples

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Gene Expression Analysis of Cancer-Associated Fibroblast (CAF) compared to Normal Fibroblast (NF) [RNA-seq]

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Gene Expression Analysis of Cancer-Associated Fibroblast (CAF) compared to Normal Fibroblast (NF) [RNA-seq]

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Effects of Arid1a knockout in murine ovarian endometrioid carcinomas with biallelic inactivation of Apc and Pten

Project description:We mated mice with floxed alleles of both Apc and Pten, to mice with floxed alleles for Arid1a, to obtain female mice with both copies of all three genes floxed. At 7 to 8 weeks of age the right ovarian bursal cavites of the mice were injected with 50 million plaque-forming units of adenovirus expressing Cre recombinase, which causes the floxed genes to be knocked out. Tumor tissue from 3 mice for each group was obtained at necropsy, RNA purified, and targets for Affymetrix arrays synthesized from the mRNAs. We used Affymetrix Mouse Genome 430 2.0 arrays, which hold 45101 probe-sets. Raw data was processed with Robust Multi-array Average algorithm (RMA). Data is log2-transformed transcript abundance estimates. We performed T-tests to compare the 3 vs 3 arrays. We supply a supplementary excel workbook that holds the same data as the data matrix file, but also holds the probe-set annotation at the time we analyzed the data, and some very simple statistical calculations, which select subsets of the probe-sets as differentially expressed. Consumers should consider obtaining more up-to-date probe-set annotation for the array platform. We have also supplied a second supplementary tar archive holding software and files to 1) perform permutation testing of the probe-set selection in order to estimate false discovery rates for the probe-sets we selected as differentially expressed, 2) perform enrichment testing of GO terms, and 3) to perform enrichment testing of KEGG pathways and 3000 curated gene sets from version 4 of the Molecular Signatures Database (MSigDB). The software is in "C".

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Gene Expression Analysis of Cancer-Associated Fibroblast (CAF) compared to Normal Fibroblast (NF) [microarray]

Project description:Analysis of differentially expressed genes in CAF associated with PDAC vs NF

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A novel 3-D organotypic culture model by co-culturing alpha-SMA positive CAF and cholangiocarcinoma cells in a collagen matrix

Project description:The increased α-smooth muscle-actin positive cancer-associated fibroblastic cells (CAF) in the desmoplastic stroma may relate to a more aggressive cancer and worse survival outcomes for intrahepatic cholangiocarcinoma (ICC) patients We developed a novel 3-D organotypic culture model by co-culturing α-SMA positive CAF and cholangiocarcinoma cells in a collagen matrix.

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Effects of Arid1a knockout in murine ovarian endometrioid carcinomas with biallelic inactivation of Apc and Pten

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2022-10-20 | GSE193280 | GEO

Gene expression in CAF-1 leaves

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