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MiRNA expression analysis of cancer-associated fibroblasts (CAFs) and normal fibroblasts (NFs) in breast cancer

ABSTRACT: To identify miRNA differentially expressed in CAFs vs matched NFs and analyze the heterogeneity of miRNA expression profiles in the two kinds of cells, we established primary cultures of CAFs and paired NFs from six resected breast tumor tissue without any radiotherapy and chemotherapy treatment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE37527 | GEO | 2012/09/28

SECONDARY ACCESSION(S): PRJNA161905

REPOSITORIES: GEO

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MiRNA expression analysis of cancer-associated fibroblasts (CAFs) and normal fibroblasts (NFs) in breast cancer

Project description:To identify miRNA differentially expressed in CAFs vs matched NFs and analyze the heterogeneity of miRNA expression profiles in the two kinds of cells, we established primary cultures of CAFs and paired NFs from six resected breast tumor tissue without any radiotherapy and chemotherapy treatment. Paired CAFs and NFs from six primary human breast carcinoma specimens were cultured,the third passage of primary cells was used in the experiments.

2012-09-28 | E-GEOD-37527 | biostudies-arrayexpress

Expression data from human normal fibroblasts (NFs) and cancer associated fibroblasts (CAFs)

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Gene expression profiles of oral normal fibroblasts (NFs) and oral carcinoma-associated fibroblasts (CAFs)

Project description:This study aims to identify genes differentially expressed in oral CAFs with respect to their normal counterparts, i.e. oral NFs. We collected oral normal mucosal tissues and oral squamous cell carcinoma (OSCC) tissues from 12 healthy people and 12 OSCC patients, respectively, at West China Hospital of Stomatology, Sichuang University, P. R. China. The tissues were isolated, cultured and purified using standard protocols to obtain oral NFs and CAFs. Agilent 4×44K Whole Genome Oligo Microarrays were used to measure the gene expression profiles of the samples. Sample preparation and hybrid reactions were performed according to the manufacture’s instructions. RNA samples from NFs and CAFs were pooled respectively before hybridization. The chips were scanned and visualized using the Agilent DNA microarray scanner. Probe set intensities were measured using Agilent Feature Extraction software (version 10.5.1.1). Raw data were normalized in the Agilent GeneSpring GX software (version 11.0) using the Agilent FE one-color scenario (mainly median normalization). Oral NFs and CAFs were obtained from tissues derived from 12 healthy people undergoing plastic surgery and 12 OSCC patiens undergoing surgical resection. RNA samples from NFs and CAFs were pooled respectively before hybridization.

2012-01-26 | E-GEOD-35356 | biostudies-arrayexpress

RNA Expression Profile of normal fibroblasts (NFs) and cancer-associated fibroblasts (CAFs) derived from human Pancreatic Ductal Adenocarcinoma.

Project description:Although how CAFs impact the tumor epithelium is being progressively unveiled, transcriptional processes of lineage plasticity in fibroblasts govern the acquisition and transition of the CAF phenotype are much less understood. Here, to explore the potential involvement of the circular RNAs (circRNAs) in fibroblast activation and phenotype acquisition, we isolated CAFs and NFs from human pancreatic cancer and paired normal pancreatic tissue. Next, we conducted circRNA profiling five CAFs and three paired NFs by high throughput sequencing. Our results showed that clusters of circRNAs were aberrantly expressed in CAFs compared with NFs, and provided potential targets for future treatment of PDAC and novel insights into PDAC microenvironment.

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Expression data from human normal fibroblasts (NFs) and cancer associated fibroblasts (CAFs) [HTA-2_0]

Project description:CAFs are the major regulators in tumor microenviroment which promote cancer progression. We want to know which mRNAs changed in human CAFs compared to NFs. We used microarrays to detail the mature mRNA expression and identified distinct classes of 2-fold changed mRNAs during this process.

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Expression data from human normal fibroblasts (NFs) and cancer associated fibroblasts (CAFs)

Project description:Expression data from human normal fibroblasts (NFs) and cancer associated fibroblasts (CAFs)

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Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [methylation profiling]

Project description:The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. Microarray gene expression analysis of the 15 matched CAF and NF cell lines identified 46 differentially expressed genes, encoding for proteins that are significantly enriched for extracellular proteins regulated by the TGF-beta signaling pathway. We have identified a subset of 11 genes that formed a prognostic gene expression signature, which was validated in multiple independent NSCLC microarray datasets. Functional annotation using protein-protein interaction analyses of these and published cancer stroma-associated gene expression changes revealed prominent involvement of the focal adhesion and MAPK signalling pathways. Fourteen (30%) of the 46 genes also were differentially expressed in laser-capture micro-dissected corresponding primary tumor stroma compared to the matched normal lung. Six of these 14 genes could be induced by TGF-beta1 in NF. The results establish the prognostic impact of CAF-associated gene expression changes in NSCLC patients. Methylation profiles of 5 pairs of were included in a molecular characterization of NSCLC fibroblast cell lines (CAFs) vs. normal lung fibroblasts (NFs). Methylation profiles of 5 paired primary NSCLC fibroblast cell lines (CAFs) and normal lung fibroblasts (NFs) were generated. Genes were determined to be hyper- and hypo-methylated based on paired analysis.

2011-04-08 | E-GEOD-27284 | biostudies-arrayexpress

Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [genome variation profiling]

Project description:The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. Microarray gene expression analysis of the 15 matched CAF and NF cell lines identified 46 differentially expressed genes, encoding for proteins that are significantly enriched for extracellular proteins regulated by the TGF-beta signaling pathway. We have identified a subset of 11 genes that formed a prognostic gene expression signature, which was validated in multiple independent NSCLC microarray datasets. Functional annotation using protein-protein interaction analyses of these and published cancer stroma-associated gene expression changes revealed prominent involvement of the focal adhesion and MAPK signalling pathways. Fourteen (30%) of the 46 genes also were differentially expressed in laser-capture micro-dissected corresponding primary tumor stroma compared to the matched normal lung. Six of these 14 genes could be induced by TGF-beta1 in NF. The results establish the prognostic impact of CAF-associated gene expression changes in NSCLC patients. Genotyping profiles of 4 pairs of were included in a molecular characterization of NSCLC fibroblast cell lines (CAFs) vs. normal lung fibroblasts (NFs). Genotyping profiles of 4 paired primary NSCLC fibroblast cell lines (CAFs) and normal lung fibroblasts (NFs) were generated. CNV was assessed using paired analysis.

2011-04-08 | E-GEOD-27289 | biostudies-arrayexpress

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