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Mus musculus

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

PROVIDER: PRJNA241180 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1191170_1.fastq.gz	Fastqsanger.gz
	SRR1191170_2.fastq.gz	Fastqsanger.gz
	SRR1191171_1.fastq.gz	Fastqsanger.gz
	SRR1191171_2.fastq.gz	Fastqsanger.gz

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Mus musculus

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

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

Project description:Gene Expression Analysis of Cancer-Associated Fibroblast (CAF) compared to Normal Fibroblast (NF)

| PRJNA241179 | ENA

Different gene expression between normal and cancer-associated fibroblasts from diffuse-type gastric cancer

Project description:To identify a cancer-associated fibroblast (CAF)-specific molecule that contributes to tumor-promoting effect, we utilized trnascriptome analysis. We performed RNA-sequencing with three normal fibroblast (NF)-CAF pairs derived from diffuse-type gastric cancer patients’ tissues. RNA-sequencing revealed several commonly increased CAF-specific genes among each pair.

2024-05-30 | GSE233331 | GEO

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

Project description:Analysis of differentially expressed genes in CAF associated with PDAC vs NF. Genetically engineered mice with spontaneous pancreas cancer were generated. Their genotype is Ptfa-cre/+:LSL KrasG12D/+;Tgfrb2flox/flox. Cancer associated fibroblasts were expanded in vitro from the tumors of these mice (CAF). Normal fibroblasts (NF) were also expanded from normal pancreas of mice. The experiement consists in comparing the expression profile of CAF vs. NF. Expanded cultures of fibroblasts in vitro from pancreas tumor and normal pancreas tissue were lyzed in TRIzol and RNA extracted from them.

2014-06-18 | E-GEOD-55870 | biostudies-arrayexpress

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

2014-06-18 | GSE55870 | GEO

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

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. 30 samples: 15 primary NSCLC fibroblast cell lines, 15 normal lung fibroblast cell lines

2011-04-08 | E-GEOD-22862 | biostudies-arrayexpress

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

Gene and miRNA expression profiling of primary cell cultures of lung fibroblasts obtained from cancer or normal tissue of lung cancer patients

Project description:There is increasing evidence for a crucial contribution of the tumor microenvironment to cancer development and progression since several stromal components, including fibroblasts, interact with cancer cells regulating their behavior and ultimately affecting tumor phenotype. To investigate the cross-talk between cancer cells and lung-derived fibroblasts we have prospectively collected surgical specimens of lung cancer and normal lung tissue and established primary fibroblast cultures from different areas of the lungs. We have generated cultures from cancer specimens (Cancer Associated Fibroblasts, CAF) and cultures from normal lung tissue either proximal (Adjacent Fibroblasts, AF) or distant from the neoplastic lesion (Normal fibroblasts, NF). Gene and miRNA expression profiles were obtained from 60 cultures to identify fibroblast properties related to cancer progression.

2017-07-10 | GSE97545 | GEO

Proteomics of high-grade serous ovarian cancer models reveals cancer associated fibroblast markers associated with outcome.

Project description:Here, we performed proteomics on whole cell lysate of three high-grade serous ovarian cancer patient derived cancer associated fibroblast (CAF) lines, four commercially available high-grade serous ovarian epithelial cancer cell lines (Kuramochi, PEO4, OVCAR8, ES2) and two immortalized normal Fallopian tube secretory epithelial cell lines (FT237, FT194). N-glycoproteomics using hydrazide-based enrichment was performed on 8/9 models. Integration of data from in vitro models with publicly available primary tissue data identified multiple novel CAF proteins that are associated with poor clinical outcomes in HGSC.

2022-11-28 | MSV000090794 | MassIVE

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