Gene and miRNA expression profiling of primary cell cultures of lung fibroblasts obtained from cancer or normal tissue of lung cancer patients
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE97545 | GEO | 2017/07/10
SECONDARY ACCESSION(S): PRJNA382261
REPOSITORIES: GEO
Similar Datasets
Project description:ABSTRACT Primary human distal lung/parenchymal fibroblasts (DLF) exhibit a different phenotype from airway fibroblasts (AF), including the expression of high levels of a-smooth muscle actin (a-SMA). The scope of the differences and the mechanisms driving them are unknown. To determine whether distinct fibroblast characteristics and function based on lung region are predicted by a broad range of genomic differences in AF vs DLF. Matched human fibroblast pairs isolated from proximal and distal lung in 18 asthmatic and 4 normal subjects were studied. Microarray analysis was performed on 12 matched fibroblast pairs (8 asthmatic and 4 normal subjects) and validated by quantitative real-time PCR (qRT-PCR). The functional impact of these molecular differences on AF and DLF was then revealed using computational approaches. Microarray data demonstrated 474 transcripts upregulated in AF, and 611 transcripts upregulated in DLF, when the asthmatic and normal fibroblasts were combined for all the analysis. Further gene ontology (GO) and network analysis identified distinct pathway activation patterns between AF and DLF, including identification of the SMAD3 and MAPK8 signaling pathways. These results demonstrated that marked molecular and functional differences exist between these two lung regional fibroblast populations. These striking differences identify multiple potential mechanisms by which AF and DLF differ in their responses to injury, regeneration and remodeling in the lungs. In order to better identify the underlying molecular differences between AF and DLF, microarray analysis was performed on 12 different matched pairs of fibroblasts (4 pairs from normal subjects and 8 pairs from asthmatics).
2011-07-21 | E-GEOD-27335 | biostudies-arrayexpress
Project description:ABSTRACT Primary human distal lung/parenchymal fibroblasts (DLF) exhibit a different phenotype from airway fibroblasts (AF), including the expression of high levels of a-smooth muscle actin (a-SMA). The scope of the differences and the mechanisms driving them are unknown. To determine whether distinct fibroblast characteristics and function based on lung region are predicted by a broad range of genomic differences in AF vs DLF. Matched human fibroblast pairs isolated from proximal and distal lung in 18 asthmatic and 4 normal subjects were studied. Microarray analysis was performed on 12 matched fibroblast pairs (8 asthmatic and 4 normal subjects) and validated by quantitative real-time PCR (qRT-PCR). The functional impact of these molecular differences on AF and DLF was then revealed using computational approaches. Microarray data demonstrated 474 transcripts upregulated in AF, and 611 transcripts upregulated in DLF, when the asthmatic and normal fibroblasts were combined for all the analysis. Further gene ontology (GO) and network analysis identified distinct pathway activation patterns between AF and DLF, including identification of the SMAD3 and MAPK8 signaling pathways. These results demonstrated that marked molecular and functional differences exist between these two lung regional fibroblast populations. These striking differences identify multiple potential mechanisms by which AF and DLF differ in their responses to injury, regeneration and remodeling in the lungs.
2011-07-22 | GSE27335 | GEO
Project description:ABSTRACT Background: Primary human distal lung/parenchymal fibroblasts (DLF) exhibit a different phenotype from airway fibroblasts (AF), including the expression of high levels of alpha-SMA. The scope of the differences and the mechanisms driving them are unknown. We hypothesized that the distinct fibroblast characteristics based on lung region predicted a broad range of genomic differences which contribute to distinctly different functional pathway activation in AF and DLF. Methods and Findings: To investigate whether comprehensive gene expression patterns vary between AF and DLF, we compared global gene expression profiles of 3 matched pairs of primary human fibroblasts isolated from proximal and distal lung. 194 transcripts were upregulated in AF, and 290 transcripts upregulated in DLF. Quantitative real-time PCR (qRT-PCR) from both asthmatic and normal subjects confirmed the validity of microarray data (n = 8). Further analysis identified distinct pathway activation patterns, including the identification of the TGF-β receptor/SMAD3 signaling pathway as critical to the phenotypic differences in AF and DLF. The functional impact of these molecular differences on AF and DLF was then analyzed using Western blot, qRT-PCR, ELISA and gene knock-down approaches. TGF-β receptor/SMAD2-3 pathway analysis confirmed the contribution of higher TGF-β1 expression and accompanying SMAD3 and JNK activation to the increased alpha-SMA level seen in DLF. There are two limitations associated with our work. First, the microarray sample size was small. Second, for ethical reasons, a large majority of our data were from asthmatic subjects, only one pair of airway and distal lung tissues from a subject without knowing preexisting lung disease matched for age and smoking status was available. In this single normal subject, the same pattern of differences existed, supporting the concept that these genomic differences are regional, rather than disease-related. Conclusions: These findings demonstrated marked molecular and functional differences for these two lung regional fibroblast populations. These results suggest that airway and parenchymal fibroblasts differ in their responses to injury, repair, and remodeling in the lungs. There are likely profound implications of these observations for understanding mechanisms of development of fibrotic lung diseases as well as approaching therapy. In order to identify the underlying molecular differences between airway- and distal lung fibroblasts, microarray analysis was performed on 3 different matched pairs of fibroblasts.
2011-07-21 | E-GEOD-19362 | biostudies-arrayexpress
Project description:Mesothelioma is an aggressive cancer of the mesothelial layer associated with an extensive fibrotic response. The latter is in large part mediated by cancer-associated fibroblasts which mediate tumour progression and poor prognosis. However, understanding of the crosstalk between cancer cells and fibroblasts in this disease is mostly lacking. Here, using co-cultures of patient-derived mesothelioma cell lines and lung fibroblasts, we demonstrate that fibroblast activation is a self-propagated process producing a fibrotic extracellular matrix (ECM) and triggering drug resistance in mesothelioma cells. Following characterisation of mesothelioma cells/fibroblasts signalling crosstalk, we identify several FDA-approved targeted therapies as far more potent than standard-of-care Cisplatin/Pemetrexed in ECM-embedded co-culture spheroid models. In particular, the SRC family kinase inhibitor, Saracatinib, extends overall survival well beyond standard-of-care in a mesothelioma genetically-engineered mouse model. In short, we lay the foundation for the rational design of novel therapeutic strategies targeting mesothelioma/fibroblast communication for the treatment of mesothelioma patients.
2024-01-26 | PXD040492 | Pride
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
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
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
Project description:ABSTRACT Background: Primary human distal lung/parenchymal fibroblasts (DLF) exhibit a different phenotype from airway fibroblasts (AF), including the expression of high levels of alpha-SMA. The scope of the differences and the mechanisms driving them are unknown. We hypothesized that the distinct fibroblast characteristics based on lung region predicted a broad range of genomic differences which contribute to distinctly different functional pathway activation in AF and DLF. Methods and Findings: To investigate whether comprehensive gene expression patterns vary between AF and DLF, we compared global gene expression profiles of 3 matched pairs of primary human fibroblasts isolated from proximal and distal lung. 194 transcripts were upregulated in AF, and 290 transcripts upregulated in DLF. Quantitative real-time PCR (qRT-PCR) from both asthmatic and normal subjects confirmed the validity of microarray data (n = 8). Further analysis identified distinct pathway activation patterns, including the identification of the TGF-β receptor/SMAD3 signaling pathway as critical to the phenotypic differences in AF and DLF. The functional impact of these molecular differences on AF and DLF was then analyzed using Western blot, qRT-PCR, ELISA and gene knock-down approaches. TGF-β receptor/SMAD2-3 pathway analysis confirmed the contribution of higher TGF-β1 expression and accompanying SMAD3 and JNK activation to the increased alpha-SMA level seen in DLF. There are two limitations associated with our work. First, the microarray sample size was small. Second, for ethical reasons, a large majority of our data were from asthmatic subjects, only one pair of airway and distal lung tissues from a subject without knowing preexisting lung disease matched for age and smoking status was available. In this single normal subject, the same pattern of differences existed, supporting the concept that these genomic differences are regional, rather than disease-related. Conclusions: These findings demonstrated marked molecular and functional differences for these two lung regional fibroblast populations. These results suggest that airway and parenchymal fibroblasts differ in their responses to injury, repair, and remodeling in the lungs. There are likely profound implications of these observations for understanding mechanisms of development of fibrotic lung diseases as well as approaching therapy.
2011-07-22 | GSE19362 | GEO
Project description:The interaction of lung epithelial and lung mesenchymal cells (fibroblasts) was investigated in a novel co-culture model of human pulmonary fibrosis. Remarkably, co-culturing both cell types induced cell-type-specific responses, including fibroblast-to-myofibroblast differentiation and epithelial-to-mesenchymal transition (EMT), which were fully dependent on direct epithelial / fibroblast contact. Primary normal human lung fibroblasts (NHLF) and normal human bronchiolar epithelial cells (NHBE) were fluorescently labelled prior to seeding, then grown either as mono or co-cultures and collected in triplicates for mRNA-seq at the start (T=0h) and after 3h and 18h. Each harvested cell culture was FACS sorted into individual NHLF and NHBE cell populations, which were then then lysed and sequenced.
2022-10-03 | E-MTAB-11832 | biostudies-arrayexpress
Project description:We obtained fibroblast cultures from fresh surgical specimen ressected from patients with primary colorectal carcinoma: normal colonic fibroblasts (NCF=9) from the normal colonic mucosa at least 5-10cm from the surgical margin, carcinoma-associated fibroblasts from the primary tumor (CAF-PT=14) and carcinoma-associated fibroblasts (CAF-LM=11) from fresh surgical specimens of liver metastases. We identified 277 probes, in common between the three types of fibroblasts, whose expression level is sequentially deregulated according to cancer progression (NCF→CAF-PT→CAF-LM; fold change Log2 normalized expression>1.5 in each step). Prediction Analysis of Microarrays was applied to obtain a 25-gene signature that better characterizes each fibroblast class. The signature is able to classify patients carrying primary tumors according to prognosis. This fact was exploited to obtain a 19-gene signature (from the 277 deregulated probes) predicting recurrence with high accuracy in stage II/III colorectal cancer patients. Signature validation has been carried out in two independent datasets and in a meta-cohort of 336 stage II/III patients. Since the 25-gene signature was obtained regardless of gene expression data of tumor specimens or patient’s clinical data, the prognostic power of this signature provides strong evidence of the link between the tumor stroma and cancer progression. Furthermore, the 19-gene signature was able to identify low-risk patients with very high accuracy, especially relevant for those high-risk stage-II patients. We hybridised fibroblast RNA in Affymetrix GeneChip 1.0 st arrays
2013-05-10 | E-GEOD-46824 | biostudies-arrayexpress