Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma

Abstract Background This study aimed to investigate the gene expression changes associated with carcinoma-associated fibroblasts (CAFs) involving in non-small cell lung carcinoma (NSCLC). Methods We downloaded the GEO series GSE22862, which contained matched gene expression values for 15 CAF and...

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Autores principales:	Wu,Xiaofen, Ruan,Lei, Yang,Yi, Mei,Qi
Lenguaje:	English
Publicado:	Sociedad de Biología de Chile 2017
Materias:	Carcinoma-associated fibroblast Non-small cell lung carcinoma Differentially expressed genes Allele-specific copy number Functional analysis
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602017000100204
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spelling	oai:scielo:S0716-976020170001002042017-04-10Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinomaWu,XiaofenRuan,LeiYang,YiMei,Qi Carcinoma-associated fibroblast Non-small cell lung carcinoma Differentially expressed genes Allele-specific copy number Functional analysis Abstract Background This study aimed to investigate the gene expression changes associated with carcinoma-associated fibroblasts (CAFs) involving in non-small cell lung carcinoma (NSCLC). Methods We downloaded the GEO series GSE22862, which contained matched gene expression values for 15 CAF and normal fibroblasts samples, and series GSE27289 containing SNP genotyping for four matched NSCLC samples. The differentially expressed genes in CAF samples were identified using the limma package in R. Then we performed gene ontology (GO) and pathway enrichment analysis and protein–protein interaction (PPI) network construction using the identified DEGs. Moreover, aberrant cell fraction, ploidy, allele-specific copy number, and loss of heterozygosity (LOH) within CAF cells were analyzed using the allele-specific copy number analysis. Results We obtained 545 differentially expressed genes between CAF and normal fibroblasts samples. The up-regulated genes are mainly involved in GO terms such as positive regulation of cell migration and extracellular region, while the down-regulated genes participate in the lung development and extracellular region. Multiple genes including bone morphogenetic protein 4 (BMP4) and transforming growth factor, beta 3 (TGFB3) are involved in the TGF-β signaling pathway. Genes including BMP4, TGFBI and matrix Gla protein (MGP) were hub genes. Moreover, no LOH event for BMP4 and MGP was found, that for sphingosine kinase 1 (SPHK1) was 70%, and for TGFBI was 40%. Conclusion Our data suggested that BMP4, MGP, TGFBI, and SPHK1 may be important in CAFs-associated NSCLC, and the abnormal expression and high LOH frequency of them may be used as the diagnosis targets of CAFs in NSCLC.info:eu-repo/semantics/openAccessSociedad de Biología de ChileBiological Research v.50 20172017-01-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602017000100204en10.1186/s40659-017-0108-9
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Carcinoma-associated fibroblast Non-small cell lung carcinoma Differentially expressed genes Allele-specific copy number Functional analysis
spellingShingle	Carcinoma-associated fibroblast Non-small cell lung carcinoma Differentially expressed genes Allele-specific copy number Functional analysis Wu,Xiaofen Ruan,Lei Yang,Yi Mei,Qi Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma
description	Abstract Background This study aimed to investigate the gene expression changes associated with carcinoma-associated fibroblasts (CAFs) involving in non-small cell lung carcinoma (NSCLC). Methods We downloaded the GEO series GSE22862, which contained matched gene expression values for 15 CAF and normal fibroblasts samples, and series GSE27289 containing SNP genotyping for four matched NSCLC samples. The differentially expressed genes in CAF samples were identified using the limma package in R. Then we performed gene ontology (GO) and pathway enrichment analysis and protein–protein interaction (PPI) network construction using the identified DEGs. Moreover, aberrant cell fraction, ploidy, allele-specific copy number, and loss of heterozygosity (LOH) within CAF cells were analyzed using the allele-specific copy number analysis. Results We obtained 545 differentially expressed genes between CAF and normal fibroblasts samples. The up-regulated genes are mainly involved in GO terms such as positive regulation of cell migration and extracellular region, while the down-regulated genes participate in the lung development and extracellular region. Multiple genes including bone morphogenetic protein 4 (BMP4) and transforming growth factor, beta 3 (TGFB3) are involved in the TGF-β signaling pathway. Genes including BMP4, TGFBI and matrix Gla protein (MGP) were hub genes. Moreover, no LOH event for BMP4 and MGP was found, that for sphingosine kinase 1 (SPHK1) was 70%, and for TGFBI was 40%. Conclusion Our data suggested that BMP4, MGP, TGFBI, and SPHK1 may be important in CAFs-associated NSCLC, and the abnormal expression and high LOH frequency of them may be used as the diagnosis targets of CAFs in NSCLC.
author	Wu,Xiaofen Ruan,Lei Yang,Yi Mei,Qi
author_facet	Wu,Xiaofen Ruan,Lei Yang,Yi Mei,Qi
author_sort	Wu,Xiaofen
title	Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma
title_short	Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma
title_full	Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma
title_fullStr	Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma
title_full_unstemmed	Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma
title_sort	analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma
publisher	Sociedad de Biología de Chile
publishDate	2017
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602017000100204
work_keys_str_mv	AT wuxiaofen analysisofgeneexpressionchangesassociatedwithhumancarcinomaassociatedfibroblastsinnonsmallcelllungcarcinoma AT ruanlei analysisofgeneexpressionchangesassociatedwithhumancarcinomaassociatedfibroblastsinnonsmallcelllungcarcinoma AT yangyi analysisofgeneexpressionchangesassociatedwithhumancarcinomaassociatedfibroblastsinnonsmallcelllungcarcinoma AT meiqi analysisofgeneexpressionchangesassociatedwithhumancarcinomaassociatedfibroblastsinnonsmallcelllungcarcinoma
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Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma

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