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Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma
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 fib...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322592/ https://www.ncbi.nlm.nih.gov/pubmed/28231844 http://dx.doi.org/10.1186/s40659-017-0108-9 |
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author | Wu, Xiaofen Ruan, Lei Yang, Yi Mei, Qi |
author_facet | Wu, Xiaofen Ruan, Lei Yang, Yi Mei, Qi |
author_sort | Wu, Xiaofen |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5322592 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-53225922017-03-01 Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma Wu, Xiaofen Ruan, Lei Yang, Yi Mei, Qi Biol Res Research Article 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. BioMed Central 2017-02-23 /pmc/articles/PMC5322592/ /pubmed/28231844 http://dx.doi.org/10.1186/s40659-017-0108-9 Text en © The Author(s) 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article 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 |
title | 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_short | 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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322592/ https://www.ncbi.nlm.nih.gov/pubmed/28231844 http://dx.doi.org/10.1186/s40659-017-0108-9 |
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