Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Illumina methylation EPIC arrays of human blood at baseline and after 18 months of dietary interventions

ABSTRACT: To highlight molecular mechanisms underlying the beneficial metabolic effects of a Mediterranean (MED) diet, a MED diet enriched in polyphenols and reduced in red/processed meat (greenMED), and a diet with healthy dietary guidelines (HDG), we analyzed their effects on the methylome in the 18-month DIRECT PLUS randomized controlled trial. The methylation arrays contains individuals from the three intervention arms (MED, greenMED, HDG) for baseline (T0). We will gladly provide further metadata upon request.

ORGANISM(S): Homo sapiens

SUBMITTER: Anne Hoffmann

PROVIDER: E-MTAB-12527 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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. This SuperSeries is composed of the following subset Series: GSE22862: Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [expression profiling_CAFs] GSE22863: Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [expression profiling_NSCLC stroma] GSE27284: Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [methylation profiling] GSE27289: Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [genome variation profiling]

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Illumina methylation EPIC arrays of human blood at baseline and after 18 months of dietary interventions

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