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Expression data from human lung FFPE samples

ABSTRACT: Expression data from human lung FFPE samples

PROVIDER: PRJNA870728 | ENA |

REPOSITORIES: ENA

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Expression data from human lung FFPE samples

Project description:Fibrinogen deposition promotes metastasis in lung because fibrinogen binds circulating tumor cells and the fibrinogen-tumor cell complex is allowed to invade in the lung tissue. We used microarrays to compare gene expression profiles of the tissues near and apart from fibrinogen deposition in non-cancer patients and cancer patients.

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Project description:Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. In this study, we investigated the feasibility of gene expression signature generation from archival FFPE materials. Nineteen cervical squamous cell carcinoma (SCC) and nine adenocarcinoma (AC) 10~16-year-old FFPE samples were profiled using Affymetrix Exon 1.0 ST arrays. A comparison of the global gene expression changes between SCC and AC revealed 1217 differentially expressed genes. Of these, 1062 showed significantly higher expression levels in SCC relative to AC, and 155 genes were found to be specifically upregulated in AC. When the 1217-gene signature was tested on a fresh-frozen human non-small cell lung cancer (NSCLC) series, it correctly separated the 58 NSCLC samples into SCC and AC. In conclusion, our results showed that clinically and biologically relevant gene expression profiles can be derived from FFPE samples with Exon array profiling.

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Gene expression profiling of FFPE breast cancer samples [Illumina DASL WG platform]

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