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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:Formalin-fixed, paraffin-embedded (FFPE) is the most common method for preserving tissue material in the clinic with millions of specimens stored in biobanks around the world. However, FFPE samples present challenges for molecular profiling, including proteomics. Nonetheless, optimized sample preparation protocols and next-generation mass spectrometers (MS) enable the analysis of FFPE samples. Here, we analyze 15 FFPE lung cancer specimens, including resected tissue and biopsies using label-free data-independent acquisition (DIA) MS proteomics. We show data from three instruments, including Orbitrap Astral, timsTOF HT, and Orbitrap Exploris. Our analysis shows that label-free proteomics offers rapid, in-depth, reproducible proteome-wide profiling of FFPE tissue samples.

2026-05-26 | PXD071948 | Pride

Gene expression profiling of human DLBCL tumor samples (FF and FFPE pairs)

Project description:We profiled human DLBCL tumor samples (FF and FFPE matched pairs) to identify the transcripts which are less prone to degradation in FFPE Keywords: DLBCL FF FFPE

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Label-free mass spectrometry-based proteomics of lung cancer FFPE glass slides

Project description:Formalin-fixed, paraffin-embedded (FFPE) is the most common method for preserving tissue material in the clinic with millions of specimens stored in biobanks around the world. However, FFPE samples present challenges for molecular profiling, including proteomics. Nonetheless, optimized sample preparation protocols and next-generation mass spectrometers (MS) enable the analysis of FFPE samples. Here, we analyze 68 FFPE lung cancer biopsies on single glass slides using label-free data-independent acquisition (DIA) MS proteomics. We show data from two instruments, Orbitrap Astral and timsTOF HT. Our analysis shows that label-free proteomics offers rapid, in-depth, reproducible proteome-wide profiling of FFPE tissue samples.

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DNA methylation of human FFPE meningioma samples

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DNA methylation of human FFPE meningioma samples

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Exon-array profiling of squamous cell carcinoma and adenocarcinoma in human cervical FFPE samples

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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