Differential effect of surgical manipulation on gene expression in normal breast tissue and breast tumor tissue.
Author(s): Pedersen IS, Thomassen M, Tan Q, Kruse T, Thorlacius-Ussing O, Garne JP, Krarup HB
Publication: Mol Med, 2018, Vol. 24, Page 57
PubMed ID: 30445902 PubMed Review Paper? No
Purpose of Paper
This paper investigated the effects of warm ischemia on gene expression profiles of normal and tumor breast tissue using Generalized Estimating Equation (GEE) analysis and Gene Set Enrichment Analysis (GSEA).
Conclusion of Paper
A total of 6166 genes were differentially expressed between normal and tumor tissue specimens and 22 pathways were upregulated in tumor tissue compared to normal tissue. For ex vivo biopsy specimens subjected to ~1 h warm ischemia, 3179 differentially expressed genes were identified between normal and tumor tissue and 667 genes were differentially expressed between ex vivo and in situ biopsy specimens (normal and tumor) with significant up-regulation of 29 pathways and down-regulation of 1 pathway in tumor specimens compared to normal specimens and 6 pathways were upregulated in both tumor and normal adjacent specimens after ischemia. Hierarchical clustering of all genes revealed no separation of tumor and normal tissue in in situ biopsy specimens but distinct clustering in ex vivo biopsy specimens subjected to ~1 h warm ischemia.
Studies
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Study Purpose
This study investigated the effects of warm ischemia on gene expression profiles of normal and tumor breast tissue. Biopsy specimens were taken from three female breast cancer patients undergoing radical mastectomy prior to (in situ biopsies) and after surgical resection of the tumor (ex vivo biopsies). In situ biopsies were taken from normal and tumor tissue immediately after anesthesia was administered, while ex vivo biopsies of the resected tumor (one biopsy/case) and normal adjacent tissue (3 biopsies/case) were collected within one hour of the in situ biopsy. The ischemia time reported likely reflects the combined warm and cold ischemia time. All biopsies were snap-frozen in liquid nitrogen and kept at −80°C until RNA extraction with a RNeasy Micro kit. RNA quantity and purity was determined by a Nanodrop spectrophotometer. RNA was amplified using the MessageAmp III RNA amplification kit and hybridized to a Human Genome U133 microarray. Hierarchical clustering of genes was performed using MultiExperiment Viewer and data were investigated using Generalized Estimating Equation (GEE) analysis and Gene set enrichment analysis (GSEA).
Summary of Findings:
GEE analysis of all biopsy specimens (in situ and ex vivo) identified a total of 6166 differentially expressed genes between normal adjacent and tumor tissue specimens with 22 pathways upregulated in tumor tissue compared to normal adjacent tissue, as determined by GSEA analysis. For ex vivo biopsy specimens subjected to ~1 h warm ischemia, 3179 differentially expressed genes were identified between normal adjacent and tumor tissue and 667 of these genes were differentially expressed compared to in situ biopsy specimens (normal and tumor). GSEA analysis revealed significant up-regulation of 29 pathways and down-regulation of 1 pathway in ex vivo tumor specimens when compared to normal adjacent specimens with 6 pathways upregulated in both specimen types after ischemia. Hierarchical clustering of all genes revealed no separation of tumor and normal adjacent tissue among in situ biopsy specimens but distinct clustering among ex vivo specimens subjected to ~1 h warm ischemia.
Biospecimens
Preservative Types
- Frozen
Diagnoses:
- Neoplastic - Normal Adjacent
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform RNA Spectrophotometry RNA DNA microarray Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Preaquisition Warm ischemia time 1 h
0 h
Biospecimen Acquisition Locale of biospecimen collection Tumor tissue
Normal/adjacent tissue