Effects of Warm Ischemic Time on Gene Expression Profiling in Colorectal Cancer Tissues and Normal Mucosa

Valeria Musella, Paolo Verderio, James Francis Reid, Sara Pizzamiglio, Manuela Gariboldi, Maurizio Callari, Milione Massimo, Loris De Cecco, Silvia Veneroni, Marco Alessandro Pierotti, Maria Grazia Daidone

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Background: Genome-wide gene expression analyses of tumors are a powerful tool to identify gene signatures associated with biologically and clinically relevant characteristics and for several tumor types are under clinical validation by prospective trials. However, handling and processing of clinical specimens may significantly affect the molecular data obtained from their analysis. We studied the effects of tissue handling time on gene expression in human normal and tumor colon tissues undergoing routine surgical procedures. Methods: RNA extracted from specimens of 15 patients at four time points (for a total of 180 samples) after surgery was analyzed for gene expression on high-density oligonucleotide microarrays. A mixed-effects model was used to identify probes with different expression means across the four different time points. The p-values of the model were adjusted with the Bonferroni method. Results: Thirty-two probe sets associated with tissue handling time in the tumor specimens, and thirty-one in the normal tissues, were identified. Most genes exhibited moderate changes in expression over the time points analyzed; however four of them were oncogenes, and two confirmed the effect of tissue handling by independent validation. Conclusions: Our results suggest that a critical time point for tissue handling in colon seems to be 60 minutes at room temperature. Although the number of time-dependent genes we identified was low, the three genes that already showed changes at this time point in tumor samples were all oncogenes, hence recommending standardization of tissue-handling protocols and effort to reduce the time from specimen removal to snap freezing accounting for warm ischemia in this tumor type.

Original languageEnglish
Article numbere53406
JournalPLoS One
Volume8
Issue number1
DOIs
Publication statusPublished - Jan 15 2013

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Warm Ischemia
Gene Expression Profiling
colorectal neoplasms
Gene expression
mucosa
Colorectal Neoplasms
Mucous Membrane
Tumors
Tissue
gene expression
Genes
neoplasms
oncogenes
Neoplasms
colon
genes
surgery
Oncogenes
Gene Expression
Colon

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Effects of Warm Ischemic Time on Gene Expression Profiling in Colorectal Cancer Tissues and Normal Mucosa. / Musella, Valeria; Verderio, Paolo; Reid, James Francis; Pizzamiglio, Sara; Gariboldi, Manuela; Callari, Maurizio; Massimo, Milione; De Cecco, Loris; Veneroni, Silvia; Pierotti, Marco Alessandro; Daidone, Maria Grazia.

In: PLoS One, Vol. 8, No. 1, e53406, 15.01.2013.

Research output: Contribution to journalArticle

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