Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples.

Zhu J, Deane NG, Lewis KB, Padmanabhan C, Washington MK, Ciombor KK, Timmers C, Goldberg RM, Beauchamp RD, Chen X
Sci Rep. 2016 6: 33273

PMID: 27623752 · PMCID: PMC5021945 · DOI:10.1038/srep33273

Defining molecular features that can predict the recurrence of colorectal cancer (CRC) for stage II-III patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed, Paraffin-Embedded (FFPE). NanoString nCounter® and Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA) are the two platforms marketed for high-throughput gene expression profiling for FFPE samples. In this study, to evaluate the gene expression of frozen tissue-derived prognostic signatures in FFPE CRC samples, we evaluated the expression of 516 genes from published frozen tissue-derived prognostic signatures in 42 FFPE CRC samples measured by both platforms. Based on HTA platform-derived data, we identified both gene (99 individual genes, FDR < 0.05) and gene set (four of the six reported multi-gene signatures with sufficient information for evaluation, P < 0.05) expression differences associated with survival outcomes. Using nCounter platform-derived data, one of the six multi-gene signatures (P < 0.05) but no individual gene was associated with survival outcomes. Our study indicated that sufficiently high quality RNA could be obtained from FFPE tumor tissues to detect frozen tissue-derived prognostic gene expression signatures for CRC patients.

MeSH Terms (13)

Colorectal Neoplasms Disease-Free Survival Female Formaldehyde Gene Expression Regulation, Neoplastic Humans Male Neoplasm Recurrence, Local Oligonucleotide Array Sequence Analysis Paraffin Embedding Prognosis Tissue Fixation Transcriptome

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