Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples.
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.
Vanderbilt University, Department of Surgery, Nashville, 37232, USA.|Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA.
Jing
J
Zhu
Vanderbilt University, Department of Surgery, Nashville, 37232, USA.|Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA.
Natasha G
NG
Deane
Vanderbilt University, Department of Surgery, Nashville, 37232, USA.
Keeli B
KB
Lewis
Vanderbilt University, Department of Surgery, Nashville, 37232, USA.
Chandrasekhar
C
Padmanabhan
Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA.|Vanderbilt University, Department of Pathology, Nashville, 37232, USA.
M Kay
MK
Washington
The Ohio State University Comprehensive Cancer Center, Columbus, 43210, USA.|Ohio State University, Division of Medical Oncology, Department of Internal Medicine, Columbus, 43210, USA.
Kristen K
KK
Ciombor
The Ohio State University Comprehensive Cancer Center, Columbus, 43210, USA.
Cynthia
C
Timmers
The Ohio State University Comprehensive Cancer Center, Columbus, 43210, USA.|Ohio State University, Division of Medical Oncology, Department of Internal Medicine, Columbus, 43210, USA.
Richard M
RM
Goldberg
Vanderbilt University, Department of Surgery, Nashville, 37232, USA.|Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA.|Vanderbilt University, Department of Cell and Developmental Biology, Nashville, 37232, USA.|Vanderbilt University, Department of Cancer Biology, Nashville, 37232, USA.
R Daniel
RD
Beauchamp
University of Miami Miller School of Medicine, Division of Biostatistics, Department of Public Health Sciences, Miami, 33136, USA.|University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, 33136, USA.
Xi
X
Chen
D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D018572:Disease-Free Survival; D005260:Female; D005557:Formaldehyde; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D008297:Male; D009364:Neoplasm Recurrence, Local / Q000235:genetics* / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016612:Paraffin Embedding; D011379:Prognosis; D016707:Tissue Fixation; D059467:Transcriptome / Q000235:genetics*
D005557:Formaldehyde