Development and Independent Validation of a Prognostic Assay for Stage II Colon Cancer Using Formalin-Fixed Paraffin-Embedded Tissue

Kennedy, Richard D.; Bylesjö, Max; Kerr, Peter; Davison, Timothy S.; Black, Julie M.; Kay, Elaine W.; Holt, Robert J.; Proutski, Vitali; Ahdesmäki, Miika J.; Farztdinov, V. M.; Goffard, Nicolas; Hey, Peter; McDyer, F; Mulligan, Karl; Mussen, Julie; O’Brien, Eamonn; Oliver, Gavin R.; Walker, Steven M.; Mulligan, Jude M.; Wilson, Claire; Winter, Andreas; O’Donoghue, Diarmuid; Mulcahy, Hugh; O'Sullivan, Jacintha; Sheahan, Kieran; Hyland, John; Dhir, Rajiv; Bathe, Oliver F.; Winqvist, Ola; Manne, Upender; Shanmugam, Chandrakumar; Ramaswamy, Sridhar; Leon, Eduardo J.; Smith, William I.; McDermott, Ultan; Wilson, Richard H.; Longley, Daniel B.; Marshall, John L.; Cummins, Robert; Sargent, Daniel J.; Johnston, Patrick G.; Harkin, D. Paul

doi:10.1200/jco.2011.35.4498

Cited by 176 publications

(152 citation statements)

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“…Amplified products were hybridized to the Almac Colorectal Cancer DSA microarray platform (Almac, Craigavon, United Kingdom; ref. 40). Following quality control, TOP1 mRNA expression data were available for a total of 688 unique samples, including 580 from patients with stage III disease.…”

Section: Top1 Mrna Expressionmentioning

confidence: 99%

DNA Topoisomerase I Gene Copy Number and mRNA Expression Assessed as Predictive Biomarkers for Adjuvant Irinotecan in Stage II/III Colon Cancer

Nygård

Vainer

Nielsen

et al. 2016

Clinical Cancer Research

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Purpose: Prospective-retrospective assessment of the TOP1 gene copy number and TOP1 mRNA expression as predictive biomarkers for adjuvant irinotecan in stage II/III colon cancer.Experimental Design: Formalin-fixed, paraffin-embedded tissue microarrays were obtained from an adjuvant colon cancer trial (PETACC3) where patients were randomized to 5-fluorouracil/folinic acid with or without additional irinotecan. TOP1 copy number status was analyzed by fluorescence in situ hybridization (FISH) using a TOP1/CEN20 dual-probe combination. TOP1 mRNA data were available from previous analyses.Results: TOP1 FISH and follow-up data were obtained from 534 patients. TOP1 gain was identified in 27% using a singleprobe enumeration strategy (4 TOP1 signals per cell) and in 31% when defined by a TOP1/CEN20 ratio 1.5. The effect of additional irinotecan was not dependent on TOP1 FISH status. TOP1 mRNA data were available from 580 patients with stage III disease. Benefit of irinotecan was restricted to patients characterized by TOP1 mRNA expression third quartile (RFS: HR adjusted , 0.59; P ¼ 0.09; OS: HR adjusted , 0.44; P ¼ 0.03). The treatment by TOP1 mRNA interaction was not statistically significant, but in exploratory multivariable fractional polynomial interaction analysis, increasing TOP1 mRNA values appeared to be associated with increasing benefit of irinotecan.Conclusions: In contrast to the TOP1 copy number, a trend was demonstrated for a predictive property of TOP1 mRNA expression. On the basis of TOP1 mRNA, it might be possible to identify a subgroup of patients where an irinotecan doublet is a clinically relevant option in the adjuvant setting of colon cancer. Clin Cancer Res; 22(7); 1621-31. Ó2015 AACR.

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Section: Top1 Mrna Expressionmentioning

confidence: 99%

DNA Topoisomerase I Gene Copy Number and mRNA Expression Assessed as Predictive Biomarkers for Adjuvant Irinotecan in Stage II/III Colon Cancer

Nygård

Vainer

Nielsen

et al. 2016

Clinical Cancer Research

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“…After isothermal amplification, 50 or 100 ng of total RNA was amplified to 4 to 7 mg of biotinylated cDNA complementary to the original mRNA. The amplification step has been optimized for RNA extracted from FFPE specimens 15,16 and has shown comparable differential expression profiles to corresponding fresh-frozen tissues. 17 After amplification, we hybridized 3.75 mg of amplified cDNA to the GeneChip Human Gene 1.0 ST Array (Affymetrix).…”

Section: Messenger Rna Expression Profiling Arraymentioning

confidence: 99%

Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues

Tyekucheva

Martin

Stack

et al. 2015

The Journal of Molecular Diagnostics

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Archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a readily available but largely untapped resource for gene expression profilingebased biomarker discovery. Several technologies have been proposed to cope with the bias from RNA cross-linking and degradation associated with archival specimens to generate data comparable with RNA from fresh-frozen materials. Direct comparison studies of these RNA expression platforms remain rare. We compared two commercially available platforms for RNA expression profiling of archival FFPE specimens from clinical studies of prostate and ovarian cancer: the Affymetrix Human Gene 1.0ST Array following whole-transcriptome amplification using the NuGen WT-Ovation FFPE System V2, and the NanoString nCounter without amplification. For each assay, we profiled 7 prostate and 11 ovarian cancer specimens, with a block age of 4 to 21 years. Both platforms produced gene expression profiles with high sensitivity and reproducibility through technical repeats from FFPE materials. Sensitivity and reproducibility remained high across block age within each cohort. A strong concordance was shown for the transcript expression values for genes detected by both platforms. We showed the biological validity of specific gene signatures generated by both platforms for both cohorts. Our study supports the feasibility of gene expression profiling and large-scale signature validation on archival prostate and ovarian tumor specimens using commercial platforms. These approaches have the potential to aid precision medicine with biomarker discovery and validation. (J Mol Diagn 2015, 17: 374e381; http://dx

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“…On the basis of a different prognostic assay, Kennedy and colleagues (29) reported that the 634-probes signature used in the ColDx test (Almac Diagnostics) also had the ability to discriminate risk of recurrence in patients with stage II colon cancer (HR ¼ 2.53; P ¼ 0.003). However, these findings did not account for the MMR characterization, and the sample size of the validation set was limited and enriched for recurrence (29). The relative merit of enhanced nodal characterization versus genomic profiling of the primary tumor is a critical question for future study.…”

Section: Discussionmentioning

confidence: 99%

“…During the last few years, gene signatures have been developed from FFPE tumor samples to identify patients with stage II colon cancer who are at higher risk of disease recurrence (28)(29)(30)(31)(32). The study by Gray and colleagues (28) was designed as a validation study based on prospectively specified retrospective analyses of the QUASAR (QUick And Simple And Reliable) trial.…”

Section: Discussionmentioning

confidence: 99%

Molecular Testing for Lymph Node Metastases as a Determinant of Colon Cancer Recurrence: Results from a Retrospective Multicenter Study

Sargent¹,

Gill

Louvet³

et al. 2014

Clinical Cancer Research

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Purpose: Recurrence risk assessment to make treatment decisions for early-stage colon cancer patients is a major unmet medical need. The aim of this retrospective multicenter study was to evaluate the clinical utility of guanylyl cyclase C (GCC) mRNA levels in lymph nodes on colon cancer recurrence.Methods: The proportion of lymph nodes with GCC-positive mRNA (LNR) was evaluated in 463 untreated T3N0 patients, blinded to clinical outcomes. One site's (n ¼ 97) tissue grossing method precluded appropriate lymph node assessment resulting in post hoc exclusion. Cox regression models tested the relationship between GCC and the primary endpoint of time to recurrence. Assay methods, primary analyses, and cut points were all prespecified.Results: Final dataset contained 366 patients, 38 (10%) of whom had recurrence. Presence of four or more GCC-positive lymph nodes was significantly associated with risk of recurrence [hazard ratio (HR) ¼ 2.46, 95% confidence interval (CI), 1.07-5.69, P ¼ 0.035], whereas binary GCC LNR risk class (HR ¼ 1.87, 95% CI, 0.99-3.54, P ¼ 0.054) and mismatch repair (MMR) status (HR ¼ 0.77, 95% CI, 0.36-1.62, P ¼ 0.49) were not. In a secondary analysis using a 3-level GCC LNR risk group classification of high (LNR > 0.20), intermediate (0.10 < LNR 0.20), and low (LNR 0.10), high-risk patients had a 2.5 times higher recurrence risk compared with low-risk patients (HR ¼ 2.53, 95% CI, 1.24-5.17, P ¼ 0.011).Conclusions: GCC status is a promising prognostic factor independent of traditional histopathology risk factors in a contemporary population of patients with stage IIa colon cancer not treated with adjuvant therapy, but GCC determination must be performed with methodology adapted to the tissue procurement and fixation technique.

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Development and Independent Validation of a Prognostic Assay for Stage II Colon Cancer Using Formalin-Fixed Paraffin-Embedded Tissue

Abstract: This gene signature represents a novel prognostic biomarker for patients with stage II colon cancer that can be applied to FFPE tumor samples.

Cited by 176 publications

References 27 publications

DNA Topoisomerase I Gene Copy Number and mRNA Expression Assessed as Predictive Biomarkers for Adjuvant Irinotecan in Stage II/III Colon Cancer

DNA Topoisomerase I Gene Copy Number and mRNA Expression Assessed as Predictive Biomarkers for Adjuvant Irinotecan in Stage II/III Colon Cancer

Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues

Molecular Testing for Lymph Node Metastases as a Determinant of Colon Cancer Recurrence: Results from a Retrospective Multicenter Study

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