Array-Based Quantitative Nuclease Protection Assay Can Reproducibly Identify Prognostic mRNA Biomarkers in Archival Mantle Cell Lymphoma Specimens
David T Yang, Matthew J Maurer, Rebecca F McClure, Mai Ming, Brian Link, Thomas M Habermann, Gene R Shaw, James R Cerhan, Brad S Kahl, Ahmet Dogan. University of Wisconsin, Madison, WI; Mayo Clinic, Rochester, MN; University of Iowa, Iowa City, IA; Marshfield Clinic, Marshfield, WI
Background: Gene expression profiling has identified several potential prognostic biomarkers in mantle cell lymphoma (MCL), a B-cell lymphoma with a variable clinical course from indolent to aggressive. However, technical limitations have hampered the translation of these findings into the clinical laboratory. Array based quantitative nuclease protection assay (qNPA) can assess gene expression in formalin-fixed paraffin-embedded (FFPE) tissue in a simple, robust manner and has potential for clinical assay development. We determined the ability of qNPA to identify prognostic mRNA biomarkers in routinely processed FFPE biopsies of MCL.
Design: Expression of 42 genes with potential prognostic significance was analyzed using qNPA in a plate based, low density format on FFPE tissue on a discovery cohort of 57 patients. Gene expression was normalized to two housekeeping genes, TBP and B2M. Cox proportional hazards models were used to assess association between individual gene expression and progression free survival (PFS). Results were validated on an independent cohort of 32 patients with a meta-analysis approach for combined results between discovery and replication cohorts.
Results: Expression of the 42 genes on the panel distinguished MCL (black) from control cases representing a variety proliferative indices using unsupervised clustering (Figure 1). 11 genes (26%) were associated with PFS (p<0.1) in the discovery cohort (Figure 2). Three of these genes (MYC, HPRT1, CDKN2A) were prognostically significant in the validation cohort (p<0.05) and an additional 3 genes (TNFRSF10B, ASPM, and SOX11) were significant in the pooled meta-analysis.
Conclusions: Array based qNPA can be utilized to develop a prognostic MCL gene expression assay with potential for adoption by the clinical laboratory.
Tuesday, March 5, 2013 9:30 AM
Poster Session III # 164, Tuesday Morning