Comparative Quantitation of Lymphoma Gene Signatures in Parallel FormalinFixed Paraffin Embedded and Frozen Tissue Lymph Nodes

Abstract Microarray gene expression profiling of frozen samples has identified Indicator genes predictive outcome in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) and there is a now a need to translate these to use in routine clinical material. In order to evaluate the use of Indicator genes as a diagnostic tool in routinely processed formalin fixed paraffin embedded tissue (FFPET), we used a simple, practical polyA PCR based method for analysis of Indicator genes in DLBCL and FL, using parallel FFPET and frozen tissue lymph nodes. PolyA PCR was used to generate polyA cDNAs from 42 archival FFPET lymph nodes and 42 parallel frozen tissue lymph nodes. These polyA cDNAs were assayed by real-time PCR for 35 Indicator genes, identified from previous microarray studies, predictive of outcome in FL and DLBCL, together with housekeeping genes. Housekeeping genes were detectable at high levels in all cases, though the 35 Indicator genes were expressed at lower levels. There was statistically significant difference in gene expression between DLBCL and FL for one of the Indicator genes, HSP27 (p ≤ 0.02). There was no correlation between the Indicator gene expression levels in the FFPET and frozen lymph nodes. The results demonstrate that gene expression in FFPET is altered from that in frozen tissue and that gene expression data from frozen tissue is therefore not transferable for use in FFPET.