Affymetrix Genechip Microarray Analysis of Renal Cell Carcinoma in Formalin Fixed Paraffin Embedded Tissue.
Kevin Fisher, Andrew N Young, Qiqin Yin-Goen, Adeboye O Osunkoya. Emory University Scool of Medicine, Atlanta
Background: The classification of RCC is important because the different subtypes are associated with distinct clinical behavior, and patients may benefit from type-specific therapeutic modalities. Previously, we used high-density microarrays to discover biomarker profiles for diagnostic classification, characterized by differential expression in RCC subtypes. However, high-density arrays are difficult to apply for clinical diagnosis due to cost, complexity and challenges with quality control. In this study, we tested the utility of Ziplex(R) Tipchip arrays (Xceed Molecular/Axela) for diagnostic classification of renal cell carcinoma (RCC) in formalin fixed paraffin embedded tissue. The Ziplex platform is designed to enable array-based testing in clinical laboratories; it is an integrated system for simple, automated hybridization to Tipchips containing ∼100 probes, followed by automated imaging in the same instrument.
Design: Gene expression was measured in formalin fixed paraffin embedded tissue from different RCC subtypes using custom Tipchip arrays, containing ∼100 biomarkers identified from our previous study using high-density arrays. The renal tumors (6 cases of clear cell RCC, 3 cases of papillary RCC, and 6 cases of chromophobe RCC) were analyzed. Total RNA was extracted from the tumors, and cRNA was synthesized and hyridized to Ziplex(R) arrays. Results were normalized against the Geomean of 44 controls genes shown to be relatively invariant among the RCC subtypes.
Results: Most biomarkers on the Ziplex(R) arrays showed gene expression patterns among the RCC subtypes that were similar to our previous results in formalin fixed paraffin embedded tissue. The following diagnostic gene expression patterns were verified with the Ziplex(R) platform: Clear cell RCC overexpressed CA9, CAV1, CP, CXCR4, IL10RA, LY6E, NNMT, PLIN2 / ADPF, TGFB1 and vimentin; Papillary RCC over expressed AMACR, BAMBI, LAMB1, SCHIP1, SLC34A2;and Chromophobe RCC over expressed ACAT1, ACSL1, BLNK, CLDN8, COX5A, BDF1, GOT1, KIT, PVALB, and SLC25A4.
Conclusions: Our study demonstrates that Affymetrix Genechip microarray analysis can be utilized in the subtyping of RCC with comparable results in formalin fixed paraffin embedded tissue. This technology delivers similar results with high-density microarrays in formalin fixed paraffin embedded tissue, and lacks the complexity and quality control challenges encountered with high-density microarrays.
Category: Genitourinary (including renal tumors)
Wednesday, March 2, 2011 9:30 AM
Poster Session V # 98, Wednesday Morning