Differential Chromosomal Copy Number Variations in Chromophobe Renal Cell Carcinoma and Oncocytoma Using High Resolution SNP Array.
Somak Roy, Amber H Hughes, Gaurav Sharma, Maureen A Lyons, Michael J Krill-Burger, Lori A Kelly, Anil V Parwani, Sheldon Bastacky, William A LaFramboise, Rajiv Dhir. UPMC, Pittsburgh, PA
Background: Chromophobe renal cell carcinoma (ChRCC) and oncocytoma (Onc) are biologically distinct renal tumors; however subsets of these tumors exhibit overlapping morphological and immunohistochemical features. High-density single nucleotide polymorphism (SNP) arrays allow genome-wide interrogation of chromosome copy number variation (CNV) and loss-of-heterozygosity at resolutions of 1-2kb. This study investigates CNV in these tumors to identify molecular changes as potential discriminants between these RCC classes.
Design: Five ChRCCs and 4 Onc with classic histologic features and non-neoplastic renal tissue from nephrectomy specimens were evaluated. DNA was purified from flash-frozen specimens. Five hundred nanograms were cut with restriction endonuclease Nsp I or Sty I followed by adaptor ligation and PCR based whole genome amplification. PCR products were purified, fragmented, denatured, labeled and hybridized to Affymetrix 6.0 SNP arrays. Results were processed to detect CNV using Genotype Console and Partek Genomics Suite (hMM modeling) to derive results between tumor and normal samples and in comparison to an in-house reference library of normal tissues (n=10).
Results: The analysis revealed significant CNV changes affecting 6116 genes in ChRCC as compared to 721 genes in Onc samples. In the ChRCCs, there was a predominance of deletions (83%, 441 CNV) over amplifications (17%, 88 CNV) detected in at least 3 of the 5 specimens. These deletions were specifically clustered on chromosomes 1 (267 CNV) and 10 (174 CNV) only, signifying loss of large portions of these structures. The amplifications were fewer and distributed among chromosomes 4, 5, 7, 8, 11, 12, 14, 15, 16, 20 and 22. In contrast, Onc demonstrated amplifications in chromosomes 2, 4, 5, 6, 7, 10, 12, 18, and 21 but at a lower frequency compared to ChRCC specimens. Unlike ChRCC, deletions in Onc specimens were atypical and unshared across this tumor class.
Conclusions: The distinct patterns of CNV including the large numbers associated with ChRCC compared to Onc may reflect different mechanisms of tumorigenesis. The prominent deletions in chromosomes 1 and 10 were specifically seen in ChRCCs. Furthermore, the amplifications were mainly clustered in chromosomes 12, 15 and 22 in ChRCCs, in contrast to Onc. These findings support the hypothesis of significant differences in the pattern of gain and loss of genetic material in the two tumor groups which can be potentially exploited to establish clinically useful diagnostic markers and identify therapeutic targets.
Category: Genitourinary (including renal tumors)
Monday, February 28, 2011 9:30 AM
Poster Session I Stowell-Orbison/Surgical Pathology/Autopsy Awards Poster Session # 107, Monday Morning