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Analysis of Cancer Proteome via Mass Spectrometry January 7 , 2007 1 Background and Significance

Tumor genomes accumulate a large number of rearrangements many of which contribute to tumor progression and lead to formation of novel fusion genes resulting in oncogenic activities (Gray and Collins 2000 [1]). Identification of fusion genes has contributed significantly to our understanding of cancer progression , yielding important predictive markers and targets for therapeutic intervention such as BCR-ABL, ERBB2, and TP53 (Ehrlich 2000 [2]). Indeed, the successful anti-leukemia drug STI-571 was designed to abrogate the aberrant activity of the BCR-ABL fusion protein resulting from the Philadelphia chromosome translocation. The breast cancer therapeutic Herceptin was designed to counteract the activity of the HER2-ERBB2 gene. STI-571 and Herceptin are examples where knowledge of fusion genes translated to therapeutics. We remark that these fusion genes can be potentially identified by a single tandem mass spectrometry (MS/MS) experiment provided there exist computational tools that are able to interpret mass-spectra from fusion proteins. Therefore, the MS-based computational approaches for the identification of fusion proteins are crucial to the understanding of tumor biology and the identification of tumor biomarkers. Rearrangements exert their oncogenic effect by disruption of genes at rearrangement breakpoints (Ar-tandi et al. 2000 [3]). Understanding of cancer is predicated upon knowledge of the architecture of malignant genomes that accumulate a large number of genome rearrangements during tumorigenesis. Despite breath-taking progress made in genomics, sequence-based analysis of tumor genomes architectures was nearly impossible, or, at best, extremely laborious until very recently (Volik et al., 2003 [4]). While recent studies suggest that the known fusion proteins in solid tumors are likely to represent only a tip of an iceberg (Mitel-man et al. 2004), SKY and other low-resolution technologies are limited to cytogenetic resolution for the localization of tumor genome breakpoints. Collins's lab (UCSF) recently developed End Sequence Profiling (ESP) approach that maps genome breakpoints associated with genome rearrangements elucidating the structural organization of tumor genomes (Volik et al., 2006 [5]) that recently enabled development of new computational tools for fine-scale analysis of tumor genome [6, 7]. Volik et al., 2006 [5] further demonstrated how putative genome breakpoints identified by ESP can be confirmed experimentally and extended ESP to the transcriptome (tESP). In the last year, other fine-scale techniques for interrogating cancer genomes emerged, most notably the PET technology developed at the Genomic Institute of Singapore [8] and the Solexa array platform. The key advantage of ESP over other competing high-throughput tumor interrogation techniques is the " …