Abstract 247: A functional genomics and a systems biology approach identify POMP as a potential therapeutic target for colorectal cancer
Authors: Camps Jordi , Hummon Amanda H. , Emons Georg , Kramer Frank , Pitt Jason J. , Grade Marian , Nguyen Quang T. , Ghadimi B. Michael , Difilippantonio Michael J. , Beissbarth Tim , Caplen Natasha J. , Ried Thomas 
Published: February 2011

Abstract
Colorectal cancer (CRC) is one of the most frequent malignancies in many parts of the world and a leading cause of cancer deaths in both men and women. The identification of rationale therapeutic targets is one possibility to provide personalized medicine to cancer patients. Our approach consisted of identifying overexpressed genes located at sites of recurrent chromosomal amplifications, as these regions are likely to harbor genes required for cancer cell survival. Thirty-one colon cancers and 15 CRC cell lines were analyzed by high-resolution array CGH and microarray gene expression profiling. RNA interference (RNAi)-based analysis identified a subset of genes whose loss-of-function (LOF) reduced the cellular viability of CRC cell lines. Consistent with previous reports, the vast majority of CRC assayed exhibited amplification of the chromosome band 13q12.13-q12.3. Among the genes residing within the 13q12.13-q12.3 amplified region showing an overexpression level of at least two-fold higher in the tumor compared to normal mucosa and whose gene silencing impaired cellular survival, we identified NUPL1, LNX2, POLR1D, CDX2, POMP, and SLC7A1. As little is know of the function of these proteins, we decided to use an unbiased systems biology approach to identify genes, pathways and networks altered following RNAi-mediated LOF of each of these candidate genes. To do this we perturbed the expression of each candidate gene through application of two or more siRNAs corresponding to each gene, followed by whole genome expression profiling to monitor cellular transcriptional responses to gene specific LOF. Concordant gene expression signatures generated using three different RNAi effectors targeting POMP, over a time-course (10, 24, 48, and 72 hours), showed that a decrease in POMP expression of more than 80% at 24 hours initially resulted in only minor downstream changes in gene expression. However, by 48 hours approximately 100 genes exhibited altered expression and by 72 hours nearly 2000 genes. At this last time point a statistically significant enrichment (p&lt;0.05) for the altered expression of genes linked to the gene ontologies of cancer, cell death, and cellular growth was observed. POMP, a proteasome maturation protein, is an essential factor for mammalian proteasome biogenesis. This dynamic loss-of-function approach revealed a regulatory network that controls the transcriptional response of colorectal cancer cells after impairing the function of the proteasome. We are also investigating whether the gene expression profiles observed following silencing of POMP resemble the transcriptomic changes that undergo cells treated with proteasome inhibitors as this may shed further light on the mechanism of action of this new class of anti-cancer drugs particularly in CRC.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 247.