Expression Genomics and p53 Biology
Systems biology seeks to explain biologic phenomenon through the net interactions of all cellular and biochemical components within a cell or organism. We present work that uses a systems approach to build the framework for predictive pharmacology. We used as a model system, the p53 transcriptional response in vitro and in human tumors. First, we analyzed transcript profiles in 251 primary breast cancers in which the p53 gene had been sequenced and identified a clinically embedded 32-gene expression signature that distinguishes p53-mutant and wild-type tumors that outperforms p53 sequencing. Thus, the transcriptional fingerprint is a more definitive downstream indicator of p53 function. Second, we identified a unique role for GSK-3beta in regulating p53 function in human colorectal cancer cells. Pharmacologic modulation of GSK-3beta markedly impaired p53-dependent transactivation of targets including p21 and Puma but promoted p53-dependent conformational activation of Bax leading to apoptosis. Thus, the cell cycle arrest after p53-mediated damage response is converted to apoptosis following exposure to a variety of chemotherapeutic agents (Tan, et al. Cancer Res. 65(19):9012-20). The success of this compound will depend on a reliable assessment of p53 status in primary tumors. Based on these observations, we sought to identify the precise mechanisms of p53 gene regulation by developing a robust approach that couples chromatin immunoprecipitation (ChIP) with the paired-end ditag (PET) sequencing strategy for unbiased and precise global localization of p53 binding sites. From a saturated sampling of over half a million PET sequences, we characterized 65,572 unique p53 ChIP DNA fragments and established overlapping PET clusters as a readout to define p53 binding loci with remarkable specificity. Based on this information, we refined the consensus p53 binding motif, identified at least 542 binding loci with high confidence, discovered 98 previously unidentified p53 target genes that were implicated in novel aspects of p53 functions such as cell adhesion and motility. Finally, we showed their clinical relevance to p53-dependent tumorigenesis in primary cancer samples (Wei CL, et al. Cell. 124(1):207-19).