DNA microarrays identification of primary and secondary target genes regulated by p53

Abstract

The transcriptional program regulated by the tumor suppressor p53 was analysed using oligonucleotide microarrays. A human lung cancer cell line that expresses the temperature sensitive murine p53 was utilized to quantitate mRNA levels of various genes at dierent time points after shifting the temperature to 328C. Inhibition of protein synthesis by cycloheximide (CHX) was used to distinguish between primary and secondary target genes regulated by p53. In the absence of CHX, 259 and 125 genes were up or down-regulated respectively; only 38 and 24 of these genes were up and down-regulated by p53 also in the presence of CHX and are considered primary targets in this cell line. Cluster analysis of these data using the super paramagnetic clustering (SPC) algorithm demonstrate that the primary genes can be distinguished as a single cluster among a large pool of p53 regulated genes. This procedure identi®ed additional genes that co-cluster with the primary targets and can also be classi®ed as such genes. In addition to cell cycle (e.g. p21, TGF-b, Cyclin E) and apoptosis (e.g. Fas, Bak, IAP) related genes, the primary targets of p53 include genes involved in many aspects of cell function, including cell adhesion (e.g. Thymosin, Smoothelin), signaling (e.g. H-Ras, Diacylglycerol kinase), transcription (e.g. ATF3, LISCH7), neuronal growth (e.g. Ninjurin, NSCL2) and DNA repair (e.g. BTG2, DDB2). The results suggest that p53 activates concerted opposing signals and exerts its eect through a diverse network of transcriptional changes that collectively alter the cell phenotype in response to stress.

Deregulated expression of pro-survival and pro-apoptotic p53-dependent genes upon Elongator deficiency in colon cancer cells

“…3A, top panels, compare lanes 3 and 4 and lanes 7 and 8, respectively). Some genes such as tumor necrosis factor receptor superfamily, member 10D (TNFRSF10D), sestrin 2 (SESN2), and BTG family member 2 (BTG2) are known to be induced by a genotoxic stress through a p53-dependent pathway [28] and both our micro-array analysis and our real-time PCR experiments indeed confirmed that these genes were induced upon 2 h of daunomycin treatment in HCT116 cells (Fig. 3B, on the left).…”

Analysis of p53/BAX in primary colorectal carcinoma: Low BAX protein expression is a negative prognostic factor in UICC stage III tumors

“…The p53 gene is a transcriptional regulator and transactivator of a growing number of specific genes implicated in the regulation of cell cycle and apoptosis. 3,36 Mutations in the p53 gene can be detected in up to 50% of various cancer entities. 37 A considerable number of studies have been performed with regard to the p53 status and its correlation to prognosis or therapeutical response in colorectal cancer.…”

Cellular response to oxidative stress: Signaling for suicide and survival*

“…These include Bax, a pro-apoptotic Bcl-2 family member (Miyashita et al, 1994), several mitochondrial proteins, Noxa, (Oda et al, 2000a), p53AIP1 (p53-regulated-apoptosis-inducing protein 1) (Oda et al, 2000b), and PUMA (p53-upregulated modulator of apoptosis) (Nakano and Vousden, 2001;Yu et al, 2001), and several genes associated with death receptor-mediated apoptosis, Fas, Killer/DR5, and PIDD (Lin et al, 2000;Wu et al, 2000). There does not appear to be a single gene that is the principal mediator of p53-induced apoptosis, but rather the response involves the activation of several apoptotic genes (Sionov and Haupt, 1999;Ryan et al, 2000;Kannan et al, 2001). In addition, there is much overlap in the pattern of genes regulated by p53 whether it results in growth arrest or apoptosis.…”