Identification of Target Genes of the p16INK4A-pRB-E2F Pathway

Abstract

Deregulation of the retinoblastoma protein (pRB) pathway is a hallmark of human cancer. The core members of this pathway include the tumor suppressor protein, pRB, which through binding to a number of cellular proteins, most notably members of the E2F transcription factor family, regulates progression through the cell division cycle. With the aim of identifying transcriptional changes provoked by deregulation of the pRB pathway, we have used cell lines that conditionally express a constitutively active phosphorylation site mutant of pRB (pRB⌬CDK) or p16 INK4A (p16). The expression of pRB⌬CDK and p16 resulted in significant repression and activation of a large number of genes as measured by high density oligonucleotide array analysis. Transcriptional changes were found in genes that are essential for DNA replication and cell proliferation. In agreement with previous results, we found a high degree of overlap between genes regulated by p16 and pRB. Data we have obtained previously for E2F family members showed that 74 of the genes repressed by pRB and p16 were induced by the E2Fs and 23 genes that were induced by pRB and p16 were repressed by the E2Fs. Thus, we have identified 97 genes as physiological targets of the pRB pathway, and the further characterization of these genes should provide insights into how this pathway controls proliferation. We show that Gibbs sampling detects enrichment of several sequence motifs, including E2F consensus binding sites, in the upstream regions of these genes and use this enrichment in an in silico filtering process to refine microarray derived gene lists.

Diffuse large B-cell lymphomas with CDKN2A deletion have a distinct gene expression signature and a poor prognosis under R-CHOP treatment: a GELA study

“…Using a global testing approach, a significant enrichment of genes regulated by the p16inka/pRb/E2F pathway in U-2 OS cells 28 as well as those containing E2F binding sites 29 was observed in DLBCL 9p21del cases ( Figure 6A). These sets of genes were highly expressed in DLBCL 9p21del , indicating that the GEP of DLBCL 9p21del is at least partially related to the loss of RB1 regulation and to the release of its downstream targets.…”

VRK1 Signaling Pathway in the Context of the Proliferation Phenotype in Head and Neck Squamous Cell Carcinoma

“…VRK1 expression is also activated by E2F and inhibited by p16 and nonphosphorylated retinoblastoma (Rb; ref. 21). VRK1 has a serine/threonine kinase activity and phosphorylates several transcription factors, including human p53 (22), and can also cooperate with the c-Jun NH 2 -terminal kinase pathway by phosphorylation of c-Jun (23) and ATF2 (24).…”

Gene expression reveals two distinct groups of anal carcinomas with clinical implications

“…Finally, we investigated expression profiling of genes selectively regulated by either CDKN2A (p16) or by E2F as reported by Vernell et al (2003). We found that hierarchical clustering based on CDKN2A (p16)-regulated genes could not reproduce the unsupervised clustering (Figure 3Ca), while genes regulated directly by E2F reproduced the unsupervised cluster analysis (Figure 3Cb).…”

“…However, the effect of high-risk HPV on global gene expression has been studied and characterised in several model systems on different microarray platforms (Chang and Laimins, 2000;Nees et al, 2001;Alazawi et al, 2002;Vernell et al, 2003;Garner-Hamrick et al, 2004;Loercher et al, 2004;Santin et al, 2005). Several biomarkers predicting both HPV status and response to treatment for several cancers have been proposed.…”

“…The number outside the big circle corresponds to genes with matching probes on the ABI chip but not included in the 8449 selection. (C) Hierarchical cluster analysis based on (Ca) CDKN2A (p16) transcriptionally regulated genes and (Cb) E2F-regulated genes, as reported by Vernell et al, 2003. expressed in several systems related to high-risk HPV infection. This included gene expression profiling of a mouse SCC model (Loercher et al, 2004), effect on overall gene expression associated with integration of HPV16 in cervix SCC (Alazawi et al, 2002), gene expression profiling of primary HPV16-and HPV18-infected early stage cervical cancer (Santin et al, 2005), effect of HPV18 E6 and E7 on global gene expression in an organotypic keratinocytes culture system (Garner-Hamrick et al, 2004), effect of HPV16 E6 and/or E7 on global gene expression in differentiating cervical keratinocytes (Nees et al, 2001) and, finally, effect of HPV31 on global gene expression in normal human keratinocytes (Chang and Laimins, 2000).…”