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The goal of our work in the Bracken lab is to unravel the molecular mechanisms of stem cell differentiation and cellular senescence, while also identifying novel molecular targets for cancer therapy. To this end, we have identified and are currently studying the function of several 'Epigenetic' regulators involved in controlling these processes.

Epigenetic Regulation of Embryonic Stem Cell Differentiation

A major challenge in modern biology is to understand how “cell fate decisions” are regulated in stem and progenitor cells. These decisions govern whether a particular stem or progenitor cell differentiates into one type of cell or another. This question has major implications for regenerative medicine as well as our understanding of the molecular events that lead to cancer. It is becoming increasingly clear that, in addition to genetic alterations, cancer development involves the alteration of gene expression patterns as a result of 'epigenetic' changes (Feinberg et al., 2006). There are already several examples of epigenetic modifiers that are deregulated in cancer, e.g. BRD4 and EZH2 (Dawson and Kouzarides, 2012). The recent advent of “cancer epigenetic therapies”, such as those using BRD4 and EZH2 inhibitors to treat certain types of cancer, have demonstrated that knowledge in this field can lead to tangible successes in cancer treatment.

The Polycomb group proteins, which include EZH2, are centrally involved in cell fate decisions (Figure 1). Our central hypothesis is that the deregulation of the function of a set of Polycomb group proteins during cell fate decisions is central to tumour initiation. We are currently experimentally addressing this hypothesis, as well as investigating novel interactions between Polycomb group proteins and other chromatin regulators and DNA binding transcription factors involved in cell fate decisions. The goal is that this research will lead to breakthroughs in our understanding of stem cell biology as well as cancer.

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Figure 1. Dynamic recruitment and displacement of Polycomb group proteins during lineage specification. The Polycomb complexes (PRC1 and PRC2)  are displaced from the promoters of one set of target genes, while being recruited to the promoters of another set of target genes during lineage specification. This model depicts an embryonic stem cell that has the potential to differentiate into three different cell types: Lymphocytes, Muscle cells and Neuronal cells. Embryonic stem cells express genes that are required to maintain their self-renewal and pluripotent state. Before the signal to differentiate, the Polycomb proteins repress the transcription of lineage-specific differentiation genes. Upon stimulation to differentiate, the Polycomb proteins are recruited to the embryonic stem cell-specific genes, independently of the type of lineage specification signal. The Polycomb proteins are then displaced from lineage-specific gene promoters during differentiation depending on the lineage specification signal. The mechanisms by which the Polycomb proteins are displaced and recruited to target genes are not well understood. In differentiated cells, Polycomb proteins silence not only the expression of embryonic stem cell genes, but also the expression of genes that encode regulators of alternative lineages. This mechanism of ‘locking’ cell fate is thought to be central to how cells maintain their identity through subsequent cell divisions. Importantly, these mechanisms are more dynamic and plastic than previously anticipated, and they are reversed during cellular reprogramming and are deregulated in cancer. Adapted from Bracken and Helin. Nature Reviews Cancer. 9, 773-784 (November 2009).

 

Transcriptional Regulation of Cellular Senescence

Cellular senescence is an irreversible arrest of proliferation. It is activated when a cell encounters stress such as DNA damage, telomere shortening, or oncogene activation. Like apoptosis, it impedes tumour progression and acts as a barrier that pre-neoplastic cells must overcome during their evolution toward the full tumourigenic state. Central to cellular senescence are the p53 and pRb tumour suppressor pathways, which are activated upon cellular stress. We are studying the role of transcriptional regulators in the control of these cellular senescence pathways. Our goal is to harness this knowledge for future cancer therapies.

Figure 2. Molecular mechanisms of cellular senescence. The p53 and pRb pathways are central to cellular senescence control. Recent evidence suggests that multiple types of cellular stress can activate the p53 pathway by common or at least partially overlapping mechanisms. Telomere attrition, radiation, cytotoxic drugs and oncogene-induced DNA replication stress have all been shown to induce the DNA damage response (DDR), resulting in the activation of the checkpoint kinases ATM/ATR and CHK1/2, and leading to p53 accumulation. p53 can also be activated downstream of p14ARF, which binds to the E3 ubiquitin ligase, MDM2, preventing the degradation of p53. MDM2 can directly bind to p53 and control its transcriptional function, as well as regulate degradation of p53 through ubiquitination. This stabilisation and accumulation of p53 allows the activation of downstream genes such as p21CIP1, and the induction of cellular senescence or apoptosis, depending on the cellular context. The p16INK4a tumour suppressor, transcriptionally upregulated in stressed cells, inhibits cyclin D-dependent kinases, thereby preventing the phosphorylation and inactivation of the retinoblastoma protein, pRb. This promotes the repressive association between pRb and the E2F1-3 pro-proliferative transcriptional activators, preventing progression through the cell cycle, and permitting the formation of a repressive or ‘closed’ chromatin structure around E2F target gene promoters, known as SAHF. Importantly, the mechanisms of  transcriptional regulation of p16INK4a and p14ARF in senescent human cells are not yet fully understood. We are actively exploring new transcriptional regulators of both these cancer pathways. Red = tumour suppressors and green = oncogenes. Adapted from Lanigan and Bracken. Oncogene. 2011 Jun 30;30(26):2901-11.

 
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