The epigenomics of cancer

Abstract

Aberrant gene function and altered patterns of gene expression are key features of cancer. Growing evidence shows that acquired epigenetic abnormalities participate with genetic alterations to cause this dysregulation. Here, we review recent advances in understanding how epigenetic alterations participate in the earliest stages of neoplasia, including stem/precursor cell contributions, and discuss the growing implications of these advances for strategies to control cancer.

Figure 1. Gene Silencing in Normal Cells

Heritable gene silencing involves, among other processes, the interplay between DNA methylation, histone covalent modifications, and nucleosomal remodeling. Some of the enzymes that contribute to these modifications include DNA methyltransferase (DNMTs), histone deacetylases (HDACs), histone methyltransferases (HMTs), and complex nucleosomal remodeling factors (NURFs). The interplay between these processes establishes a heritable repressive state at the start site of genes resulting in gene silencing. Physiologically, silencing is critical for development and differentiation. Pathologically, silencing leads to diseases such as cancer. Recent evidence suggests global changes in all three processes in cancer, perhaps reflecting their interrelationships.

Figure 2. An “Epigenetic Gatekeeper” Prevents Early Tumor Progression

Epigenetic silencing of genes p16, SFRPs, GATA-4 and -5, and APC (red X) in stem/precursor cells of adult cell-renewal systems may serve to abnormally lock these cells into stem-like states that foster abnormal clonal expansion. These genes are termed “epigenetic gatekeepers” because their normal epigenetic pattern of expression should allow them to be activated during stem/precursor cell differentiation as needed to properly control adult cell renewal. The repertoire of abnormal gene silencing then allows abnormal survival of the cells in the setting of chronic stress, such as inflammation (see Figure 3). The resulting preinvasive stem cells become “addicted” to the survival pathways involved so that selection for mutations in genetic gatekeeper genes provide an even stronger stimulus for further tumor progression. The bulk of the resulting tumor is composed of a sub-population of cancer stem cells and neoplastic progeny.

Figure 3. Networks of Gene-Silencing Events

Such networks help to foster early and later steps during neoplastic progression. Examples of early gene silencing (red X) occur at multiple points in key tumor control pathways to allow abnormal cell survival after stress and early clonal expansion. These epigenetic events are shown as provoking disruptive crosstalk between the pathways facilitating this expansion. Examples of gene-silencing events that foster subsequent silencing events (green arrows linking SIRT1 to silencing of GATA-4 and -5 and SFRPs) are depicted.

Figure 4. Strategies for Epigenetic Therapy

Epigenetic therapy with DNA methylation inhibitors (DNMTi) and HDAC inhibitors (HDACi) is now a reality. While these agents are currently approved as single agents, combination therapies are likely to gain traction in the future because of the inherent self-reinforcing nature of silencing mechanisms (see Figure 1). Future breakthroughs could come from the use of epigenetic drugs to activate miRNAs or the use of drugs to target cancer stem cells after tumor debulking by standard chemotherapy.