Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

Abstract

This year is the tenth anniversary of the publication in this journal of a model suggesting the existence of 'tumour progenitor genes'. These genes are epigenetically disrupted at the earliest stages of malignancies, even before mutations, and thus cause altered differentiation throughout tumour evolution. The past decade of discovery in cancer epigenetics has revealed a number of similarities between cancer genes and stem cell reprogramming genes, widespread mutations in epigenetic regulators, and the part played by chromatin structure in cellular plasticity in both development and cancer. In the light of these discoveries, we suggest here a framework for cancer epigenetics involving three types of genes: 'epigenetic mediators', corresponding to the tumour progenitor genes suggested earlier; 'epigenetic modifiers' of the mediators, which are frequently mutated in cancer; and 'epigenetic modulators' upstream of the modifiers, which are responsive to changes in the cellular environment and often linked to the nuclear architecture. We suggest that this classification is helpful in framing new diagnostic and therapeutic approaches to cancer.

Figure 1. Functional classification of cancer genes and their contribution to malignancy

Ageing, inflammation and chronic exposure to carcinogens impinge on epigenetic modulators, such as adenomatous polyposis coli (APC) and signal transducer and activator of transcription 3 (STAT3), that fine tune and regulate the function of epigenetic modifiers — for example, TET methylcytosine dioxygenase 2 (TET2) and AT-rich interaction domain 1A (ARID1A) — to bring about changes in the expression of epigenetic mediators — for example, sex-determining Y-box 2 (SOX2) and OCT4 — whose gene products regulate developmental potential. Chronic exposure to a fluctuating, cancer-predisposing environment and ageing promote the selection for epigenetic heterogeneity in vulnerable populations of somatic stem cells and progenitor compartments. Mutations in modulators and modifiers are often selected for during cancer development, which leads not only to increased cell proliferation, but also to the unscheduled expression of mediators that, in turn, inhibit differentiation and promote epigenetic plasticity by affecting the epigenetic modulators and modifiers in a feedback loop. The mechanism of epigenetic instability involves the erosion of barriers against dedifferentiation, such as large organized chromatin K9 modifications (LOCKs) overlapping with lamina-associated domains (LADs), and the emergence of hypomethylated blocks that contain the most variably expressed domains of the tumour genome and interfere with normal differentiation. Increased transcriptional noise at developmentally regulated genes is paralleled by the redistribution of super-enhancers from cell-fate-determining genes to oncogenes that further stabilize the cancer cell state. Stochastic changes in unstable chromatin states lead to the continuous regeneration of epigenetic heterogeneity that manifests as increased cellular entropy and provides the basis for the selection of the fittest during cancer evolution. BRD4, bromodomain containing 4; KLF4, Kruppel-like factor 4.

Figure 2. Change in cell state towards cancer stem cell states induced by reprogramming of the 3D epigenome

This hypothetical scheme explains how epigenetic mediators (for example, OCT4) might reprogramme the epigenome to tip over normal somatic stem cells or differentiated progenitor cells into cancer stem cell states displaying phenotypic heterogeneity. Large organized chromatin K9 modifications (LOCKs) (red cloud) overlapping with lamina-associated domains (LADs) are hypothesized to be largely absent in somatic stem cells (left panel) to ensure epigenetic flexibility associated with the multipotent state. The coordination of cell-type-specific repressed states (right panel) within the LOCKs/LADs is facilitated by epigenetic modifiers establishing multiple layers of epigenetic modifications, such as H3K9me2, H3K9me3, and DNA methylation. The localization of LOCKs/LADs to the lamina leads to the separation of active and inactive domains to reduce transcriptional noise and to provide barriers for dedifferentiation. Conversely, the unscheduled activation of epigenetic mediators leads to the erosion of LADs/LOCKs and the emergence of hypomethylated blocks during the neoplastic process. This, in turn, induces phenotypic heterogeneity by increasing the variability in expression and the probability of switches between the diverse cellular states within the tumour. A loss of LOCKs is postulated, moreover, to interfere with the constraints of enhancer–promoter communication within and between topologically associated domains (TADs), enabling the clustering of oncogenic super-enhancers and expression domains (green circles) to coordinate the expression of oncogenic pathway members (centre panel).

Figure 3. Waddington landscape of phenotypic plasticity in development and cancer

a. The Waddington landscape of development is adapted to compare cellular states of different entropy during normal differentiation (left side of image) and in cancer (right side of image). The developmental potential of normal somatic stem cells (grey balls) positioned on the top of the hill correlates with high entropy, which is mediated by cellular heterogeneity (different shades of grey). During differentiation, cells are guided towards well-defined cell fates (light blue and brown balls) with lower entropy, paralleled by a decrease in transcriptional noise and the stabilization of cell states (deepening of the valleys or canalization). Cancer stem cell (CSC) states (yellow ball) arise when epigenetic instability interferes with normal differentiation and leads to the erosion of barriers against dedifferentiation — for example, via the erosion of large organized chromatin K9 modifications and the emergence of hypomethylated blocks. In a similar manner to normal differentiation, CSCs with higher entropy occupy higher altitudes on the hill than cancer cells (orange and red balls), although the difference is smaller than between normal stem cells and differentiated progeny. Increased transcriptional noise (shallow valleys) and stochastic switches between diverse cell states (arrows between valleys) are regulated by the interplay between epigenetic modulators, modifiers and mediators, the deregulated epigenome and fluctuating environmental cues (for example, inflammation, repeated exposure to carcinogens, ageing or an overactive WNT pathway). Finally, cellular heterogeneity (yellow, orange and red balls) within the tumour eventually enables selection mechanisms to drive the growth of the fittest clone. b. Illustration of the role of epigenetic modifiers, modulators and mediators on the Waddington landscape described in part a. Epigenetic modulators (pink hexagon) regulate the activity of epigenetic modifiers (green triangles) that induce the ectopic expression of epigenetic mediators. Mediators dynamically alter the contour of the landscape via feedback loops that target epigenetic modifiers such as chromatin modifications (blue circles), lamin proteins (yellow circles) and chromosomal interactions (new loop on right). The expression of epigenetic mediators thus produces a shift in the epigenetic landscape, enabling the sampling of aberrant developmental outcomes displaying increased phenotypic plasticity in neoplastic or pre-neoplastic cells. APC, adenomatous polyposis coli; DNMT, DNA methyltransferase; SOX2, sex-determining Y-box 2; STAT3, signal transducer and activator of transcription 3; TET, TET methylcytosine dioxygenase.