Nature Reviews Cancer 9, 773-784 (November 2009) | doi:10.1038/nrc2736
Polycomb group proteins: navigators of lineage pathways led astray in
cancer
Adrian P. Bracken & Kristian Helin
Abstract
The Polycomb group (PcG) proteins are transcriptional repressors that regulate
lineage choices during development and differentiation. Recent studies have
advanced our understanding of how the PcG proteins regulate cell fate decisions
and how their deregulation potentially contributes to cancer. In this Review we
discuss the emerging roles of long non-coding RNAs (ncRNAs) and a subset of
transcription factors, which we call cell fate transcription factors, in the
regulation of PcG association with target genes. We also speculate about how
their deregulation contributes to tumorigenesis.
Considerable attention is currently focused on identifyingthe events that lead to
the development of so-called 'tumour-initiating cells', as understanding this
might facilitate the design of more effective cancer therapies1, 2, 3. It is
becoming increasingly evident that, in addition to genetic alterations, tumour
development involves the alteration of gene expression patterns owing to
epigenetic changes4. Recent studies have implicated the Polycomb group
proteins (PcG proteins) as key contributors to these changes5, 6, 7, 8, 9. The PcG
proteins form multiprotein repressive complexes, called Polycomb repressive
complexes (PRCs), which repress transcription by a mechanism that probably
involves the modification of chromatin (Fig. 1).
Figure 1 | Coordinated action of Polycomb repressive complexes.
Several genetic studies in different organisms have firmly established the vital
and conserved roles for PcG proteins in embryonic development and adult
somatic cell differentiation10. Moreover, recent studies have demonstrated that
the PcG proteins are required for maintaining the correct identities of stem,
progenitor and differentiated cells11. The genome-wide mapping of PcG target
Two major Polycomb repressive complexes (PRCs) have been described. The PRC2 complex
contains the histone methyltransferase enhancer of zeste homologue 2 (EZH2), which together
with embryonic ectoderm development (EED) and suppressor of zeste 12 homolog (SUZ12)
catalyses the trimethylation of histone H3 at lysine K27 (H3K27me3). The EZH2 SET domain
confers this activity. Multiple forms of the PRC1 complex exist and these contain combinations of
at least four PC proteins (CBX2, CBX4, CBX7 and CBX8), six PSC proteins (BMI1, MEL18, MBLR,
NSPC1, RNF159 and RNF3), two RING proteins (RNF1 and RNF2), three PH proteins (HPH1,
HPH2 and HPH3) and two SCML proteins (SCML1 1 and SCML2). Some results have suggested
that PRC1 complexes are recruited by the affinity of chromodomains in chromobox (Cbx)
proteins to the H3K27me3 mark. PRC1 recruitment results in the RNF1 and RNF2-mediated
ubiquitylation of histone H2A on lysine 119, which is thought to be important for transcriptional
repression. PC, Polycomb; PSC, Posterior sex combs ; SCML, Sex combs on midleg .
genes in mammalian cells has offered scientists the opportunity to start to
unravel the molecular mechanisms of PcG protein action12, 13, 14. The PcG
proteins have been found to bind and repress the promoters of genes that
encode proteins with key roles in cell fate determination in many different
cellular lineages. Although these data support the large body of evidence that
points to crucial roles for the PcG proteins in both development and adult
homeostasis, we are only beginning to understand how the PcG proteins actually
regulate their target genes.
Initial studies have established that the PcG proteins are displaced from certain
target genes, for example the homeobox (Hox) genes, on their transcriptional
activation during differentiation13, 14, 15. However, subsequent studies
demonstrated that the binding of PcG proteins is much more dynamic than
anticipated, showing that the PcG proteins are also recruited to the promoters of
certain genes in response to differentiation signals and, importantly, that this
recruitment is required for their silencing during differentiation15, 16, 17, 18,
19. On the basis of these results, we and others have proposed a model in which
the PcG proteins function dynamically during development and differentiation to
lock off the expression of alternative cell fate regulators in any particular lineage
(Fig. 2). In this Review we propose that the deregulation of these mechanisms is
central to tumour initiation.
Figure 2 | Dynamic recruitment and displacement of Polycomb group proteins
during lineage specification.
PcG proteins and cancer
The PcG proteins are essential for the maintenance of both normal and cancer
stem cell populations20, 21, 22. This is partly attributed to their ability to bind to
and repress the CDKN2B and CDKN2A loci, which encode the tumour
suppressors INK4B (encoded by CDKN2B), INK4A and ARF (both encoded by
CDKN2A)21, 23, 24, 25, 26, 27, 28, 29, 30, 31. INK4A and INK4B function
upstream in the RB pathway, and ARF functions upstream in the p53 pathway25,
32. In addition to frequent genetic alterations, this locus is often epigenetically
silenced by DNA methylation in cancer, and the PcG proteins have been proposed
to contribute to this26. Many additional PcG target genes accumulate DNA
methylation on their promoters in cancer, such as Wilm's tumour 1 (WT1),
retinoic acid receptor-beta (RARB), kruppel-like factor 4(KLF4), inhibitor of DNA
binding 4 (ID4), GATA binding protein 3 (GATA3) chromodomain helicase DNA
The Polycomb group (PcG) proteins 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 a progenitor or stem cell that has the potential to differentiate into three different lineages: A, B or
C. As an undifferentiated cell it expresses 'stem cell genes' that are required to maintain its proliferative
undifferentiated state. Before the signal to differentiate, the PcG proteins repress the transcription of
lineage-specific differentiation genes. On stimulation to differentiate, the PcG proteins are recruited to the
stem cell-specific genes, independently of the type of lineage specification signal. The PcG proteins are
then displaced from lineage-specific gene promoters during differentiation depending on the lineage
specification signal. The mechanisms by which the PcG proteins are displaced and recruited to target
genes are not well understood. In differentiated cells, PcG proteins silence not only the expression of 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.
binding protein 5 (CHD5) and PU.1 (also known as SPI1)13. The reports that
enhancer of zeste homologue 2 (EZH2)33 and chromobox homologue 7
(CBX7)34 can physically associate with DNA methyltransferases (DNMTs)
suggest a mechanism whereby the PcG proteins directly contribute to the altered
DNA methylation profiles that are observed in multiple cancer types. In fact, PcG
target genes are as much as 12 times as likely to be aberrantly silenced by DNA
methylation in cancer as non-PcG target genes7, 8, 9 and poorly differentiated
and aggressive human tumours show preferential repression of PcG target
genes6. Taken together, these results suggest a possible scenario in which PcG
proteins and DNA methylating enzymes (such as DNMTs) cooperate to
aberrantly silence pro-differentiation and anti-proliferative genes, which leads to
the accumulation of a population of cells unable to respond to differentiation
signals. It is thought that the consequent block of differentiation may allow these
tumour-initiating cells to linger and accumulate the additional epigenetic and/or
genetic alterations necessary to develop into a tumour.
However, a key question remains unanswered: what triggers the aberrant
silencing of PcG target genes that is observed in many cancer types? One
potential scenario is that PcG proteins, such as EZH2 and BMI1, become
aberrantly upregulated, leading to the progressive recruitment of DNMTs to PcG
target genes, a switch to a more permanent transcriptional silencing and the
generation of tumour-initiating cells. Supporting evidence for this hypothesis
includes the fact that several PcG proteins are highly expressed in cancer10. For
example, BMI1 is amplified and overexpressed in B cell lymphoma and functions
as an oncogene that cooperates with Myc in a mouse model of lymphoma35, 36,
37, 38. Similarly, suppressor of zeste 12 homologue (SUZ12) is translocated in
endometrial cancer39, and EZH2 is amplified and highly expressed in many
tumour types40, 41, 42, 43, 44, 45, 46, 47. Potentially contributing to these
increased EZH2 levels, the microRNA miR-101 has recently been reported to
directly target EZH2 and is itself deleted in some cancers48, 49. However,
despite the functional evidence for a role of PcG proteins, particularly BMI1, in
the development of cancer, the higher levels of these proteins frequently
observed in tumours could partly be a consequence of the high proportion of
proliferating and/or 'stem-like' cells in tumours. For example, BMI1 has been
reported to be highly expressed in normal stem cells50 and EZH2 expression
correlates with proliferation rate as it is controlled by the RB–E2F pathway41.
Therefore, in this Review we discuss an alternative and complementary
hypothesis in which PcG proteins are led astray in cancer by the deregulation of
factors that are required for their association to target genes. We propose that
the deregulation of these factors directly contributes to the aberrant modulation
of transcriptional programmes observed in many cancers.
PcG recruitment to target genes
PcG proteins do not have the ability to bind specific DNA motifs. Therefore, a key
mechanistic question concerns how they are recruited to and displaced from
their target genes during lineage specification. The answer to this question not
