EZH2: biology, disease, and structure-based drug discovery

Abstract

EZH2 is the catalytic subunit of the polycomb repressive complex 2 (PRC2), which is a highly conserved histone methyltransferase that methylates lysine 27 of histone 3. Overexpression of EZH2 has been found in a wide range of cancers, including those of the prostate and breast. In this review, we address the current understanding of the oncogenic role of EZH2, including its PRC2-dependent transcriptional repression and PRC2-independent gene activation. We also discuss the connections between EZH2 and other silencing enzymes, such as DNA methyltransferase and histone deacetylase. We comprehensively address the architecture of the PRC2 complex and the crucial roles of each subunit. Finally, we summarize new progress in developing EZH2 inhibitors, which could be a new epigenetic therapy for cancers.

Figure 1

Possible architecture of the PRC2 complex. (A) Models of the fly and human PRC2 complexes. The subunits and interactions between them are shown. (B) Domain organizations of each subunit in the human PRC2 complex. Domain “1”, binding region for PHF1 in human cells and PCL in flies; domain “2”, binding region for SUZ12; CXC, cysteine-rich domain; SANT, domain that allows chromatin remodeling protein to interact with histones; SET, catalytic domain of EZH2; VEFS, VRN2-EMF2-FIS2-SUZ12 domain; WD, WD-40 domain; WDB, WD-40 binding domain; Zn, Zn-finger region.

Figure 2

A model for the collaboration of epigenetic silencing enzymes, including core of the PRC2 complex, DNA methyltransferase (DNMT), and histone deacetylase (HDAC). In this model, if K27 is pre-acetylated, HDAC may first deacetylates it, and then the target genes are silenced through the methylation of K27 by PRC2. DNMTs may also be recruited by PRC2, and after methylating CpG DNA of target genes, making the chromatin state more deeply silenced. Ac, acetylation; and Me, methylation.

Figure 3

A model of the EZH2 functional switch from a polycomb repressor to a transcriptional activator in castration-resistant prostate cancer. PI3K/AKT pathway activation can lead to phosphorylation of EZH2 at Ser21. This phosphorylation event shifts EZH2 from a transcriptional repressor associated with PRC2 to a transcriptional co-activator cooperating with AR, using an intact SET methyltransferase domain.

Figure 4

Crystal structures of EED complexes or NURF-55 complexes. (A) The EZH2 N-terminal peptide (residues 39-68) binding to the bottom of the EED WD domain (PDB code: 2QXV). (B) H3K27me3 binding to an aromatic cage (top) on EED (PDB code: 3IIW). (C) Side view of the EED structure for comparing the binding of the EZH2 peptide and H3K27me3. (D) SU(Z)12 N-terminal peptide (residues 79-91) binding to the S/H-site of NURF-55 (PDB code: 2YBA). (E) Histone H31-19 peptide binding to the C-site of NURF-55 (PDB code: 2YB8).

Figure 5

Structure-based sequence alignment of selected SET domains containing histone methyltransferase. The alignment includes Clr4 (NP_595186), Dim5 (AAL35215), SUV39h1 (NP_003164), G9a (S30385), EZH2 (NP_004447), SET7/9 (NP_085151), SET8 (NP_065115), and vSET (AAC96946). The conserved sequence are highlighted with green boxes. Abbreviations: Hs, Homo sapiens; Nc, Neurospora crassa; Sp, Schizosaccharomyces pombe. The catalytic sites are indicated with star, and mutations of Y641 and A677 are indicated with triangles.

Figure 6

Structures of the protein methyltransferase SET domain. Zinc atoms are shown in grey spheres. (A) Clr4_Sp (PDB code: 1MVX). (B) Dim5_Nc complexed with H3K9 (pink sticks) and SAH (yellow sticks) (PDB code: 1PEG). (C) SET7/9_Hs complexed with H3K9 peptide and SAH (PDB code: 1O9S). (D) G9a-like protein methyltransferase complexed with BIX-01294 (cyan sticks) and SAH (PDB code: 3FPD). (E) SET8 complex with SAH (PDB code: 1ZKK). (F) vSET from virus complexed with peptide and SAH (PDB code: 2G46).

Figure 7

PRC2 subunit composition and modes of inhibition. Three types of inhibitors are indicated: SAM competitive inhibitors, SAH, and DZNep as an SAH hydrolase inhibitor.