Class I HDACs Affect DNA Replication, Repair, and Chromatin Structure: Implications for Cancer Therapy

Abstract

Significance: The contribution of epigenetic alterations to cancer development and progression is becoming increasingly clear, prompting the development of epigenetic therapies. Histone deacetylase inhibitors (HDIs) represent one of the first classes of such therapy. Two HDIs, Vorinostat and Romidepsin, are broad-spectrum inhibitors that target multiple histone deacetylases (HDACs) and are FDA approved for the treatment of cutaneous T-cell lymphoma. However, the mechanism of action and the basis for the cancer-selective effects of these inhibitors are still unclear.

Recent advances: While the anti-tumor effects of HDIs have traditionally been attributed to their ability to modify gene expression after the accumulation of histone acetylation, recent studies have identified the effects of HDACs on DNA replication, DNA repair, and genome stability. In addition, the HDIs available in the clinic target multiple HDACs, making it difficult to assign either their anti-tumor effects or their associated toxicities to the inhibition of a single protein. However, recent studies in mouse models provide insights into the tissue-specific functions of individual HDACs and their involvement in mediating the effects of HDI therapy.

Critical issues: Here, we describe how altered replication contributes to the efficacy of HDAC-targeted therapies as well as discuss what knowledge mouse models have provided to our understanding of the specific functions of class I HDACs, their potential involvement in tumorigenesis, and how their disruption may contribute to toxicities associated with HDI treatment.

Future directions: Impairment of DNA replication by HDIs has important therapeutic implications. Future studies should assess how best to exploit these findings for therapeutic gain.

FIG. 1.

Classification of the nonsirtuin HDAC families. Eleven human HDACs are pictured (class III HDACs, the sirtuins, are not included). Class I HDACs are largely nuclear and are related to the yeast protein Rpd3 within the conserved, deacetylase domain (DAC). Class II HDACs are related to the yeast Hda1 protein. Class IIa proteins have a number of N-terminal serine phosphorylation sites (S), which facilitate cytoplasmic shuttling. Class IIb HDACs contain tandem deacetylase domains (only a partial domain in the case of HDAC10). In addition, HDAC6 contains an SE14 repeat domain, important for its cytoplasmic retention, and a ubiquitin-binding zinc finger domain (PAZ domain). HDAC11 is the sole member of the class IV HDACs and shows homology with both class I and class II HDACs. HDAC, histone deacetylase.

FIG. 2.

Recruitment of HDAC-containing repressor complexes by the BCL6 proto-oncogene. Gene rearrangements involving BCL6 are commonly associated with diffuse large B-cell lymphoma. BCL6 represses target gene expression (A) through the recruitment of both HDAC1- and HDAC2-containing Sin3a complexes (B), as well as through the recruitment of HDAC3-containing NCoR/SMRT complexes (C). In addition, BCL6 is itself regulated by acetylation. Acetylation of BCL6 inhibits its ability to bind DNA, and the deacetylation of BCL6 has been ascribed to both Sirtuin and HDAC activities (10). NCoR, nuclear hormone co-repressor; SMRT, silencing mediator of retinoid or thyroid-hormone receptors.

FIG. 3.

The HDAC co-repressor association is mediated by Ins(1,4,5,6)P₄. Crystallography studies have solved the structure of the interaction between the SMRT DAD (upper left) and human HDAC3. These studies have revealed the requirement of the inositol tetraphosphate molecule [Ins(1,4,5,6)P₄, arrow] for both the stabilization and activation of the HDAC-corepressor complex (127). DAD, deacetylase activating domain.

FIG. 4.

Changes in chromatin structure and histone acetylation are linked to DNA replication. HDACs 1, 2, and 3 localize to replication forks, and the disruption of HDAC function slows replication fork progression. This could be through direct effects on the replication machinery, as replication factors such as PCNA are regulated through acetylation. Alternatively, newly synthesized histones are acetylated on H4K5K12 before deposition onto nascent DNA. Histone chaperones, such as CAF-1, are important for histone deposition and associate with HDACs. Furthermore, HDACs 1, 2, and 3 have been implicated in the removal of histone deposition marks (H4K5 and H4K12), which is critical for chromatin maturation and the disruption of which can contribute to replication stress. CAF-1, chromatin assembly factor 1; PCNA, proliferating cell nuclear antigen.

FIG. 5.

TCGA identifies mutations and/or copy number alterations in HDACs 1, 2, and 3. Cancer genome sequencing analyses coordinated by the Cancer Genome Atlas have revealed alterations, including mutation, amplifications, and deletions of HDAC1, 2, and 3 in a number of tumor types (18, 33).