Role of Histone Acetyltransferase Inhibitors in Cancer Therapy

Abstract

The development of cancer is a complex phenomenon driven by various extrinsic as well as intrinsic risk factors, including epigenetic modifications. These post-translational modifications are encountered in diverse cancer cells and appear for a relatively short span of time. These changes can significantly affect various oncogenic genes and proteins involved in cancer initiation and progression. Histone lysine acetylation and deacetylation processes are controlled by two opposing classes of enzymes that modulate gene regulation, either by adding an acetyl moiety on a histone lysine residue by histone lysine acetyltransferases (KATs) or via removing it by histone deacetylases (KDACs). Deregulated KAT activity has been implicated in the development of several diseases including cancer and can be targeted for the development of anti-neoplastic drugs. Here, we describe the predominant epigenetic changes that can affect key KAT superfamily members during carcinogenesis and briefly highlight the pharmacological potential of employing lysine acetyltransferase inhibitors (KATi) for cancer therapy.

Introduction

It has been well established that post-translational modifications on histone and non-histone proteins such as phosphorylation, acetylation, and methylation can regulate multiple cellular processes. Epigenetic modifications in chromatin structure regulate gene expression. Euchromatin, which is loosely packed DNA, exhibits greater transcriptional activity, whereas heterochromatin, the tightly packed form, displays reduced transcriptional activity. Various chromatin remodeling complexes can disrupt and remodel the nucleosome structure by increasing DNA accessibility. Two groups of chromatin-modifying complexes have been described: the ATP-dependent complex and covalent histone modifications. The homeostasis of histone modifications is established and maintained by a range of enzymes including, but not limited to, histone lysine acetyltransferases (KATs) and histone lysine deacetylases (KDACs). Histone modifications are important regulators of gene transcription and modulate dynamic processes that affect nucleosomes. Several lines of evidence suggest that deregulated acetylation is implicated in cancer development. Long noncoding RNAs have also been shown to be necessary for targeting histone-modifying activities. Comprehensive global acetylome analysis has shown thousands of acetylation sites on numerous proteins, not necessarily confined to the nucleus. Currently, public repositories report more than 35,000 acetylation sites in human cells. Aberrant histone modifications contribute to human diseases such as cancer, neurodegenerative diseases, and infections, including inflammation. Several pro-inflammatory cytokines such as tumor necrosis factor α, interleukin 1β, and other stimulants such as lipopolysaccharides can promote histone acetylation. In addition to their nuclear function, the levels of circulating histones and nucleosomes may be enhanced under pathological conditions, indicating their potential as novel therapeutic targets.

Major KAT Families

Based on cellular localization, KATs are classified into two types: nuclear or cytoplasmic KATs. Nuclear KAT families are further classified based on their structural homology and enzyme transfer mechanisms. Five distinct families have been identified with different targets and functions: GCN5-related N-acetyltransferase (GNAT), CREB-binding protein and its paralog p300 (p300/CBP), MYST, and the nuclear receptor coactivator factor (NRCF) family. Approximately 100 protein substrates have been described for p300/CBP, which acetylates both histone and non-histone proteins, such as p53. The MYST family is the largest and most diverse and is primarily involved in DNA repair and gene silencing. Members include MOZ, YBF2/Sas3, Sas2, MOF, and Tip60, characterized by a conserved domain with an acetyl-CoA binding site, a C2HC zinc finger, and a helix-turn-helix DNA-binding domain. The KAT family also exhibits variations in structural features, such as PHD fingers, zinc fingers, and chromodomains. Recently, a novel family of histone acetyltransferases known as camello has been identified, which can acetylate histone H4 in zebrafish development and localizes in the perinuclear space. Cytoplasmic KATs are responsible for acetylation of newly synthesized histone proteins, and include HAT1, HAT2, HatB3.1, Rtt109, and HAT4.

p300/CBP Family

The p300/CBP family consists of two members, CBP (CREB-binding protein) and its paralog p300. These proteins have similar structures and functions, including a 500-amino acid KAT domain with high sequence similarity, a bromodomain, and three cysteine-histidine-rich domains that facilitate protein-protein interactions. p300/CBP serves as a coactivator for many transcription factors and plays a pivotal role in assembling and mobilizing basal transcriptional machinery. They interact with at least 400 different cellular proteins, including c-Myc, c-Myb, β-catenin, hypoxia-inducible factor 1, tumor suppressor protein p53, androgen receptor, estrogen receptor, and CREB. These interactions are important events in the transcription of various downstream genes, consistent with the functions of p300/CBP as transcriptional coactivators.

GNAT Family

The superfamily of general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) was first reported in the late 1990s. There are currently at least 17 distinct GNAT family members known, all sharing a similar HAT domain and a conserved bromodomain at the C-terminal, enabling attachment to lysine residues. Notably, GCN5 (KAT2A) and pCAF (KAT2B) are important in gene transcription, acetylating several transcription factors and regulating their function. GNATs control numerous cellular processes such as DNA replication and repair, metabolism, key signaling pathways, and the development of diseases including cancer.

MYST Family

The MYST family of KATs are an evolutionarily conserved group of enzymes that share a conserved MYST domain, including a zinc finger domain and an acetyl-CoA binding domain. The MYST family comprises five important enzymes: MOZ, Tip60, MOF, MORF, and HBO1. These acetyltransferases are found in various protein complexes and regulate gene transcription. In cancer, the levels of MYST acetyltransferases are often altered. For example, Tip60 expression is frequently downregulated in melanoma, cervical, colorectal, and gastric cancers. hMOF, another MYST family member, is the main acetyltransferase for H4K16, and its loss causes deregulation of this modification. hMOF deficiency is observed in gastric, renal, colorectal, ovarian, breast, and other cancers, serving as a prognostic biomarker for these diseases.

Nuclear Receptor Coactivator Family and Transcription Factor-Related KAT Family

The nuclear receptor coactivator family includes steroid receptor coactivators (SRC-1, -2, and -3). These proteins are ubiquitous and well characterized. All three SRCs form multiprotein complexes to activate transcription by nuclear receptors and other factors. They each have intrinsic KAT domains at the carboxy-terminus, specific for histone H3 and H4. SRC-1 and SRC-3 predominantly acetylate histone H3 and H4, and SRC-3 can also acetylate these histones in mononucleosomes. Transcriptional coactivator complexes possess intrinsic histone acetyltransferase activity, directly linking chromatin acetylation to transcriptional activation. Additionally, some TATA-box binding protein-associated factors (TAF) and TFIIIC have KAT activity. Furthermore, cytosolic KAT1 acetylates H2A, while KAT4 promotes acetylation of cytosolic H4 to enhance nucleosome assembly.

Lysine Acetylation in Cancer

Intrinsic and extrinsic environmental signals can be converted into cellular responses through control of gene expression, in which N-ε-lysine acetylation plays a key role. This post-translational modification is catalyzed by KATs, which act as “writers,” and reversed by KDACs, the “erasers.” The acetylation event was first observed decades ago, primarily in histones, and is now recognized as an important epigenetic modification contributing to the development of many human diseases, including cancer. Lysine acetylation influences the expression of genes involved in proliferation, apoptosis, differentiation, and other processes critical for cancer initiation and progression. Dysregulation may occur through overexpression, mutation, or altered activity of KATs, leading to aberrant transcriptional programs. Consequently, targeting KATs with small molecule inhibitors has emerged as a potential therapeutic strategy in oncology.

KAT proteins regulate a wide spectrum of oncogenic and tumor suppressor pathways. For instance, mutations or dysregulation in p300 and CBP have been associated with various forms of leukemia, solid tumors, and lymphomas. Loss of KAT activity or expression can lead to the silencing of tumor suppressor genes, whereas aberrant activation can enhance the expression of oncogenes. Some KATs also modify non-histone proteins, including p53, thereby influencing their function, localization, and stability.

It is noteworthy that KATs not only affect nuclear proteins but also acetylate cytoplasmic and mitochondrial proteins, thereby expanding their regulatory impact to metabolic processes and cell signaling beyond chromatin. The diverse roles of lysine acetylation and the widespread deregulation of KATs in human cancers underscore the therapeutic significance of modulating KAT activity, potentially reversing aberrant gene expression programs that drive malignant transformation and progression.

Lysine Acetylation in Breast Cancer

Breast cancer is among the most common cancers worldwide, and mounting evidence links histone acetylation patterns and KAT activity to its development and progression. Mutations, deletions, and abnormal expression of KATs such as p300, CBP, and some MYST family members have been documented in breast tumors. For example, downregulation of hMOF in breast cancer cells correlates with poor prognosis and aggressive disease. Similarly, the KAT activity of p300 and CBP is critical for the transcription of genes involved in cell cycle control, DNA repair, and apoptosis.

Overexpression of p300 and CBP in some breast cancers has been associated with advanced disease stage and chemotherapy resistance. Conversely, loss-of-function or reduced expression of these KATs impairs p53 function and facilitates tumor progression. Additionally, KATs are involved in modulating the activity of hormone receptors: p300 and CBP function as coactivators of the estrogen receptor (ER), influencing the expression of ER-regulated genes critical for tumor cell growth and survival.

Histone acetylation levels, particularly of H3K27 and H4K16, are often decreased in breast cancer tissues compared to normal breast epithelial cells. This loss of acetylation may lead to chromatin compaction and silencing of genes that guard against malignancy. KATs further contribute to the development of resistance to endocrine therapies in ER-positive breast cancers, and their pharmacological inhibition has been proposed as a strategy to overcome this challenge.

Lysine Acetylation in Lung Cancer

In lung cancer, global abnormalities in histone acetylation are frequently observed. Decreased acetylation of specific lysines on histone H4 and H3 is correlated with poor prognosis in non-small cell lung cancer (NSCLC) patients. Dysregulation of KATs, including p300 and members of the MYST family, has also been linked with tumor development. For instance, alterations in Tip60 and hMOF expression are commonly noted in lung adenocarcinomas.

The acetylation status of non-histone proteins, such as the tumor suppressor p53, is another critical factor in lung cancer biology. Acetylation of p53 by KATs enhances its stability and transcriptional activity, promoting cell cycle arrest and apoptosis. Malfunction or loss of KAT function impairs p53-mediated tumor suppressor pathways, thereby contributing to tumorigenesis.

In lung cancers, aberrant KAT activity influences numerous cellular pathways, modulating not only gene transcription but also responses to DNA damage and cellular stress. Targeting acetylation-dependent pathways using specific KAT inhibitors presents a new avenue for therapeutic intervention.

Lysine Acetylation in Gastric Cancer

Gastric cancer displays significant dysregulation of both histone and non-histone lysine acetylation. Downregulation of hMOF and Tip60 is recurrently observed in primary gastric tumors, which is often accompanied by a reduction in histone H4K16 acetylation—an established mark of open chromatin and active gene expression. This aberrant acetylation profile is associated with the silencing of tumor suppressor genes and a poor clinical outcome.

Genetic studies have identified frequent mutations and deletions in KAT genes, such as p300, in gastric cancer cases. Reduced p300 and CBP activity not only affects histone acetylation but also compromises the function of non-histone proteins required to prevent tumor initiation. Loss of MYST family member activity similarly impairs DNA repair mechanisms and enhances genomic instability.

Overall, the complex modulation of acetylation status by multiple KATs shapes the transcriptome and proteome of gastric cancer cells, influencing their ability to proliferate, metastasize, and resist therapy. As with other cancers, targeting KAT activity is being explored as a means to restore normal acetylation patterns and inhibit tumor progression.

Lysine Acetylation in Hematological Malignancies

The role of KATs in hematological cancers such as leukemia and lymphoma is well established. Chromosomal translocations involving KAT genes such as CBP, p300, and MYST family members are common in acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), and certain lymphomas. For example, fusions of MOZ and CBP or p300 with other transcriptional regulators can result in aberrant acetyltransferase activity and lead to malignant transformation.

Altered expression levels of KATs are detected in leukemia and are associated with impaired differentiation, increased proliferation, and resistance to apoptosis in malignant cells. The p300/CBP family’s ability to acetylate both histone and non-histone substrates is critical for regulating gene expression networks in hematopoietic cells.

KAT mutations often create dependency on compensatory survival pathways, providing an opportunity for targeted therapy. Several KAT inhibitors are in preclinical and clinical development for the treatment of hematological malignancies, aiming to correct the transcriptional imbalances underlying the disease.

Lysine Acetylation in Nasal Cancer

Although less prevalent, nasal cancers also exhibit aberrant patterns of lysine acetylation. Recent studies have shown abnormal expression of KATs, specifically members of the GNAT and MYST families, in nasal carcinoma. These alterations affect the regulation of cell proliferation, apoptosis, and the immune response to tumor cells. The detailed molecular mechanisms are still being elucidated, but targeting acetyltransferase activity may offer promising strategies for intervention in nasal cancers.

KAT Inhibitors

The discovery and development of small molecule inhibitors targeting histone lysine acetyltransferases have opened new possibilities for cancer therapy. KAT inhibitors (KATi) aim to reduce aberrant acetylation profiles, restore normal gene expression, and suppress the proliferation and survival of cancer cells. Such inhibitors can be classified into several categories, including natural product-derived inhibitors, synthetic compounds, and bisubstrate analogs.

Natural compound KAT inhibitors such as curcumin, anacardic acid, garcinol, plumbagin, and epigallocatechin-3-gallate (EGCG) display varying degrees of selectivity toward specific KAT families. These compounds modulate acetylation status and exhibit anti-cancer effects in diverse preclinical models. Synthetic KAT inhibitors have been developed to increase potency and selectivity, and several are nearing clinical evaluation.

The design of bisubstrate inhibitors, which mimic both the lysine substrate and acetyl-CoA donor, represents a novel strategy to achieve high specificity for particular KAT enzymes. Continuous research in this area is expected to yield more selective and effective therapeutic options.

Bisubstrate Inhibitors

Bisubstrate KAT inhibitors are a new class of molecules designed to simultaneously target the substrate and cofactor binding sites of KATs. These compounds exhibit improved selectivity and potency compared to traditional inhibitors by closely mimicking the enzyme’s natural substrates and cofactors. By occupying both binding pockets, bisubstrate inhibitors effectively block the catalytic activity of KATs, offering the potential for precise modulation of acetylation patterns in cancer cells.

Natural Product Based KAT Inhibitors

Several natural products have demonstrated KAT inhibitory activity and shown promise as anti-cancer agents. Curcumin, anacardic acid, garcinol, plumbagin, and EGCG are among the most widely studied natural KAT inhibitors. These compounds act through multiple mechanisms, including direct inhibition of KAT enzymatic activity, modulation of gene expression, and interference with cellular signaling pathways. Research continues to explore the therapeutic potential and bioavailability challenges associated with natural KAT inhibitors.

Conclusion and Perspectives

In conclusion, histone lysine acetyltransferases are critical regulators of gene expression through their influence on chromatin dynamics. Dysregulation of KAT activity contributes to tumor initiation, progression, and resistance to therapy across a variety of human cancers. The development of KAT inhibitors represents a promising therapeutic approach aimed at correcting aberrant acetylation patterns and restoring normal gene regulation. Further research into the structural biology, selectivity, and pharmacodynamics of KAT inhibitors will accelerate the translation of these compounds into the clinic, potentially improving outcomes for patients NEO2734 with cancer and other diseases linked to epigenetic dysregulation.