Epigenetic regulation refers to alterations to the chromatin template that collectively establish differential patterns of gene transcription. Post-translational modifications of the histones play a key role in epigenetic regulation of gene transcription. In this review, we provide an overview of recent studies on the role of histone modifications in carcinogenesis. Since tumour-selective ligands such as tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) are well-considered as promising anti-tumour therapies, we summarise strategies for improving TRAIL sensitivity by inhibiting aberrant histone modifications in cancers. In this perspective we also discuss new epigenetic drug targets for enhancing TRAIL-mediated apoptosis.
In humans, the genetic information (DNA) is contained in 23 chromosome pairs. These chromosomes are composed of DNA and histone proteins that form highly condensed chromatin. In parallel to genetics, the term “epigenetics” was originally defined to describe heritable changes that are not encoded in the DNA. Currently, epigenetics is used as a common term to describe chromatin modifications that regulate DNA-based processes including heritable and non-heritable changes[
Among various strategies to treat cancers, the selective induction of cellular apoptosis in cancer cells is considered as a promising therapeutic strategy. A well-known ligand to induce apoptosis is tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL). Dulanermin is a TRAIL-based therapeutic containing amino acids 114-281 of human TRAIL, which has been developed as a clinical anti-cancer drug. An early phase I clinical study showed that dulanermin was well-tolerated by patients with advanced cancer. However, only 3% of the patients in this study responded to dulanermin treatment for a period longer than 6 months[
In this review, we provide an overview of post-translational modifications of histones and the enzymes involved in the addition or removal of these modifications. We discuss small molecules targeting these enzymes and their anti-tumour effects. We connect this to targets involved in apoptosis as potential approach in cancer therapy. Finally, we summarize the current understanding of epigenetic mechanisms involved in sensitivity to TRAIL-induced apoptosis.
Histones are the central components of nucleosomes, in which a DNA string wraps around an octamer containing two copies of four core histones (H3, H4, H2A and H2B). These nucleosomes are organized like “beads” on DNA strings and are connected by histone protein H1 and further compacted to 30 nm-chromatin fibres, which are eventually condensed to form a chromosome. Therefore, histones provide structural support for chromosomes to provide organized packing of the DNA inside the nucleus. Unstructured histone tails are excluded from nucleosome cores and these tails are rich in lysine and arginine residues. Lysine residues are positively charged and provide charge-charge interactions with the negatively charged DNA, thus compacting the chromatin structure. Post-translational modifications occur mostly on the
Histone modifications
Amino acids | Modifications | Positions | Nomenclature | Ref. |
---|---|---|---|---|
Arginine | Methylation | *H3R2/R8/R17/R26, H4R3, H2AR3 | R-me1, R-me2s, R-me2a | [ |
Citullination | *H3R2/R8/R17/R26/R42, H4R3, H2A, and H1 | R-citrulline | [ |
|
Lysine | Methylation | *H3K9/K4/K36/K79/K27, H4K5/K20 | K-me1, K-me2, K-me3 | [ |
Acetylation | *H3K9/K14/K56, H4K5/K12/K16 | K-acetyl | [ |
|
Propionylation | *H3K14 | K-propionyl | [ |
|
Butyrylation | *H3K14, H4K5/K8 | K-butyryl | [ |
|
2-hydroxyisobutyrylation | H2AK5/9/36/74/75/95/118, H2BK5/12/20/23/24/34/43/46/57/85/108/116/120,
|
K-2-hydroxyisobutyryl | [ |
|
Malonylation | *H2AK119 | K-malonyl | [ |
|
Succinylation | *H3K79 | K-succinyl | [ |
|
Crotonylation | H2AK36/118/119/125, H2BK5/11/12/15/16/20/23/34
|
K-crotonyl | [ |
*Specific positions which were identified to have certain effects in nuclear processes
Biologically, arginine methylation refers to a reaction in which a methyl group is transferred from
In contrast to arginine methylation, it is less clear which enzymes catalyse arginine demethylation. JMJD6 was initially reported to demethylate H3R2 and H4R3[
A recently identified arginine post-translational modification is citrullination. This post-translational modification was already found in dozens of proteins, such as proteases, metabolic enzymes, and histones. The citrullination of histones is well-known to be involved in the formation of neutrophil extracellular traps (NETs), which is connected to innate immunity. In the process of clearing bacteria, the neutrophils secrete DNA, histones, and intracellular proteins to the extracellular space where they form NETs[
Lysine methylation is tightly regulated by “writers” (KMTs, methyltransferases) and “erasers” (KDMs, demethylases). Similar to PRMTs, KMTs also employ SAM as co-factor to transfer one, two, or three methyl groups to specific histone lysine residues. More than 50 human KMTs and 30 KDMs have been identified[
A classically studied lysine modification is acetylation of histone lysine residues. In a lysine acetylation reaction, an acetyl group from acetylated coenzyme A is transferred to the e-amino from a lysine residue, which results in neutralization of the positive charge and thus weakening of the electrostatic interaction with the DNA. This change leads to a more open chromatin structure, which allows access of DNA binding proteins. In general, acetylation is related to increased gene transcription, while deacetylation is connected to repression of gene transcription
Acetylation or deacetylation of histone lysine residues is catalysed by HATs and HDACs, respectively. Lysine acetylation is connected to loosening of the chromatin structure. This change enables DNA binding and eventually leads to activation of gene transcription. In contrast, deacetylation closes the chromatin structure and represses gene transcription. HATs: histone acetyltransferases; HDACs: histone deacetylases
Besides histone lysine acetylation, recent studies show that other short-chain CoAs, such as propionyl-CoA, butyryl-CoA[
Besides the aforementioned methylation and acetylation, other types of post-translational modifications are identified on histones, such as lysine ubiquitinoylation, sumoylation and ADP-ribosylation. These modifications are mostly reported to relate to DNA damage and repair. Moreover, phosphorylation of histone serine and threonine residues is a globally found modification, which plays important roles in diverse nuclear processes. Details for these modifications are discussed in recent reviews[
Overexpression of PRMTs has been observed in various types of human cancers[
Inhibitors of histone methylation in clinical studies
Name | Type of histone modification | Target | Clinical phase | Condition or disease in clinic | Disease in preclinical studies |
---|---|---|---|---|---|
Pinometostat
|
Lysine methylation | DOT1L | 1 | Advanced acute leukemia, particularly MLL-r[ |
Rearranged mixed lineage leukemia (MLL-r)[ |
CPI-1205 | EZH2 | 1 | B-cell lymphomas[ |
B-cell lymphomas[ |
|
Tazemetostat
|
2 | Elapsed or refractory B-cell non-Hodgkin lymphoma and advanced solid tumours[ |
Non-Hodgkin lymphoma[ |
||
GSK2879552 | LSD1 | 1 | Relapsed or refractory SCLC[ |
Small cell lung carcinoma[ |
|
JNJ-64619178 | Arginine methylation | PRMT5 | 1 | Relapsed/refractory B cell non-Hodgkin lymphoma (NHL) or advanced solid tumours | Human NSCLC and SCLC cancer mouse xenograft models[ |
GSK3326595
|
PRMT5 | 1 | Advanced or metastatic solid tumours and non-Hodgkin’s lymphoma[ |
Hematologic and solid tumour cells lines[ |
|
GSK3368715
|
Type I PRMTs | 1 | Solid tumours and diffuse large B-cell lymphoma | Lymphoma and AML cell lines[ |
SCLC: small cell lung cancer; NSCLC: non-small-cell lung carcinoma; AML: acute myeloid leukemia
Numerous studies have shown that mutation, dysregulation, or overexpression of lysine modifying enzymes such as KMTs, KDMs, HATs, or HDACs are associated with cancers and other diseases. Therefore, these enzymes were recognized as potential drug targets for cancer treatment[
As listed in
Previously, the FDA approved several pan-HDAC inhibitors for the treatment of cancers. For instance, vorinostat (SAHA) is approved for the treatment of cutaneous manifestations of cutaneous T-cell lymphoma[
Specific HAT and HDAC inhibitors developed between 2009 and 2019, and their applications in cancer
Name | Target | Links to cancer |
---|---|---|
BG45 | Class I HDAC | multiple myeloma[ |
TMP-195 | Class IIa HDAC | Breast tumour[ |
LMK235 | HDAC4,5 | Chemoresistant cancer cells[ |
Tubastatin A | HDAC6 | cholangiocarcinoma[ |
Ricolinostat (ACY-1215) | multiple myeloma[ |
|
SKLB-23bb | solid and hematologic tumour[ |
|
Cay 10603 | Burkitt’s lymphoma[ |
|
Nexturastat A | myeloma[ |
|
PCI-34051 | HDAC8 | neuroblastoma[ |
A485 | P300/CBP | myeloma[ |
HAT: histone acetyltransferase; HDAC: histone deacetylase
In comparison to HDAC inhibitors, the development of potent and specific HAT inhibitors is lagging. C646 was firstly considered as a p300 and CBP selective inhibitor[
Bromodomains are protein modules that are present in 46 different human proteins[
TRAIL is a member of the TNF superfamily and it binds to five receptors, including death receptor 4 (DR4), death receptor 5 (DR5), decoy receptor 1 (DcR1), decoy receptor 2 (DcR2), and osteoprotegerin. DR4 and DR5 both contain an intracellular death domain (DD), which initiates apoptotic signalling transduction. In contrast, DcR1 and DcR2 do not induce apoptosis due to the truncated DD in DcR1 and the absent DD in DcR2. The mechanisms of TRAIL-induced apoptosis have been intensively investigated and pathways identified are shown in
TRAIL-induced apoptotic pathways. After trimerization, TRAIL binds to death receptors, which triggers the formation of the DISC and activates caspase-8/10. Subsequently, activated caspase-8/10 induces cleavage of caspase-3/7, which leads to apoptosis. On the other hand, cleaved caspase-8/10 can also recruit Bid to trigger apoptosis via the intrinsic pathways. The intrinsic pathway is usually activated by DNA damage followed by p53 activation, whereas TRAIL-induced intrinsic apoptotic pathway is independent of p53. Interestingly, p53 has also been found to regulate TRAIL receptors DR4, DR5, DcR1, and DcR2[
Anti-apoptotic proteins are also involved in these apoptotic signalling pathways. For instance, cellular-FLIP (c-FLIP) and cellular inhibitors of apoptotic proteins (cIAP1 and cIAP2) disturb the formation of DISC. X-linked IAP (XIAP) and survivin, on the other hand, block executioner caspases and the apoptosome. Moreover, anti-apoptotic Bcl-2 family members, like Bcl-2, Bcl-XL, Mcl-1, and Bfl-1 are able to prevent MOMP.
Although, TRAIL has promising tumour-cell selective apoptosis-inducing properties, various tumour cells are resistant to TRAIL treatment. Therefore, it is important to improve TRAIL-sensitivity. Here, we discuss the strategies of improving TRAIL-sensitivity by targeting histone modifying enzymes that are involved in methylation and acetylation. Examples of the use of selective inhibitors as TRAIL sensitizers to overcome TRAIL-resistance are shown in
Improved TRAIL-induced apoptosis pathway using inhibitors targeting enzymes in histone modifications
Target | Small molecule | Regulation mechanisms | Cancer type | Ref. |
---|---|---|---|---|
Euchromatic histone-lysine |
BIX-01294 | Downregulation of Survivin and Upregulation of DR5 | Renal carcinoma | [ |
Upregulation of DR5 | Breast cancer | [ |
||
PRC2 | Retinoic acid (RA) or 3-deazaneplanocin A (DZNep) | Increased DR5 transcript level | Colon cancer | [ |
Class I HDAC | Entinostat
|
Restore expression of Coxsackie Adenovirus receptor | Prostate cancer | [ |
Upregulation of DR4, DR5, Bax, Bak | Breast cancer | [ |
||
Decrease degradation of endogenous TRAIL | Anaplastic thyroid carcinoma | [ |
||
Expression of endogenous TRAIL | Acute myeloid leukemia | [ |
||
HDAC3 | RGFP966 | Upregulation of DR4 | Colon cancer | [ |
HDAC8 | PCI34051 |
The enzyme EHMT2 catalyses the dimethylation of H3K9me2, which is associated with silencing of tumour suppressor genes. The PRC2 complex plays an important role in H3K27me3, which is also related to transcriptional repression of tumour suppressor genes. When combined with TRAIL, inhibitors of either EHMT2 or PRC2 increase the number of apoptotic cells through upregulation of DR5[
Additionally, a recent study shows that silencing KDM2B, a H3K36-specific histone demethylase, can cause a de-repression of a pro-apoptotic gene Harakiri (HRK) in glioblastoma multiforme cells. This study also shows that the silencing of KDM2B cooperates with TRAIL to reduce cell viability[
As discussed above, EZH2 is a promising therapeutic target for lymphoma. Therefore, EZH2-specific inhibitors may enhance the sensitivity of lymphoma cells to TRAIL. Additionally, another methyltransferase PRMT5 has been identified as a novel TRAIL receptor binding protein at the plasma membrane, which is involved in the early stage of signal initiation for induction of the NF-κB signalling pathways[
Previously, studies have shown that the combination of pan-HDAC inhibitors, such as panobinostat, with TRAIL downregulates anti-apoptotic proteins, c-FLIP and XIAP, thereby improving sensitivity to TRAIL[
Moreover, highly acetylated Ku70, a DNA repair protein, disrupts the formation of the Ku70-FLIP complex and triggers the degradation of FLIP by polyubiquitination. Therefore, using the HDAC inhibitor vorinostat increases apoptosis through the stabilization of the Ku70-FLIP complex in colon cancer models
Interestingly, the BET inhibitor JQ1 was reported to reduce the expression of c-FLIP and XIAP at mRNA and protein level in KRAS-mutated NSCLC cells. Combined JQ1 with TRAIL significantly enhanced apoptosis[
Due to intensive research efforts over the past decades, the knowledge of epigenetic regulation in carcinogenesis is expanding rapidly. This knowledge provides new insights into the role of histone modifications in oncogenic gene transcription. Consequently, histone modifying enzymes have been recognized as drug targets. In this review, we summarize recent discoveries involving histone modifications and the enzymes involved. We focus on small molecules targeting these enzymes involved, and we highlight their effects on TRAIL-induced apoptosis. Finally, we indicate new targets in
Conceptualization: Zhang BJ
Writing original draft, review and editing: Zhang BJ, Chen D, Dekker FJ, Quax WJ
Figure creating: Chen D
Resources: Dekker FJ, Quax WJ
Funding acquisition, Supervision: Quax WJ
Not applicable.
This research was partly funded by The Dutch Technology Foundation (STW) (No. 11056) and European Fund for Regional Development (KOP/EFRO) (No. 068 and No. 073). Zhang BJ and Chen D have received a PhD scholarship from China Scholarship Council.
All authors declared that there are no conflicts of interest.
Not applicable.
Not applicable.
© The Author(s) 2020.