Epigenetic priming (also known as gene priming) is the modification to a cell's epigenome whereby specific chromatin domains within a cell are converted from a closed state to an open state, usually as the result of an external biological trigger or pathway, allowing for DNA access by transcription factors or other modification mechanisms. The action of epigenetic priming for a certain region of DNA dictates how other gene regulation mechanisms will be able to act on the DNA later in the cell’s life. Epigenetic priming has been chiefly investigated in neuroscience and cancer research, as it has been found to play a key role in memory formation within neurons [1] and tumor-suppressor gene activation in cancer treatment [2] respectively.
Epigenetic priming refers to a latent epigenetic state triggered by a stimuli, such as a drug or environmental changes. The epigenetically primed state is characterized by chromatin loosening, which is the change of chromatin state from heterochromatin (tightly bound and inaccessible) to euchromatin (loosely bound and fully accessible), which leads to an increased transcription of certain genes as a result of the easier access and binding of transcription factors. [1] The triggering signal is effectuated by various epigenetic mechanisms, the most prominent of which are histone acetylation and histone methylation. Most of the epigenetic agents involved in histone modifications, such as histone deacetylase (HDAC) variants, are non-targeted, meaning the loosening and tightening of the chromatin is unspecific within the cell. [3] Therefore, epigenetic priming and resultant gene transcription occurs throughout the cell and affects a large variety of chromatin sites.
Chromatin remodeling processes such as histone acetylation and methylation are reversible, and euchromatin sites resulting from epigenetic priming are eventually converted back to heterochromatin by reversal agents such as histone deacetylase. Thus, priming may be artificially controlled by inhibiting these reversal agents within the cell so that the chromatin remains open. Among these approaches, the most well studied is HDAC inhibition.
In order to maintain the epigenome plasticity, enzymes that add (writers) and remove (erasers) the different epigenetic marks are needed. As exemplified by histone acetylation in the Epigenetic Priming Model figure above, there is an interplay between these writers and erasers that allows the genome to be responsive to external or internal stimuli. In the case of acetylation, histone acetyltransferases add acetyl groups to the histones and histone deacetylases (HDAC) remove them. Both are present within a cell at a given time, meaning that an acetylated (open) region of chromatin might be reverted to closed form. HDAC inhibition ensures that chromatin is left in an open state by prohibiting the open to closed transition, leading to lasting gene expression and other epigenetic activity.
Epigenetic priming was first described in cancer research when epigenetic alterations on tumor-suppressor genes (TSG) were found to be drivers of carcinogenesis. [2] Epigenetic alterations (e.g. DNA methylation) resulting in TSG inactivation as a common means of tumor formation. Contrary to regular DNA mutations common in cancer, methylation is reversible, provided that the chromatin is adequately open to allow hypomethylating agents to access the DNA and prevent methylation. Therefore, priming was investigated as a ‘pre-treatment’ to sensitize the tumerogenic cells to hypomethylating chemotheraputics such as decitabine. [2] Many types of cancer (e.g. gastric) are known for having aberrant epigenetic changes, particularly in DNA methylation. In contrast to DNA mutations which cannot be easily changed through treatment, these aberrant epigenetic changes allow for a reversible treatment avenue.
Epigenetic agents have proved to increase expression of aberrantly silenced genes (i.e. Runx3, Tnf, Pycard, Fas) in mice models after 5-aza-CR treatment . [4] Thus, helping overcome cancer-induced cell dysfunction. Additionally, epigenetic priming has been shown to enhance cytotoxicity of cancer drugs (i.e. SN38 and CDDP), showing promising results in lung and ovarian cancer. [5] Due to their proven effectivity, the FDA approved 5-azacytidine, romidepsin and other DMNT inhibitors (i.e. 5-azacytidine, hydralazine, 5-Aza-2’-deoxycytidine) and HDAC inhibitors (i.e. romidepsin, belinostat, panobinostat) for clinical use . [4] [6]
Several clinical trials have been performed to assess the safety and effectivity of epigenetic therapy as a pretreatment in cancer therapy. Preclinical usage of epigenetic agents like 5-azacytidine (DNMT inhibitor) and romidepsin (HDAC inhibitor) sensitizes cancer cells for further treatment. Some examples of clinical trials performed are listed below.
Epigenetic treatment with 5-azacytidine (5-AZA) and romidepsin before pembrolizumab administration was tested for safety in a clinical trial from 2016 - 2018. Drug administration (5-AZA, romidepsin, 5-AZA + romidepsin) was followed for 14 days in 24 patients between 40–69 years old. Side effects in groups included diarrhea, nausea and fatigue. Moreover, lack of appetite, anemia and thrombocytopenia were independent of the drug combination received by the patient. After this study, epigenetic agent 'pretherapy' with 5-AZA and romidepsin followed by pembrolizumab treatment was deemed feasible and overall safe for patients. [7]
Gastric cancer is heavily influenced by epigenetic aberrations. Analysis showed that DNA methylation changes have a higher influence on gastric cancer than point mutations. A phase I study on gastric cancer 5-AZA pretreatment in combination with epirubicin, oxaliplatin and capecitabine was successful. [8] The epigenetic intervention was fruitful in demethylating loci (i.e. CDKN2A, ESR1, HPP1, MGMT, TIMP3) abnormally methylated in gastric carcinomas.
A phase I study explored the feasibility of epigenetic priming with decitabine in patients with Acute Myelogenous Leukemia (AML) followed by cytarabine and daunorubicin treatment. Patients were treated two weeks before the immunotherapy either with 1 hour infusion (group A) or continuous infusion for 3, or 7 days (group B). Group B showed higher levels of hypomethylation after treatment than group A, but neither showed toxicity by the epigenetic agent. Finally, no significant side effects were encountered. [9]
Older patients with AML diagnosis have poor prognosis, lower rates of complete remission and worsening of overall survival. A phase 2 study was performed evaluating the efficacy and safety of epigenetic priming through decitabine in elderly patients with AML. In 2015, 46 patients who were not candidates for intensive chemotherapy enrolled in the study. Treatment consisted of continuous IV administration of decitabine, followed by 5 days of cytarabine immunotherapy. Patients continued with a second cycle if evidence of disease was found on 15 day bone marrow biopsy, otherwise, they proceeded with decitabine maintenance. The study showed that pretreatment with decitabine followed by cytarabine promoted a higher number of complete remissions (70%) in older patients with AML. [10]
It is believed that epigenetic modifications, and in particular those which perform epigenetic priming, are fundamentally responsible for the encoding of memory within neurons. This idea is supported by various pieces of evidence. Firstly, despite inhibition of protein synthesis during memory formation, memories may be retrieved later on. [11] This, along with the discovery that long-term memory can be restored after synapse deterioration, [12] suggests synaptic structuring (which requires protein synthesis during memory formation) is not the fundamental source of engram encoding within a cell. [13] Furthermore, in mice it has been found that proper histone acetytransferase function is required for memory formation [14] [15] and that HDAC inhibition in neurons can improve learning behavior and long-term memory. [16] An explanation is that, when present in combination with memory-associated neural activity, HDAC inhibitors (HDACi) allow chromatin to remain open and increase transcription of genes that remodel synapses, resulting in increased plasticity and improved memory formation. [13] [17] As a result of these observations, it has been proposed that epigenetic priming is the initial phase of memory formation. [13]
It has been found that different forms of long-term memory are associated with different types of histone acetylation, such as acetylation of H3 versus H4. [15] This suggests that epigenetic priming in neurons which result in different memory profile expressions may be encoded by different histone acetyltransferases. Thus, although the mechanisms that loosen chromatin are unspecific in their target, likely have specificity depending on which ones are activated. In a similar vein, it is believed that the action of different of priming agents, such as the varieties of histone acetyltransferases, may combine to create a stacking effect on neuron chromatin, resulting in significantly increased expression of the associated genes.[ citation needed ]
Epidemiological and experimental studies have shown that environmental factors during early development, such as maternal nutrition and body composition, can influence the metabolic phenotype of the offspring. [18] Epigenetic priming is thought to mediate the persistent changes in gene expression that could eventually lead to metabolic syndrome. [19] Potentially, these induced metabolic disruptions benefit progeny developing in a low resources environment to increased success later in life. [18] The Agouti mouse exemplifies a variation of the aforementioned effect of early environmental exposures on offspring’s fitness. [20]
Histone deacetylases (EC 3.5.1.98, HDAC) are a class of enzymes that remove acetyl groups (O=C-CH3) from an ε-N-acetyl lysine amino acid on both histone and non-histone proteins. HDACs allow histones to wrap the DNA more tightly. This is important because DNA is wrapped around histones, and DNA expression is regulated by acetylation and de-acetylation. HDAC's action is opposite to that of histone acetyltransferase. HDAC proteins are now also called lysine deacetylases (KDAC), to describe their function rather than their target, which also includes non-histone proteins. In general, they suppress gene expression.
Decitabine, sold under the brand name Dacogen among others, acts as a nucleic acid synthesis inhibitor. It is a medication for the treatment of myelodysplastic syndromes, a class of conditions where certain blood cells are dysfunctional, and for acute myeloid leukemia (AML). Chemically, it is a cytidine analog.
Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation.
Histone deacetylase inhibitors are chemical compounds that inhibit histone deacetylases. Since deacetylation of histones produces transcriptionally silenced euchromatin, HDIs can render chromatin more transcriptionally active and induce epigenomic changes.
Chromatin remodeling is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression. Such remodeling is principally carried out by 1) covalent histone modifications by specific enzymes, e.g., histone acetyltransferases (HATs), deacetylases, methyltransferases, and kinases, and 2) ATP-dependent chromatin remodeling complexes which either move, eject or restructure nucleosomes. Besides actively regulating gene expression, dynamic remodeling of chromatin imparts an epigenetic regulatory role in several key biological processes, egg cells DNA replication and repair; apoptosis; chromosome segregation as well as development and pluripotency. Aberrations in chromatin remodeling proteins are found to be associated with human diseases, including cancer. Targeting chromatin remodeling pathways is currently evolving as a major therapeutic strategy in the treatment of several cancers.
Romidepsin, sold under the brand name Istodax, is an anticancer agent used in cutaneous T-cell lymphoma (CTCL) and other peripheral T-cell lymphomas (PTCLs). Romidepsin is a natural product obtained from the bacterium Chromobacterium violaceum, and works by blocking enzymes known as histone deacetylases, thus inducing apoptosis. It is sometimes referred to as depsipeptide, after the class of molecules to which it belongs. Romidepsin is branded and owned by Gloucester Pharmaceuticals, a part of Celgene.
Cancer epigenetics is the study of epigenetic modifications to the DNA of cancer cells that do not involve a change in the nucleotide sequence, but instead involve a change in the way the genetic code is expressed. Epigenetic mechanisms are necessary to maintain normal sequences of tissue specific gene expression and are crucial for normal development. They may be just as important, if not even more important, than genetic mutations in a cell's transformation to cancer. The disturbance of epigenetic processes in cancers, can lead to a loss of expression of genes that occurs about 10 times more frequently by transcription silencing than by mutations. As Vogelstein et al. points out, in a colorectal cancer there are usually about 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. However, in colon tumors compared to adjacent normal-appearing colonic mucosa, there are about 600 to 800 heavily methylated CpG islands in the promoters of genes in the tumors while these CpG islands are not methylated in the adjacent mucosa. Manipulation of epigenetic alterations holds great promise for cancer prevention, detection, and therapy. In different types of cancer, a variety of epigenetic mechanisms can be perturbed, such as the silencing of tumor suppressor genes and activation of oncogenes by altered CpG island methylation patterns, histone modifications, and dysregulation of DNA binding proteins. There are several medications which have epigenetic impact, that are now used in a number of these diseases.
While the cellular and molecular mechanisms of learning and memory have long been a central focus of neuroscience, it is only in recent years that attention has turned to the epigenetic mechanisms behind the dynamic changes in gene transcription responsible for memory formation and maintenance. Epigenetic gene regulation often involves the physical marking of DNA or associated proteins to cause or allow long-lasting changes in gene activity. Epigenetic mechanisms such as DNA methylation and histone modifications have been shown to play an important role in learning and memory.
Embryonic stem cells are capable of self-renewing and differentiating to the desired fate depending on their position in the body. Stem cell homeostasis is maintained through epigenetic mechanisms that are highly dynamic in regulating the chromatin structure as well as specific gene transcription programs. Epigenetics has been used to refer to changes in gene expression, which are heritable through modifications not affecting the DNA sequence.
The epigenetics of schizophrenia is the study of how inherited epigenetic changes are regulated and modified by the environment and external factors and how these changes influence the onset and development of, and vulnerability to, schizophrenia. Epigenetics concerns the heritability of those changes, too. Schizophrenia is a debilitating and often misunderstood disorder that affects up to 1% of the world's population. Although schizophrenia is a heavily studied disorder, it has remained largely impervious to scientific understanding; epigenetics offers a new avenue for research, understanding, and treatment.
Epigenetic regulation of neurogenesis is the role that epigenetics plays in the regulation of neurogenesis.
Epigenetic therapy refers to the use of drugs or other interventions to modify gene expression patterns, potentially treating diseases by targeting epigenetic mechanisms such as DNA methylation and histone modifications.
Neurodegenerative diseases are a heterogeneous group of complex disorders linked by the degeneration of neurons in either the peripheral nervous system or the central nervous system. Their underlying causes are extremely variable and complicated by various genetic and/or environmental factors. These diseases cause progressive deterioration of the neuron resulting in decreased signal transduction and in some cases even neuronal death. Peripheral nervous system diseases may be further categorized by the type of nerve cell affected by the disorder. Effective treatment of these diseases is often prevented by lack of understanding of the underlying molecular and genetic pathology. Epigenetic therapy is being investigated as a method of correcting the expression levels of misregulated genes in neurodegenerative diseases.
Human herpes viruses, also known as HHVs, are part of a family of DNA viruses that cause several diseases in humans. One of the most notable functions of this virus family is their ability to enter a latent phase and lay dormant within animals for extended periods of time. The mechanism that controls this is very complex because expression of viral proteins during latency is decreased a great deal, meaning that the virus must have transcription of its genes repressed. There are many factors and mechanisms that control this process and epigenetics is one way this is accomplished. Epigenetics refers to persistent changes in expression patterns that are not caused by changes to the DNA sequence. This happens through mechanisms such as methylation and acetylation of histones, DNA methylation, and non-coding RNAs (ncRNA). Altering the acetylation of histones creates changes in expression by changing the binding affinity of histones to DNA, making it harder or easier for transcription machinery to access the DNA. Methyl and acetyl groups can also act as binding sites for transcription factors and enzymes that further modify histones or alter the DNA itself.
Epigenetics of depression is the study of how epigenetics contribute to depression.
Neuroepigenetics is the study of how epigenetic changes to genes affect the nervous system. These changes may effect underlying conditions such as addiction, cognition, and neurological development.
Pharmacoepigenetics is an emerging field that studies the underlying epigenetic marking patterns that lead to variation in an individual's response to medical treatment.
H4K16ac is an epigenetic modification to the DNA packaging protein Histone H4. It is a mark that indicates the acetylation at the 16th lysine residue of the histone H4 protein.
H4K12ac is an epigenetic modification to the DNA packaging protein histone H4. It is a mark that indicates the acetylation at the 12th lysine residue of the histone H4 protein. H4K12ac is involved in learning and memory. It is possible that restoring this modification could reduce age-related decline in memory.
Epigenetics of chronic pain is the study of how epigenetic modifications of genes affect the development and maintenance of chronic pain. Chromatin modifications have been found to affect neural function, such as synaptic plasticity and memory formation, which are important mechanisms of chronic pain. In 2019, 20% of adults dealt with chronic pain. Epigenetics can provide a new perspective on the biological mechanisms and potential treatments of chronic pain.