There is a definite  gender bias  in the distribution of ASD.  There are about four times as many affected males across the ASD population.  Even when patients with mutations in  X-linked genes  ( MECP2  and  FMR1 ) are excluded, the gender bias remains.  However, when only looking at patients with the most severe cognitive impairment, the gender bias is not as extreme.  While the most obvious conclusion is that an X-linked gene of major effect is involved in contributing to ASD, the mechanism appears to be much more complex and perhaps epigenetic in origin. [ 25 ]


Based on the results of a study on females with  Turner syndrome , a hypothesis involving epigenetic mechanisms was proposed to help describe the gender bias of ASD.  Turner syndrome patients have only one X chromosome which can be either maternal or paternal in origin.  When 80 females with  monosomy  X were tested for measures of social cognition, the patients with a paternally derived X chromosome performed better than those with a maternally derived X chromosome.  Males have only one X chromosome, derived from their mother.  If a gene on the paternal X chromosome confers improved social skills, males are deficient in the gene.  This could explain why males are more likely to be diagnosed with ASD. [ 53 ]


In the proposed model, the candidate gene is silenced on the maternal copy of the X chromosome.  Thus, males do not express this gene and are more susceptible to subsequent impairments in social and communication skills.  Females, on the other hand, are more resistant to ASD. [ 54 ] [ 55 ] [ 56 ] [ 57 ]  Recently a cluster of imprinted genes on the mouse X chromosome was discovered; the paternal allele was expressed while the female copy was imprinted and silenced. [ 58 ] [ 59 ]  Further studies are aimed at discovering whether these genes contribute directly to behavior and whether the counterpart genes in humans are imprinted. [ 25 ]


Epigenetic alterations of the methylation states of genes such as  MECP2  and  EGR2  have been shown to play a role in autism and autism spectrum disorders.  MECP2 abnormalities have been shown to lead to a wide range of phenotypic variability and molecular complexities. [ 60 ]   These variabilities have led to the exploration of the clinical and molecular convergence between  Rett syndrome  and autism. [ 60 ]


Sleeping  and  language impairments , seizures, and developmental timing are common in both autism and Rett syndrome (RTT).  Because of these phenotypic similarities, there has been research into the specific genetic similarities between these two pervasive developmental disorders.  MECP2 has been identified as the predominant gene involved in RTT. It has also been shown that the regulation of the MECP2 gene expression has been implicated in autism. [ 61 ]   Rett syndrome brain samples and autism brain samples show immaturity of  dendrite spines  and reduction of cell-body size due to errors in coupled regulation between MECP2 and EGR2. [ 62 ]    However, because of the multigene involvement in autism, the MECP2 gene has only been identified as a vulnerability factor in autism. [ 63 ]   The most current model illustrating MECP2 is known as the transcriptional activator model.


Another potential molecular convergence involves the  early growth response gene-2  (EGR2). [ 60 ]   EGR2 is the only gene in the EGR family that is restricted to the central nervous system and is involved in  cerebral development  and  synaptic plasticity . [ 60 ]   EGR2 expression has been shown to decrease in the cortexes of individuals with both autism and RTT. [ 64 ]   MECP2 expression has also been shown to decrease in individuals with RTT and autism.  MECP2 and EGR2  have been shown to regulate each other during  neuronal maturation . [ 64 ]  A role for the dysregulation of the activity-dependent EGR2/MECP2 pathway in RTT and autism has been proposed. [ 64 ]  Further molecular linkages are being examined; however, the exploration of MECP2 and EGR2 have provided a common link between RTT, autism, and similarities in phenotypic expression.


Folate pathways have been studied to be potential predictors of ASD. A few genetic polymorphisms such as folate hydrolase 1 and hydroxymethyltransferase 1 along with  hyperhomocysteinemia  were used as risk factors to develop an  artificial neural network  (ANN). Studies showed that this model was around 63.8% accurate in predicting ASD risk, implying a moderate association between genetic polymorphisms of the folate pathway and autism risk. [ 41 ]
*8*


The most important methyl donor for DNA methylation is 5-methyl-tetrahydrofolate. Consequently, any changes in folate levels or folate metabolism could significantly impact DNA methylation and contribute to what causes autism. This idea is what makes folate pathways a potential predictor of ASD because genetic  polymorphisms  of the folate pathway could have different effects on DNA methylation. In general, lower folate levels in pregnant women have been associated with increased ASD risk. The effect of enhancing folate levels on the symptoms of ASD are still being researched and have yet to be confirmed. [ 65 ]


Epigenetics of autoimmune disorders  is the role that  epigenetics  (heritable changes that do not involve alterations in DNA sequences) play in  autoimmune diseases . Autoimmune disorders are a diverse class of diseases that share a common origin. These diseases originate when the  immune system  becomes dysregulated and mistakenly attacks healthy tissue rather than foreign invaders. These diseases are classified as either local or systemic based upon whether they affect a single body system or if they cause systemic damage.


Whether someone develops an autoimmune disorder is dependent on genetics as well as environmental factors. Some families show genetic predisposition for these conditions, however genetics alone is often not sufficient to explain whether someone will develop an autoimmune condition. Smoking, stress, and diet can produce epigenetic modifications to the genome that alter the regulation of immune system-specific genes leading to the onset of these conditions.


The main mechanisms of epigenetic alterations are  DNA methylation ,  histone modifications , and regulation by  non-coding RNAs .  These epigenetic changes regulate the expression of genes, including those involved in the immune system, and therefore these modifications play a role in the onset and symptoms of different systemic and local autoimmune diseases. [ 1 ]


DNA methylation  is an epigenetic modification that interferes with transcription and causes decreased levels of gene expression. The addition of methyl groups to DNA nucleotides inhibits transcription by creating a surface that transcription factors are unable to bind. Additionally, DNA methylation recruits methyl-CpG-binding domain proteins that signal for the formation of co-repressor complexes that alter chromatin structure and further inhibit transcription. A hypermethylated DNA state is associated with gene silencing while a hypomethylated DNA state is associated with increased levels of transcription and gene expression. DNA methylation is carried out by  DNA methyltransferases  (DNMTs) which attach methyl groups at the 5th position of a cytosine nucleotide. In vertebrates, gene expression is modulated in particular by methylation within a region of the genome known as a  CpG island , a region near a gene's promoter that contains a high percentage of cytosine and guanine nucleotides. [ 2 ]  DNA demethylation is carried out by  ten-eleven translocation (TET) enzymes  which convert  5-methylcytosine (5mC) into hydroxymethylcytosine (5hmC), leading to the demethylation of that segment of DNA and an increase in gene expression. TET inhibitors have been identified as potential treatments for autoimmune diseases, particularly  rheumatic  ones. [ 3 ]


Histone modification , resulting in conformational changes to protein binding sites, is involved in autoimmune disorders. Histone acetylation leads to increased transcription by promoting gene expression. Primarily, histone acetylation increases gene expression by reducing cross-linking between neighboring  nucleosomes . Preventing this interaction between adjacent nucleosomes serves as a key driver of condensation. Additionally, histone acetylation also interferes with the electrostatic interaction between positively charged histones and negatively charged DNA by neutralizing some of the positive charges on the histone tails. This helps further promote gene expression by causing the histones to relax their grip on the DNA. Although acetylation helps to make DNA more accessible for transcription, histone acetylation's ability to make  chromatin remodeling  more likely to occur is an extremely important part in its ability to alter gene expression. This remodeling allows condensed  heterochromatin  to transform into a more relaxed  euchromatin  which is associated with higher levels of gene transcription.


Acetylation also functions as a way of recruiting transcription factors that promote gene expression. One way this recruitment occurs is through the activity of  TAF1  (TATA-box binding protein associated factor 1) which contains a double  bromodomain  and can detect very low levels of histone acetylation. TAF1 detects acetylation and then recruits transcription factors to the acetylated region. Acetylation frequently occurs near promoter regions and is recognized by TAF1 which tethers TFIID to this region in order to increase the likelihood of TFIID locating the core promoter and initiating transcription. TAF1 also behaves as a HAT ( histone acetyltransferase ) and acetylates nearby histones at an increased frequency. Acetylation also prevents the addition of repressive marks to the DNA. [ 3 ]


Normally,  histone deacetylases  (HDACs) serve to remove acetyl groups from the lysine residue of the histone causing a decrease in gene expression. HDAC activity is involved in the pathology of autoimmune diseases, such as in rheumatoid arthritis where HDAC activity is low in the synovial tissues. [ 4 ]  Histone methylation is also implicated in autoimmune disorders. This can be by inhibition of histone methylation such as in systemic sclerosis or by elevated histone methylation at certain gene loci in Type I diabetes. [ 4 ]


Histone modification can give rise to rheumatic, endocrinological, and gastrointestinal autoimmune disorders. Histone modification leads to either activation or repression of gene expression depending on the disorder. Suberanilohydroxamic acid (SAHA), also known as Vorinostat, inhibits the activity of HDACs. Vorinostat has shown promise as a treatment for immune system dysfunctions. Vorinostat, by inhibiting HDACs, can treat cutaneous T cell lymphoma. Though epigenetics-based treatments for autoimmune rheumatic disorders does not exist yet, Vorinostat's function in treating T cell lymphoma is a basis for a path to epigenetics-based treatment of autoimmune rheumatic disorders. [ 3 ]


Micro-RNAs  (miRNAs) are small RNA fragments, 18–23 nucleotides in length, that act to regulate gene expression post-transcriptionally. [ 3 ]  miRNAs play a critical role in modulating the immune response since they influence whether or not the mRNA transcribed from specific immune related genes will go on to be translated into protein or not. Alteration of different miRNA levels is associated with autoimmune disease pathogenesis and symptoms. Depending on the disorder, upregulation or downregulation of a specific type of miRNA may be observed. miRNAs negatively regulate gene expression by binding to complementary mRNA sequences within the 3' untranslated region (3' UTR). [ 3 ]  This process of miRNA activity begins with the synthesis of pri-miRNA in the nucleus by RNA polymerase II which is then converted into pre-miRNA. This pre-miRNA exits the nucleus and is cut by  Dicer  into a double stranded RNA with one of the strands binding to the RISC complex. This binding leads to the association of the miRNA with its target mRNA sequence and encourages the degradation of the mRNA or represses translation of the mRNA, decreasing gene expression. [ 5 ]  miRNA can also affect gene expression via the binding of RNA-induced transcriptional silencing (RITS) complex. The binding of the RITS complex to miRNA allows for post-transcriptional histone modifications such as methylation to be made further altering gene expression. [ 1 ]


Long non-coding RNAs have also been identified as playing an important role in gene expression. These lncRNAs are RNAs that are more than 200 nucleotides in length but are not transcribed into any functional protein. They have been identified to play a role in the epigenetics of diseases such as discoid lupus erythematosus and rheumatoid arthritis. One method by which lncRNAs regulate gene expression is through the process of X inactivation which functions as a way to provide dosage compensation. In X-inactivation, Xist (X-inactive specific transcript) lncRNA is transcribed and coats the Xi chromosome that will be inactivated, beginning the process of chromosome condensation and repression of genes on that X chromosome. [ 6 ]  Still, more research is needed to further understand the mechanisms these lncRNAs use in order to regulate gene expression. [ 3 ]


Systemic autoimmune diseases  are those that effect multiple organ systems rather than targeting a single type of tissue or organ system.


Rheumatoid arthritis  is a degenerative autoimmune disease that causes damage and inflammation to a patient's joint and can affect bodily systems involving the heart, lungs, nerves, eyes, bones, and skin. Global DNA hypomethylation is a hallmark of Rheumatoid Arthritis and is observed in the early stages of this disease, when joint degeneration begins. [ 3 ]  Those who suffer from RA have a global decreased level of methylation on many DNA promoter regions including those associated with normal immune system and joint function. This overexpression from hypomethylation is observed in various genes such as ITGAL, CD40LG, PRF1, and more. Taking a closer glance at those who suffer from RA, it can be observed that within the synovial cells, there is a level of hypomethylation which is proposed to cause the expression and overproduction of the cytokines which perpetuate the inflammatory response causing inflammation within the synovial fluid, which is the fluid that exists between the joints. [ 7 ]  Typically, healthy joints have a thin layer of synovial tissue that lines the cavities of the joints. However, as an increase number of immune cells begins to penetrate the tissue, the synovial tissue begins to form a thick lining layer that consists of different macrophages and synovial cells. [ 8 ]  Hypomethylation of CD40LG, which will make the T-cells within the immune response, can lead to T-cell overexpression and becomes a contributing factor to how Rheumatoid Arthritis functions within an inflammatory response. Patients with RA often display anti-cyclic citrullinated peptide (anti-CCP) antibodies and have hypomethylation of the retrotransposon gene L1, as well as decreased methylation at the  Il6  and  ERa  promoter. [ 9 ]  TET proteins, more specifically the TET1-TET3 enzymes and TET2 in T cells can demethylate DNA which helps to set and clarify the early stages of RA. [ 3 ]   The RA development from demethylation of histones in the patient can lead to expression of high levels of IL-6 which causes destruction in the joints. [ 3 ]  miRNAs also play an important part in rheumatoid arthritis development as well, particularly the upregulation of miRNA-146a and miRNA-150. Although more research is needed, lncRNAs have been implicated to play a role in this disease since current treatments used for this disorder show altered expression of 85 different lncRNAs in RA patients on tocilizumab and  adalimumab. [ 3 ]


As a systemic disease, RA can develop other complications and cause damage to tissues and organs besides the joints, which include the heart, lungs, bones, skin, and eyes. In regard to the heart, RA patients typically experience some form of heart disease such as pericarditis, myocarditis, and coronary artery disease. Because the synovial tissue and circulating immune cells release pro-inflammatory cytokines (TNF-α and IL-6), this leads to systemic inflammation and the overexpression of T-cell and B-cell lymphocytes. Autoantibodies, antibodies that react with self-antigens, in RA then affect the structures of the cardiovascular system, such as the myocardium and heart valves, thus leading to various forms of cardiovascular disease. [ 10 ]  Osteoporosis is another common systemic disease that can occur along with RA. Systematic inflammation, autoantibody circulation in the body, and the secretion of pro-inflammatory cytokines work together to contribute to the bone erosion and fragility in RA patients. The inflammatory cytokines decrease osteoblastogenesis while promoting osteoclastogenesis, which is why bone loss is more likely to occur, especially around the joints of those who suffer from RA. [ 10 ]  Osteoblastogenesis refers to the process by which osteoblasts, the cells responsible for bone formation, are generated and differented to develop and maintain the bone. Meanwhile, osteoclasts, cells involved with the dissolution and reabsorption of old bone tissue, are involved in the process of osteoclastogenesis. [ 11 ]


There are several environmental risks factors that also contribute to the development of rheumatoid arthritis through epigenetic modifications induced by external stimuli, which include smoking and air pollution. The main source of air pollution has come from heavy traffic, fuel burners, forest fires, and solid fuel combustion, which usually contain a mixture of particles and gases such as nitrate,  sulfur dioxide , ozone, and carbon monoxide. [ 12 ]  These pollutants can release reactive oxygen species that can be easily inhaled into the respiratory tract to activate nuclear factor ƙappa B (NF-ƙB), an important regulator for pro-inflamatory cytokine production in RA. This process leads to an excess production of T helper lymphocyte type 1 (Th1) cytokines that migrate to tissues in the synovial joints, further promoting inflammation. [ 12 ]  In addition, smoking has been found to be one of the most common environmental risk factor for developing RA as it affects the lung tissue and alters the expression of sirtuins (SIRT) in the body. SIRT is a deacetylase protein that is involved in modifying histone and non-histone proteins, and it is essential for the body's ability to adapt as it helps to maintain the stability of the genome when cells are using epigenetic mechanisms to respond to stress. [ 13 ]  Other general risk factors for rheumatoid artithritis include sex, age, family history, and excess weight. Women are more likely to develop RA compared to men, and RA typically begins developing in middle-aged adults. [ 14 ]


Because rheumatoid arthritis is caused by certain epigenetic mechanisms involved in regulating biological processes, these epigenetic alterations have been found to be reversible and could be altered by diet, drugs, and other environmental factors. For example, inhibition of a  of the histone deacetylase HDAC6i can ameliorate collagen type II - induced arthritis.  [ 15 ]  This suggests that prevention and therapy of diseases that target the epigenetic mechanisms could help to treat chronic inflammatory diseases. Efforts have been made to create drugs that either change or restore the original epigenetic mechanisms that occur within the body, and some DNA methyltransferase inhibitors have already been used to treat inflammatory conditions such as pancreatitis. [ 13 ]  However, more clinical trials and testing still needs to be done before these drugs can be approved.


Systemic lupus erythematosus  is the most common form of lupus and is a condition in which the immune system attacks healthy bodily tissue causing wide-spread inflammation and tissue damage across many organ systems. Hypomethylation is observed across the epigenome in those with systemic lupus. The promoter regions of many genes including ITGAL, CD40LG, and CD70 are shown to be hypomethylated as well as the 18S and 28S ribosomal gene promoters. In particular, this DNA hypomethylation is thought to alter the chromatin structure of T cells enhancing the immune and inflammatory response observed in those with this condition. [ 7 ]  Genome wide it has been shown that when comparing the epigenomes of pairs of identical twins in which one twin is afflicted by the condition and one is not, the twin possessing the condition shows global decreases in methylation of their genomes. This hypomethylation causes genes that are traditionally repressed by methylation to be overexpressed particularly in CD4+ T cells. It has been suggested that inhibition of DNMT1 produces the loss of methylation observed in those afflicted by systemic lupus. DNMT1 is a  DNA methyltransferase that maintains methylation patterns across the process of DNA replication, ensuring that new copies of DNA contain the methylation pattern observed on the original parent strand. Inhibition of DNMT1 causes methylation patterns to be lost across generations and epigenome-wide hypomethylation is observed as a result. In particular, it has been observed that DNMT1 expression is lower in immune T-cells. [ 16 ]  Levels of DNMT1 is partly regulated by the ERK signaling pathway in the body. In patients with SLE, ERK activity has been found to be reduced in lupus CD4+ T-cells. When ERK activity is suppressed, it causes there to be a reduction in DNMT1 expression and DNA hypomethylation levels increases. Because of this, the DNA of CD4+ T-cells in SLE patients becomes hypomethylated, which causes them to be autoreactive when encountering self-class MHC II molecules. [ 17 ]  Because it is a systematic disease, SLE can also affect many other body systems including the kidneys, brain, central nervous system, blood system, lungs, and heart. [ 18 ]  There is no cure for SLE but treatments aim to control inflammation, alleviate pain and damage to the joints, prevent disease flares, and minimize organ damage. [ 19 ]


Several environmental factors such as smoking, viral infections, various chemicals, and UV light, have been found to induce oxidative stress that leads to inhibition or reduction of DNMT1 levels, which reduces DNA methylation in CD4+ T-cells and can prompt autoimmunity. In patients with SLE, the disease can be triggered or induced by exposure to UV light with its effects appearing to be dose dependent. UV-B light can induce apoptosis of dermal cells, and this can release large amounts of autoantigens and pro-inflammatory cytokines, which can trigger systematic inflammation. [ 17 ]  Additionally, vitamin D has been found to have a role in SLE activity. Vitamin D has a protective role in regulating the immune system and possibly in the regulation of gene expression important for SLE pathogenesis. Deficiency of vitamin D has also been shown to be associated with higher lupus disease activity as there seems to be a decrease in the proliferation and production of the IgG immunoglobulin. [ 17 ]  Although there is no clear association, smoking and drinking have also been reported as potential environmental risk factors for SLE.


Systemic sclerosis  (SSc) is an autoimmune disease characterized by system wide excessive collagen deposits. It can affect several bodily systems including the skin, internal organs, lungs, heart, kidneys, musculoskeletal system, and the gastrointestinal tract. [ 20 ]  It causes the patient's skin and connective tissues to tighten and harden due to the uncontrolled accumulation of extracellular matrix proteins on the joints and various internal organ system which can lead to premature death in patients. [ 7 ]  Fli1 is a transcription factor that negatively regulates collagen production such that the higher the Fli gene expression, the less collagen is produced. In SSc patients, hypermethylation of CpG islands in the Fli1 promoter region is observed, inhibiting transcription of the Fli gene and increasing collagen production beyond normal levels causing collagen build-up and an overproduction of fibrous connective tissue. This causes joint damage, scarring, and thickening of the skin. Patients with SSc are also observed to have decreased levels of DNA methyltransferases (DNMTs) in their CD4+ T cells which play an important role in the immune system. This reduced methylation is associated with immune dysfunction and the progression of SSc and its inflammatory effects, however more research is needed to further understand this implication. [ 9 ]  Patients with systemic sclerosis also display hypomethylation of the collagen genes COL23A1 and COL4A2. This overexpression of these collagen genes leads an overproduction of collagen characteristic to tissue fibrosis. The TGF-β signaling pathway and Wnt/β-catenin signaling pathway also play an important role in this disease. The TGF-β signaling pathway is responsible for several cellular responses from cell differentiation and migration in developing cells to regulating homeostasis within an immune response in the body.  The TGF-β signaling pathway is involved in that activation of fibroblast which precedes fibrosis. The gene, ITGA9 which codes for alpha integrin 9 and is involved in this pathway, is hypomethylated in those with this condition leading to overexpression of integrins which leads to fibrosis as wells as provides positive feedback to this pathway further encouraging fibroblast activation. [ 21 ]  An Integrin is a type of receptor that is a transmembrane receptor meaning it is able to communicate from cell to cell and help the cell attach and adhere to nearby cells.


There are several different types of environmental risk factors that can affect autoimmune diseases. Frequency exposure to crystalline silica dust has been recognized as a risk factor for SSc. SSc patients with occupational exposure to silica has been shown to be a factor in the pathogenesis of the disease. Additionally, organic solvent exposure has been found to be a risk factor for the disease, although the specific agents involved have not been identified. [ 22 ]


Because epigenetics has been recognized as a contributor to SSc pathogenesis, epi-drugs have been tested as potential therapeutics for the disease. Drugs targeting certain miRNAs in SSc to replace or inhibit them have been found to reduce some fibrosis effects. However, several issues including inconsistent results of epigenetic modifications and problems getting the treatment to the proper tissues means that no definitive epi-drug has been created for the disease. [ 23 ]


Local dermatological autoimmune disorders are those that effect skin and mucous membranes.


Discoid lupus erythematosus  is one of the most common cutaneous diseases characterized by an attack on healthy epidermal tissue by the immune system leading to lesions on the skin, inflammation, and rashes. Localized DLE lesions will occur on the face, ears, and scalp. Disseminated DLE, below the neck lesions, is unusual if localized DLE lesions are absent. [ 24 ]  DLE lesions can result in pigment changes, scarring of the skin, potential hair loss, and rare occurrences of squamous cell carcinoma. [ 24 ]  Differential expression, a significant observed difference in expression levels ,  of lncRNAs and circRNAs, identified in a study by Xuan et al., [ 25 ]  alter the mucosa, which is the inner lining and moist part of the epidermis such as inside the mouth and nose; this differential expression affected by DLE causes this tissue to become inflamed and crusty at times. The mucosa serves as a key part in the pathology of this disease. [ 26 ]  There are transcripts such as lncRNA and circRNAs that have been found to be expressed in affected tissues of those who have DLE. These transcripts were more heavily expressed in the tissue of those affected by DLE as compared to control unaffected healthy tissue. The pattern of expressed lncRNAs and circRNAs helps to discriminate against affected tissue of DLE and healthy unaffected tissues establishing a useable pattern for reference. [ 26 ]  Additionally,  discovered through analysis of the function and expression of lncRNA, lncRNAs are correlated with the expression of  Il19, CXCL1, CXCL11, and TNFSF15 which all are related to an immune response helping to identify the pathway in which DLE is manifested epigenetically by the abnormal expression of IncRNA. Another key portion of the study performed by Xuan et al. was the identification of STAT4 as a key transcription factor responsible for influencing the regulation of many target genes involved in DLE. [ 26 ]  STAT4 is a very important transcription factory as it is correlated with the pathogenesis and this the progression of DLE, many of the STAT4 genes targets have been seen to act to enrich various functional pathways involved in progression.


Psoriasis  is an inflammatory skin condition characterized by T-cell activation and the development of scaly red patches on the skin caused by the overproduction of skin cells. [ 27 ]  Psoriasis can be broken down into plaque psoriasis and psoriatic arthritis.  Psoriatic arthritis  differs from plaque psoriasis because the psoriatic skin lesions are also accompanied by inflammation, joint pain, and joint stiffness attributed to immune system complication produced by psoriasis. [ 28 ]  Psoriatic arthritis patients secrete high levels of immune-regulated cytokines and chemokines. It has been shown that epigenetics modifications play a prominent role in the symptoms and pathogenesis of this condition. Alterations in miRNA expression levels are one of many epigenetic modifications that accompany the onset of this disease. In particular, miRNA-203 levels are decreased in those with psoriatic arthritis and this has been linked to psoriasis pathogenesis. [ 3 ]  miRNA-203 is responsible for targeting suppressors of cytokine signaling 3 (SOC3) and ensures that the immune response is kept in check. However, when miRNA-203 levels are low, cytokine signaling occurs at a high level leading to a heightened immune response. Developing a treatment that can increasing miRNA-203 levels has been implicated as a way to decrease the inflammatory immune response observed in patients with this condition. Abnormal expression of HDACs and HATs have also been observed in patients with psoriasis. [ 3 ]  Peripheral blood mononuclear cells, which are a collection of immune system cells, exhibit a global decrease in acetylation of histone 4 in psoriasis patients as well as increased HDAC-1 levels. HDAC inhibitors have been identified as a potential treatment for psoriasis as well as many other inflammatory autoimmune disorder. [ 29 ]


Sjorgen's syndrome  is a dermatological autoimmune disorder that targets exocrine glands [ 30 ]  and attacks lacrimal and salivary glands causing a decrease in the secretion of tears and saliva. This results in inflammation, dry eyes, and dry mouth. Patients with this condition experience a buildup of white blood cells in the salivary glands known as lymphocytic infiltrate. The first confirmed case of Sjogren's syndrome was reported in 1892. [ 31 ]  Current research is largely focused on the innate immune system's role in the pathogenesis of this diseases. [ 3 ]  In Sjorgen's patients, miRNA-146a is upregulated in PBMCs and is associated with the pathogenesis of this disease. miRNA-146a plays an important role in regulating the immune system by providing negative feedback to toll-like receptor (TLR) signaling which is used to engage the innate immune response. When miRNA-146a is upregulated, this negative feedback to TLR signaling decreases leading to inflammation and a heightened immune response that can damage healthy cells such as those in the lacrimal and salivary gland. [ 32 ]  miRNA-150 and miRNA-149 are also upregulated in the salivary glands and lymphocytes of those with Sjorgen's. These miRNAs are targeted to mRNAs that play an important role in immune function and regulating pro-inflammatory cytokine levels. The overexpression of these miRNAs thus leads to a heightened and dysregulated immune response. [ 7 ]  Epigenetic alterations to the genes of CD4+ T-cell in the immune system are also observed in this condition. Specifically, research has linked hypomethylation of CD70, a T-cell costimulatory gene, to the development of Sjogren's syndrome. [ 33 ]  Decreased expression of the  FOXP3  gene, which leads to DNA hypermethylation, is also observed in these CD4+ T-cells. This causes CpG hypermethylation leading to the downregulation of many cells that are essential for keeping the immune system in check. [ 33 ]


Alopecia Areata  is a dermatological autoimmune condition where the immune system attacks the immune system and causes patchy or total hair loss usually affecting the scalp and face but can cause hair loss on the whole body. [ 34 ]  The cause of alopecia areata is unknown and typically people with the condition have no other symptoms. Genetic and environmental factors, like stress, are believed to trigger an episode of the condition. [ 35 ]  This condition was described as “bite alopecia” over 3500 years ago by Cornelius Celsus. The modern term was not used until the early 1700s to late 1800s. [ 36 ]


In a study done by Zhou et al. [ 37 ]  a significant increase in DNA methylation, specifically T-cells, was detected after the analysis of peripheral blood mononuclear cells in patients with AA compared to healthy control cells. Other areas of increased expression included DNA methylation-regulating enzymes, RANTES, E1A binding protein p300, and HDAC1. There were also decreased levels of HDAC2, HDAC7, and LSD1 expression shown in the peripheral blood mononuclear cells. [ 35 ]  A notable protein in patients with AA is the HDAC1 protein. It has become a more heavily studied protein because of a study with postnatal dermal cells in mice conducted by Park et al. [ 38 ]  that has shown that a HDAC inhibitor, that is known for upregulating genes that effect hair follicle pathways, is causing HDAC 1 dysregulation in AA patients. This dysregulation is causing patients with AA to have higher serum levels of HDAC1. [ 39 ]


Hashimoto's thyroiditis  is an endocrine disease in which a patient's immune system attacks their thyroid gland. Hashimoto's thyroiditis usually manifests via hypothyroidism, which is characterized by the build up of white blood cells in the thyroid and the production of thyroid autoantibodies. Research suggests a strong genetic susceptibility when it comes to autoimmune thyroid diseases like Hashimoto's thyroiditis as well as an epigenetic role in the pathology of Hashimoto's thyroiditis. The thyroglobulin (Tg) gene, a gene involved in the synthesis of the thyroid hormones, thyroxine and triiodothyronine, plays an important role in the pathogenesis of Hashimoto's thyroiditis. In those with Hashimoto's, an alteration in the histone methylation pattern at the thyroglobulin (Tg) promoter has observed causing decreased gene expression and thus decreased production of thyroid hormones. IRF-1 is a transcription factor for Tg whose binding is impacted by histone methylation patterns. [ 40 ]


Skewed X chromosome inactivation has also been implicated in autoimmune thyroid diseases.  X chromosome inactivation  is a process by which one of the two X chromosomes in females is silenced by being converted into transcriptionally inactive heterochromatin. Skewed X chromosome inactivation is an imbalance in the amount of inactivation that occurs between maternal and paternal X chromosomes leading to the favoring of expression of one X chromosome over the other. In studies of Graves' and Hashimoto's disease, the skew of X chromosome inactivation towards one X chromosome over another in the same tissue is markedly high compared to the control without Graves' or Hashimoto's disease; however, it is not clear why preferential expression of a single X chromosome increases the risk of these diseases. Skewed X chromosome activation in one study defined it to be a 80:20 ratio of activation of one X chromosome over another in the same tissue. [ 41 ]  In Turner syndrome, a chromosomal abnormality in which a person exhibits X chromosome monosomy, patients are at a great risk of developing autoimmune thyroid disease since their genotype mimics an extreme form of X chromosome inactivation since there is only one X chromosome that can be expressed. Though there is no definite mechanism by which skewed X chromosome inactivation influences autoimmune thyroid disease, one possibility being studied is that skewed XCI in the thymus may lead to a lack of thymic expression, ultimately leading to inadequate T cell deletion. X chromosome inactivation is a common and widely-studied epigenetic phenomenon.


Graves' disease  is an autoimmune disease involving thyrotoxicosis, in which the body is affected by the overproduction of thyroid hormone as a result of the immune system attacking the thyroid gland. The overproduction of thyroid hormone is termed hyperthyroidism. Thyrotoxicosis can be caused by hyperthyroidism, thyroiditis, and other conditions. This is generally due to an increase in immunoglobulin antibodies that activate thyroid-stimulating hormone receptor. [ 42 ]  Like Hashimoto's thyroiditis, Graves' disease is qualified as an autoimmune thyroid disease. The epigenetic processes involved in Hashimoto's thyroiditis are also involved in Graves' disease. Namely, these are the modification of histone methylation in Tg and skewed X chromosome inactivation. In the specific case of Graves' disease, discoveries have been made showing the involvement of abnormal DNA methylation at certain CpG sites. This abnormal DNA methylation leads to interferon signaling and other dysregulated immune system-related processes in cases of Graves' disease. The CpG promoter regions of many genes expressed in immune cells are shown to be hypomethylated in epigenetic analysis of Graves' disease patients, meaning that these genes are over-expressed in these immune cells. For example, CD40L protein levels are observed to be high in patients recently diagnosed with Graves' disease. It has been shown that hypomethylation is observed at the CD40L gene. This gene codes for the CD40 ligand protein that binds the CD40 receptor and this binding activates an immune response. The over expression of this gene thus has been attributed to the onset of autoimmune-mediated hyperthyroidism. Additionally, histone methylation in peripheral blood mononuclear cells is abnormal in individuals with Graves' disease. This abnormality, which manifests as hypermethylation, is observed in epigenetic modifier genes such as the CD3 gene family that regulates T cell behavior as well as the expression of other immune function genes. This results in a decrease of the expression of CD3 gene family members in individuals with Graves' disease. [ 43 ]  Additionally, the differential expression of certain non-coding RNAs has recently been implicated in the development of Graves' disease, however more research is needed. These non-coding RNAs could potentially serve as biomarkers for Graves' disease diagnosis upon further study. [ 42 ]


Type I diabetes  is an endocrinological disease in which the immune system's T cells attack the beta cells of the pancreas, disrupting the production of insulin. Though the pathology of Type I diabetes is still being studied, certain epigenetic mechanisms have been implicated in Type I diabetes. Type I diabetes is characterized by global hypermethylation that arises as a result of alterations to homocysteine metabolism. Increased methylation of promoter regions is thought to alter gene expression in ways that cause immune cell dysfunction. Homocysteine metabolism occurs via two pathways. One pathway breaks homocysteine into methionine and then into S-adenosylmethuionine (SAM). Another pathway, the transsulfuration pathway, through numerous steps breaks homocysteine down into glutathionine. Type I diabetics demonstrate insulin insufficiency and this decrease in insulin levels inhibits transsulfuration needed for one of the two pathways of homocysteine breakdown. As a result, homocysteine levels rise and the pathway that converts homocysteine → methionine → SAM becomes the primary method of homocysteine breakdown. In order to accommodate this, DNMTs in S-adenomethionine catalyze methionine breakdown and cause enhanced DNMT activity which leads to global hypermethylation which causes widespread changes to gene expression. [ 7 ]  DNA demethylation is observed at the gene for HOXA9 transcription factor and DNA hypermethylation is observed at the FOXP3 immune response gene promoter region. [ 9 ]   HOXA9  codes for a protein involved in hematopoietic stem cell generation and is hypomethylated in the case of Type I diabetes. [ 44 ]  Recently, an enrichment of differentially variable CpG positions has been identified, which indicates the involvement of altered DNA methylation levels in Type I diabetes pathogenesis. [ 9 ]  More study is needed on this front. Increased DNA methylation variability in immune effector cells in type I diabetes has also demonstrated the involvement of DNA methylation in other processes related to type I diabetes' pathogenesis as well. [ 45 ]


Celiac disease  is a disease in which the small intestine is damaged in those whose bodies are unable to process gluten because of a T cell response that is activated when gluten, from foods such as wheat or rye, is present in the intestines. Several epigenetic mechanisms are implicated in celiac disease, such as DNA methylation, histone modification, and non-coding RNAs. These epigenetic mechanisms are involved in the pathogenesis of celiac disease as well as altered in those with a predisposition for celiac disease. [ 46 ]  Furthermore, unusual methylation in the genes involved in the core NF-κB pathway, a regulator of innate immunity, is implicated in the pathogenesis of celiac disease. [ 46 ] [ 47 ]  A high rate of DNA methylation of CpGs contributes to the development of small bowel adenocarcinomas, which are malignant tumors, in individuals with celiac disease. This CpG hypermethylation is correlated to the loss of expression of the  MLH-1  gene, which is involved in DNA repair. Furthermore, hypermethylation of the  APC gene , a tumor suppressor gene, has been found to cause defects in the mismatch repair mechanisms in individuals with celiac disease. [ 46 ]  An increase in histone acetylation, specifically H3K27ac, has also been found in celiac disease biopsies. When comparing the genes of three different cytokines in response to cytotoxic T lymphocytes in celiac biopsies, an increase in H3K27ac in the promoter and enhancer regions was found in the cytokine INFꞵ genes. [ 46 ]  The regulation of certain microRNAs differs significantly in individuals with celiac disease compared to individuals without celiac disease. These differences were found to come in the form of downregulation of some microRNAs and upregulation of others. This differential regulation likely occurs for microRNAs involved in modulating intestinal barrier function, though more study is needed specific to celiac disease. [ 47 ]


Multiple sclerosis  is a neurological disease characterized by the immune system attacking and destroying the myelin sheaths that coat nerve fibers. Destruction of these sheaths leads to the slowing or loss of electrical transmission of messages across nerve cells and as a result, patients experience weakness, pain, and vision loss. It has been shown that vitamin D deficiency is associated with alteration to epigenetic markers and MS pathogenesis. [ 2 ]  Vitamin D plays an important role in suppressing autoimmunity and in particular Th17 autoimmunity. Th17 is a subset of T helper cells that secrete pro-inflammatory interleukin(IL)-17. Traditionally vitamin D  suppresses transcription of IL17 via recruitment of HDAC2 to the IL17A promoter, however in those deficient in vitamin D, IL17 transcription is increased leading to a heightened inflammatory immune response. Increased expression of miRNA-326 in PBMC cells is also prevalent in those with MS and is known to encourage Th17 cell differentiation. [ 48 ]  Histone H3 citrullination, which alters the methylation of arginine residues and consequently chromatin structure and gene expression, has  been shown to be increased in the brains of MS patients as well. Although more research is needed to understand the mechanism of how histone H3 citrullination contributes to demyelination, research demonstrates that inhibitors of the enzymes involved in this citrullination improve the outlook and progression of this disease. [ 49 ]


Myasthenia gravis  is an autoimmune disease that causes weakness and dysfunction of the patient's skeletal muscles as a result of extensive neurological damage that destroys the communication between the nerves and the muscles. It has been found that individuals who have Myasthenia Gravis possess high levels of the acetylcholine receptor antibody, AchR-Ab, which recruits the immune system to destroy the ACh receptors present at neuromuscular junctions. A significantly higher levels of methylation in the CTLA-4 region is observed in MG patients compared to controls. CTLA-4 gene expression serves as a negative regulator of T-Reg cells and suppress the immune response. When there is a blockade of expression of the CTLA-4 region, as is seen in those with MG, increased T-cell activation occurs and a heightened immune response is observed. The expression of the CTLA-4 generating cytokines that regulate AchR-Ab autoantibodies require further exploration to better understand their mechanism of action. [ 50 ]


Epigenetics of bipolar disorder  is the effect that  epigenetics  has on triggering and maintaining  bipolar disorder .


Bipolar disorder is a chronic mood disorder, characterized by manic and depressive episodes. The symptoms of a manic episode include high mood, low sleep, and reduced inhibition, while the symptoms of a depressive episode include low mood, lethargy, and reduced motivation. There are different types of bipolar disorders; the two most common are bipolar I and bipolar II. Patients are diagnosed with bipolar disorder I if their manic episodes last at least seven consecutive days and they experience major depressive symptoms over the course of two weeks. In bipolar disorder II, patients experience shorter hypomanic episodes or manic symptoms that have less disruptive impacts on their daily lives. Sometimes patients can experience extreme cycling where they experience four or more episodes of mania and major depression in one year. [ 1 ]  In addition to affecting mood, people who have bipolar disorder often deal with impaired cognitive abilities, where memory, speech, attention and decision-making skills are all impacted. Bipolar disorder has one of the highest rates of suicide amongst psychiatric disorders, as well as high comorbidity rates with alcohol and substance use disorders. [ 2 ]


Bipolar disorder has  a genetic component . [ 3 ]  This means that the sequence of  nucleotides  in  DNA  contains information that can lead to bipolar disorder in individuals. Researchers determined that bipolar disorder has a genetic component by comparing individuals who have been diagnosed with the disorder and those who have not. However, findings are inconsistent as to what specific  genes  are involved.


The trouble that researchers have had in conclusively identifying genes that cause bipolar disorder has led them to search for an epigenetic component to bipolar disorder. Epigenetics is the study of heritable  phenotypes  that occur without changes to the primary DNA sequence. Typically, epigenetics focuses on the  expression  and regulation of genes. Common epigenetic mechanisms include  DNA methylation , and  histone modification . More research into the epigenetics behind bipolar disorder is required to reach a firm conclusion, however current results have yielded promising information that supports the idea that bipolar disorder is caused by a combination of genetic and epigenetic factors.


DNA methylation is a commonly researched form of epigenetic modification for its role in decreasing gene expression. DNA methylation works by adding methyl groups to DNA molecules. These affect the activity of gene without actually changing the DNA sequence. DNA methylation has been shown to recruit proteins, like DNA-methyl binding proteins and  polycomb proteins , that are implicated in gene repression and prevent  transcription factors  from binding to DNA. [ 4 ]  DNA methylation has also been shown to affect the expression of genes with important neuronal implications, such as the  BDNF gene  and  serotonergic  genes. [ 4 ]


The  brain-derived neurotrophic factor  (BDNF) gene plays a role in the growth, differentiation, and maintenance of  neurons . There have been consistent differences observed between bipolar disorder patients and controls in the cytosine methylation levels of the BDNF gene  promoter regions  3 and 5. The type of methylation at these regions is methylation of cytosine nucleotides. Typically, hypermethylation of these promoter regions is observed in patients with bipolar disorder. Hypermethylation of the BDNF genes in neurons from frontal cortex was observed in patients with bipolar disorder. When the promoter of the BDNF genes is hypermethylated, BDNF's expression is reduced and therefore decreased levels of BDNF. [ 5 ]  Furthermore, patients with bipolar disorder have been shown to have lower levels of BDNF mRNA, [ 6 ]  showing that the increased methylation is indeed producing lower amounts of transcript. Decreased levels of BDNF have also been found in post mortem tissues of people who committed suicide [ 7 ]  and people with schizophrenia. [ 8 ]  However, BDNF gene promoter region 1 did not have major differences in methylation level between bipolar disorder groups and control groups. When taking into consideration pharmaceutical treatment, subjects who are on both mood stabilizers and antidepressants are found to have higher levels of DNA methylation at this gene than those who are only on mood stabilizing treatments. [ 4 ]  Positive correlations have been found between BDNF increased methylation levels and childhood trauma, severity of depression, impulsivity, and hopelessness. [ 8 ]  Patients with bipolar disorder and in a depressive states have far more methylation of the promoter for BDNF than patients in manic or mixed states. [ 5 ]  There is a strong body of evidence implicating BDNF as a critical component within bipolar disorder. Changes in methylation of this gene or its regulatory sequences can affect the levels of BDNF within an individual.


The neurotransmitter  serotonin  is known for its function as a mood stabilizer and its role in regulating a variety of nervous system functions such as sleep, memory, learning, and mood. Low serotonin levels are typically observed in the depressive phase of bipolar disorder 1. [ 9 ]  Increased methylation of the  5-HTT transporter  and  5-HTR1A receptor  genes of the serotonergic system were observed in individuals with bipolar disorder. [ 4 ]


The 5-HTT transporter is responsible for the reuptake of serotonin from the synaptic cleft back into the presynaptic cell after initial release. This function halts the effect of serotonin on the receptors on the post-synaptic cell and allows the presynaptic cell to replenish its stores of the neurotransmitter. Hypermethylation of the genes encoding this transporter lead to reduced expression of this transporter, and the resulting decrease in presynaptic reuptake is thought to decrease overall serotonin levels in the brain.


5HTR1A receptors are found all throughout the brain, involved in many central nervous system functions like sleep, sex drive, and mood. One of the main functions of this receptor is its role as an  autoreceptor  on neurons that release serotonin. Binding of serotonin to the 5HTR1A receptor on a serotonergic neuron initiates a negative feedback loop that halts further release of serotonin by the neuron. This results in diminished serotonin-induced effects in the post-synaptic cells and maintains the stores of this neurotransmitter in the presynaptic cell. Methylation of the promoter region in the gene encoding the 5HTR1A receptor decreases the concentration of this receptor throughout the brain. Thus, the negative feedback loop regulating the transmission of serotonin is diminished, leading to longer periods of serotonin binding to post-synaptic cells and decreased presynaptic stores of serotonin.


The two genes above are the most researched ones; however, there are still some other genes that are found to have different levels of methylation compared to control patients. An example of this is in the KCNQ3 gene. This gene encodes a  potassium channel  which function to prevent hyperexcitability of a neuron. In the CpG region of exon 11, one observes individuals with bipolar disorder having significantly lower methylation levels compared to individuals who do not have bipolar disorder. [ 5 ]  This data was collected from post-mortem individuals that had bipolar disorder. There was no overall conclusion on the effect of this methylation difference on gene expression; however, it is clear that further research should be conducted on this gene. [ 10 ]


Bipolar disorder is classified as a  mood disorder  which is a classification of mental and behavioral disorders that include characteristics such as manic episodes, depressive episodes, recurrent depressive disorders, and persistent mood disorders and more. [ 1 ]   Major depressive disorder  is a type of mood disorder commonly known as clinical depression and it is categorized by an individual having low mood, low self-esteem, and loss of pleasure in activities the individual once enjoyed. [ 11 ]  Bipolar Disorder and Major Depressive Disorder have been closely linked due to the similar depressive symptoms and similar  monoaminergic  systems that have been thought to underlie these conditions. Much of the research for bipolar disorder is done in conjunction with studies of other diseases, most commonly  schizophrenia  and major depressive disorder. Bipolar disorder overlaps with schizophrenia in the possible psychotic features in both of these disorders and the depressive episodes in bipolar disorder are similar to those in major depressive disorder. Despite being different disorders, the similarity in overlapping symptoms suggest that there are common underlying biological regulatory systems that are being disordered and has resulted in research for these disorders yielding similar results. Family, twin, and adoption studies have yielded results that there is a genetic component to mood disorders. Genetic mapping studies have tried to find the genes responsible for these mood disorders, however, they have not produced consistent results. Researchers have yet to definitively pinpoint a genetic polymorphism or mutation that underlies these disorders. [ 1 ]


Bipolar disorder has been found to be  comorbid  with several other disorders. Anxiety disorder comorbidity with bipolar disorder is common, as half of people with bipolar disorder are likely to be diagnosed with some form of anxiety disorder. [ 12 ]  Schizophrenia and bipolar disorder are also considered to be comorbid, [ 13 ]  and it has been found that abnormalities in white matter, including the level of myelination and organization of axonal fibers, are common to both conditions. [ 14 ]  Bipolar disorder has also been found to be comorbid with obsessive compulsive disorder and it has resulted in higher suicide rates for comorbid patients than noncomorbid patients.


Increasingly, evidence points towards abnormalities in epigenetic mechanism as a reason behind mood disorders such as major depressive disorder and schizophrenia. Alterations in methylation and histone modification have been found to be underlying epigenetic mechanisms in these disorders. Hypomethylation of the genes for  catechol-O-methyltransferase  (MB-COMT), an enzyme that is responsible for breaking down catecholamines, were found in both schizophrenia and bipolar disorder patients. Catecholamines are known for being important mood regulators. Hypomethylation of these genes suggests that an increased production of this enzyme results in an increased degradation of neurotransmitters, such as dopamine, and could provide an epigenetic and molecular reason as to why these mood disorders form.


Brain-derived neurotrophic factor (BDNF) plays a major role in both bipolar disorder and major depressive disorder. BDNF is a  neurotrophin  that is critical for development due to its role in plasticity and stress response. [ 1 ] [ 5 ]  Hypermethylation of the promoter for the BDNF genes has been found in patients both with bipolar disorder and major depressive disorder. [ 1 ]  When the promoter of the BDNF genes is hypermethylated, BDNF's expression is reduced and therefore decreased levels of BDNF. Patients with bipolar disorder and in a depressive states have far more methylation of the promoter than patients in manic or mixed states. [ 5 ]  This confirms BDNF's essential role in the formation of depressive states and explains why it is present in both bipolar disorder and major depressive disorder as both disorders are categorized by depressive states. Lower expression of BDNF in the frontal cortex and hippocampal region has also been shown in schizophrenia patients and within these patients, methylation of the promoter site was a common occurrence. [ 8 ]  BDNF is clearly a critical protein in the body and lower levels of it can have critical consequences for a person whether it's bipolar disorder or another serious mental health condition.


The most common current treatments for bipolar disorder involve utilizing  mood stabilizers  in order to prevent and treat manic and depressive episodes.  Lithium  is the most common mood stabilizer used and is considered the most effective. Other drugs that are commonly prescribed include  anticonvulsants  such as  valproic acid ,  lamotrigine ,  carbamazepine , and  oxcarbazepine . [ 1 ]  However, current treatments yield mixed results as within one year of receiving treatment, it has been found that 37% of BD patients relapse back into a depressive or manic episode. Within two years of receiving treatment, that number increases to 60% of patients who have a relapse. There are some patients who are thought to be treatment resistant. [ 1 ]  Patients who do not significantly respond to treatment for 6 weeks in mania, 12 weeks in bipolar disorder depression and 12 months or longer for long-term treatment are categorized as having treatment-resistant bipolar disorder. [ 1 ]  While most current drugs and treatments are meant to stabilize the patients mood or control mood swings, they have not been shown to improve the decline of cognitive abilities and, in fact, could magnify cognitive decline. [ 1 ]  Given the current lack of treatments that mainly effect neurotransmitter levels, researchers think that epigenetic treatments may be a potential solution given the epigenetic factors in bipolar disorder.


Besides pharmacological treatment of bipolar disorder, psychotherapy is also utilized. Individuals with bipolar I and II who underwent family-focused therapy alongside pharmaceutical treatment were found to have around 30 percent less relapse and re-hospitalization than bipolar individuals who didn't. However, the efficacy for cognitive-behavioral therapy is more inconclusive with different studies either saying it helped or there was no difference. [ 15 ]  In regards to the epigenetics of psychotherapy treatment, there is no strong research investigating correlation between the two.


Histone deacetylase  inhibitors and  DNA methyltransferase  inhibitors are commonly used in the treatment of bipolar disorder.  Olanzapine , a medication used to treat both bipolar disorder and schizophrenia, has been shown to induce DNA methylation changes in  dopamine  receptor genes. It has been found that methylation increases in the hippocampus specifically, which was identified in rat populations. [ 16 ]  Olanzapine has been shown to be effective in decreasing manic symptoms, but its impact on depressive symptoms has not been statistically significant. [ 17 ]


Quetiapine , an antipsychotic, has also been found to modulate DNA methylation. It binds favorably to  5-HT2A receptors , serotonin receptors that are implicated in bipolar disorder, alcohol use disorder, and depression. [ 18 ]  It has also been seen to increase DNA methylation. [ 16 ]  This drug has been tested on patient populations with bipolar disorder II, and it has been successful in alleviating mood symptoms and decreasing patients' overall scores on the  Young Mania Rating Scale . [ 17 ]  This scale is relevant to bipolar individuals as it measures the severity of their mania and these decreased scores prove the effectiveness of Quetiapine.


Valproic acid, an HDAC1 inhibitor that is used to treat schizophrenia and bipolar disorder, has been shown to reverse the hypermethylation of the  Reln gene  that has been observed in patients with schizophrenia. Histone deacetylase proteins reverse the acetylation of histone proteins, suppressing DNA expression. Thus, HDAC1 inhibitors allow the acetyl groups attached to histones to remain in place. Acetyl groups on histone proteins can act as binding sites for  bromodomain-containing proteins  and other chromatin-remodeling proteins that promote transcription initiation. As DNA methylation decreases DNA suppression, these remaining acetyl groups on certain genes may recruit proteins that reverse methylation.


Valproic decreases DNA methylation at the CpG island of the Cdkn p21 promoter. It is believed that Reln genes could influence therapeutic response in bipolar disorder as well, especially since valproic acid is already being used as a treatment for bipolar disorder. [ 5 ]


Lithium has been shown to significantly decrease methylation at the BDNF promoter IV along with an increase in BDNF mRNA levels in rats. This is important since the BDNF gene is believed to be associated with bipolar disorder pathophysiology. Lithium is also known as a histone deacetylase inhibitor.


In general, selective serotonin  reuptake inhibitors  are associated with the decrease of DNA methylation at the  S100a10  gene promoter region. It is important to note that these findings were in rats; however, it is still believed to be useful in humans as well and that there are not many human studies that have investigated these epigenetic mechanisms. Overall, this indicates the large impact of DNA methylation in bipolar disorder treatment, as well as indicates the implication of epigenetics of bipolar disorder in general.


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. [ 1 ]  Epigenetics can provide a new perspective on the biological mechanisms and potential treatments of chronic pain.


Chronic pain  is often caused by peripheral tissue inflammation or nerve and tissue damage. Chronic pain can have a variety of causes, but one potential cause is the production of a  pain wind-up , which is an increase in pain intensity in response to persistent activation of pain signals. This persistent pain reduces the threshold to feel pain over time and amplifies the pain response at the site of injury and surrounding areas. [ 1 ]


Around 100 million adults have chronic pain in the US, and the economic loss caused by chronic pain is around 600 million dollars. Chronic pain and accompanying chronic health conditions take a physical and mental toll on those who suffer from them. Rates of depression have been shown to be higher in people with chronic pain, and it has been found to be highly comorbid with PTSD. [ 2 ] [ 3 ]


As for treatment, there are predominantly two options: opioids and anti-inflammatory drugs. These drugs target the side effects of chronic pain and help manage the pain. However, they don't address the root cause of the pain and often have bad side effects and risk for substance abuse. For example, while opioids can be beneficial for some, it can be harmful for others. Some adverse effects of opioids include impaired immune system, physical dependence, and overdose.


Understanding the epigenetic modifications associated with chronic pain will potentially help identify the biological mechanism of its development and inform future treatment plans.


Epigenetic alterations involve lasting changes in gene expression, without changes in DNA sequence, but are instead due to a chemical modification of, or a persistent addition to the chromatin. They can enhance or suppress gene expression, and there are a variety of mechanisms through which this occurs. The major mechanisms of epigenetic alterations include DNA methylation, histone modifications (methylation, acetylation, phosphorylation etc.), and non-coding RNA regulation of gene expression. For the purpose of this topic, this article will focus on the first two.


In  histone methylation , methyl groups are added to individual amino acids in histone proteins, and gene expression can be enhanced or repressed, depending on the location and degree of methylation on any given histone. Epigenetic alterations in gene expression are responsive to changes in an organism's experience and environment, making it a dynamic and intriguing field of study.


The methylation of Lys27 histone H3 at a proinflammatory cytokine promoter (MCP-3) has been shown to decrease in spinal injury models. This decrease in methylation increased the production of pro-inflammatory cytokines, which regulate immune system function, long-term. This was shown to lead to central sensitization and a neuropathic, or chronic, pain-like state. [ 4 ]


In addition to histones, certain regions of DNA undergo frequent epigenetic modifications. CpG islands are regions of DNA in which there is a high density of CpGs, nucleotides cytosine and guanine linked by a phosphate group. They are frequently methylated, and their modification has important implications in changing gene expression. Within rodent inflammatory pain models, levels of methylation of  CpG islands  in DNA have been linked to the nociceptive, or pain, threshold. [ 1 ]


In regards to clinical relevance, hypermethylation of CpG islands are very often seen in cancerous cells, which is a disease strongly associated with chronic pain. Recent human studies have suggested the hypermethylation of CpG islands in malignant cells may be associated with enhanced production of pro-nociceptive peptides, providing a potential explanation for cancer-induced pain. Research in the field points to pharmacological intervention of DNA methylation as a promising new direction. [ 1 ]


Histone acetylation  is the process where acetyl groups are added to the histone by histone acetyltransferase (HATs). Histone acetylation promotes gene expression by making the DNA more accessible for transcription. The removal of these acetyl groups is done by histone deacetylases (HDACs). Histone acetylation has been found to play a part in pain sensitivity and chronic pain development.


The sensitization of nociceptive neurons, which are responsible for transmitting pain signals, is thought to be an important aspect of chronic pain. In this context,  sensitization  is the increased sensitivity of a neuron's response to a stimulus after persistent, repetitive activation. Recent studies have shown a possible association between histone acetylation and nociceptive sensitization. Histone acetylation in the dorsal horn of the spine has been shown to affect nociceptive sensitivity in animal models. The upregulation of HDAC1 and decrease in histone H3 acetylation in the dorsal horn of the spine was found to be adaptations that increase pain sensitivity. The administration of a general HDACi, which is an HDAC inhibitor, helps to alleviate the hyperalgesia, or, and allodynia caused by a spinal injury. It also reversed the increased HDAC1 expression and the reduction of histone H3 acetylation. This experiment was done with other general HDACis, and similar results in the pain alleviation were found. [ 1 ]


Histone acetylation also plays a role in inflammatory pain. Induced inflammatory pain caused an increase in the production of HDAC2 proteins in the dorsal horn. The administration of HDACis, such as SAHA, suberanilohydroxamic acid, and TSA, trichostatin A, caused a decrease in hyperplasia and an increase in histone acetylation in the superficial layers of the spinal cord. [ 1 ]


HDAC inhibitors can also relieve pain sensation by repressing the over acetylation of histone H3 in the promoter region of inflammatory proteins and chemokine CC receptors. Intrathecal injection of a HDAC inhibitory can reverse the CCI-induced hyperalgesia and mechanical allodynia. [ 5 ]


H3K9 methylation is an important part of the neuropathic pain pathway. The main markers for chronic neuropathic pain are a rise in excitability in primary afferent neurons and a decrease in potassium channel expression in primary sensory neurons. Peripheral nerve damage causes prolonged downregulation of voltage-gated potassium channels. This downregulation causes dorsal root ganglion neurons to be hyper excited and increases pain sensitivity overall. There was an increase in G9a expression and its product H3K9me2 when a nerve injury occurred. A chromatin-immunoprecipitation assay showed that there was a rise in protein enrichment of H3K9 at promoter regions of potassium channel genes. This caused the downregulation of the voltage-gated potassium channels in subunit Kcna2 in the dorsal root ganglion (DRG). A knockout of G9a in the DRG neurons resulted in the regular expression of potassium channels and no development of chronic pain after nerve injury. [ 6 ] [ 7 ]  Another important role of H3K9me2 is its effect on opioid receptors. The MOR receptor is expressed in DRG neurons and is crucial for the pain-relieving effect of MOR agonists. Nerve damage was shown to cause a decrease in the expression of MORs in DRG. Nerve injury causes an increased enrichment of H3K9me2 at the promoter site of the MOR gene, causing the repression of the gene. A knockout of G9a restores the MOR expression and analgesic effect of morphine after injury. [ 6 ]


H3K27me3 is a repressive mark that is mediated by the PCR2 complex. PCR2 has a methyltransferase EZH2. Nerve damage stimulates EZH2 expression and increases the enrichment of H3K27me3 at the promoter site of potassium channel genes. Although the injury of nerves does increase EZH2 expression, the inhibition of EZH2 has minimal effect on management of chronic pain. [ 6 ]


GAD65,  glutamic acid decarboxylase 65, expression is also found to play a part in chronic  pain. Long lasting inflammatory and neuropathic pain decreased the expression of GAD65 in the nucleus raphe magnus, which is in the ventral medulla. The nucleus raphe magnus utilizes HDACs to mediate histone hypoacetylation for pain control. The decrease of GAD65 leads to reduced GABA  synaptic inhibition. The treatment of HDACis in nucleus raphe magnus caused increased expression of GAD65, normal GABA synaptic inhibition, and ceased oversensitivity. [ 8 ]


Arginine methylation is the process where protein arginine methyltransferases, PRMTs,  add methyl groups on arginine residue. Nerve injury has a significant effect on these PRMTs' activity. In the DRG of mice, peripheral nerve damage increases the expression of PRMT4 and decreases the expression of PRMT8 and PRMT9. PRMT8 is special because it is mainly expressed in the nervous system and catalyzes arginine methylation for dendritic spine maturation and synaptic plasticity. The reduction of PRMT8 leads to a decreased amount of NMDA receptor subunit GluN2A. This reduced level of GluN2A and PRMT8 leads to hypersensitivity to pain. In terms of PRMT4, the knockout of PRMT4 has shown to decrease pain hypersensitivity, but it is not clear which genes or proteins are responsible for this interaction. [ 6 ]


Noncoding RNAs also play a role in chronic pain. They include long ncRNAs, circular RNAs, antisense RNAs, and microRNAs, which all regulate transcription, translation, and mRNA stability. Neural pain can increase the expression of certain antisense ncRNAs through transcription factors, which can turn on and off genes associated with pain. A decreased level of Ds-lncRNA, which is a long ncRNA,  after neural injury enhances the binding of  RALY, an RNA cofactor, to RNA polymerase II. This causes an increased G9a expression which increases pain awareness. [ 6 ]


One potential treatment option is inhibiting the deacetylation of histones. There are eighteen identified HDAC genes, and they have varying effects on the nervous system. Intrathecal injection of HDAC inhibitors resulted in the reduction of inflammatory pain in rats. The administration of HDAC inhibitors increase the activity of glutamate decarboxylase promoters GAD65 and GAD67, which are normally involved in enhancing GABA inhibition and reducing pain. [ 9 ]  This experiment suggests that blocking the removal of acetyl groups on histone could be the way to manage chronic pain. An example of an HDAC inhibitor in use is Valproic acid. Valproic acid is a substance used to treat seizures, but it is now in a trial to treat migraines by blocking HDACs. Givinostat is another HDAC inhibitor that is being reviewed in treating juvenile arthritis pain. [ 10 ]


Another potential therapeutic mechanism is histone methylation. There is little research on this particular epigenetic mechanism as it relates to chronic pain. However, folate, a prenatal vitamin, has been shown to be an important cofactor in DNA methylation during pregnancy. More research needs to be done before folate can be suggested as a potential therapeutic. [ 10 ]


DNA methylation inhibitors showed a potential to treat chronic pain. A study found there was an increase in DNA methylation in mice's spines after a chronic injury. An intrathecal injection of DNMT inhibitor reduced this methylation increase and also the hypersensitivity to pain in the spine. Also DNMT inhibitor, zebularine, also was shown to reduce thermal hyperplasia after chronic stress. [ 11 ]


Cocaine addiction  is the compulsive use of cocaine despite adverse consequences. It arises through epigenetic modification (e.g., through  HDAC ,  sirtuin , and  G9a ) and transcriptional regulation (primarily through  ΔFosB 's  AP-1 complex ) of genes in the  nucleus accumbens .


Histone deacetylase inhibitors  (HDAC inhibitors) have been implicated as a potential treatment for  cocaine  addicts.   HDACs  are enzymes that can deacetylate the  histones  associated with genes. This can activate genes for transcription.  Several experiments have shown that inhibiting HDACs involved in histone  H3K9  deacetylation reduces  drug seeking behavior .


It has been known that  epigenetic regulations , such as the  methylation  of H3K9, have a key role in the mechanism of  addiction . Recent studies have shown that administering HDAC inhibitors can help reduce the craving for cocaine in rats. [ 1 ]   Trichostatin A  (TsA) is an HDAC inhibitor associated with reduced cocaine-seeking behaviors; it inhibits HDAC classes 1, 3, 4, 6, and 10. Since this HDAC inhibitor has such a significant effect on cocaine-seeking behaviors, scientists have speculated about their ability to reduce a person who is addicted to cocaine's risk of relapse in the rat model system during rehab.


After several tests in which rats were exposed to cocaine followed by either an HDAC inhibitor or a placebo, it was found that HDAC inhibitors had a significant effect on lowering cocaine-seeking behavior. [ 1 ]  This also suggests an epigenetic mechanism involved in HDAC chromatin regulation. The data is crucial to proving the hypothesis that trichostatin A can remodel chromatin structure and prevent behavioral changes following cocaine exposure. Tests also revealed that HDAC inhibitor administration can not only prevent addiction but also helps reduce the risk of relapse in cocaine addicts in the rat model system. [ 1 ]


As the previous findings suggest, chronic cocaine use caused both alterations in the chromatin remodeling activity of  HDACs  and drug-seeking behavior.  Renthal et al. [ 2 ]  focused specifically on the  class II histone deacetylase ,  HDAC5  since it was known to have activity-dependent regulation in neurons. In fact, they found that HDAC5 was a central regulator of the actions of chronic cocaine use and contributed to the behavioral adaptations with its deacetylase activity. Chronic cocaine injections increased HDAC5  phosphorylation  at Ser259 in the  nucleus accumbens  (NAc) within 30 minutes.  This provides docking sites for 14-3-3 proteins, which mediate the export of HDAC5 out of the nucleus.  They also found that  CaMKII  was necessary for depolarization-induced HDAC5 phosphorylation in NAc tissue, highlighting its role as a  kinase  for HDAC5.  Experiments with  mutant proteins  and HDAC inhibitors suggested that HDAC5's action is mediated through its catalytic histone deacetylase domain. Rapid phosphorylation and the export of HDAC5 from the nucleus following cocaine use most likely leads to increased "pulses" of acetylation, targeted gene activation, and behavioral adaptations to long-term cocaine exposure.


The second set of experiments that Renthal et al. [ 2 ]  performed showed that chronic cocaine use induced upregulation of the  NK 1  receptor  protein in HDAC5 knockout mice, which is associated with hyperacetylation of  H3  at the NK1R gene promoter.  The NK1R gene promoter has been associated with enhanced response to cocaine reward, meaning HDAC5 in normal genomes may decrease cocaine reward with chronic cocaine exposure.  They also found key pathways that were implicated in neural plasticity and reward behavior, which included  DA receptor  signaling,  ATF2 / CREB  signaling,  NF-κB ,  NFAT ,  cytoskeletal remodeling  proteins, and  ion channels .  Their data implicated  chromatin  remodeling as a mechanism that drives altered gene activation and behavioral responses to cocaine.  With this information, they concluded that within normal (wild-type) genomes, the response to chronic cocaine includes phosphorylation of HDAC5 and export of the deacetylase out of the nucleus to activate downstream target genes.  Between exposure and 24 hours after, HDAC5 returns to the cell nucleus to limit the expression of these cocaine-regulated genes by  histone deacetylation .  Their experiments with HDAC5 knockout mice lent additional support for this hypothesis.  Since HDAC5 isn't there to limit the gene's expression, it begins to accumulate with repeated cocaine exposure, with the result being increased sensitivity to cocaine reward.


Modifications to  histones  such as methylations and acetylations can change gene expression patterns by activating or deactivating a region of DNA for  transcription . The  H3K9  position has been shown by several studies to be altered by chronic cocaine use.


Addictive behavior observed from long-term cocaine users can be due to changes in the gene expression profiles in the brain's reward circuitry.   Most research has been focused on the active regions of the reward-related genes, but Maze et al. [ 3 ]  focuses at what happens to the  heterochromatic regions .  Maze et al. [ 3 ]  showed that heterochromatic regions in the  nucleus accumbens  (NAc), a major reward circuit in the brain, are significantly altered in the H3K9me3 position.  Acute cocaine exposure leads to a rapid increase in H3K9me3 within half an hour and decreases back to normal levels within 24 hours.  Chronic cocaine exposure leads to a slower increase in H3K9me3 within an hour (although it reaches the same level as acute by this time) and a 50% decrease from normal baseline levels within 24 hours.  This chronic exposure was proposed to decrease heterochromatinization (destabilization) within this brain region in patients given repeated cocaine exposure, which implies that the long-term addictive behaviors are affected by this epigenetic mark.  They used  ChIP-seq  to provide supporting evidence that the H3K9me3 modification is mainly localized to  intergenic regions .  In these areas of the genome, 17 regions of  repeat elements  ( SINEs ,  LINEs ,  LTRs , etc.) had significant H3K9me3 state changes in chronic cocaine exposure mouse models.  They used  quantitative PCR  to determine that of these significant elements, the LINE-1 region showed a significant increase in expression levels.   LINE-1  is a  retrotransposon , so expressing it inappropriately can activate the transposon to insert itself within important genes and destabilizing the DNA.  They conclude their findings by suggesting that LINE-1 retrotransposon insertions cause inappropriate or disrupted expression of genes leading to the  addictive behavior .


Like Maze et al., [ 3 ]  studies by Covington et al. [ 4 ]  focused on histone modification in the nucleus accumbens.  They suggest that the H3K9me2 modification in this area of the brain plays a role in the  stress  and  depression  pathway.  Their idea was that cocaine modifies this epigenetic mark and that this increases an addicted person's vulnerability to stress and depression, which leads to the addictive effects of these reagents.  A  methyltransferase ,  G9a , was found to have reduced expression in the nucleus accumbens in cocaine addicts, therefore causing reduced H3K9me2 levels.  The genes that are unsilenced via acetylation of the heterochromatin abnormally express the genes involved in  BDNF - TrkB - CREB  signaling pathway. This causes enhanced phosphorylation of CREB downstream in the pathway.  CREB causes enhanced acetylation and dis-regulation of the stress and depression signaling pathways.


Cocaine induces epigenetic changes that lead to  neuronal morphology  and behavioral changes. Most changes have to do with the disruption of  heterochromatin  caused by reduced levels of methylation on histones, namely H3K9. This decrease is mediated by the repression of G9a, a  histone-lysine N-methyltransferase  which is regulated by  ΔFosB .  ΔFosB is a cocaine-induced transcription factor that accumulates in the nucleus accumbens (NAc) and acts to repress G9a. When ΔFosB is overexpressed, G9a levels are reduced, and H3K9 dimethylation levels are reduced in the NAc. Maze et al. [ 5 ]  was interested in determining how the reduced levels affects the behavior of cocaine users. Several studies were done in rats and it was concluded that G9a overexpression, and thus the presence of H3K9 dimethylation, caused a decreased preference for cocaine in rats. [ 5 ]  Researchers then looked at the nuclear volume of rats exposed to cocaine and found that down-regulation of G9a increased the amount of  dendritic spines  in the nucleus accumbens leading to increased cocaine-seeking behavior.


Only in the nucleus accumbens do G9a levels matter for cocaine addiction. Studies have been done in which G9a levels and H3K9me2 levels were changed in other areas of the brain, but these other locations had no effect on the cocaine-seeking behavior of rats.


The role of  sirtuin  deacetylases have also been shown to play a role in mediating cocaine addiction. [ 6 ]   To determine their role, the two transcription factors previously mentioned, ΔFosB and CREB, first had to be analyzed. It has been previously stated that ΔFosB increases the cocaine-seeking behavior of users. This is because ΔFosB has a uniquely stable structure that allows it to persist and accumulate in the body. Unlike ΔFosB, CREB is responsible for reducing sensitivity to cocaine which causes negative symptoms during the withdrawal period. Each of these transcription factors increases the cocaine-seeking behavior of addicts.  Once this connection between transcription factors had been established, the researchers were curious if other genes caused addictive behaviors too and explored the ones that were significant markers for cocaine addiction, one of which, was the  sirtuin  gene family.  Sirtuins are Class III NAD-dependent  histone deacetylases . Not only do sirtuins deacetylate histones, but are also responsible for the deacetylation of  tubulin ,  p53 , and  NFKB . Several studies have explored the role sirtuins played in cocaine-seeking behavior. In one set of experiments, it was found that a significant increase in ΔFosB in the nucleus accumbens led to ΔFosB binding to the  SIRT2  promoter. [ 5 ]  This increased binding caused acetylation of  H3  which is associated with increased Sir2 mRNA. It was also found that the H3 acetylation induced by cocaine increased Sirt1 in the nucleus accumbens. Thus, repeated cocaine use causes an increase in both Sirt1 and Sirt2.  Scientists were then interested in determining how increased  Sirt1  and Sirt2 affected nuclear volume because it has been previously shown that repeated cocaine use does so. Scientists studying Sirt1 and Sirt2 have also found that these transcription factors led to increased nuclear volume. Therefore, it has been concluded that ΔFosB, CREB, Sirt1, and Sirt2 all play an integral role in cocaine-seeking behaviors.


Kumar et al. [ 7 ]  focused on how acute and chronic cocaine exposure affected the  striatum , which is another area of the brain involved in the reward and locomotor pathways.  To study the molecular actions of cocaine in this region, researchers studied the histone modifications of three different promoters:  cFos ,  BDNF , and  Cdk5 .  They saw that  cFos , which is normally expressed immediately after neurons fire action potentials, had high levels of  H4  acetylation within 30 minutes of a cocaine injection – but no histone modifications were seen with chronic cocaine use.  These results suggested that this promoter is activated by acute cocaine use and possibly means that the neurons it regulates fire rapidly during acute cocaine exposure, yet are not affected by long-term use.   BDNF  has been implicated as a critical regulator in drug dependency, and Cdk5 is implicated in the regulation of  cell proliferation  genes.  Both of these promoters were induced by chronic cocaine use (H3 hyperacetylation).  Altering the natural acetylation states of these promoters in acute and chronic cocaine users altered the locomotor and reward responses to cocaine.  This suggests that the behavioral activity observed by cocaine users can be attributed, in part, to the histone modifications at these promoter sites.


McClung et al. [ 8 ]  discuss the gene expression profiles of previously mentioned CREB and ΔFosB  as they are involved in cocaine use.  These transcription factors have been shown to play a role in the short-term and long-term adaptive changes in the brain.  CREB has been implicated in learning, memory, and depression and enriched in cocaine users within the nucleus accumbens. CREB seems to upregulate many genes in its pathway within the reward regions of the brain. It also seems to reduce the rewarding effects of cocaine and leads to depressive-like behaviors instead. The gene expression changes by CREB are induced by short-term cocaine treatment and eventually go back to normal.  They also focused on ΔFosB, which is in the family of FosB proteins. While most of these proteins have been implicated in short-term dependence gene expression changes, McClung et al. [ 8 ]  demonstrated that ΔFosB gene expression changes in the NAc were induced by short-term and long-term cocaine exposure.  Short-term cocaine exposure leads to the same expression profiles of upregulated genes as CREB did creating the reduced rewarding effects seen.  However, long-term exposure leads to a different expression profile leading to increased rewarding effects. They suggested that ΔFosB acts as a  repressor  and somehow interacts with the CREB pathway and indirectly leads to the same short-term effects seen, but over time, acts to upregulate genes within its own pathway leading to the increased rewarding effects.  It is unknown how these two pathways interact, but they have shown that there is some overlap.


Also involved in the CREB-Fos protein pathways is the  dopamine D1 receptor  (DRD1), expressed in neurons in the  nucleus accumbens  and  caudate putamen  regions.  Zhang et al. focused on this receptor, as it is known to mediate the effects of cocaine. [ 9 ]    When stimulated, it increases  cAMP  levels, in turn leading to  CREB  activation.   They had observed previous cocaine injections led to a direct increase in D1 receptor sensitivity. Through lines of D1 receptor mutant mice, it had also been implicated in mediating both the locomotor sensation and rewarding effects of cocaine.  Acute cocaine injections induced c-fos and CREB expression via D1 receptors and repeat cocaine administration, which is associated with long lasting  AP-1 transcription complexes  containing ΔFosB.  Persistent ΔFosB expression in D1 receptors in nucleus accumbens led to a significant increase in the locomotor-stimulating and rewarding effects of cocaine.  Conversely, an increase of CREB was shown to decrease the rewarding effects of cocaine.
Zhang et al. also used  microarrays  to identify specific genes induced by chronic cocaine use, which depend on a functional D1 receptor 24 hours after cocaine withdrawal. [ 9 ]   There were 109 genes identified that were either up or down-regulated by 1.2 fold or more in the caudate putamen D1 receptor mutant mice after repeat injections.  The expression of these genes was totally normal in mice with functional D1 receptors, suggesting chronic cocaine use had a direct influence on mediating these genes through a functional DRD1 receptor  They found genes belonging to a number of functional groups, and chose six candidate genes from three of these functional groups to verify their differential expression in the caudate putamen.  For each gene, researchers verified the dependency of their expression on the D1 receptor after cocaine treatment using  Trichostatin A  or other  receptor antagonists .  Specifically, they focused on the genes encoding  extracellular  factors, receptors, modulators, and intracellular signaling molecules.  These can be regulated by chronic cocaine treatment via D1 receptors, and all of the genes contain AP-1 transcriptional complex binding sites in their promoter regions.   For extracellular signaling molecules, they looked at the expression of the genes  IGFBP6  and  SDF1 .  Both of these were induced in the caudate putamen in wild-type mice but attenuated in the D1 receptor mutants.  This suggests that IGFBP6 and SDF1 can be induced by repeat cocaine administration, and also that this interaction is partially dependent on a functional D1 receptor.


Zhang et al. had previously seen that chronic cocaine administration leads to increased  dendritic branching  and spine density on medium spine neurons and  prefrontal cortex   pyramidal neurons , which may contribute to cocaine-induced  neuroadaptations . [ 9 ]  When investigating the genes that were receptors and modulators, they found that expression of the  sigma 1 receptor  and  RGS4  was not upregulated after repeat cocaine administration in DA D1 receptor mutants, suggesting functional  dopamine D1 receptor  is necessary for their induction.  This receptor had been seen to modulate the rewarding effects of cocaine, and receptor antagonists had blocked the acute locomotor stimulating effect and lowered behavioral sensitization.  Changes in the sigma 1 receptor have been shown to modulate dopamine release, so shifts in its expression can change the behavioral responses to cocaine with pre and post-synaptic influences.  They knew that  RGS4  proteins can modulate  G-protein-coupled receptor  function, and since  RGS4  levels can increase or decrease in response to D1/ D2  receptor stimulation it could be involved in alterations of the signal transduction pathway after D1 receptor activation from repeat cocaine stimulation.


For the genes that encoded  intracellular signaling  molecules, Zhang et al. focused on the  Wrch1  gene. [ 9 ]   After experimentation researchers found  Wrch1  was upregulated by repeat cocaine injections in the caudate putamen in D1 receptor mutants.  There was no change in wild-type mice, leading them to believe that  Wrch1  may inhibit cocaine-induced and D1 receptor-mediated behavioral changes. A key member of the  Wnt signaling pathway ,  β-catenin , was thought to be induced by chronic cocaine administration (which had been true in the nucleus accumbens) but acute cocaine reduced expression in the caudate putamen whereas chronic cocaine injections decreased expression even in the NAc in D1 receptor mutants.  This pathway influences Wrch1, so it can also influence cocaine-induced neuroadaptations.  Lastly, they found that  CaMKII-α  was not upregulated as expected, and CD2 was downregulated in D1 receptor mutants after chronic treatment.   These results suggest gene expression changes are definitely induced by chronic cocaine exposure via the D1 receptor and most at AP-1 binding sites.


Contrary to most studies focusing on the  nucleus accumbens , Febo et al. [ 10 ]  suggested that the reward brain circuitry is not the only system involved in addictive behaviors.  Previous knowledge has suggested that stimulants induce changes in gene expression in the main parts of  mesolimbic  circuitry (including the  ventral tegmental area ,  ventral striatum /nucleus accumbens, and  prefrontal cortex ) and play a big role in development and maintenance of addicted state and  chromatin remodeling . They applied this knowledge to investigate whether these gene expression changes are involved in cocaine-related behavioral and molecular adaptations. They found unexpected patterns of brain activation in awake rats that were exposed to  sodium butyrate , an  HDAC inhibitor  (or HDACi).  An acute dose resulted in widespread BOLD ( blood-oxygen-level dependent ) activation in the  forebrain  and  midbrain , but cocaine-induced activation was significantly attenuated after repeat exposure.  Sodium butyrate co-treatment with cocaine restored pronounced BOLD activation after successive cocaine treatments.  These suggest that the brain's initial response to repeated cocaine exposure triggers a  desensitization  mechanism which can be overturned by pretreatment with sodium butyrate.  The neural circuitry for the epigenetic modifications contributing to cocaine sensitivity was not limited to the  mesocorticolimbic dopamine system  ("reward system") as they expected.  Instead, they saw corticolimbic circuitry (implicated in  emotion  and  memory ) had a bigger role in HDACi related alterations of reward behaviors.  Evidence that HDACi-mediated enhancement of a stimulant's sensitizing effects is context-specific, and involves associative learning.


As of May 2014 [update] , there is no effective approved  pharmacotherapy  for cocaine addiction. [ 11 ] [ 12 ]   HDAC inhibitors  have been implicated as a potential treatment for cocaine addiction.


Cognitive behavioral therapy  is currently the most effective clinical treatment for psychostimulant addiction in general. [ 13 ]


Epigenetics of depression  is the study of how  epigenetics  (heritable characteristics that do not involve changes in DNA sequence) contribute to depression.


Major depressive disorder  is heavily influenced by environmental and genetic factors. These factors include  epigenetic  modification of the genome which may result in a persistent change in  gene expression  without a change in the actual DNA sequence.  Genetic and environmental factors can influence the genome throughout a life; however, an individual is most susceptible during childhood. [ 1 ]  Early life stresses that could lead to major depressive disorder include periodic maternal separation, child abuse, divorce, and loss. [ 2 ] [ 3 ]  These factors can result in epigenetic marks that can alter gene expression and impact the development of key brain regions such as the hippocampus. [ 4 ] [ 2 ]  Epigenetic factors, such as   DNA methylation , could serve as potential predictors for the effectiveness of certain antidepressant treatments, as well as show associations with depression symptoms. [ 5 ] [ 3 ]  The use of antidepressants can be also associated with changes in DNA methylation levels. [ 6 ]  Identifying gene with altered expression could result in new antidepressant treatments. [ 3 ]


Histone deacetylases  (HDACs) are a class of enzymes that  remove acetyl groups from histones . Different HDACs play different roles in response to depression, and these effects often vary in different parts of the body. In the  nucleus accumbens  (NaC), it is generally found that H3K14 acetylation decreases after chronic stress (used to produce a depression-like state in rodent model systems). However, after a while, this acetylation begins to increase again, and is correlated with a decrease in the activity and production of  HDAC2 . [ 7 ]  Adding HDAC2i (an  HDAC2 inhibitor ) leads to an improvement of the symptoms of depression in animal model systems. [ 4 ]  Furthermore, mice with a  dominant negative  HDAC2 mutation, which suppresses HDAC2 enzymatic activity, generally show less depressive behavior than mice who do not have this dominant negative mutation. [ 8 ]   HDAC5  shows the opposite trend in the NaC. A lack of HDAC5 leads to an increase in depressive behaviors. This is thought to be due to the fact that HDAC2 targets have antidepressant properties, while targets of HDAC5 have depressant properties. [ 4 ]


In the  hippocampus , there is a correlation between decreased  acetylation  and depressive behavior in response to stress. For example, H3K14 and H4K12 acetylation was found to be decreased, as well as general acetylation across  histones H2B  and  H3 . [ 9 ] [ 10 ] [ 11 ]  Another study found that  HDAC3  was decreased in individuals resilient to depression. In the hippocampus, increased HDAC5 was found with increased depressive behavior (unlike in the nucleus accumbens). [ 4 ] [ 11 ] [ 12 ]