User:RG2022/Rhea Gogia Week 4

= Epigenetics of Schizophrenia =

Heritability- Genetics
Studies have shown that epigenetic changes can be passed on to future generations through meiosis and mitosis. These findings suggest that environmental factors that the parents face can possibly affect how the child's genetic code is regulated. Research findings have shown this to be true for patients with schizophrenia as well. In rats, the transmission of maternal behavior and even stress responses can be attributed to how certain genes in the hippocampus of the mother are methylated. Another study has shown that the methylation of the BDNF gene, which can be affected by early life stress and abuse, is also transmittable to future generations.

''Schizophrenia is induced by both environmental and genetic factors. It has been calculated that the heritability of schizophrenia is around 80%, and within that heritability 30% of the variability comes from single nucleotide polymorphisms and another 30% from large copy number variants (CNVs). Heritability represents the percentage in variability in a trait that comes from genetic differences. It has also been shown that having direct family members that are diagnosed with schizophrenia increases the rate of developing schizophrenia by 9 times. Monozygotic and dizygotic twin studies have also shown that schizophrenia has significant heritability, as monozygotic twin pairs developed schizophrenia (when one twin was already diagnosed with schizophrenia) at a higher rate than dizygotic twin pairs. Another study investigated the rates of schizophrenia of adoptees: adoptees with a genetic history of schizophrenia that were adopted by non-schizophrenic parents were seen to be diagnosed with schizophrenia at higher rates than adoptees without a biological history of schizophrenia but raised with adoptive parents diagnosed with schizophrenia. However, the extent to which interactions between environmental and genetic factors contribute to the development of schizophrenia is uncertain.''

''Maternal immune responses are involved in schizophrenia development. A 2019 study found that, in mice models, maternal immune activation may be involved in the regulation of the ARX gene expression that contributes to the GABA dysfunction commonly implicated in schizophrenia. Most maternal effects involved in schizophrenia development have to do with immune system activation and associated cytokine and neurogenesis mechanisms rather than genetic changes.''

''Paternal genetic effects are seen to be involved in the rate of development of schizophrenia. A 2021 study showed that advanced paternal age was associated with higher schizophrenia risk. In the study, the paternal ages were grouped into 5-year increments, and it was seen that as the increments increased, so did the risk of developing schizophrenia. It is hypothesized that advanced paternal age increases schizophrenia risk because fathers pass down three to four times more de novo mutations than do mothers. It is estimated that 2 new de novo mutations are created a year, resulting in fathers with an advanced age passing down more mutations to their offspring, which may explain the increased rates of schizophrenia'''. '

''In some circumstances, it has been shown that environmental factors can increase the risk of schizophrenia when combined with a family history of psychosis. ''

Genes Associated with Schizophrenia
Among the many genes known to be associated with schizophrenia, a few have been identified as particularly important when studying the epigenetic phenomena underlying the disease.


 * GAD1- GAD1 codes for the protein GAD67, an enzyme that catalyzes the formation of GABA from glutamate. Individuals with schizophrenia have shown a decrease in GAD67 levels and this deficit is thought to lead to working memory problems, among other impairments.
 * RELN- RELN codes for reelin, an extracellular protein that is necessary for formation of memories and learning through plasticity. Reelin is thought to regulate nearby glutamate producing neurons.

Both proteins are expressed by GABAergic neurons. Several studies have demonstrated that levels of both reelin and GAD67 are downregulated in patients with schizophrenia and animal models.
 * BDNF - Brain-derived neurotrophic factor, BDNF, is another important gene in the study of schizophrenia genetics. BDNF plays a crucial role in cognition, learning, memory formation, and vulnerability to social and life experiences.

Genome-wide association studies (GWAS) have confirmed the presence of other genes thought to be involved in the regulation of schizophrenia. Several genes that GWAS have determined to be associated with schizophrenia include genes involved in neurodevelopment, including glutamatergic signaling, synaptic transmission, and the regulation of voltage-gated calcium channels. ''This includes the GAD1 and RELN pathways denoted above as well as BDNF. Another important gene is the Dopamine Receptor 2 gene, which encodes a dopamine receptor (D2), a primary target of many of the antipsychotic drugs that are used to treat patients with schizophrenia. Chromosomal regions containing a large number of CNVs are reported to lead to increased susceptibility to schizophrenia.''

Copy Number Variants (CNVs) have also been reported to be associated with schizophrenia, particularly in chromosomal regions with large amounts of CNVs. A CNV located at the gene NRXN1, which encodes a neurexin protein involved in synaptic transmission, is thought to cause a loss-of-function mutation that is associated with the development of schizophrenia. Loss-of-function mutations at the gene encoding histone H3 methyltransferase, an important enzyme for epigenetic histone modification, have also been implicated in gene-association studies for schizophrenia. ''Histone modification is not the only epigenetic mechanism thought to be commonly associated with schizophrenia. Analyzing schizophrenia-associated genes reveals that risk loci are commonly found near DNA methylation quantitative trait loci (which affect CpG methylation), which have post-transcriptional modifications uniquely correlated to schizophrenia and produce splice variants with strong chromatin associations. DNA methylation, post-transcriptional modification and splice variation, and chromatin modifications are all prominent epigenetic mechanisms, and their association with schizophrenia-risk-associated loci indicates that these mechanisms may play a significant role in the development of the disease.''

Moving away from GWAS, linkage studies have proved to be unsuccessful due to the interaction of several different genes that are all involved in the development of schizophrenia. There are also few specific SNPs majorly involved in the development of schizophrenia, however groups of SNPs could account for 30% of the genetic susceptibility for developing schizophrenia.

Epigenetic alterations
Although research is ongoing, studies have shown that there are several mechanisms of epigenetic regulation associated with schizophrenia. Evidence in this area is still sparse, and just as genetic culprits for the disease remain nebulous, there is no definite answer to what epigenetic alterations should be expected in patients with schizophrenia.

DNA methylation
Differential DNA methylation has been identified in the schizophrenic epigenome across 4 different regions of the brain. Hypermethylation of genes in neurotransmitter pathways (including GAD1, RELN, and the serotonin pathway) as well as hypomethylation of genes in other pathways (such as the dopaminergic pathway) have been observed in schizophrenic patients. A broad range of genomic methylation patterns have been observed in patients with schizophrenia, and although a definite explanation is not in place, there are enough consistent abnormalities to suspect that differential methylation may play a substantial role in the pathogenesis of schizophrenia.

Histone modification
Another important mechanism of regulation is post-translational histone modifications such as histone methylation, phosphorylation, ubiquitination, and acetylation in parts of the genome associated with schizophrenia. A prominent example is the increased repressive methylation of histone 3 (H3K9me2), which has been associated with both age of disease onset and treatment resistance. Investigations into these epigenetic regulations indicate that therapeutic pathways targeting epigenetic mechanisms like differential methylation and acetylation may be beneficial.

Epigenetic Markers Associated with Famine
''In addition to epigenetic effects as a result of maternal influence during important stages of neurodevelopment, studies show that nutrient deprivation can result in epigenetic modifications that are maintained from generation to generation.  Historically, famines are thought to cause changes in epigenetic regulation within the human genome. Specifically, deprivation of nutrients is thought to alter methylation patterns in mammals, and several case studies have shown that periods of famine are positively correlated to increased incidences of schizophrenia in certain populations. Babies born during periods of famine were up to twice as likely to develop schizophrenia or schizophrenia spectrum disorder. Thus, researchers believe that the development of schizophrenia is linked to nutrient deprivation. The leading hypothesis for how this is accomplished is via subtle epigenetic alterations following nutrient deprivation, such as the hypermethylation of genes in neurotransmitter pathways, since it is well documented that dietary restriction has an effect on DNA methylation states. This line of thinking is further supported by studies showing that deficiencies in certain nutrients, including choline, folate and vitamin B12 which are required for the creation S-adenosylmethionine (SAM), are also linked with increasing the epigenetic factors associated with increased risk of schizophrenia. Evidence is still mounting in this area, but the existing correlations are notably strong.''

Environmental risks and causes
While there haven't been many studies linking environmental factors to schizophrenia-related epigenetics mechanisms at this point in the field, a few studies have shown interesting results. Advanced paternal age is one of the risk factors for schizophrenia, according to recent research. This is through mutagenesis, which cause further spontaneous changes, or through genomic imprinting. As the parent ages, more and more errors may occur in the epigenetic process. There is also evidence of the association between the inhalation of benzene through the burning of wood and schizophrenic development. This might occur through epigenetic changes. Methamphetamine has also been linked to schizophrenia or similar psychotic symptoms. A recent study found that methamphetamine users had altered DNMT1 levels, similar to how patients with schizophrenia have shown abnormal levels of DNMT1 in GABAergic neurons.

''Research has shown that there is not a 100% likelihood for genetically inheriting schizophrenia- as in monozygotic twin pairs, when one twin is diagnosed with schizophrenia, there is only a 50% chance that the other twin will also be diagnosed with schizophrenia. This finding shows that environmental influences play a role in the development of schizophrenia.''

''Maternal effects have also been shown to increase the rate of schizophrenia. It has been hypothesized that babies born in winter and spring have higher rates of schizophrenia than babies born in the summer and fall because of the increase in respiratory infections during the colder months. Furthermore, a study showed that maternal respiratory infection increased the rate of schizophrenia “three- to sevenfold,” and if the mothers would not have gotten the respiratory infection, “14 to 21% of schizophrenia cases would have been prevented.” The relative amounts of pro-inflammatory and anti-inflammatory compounds found in maternal serum are associated with the onset of schizophrenia, as seen in studies in which amounts of interleukin 6 and interleukin 10, pro- and anti- inflammatory, respectively, were manipulated. It was reported that increasing the amount of interleukin 10 or decreasing the amount of interleukin 6 lessened the effects of the immune system on the fetus.  These long-lasting impacts may indicate an epigenetic effects in the offspring, however, it remains unconfirmed. A 2018 study found that patients with schizophrenia had hypomethylation--associated with increased expression of a gene-- of the IP6 promoter region compared to the control subjects.''

''DNA methylation patterns have been linked with increased schizophrenia risk. Specifically, the hypermethylation of the promoter region has been reported to suppress expression of reelin (RELN) in the frontal and prefrontal cortex. Higher DNA methylation levels of RELN promoters has been observed in schizophrenic patients. Several other genes, including GABAergic, dopaminergic, and serotonergic genes, have also been found to have different methylation in patterns in those afflicted with schizophrenia. Those with schizophrenia have also been noted to have increased amounts of DNMT1, which is involved in the regulation of methylation at CpG sites. Jaffe et al. recently found that 2104 CpG sites were differently methylated in the prefrontal cortex those with schizophrenia as compared to those without schizophrenia. Most notably, the differentially methylated sites were found in genes having to do with "embryonic development, cell fate commitment, and nervous system differentiation" as well as the time period between late gestation and early life.''

''Prenatal Maternal Stress (PNMS) is also associated with schizophrenia and schizophrenia spectrum disorders (SSD). Several studies have shown that increased PNMS is linked to decreased fetal growth in males who later develop SSD. It has also been found that PNMS leading to increased morbidity and mortality outcomes are also associates with increased risk of SSD development in males. PNMS, especially in early pregnancy, has also been associated to motor deficiencies and behavioral difficulties in the pre-morbid period before schizophrenia onset, most notably in males.''

Epigenetic Therapeutics
Since epigenetic changes can be reversed with pharmacological treatments and drugs, there is a great deal of promise in developing treatments. As many have pointed out, schizophrenia is a lifelong disorder that had widespread effects. Thus, it may not be possible to fully reverse the disease. ''Although irreversible, the lives of patients with schizophrenia can be greatly improved through treatments that alleviate symptoms. Treatments like anti-psychotic medications for schizophrenia are effective, but they often have serious side effects, and medical practitioners are always looking to improve patients' treatment outcomes. Recent studies indicate that it may be possible to improve upon existing treatments through epigenetic means. This provides a promising new direction for disease management. Pharmaceuticals that directly affect epigenetic markers could be used to improve the efficacy of a patient's current treatment or serve as an updated treatment regiment altogether.''

''As previously discussed, schizophrenia is associated with elevated levels of gene methylation and repressive histone marks, including H3K9me2. Mood stabilizers have become a therapeutic method of interest in treating schizophrenia due to their ability to reverse epigenetic alterations like repressive histone marks. Mood stabilizers that are known to target epigenetic markers associated with schizophrenia include lithium, valproate, lamotrigine, and carbamazepine.''

Targeting Histone Modifications
HDAC (histone deacetylase) inhibitors are one class of drugs that are being investigated. The reelin and GAD67 genes (which are expressed less in schizophrenic animal models) are both upregulated after treatment with HDAC inhibitors. Furthermore, there is the added benefit of selectivity, as HDAC inhibitors can be specific to cell type, tissue type, and even regions of the brain. Just as there are many types of HDAC enzymes, there are several selective HDAC inhibitors that can be used to target HDACs specific to certain types of cells to accomplish this selectivity.

Valproate, a psychotropic drug, is an HDAC inhibitor that is frequently used to treat patients with schizophrenia. Valproate leads to both increased H3 and H4 acetylation as well as increased GAD67 and reelin mRNA levels in lymphocytes. Lithium has also been shown to be highly effective at increasing histone acetylation and presence of GAD67 and reelin transcripts in patients experiencing psychotic symptoms.

HMT (histone demethylase) inhibitors also act on histones. They prevent the demethylation of the H3K4 histone protein and open up that part of the chromatin. Tranylcypromine, an antidepressant, has been shown to have HMT inhibitory properties, and in a study, treatment of patients with schizophrenia with tranylcypromine showed improvements regarding negative symptoms.

''In early studies, imipramine, an antidepressant drug, was shown to be able to remove the repressive epigenetic mark H3K9me2. Decreasing repression at this marker appears to improve treatment outcomes for patients taking antipsychotic medications. ''

Targeting DNA methylation
Among long-term antipsychotic users, post-mortem tissue analysis finds that genes that are typically methylated in patients with psychosis are hypomethylated after lifelong antipsychotic use. ''In other words, anti-psychotic drugs are able to reduce methylation of genes in long-term users. Removing repressive epigenetic marks is only part of how these drugs modify the epigenome of patients with psychotic symptoms. Antipsychotics are associated with both the induction and inhibition of DNA methylation, which can lead to the simultaneous upregulation and downregulation of different genes in patients. While significant variation in methylation patterns have been recorded in patients using antipsychotic drugs, the evidence in this area is not yet sufficient to determine the exact mechanism underlying how these drugs influence methylation. Schizophrenia is a complex, multifaceted illness, and the variety of methylation patterns observed affirms this knowledge.''