Chronic Neurological Disorders: Genetic and Epigenetic Markers for Monitoring of Pharmacotherapy
Correspondence Address: Source of Support: None, Conflict of Interest: None DOI: 10.4103/0028-3886.314522
Source of Support: None, Conflict of Interest: None
Keywords: Alzheimer's disease, epigenetic markers, genetic markers, multiple sclerosis, Parkinson's disease, pharmacotherapy
Key Message: Association of genetic and epigenetic markers with potential to affect treatment in Multiple Sclerosis (MS), Alzheimer′s disease (AD) and Parkinson′s disease (PD) has been reviewed in this article. MS treatment response has a significant association with genetic markers like HLA genes, lipid-specific IgM oligoclonal bands, type I IFN-responsive genes, and epigenetic factors like SIRT1 expression and miR related factors. AD treatment effect varies with changes in genetic factors like ApoEε4allele, PS I and II, Tau phosphorylation, neuroinflammatory factors, and factors affecting methylation like folate and hyper/hypo-methylated genes. PD prognosis is affected through genetic factors like polymorphisms in dopamine receptor genes (DRD2), COMT and DDC metabolism genes, and epigenetic factors like ?-synuclein, LRRK2 and histone proteins (H4K5, K8, K12, K16).
With an enhanced life expectancy in the developing world, the burden of chronic neurological diseases has augmented significantly and affected health worldwide. As per the Global Burden of Disease (GBD; 2015) data, neurological disorders result in 250 million disability-adjusted life years (DALYs). Out of the total causes of global DALYs, 10.2% are due to Alzheimer's disease(AD), multiple sclerosis (MS), and Parkinson's disease (PD).These disorders are responsible for over 20% of deaths related to neurological disorders. It is estimated that around 30 million Indians suffer from neurological disorders (excluding neuroinfections and traumatic injuries). Along with high incidence and prevalence rates, it is interesting to note the varied treatment responses to the currently available pharmacotherapy for these diseases among the patients. For e.g., patients with AD respond variably to cholinesterase inhibitors. Levodopa (L-DOPA), which is the mainstay of treatment for PD, shows effects that may range from motor fluctuations and dyskinesia to psychosis and hallucinations. The varied response seen in MS patients to interferon-beta (IFN-β) treatment is also well-known. The current method of monitoring therapeutic outcomes in such diseases is through clinical endpoints, which is largely subjective in nature and would differ from one tertiary health care center to another. In addition, the clinical endpoints are likely to be misinterpreted by health care professionals, leading to delayed or incorrect pharmacotherapy. Neurodegenerative disorders, such as AD, are mostly diagnosed clinically after 15–20 years of the initial neuronal insult; thereafter, the only option available is to provide short-term symptomatic relief to patients via drug modifications rather than long-term therapeutic monitoring. Another option is using radiological endpoints as markers of therapeutic response. This exercise is quite futile as most diseases progress over time and regular radiological check-ups will only increase the workload and financial burden of an already overburdened health setup in a developing country. In this context, there is an immense role of pharmacogenomics and personalized treatment, and this is feasible through advanced genetical screening methodology. The personalization or tailoring of treatment is one way that the treatment outcome/prognosis of the disease may be improved.
In this article, we have explored the genetic and epigenetic markers for three chronic neurological disorders, i.e., MS, AD, and PD, and briefly discussed them. We hope that soon, therapeutic monitoring in these chronic neurological disorders will be based on genetic and epigenetic biomarkers for better and early management.
This study collected articles relevant to genetic and epigenetic markers in the disease like MS, AD, a PD. A literature search was performed in PubMed (January 1999–September 2018). The search strategies adopted in this study included combinations of MeSH headings, such as “Genetic markers,” “Epigenomics,” “Epigenetics” along with “Multiple Sclerosis,” “Alzheimer's Disease,” or “Parkinson Disease.” The reference lists of all articles selected from the searches were inspected. Two authors independently searched the databases for the collection of articles. One reviewer screened the articles to find out potentially relevant studies satisfying the inclusion and exclusion criteria and reduce duplication of studies by checking the titles and abstracts obtained from the literature searches. All authors resolved disagreements about study inclusion by discussion. The types of articles included were peer-reviewed original research articles, including randomized control trials (RCTs), open-label studies, and animal experimental studies. The study excluded letters to editors, expert opinion articles, and case studies. Articles were screened for the presence of keywords in titles or abstracts. Studies involved participants with clinically confirmed MS, AD, and PD at all stages of their illness, both sexes and any age. Animal studies involving the above disease conditions and induced disease models were included. The interventions in these studies included assessment of genetic and epigenetic markers as primary or secondary objectives and correlation with the above disease conditions. The outcomes considered were the identification of any genetic and epigenetic marker that has a significant correlation with the disease.
PubMed found 4,381 potential articles by update searches, out of which, 715 were screened based on the period of evaluation (1999–2018) and removal of duplicates [Figure 1]. After screening for eligibility of potential articles, 65 studies were included in this review. Potential bias in the review process was that the research question was focused to include only three neurodegenerative diseases, i.e., MS, AD, and PD. However, there are several other neurodegenerative diseases for which genetic and epigenetic markers have been assessed, which were not considered in this review. During selection, we focused on the period between 1999–2018, which is also a limitation as studies before this period with significant results are not considered.
The concern with MS is that unlike other major chronic neurological disorders, MS causes disability in young adults. Current pharmacotherapy is largely classified based on the subjective clinical response of the patient. Acute attack demands swift treatment with glucocorticoids and adrenocorticotropic hormone (ACTH), whereas disease-modifying agents, such as IFN-β, glatiramer acetate (GA), mitoxantrone, natalizumab, and fingolimod is the mainstay of treatment. Episodes of severe pain require analgesics, antispasmodic, and antidepressants. It has been reported that several genetic and epigenetic factors are associated with treatment response in MS as mentioned in [Table 1].
Genetic factors affecting pharmacotherapy
Human leukocyte antigen genes
The human leukocyte antigen (HLA) DRB1*1501 allele is one such factor that has gained notoriety over the past decade in the field of MS because of its pathological potency rather than being just a diagnostic biomarker. Yates et al. (2015) showcased that motor cortical demyelination was comparatively higher in younger cases carrying the HLA-DRB1*15 allele and had more severe motor cortical parenchymal and meningeal T-cell inflammation compared with HLA-DRB1*15 negative cases. Gross et al. (2011) investigated this marker in a retrospective study on patients treated with GA. According to the results, a single nucleotide polymorphism (SNP) on the HLA-DRB1*1501 allele (rs17445836A) did have a variation in the event-free survival (EFS) rate. Homozygotes for this mutation showed a longer EFS on GA than on IFN-β. Studies performed by Mazdeh et al. (2016) showed that an increased frequency of HLA-DRB1*04 allele and a decreased frequency of HLA-B*15 were linked with a better outcome in patients on IFN-β treatment. At the onset of the treatment, a substantial proportion of MS patients develop neutralizing antibodies (NABs) against IFN-β. It has been found that at the genetic level, patients with SNP on HLA region rs9272105 are at an increased risk of developing NABs, which ultimately decreases the efficacy of IFN-β.
Lipid-specific immunoglobulin M oligoclonal bands
Predicting the therapeutic efficacy of drugs treating MS does not always require expensive genetic (HLA) testing. The presence of antibodies of the immunoglobulin M (IgM) class, specifically lipid-specific IgM oligoclonal bands (LS-OCMB) in the cerebrospinal fluid (CSF) are associated with an aggressive form of the disease. In a study performed by Villar et al. (2005), autoreactive B cells were found to play a crucial role in the pathogenesis of MS. They observed that most B-cell lymphocyte antigen CD19 and CD5 positive present in the CSF have lost their CD20 expression, showing a phenotype characteristic of differentiated B-cells competent in secreting higher amounts of Igs. The final targets of these IgM antibodies are the components of the myelin sheath. Apart from their prognostic significance, these Igs also have a therapeutic significance. Bosca et al. (2010) demonstrated that LS-OCMB positive patients have an increased probability of relapse in the first year of treatment while they are on IFN-β therapy as compared with LS-OCMB negative patients. In addition, these patients showed a higher Expanded Disability Status Scale (EDSS) score at the end of 3 years (follow-up). Both the groups were statistically nonsignificant for the presence of NABs. This study clarified that LS-OCMB can be used as a surrogate marker to assess IFN-β response. Also, it is important to note here that patients with LS-OCMB have a reduced risk of developing progressive multifocal leukoencephalopathy (PML) during treatment with natalizumab. The risk of PML with natalizumab is well-documented (this side effect led to natalizumab's withdrawal in 2005 and reintroduction in 2006 after establishing a global risk management program).
Type I interferon-responsive genes
IFN-β (United States Food and Drug Administration [USFDA] approval: 1993) continues to remain the mainstay among treating agents that are considered “disease-modifying” when spoken in the context with MS. The various mechanisms by which IFN-β acts have been mentioned in detail by Airas et al. (2007). However, the efficacy and tolerability of IFN-β are not the same in all patients of MS. A meta-analysis consisting of a combined total of 3,980 MS (different varieties) patients conducted by Nikfar et al. (2010) is evidence of this claim. The justification for carrying out this study was the fact that many patients do not show any response to IFN-β. A study conducted by Hundeshagen et al. (2012) found increased endogenous IFN activity in a subset of MS patients before initiation of IFN-β treatment. Polymorphisms in such genes can lead to variation in the therapeutic outcome. For example, as noticed in the case of polymorphism in interferon regulatory factor 5 (IRF5) (rs2004640) has been associated with negative treatment response, whereas polymorphism in interleukin 10 (IL10; rs1800896, rs1800871, rs1800872) is associated with a positive outcome.
Epigenetic factors affecting pharmacotherapy
Decreased expression of sirtuin 1
It has been observed that relapse in MS patients has a correlation with decreased levels of sirtuin 1 (SIRT1), a class III histone deacetylase (HDAC). The basic science of SIRT1 or any other HDAC is that their action results in tight packing of the nucleosomes, which restricts the binding of transcription factors, thereby inducing chromatin silencing. Therefore, SIRT1 could be an important biomarker in predicting the likelihood of a future MS relapse episode in a patient and may lead to drug dose modification beforehand. In addition, unlike genomic factors, epigenetic changes are modifiable, SIRT1 may prove to be a new potential therapeutic target in the management of MS.
Like HDAC enzymes, micro ribonucleic acid (miRNA) is another epigenetic tool that leads to RNA silencing and post transcriptional regulation of gene expression. One important miRNA that has gained importance is miR-26a, which has been shown to downregulate T helper 17 (Th17) cell function in animal autoimmune encephalitis models. Inhibition of miRNA-26a may lead to increased levels of Th17-dependent cytokines, leading to exacerbation of clinical signs and symptoms of the disease. Similar findings have been replicated in human studies via quantification of miR-26a in peripheral blood mononuclear cells (PBMC) of MS patients. Not only does miR-26a play an important role in the pathogenesis of MS (and has the potential to be a prognostic marker), it might also have a significance in assessing therapeutic outcomes of treatment. While administering IFN- β, it was analyzed by Felice et al. (2014) that the level of miR-26a-5p was varied in response to IFN-β. It was higher in relapsing–remitting MS (RRMS) patients treated with IFN-β after 3 months of treatment interval and remained stable at 6 months interval in all patients. As a result, it was concluded that miRNA profiling could be a useful epigenetic marker for predicting IFN- β efficacy.
While MS is a disease of young adults, Alzheimer's is a chronic neurodegenerative disorder that affects millions worldwide and is the most prevalent in the older age group. It is also the most common form of dementia seen in clinical practice. Considering that the treatment of AD is mostly symptomatic, and as therapy for such chronic disorders is lifelong, it is important to understand various genetic and epigenetic markers [Table 2] that may affect the therapeutic outcome of AD.
Genetic factors affecting Alzheimer's disease pharmacotherapy
Apolipoprotein E allele
Apolipoprotein E (ApoE) is a genetic factor that affects the more common form of AD (sporadic and late-onset) and has three common polymorphisms in the ApoE gene, ε2, ε3, and ε4. Except for ε2, the other variants have an association with AD with the highest risk being in people carrying the ε4 allele. Binding of ApoE-associated lipoproteins to Aβ peptide leads to synaptic dysfunction and neurodegeneration in AD patients. In addition, an increase in the number of ApoE4 allele copy correlates with a decrease in choline acetyltransferase (ChAT) activity. Thus, it is safe to say at this point that more significant the influence of ApoE4 on disease activity, more severe is the cholinergic deficit. Whether ApoE4 has an effect on the therapeutic outcome after cholinesterase inhibitor administration in a patient with AD is debatable with some studies finding a positive correlation, whereas others refuting this claim. Cacabelos et al. carried out a study in 2007 on the Spanish population to check the effect of CYP2D6 distribution on the therapeutic outcome of cholinesterase inhibitors. CYP2D6-related extensive metabolizers and intermediate metabolizers were the best responders whereas poor metabolizers and ultra-extensive metabolizers responded the worst to treatment. In addition, the presence of ApoE4 allele in genetic clusters integrating cytochrome P450 2D6 (CYP2D6) and ApoE genotypes deteriorates the therapeutic outcome. Wang et al. (2014) studied the ApoE allele to check whether cholinesterase inhibitors affect the resting-state functional connectivity magnetic resonance imaging (rs-fcMRI). They discovered that ApoE carriers responded better to cholinesterase inhibitors (donepezil) than noncarriers. Such conflicting results might arise from a difference in cholinesterase inhibitor pharmacodynamics and follow-up periods of patients. It is important to understand the baseline characteristics of each patient group, whether they are on concomitant therapy and the duration of disease. Only then can we achieve a conclusion.
Tauopathy encompasses a wide variety of diseases, such as AD, frontotemporal degeneration, corticobasal degeneration, progressive supranuclear palsy, and Pick's disease. Cyclin-dependent kinase-5 (CDK-5) inhibitors for tau deposit-associated dementia have been developed. However, because of poor clinical efficacy, none have received FDA approval. Pathophysiology of tau is related to the microtubule-associated protein (MAP; tau protein) being hyperphosphorylated. This leads to its detachment from the microtubules (essential in neuronal axons as they provide tracks for the transport of vesicles and organelles) making them unstable. This accompanied by phosphorylated tau aggregate to form neuro-fibrillary tangles (NFT), which form the basic pathology behind more than 20 known tauopathies. All stages that lead to phosphorylation of tau protein to the formation of NFT have been targeted in preclinical studies and cell lines. One such agent is lithium, which is a well-known inhibitor of glycogen synthase kinase 3β (GSK-3ß; a nonspecific phosphorylator of tau protein). Preclinical studies in triple transgenic mice have shown positive results. A meta-analysis from 2015 confirmed that the use of lithium in AD patients resulted in significantly lesser memory impairment than patients who were on placebo. Lithium is currently being used off-label in patients with another tauopathy called chronic traumatic encephalopathy (CTE), as these patients are at an increased risk of bipolar disorder and suicide.
Presenilins are catalytic subunits of the gamma (γ) secretase protease complex. They originate from two genes, namely, PS1 and PS2. As their name suggests, they are associated with early-onset AD. In their study, Zamani et al. (2011) reported the effect of PS2 association with rivastigmine efficacy. They found that patients with the PS2 + A/–A genotype and bigenic genotypes of + A/–A E3/E3 and + A/–A E 3/E4 were the best responders to rivastigmine therapy, and those with the PS2 + A/+A were the worst responders.
The neuropathological hallmarks of AD are Aβ plaques and NFT. However, inflammatory insult starts much earlier, initiating neurodegeneration that leads to signs of cognitive impairment later on in life. In fact, neuroinflammation is central to all subsequent pathologies leading to AD. However, the clinical trials conducted till now have not taken into account individual predisposition to increased inflammatory activity before administering anti inflammatory medication. In addition, most of the anti inflammatory drugs were compared in parallel studies against placebo, making it difficult to propose whether individuals with increased neuroinflammation would respond differently to current pharmacotherapy. This has given rise to dichotomous results, wherein some studies show an improvement in cognitive impairment and some show no increased efficacy., It is difficult to reach a conclusion at this stage.
Epigenetic factors affecting Alzheimer's disease pharmacotherapy
The relationship between folate and Alzheimer's disease
It is important to understand the epigenetic mechanism of the transcriptional arrest. DNA methylation takes place at various cytosine-phosphate-guanine (CpG) sites via a DNA methyltransferase enzyme. S-adenosyl methionine (SAM) acts as the methyl donor. Cytosine is converted to 5' methyl-cytosine. The end product is methyl-CpG-binding proteins that are instrumental in causing transcriptional arrest. Many factors could change DNA methylation patterns and alter the levels of gene expression. One such compound is folate, which helps in the conversion of homocysteine to methionine, which then is converted into SAM. It can be comfortably concluded that a decrease in the levels of folate would lead to a decrease in SAM, thereby cause lesser transcriptional arrest. Folate deficiency has been shown to cause global hypomethylation. Inspired by similar findings, the Baltimore Longitudinal Study of Aging (BLSA) followed 579 elderly volunteers for more than nine years and recorded their vitamin intakes. Among them, 57 subjects developed AD over that time period. Among the intake of various vitamins taken into consideration (E, C, folate, B12, B6, and carotenoids), BLSA was able to finalize that intake of folate at or above the Recommended Dietary Allowance (RDA) is associated with a reduced risk of AD. It is, therefore, safe to say that despite the best symptomatic care, dietary folate level monitoring (as a therapeutic indication) should also become a regular part of outpatient department (OPD) visits for AD patients.
In animal studies, it has been shown that another epigenetic mechanism, i.e., histone tail modification also affects the pathophysiology of AD. Many HDAC inhibitors (HDACi), such as sodium butyrate, trichostatin A, and vorinostat have been preclinically tested and shown positive results. Whether histone tail modification affects therapy with cholinesterase inhibitors or memantine is yet to be demonstrated.
Methylation and deacetylation mechanisms
Many recent studies have shown the effect of multiple epigenetic mechanisms and the effect they have on disease and treatment outcomes in patients with AD. Cohort studies analyzing postmortem brains have shown an increase in hypermethylation of genes such as Ankyrin 1 (ANK1) in the entorhinal cortex. Similar studies on Bridging integrator 1 (BIN1), Cadherin-3 (CDH3), Rhomboid 5 (RHBDF2) and DUSP 22 have shown a correlation between the level of hypermethylation and severity of AD sometimes via increased tau production., Many hypomethylated and deacetylated genes have been implicated in the pathology of AD [Table 2]. Although it is safe to say based on recent researches that these epigenetic factors play a role in disease severity, it is early to comment on whether they may affect pharmacotherapy.
PD involves a broad spectrum of clinical manifestations. Understanding genetic and epigenetic processes that affect therapy is important to provide adequate therapeutic benefit to all patients [Table 3].
Genetic factors affecting Parkinson's disease pharmacotherapy
Dopamine receptor genes
Among all dopaminergic receptor genes, the one that has appealed researchers the most is the dopamine receptor gene “DRD2” (chromosome 11q22-q23), especially its association with Taq1A polymorphism. This phenomenon was shown to not just increase the risk of PD in certain racial subgroups but also to interfere with the drug metabolism of various drugs used to treat this chronic neurological disorder. Apart from its impact on the course of the disease, the DRD2 Taq1A polymorphism has been associated with drug-induced dyskinesia, the onset of hallucinations, and sleep attacks. Taq1A polymorphism is an SNP that leads to substitution within the eleventh ankyrin repeat of the ankyrin repeat and kinase domain containing 1 (ANKK1; Glu713Lys of 765 residues). ANKK1 enzyme is involved in signal transduction pathways and is a member of the Ser/Thr protein kinase family. Although this enzyme (ANKK1) is encoded by the ANKK1 gene, it influences PD pharmacogenomics because of its close location with the DRD2, which is the eventual landmark for most anti-Parkinson's drugs.
Catechol-o-methyltransferase (COMT) metabolizes dopamine and its gene is located at chromosome 22q11. Genetic variation because of polymorphisms is bound to occur. Two most notable polymorphisms that may require therapeutic adjustment are:
Oral L-DOPA is the most widely used anti-Parkinson's drug and has been in clinical use for close to five decades. A bulk of its pharmacokinetics depends upon its interaction with dopa-decarboxylase (DDC), an enzyme that converts L-DOPA to dopamine. Located at chromosome 7p12, the DDC gene is also subject to polymorphisms as noticed by Devos et al. (2014). In their study, 33 patients underwent a challenge with L-DOPA and benserazide (peripherally acting aromatic L-amino acid decarboxylase). At the baseline, the patients were genotyped for two specific polymorphisms, i.e., rs921451 and rs3837091. The primary endpoint was the motor response to L-DOPA, whereas the pharmacokinetic parameters were plasma levels of L-DOPA and dopamine. While the presence of the polymorphisms did show a significant change in the primary endpoint, there was no significant contrast in the secondary endpoints.
Epigenetic factors affecting pharmacotherapy
α-synuclein is the principal component of the Lewy body, the hallmark inclusion body of PD. The amount of neurodegeneration in a brain suffering from PD shows a direct correlation with the quantity of Lewy bodies deposited. As mentioned in the case of epigenetic factors with respect to AD, epigenetic factors also play a key role here. Although α-synuclein has been found in other chronic neurological disorders, its location in the brain determines the type of disease the patient may suffer from, e.g., hypomethylation at α-synuclein intron 1 in the substantia nigra is specific to PD. In turn, this hypomethylation leads to an increase in α-synuclein associated Lewy bodies production and deposition in the diseased brain.
Until now, we were mostly discussing the impact of genetic and epigenetic markers on therapy, but the effect of therapy (L-DOPA) on a marker (α-synuclein levels) is yet to be discussed. Schmitt et al., (2015) noticed in their study on 490 sporadic PD patients, the epigenetic off-targets of L-DOPA, stating that L-DOPA reversed hypomethylation of α-synuclein in a dose-dependent manner. Concurrent medication in patients with PD may also have an effect on the pathogenesis of the disease. Patients taking nonselective beta-blockers, such as propranolol, may be at risk of increased Lewy bodies (clumps of α-synuclein) accumulation, whereas β-2 agonists may have a delay in the onset of PD.
Other epigenetic factors
Two important epigenetic factors require mentioning. The first being Leucine-rich repeat kinase 2 (LRRK2). In a 2018 meta-analysis, it was found that carriers of the LRRK2-G2019S mutation were predominantly female patients with a positive family history of early-onset PD. This group of individuals, when compared with noncarriers, showed a better response to L-DOPA and had an increased tendency to develop dyskinesia and motor fluctuations later on in life. Habibi et al. have clearly described the effects of various epigenetic mechanisms, such as methylation, acetylation, phosphorylation, and ubiquitylation on histone proteins and their effect on PD pathology. Their effect on pharmacotherapeutic outcomes remains to be discovered.
Chronic neurological disorders are a major health burden worldwide. Monitoring pharmacotherapy based solely on clinical endpoints may suffer from investigator bias as dose modulation is in the hands of the clinician. In the last two decades, there have been giant leaps in the field of genetics and epigenetics. In this article, we have tried to summarize the genetic and epigenetic markers that may influence drug pharmacokinetics and pharmacodynamics, thereby require monitoring. This article attempted to bring a majority of genetic and epigenetic factors onto a single platform. This study compiled the biomarkers already studied by different authors from a research point of view, which can have potential clinical applications for prognostic and therapeutic outcomes. The main disadvantage is the unfamiliarity of many such biomarkers in a clinical setting and the cost factor associated with such analysis in the current times. As the health care system develops and reaches newer heights, we expect more and more of these biomarkers to be used as pharmacotherapeutic outcome indicators.
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Conflicts of interest
There are no conflicts of interest.
[Table 1], [Table 2], [Table 3]