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Handbook of Epigenetics. http://dx.doi.org/10.1016/B978-0-12-805388-1.00021-3Copyright © 2017 Elsevier Inc. All rights reserved.

21Epigenetics, Stem Cells, Cellular Differentiation, and Associated

Hereditary Neurological DisordersBhairavi Srinageshwar*, Panchanan Maiti*,**,

Gary L. Dunbar*,**, Julien Rossignol**Central Michigan University, Mt. Pleasant, MI, United States;

**Field Neurosciences Institute, Saginaw, MI, United States

INTRODUCTION TO EPIGENETICS

Epigenetics is defined as structural and functional changes occurring in histones and DNA, in the absence of alterations of the DNA sequence, which, in turn, has a significant impact on how gene expression is altered in a cell [1]. The term “epigenetics” was coined by the famous developmental biologist, Cornard Hal Wad-dington, as “the branch of biology that studies the causal interactions between genes and their products, which bring the phenotype into being”[2]. Epigenetics bridge the gap between the environment and gene expression, which was once believed to function independently [3]. Epigenetic changes can lead to increase or decrease in gene expression, thereby activating and/or deactivating genes, depending on the nature of the epigenetic con-trol. Some of the most important histone modifications include: (1) methylation; (2) acetylation; (3) phosphory-lation; (4) ubiquitination; and (5) SUMOylation and DNA modification, including DNA methylation. These

changes are discussed in detail elsewhere [3,4], but are briefly described later as an overview for this chapter.

DNA methylation. DNA methylation and some of the histone modifications are interdependent and play an important role in gene activation and repression during development [5]. DNA methylation reactions are cata-lyzed by a family of enzymes called DNA methyl trans-ferases (DNMTs), which add methyl groups to a cytosine base of the DNA at the 5’-end, giving rise to the 5’-methyl cytosine. This reaction can either activate or repress gene expression, depending on the site of methylation and it can also determine how well the enzymes for gene tran-scription can access the DNA that is wrapped around the histone [6].

Histone methylation. Trimethylation of lysine at position 4 on histone 3 (H3K4me3) promotes gene transcription (i.e., gene activation), whereas trimethylation of lysine at position 27 on histone 3 (H3K27me3) inhibits gene transcription (i.e., gene silencing). Alternate gene acti-vation and repression promote a balanced dose of gene

O U T L I N E

Introduction to Epigenetics 323

Epigenetics and the Human Brain 324Stem Cells 324Eukaryotic Chromosomal Organization 325

Histones and Their Structure 325Epigenetics and Neurological Disorders 326

Conclusions 335

References 336

324 21. EPIGENETICS, STEM CELLS, CELLULAR DIFFERENTIATION, AND ASSOCIATED HEREDITARY NEUROLOGICAL DISORDERS

V. FACTORS INFLUENCING EPIGENETIC CHANGES

expression, which is required for those genes involved in overall development and maturation of organisms. This ensures that only appropriate genes are turned “ON” and “OFF” at any given point of time [7]. Huntington’s disease (HD), Parkinson’s disease (PD), and multiple sclerosis (MS) are some of the diseases that are caused by abnormal DNA methylation pattern. These are discussed in more detail in later sections of this chapter.

Histone acetylation. DNA acetylation involves the acetylation of lysine residue, which is catalyzed by the enzymes, histone acetyltransferases (HATs), and histone deacetylases (HDACs), which have opposing effects on each other. HATs transfer acetyl groups to lysine, whereas HDACs remove acetyl groups from lysine. However, presence or absence of an acetyl group (CH3CO) on a lysine residue alters the charge on the amino acid and can decrease the interaction of the N-terminal region of histones with the negatively charged phosphate groups of DNA. These events are involved in transformation of the condensed chromatin into a more relaxed structure, which can induce gene expression [8].

Histone phosphorylation. Phosphorylation involves addi-tion of phosphate group to threonine, serine, and tyrosine residues. Phosphorylation of serine at position 139 on histone 2 (H2) occurs as a response to DNA damage dur-ing cell cycling. This relaxes the chromatin; thereby the proteins or factors responsible for repairing the damaged regions of the DNA have greater access to the DNA, which aids in the recovery of the DNA damage. Moreover, phos-phorylation of threonine and serine residues on histone 3 (H3) facilitates regulation of gene expression [9]. Histidine phosphorylation is one of the epigenetic modifications occurring in the prokaryotic cells and in lower eukaryotes that plays a major role in cell signaling. The histidine is phosphorylated at the imidazole ring, but occurs only on those nitrogen atoms that are unprotonated [10].

Histone ubiquitination and SUMOylation. Ubiquitina-tion and SUMOylation are associated with posttransla-tional modifications that regulate transcription of gene and protein translation activities. It is well established that the addition of ubiquitin molecules to proteins facil-itate targeted protein degradation. In addition to ubiqui-tin, various small ubiquitin-like molecules (SUMO) are observed in cells, known as small ubiquitin-related mod-ifier. These molecules have activities, which are similar to ubiquitin and can attach covalently to those proteins, which are involved in changing chromatin structure and gene expression [3].

EPIGENETICS AND THE HUMAN BRAIN

Generation of neurons and glial cells from progeni-tor cells involve epigenetic mechanisms that take place throughout the developmental stages of the brain.

The outer layer of the embryo, called ectoderm, forms the central nervous system, and during the process of development, DNA methylation controls the epigen-etic mechanisms of the embryonic cells. For example, to prevent the differentiation of nonneuronal cells into mature neurons, the proneural genes, as well as gene which are associated with proteins involved with neu-rogenesis, such as the brain-derived neurotrophic factor (BDNF) gene, are silenced by DNA methylation at their promoter region. However, DNA remethylation can take place on a neuronal gene, such as Sox2 [11], which allows for the selective initiation of neuronal develop-ment. Similarly, during initial development of the cor-tex, the genes involved in the formation of glial cells are suppressed by DNA methylation, promoting the forma-tion of more neurons during the early stages of neuro-nal development. Eventually, during the later stages of cortical development, the DNA methylation is reversed, leading to the generation of glial cells [12,13]. Some of the genes involved in postnatal neurogenesis are Sox2, Dlx2, Sp8, and Neurog2 and those involved in the for-mation of glial cells are Sparcl1 and Nkx2-2. It has been shown that during the differentiation of neural stem cells (NSCs) or progenitor cells, DNA methylation is facilitated by DNMT3a, which silences the genes Sparcl1 and Nkx2-2, leading to the inhibition of glial cell for-mation and promotion of mature neuron development from NSCs [14]. It is also believed that the normal aging process in humans is associated with modification of the epigenome in the brain, affecting certain genes related to neurogenesis, especially within the cortex [15]. This process leads to the disruption of synapses, abnormal neurotransmission, and is associated to age-related dis-orders [16]. However, a comprehensive description of the epigenetic mechanisms related to aging is beyond the scope of this chapter.

Stem Cells

Dysregulation of epigenetic mechanisms has a direct impact on gene expression patterns that lead to abnor-mal gene functions, which form the basis of most of the genetic disorders (monogenic or polygenic) in humans. Environmental stress can also alter epigenetic mecha-nisms, which could become a cause for the predisposi-tion of certain diseases, such as autism, schizophrenia, and congenital heart disease [17]. This chapter focuses on the role of epigenetics and epigenetic changes that take place during stem cell differentiation, which can be used as a potential therapy for neurological diseases. Stem cells have a unique property of proliferation, dif-ferentiation, and self-renewal. Stem cell plasticity is an important characteristic and is based on the degree of pluripotency, which is the ability of a cell to differenti-ate into another cell lineage. Stem cells can be classified

EPIGENETICS AND THE HUMAN BRAIN 325


as: (1) totipotent, such as embryonic stem cells (ESCs) of the morula, which can be differentiated into any cell type, including placental cells; (2) pluripotent, such as induced pluripotent stem cells (iPSCs), which can be dif-ferentiated into any cell type, except for placental cells; and (3) multipotent, such as mesenchymal stem cells (MSCs) and neural stem cells (NSCs), which can be dif-ferentiated into many, but not all, cell types.

ESCs are highly unspecialized and can form any type of specialized cells under appropriate conditions and environments. ESCs divide and renew themselves, which make them appropriate candidates for regenera-tive medicine or cell replacement therapy [18]. Previ-ously, we have reviewed the role of epigenetics in MSCs, NSCs, and iPSCs and their association with neurode-generative diseases [19]. In addition, the basics of stem cells, and the various epigenetic mechanisms associated with them, are explained comprehensively in the previ-ous edition of this book. Therefore, the aim of the pres-ent chapter is to discuss the role that epigenetics of stem cells might play in a subset of neurological diseases.

Some of the inherited genetic disorders that occur as a consequence of abnormal epigenetic mechanisms include: (1) HD; (2) PD; (3) Rett Syndrome (RTT); (4) spinocerebellar ataxia (SCA); and (5) MS. Currently, stem cell–based therapies are being tested as a potential treatment for these diseases. A sampling of these treat-ment strategies are outlined in this chapter and include examples of: (1) transplants of bone marrow-derived mesenchymal stem cells (BM-MSCs) for treating HD; (2) transplants of neural stem cells (NSCs) for treating PD; (3) transplants of induced pluripotent stem cells (iPSCs) for treating RTT; (4) transplants of umbilical cord-derived mesenchymal stem cells (UC-MSCs) for treating SCA; and (5) transplants of hematopoietic stem cells (HSCs) for treating MS. These treatment strategies and the epigenetic mechanisms involved with these dis-orders are summarized in Table 21.1.

To better understand the role of epigenetics in neuro-logical disorders, a working knowledge about histones,

chromosomes, and the general hierarchy in the chromo-somal organization, is needed, which is briefly reviewed in the next section.

Eukaryotic Chromosomal Organization

The strands of DNA are about 2 nm wide and are packed around the core of four pairs of histone pro-teins (H2A, H2B, H3, and H4), forming the nucleosome, which is the first level of chromosomal organization (Fig. 21.1). These nucleosomes are the building blocks of the chromatin structure, which is about 30 nm in diam-eter. The formation of chromatin structure involves the fifth histone, H1, which is near the adjacent nucleosome, thereby compacting the nucleosome or chromatin to form chromatin coils, which are about 300 nm in diam-eter. These fibers are further condensed to make loops of 700 nm in diameter, which, in turn, form the intact metaphase chromosomes, which are about 1400 nm wide [28].

Histones and Their Structure

The genome consists of two molecules of each his-tone protein (H2A, H2B, H3, and H4) giving rise to an octamer, which is made of about 130 amino acids. The nucleosome, as discussed before, consists of DNA, that is, 146–147 nucleotides long, making about 1.65 turns around the octamer. The core histones are highly con-served in eukaryotes, having a “tail” at their N-terminal end where the epigenetic modifications, such as meth-ylation, acetylation, and/or phosphorylation, take place. These regulate the chromatin structure, which has an impact on recruiting various proteins involving activation and repression of gene expression [28,29]. Defects in chromatin organization and deficiency of enzymes lead to various forms of human diseases, such as RTT, Rubinstein–Taybi syndrome, and Coffin–Lowry syndrome [30].

TABLE 21.1 An Overview of Various Epigenetic Mechanisms Associated With Neurodegenerative Diseases

Neurodegenerative disease Stem cell based therapy Epigenetic mechanism involved with disease

HD BM-MSCs Histone 3 (H3) methylation leading to reduced trophic factors [20]

PD NSCs DNA methylation leading to metabolic defects [21]

RTT iPSCs Point mutations in MeCP2 gene leading to defective epigenetic regulatory molecules [22]

SCA UC-MSCs Methylation and acetylation of histone leading to reduced RNA expression [23,24]

MS HSCs DNA methylation, histone acetylation and posttranscriptional modification by miRNA leading to compromised immune response [25–27]

HD, Huntington’s disease; MS, multiple sclerosis; PD, Parkinson’s disease; RTT, Rett syndrome; SCA, spinocerebellar ataxias.



Epigenetics and Neurological Disorders

Huntington’s Disease and Mesenchymal Stem CellsHuntington’s disease (OMIM #143100) is a devastat-

ing, fatal, autosomal dominant neurodegenerative dis-order, which most profoundly affects the striatal region of the brain. The disease is characterized by cognitive, motor, and psychiatric disturbances [31]. There is atro-phy and loss of the medium spiny GABAergic neurons in the caudate and putamen regions of the striatum, which leads to motor and cognitive impairment [32]. The disease is due to the expansion of CAG repeats in the Huntingtin gene (HTT), which produces mutant huntingtin protein (mHTT) that is highly toxic, leading to the signs and symptoms of the disease [33].

Currently our laboratory is investigating the role of transplanting BM-MSCs and UC-MSCs as a potential treatment for HD. We have shown that BM-MSCs cre-ate an optimal microenvironment in the striatum that slows the progression of neuronal loss and dysfunction by restoring the various neurotrophic factors, includ-ing BDNF, which is down regulated in HD. In our pre-vious studies, we transplanted BM-MSCs, which were genetically altered to overexpress BDNF, into the striata of YAC128 mice (a slowly progressing, transgenic HD mouse model, which carries the entire human mHTT gene) and R6/2 mice, (fast-progressing, transgenic HD mouse model, carrying exon 1 of human mHTT gene), and observed profound neuroprotective effects, includ-ing a significant reduction in the motor symptoms of the

FIGURE 21.1 The eukaryotic chromosomal organization. The steps showing the chromosomal organization involved in condensation of a 2 nm wide DNA wrapping around the histone molecules to form the nucleosome, which in turn twists to form coils (30 nm) and loops (300 nm) which further condenses into a 1400 nm wide chromosome [28].



disease. These observations suggest that manipulation of BM-MSCs could be a potential therapeutic for allevi-ating HD pathology [34–36].

The Huntingtin gene. The normal HTT protein is local-ized in the cytoplasm, whereas mHTT is found in the nucleus, as well as in the cytoplasm. Though both wild type HTT and the mHTT can interact and inhibit acet-yltransferase function, the actual presence of the mHTT in the nucleus was shown to be specifically responsible for interfering with the acetylation of histones [37]. The cognitive symptoms observed in HD are linked to the hypermethylated status of certain genes, such as Sox2 and Pax6. Because these genes play vital roles in the pro-liferation and maintenance of neural stem cells, which eventually become neurons, alterations of their struc-ture may contribute to subsequent dysfunctions, such as an impairment of hippocampal neurogenesis [38]. Similarly, the hypoacetylation of certain genes, such as BDNF gene, has been found in HD patients and animal models of HD. The CREB binding protein (also known as CREBBP) is a histone acetyltransferase and a tran-scriptional cofactor that regulates histone acetylation and gene activation. When the mHTT interacts with the CREB binding protein, it loses its transcriptional activa-tor and HAT functions, which lead to hypoacetylation of histones. This in turn, leads to transcriptional dys-regulation of certain genes in the neurons in HD brain [39]. Later, it was found that defects, other than DNA methylation and acetylation, are involved in HD. Lee and coworkers [40] investigated the role of microRNA molecules (miRNA) and found lower levels of 9 types of miRNA in 12-month-old YAC128 and 10-week-old R6/2 mice. Understanding the defective epigenetic mecha-nisms in HD has led to the use of HDAC inhibitors and miRNA as potential treatments for this disease.

HD and BDNF. BDNF is an important neurotropic factor, which is expressed abundantly in different brain regions. H3K4me3 is a histone involved in transcription of the BDNF gene, which is significantly reduced in the cortex of the HD brain. BDNF is expressed in the corti-cal neurons that project into the striatum and has been shown to be essential for the survival of striatal neurons. As mentioned earlier, histone methylation leads to gene silencing and histone acetylation leads to gene activa-tion. However, H3K4 is an exception because either methylation or acetylation of this histone leads to gene activation. Modification of H3K4me3 is widely studied and is of interest to researchers because H3 is associ-ated with the promoters of the genes that are actively transcribed (e.g., BDNF) [41]. Research using chromatin immunoprecipitation (ChIP) analysis has revealed a cor-relation between BDNF expression and H3K4me3 levels in HD [20]. In the brain, repressor element-1 silencing transcription factor/neuron-restrictive silencer fac-tor (REST/NRSF) is the main factor that recruits other

cofactors to regulate neuronal gene expression. REST, a transcriptional repressor, plays a major role in the regu-lation of the BDNF gene. Under normal circumstances, REST binds with the HTT in the cytoplasm, but in the case of mHTT, there is no interaction between the REST and HTT (Fig. 21.2). This leads to nuclear transloca-tion of the REST, which then inhibits BDNF expression, resulting in neurodegeneration. REST not only targets BDNF gene, but also influence other neuronal genes that are down regulated in HD [41].

These findings show that rescue of REST-regulated genes may prove to have a promising therapeutic effect on HD. H3K4me3 levels are significantly lower at the REST region of the BDNF gene in the cortex when com-parisons are made between 8 and 12-week old R6/2 mice. H3K4me3 not only regulates BDNF gene expression, but also has an impact on other genes, a postulate that was confirmed by transcriptome analysis and genome-wide analysis, which revealed that there are about 98 major genes showing differential expressions in the cortex and the striatum in 12-week old R6/2 mice. In the cortex, the differentially expressed genes are associated with neuro-transmission (e.g., Grla3, Grm4, and Bagra5), G-protein signaling (e.g., Rgs9 and Arpp21), synaptic transmis-sion (e.g., Snap25 and Rph3a), inflammation (e.g., C4a and Dusp6), and calcium signaling (e.g., Scn4b, Hpca, and Itpr1). In the striatum, the differentially expressed genes are associated with neurotransmission (e.g., Drd2, Grm3, and Gabrd), G-protein signaling (e.g., Rgs9 and Arpp21), synaptic transmission (e.g., Snapr and Dlg4), and calcium signaling (e.g., Scn4b, Hpca, and Itpr1) [20].

Stem cell therapy for HD. MSCs are adult stem cells that are abundantly present in bone-marrow (BM). MSCs can also be derived from umbilical cord (UC) and adipose tissue (AT). The MSCs, derived from BM and AT, have a greater survival rate, when compared to the MSCs derived from other sources [43]. BM-MSCs can differen-tiate into osteogenic, adipogenic, and chondrogenic lin-eages. However, by triggering an epigenetic mechanism, these MSCs can differentiate into a neuronal-like lineage.

FIGURE 21.2 Role of REST in downregulation of BDNF in HD. (A) The wild-type HTT protein binds to the REST protein in the cy-toplasm, thereby preventing the REST molecule to bind to the BDNF promoter. (B) The mHTT fails to bind to the REST which causes REST to bind to BDNF promoter and inhibits trophic factor transcription leading to reduced BDNF expression as seen in HD brain [42].



This can be achieved by passaging the MSCs and every time the MSCs get passaged, a series of methylation and acetylation reactions take place [44].

Recently, we have found that MSCs at higher pas-sages (passaged about 40–50 times prior to transplan-tation) have more therapeutic efficacy for alleviating motor symptoms in the R6/2 mice, compared to lower-passaged MSCs (passaged about 3–8 times prior to transplantation). This study showed that passaging the cells up to 40–50 times produces a subpopulation of MSCs that have the potential to create an optimal envi-ronment within the transplantation site in the striatum, as well as generating BDNF, which is usually deficient in HD brains [36]. Genes that are associated with steering the MSCs toward osteogenic, adipogenic, and chondro-genic lineages, such as osteopontin (OPN), peroxisome proliferator-activated receptors gamma 2 (PPAR-γ2), and fatty acid binding protein 4 (FABP4), undergo methyla-tion and histone acetylation, as the cells are passaged, thereby reducing differentiation into osteogenic, adipo-genic, or chondrogenic lineages [44,45]. The acetylation status of H3K9 at the promoter regions of these genes undergoes changes, thereby leading to less activation [46]. Therefore, when higher passaged MSCs are trans-planted into animal models, the environment at the transplantation site is more favorable for increasing BDNF, which is required for neuronal survival and alle-viating symptoms of HD [36].

Similarly, in another study, we genetically modified the BM-MSCs to overexpress BDNF and transplanted these cells into the striatum of the YAC128 mice. The mice, which received BM-MSCs that overexpressed BDNF showed improvement in motor coordination, compared to YAC128 mice, which did not receive BM-MSCs that overexpressed BDNF [34]. Interestingly, one of our previous studies involved transplantation of UC-MSCs into the striata of the R6/2 mice and though these mice showed reduction in both spatial memory and motor deficits, the extent of behavioral sparing was slightly higher when BM-MSCs were used, suggesting that the source of the MSCs may affect their efficacy when transplanted [35].

Conclusions for epigenetics in HD. The epigenetic altera-tions of genes, such as OPN, PPAR-γ2, and FABP4, steer MSCs away from osteogenic, adipogenic, and chondro-genic lineages as a function of cell passaging and may play an important role in driving these stem cells into a neuronal-like lineage. The aforementioned studies show that MSCs have a therapeutic effect on HD and by uti-lizing higher-passaged MSCs, the transplants appear to be more efficacious than using lower-passaged MSCs. However, the higher-passaged MSCs may have less clinical utility, because they are more susceptible to other epigenetic effects and tumor formation follow-ing transplantation, as they have been shown to carry

chromosomal abnormalities that may adversely affect survivability and successful engraftment at the trans-plantation site [47]. Therefore, even though higher-passaged MSCs may have a stronger therapeutic effect for HD, it is important to study the epigenetic mecha-nisms of MSCs at different passages to select a subpopu-lation of cells that will show their maximum therapeutic effects, without adverse effects.

Epigenetic mechanisms play an important role in the dysregulation of genes that are associated with the secretion of trophic factors, such as BDNF, as described previously. Therefore, targeting epigenetic markers and improving the expression of BDNF may prove to be beneficial in alleviating the signs and symptoms of HD [20].

Although various studies have described histone modifications and histone variants that are associated with HD, including phosphorylation of histone 2 vari-ants observed in HD cell line and in R6/2 mouse model [48], a detailed description of this and many other his-tone variations is beyond the scope of this chapter.

Parkinson’s Disease and Neural Stem CellsParkinson’s disease (OMIM #168600) is a late-onset

neurodegenerative disease, mainly affecting individuals of about 65–85 years of age. The disease is characterized by impairment of both motor and nonmotor symptoms, including rigidity, bradykinesia, tremor, postural insta-bility, depression, abnormal sleep patterns, cognitive dysfunction, and autonomic insufficiency [21,49]. PD is due to the degeneration of dopaminergic neurons in substantia nigra, pars compacta (SNpc). The genetic fac-tors, such as mutations in PARK genes and environmen-tal factors, such as aging and exposure to neurotoxins, contribute to the disease [50,51]. As such, PD can be caused either by sporadic mutations or can be inher-ited. Major gene candidates that are associated with PD, include PARK genes, leucine-rich repeat kinase 2 gene (LRRK2), and the α-synuclein gene (SNCA). The muta-tions in PARK gene family (PARK 1–15) and SNCA show Mendelian inheritance patterns, suggesting familial PD. Sporadic PD is caused by variants found in SNCA and LRRK 2 genes. PD also shows polygenic and complex inheritance patterns, combined with environmental factors [21].

Impairment of one-carbon metabolism in PD. The group of metabolic reactions consisting of various enzymes and coenzymes that are involved in various biological functions that involve lipid metabolism, redox reaction, and methylation reaction is known as one-carbon metab-olism. These metabolic activities take place by utilizing glucose, amino acids, such as serine and glycine, and vitamins, such as B12 and B6 [52]. Therefore, impairment in DNA methylation is a part of one-carbon metabolism that is found in PD.



As mentioned earlier, DNA methylation is one of the major epigenetic modifications that ensures condensa-tion or relaxation of chromatin structure, depending on the methylation status of the DNA that is wrapped around the histones. The chemical reaction is catalyzed by DNMT1, where cytosine gets methylated to form 5′methyl-cytosine, a reaction that involves two major molecules, S-adenosylmethionine (SAM), and S-adeno-sylhomocysteine (SAH). SAM is a universal methylating agent produced from folate and homocysteine (HCY), which methylates histones and DNA [21]. SAM, SAH, and HCY are some of the biomarkers of the metabolic pathway associated with the one-carbon metabolism [53]. Hence, the DNA methylation potential depends on the levels of SAM and the potential of DNMT1 to cata-lyze the reaction and transfer the methyl group to cyto-sine. This reaction was found to be impaired in many neurodegenerative diseases, especially in genes asso-ciated with Alzheimer’s disease (AD) and PD. Due to defects in one-carbon metabolism, the rate of methyla-tion decreases, leading to increased gene expression. An example of such defects in metabolism was found dur-ing the analysis of methylation status of the SNCA gene in PD patients [21].

The SNCA gene. The α-synuclein protein is important for dopaminergic neurogenesis during early embryonic development. The Lewy bodies found in PD consist of SNCA and protein inclusion bodies, which lead to dis-ease pathogenesis. Lower levels of SNCA are associated with loss of dopaminergic neurons during embryonic stage, whereas increased expression of SNCA may be a risk factor or a threat during later stages [54]. The genetic abnormalities associated with SNCA that lead to PD are the point mutations and copy number variants. Previous studies have reported that the mutation of the SNCA genes found in dopaminergic neuron, results in decreased methylation, leading to mono-allelic expres-sion of the gene. However, mRNA levels from this single allele exceed that of the control subjects having normal biallelic expression. Methylation status of the intronic regions (human intron 1 having 66 CpG sites) of the SNCA gene was found to be similar to those reported in previous studies, especially in reference to the cortex and substantia nigra regions of the brain [55,56]. The miRNA also plays a role in regulating the gene expres-sion of SNCA. Doxakis [57] has analyzed two of the major miRNA of the brain, mi-RNA7 and mi-RNA153, and found that overexpression of these miRNAs in neu-ronal culture lowered the SNCA levels.

The PARK gene. The majority of PARK gene muta-tions are also associated with juvenile form of PD. Cai and coworkers [58] investigated about 33 CpG regions on the PARK gene promoter in three groups of indi-viduals, including PD patients carrying PARK gene mutations, PD patients without PARK gene mutations,

and age-matched controls. DNA methylation analysis revealed that there was no significant difference in meth-ylation status between the three groups, which suggests that PARK gene methylation does not contribute in the PD pathogenesis.

Stem cell therapy for PD. More than half of the dopami-nergic neurons are lost in SNpc before the actual onset of PD [59]. There are various studies and literature reviews that have investigated the role of neural stem cells in PD [49,54,60] and the importance of neurotrophic fac-tors, particularly glial cell line-derived neurotrophic fac-tor (GDNF). The NSCs are multipotent stem cells that are specifically found in the subventricular zone (SVZ), subgranular zone (SGZ), and the dentate gyrus (DG) of the hippocampus. The environment at these regions are the most favorable for the differentiation of NSCs into neurons [61]. Sanberg [60] has discussed the role of transplantation of undifferentiated NSCs into the stria-tum of a primate model of PD and indicated that NSCs were able to survive and migrate to the site of neuro-degeneration and replace the lost neurons. The animals recovered from their behavioral deficits. Redmond and coworkers [62] also transplanted undifferentiated NSCs into the primate model of PD and found that though, these undifferentiated NSCs had therapeutic effect, only a small population of these NSCs partially differentiated into dopaminergic neurons, due to a less-than optimal microenvironment at the site of transplantation. These studies indicate that the partially differentiated NSCs migrate to the substantia nigra, through the nigrostriatal pathway, following their unilateral transplantation into the striatum. However, these finding suggest that cell replacement therapy provides only minimal neuropro-tective effects.

Other approaches, such as dopamine replacement therapy and deep brain stimulation (which decrease tremor and rigidity), also failed to show neuroprotec-tive effects. GDNF is well known to increase surviv-ability of dopaminergic neurons, and delivering GDNF into the brain of PD animal models, such as MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine)-treated rhesus monkey [63] and 6-OHDA (6-hydroxydopamine) injected rats [64,65], were shown to be neuroprotective. Overall, GDNF is critical for establishing the nigrostria-tal dopamine system during development and plays an important role in protecting dopaminergic neurons from degeneration by maintaining their morphology and neurochemical and biochemical reactions that are taking place in them, as well as ensuring proper neuronal dif-ferentiation and long-term survivability of neurons [66].

Open-labeled clinical trials using GDNF showed tol-erance and clinical benefits in patients within 3 months of treatment, but randomized clinical trials failed to reveal significant benefits [67]. Deng and coworkers [68] have shown that the cotransplantation of dopaminergic



neurons and NSCs can reduce motor symptoms in a rodent model of PD. However, to increase the number of NSCs that differentiate into dopaminergic neurons, the overexpression of nuclear receptor (Nurr1) and fac-tors, derived from local type 1 astrocytes, are necessary. Wagner and coworkers [69] showed that NSCs having these factors were able to differentiate into dopaminer-gic neurons, compared to NSCs that did not express these factors. Similarly, Nurr1 and Pitx3 are needed to produce dopaminergic neurons from embryonic stem cells. Nurr1 is a nuclear hormone receptor that is involved in the dopaminergic neurogenesis, while Pitx3 is a transcription factor that is important for the differ-entiation and maintenance of dopaminergic neurons in the mid-brain. Nurr 1, along with Pitx3, influences the expression of some of the genes involved in production of dopamine, such as tyrosine hydroxylase (TH) and dopamine transporter (DAT), which are associated with dopamine signaling [70]. Nurr1 is usually present in a silenced state when not combined with Pitx3. This is due to the binding of silencing mediator of retinoic acid and thyroid hormone receptor (SMRT) that leads to HDAC-mediated silencing of Nurr1. However, in the presence of Pitx3, the binding of SMRT is reduced and Nurr1 is activated, thereby the Nurr1-Pitx3 complex can bind to the promoter of TH and DAT genes and activate them. Therefore, Nurr1, on its own, cannot activate the target genes associated with dopamine production [71].

Conclusions for epigenetics in PD. The familial form of PD involves defects in epigenetic mechanisms, such as one-carbon metabolism reaction, which is associated with defects in rate of DNA methylation that leads to PD. The rate of transfer of methyl group to the cytosine by DNMT1 has been highly reduced, thereby interfering with the one-carbon metabolism, which was confirmed by measuring SAM and SAH, the biomarkers of the one-carbon metabolism associated with DNA methyla-tion. Similarly, abnormal increase in expression of cer-tain miRNAs leads to decreased SNCA gene expression, which is also associated with this disease. Cell replace-ment therapy to increase production of GDNF through transplantation of partially differentiated NSCs has proven, thus far, to have only limited efficacy. To achieve conversion of NSCs into dopaminergic neurons, the expression of Nurr1 and Pitx3 are required. The com-plex formed between Nurr1 and Pitx3 is associated with increased gene expression of TH and DAT, which, in turn, increases the production of dopamine. Therefore, complexing Nurr1 and Pitx3 is necessary, since Nurr1, per se, is considered to be in a silenced state, and binding with Pitx3 leads to the activation of the complex.

Rett Syndrome and Induced Pluripotent Stem CellsRett syndrome (OMIM #312750) is a X-linked auto-

somal dominant progressive neurodevelopmental

disorder affecting, predominantly, the female popula-tion and classified as one of the autism-spectrum dis-orders (ASDs). The classical symptoms of this disease include speech disability, stereotypic hand use, autistic characteristics, and seizures that gradually develop after 18 months of age [22]. The cause of the disease is associ-ated with point mutations in methyl-CpG binding protein 2 gene (MeCP2), although there are other sets of genes and environmental factors that contribute to the onset of this disease. Most of the mutations observed in MeCP2 gene are point mutations (missense or nonsense). Some of the hotspots include: (1) p. R133C and p. T158M, found in the methyl binding domain (MBD); and (2) p. R306C, p. R168X, p. R294X, and p. R255X located in transcriptional repression domain (TRD) [72–75]. The MeCP2 gene has a major role to play in the epigenetic regulation of vari-ous gene expressions related to ASD [72]. The domains of MeCP2 gene, such as the MBD and TRD, are involved in chromatin remodeling and protein interactions, respectively [76].

MeCP2 gene and its function. MeCP2 gene is involved in coding an epigenetic regulatory molecule, and muta-tions or large-scale deletions, duplications, and insertions of MeCP2 cause RTT syndrome. RTT can be classified into two categories, either atypical RTT or classical RTT. More than 95% of the patients having mutation in MeCP2 gene are considered having classical RTT. In general, MeCP2 binds to the DNA via the MBD and silences the gene. Similarly, the MeCP2 protein helps with chroma-tin remodeling by binding to the DNA via its TRD. The methylation of histone 3 at lysine position 9 (H3K9me) is achieved by MeCP2, thereby silencing the gene to which it is bound [22]. However, Yasui and coworkers [77] have extensively studied the MeCP2 binding sites on the genes and found that only about 6% of the CpG islands are bound by MeCP2. Their study indicated that: (1) the main function of MeCP2 is not associated with silenc-ing the methylated regions of the gene and (2) the genes having the maximum methylation status are not bound by MeCP2. Previous publications have shown that the human genome has methylated cytosine as 5-hydroxy-methylcytosine (5hmC) and 5-methylcytosine (5mC). It has been shown that 5hmC is found abundantly in neu-ronal genes that are active and that MeCP2 has a very high affinity toward 5hmC compared to 5mC, which plays a major role in how the gene expressions are regu-lated in neurons (Fig. 21.3).

An interesting finding is that the MeCP2 competes with the histone, H1, to bind to the nucleosome, indi-cating that the levels of H1 and MeCP2 are not always corelated with each other, especially in neurons. The finding that MeCP2 gene is associated with activating genes when bound to 5hmC, as well as with silencing the genes when linked with H3K9, underlies the dual nature of the protein. Therefore, there are some genes that are



down regulated when MeCP2 is lost and upregulated with increased MeCP2 gene expression [78].

iPSC models of RTT. Induced pluripotent stem cells have been used as a cell model for RTT [79]. Takahashi and Yamanaka [80] first reprogrammed the somatic cells into iPSCs by overexpressing four major genes, such as Oct3/4, Sox2, Klf4, and c-Myc, which are now collectively known as the Yamanaka factors. Reprogramming of iPSCs involves loss and gain of DNA methylation on H3 at lysine positions 27 (H3K27me3) and 4 (H3K4me3), as the cells get transformed from somatic stage, to pluripo-tent stage as has been discussed in detail in our previ-ously work [19].

The iPSCs derived from the RTT patients have been reprogrammed to form neurons, which show signifi-cant pathological changes, such as reduced nuclear size, lower expression of neuronal markers, reduced den-dritic spine density, loss of synapses, and lower levels of intracellular calcium. Electrophysiological analysis of neurons obtained from the RTT-derived iPSCs show decreased excitatory and inhibitory postsynaptic poten-tial (EPSP and IPSP). Although cell replacement research for RTT using iPSC transplantation has not been trans-lated to the clinic, the in vitro remodeling of fibroblasts derived from the RTT patients to form iPSCs have been successfully achieved by Marchetto and coworkers [81]. These findings are paving the way toward a bet-ter understanding of the pathophysiology of the disease and for identifying drugs or treatments that are patient- or mutation-specific [81,82].

Conclusions for epigenetics in RTT. In general, it has been assumed that MeCP2 usually silences the gene to which it is associated, but subsequent studies have indicated that this might not always be the case. The MeCP2 gene can increase, as well as decrease, the gene expression depending on the methylation

status, thereby emphasizing the dual role of the gene. Although both RTT syndrome and iPSCs have well-known and strong epigenetic components, the use of iPSCs for treating RTT has not been investigated. The stem-cell-based model of RTT is very useful to study a specific mutation leading to a phenotype-genotype correlation and correcting the mutated RTT-iPSCs, in vitro, and then transplanting them may prove to be a future treatment for RTT. Given that highly specific and targeted cell replacement therapy can be achieved using the corrected iPSCs, utilizing epigenetically cor-rected iPSCs for treating RTT syndrome is worthy of further investigation as such an approach has signifi-cant promise.

The Spinocerebellar Ataxia and Mesenchymal Stem Cells

SCAs are a group of neurodegenerative disorders that are caused by trinucleotide repeat expansions (mainly CAG expansions that lead to elongated poly-glutamine tracts). There are about 30 different genes responsible for the disease that is inherited in an auto-somal dominant pattern. SCA patients have neuronal degeneration in cerebellum, brain stem, and spinal cord. The main characteristics of this disease are related to retinopathy, neuropathy, cognitive dysfunction, and dementia [83]. Unfortunately, there is no cure for SCAs. Approximately 28 different types of SCAs have been discovered so far, with the most common forms being SCA1, SCA2, SCA3, and SCA7. A detailed description of the different types of SCAs is discussed by Paulson [84]. Interestingly, SCA1, SCA2, SCA3, SCA6, SCA7, and SCA17 are due to the repeat expansion in the cod-ing regions of the gene, whereas SCA8, SCA10, SCA12, and SCA31 have repeat expansions in the noncoding regions of the gene [84].

FIGURE 21.3 Function of MeCP2 gene. MeCP2 regulates the transcription of certain genes in the brain by binding to 5-methylcytosine (5mC). The main function of MeCP2 gene is not just silencing the gene to which it is bound, but also has the ability to increase the transcription of genes, such as BDNF, ORPM1, and CREB 1 [15].



SCA1 (OMIM #164400);

SCA1 mainly affects the brain stem and Purkinje cells of cerebellum and is characterized by ataxia of limbs and abnormal gait, leading to chorea. Assessments of expanded Ataxin1 gene having 82 CAG repeats in the cerebellar Purkinje cells in SCA1 animal models have shown reduced gene expression, which is involved in signal transduction and calcium homeostasis [85]. Ataxin 1 interacts with two major proteins, the retinoid acid receptor-related orphan receptor α (RORA, a type of HAT), and acetyltransferase tat-interactive protein 60 (Tip60, MW 60kDa), which is a nuclear receptor coactiva-tor that helps in the interaction of RORA [using ATXN1 with HMG-box protein 1 (AXH) domain of ATXN1]. However, in the presence of the mutant Ataxin 1 gene or protein, the interactions with Tip60 and RORAα are disrupted, which lead to disease pathogenesis [86].

SCA 7 (OMIM # 164500);

The symptoms associated with SCA 7 include cerebel-lar neurodegeneration and retinal degeneration. Similar to SCA 1, SCA7 also interacts with transcription factor cone-rod homeobox protein (CRX). CRX is a transcrip-tion activator of genes that are involved in formation of photoreceptors in the eyes. The interactions of mutant SCA7 with CRX cause abnormal formation of the pho-toreceptors, leading to retinal degeneration. Although the actual function of Ataxin 7 gene is unknown, it has recently been shown that Ataxin 7 is a subunit of HATs [23]. Therefore, the mutant form of the protein is involved in the alteration of HATs, which eventually leads to the disruption of histone acetylation.

SCA 8 (OMIM # 608768);

SCA 8 is due to the combined repeat expansion of CTG and CAG in the Ataxin 8 gene. Chen and coworkers [24] studied the SCA 8 cell line, or transcript known as ATXN8OS. Epigenetic analysis of this transcript revealed increased levels of H3K9me2 and hypoacetylation of H3K14 that led to repression of ATXN8OS RNA in cell lines that have 157 repeats. Similarly, methylation of argi-nine residues and phosphorylation of serine or threonine were found in the cell lines with about 88 repeats, which eventually led to decreased RNA expression.

Stem cell therapy for SCA. Although preclinical and clinical trials have been conducted using drugs, anti-oxidants, and neurotrophic factors, none of these tri-als were successful in alleviating the symptoms in SCA patients [87]. However, UC-MSCs transplantations in a mouse model of SCA produced promising effects. The major advantages of using UC-MSCs are: (1) there are no ethical issues that arise from their use; (2) they are highly multipotent stem cells; and (3) they have immunosup-pressive properties, resulting in reduced risk of tumor formation posttransplantation. Using SCA mice, Zhang

and coworkers [88] showed that UC-MSCs provided a therapeutic effect on these animals, including the resto-ration of motor functions at 8 weeks posttransplantation. The results of this study also showed that the cerebellar atrophy and the number of cells undergoing apoptosis were reduced. There was also an increased production of growth factors, such as insulin-like growth factor-1 (IGF-1) and vascular endothelial growth factor (VEGF). Jin and coworkers [89] performed intravenous and intra-thecal transplantation of UC-MSCs into patients affected with SCA and found that UC-MSCs are safe and have the capacity to alleviate the symptoms in SCA patients.

Another clinical study, conducted by Dongmei and coworkers [90] showed that transplantation of UC-MSCs could alleviate the symptoms of SCA, without any side effects, when evaluated using International Cooperative Ataxia Rating Scale (ICARS) and Activity of Daily Liv-ing Scale (ADL). Most importantly, these clinical find-ings provide converging evidence with the preclinical experimental results that UC-MSCs are safe and capable of alleviating the symptoms of SCA, indicating a poten-tially safe and efficacious therapy for SCA.

Conclusions for epigenetics in SCA. There is a strong cor-relation between epigenetic defects in the genes Ataxin 1, Ataxin 7, and Ataxin 8 and the neuropathological phe-notypes associated with SCA in patients. Each ataxin type has its own associated epigenetic mechanism. For example, the Ataxin 1 is a complex that is associated with RORA and Tip60, which are acetyltransferases and the interaction with them is disrupted in the presence of mutant Ataxin 1. Similarly, Ataxin 7 is a part of HAT and presence of mutant Ataxin 7 leads to improper histone acetylation. Detailed analysis of SCA 8 cell line revealed hyper- and hypomethylation of H3K9 and H3K14, respectively. [24]

To the best of our knowledge, there are no epigenetic mechanisms related to the UC-MSCs that would drive the cells to take on a specific neuronal phenotype that would confer significant therapeutic effects. However, previous studies have shown a favorable safety profile and beneficial therapeutic effects of UC-MSCs for SCA.

Multiple Sclerosis and Hematopoietic Stem CellsMultiple sclerosis (OMIM #126200) is an autoim-

mune neurological disease characterized by the loss of myelin sheath, leading to demyelination and neurode-generation of brain and spinal cord. The majority of the affected individuals are females between 20 and 40 years of age. In MS, the T-lymphocytes become stimulated by various factors, which, in turn, activate the inflamma-tory pathways, leading to the symptoms of the disease [91]. MS involves the genetic, epigenetic, and environ-mental factors (nutritional status). Epigenetic causes include: (1) DNA methylation; (2) posttranscriptional modification by miRNA; and (3) histone acetylation,



such as what occurs with the HLA-DRB 1 (human leu-kocyte antigen having beta chain) gene on chromosome 6, which is responsible for the production of major his-tocompatibility complex class II (MHC class-II) antigen and which plays an important role in immune response mechanisms [25,92]. The environmental factors include vitamin D deficiency and frequent smoking which, in turn, leads to epigenetic changes observed in MS.

DNA methylation in MS. Baranzini and coworkers [93] were the first to study the RNA transcriptome sequences and the epigenome sequences of CD4+ T-lymphocytes from three sets of MS-discordant, monozygotic twins, and found that there were no significant differences in the DNA methylation patterns. However, based on this study, alterations in DNA methylation patterns, as a cause of the disease cannot be ruled out, because the sample size was too small to make definitive conclu-sions. Other studies have shown that DNA methylation could be the cause of MS [94].

The methylation of CpG islands in some of the genes may be responsible for the disease, because the methyla-tion pattern determines how the two different types of T-helper-cells (Th1 and Th2) are formed, which, in turn, gives rise to cytokines, such as interferon-gamma (IFN-γ), interleukin-2 (IL-2), interleukin-4 (IL-4), and tumor necrosis factor-α (TNF-α). In MS, there is a dominance of IFN-γ expression associated with Th1, compared to IL-4 molecules that are associated with Th2. There-fore, abnormal DNA methylation pattern that is found in the promoter region of IFN-γ may explain why the immune response by Th1 is greater than Th2, leading to the pathophysiology of the disease (Fig. 21.4). Similarly, DNA methylation or histone deacetylation is associated with the IL-4 genes, leading to the gene silencing. HDAC inhibitors are given as a potential treatment for MS, because they lead to reduction in inflammation, demy-elination, and neuronal degeneration [95].

Epigenetics not only control cytokine gene activation in MS, but also affects myelin structure, by regulating myelin basic protein (MBP). For example, hypomethyl-ation of an enzyme, called peptidyl-arginine deiminase 2 (PAD 2), has been observed in MS [96]. This enzyme is responsible for conversion of arginine to citrullin and its level is increased in MS. Due to overactivation of PAD 2, the MBP is citrullinated and becomes vulnerable for degradation by the myelin-associated proteases, such as cathepsin D. This further leads to a reduced binding capacity of the MBP, causing lipid vesicle fragmentation, which, in turn, leads to the myelin breakdown observed in MS [96] (Fig. 21.5).

Micro-RNA. In vitro analysis of MS induced lesions and pooled cells have shown that there were about ten miRNAs that were upregulated, especially mi-RNA155 and mi-RNA326. However, mi-RNA326 is more com-monly associated with disease relapse, rather than being

directly associated with the initiation of the disease. It was found that the patients have more severe form of disease; following relapse, and showed a high expres-sion of mi-RNA326 (Table 21.2). This, in turn, leads to higher activation of T-cells and increased expression of inflammatory cytokines, which then results in abnormal immune response, leading to MS [26].

Histone Acetylation. In 2007, the International Multiple Sclerosis Genetics Consortium (IMSGC) conducted a genome-wide association study (GWAS) that included about 12,000 subjects. It was found that two genes, other than HLA-DRB 1, are associated with MS. Single nucleo-tide polymorphisms (SNPs) in interleukin-2 receptor α gene (IL2RA) and interleukin-7 receptor α gene (IL7RA) were found to be risk factors for MS. Again, in 2011, IMSGC conducted another GWAS study and found that abnormalities in some of the genes involved in cytokines and signal transduction pathways cause MS, reinforcing the fact that the most commonly affected gene by histone acetylation was the HLA-DRB 1 gene [25].

Stem cell therapy for MS. Among different stem cell pop-ulations, HSCs have drawn a special attention for use as a potential therapy of MS, because of their multipotency. These stem cells differentiate into a very large popula-tion of cells, including all functional types of blood cells, B-cells, T-cells, and many other cell types, which make them a promising candidate for therapy of many dis-eases [97]. The first therapy trials using HSCs was started

FIGURE 21.4 Impact of DNA methylation on T-cells. Compro-mised immune response exerted by Th1 and Th2 cells (dominance of IFN-γ over IL-4) is due to DNA methylation that leads to MS.



in 1995, followed by a second successful therapy trial on humans in 1998. These studies revealed that scores on the Expanded Disability Status Scale (EDSS) improved for patients who received the HSCs, confirming their use as a potential treatment for this disease [98,99]. However, subsequent clinical trials [100] revealed that patients who have a severe form of this disease (based on their EDSS score) and who received the transplants did not show significant benefits from the cell treatment. It is possible that these stem cells may exert their beneficial effects only during the early stages of disease and not after the disease has progressed to its severe stage [100]. Most of the transplants associated with the HSCs are autogenic in nature, because allogeneic or HLA-matched transplants cause an increase in mortality [91].

Atkins and Freedman [101] reviewed the pros and cons of using HSCs as a potential treatment for MS. One of the major advantages of using HSCs is that once

they are extracted from bone-marrow and transplanted into MS patients, the B-cells, and, especially the T-cells, mature and become activated, which play a major role in boosting the immune levels. However, because it is important to ensure that other immune cells, such as macrophages, do not populate the regions near the graft, it is advisable to use immune ablative conditioning regi-mens to achieve the maximum benefit from the T-cells.

A phase II clinical trial conducted by Mancardi and coworkers [102] was reported recently in 2015, which showed that autologous HSC transplantation resulted in suppression of lesion-induced inflammation. These results are based on a 4-year follow up of patients having a progressive or a relapsing form of the disease.

Collectively, these studies show that HSCs, due to their multipotent and immunomodulatory properties, have a significant promise for producing an effective therapy for MS.

FIGURE 21.5 Comparison of citrullinated myelin in normal and MS patients. Hypomethylation causes increase in the production of enzyme peptidyl-arginine deiminase 2 (PAD 2) leading to increased citrullinated myelin basic protein, thus gives abnormal structure and thereby myelin breakdown in MS patients [92].

TABLE 21.2 Roles of Different Types of miRNA in MS

miRNA Role in MS

mi-RNA155 Dysregulation of gene expression in CD4+ cells and peripheral blood mononuclear cells [27]

mi-RNA326 Dysregulation of gene expression in CD4+ [27]

mi-RNA18b, mi-RNA493, and mi-RNA599 Increased expression in relapse remitting MS [27]

CONCLUSIONS 335


Conclusions for epigenetics in MS. The compromised immune response seen in MS is due to the epigenetic mechanisms that affect the T-cells and the cytokines, which form the major molecules or proteins of the immune system. Hypomethylation of PAD 2 enzyme is observed in patients affected with MS, which leads to the breakdown of the MBP. Further analysis showed that miRNA, such as mi-RNA155, mi-RNA326, mi-RNA18b, mi-RNA493, and mi-RNA599 are associated with MS. The GWAS study and other studies have shown that HLA-DRB 1 is the main candidate gene for MS. However, there are some SNPs associated other genes, such as IL2RA and IL7RA, that pose a risk factor for this disease. HSCs have been used as a stem-cell-based therapy for MS, whereby their activation of the T-cells improve immune responses, producing favor-able outcomes.

CONCLUSIONS

Epigenetics not only play a role in determining the stem cell fate, but also form the underlying bases of neurodegenerative diseases, such as HD, PD, RTT, SCA, and MS, as discussed in this chapter. Although the genetic bases of these diseases vary, the epigenetic causes are similar. For example, alterations in the levels of DNA methylation and histone acetylation gives rise to SCA and MS. Understanding the epigenetic mecha-nisms of stem cells is an important aspect that needs to be carefully considered when designing strategies to achieve optimal efficacy and efficiency when cell replacement therapy for neurodegenerative diseases is being considered.

In order to translate and improve the outcomes of clinical trials, further research on how epigenetics drive stem cell fate is necessary. For example, because the use of MSCs for treating HD has been predominantly used in preclinical trials, researchers should be cogni-zant that the subpopulation of cells being used is the direct function of the number of passages these cells have undergone. Though higher passaged MSCs have proven to be highly beneficial in restoring the motor symptoms associated with HD, there is also a risk of chromosomal abnormalities that would lead to tumor formation or other adverse effects. Therefore, study-ing the epigenetic mechanism of MSCs to provide an effective cell replacement therapy is necessary. Some diseases, such as RTT have an epigenetic basis, which makes them excellent candidates for the yet-to-be-developed epigenetic-driven stem-cell replacement therapies. As such, a mutation corrected RTT-iPSC cell line for the transplantation may prove to be a prom-ising therapeutic approach. Similarly, identifying the

dysregulated epigenetic markers in each disease (such as H3K4me3 in HD and H3K9 and H3K14 in SCA8) may lead to designing a more targeted therapy for such neurological disorders. Addressing these types of issues and furthering our knowledge about the epigen-etic mechanisms of stem cells and the diseases associ-ated with epigenetic alterations could pave way toward developing more effective and long-lasting therapeutic approaches.

AbbreviationsADL Activity of Daily Living ScaleASDs Autism-spectrum disordersAT Adipose tissueBDNF Brain derived neurotrophic factorBM Bone marrowBM-MSCs Bone marrow-derived MSCscAMP Cyclic adenosine monophosphateCBP CREB-binding proteinChIP Chromatin immunoprecipitationCRE cAMP response elementCREB CRE-binding proteinCRX Cone-rod homeobox proteinDAT Dopamine transporterDNMTs DNA methyl transferasesEDSS Expanded Disability Status ScaleEPSP Excitatory post-synaptic potentialESCS Embryonic stem cellsGDNF Glial derived neurotrophic factorGWAS Genome-wide association studyHATs Histone acetyltransferasesHD Huntington’s diseaseHDACs Histone deacetylasesHLA-DRB Human leukocyte antigen having beta chainHSCs Hematopoietic stem cells HSCs6-OHDA 6-Hydroxydopamine5hmC 5-HydroxymethylcytosineICARS International Cooperative Ataxia Rating ScaleIFN α Interferon αIGF-1 Insulin-like growth factor-1IL-2 Interleukin-2IL-4 Interleukine-4iPSCs Induced pluripotent stem cellsLRRK2 Leucine-rich repeat kinase 2 geneMBD Methyl binding domainMBS Myelin basic proteinMeCP2 Methyl-CpG binding protein 2 geneMHC class-II Histocompatibility complex class II5mC 5-MethylcytosinemHtt Mutant huntingtin proteinmiRNA MicroRNAMPTP 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridineMS Multiple sclerosisMSC Mesenchymal stem cellsNRSF Neuron-restrictive silencer factorNSCs Neural stem cellsPAD 2 Peptidyl-arginine deiminase 2PD Parkinson’s diseasePSP Inhibitory post-synaptic potentialREST Repressor element-1 silencing transcription factorRTT Rett syndrome



SAH S-adenosylhomocysteineSAM S-adenosylmethionineSCA Spinocerebellar ataxiaSGZ Subgranular zoneSMRT Silencing mediator of retinoic acid and thyroid hor-

mone receptorSNCA α-SynucleinSNpc Substantia nigra, pars compactaSUMO Small ubiquitin-like moleculesSVZ Subventricular zoneTh T-helper-cellsTH Tyrosine hydroxylaseTNF-α Tumor necrosis factor-αTRD Transcriptional repression domainUC Umbilical cordUC-MSCs Umbilical cord derived MSCsVEGF Vascular endothelial growth factor

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Further ReadingCoppede F. Genetics and epigenetics of Parkinson’s disease. ScientificWorldJournal 2012;2012:e489830.












































































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