Unspecialized, self-renewing stem cells have extraordinary application to regenerative medicine due to their multilineage differentiation potential. Stem cell therapies through replenishing damaged or lost cells in the injured area is an attractive treatment of brain trauma and neurodegenerative neurological disorders. Several stem cell types have neurogenic potential including neural stem cells (NSCs), embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and mesenchymal stem cells (MSCs). Currently, effective use of these cells is limited by our lack of understanding and ability to direct lineage commitment and differentiation of neural lineages. Heparan sulfate proteoglycans (HSPGs) are ubiquitous proteins within the stem cell microenvironment or niche and are found localized on the cell surface and in the extracellular matrix (ECM), where they interact with numerous signaling molecules. The glycosaminoglycan (GAG) chains carried by HSPGs are heterogeneous carbohydrates comprised of repeating disaccharides with specific sulfation patterns that govern ligand interactions to numerous factors including the fibroblast growth factors (FGFs) and wingless-type MMTV integration site family (Wnts). As such, HSPGs are plausible targets for guiding and controlling neural stem cell lineage fate. In this review, we provide an overview of HSPG family members syndecans and glypicans, and perlecan and their role in neurogenesis. We summarize the structural changes and subsequent functional implications of heparan sulfate as cells undergo neural lineage differentiation as well as outline the role of HSPG core protein expression throughout mammalian neural development and their function as cell receptors and co-receptors. Finally, we highlight suitable biomimetic approaches for exploiting the role of HSPGs in mammalian neurogenesis to control and tailor cell differentiation into specific lineages. An improved ability to control stem cell specific neural lineage fate and produce abundant cells of lineage specificity will further advance stem cell therapy for the development of improved repair of neurological disorders. We propose a deeper understanding of HSPG-mediated neurogenesis can potentially provide novel therapeutic targets of neurogenesis. Stem cells are unspecialized cells capable of self-renewal and differentiation into specialized cell types under appropriate conditions.Neurogenesis is defined as the generation of functional neurons from neural precursors and is the first step in neural development, followed by axon guidance and synaptogenesis.Neural stem cells, embryonic stem cells, induced pluripotent stem cells, and mesenchymal stem cells are all capable of differentiating into neural cell types.Neurological disorders, including traumatic brain injuries and neurodegenerative diseases are commonly characterized by the loss of neural cells—current treatments provide some symptomatic improvement thus stem cell therapy in the form of cell/tissue replacement is a promising alternative.Heparan sulfate proteoglycans (HSPGs) are ubiquitous molecules on the cell surface and in the extracellular matrix which act as intermediaries between the extracellular matrix and intracellular signaling pathways, playing critical roles in numerous cellular activities.Syndecans, glypicans, and perlecan HSPGs carry heparan sulfate (HS) chains as a constant feature. They are expressed sequentially throughout mammalian neural development as progenitor cells progress through lineage differentiation.Emerging biomimetic strategies are designed to mimic the interactions between HSPGs and key growth factors of neural lineage specification. These molecules may enable greater efficacy than natural HS GAGs in promoting neural differentiation, and are promising approaches for improving and advancing stem cell therapies for the treatment of neurological disorders.Stem cells have the ability to self-renew through cell division and the capability to generate specialized cell types through differentiation under appropriate conditions  and epidermal growth factor (EGF) , and from multiple regions of the embryonic brain. NSCs can be propagated F) Gage, . In cultF) Gage, . DiffereF) Gage, . Some coF) Gage, . ChallenF) Gage, .in vitro through methods that recapitulate the embryonic neural development process , a major constituent of the ECM, are comprised of a core protein to which several GAG chains covalently attach at specific sites  residue is the commitment step of HS biosynthesis, a process catalyzed by exostosin-like 3 (Extl3)  family of enzymes. This is a partial process as NDSTs modify GlcNAc in clusters, leaving modified regions  interposed between unmodified regions  , then glucosaminyl 6-O sulfotransferases (HS6ST) followed by glucosaminyl 3-O sulfotransferases (HS3ST), concluding the modification process in the Golgi apparatus  and/or by the endoglycosidase heparanase (HPSE), further enhancing the heterogeneity and complexity of HSPGs  carry HS chains with more 2-O sulfation, similar to EB formation from ESCs  and glypicans (GPCs) membrane-bound; perlecan, agrin, and type XVIII collagen secreted into the ECM; and serglycin localized to secretory vesicles   where it regulates proliferation and maintenance of NPCs Figure . Also inO and 6-O-sulfated sites on the HS chains carried by SDC3 interact with FGF2  expresses SDC1 and SDC3 where 2-GPCs are a family of HSPGs attached to the exocytoplasmic surface of the plasma membrane via a glycosylphosphatidyl-inositol (GPI) anchor (Feng et al., in vivo, NSCs in vitro (Hagihara et al., in vivo and in cultured rodent dentate granule neurons. HSPGs, particularly GPC4, were found to be novel presynaptic receptors of LRRTM, binding preferentially to postsynaptic LRRTM4 and not LRRTM2 via HS chains (de Wit et al., GPC4 is most predominantly expressed during mouse neural development in the ventricular zone of the telencephalon, and acts as a modulator of FGF2 to maintain NSC and NPC proliferation and self-renewal (Hagihara et al., During gliogenesis, both OPCs and oligodendrocytes express GPC1 Figure . AstrocyOur work in hNSCs has also demonstrated that as the cells differentiate toward the neuronal lineage, SDC4, GPC1, GPC2, GPC3, and GPC6 are all up-regulated. Interestingly, expression of these genes was observed to be lower than the level observed in the more neuronal lineage-restricted nhNPCs, where higher gene expression levels of SDC2, 3, 4 as well as GPC1, 2, 3, and 6 were observed, similar to murine studies (Oikari et al., +CD133+ NSCs owing to the inability to induce cell cycle progression via cyclin D2 (Kerever et al., During mammalian neural development, the HSPG perlecan is expressed in the basal lamina of the neuroepithelium, a crucial component of the neural niche (Ford-Perriss et al., In vitro studies by Nakamura et al. (a et al.  demonstra et al. . With itThe emerging evidence of a central role for HSPGs in regulating neural stem cell lineage fate may provide opportunities to better understand and control lineage specification and to fully exploit the use of stem cells as effective therapeutics. With HSPGs involved at all stages of stem cell maintenance and neurogenesis, including proliferation, self-renewal, differentiation, migration, and maturation, multiple opportunities exist to develop improved therapeutics.Stem cell fate can be directed through exogenous and synthetic HSPGs and GAGs. Exogenous heparin, the highly sulfated analog of HS, is a widely utilized means of enhancing HS-mediated stem cell proliferation and self-renewal Figure . The stuHarnessing HSPG and growth factor interactions has also resulted in various forms of HS mimetics and synthetic glycopolymers that mimic natural occurring HSPGs and their function during stem cell neural differentiation. These strategies have produced synthetic glycopolymers with even higher efficacy than heparin Figure . In otheDespite no current long-term/permanent therapies, stem cells have potential in cell/tissue replacement therapies for neurological disorders. Successful therapies require regimens for differentiating stem cells into desired lineages with high efficiency and yield. Current approaches include combinations of growth factors and chemicals, which often correlate with relatively poor yield of desirable cell types, and poor therapeutic efficacy. To overcome these challenges, a comprehensive understanding of the extrinsic and intrinsic signals regulating neural stem cell fate must be defined.Identification of specific HSPGs and HS sulfation patterns as they are expressed throughout neural lineage progression will allow for distinction between neuronal, astrocyte and oligodendrocyte lineage specification and enhance derivation of these cell types from the stem cell state. HS sulfation motifs are specific for each cell type and it is essential to characterize HS structural changes in specific stem cell models. Further research, particularly in the human biological system, is required to identify point/s of intervention during neurogenesis. HS biomimetics to mimick HSPG core proteins and/or specific HS moieties are promising strategies for enriching current stem cell therapies, with more rigorous analysis required for their routine, reproducible and safe integration into therapeutic applications. Forthcoming work examining the intrinsic mechanisms governing the influence of HSPGs in mediating neural stem cell fate will likely enable better cell isolation techniques, as well as the development of tailored production of specific neural cell types for various applications and treatment requirements, and promote advances in biomimetic engineering.CY developed the concept and drafted the manuscript. LH conceived of the manuscript, supervised the structure and design of the manuscript, revised the manuscript, and approved the final version. LG revised the manuscript and approved the final version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


UCP1) gene variants and CMDs. UCP1 activity is essential for brown adipose tissue (BAT)-mediated thermogenesis. Experimental animal studies and epidemiological studies in humans highlight the significance of BAT-mediated thermogenesis in protecting against obesity and maintaining a lean phenotype. We hypothesize that the genetic variation in UCP1 gene expression observed among different ethnic groups could contribute to the ethnic-specific predisposition to CMD development. Constructing such prevalence maps of UCP1 gene variants could contribute significantly into identifying high-risk ethnic groups predisposed to the development of CMDs, and further shaping public health policies by the improvement of existing preventive and management strategies.Cardio-metabolic diseases (CMDs) comprise a cluster of risk factors that contribute to chronic pathological conditions with adverse consequences for cardiovascular function and metabolic processes. A wide range of CMD prevalence rates among different ethnic groups has been documented. In view of accumulated evidence, there is a trend toward increasing CMD prevalence rates in Eastern Europe and Western Asia. Numerous studies have revealed an association between uncoupling protein 1 ( Figure 1)  estimates that by 2030 more than 23 million patients affected by cardiovascular diseases (CVDs) – the leading cause of death globally – will die annually , while digure 1) .UCP1) gene is located in chromosome 4 of the human genome and is considered to be involved in the pathogenesis of CMDs due to its major role in thermogenesis and energy metabolism  associated with the CP1 gene . The intUCP1 gene variants and CMDs, we hypothesize that the ethnic-specific predisposition to CMDs could be attributed, at least partially, to the diverse prevalence of specific UCP1 gene variants among different ethnic groups. Such an increased susceptibility to the development of CMDs has been observed specifically in ethnic groups in Eastern Europe and Western Asia . Large population-based studies are thus required to investigate the CMD-related association of specific UCP1 gene variants among different ethnic groups. Information on ethnic-specific genotypes’ frequencies of the analyzed UCP1 gene variants could be used to identify those ethnic groups at high-risk of developing CMDs, and further explain to an extent the high CMD prevalence rates observed in Eastern Europe and Western Asia.On the grounds of experimental evidence corroborating an association of UCP1 gene variants and CMDs, often yielding to controversial results. A number of independent genetic association studies suggested an association between UCP1 gene variants and obesity, type 2 diabetes mellitus, body fat distribution, and metabolic syndrome-related traits  and/or socio-economic  factors could significantly contribute to define the association between the genetic variation in UCP1 gene and CMDs, by fully adjusting for such potential confounders. The emerging field of human social genomics highlights the importance of the contemporary dynamic social adverse conditions on influencing ones genotype and hence further shaping the susceptibility to chronic diseases. On the other hand, gene variants can also alter genotypic response to socio-environmental adversities by activating different molecular pathways and factors, and thus enhancing or reducing the risk for chronic disease . Participants will be white Caucasians of European and Western Asian origin. They will be weighed, their height will be measured, and their BMI will be calculated. Blood pressure will be assessed. Percent body fat will be measured three times, and waist-to-hip ratio will be calculated. Further, after an overnight fast, plasma glucose will be measured. Environmental and socio-economic factors will be determined by using standardized questionnaires. The seven most commonly studied UCP1 gene variants  will be genotyped. Genomic DNA will be extracted from whole blood and each UCP1 gene variant will be assessed by Real Time Taqman method. To our knowledge only three studies have conducted in vitro or in vivo studies to characterize the function of two specific UCP1 gene variants (rs1800592 and rs7687015)  . We aim,UCP1 gene variants on CMD prevalence in a very large and ethnically diverse sample of patients and healthy individuals will identify high-risk ethnic groups for developing CMDs. Further, the study of UCP1 gene variants-environment interactions will define a strong association between UCP1 gene variants and CMD development.This proposed investigation of the combined effect of the most commonly studied Cardio-metabolic diseases constitute a serious public health concern with a substantial impact not only on life expectancy  but alsoUCP1 gene variants that could predispose certain ethnic groups to the development of CMDs could assist in the design of effective preventive and management practices, with beneficial outcomes for the public health care services. UCP1 gene variants have been associated with high levels of low-density lipoprotein (LDL) cholesterol and diastolic blood pressure, as well as with low levels of high-density lipoprotein (HDL) cholesterol  was responsible for the conception and design of the work and was involved in drafting and revising the manuscript. PS was responsible in drafting and revising the manuscript. LY, LN, LK, AK, AS, AC, GM, and YS participated in the conception of the work, read and approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Mesoporous solids, which were prepared from inorganic-surfactant mesostructured materials, have been investigated due to their very large surface area and high porosity, pore size uniformity and variation, periodic pore arrangement and possible pore surface modification. Morphosyntheses from macroscopic morphologies such as bulk monolith and films, to nanoscopic ones, nanoparticles and their stable suspension, make mesoporous materials more attractive for applications and detailed characterization. This class of materials has been studied for such applications as adsorbents and catalysts, and later on, for optical, electronic, environmental and bio-related ones. This review summarizes the studies on the chemistry of mesoporous silica and functional guest species (host–guest chemistry) to highlight the present status and future applications of the host–guest hybrids. Surfactant aggregates (surfactant mesophases) were found to be useful to produce mesoscopic structures. The preparation method, characterization and application of mesoporous silicas and other mesostructured and mesoporous solids have been a hot topic in current materials chemistry after the discovery of mesoporous silicas . The periodic mesostructures are prepared by the complexation of silica source with such surfactants as quaternary ammonium salts and block co-polymers as templates (structure directing agents) . The inoIn addition to the structural and the compositional variations mentioned above, the morphosyntheses have mesoporous silicas more attractive for application in optics, electronics, and medical and biological fields , 4, 15. in situ formation (polymerization and growth) in the mesopore. It is also possible to obtain hybrids by co-precipitation (co-polymerization) of guest species with silica sources during the synthesis of the precursors of mesoporous materials (inorganic-surfactant mesostructures). Multiple functionalization has also been done by grafting various functional groups [Eu(TTA)4] into mesoporous silicas. The adsorbed complex exhibited higher UV stability and longer excited state lifetime 2+) into mesoporous silicas from the viewpoint of the spatial distribution of [Ru(bpy)3]2+ inside the mesopore, how to control the spatial distribution and how the spatial distribution affects the performances of the resulting host–guest systems. The host–guest systems composed of [Ru(bpy)3]2+ and mesoporous silicas have been investigated for possible applications for catalyst, electrode, etc [3]2+ onto mesoporous silicas with the average pore sizes of a few nanometers was conducted from dimethylformamide solution of [Ru(bpy)3]2+ chloride [3]2+ adsorbed was controlled up to less than 1 mass% at a maximum. Dehydration of [Ru(bpy)3]2+-mesoporous silicas induced the aggregation of [Ru(bpy)3]2+ ions adsorbed, which was shown by the efficient luminescence self-quenching. The luminescence was intensified dramatically upon hydration of the samples, suggesting that the aggregated [Ru(bpy)3]2+ ions were de-aggregated to be dispersed molecularly in the mesopore. Thus, the states of the guest species are affected not only by the host–guest interactions but also by the co-adsorbed species. This is an important difference between the host–guest systems with ruthenium(II) complex cation (abbreviated as 2+-containing FSM  was used as a photocatalyst to oxidize benzene to phenol [3]2+ and mesoporous silicas using modified mesoporous silicas [3]2+) has been controlled within 0.8 μ mol m−2 mesopore surface or 1.0 mol L−1 mesopore pore volume not only by the varied loading of molecular catalyst but also by the surface density (or concentration) of immobilized functional unit (sulfonated phenyl group), which interacts with the molecular catalysts). As mentioned above, these characteristics are important to design the open space for the access and diffusion of reactants and products and the efficiency of activation (photo-excitation). (figure The adsorption of a monomer and subsequent polymerization of the monomer in the mesopore have been investigated. Poly(aniline) and poly(acrylonitrile) were synthesized in MCM-41 with the pore diameter of 2.5 nm –211. Ngu3.3.Anisotropy of the guest species included in mesoporous materials has also been a topic of interest toward three dimensionally controlled geometry of the host–guest system. This kind of research became available after the progresses of hierarchically controlled mesostructure preparation and characterization , 214–217In addition to the films, pore geometries of well-defined (and anisotropic) particles have been a topic of interest. As to the mesoporous silica spherical particles, Yano and Fukushima reported the radially arranged one-dimensional pore , which c4.Due to the ability of mesopores to accommodate various kinds of guest species, the variations in the host–guest systems are huge, which accounts for the rich materials chemistry on this topic. The structures are determined by the selection of host and guest and the interfacial design of host–guest interactions. The location of guest species varies: at the external/internal surface, inside the pore, at the entrance to the pore, and within the framework. For each possible location, the homogeneity, density and orientation of the guest species should be considered in multi-length scales. The spatial distribution  and host–guest interactions affect the diffusion and stability of the guest species, which are worth investigating further . The conPossible applications of host–guest complexes of mesoporous silicas proposed include catalyst, adsorbent, drug carrier, sensor and photonics. The spatial distribution of guest species  can be designed to initiate desired reactions in catalyst applications, to bind target species strongly in adsorbent applications, to accommodate drug molecules in drug delivery applications, to react with target molecules selectively in sensing applications, etc. Accompanied by the accommodation of functional units/guest species, the remaining nanospaces after the attachment of functional units or the inclusion of guest species should be considered geometrically, topologically and chemically for efficient diffusion of reactants and products  and adsorbates (during adsorption), for controlled up-take and release of drug (in drug delivery) and for possible molecular recognition (in sensing). In addition, the dynamic behavior of the functional units on the pore surface, which change its conformation and position to fit the resulting host–guest complexes in more stable states (induced fits), has been examined recently –235.Besides the organic compounds, inorganic nano-species such as heteropolyacids, semiconductor nanoparticles and nanocarbons have been encapsulated in the mesoporous silicas. The host–guest complexes of mesoporous and mesostructured transition metal oxides and sulfides, metals, carbons and polymers have an opportunity to which mesoporous silicas do not have access. Thus, utilizing a supramolecular templating strategy can provide a huge variety of nanostructured materials from diverse building units including both host and guest. The unlimited variations and possibilities in the construction of the host–guest systems derived from the mesoporous and mesostructured materials will be investigated for the practical applications, where precise design of the structures (both static and dynamic) of host–guest complexes are of great importance.


Prenatal infection is an environmental risk factor for various brain disorders with neurodevelopmental components, including autism spectrum disorder and schizophrenia. Modeling this association in animals shows that maternal immune activation negatively affects fetal brain development and leads to the emergence of behavioral disturbances later in life. Recent discoveries in these preclinical models suggest that epigenetic modifications may be a critical molecular mechanism by which prenatal immune activation can mediate changes in brain development and functions, even across generations. This review discusses the potential epigenetic mechanisms underlying the effects of prenatal infections, thereby highlighting how infection-mediated epigenetic reprogramming may contribute to the transgenerational transmission of pathological traits. The identification of epigenetic and transgenerational mechanisms in infection-mediated neurodevelopmental disorders appears relevant to brain disorders independently of existing diagnostic classifications and may help identifying complex patterns of transgenerational disease transmission beyond genetic inheritance. The consideration of ancestral infectious histories may be of great clinical interest and may be pivotal for developing new preventive treatment strategies against infection-mediated neurodevelopmental disorders. Typically, neurodevelopmental disorders are characterized by a heterogeneous group of symptoms affecting cognitive functions, emotions and behavior, thereby undermining basic human processes of perception and judgment. In view of their chronicity and severity, neurodevelopmental disorders impose tremendous burdens on the affected individuals, and in turn, on their families and society in general.3Disruption of normal brain development is implicated in a number of neuropsychiatric diseases with neurodevelopmental origins, including schizophrenia, autism spectrum disorder and bipolar disorder.4 various environmental factors appear to increase the risk for neurodevelopmental disorders.5 Many of these factors operate during critical periods of central nervous system development. One of these factors is prenatal exposure to infection, which is increasingly recognized to play an important etiological role in various brain disorders with neurodevelopmental components, including schizophrenia,6 autism spectrum disorder8 and bipolar disorder.9 Hence, prenatal exposure to immune challenges may be best viewed as a general vulnerability factor for neurodevelopmental brain disorders rather than a disease-specific risk factor.11 Indeed, the adverse effects induced by prenatal infection may reflect an early entry into a deviant neurodevelopmental route, but the specificity of subsequent disease or symptoms is likely to be influenced by the genetic and environmental context in which the prenatal infectious process occurs. This notion is consistent with the emerging evidence suggesting that seemingly remote disorders, such as schizophrenia, autism spectrum disorder and attention-deficit/hyperactivity disorder share considerable amounts of risk factors and brain dysfunctions.11 The presence of shared genetic and environmental risks among these illnesses has led to the proposal that they might lie along a continuum of genetically and environmentally induced neurodevelopmental causalities,12 wherein prenatal infection may be one of the many factors that shape the eventual pathological outcomes.Besides genetic contributions,13 On the basis of human epidemiological findings, a number of translational rodent models have been established to explore the consequences of prenatal immune activation on brain and behavioral development. These models are based on maternal gestational exposure to specific infectious agents such as influenza virus or immune activating agents such as the bacterial endotoxin lipopolysaccharide or the viral mimic poly(I:C) (=polyriboinosinic–polyribocytidylic acid). Converging evidence from these models suggests that prenatal immune activation can negatively affect early fetal brain development and change the offspring’s neurodevelopmental trajectories, which in turn can lead to the emergence of behavioral and cognitive disturbances in later life.16 The long-term behavioral and cognitive abnormalities induced by prenatal immune challenges in rodent models have already been extensively reviewed elsewhere  and have recently been extended to models using primates with more advanced cortical development and functions.20The epidemiological link between prenatal infection and increased risk of neurodevelopmental brain disorders also receives strong support from experimental work in animal models.22 The present review summarizes and integrates novel findings supporting this hypothesis and highlights how infection-mediated epigenetic reprogramming could be a molecular mechanism shaping disease risk across generations.Despite the advances in this research field, the mechanisms whereby prenatal infection leads to long-term effects on central nervous system functions are only partially understood. In keeping with the crucial role of epigenetic remodeling in early development, it has recently been postulated that epigenetic modifications may be a critical molecular mechanism by which prenatal immune activation can mediate changes in brain development and functions.235 and Silasi et al.23). Only some of these pathogens are vertically transmitted and directly invade the fetal system. One prominent example showing transplacental transmission is rubella, which has long been known to be responsible for a spectrum of developmental abnormalities referred to as the congenital rubella syndrome.24 The majority of pathogens, however, stay refined to the maternal host upon infection during pregnancy.23 Even when lacking vertical transmission, maternal infection during pregnancy can induce long-term effects on the offspring, suggesting that the association between prenatal infection and neurodevelopmental disorders is, to a large extent, driven by factors that are common to all infections. In support of this notion, rodent studies provide substantial evidence for the hypothesis that inflammatory cytokines are one of the key players in re-wiring ongoing developmental processes into pathological trajectories following prenatal infection.27 Cytokines are increased during the acute phase response to infection and are important mediators of the host’s defense against infectious agents.29 In the context of prenatal infection, some of the maternally produced cytokines can be transferred via the placenta, as shown in animals and human placental tissue,31 and contribute to cytokine imbalances in the fetal system. In addition, the placenta and fetal organs can mount increased cytokine production in response to maternal infection.34Infection during pregnancy induces a spectrum of pathophysiological changes in the maternal host and fetal compartments.35 and can exert cytotoxic effects. Similar to cytokines, reactive oxygen species levels typically rise in response to an infection, which in turn can trigger oxidative stress in the fetal environment and negatively affect fetal brain development, both in humans and in animal models.36The post-acute effects of maternal infections are not limited to cytokine-associated inflammatory responses but further involve other pathophysiological processes, including nutrient deficiency and oxidative stress . Oxidati37 Reduction in food intake might indeed be of great relevance in the context of prenatal infection, with several studies highlighting a significant link between prenatal malnutrition and pathological brain development.39 Studies in rats and mice suggest that the association between prenatal malnutrition and neurodevelopmental disorders might result, at least in part, from a reduction in the availability of micronutrients such as zinc and iron, which are crucial for normal brain development.41Reduced availability of macro- and micronutrients for the fetus is yet another important post-acute effect of maternal infection . The inf42 Maternal infections also typically disrupt the circulation and architecture of the placenta,44 as shown by studies in rodents and humans, which in turn can induce placental insufficiency and reduce the delivery of oxygen and essential nutrients to the developing offspring  dinucleotides.45 When located in distinct genomic regions such as gene promoter or enhancer sites, DNA methylation typically acts to repress gene transcription.45 Silencing of gene transcription by DNA methylation can be mediated by direct interference with the binding of transcription factors or enhancers to recognition elements that contain CpG dinucleotides, or through recruitment of methylated DNA-binding factors that in turn attract chromatin-inactivating complexes including histone deacetylases and histone methyltransferases. Finally, miRNAs are a class of small non-encoding RNAs (~22 nucleotides long) that can control target gene expression post-transcriptionally.45 Interestingly, recent studies have demonstrated that epigenetic mechanisms, such as DNA methylation, not only regulate the transcription of protein-encoding genes, but also the expression of miRNAs.46 Conversely, miRNAs can control the expression of important epigenetic regulators, including DNA methyltransferases and histone deacetylases. Hence, there is a dynamic regulatory network between different epigenetic pathways, which altogether organize gene expression profiles through transcriptional or post-transcriptional mechanisms.46‘Epigenetics’ refers to the combination of mechanisms that confer long-term and heritable changes in gene expression without altering the DNA sequence itself.rocesses , includi45 Interestingly, transcriptional changes in the brain occur more frequently during prenatal life as compared to any other age in life.47 A temporally precise and specific regulation of gene expression thus seems indispensable for normal brain development. This regulatory process involves methylation-related epigenetic modifications, which allow a fine-tuning of fetal gene expression according to specific stages of brain development.50 A critical role for DNA methylation in early brain development is also supported by the dynamic expression of DNA methyltransferases during prenatal life,51 and by studies using transgenic mouse models showing neurodevelopmental deficits in mice with mutations in the methyl-CpG-binding protein 2 (Mecp2) gene.53 Furthermore, mice lacking distinct DNA methyltransferases (DNMTs) in the forebrain have been found to display severe learning and memory deficits, as well as impaired synaptic plasticity.55A growing number of studies highlight the importance of epigenetic mechanisms in normal brain development.56 Furthermore, Fischer et al.57 demonstrated in a mouse model of neurodegenerative disorders that increasing histone acetylation could promote synaptogenesis and augment cognitive functions.In addition to epigenetic processes involving DNA methylation, several other epigenetic mechanisms appear to be critical for neuronal development and functions. For example, it has been shown that histone modifications can regulate the conversion of oligodendrocytes into neural stem cells.59 Moreover, a recent study reported distinct temporal patterns of miRNA expression in the brain throughout gestation, and from early neonatal to adult life.60 The developmentally regulated pattern of miRNA expression is indicative of a functional role of these molecules in normal brain development. However, our understanding of how miRNA can influence neurodevelopmental processes is still in its infancy and warrants further investigations.Accumulating evidence suggests that miRNAs may similarly play a role in central nervous system development. For example, it has been shown that miRNAs in specific neuronal or glial cell populations show a dynamic expression pattern during brain development.61 stable epigenetic modifications may represent an important mechanism by which exposures to early-life environmental adversities can induce pathological consequences, even across multiple generations. Transgenerational transmission of disease susceptibility or epigenetic modification has been observed following early-life exposure to various environmental adversities  treatment in mice has also been found to alter histone modifications in the offspring. More specifically, offspring of poly(I:C)-treated mice displayed changes in promoter-specific histone acetylation and corresponding transcriptional changes, the latter of which affected genes associated with neuronal development, synaptic transmission and immune signaling.87Several recent studies sought to examine the putative effects of prenatal infection on epigenetic processes. Using a rat model of poly(I:C)-induced maternal immune activation, Hollins et al.88 found that prenatal exposure to the viral mimic poly(I:C) caused global changes in the level of DNA methylation in the adolescent mouse brain, including Mecp2 promoter hypomethylation. A recent study by Labouesse et al.89 extended those findings by assessing correlations between DNA-related epigenetic modifications, expression levels of corresponding genes and behavioral deficits. The authors showed that prenatal viral-like immune activation by poly(I:C) in mice induced methylation-related promoter remodeling of GAD1 and GAD2 in the prefrontal cortex. GAD1 and GAD2 encode for two isoforms of the rate-limiting enzyme for γ-aminobutyric acid biosynthesis. It was shown that offspring born to immune-challenged mothers displayed GAD1 and GAD2 promoter hypermethylation and associated reductions in the expression of the corresponding mRNA transcripts (GAD67 and GAD65), which in turn correlated with deficits in social interaction and impairments in working memory.89 These findings suggest that methylation-related epigenetic modifications at presynaptic GABAergic systems may represent a mechanism whereby maternal infection during pregnancy can induce long-term behavioral impairments in the offspring.Accumulating evidence suggest that prenatal infection can also cause stable changes in DNA methylation. For example, Basil et al.90 examined genome-wide DNA methylation differences at single-nucleotide resolution by capture array bisulfite sequencing in the adult prefrontal cortex. It was shown that offspring of immune-challenged mothers displayed hyper- and hypomethylated CpGs at numerous loci and at distinct genomic regions.90 The differences in methylation were again associated with transcriptional changes of the corresponding genes, suggesting that the infection-induced epigenetic modifications had a functional impact on gene expression.90Using the same mouse model of poly(I:C)-induced maternal immune activation, a recent study by Richetto 88 or in late (GD15 and beyond)89 gestation causes such changes. Recent evidence suggests, however, that the timing of viral-like immune challenge critically determines the specificity of infection-mediated epigenetic modifications,90 since early and late gestational window clearly differ in terms of methylation-related epigenetic modifications they induce.Taken together, these findings indicate that prenatal infection can cause lasting changes in the offspring’s epigenome. The available data thus far show that viral-like maternal immune activation in early/middle (between gestation day (GD) 9 and 12)92 at least when the immune challenge was induced in early/middle pregnancy . Interestingly, one study reported a transgenerational transmission of behavioral abnormalities mostly via the paternal lineage, which extended to the third (F3) generation of offspring  of gestationally immune-challenged mothers could be transmitted across subsequent generations (F2 and F3) without any further immune exposures. Using the prenatal poly(I:C) administration model in mice, it was repeatedly shown that some of the behavioral abnormalities are not only present in the direct descendants of immune-challenged mothers, but are transmitted to the subsequent generations,ffspring .92 The p21 Once the primordial germ cells are sexually differentiated, oocytes and male germ cells have different developmental dynamics; following sexual differentiation, the oocyte enters into meiosis and arrests until puberty, while male germ cells go into arrest until birth, when they undergo a phase of proliferation and then complete meiosis during puberty.93It remains to be determined further, however, why early-life adversities such as maternal infection largely spare the female germ cells. One possible explanation may relate to the differential developmental dynamics of male and female gametes. Germ cells start developing shortly after fertilization and rapidly proliferate until they migrate to the genital ridge, where sex determination occurs.92 Using next-generation mRNA sequencing, it was shown that prenatal poly(I:C)-induced immune activation caused widespread gene expression changes in the brains of both the F1 and F2 generations. Intriguingly, while some transcriptional changes were uniquely present in either F1 or F2 offspring, others were common to both generations. Hence, the prenatal infection-induced transgenerational transmission of behavioral abnormalities  or IL-17a can mimic the long-term consequences of prenatal viral-like immune activation in mice.26 Conversely, elimination of these cytokines from the maternal immune response by genetic interventions or blocking antibodies attenuates the long-term effects of prenatal immune challenge on brain and behavior.26As mentioned above, epidemiologic studies suggest that the risk of neurodevelopmental disorders is increased after prenatal exposure to a variety of viral, bacterial or protozoan pathogens, including those that are not vertically transmitted to the fetus. Based on these findings, it has been proposed that cytokine-associated inflammatory processes may be key in mediating the negative effects of maternal infection.et al.95 demonstrates that IL-6 increases the expression and biological activity of DNMT1. Some of the changes in DNMT1 activity may result from phosphorylation of the enzyme following exposure to IL-6, and the subsequent activation of downstream signaling pathways such as the AKT pathway.95 While most of the initial findings linking cytokines to epigenetic effects stem from experiments with cancer cell lines, it is likely that IL-6 regulates DNMT1 in several distinct cell types, including neurons and other brain cells. It was shown that IL-6 and DNMT1 can also influence cell migration,96 a process which is also essential in neurodevelopment. Recent studies also identified a direct influence of IL-17a on the epigenetic machinery through the modulation of histone deacetylases (HDACs). More specifically, IL-17a was shown to inhibit HDAC activity via the phosphoinositide-3-kinase (PI3K) pathway.97 Finally, one study found that TNF-alpha increases histone acetylation activity,98 suggesting that this inflammatory cytokine can act on the epigenetic machinery as well.Given these findings, it appears plausible that enhanced expression of inflammatory cytokines may be one of the factors that can directly alter epigenetic programs in the event of prenatal infection. In support of this notion, a study by Hodge 88 Mecp2 is important for epigenetic regulation due to its ability to bind to methylated DNA and to chromatin modifying complexes such as HDACs. Therefore, Mecp2 is considered both an epigenetic ‘reader’ and a ‘writer’ (for review see Ausio99). Additional research is required, however, to examine more directly whether the effects of prenatal immune activation on Mecp2 promoter hypomethylation involves specific cytokines or other pathophysiological processes associated with inflammation.Exposure to prenatal inflammation stimuli has also been shown to cause Mecp2 promoter hypomethylation.Taken together, there is initial evidence supporting a role of cytokines in modulating the epigenetic machinery in the event of prenatal infection. Hence, increased fetal expression of inflammatory cytokines may be one of the upstream factors causing epigenetic reprogramming and associated neurodevelopmental changes in offspring of gestationally infected mothers.100 Vice versa, mouse monocytes, under conditions of folate deficiency, show a 2- to 3-fold increase in the expression of several inflammatory cytokines, such as IL1b, IL-6 and TNFα.101 Folic acid has also long been implicated in neurodevelopmental processes, as exemplified by the presence of spina bifida in offspring of mothers who were deprived from folic acid during pregnancy.102 Moreover, imbalances in folate levels during pregnancy represent an important, epidemiologically valid risk factor for later psychiatric disease.103 Besides its established etiological role in neurodevelopmental disorders,104 low levels of folate are also present in patients diagnosed with schizophrenia.105 There is a growing body of evidence linking folic acid deficiency with autism as well.108 Interestingly, maternal folic acid supplementation has been associated with beneficial effects on neurodevelopment and autism.103 Moreover, mothers of children with autism have a significantly lower mean folic acid intake during early pregnancy compared to mothers of children with autism spectrum disorder.107As previously discussed, maternal infection typically leads to temporary reduced food consumption, thereby reducing nutrient availability for the developing organism . Besides109 folic acid is likely to have a direct influence on epigenetic processes during normal prenatal development. Indeed, a recent study identified a striking correlation between maternal folic acid and methylation status of a variety of genes in the offspring, some of which are related to neurological functions and to embryonic development.110 In the pathological context of maternal infection, decreased availability of folic acid may affect methylation-related epigenetic processes in the fetus, thereby contributing to infection-mediated epigenetic programming. Even though biologically plausible, however, this hypothesis still awaits direct examination in future studies.Representing one of the major dietary sources for methyl groups,111 There is a clear symbiotic link between host and microbe, wherein the microbiota is also key mediating for gene–environment interactions relevant to various physiological processes.112 Whereas initial studies mainly focused on obesity-related changes in the microbiome and its contribution to the disease phenotype, it has recently been shown that the microbiome can also influence behavior and contribute to brain development and function (for review see Cryan and Dinan113). While the fetal environment was initially thought to be entirely sterile, recent evidence suggests that some bacteria are present in the amniotic fluid114 and the placenta.115 One implication of these new discoveries is that the microbial composition of the developing offspring may be sensitive to environmental changes even during prenatal stages of life. In support of this notion, a recent study in mice demonstrated that prenatal viral-like immune activation alters the offspring’s composition of the gut microbiota.116 Notably, some of the main metabolic products of the gut microbiota are short-chain fatty acids, including sodium butyrate. Sodium butyrate can readily cross the blood–brain barrier and has been shown to modulate the expression of various genes in the prefrontal cortex, particularly those involved in neuronal excitation or inhibition.117 At the same time, sodium butyrate can interact with the epigenetic machinery by inhibiting HDACs.118 Therefore, aside from being a bacterial metabolite and a major source of energy for intestinal epithelial cells, sodium butyrate represents an efficient epigenetic regulator. Future studies are warranted in order to investigate whether infection-induced changes in gut microbiota may induce downstream changes in sodium butyrate, which in turn may affect the epigenetic machinery. Such changes would possibly also affect the fetus’ germ cells, and thereby, they could also contribute to the transgenerational transmission of behavioral traits induced by maternal immune activation.The recent years have witnessed an increasing interest in the role of the microbiome in health and disease. The human body is composed of a complex ecosystem of microbial cells, approximating the same number as the number of human cells in the human body.34 In support of this notion, numerous rodent studies highlighted a critical influence of the precise timing of prenatal infection with regards to its long-term brain and behavior consequences in the offspring.120An important aspect that warrants further investigation relates to the potential influence of the precise timing of prenatal immune activation, both in terms of its effects on the offspring’s epigenome and on the transgenerational transmission of pathological traits. Exposure to environmental insults during distinct gestational stages likely affects different neurodevelopmental events, developing brain regions, and cellular maturational processes, which in turn might shape the specificity of long-term brain dysfunctions in the offspring.122 It thus follows that maternal immune activation induces differential epigenetic modifications in the offspring depending on the precise timing of exposure. Indeed, a recent mouse study provided the first line of evidence suggesting that the epigenetic effects of prenatal immune activation are critically influenced by the timing of prenatal immune challenge.90 While immune activation in early and late gestation affected a relatively small number of common genes, the two prenatal conditions mostly showed methylation differences in distinct loci.90 Moreover, the differential epigenetic effects of early and late prenatal immune activation were associated with distinct transcriptional changes and behavioral abnormalities.90 Against this background, it appears essential to further explore whether and how timing-dependent effects are also reflected by the nature of the transgenerational effects induced by prenatal infection.It has long been recognized that epigenetic processes follow timed developmental patterns during embryogenesis and fetal development.123 has moved the risks of prenatal infection in the spotlight of public attention.The investigation of possible immune mechanisms in neurodevelopmental disorders is a long-standing area of research that continuously attracts the attention from basic scientists and clinicians alike. Within this neuroimmune framework of brain disease, a great deal of interest has been centered on the possible contribution of infections in prenatal life. The recent outbreak of Zika virus and its accompanying risk for severe brain anomalies such as microcephaly127 Against these backgrounds, the novel findings of infection-mediated epigenetic modifications raise the intriguing possibility that prenatal exposure to immune challenges may be one of the environmental factors causing epigenetic abnormalities in these disabling brain disorders. Since at least some of these epigenetic modifications may be modifiable throughout life,128 these findings may help to open new avenues for symptomatic or even preventive treatments in subjects with prenatal infectious histories.Modeling the consequences of prenatal infection in animals has led to the new discoveries that this early-life adversity induces stable epigenetic modifications in the offspring. There is increasing recognition of and evidence for altered epigenetic programming in the pathogenesis of neurodevelopmental disorders, including schizophrenia, autism and bipolar disorder.129 Hence, there are obvious challenges for future attempts to implement vaccinations as preventive means against infection-mediated neurodevelopmental disorders. The continuous implementation and integration of preclinical studies and human epidemiological research will be pivotal in overcoming these hurdles and may eventually help reducing or even preventing the burdens associated with infection-mediated neurodevelopmental disorders.The transgenerational transmission and modification of brain pathology following prenatal immune activation highlights a novel pathological aspect of this early-life adversity in shaping disease risk across generations. Given that prenatal infection is implicated in a variety of neurodevelopmental brain disorders, these new findings appear relevant to brain disorders independently of existing diagnostic classifications and may help identifying complex patterns of transgenerational disease transmission beyond genetic inheritance. These discoveries may further emphasize the importance for global health strategies in focusing on the development and promoting vaccinations, in particular for women who are pregnant or those who plan to become pregnant. Indeed, vaccinations may have the potential to prevent a wide spectrum of neuropsychiatric and neurological disorders associated with prenatal infection, and they may even prevent possible pathological effects across generations. Unfortunately, the limited access to vaccines in certain countries, along with the continuous trend against vaccinations within certain groups of the society, have led to a resurgence of serious infectious diseases, including measles, rubella and polio.


JAK2, CALR, and MPL genes in the majority of patients with myeloproliferative neoplasms (MPN) affords the opportunity to utilise these mutations as markers of minimal residual disease (MRD). Reduction of the mutated allele burden has been reported in response to a number of therapeutic modalities including interferon, JAK inhibitors, and allogeneic stem cell transplantation; novel therapies in development will also require assessment of efficacy. Real-time quantitative PCR has been widely adopted for recurrent point mutations with assays demonstrating the specificity, sensitivity, and reproducibility required for clinical utility. More recently, approaches such as digital PCR have demonstrated comparable, if not improved, assay characteristics and are likely to play an increasing role in MRD monitoring. While next-generation sequencing is increasingly valuable as a tool for diagnosis of MPN, its role in the assessment of MRD requires further evaluation.The presence of acquired mutations within the JAK2 V617F mutation, now over a decade ago, revolutionised the molecular diagnosis of MPN as this mutation is present in up to 95% of patients with PV and in approximately 50–60% of patients with ET and PMF. Subsequent identification of further disease initiating mutations, such as those in JAK2 exon 12, MPL exon 10, and CALR exon 9, allows the implementation of molecular diagnostic algorithms that are able to identify a clonal marker of disease in the vast majority of classical MPN patients. Numerous other myeloid-associated mutations have been additionally detected in MPN patients whose acquisition appears to influence the phenotype and disease course [The Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) are clonal hematopoietic diseases characterised by bone marrow proliferation of one or more of the myeloid cell lineages with no marked alterations in cellular maturation. MPNs classically comprise the clinically and pathologically related polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). In PV and ET, the potential exists for the disease to transform to a myelofibrotic stage and, together with PMF, transform to acute myeloid leukemia. Identification of the JAK2, CALR, and MPL “driver” mutations allows them to be utilised for diagnosis, but quantitatively, they may serve as markers of minimal residual disease (MRD), an additional, valuable indicator of depth of response to therapeutic intervention. To date, the clinical validity of determining JAK2, CALR, and MPL MRD responses has been demonstrated with several modalities including interferon alpha, JAK 1/2 inhibitors, and allogeneic stem cell transplantation (ASCT). Novel targeted agents for MPN in development include specific JAK2 inhibitors, histone deacetylase inhibitors, hypomethylating agents, heat shock protein 90 inhibitors, PI3-AKT-mTOR inhibitors, and telomerase inhibitors, all of which, alone or in combination with established therapies, will require assessment of efficacy [The primary treatment goals in MPN are to avoid thrombosis and bleeding, treat MPN related symptoms, improve quality of life, and minimize risk of malignant transformation and/or post-ET/PV myelofibrosis. However, the presence of theThe presence of recurrent point mutations facilitates the use of allele-specific quantitative PCR (qPCR) which has become widely adopted. Emerging approaches and platforms that are becoming increasingly implemented in the diagnostic setting with potential application for MRD monitoring include digital PCR (dPCR) and next-generation sequencing (NGS). This review will provide a brief overview of those methods already integrated into practice and consider those in development in regard to their clinical applicability to monitor MRD with respect to the three main types of MPN driver mutations. JAK2 V617F or MPL exon 10 point mutations at an allele burden of approximately 1–3% [ BCR-ABL1 monitoring into the routine clinical management of chronic myeloid leukemia, a variety of allele-specific qPCR approaches have been widely adopted. Comparative studies have demonstrated the superior sensitivity of qPCR especially after calibration to common standards [ JAK2 V617F allele burden by qPCR [ MPL exon 10 are present in approximately 5% of ET and <10% of PMF patients. This low frequency, compared to the JAK2 V617F and CALR exon 9 mutations, may explain that while several, sensitive qPCR-based techniques have been described for detection of the MPL exon 10 mutations at diagnosis [ CALR exon 9 are the most recently discovered MPN driver mutations. While semiquantitative, diagnostic fragment length analysis (FLA) has been extensively embraced, qPCR methods have been hampered by the variety of indels observed. However, recent studies focusing on the common type 1 deletion and type 2 insertion mutations that account for approximately 80% of all indels have exhibited improved specificity and sensitivity necessary for MRD purposes [Initial Sanger sequencing was superseded by pyro-sequencing, melt curve analysis, and allele-specific PCR for routine diagnostics because of its limited sensitivity and therefore inability to detect low mutation allele burdens. Remaining diagnostic methodologies vary in their sensitivity but should allow for the routine detection of theely 1–3% , 5. Asse by qPCR , 9 but aiagnosis –13, therpurposes . JAK2 V617F is the most frequent mutation in MPN, considerable effort has been afforded in addressing the clinical usefulness of using this mutation as an MRD marker in several treatment modalities. Hydroxyurea (HU) is one of the most widely used cytoreductive agents used in the treatment of PV and ET with initial reports suggesting that HU was able to suppress JAK2 V617F levels by >30% in approximately half of patients, a phenomenon observed early in disease course [ JAK2 V617F allele burden before treatment [ JAK2 V617F allele burden which either remains stable or only exhibits minor fluctuations over prolonged treatment periods [As thee course , 16. Whe periods –20.α) is able to induce hematological responses in MPN patients but its use has been constrained by the side effects of the relatively large doses employed. Nonetheless, sustained molecular responses are observed in the majority of PV and ET patients who remain on treatment with complete elimination of the detectable JAK2 V617F clone in selected cases [α [ JAK2 V617F responses, including complete molecular remission, in the majority of patients [Interferon alpha  and type 2 (5 bp insertion) that account for more than 80% of CALR mutations. Initial attempts for qPCR of these common CALR mutations resulted in limited sensitivities of 1-2%, comparable to other molecular screening approaches [ CALR mutations [In order to improve sensitivity and given the variety ofproaches . Developutations . JAK2 V617F, even at low allele burdens of 0.1%, indicating clinical utility for MRD monitoring [An emerging approach for the detection and quantitation of MPN-associated mutations is digital PCR (dPCR) which can achieve quantitation of the target allele without the requirement for standard curve construction or comparison to a reference gene. Partition of the template DNA into multiple PCR reactions is achieved by either droplet formation or nanofluidics, resulting in improved sensitivity and accuracy with minimal requirements for validation and standardization . Comparinitoring –58; howe CALR allele burdens by dPCR has recently been applied to PMF patients in the post-ASCT setting with considerable improvements observed in the detection and quantitation of type 1 and type 2 CALR mutants. As compared to FLA or qPCR, dPCR was capable of detecting delayed clearance of MRD after ASCT and earlier detection of increasing MRD levels prior to clinical relapse [ CALR mutant allele burden and, in one case, disappearance of the mutant clone at the time of transformation to acute myeloid leukemia [The accurate determination of mutant relapse , 60. Seqleukemia . JAK2 V617F MRD levels and demonstrated appreciable correlation with a qPCR approach [The capacity of next-generation sequencing (NGS) technologies, platforms, and accompanying bioinformatics pipelines to simultaneously sequence multiple genes and identify mutations with high specificity and comparable sensitivity lends itself to MPN molecular diagnostics in which a considerable degree of genomic complexity occurs. Targeted exon sequencing allows the identification of several mutations that not only demonstrate clonality but also have prognostic and therapeutic significance , 63. Whiapproach .Implementation of which MRD approach to adopt requires consideration of which cohort of patients to screen and technical aspects of the selected assays as discussed above. In addition harmonization of MRD data requires efficient handling and standardization of how results are to be reported  and alsoThe identification of multiple gene defects and deregulated signalling pathways in MPN has, in turn, propagated expansion of clinical research into specific inhibitors targeting these aberrations. The addition of MRD monitoring is likely to supplement these interventions in providing an individualized pathway of patient management.


Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques.Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in  Drosophilamelanogaster only 16 years ago  genome organization for its function. Genetic evidence for long-range effects in the regulation of gene expression was linked to a role of heterochromatin in gene silencing  pairing. Originally, Ed Lewis identified transvection at the bithorax complex  allele, in which a block of ∼2 Mb of heterochromatin containing the AAGAG satellite sequence is inserted in the coding region of the bw gene. Strikingly, when the Dbw allele is heterozygous to a wild-type (WT) copy of bw, this copy is repressed by Dbw. The repression involves a contact between the two alleles in trans, and the repositioning of the WT allele from its normal nuclear location toward centromeric heterochromatin 3-9. Even at such coarse-grained partitioning, the chromatin of transcriptionally active genes is represented by two distinct (red and yellow) states, suggesting that gene expression is accompanied by multiple distinct chromatin remodeling processes. Finally, in this classification, the major part of the transcriptionally inactive genome was assigned to black chromatin, with poorly understood and possibly repressive properties.The striking banding pattern of  domains . However protein . DamID h protein  of bindi protein , Filion Drosophila transcripts and small RNAs  may get averaged out during the analysis. Therefore, although any two genes or regulatory elements assigned to the same chromatin type are likely to share many properties, their functional behavior may still be different.Shortly after, followed a comprehensive analysis of the fly chromatin landscape by the large-scale model organism encyclopedia of DNA elements (modENCODE) project. This project produced detailed ChIP profiles of chromatin components and mapped ications . The ninDrosophila genome into distinct chromatin types is in many ways connected to its architectural organization in 3D space.To conclude, the distribution of post-translationally modified histones and nonhistone chromatin components defines distinct combinatorial patterns that partition the genome into domains with distinct chromatin types. At a chromosome scale view, we can see pericentric regions  and chromosome 4 embedded within chromatin domains rich in H3K9me2/me3 and HP1 and the rest of the genome (sometimes collectively referred to as euchromatin) represented by ∼10- to 200-kb domains of black/void chromatin alternating with similar-sized domains enriched in H3K27me3/Polycomb proteins or clusters of short domains with chromatin types characteristic of active genes. As we discuss in the following section, the segmentation of the linear Drosophila, the size of TADs in human and mice is on the order of 1 Mb on average. In both human and flies, inactive TADs roughly correspond to regions of strong attachment to the nuclear lamina [lamina-associated domains (LADs)], whereas active TADs are characterized by lower frequencies of lamina association . However, another contribution to this observation may come from the dynamics of chromatin motion. Indeed, chromatin moves with a specific speed inside the nucleus, which depends on chromatin type and position within the chromosome  . Many ofin situ DNA hybridization (DNA FISH) using whole chromosome probes. In such DNA FISH experiments, each chromosome appears to occupy a distinct portion of the nuclear space. In addition to these generic interactions, other much more specific interactions may occur between individual regulatory regions in the genome. First, a recent survey of interactions between a large set of embryonic enhancers and promoters identified specific interactions not only between each enhancer and its cognate neighboring gene promoter target, but also include very-long-range interactions with genes located hundreds of kilobases and several TADs away. Furthermore, these interactions are largely preset, before the time at which the target gene of each of these enhancers will start to be activated . Using DNase I accessibility assay, specialized chromatin structures (scs) and scs′ to flank the Hsp70 locus and proposed that those define the boundaries of the heat-shock puff. As would be expected from such boundary elements, scs and scs′ turned out to “insulate” the expression of a reporter gene from the influence of the surrounding chromatin , Mod(mdg4), and Cp190 proteins , CTCF, BEAF-32, Ibf1, Ibf2, Pita, ZIPIC , Dwg, and GAF (the product of the Trithorax-like gene) (mod(mdg4) gene  forms homo- and heterotypic multimers with the BTB/POZ domains of several other members of the tramtrack group (Cp190 and mod(mdg4) genes have distinct phenotypes , the candidate glue proteins, share genomic binding sites with many DNA binding proteins of the first group . This viHow could the elements that facilitate transient looping contacts delimit the boundaries of combinatorial patterns of chromatin modifications (chromatin states)? One scenario that is easy to envision is when histone modifications are produced via looping interactions of a protein complex anchored at a fixed chromatin site. For example, Polycomb complexes anchored at PREs (see below for details) loop out and trimethylate H3K27 at extended distances from their principal binding sites , the transition between the two kinds of chromatin is likely to appear as TAD boundary. Consistently, combinations of histone modifications typical of active genes can predict the positions of many Drosophila TAD borders  gene was then described as a separate locus that represses Hox genes outside their appropriate expression domains  could recruit PcG proteins also when they were inserted in transgenic constructs, where they could drive repression of reporter genes . The anaion loci . Since tion loci . Brieflyion loci . With anion loci , which fPsc and Su(z)2 to a murine protooncogene named Bmi-1 strongly suggested that, in addition to its requirement during development, the appropriate regulation of PcG function is also required to prevent the emergence of cancer. Since then, countless reports have corroborated this hypothesis . This large complex contained Pc, Polyhomeotic (Ph), Posterior Sex Combs (Psc), and RING1 (the product of the Sex Combs Extra gene) as stoichiometric components, as well as Sex Combs on Midlegs (Scm) in substoichiometric amounts (esc, which has a paralog called escl (ph and Psc loci (i.e., PC, PH, PSC, and SCE, whereas in noncanonical PRC1 variants, PC and PH homologs are absent and the ncPRC1-specific RYBP proteins are present instead. Furthermore, specific types of PSC paralogs characterize specific ncPRC1 variants and other proteins are present in some of them (Similar phenotypes observed in PcG mutants and the colocalization of PcG proteins in polytene chromosomes strongly suggested that PcG proteins act in concert, possibly via formation of biochemical complexes, to recognize repressed transcriptional states and to propagate them through cell division. Furthermore, their increased silencing activity in the presence of homologous PREs suggested that long-range interactions in the 3D nuclear space may reinforce silencing. Co-immunoprecipitation studies provided first evidence for molecular interactions among  amounts . AlthougPsc loci . Detailei.e., simultaneously decorated by the activating mark H3K4me3 (In parallel to the biochemical characterization of PcG complexes, a large body of work has been dedicated to describe and understand their genome-wide distribution. Initial work in flies paralleled human and mouse studies . In the  H3K4me3 . AlthougFab-7, which contains a PRE flanking a chromatin insulator, were shown to be able to frequently contact the endogenous Fab-7 element even when inserted in a different chromosome (i.e., insulators can drive associations in the 3D space of the cell nucleus of their target elements. If these elements are in a repressed state, their association is accompanied and possibly stabilized by PcG components, whereas if they are active, TrxG proteins assist their association to transcriptionally active regions of the nucleus (One intriguing observation that came from the comparison of genome-wide location with microscopy studies, done either by immunofluorescence or by analysis of GFP-fusion proteins of the PcG, is that PcG components stain as foci in the nucleus  Figure . AlthougThese data suggested that a cooperation between PcG proteins, TrxG proteins, and insulators may lead to higher-order organization of a large set of genomic loci. This idea is at least partly supported by several lines of evidence. First, the analysis of nuclear positioning of Hox genes has shown that the bithorax and the antennapedia complexes colocalize in nuclei in which Hox genes are corepressed (Drosophila has been a pioneering model system to identify and describe the connection between 3D organization of the genome and its function. Some important aspects of this organization, for instance, the compartmentalization of the genome parts to specific subnuclear locations, such as the nuclear lamina or the nucleolus, were not discussed in this review due space limitations. Nevertheless, the examples provided here clearly show that the genome cannot be reduced to a string of DNA nucleotides and that all levels of higher-order genome organization, from the nucleosome to chromatin fibers, chromosomal domains, chromosome territories, and chromosome localization within nuclear space, must be considered. A great amount of work is still required to dissect the links between each of these organizational levels and various aspects of genome function. Part of this work will likely involve the analysis of chromosome architecture of specific cell types or developmental stages, similar to the recent analysis of the spatial regulation of the bithorax complex along the anteroposterior body plan during embryogenesis (For decades Drosophila will continue to be instrumental in our quest to achieve this goal.As studies that connect disruptions of TADs to pathological rewiring of enhancer–promoter interactions and heritable malformations in human patients started to emerge . We have


Targeted therapy is able to identify cancer patients with dissimilar genetic defects at cellular level for the same cancer type and consequently requires individualized approach for treatment. Cancer therapy begins to shift steadily from the traditional approach of “one regimen for all patients” to a more individualized approach, through which each patient will be treated specifically according to their specific genetic defects. Personalized medicine accordingly requires identification of indicators or markers that guide in the decision making of such therapy to the chosen patients for more effective therapy. Cancer biomarkers are frequently used in clinical practice for diagnosis and prognosis, as well as identification of responsive patients and prediction of treatment response of cancer patient. The rapid breakthrough and development of microarray and sequencing technologies is probably the main tool for paving the way toward “individualized biomarker-driven cancer therapy” or “personalized medicine”. In this review, we aim to provide an updated knowledge and overview of the current landscape of cancer biomarkers and their role in personalized medicine, emphasizing the impact of genomics on the implementation of new potential targeted therapies and development of novel cancer biomarkers in improving the outcome of cancer therapy.Cancer therapy agents have been used extensively as cytotoxic drugs against tissue or organ of a specific type of cancer. With the better understanding of molecular mechanisms underlying carcinogenesis and cellular events during cancer progression and metastasis, it is now possible to use  However, there is a debate involving the qualification any substance or molecule which may be measured in bio-specimen and that may be associated with health-related outcomes”. From our point of view, this definition is too wide and should involve the specific association of biomarkers with the patient’s clinical outcome as well. Therefore, it is quite acceptable that the better definition was documented by the Biomarkers Definitions Working Group as “it is a biological molecule that is fairly evaluated as an indicator of normal physiological, pathological processes or pharmacological responses to a therapeutic intervention” Advanced progression in genomics has highlighted particular molecular events that lead to cancer such as DNA mutations, gene amplifications, and chromosomal rearrangements Recent advance in personalized medicine accordingly requires development of indicators or markers that help when choosing the suitable patients to treat with such therapy, and which therapy will be mostly effective for a patient i.e., DNA biomarkers, DNA tumor biomarkers, and general biomarkers Cancer “tumor” is considered as a disease that includes alterations of DNA at cellular level, and such alterations within tumor could be measured Distinct from DNA biomarkers, DNA tumor biomarkers represent the biomarkers specific to a particular cancerous tumor Prognostic biomarkers aim to predict the disease progression, whereas predictive biomarkers aim to detect the treatment response Development of new biomarkers involves multiple stages, starting initially by discovery and preclinical exploration in basic studies, then validation of the biomarker through clinical studies to identify its potential capacity for establishment of disease whether retrospectively or prospectively, and followed by clinical implementation Pepe et al. The shortage of the process of standardized validation is the biggest challenge for adoption of biomarkers in personalized medicine practice, which may be on account of the heterogeneity of tumor kinds, therapies, and the testing process itself The rapid development of high-throughput methods enables the integrated omics technologies, that include broad-spectrum platforms as genomics, transcriptomics, proteomics, epigenomics, and metabolomics analyses Proteomics-based techniques include mass spectrometry, liquid chromatography, tandem mass spectrometry, protein arrays, and antibody assays Moreover, transcriptomics analyses examine the level of gene expression as the proxy of gene activity ALX1 in non-small-cell lung cancer (NSCLC) and RASSF1A in prostate cancer, were found to be prognostic and correlate with relapse-free survival of the patients Epigenetic changes, including modification of histones, chromatin, or DNA methylation status, may affect the gene expression patterns without alteration of DNA sequences For traditional clinical procedure with cancer patients, the selection of appropriate chemotherapy is based mainly on histopathological assessment of the tumor and the primary organ from which the tumor originates MGMT promoter Biomarkers have been categorized mainly into predictive and prognostic markers, although some biomarkers might be applied for both purposes, such as methylation of The emergence of “omics” technologies, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics, may be the backbone toward the discovery of novel prognostic and predictive biomarkers for cancer patients BRCA1), breast cancer 2 gene (BRCA2), TP53, and Ataxia-Telangiectasia mutated (ATM), expose patients to an elevated risk for breast cancer BRCA2 in one allele impairs BRCA2 protein synthesis and inactivates repairing system S-transferase (GSTP1 and GSTM1) and G158A polymorphism in prostate-specific antigen gene may increase risk for prostate cancer APC) are at risk for familial adenomatous polyposis, an autosomal dominant type of inherited genetic disorder that is characterized by increased possibility of polyps and cancer of the gut, such as colorectal cancer (CRC) Prognostic biomarkers are used to monitor anti-cancer therapy, to assess the cancer grade, and to detect occurrence of remission or recurrence in individual patients BCL2, GRB7, KRT6B, KRT17, and CDH3 in breast cancer patients prior to the therapy could predict the outcomes. Given the advantages in analyzing gene expression for prediction of response to therapy, print tests show great value for personalization of cancer therapy and assessment of the possible benefits of applied therapy A quick detection of genetic mutations in the pathogenesis of complex genetic disorders is facilitated by the genome-wide association studies and discover of various pharmacogenetic biomarkers In addition, presence of miRNA molecules could be correlated to certain types of cancer, such as hepatocellular carcinoma (HCC) Alterations in DNA methylation may also be considered a good prognostic biomarker. Hypermethylation would block the promoter sites of oncogenes or tumor suppressor genes in cancer tissues, thus leading to the loss of expression or alterations of the genes In addition, the appearance of CTCs in blood may also be considered prognostic factors as well. Cells originating from the tumor may be released into circulation after passing through the vascular bed and vessel wall KRAS) gene mutation is one of the alterations in the occurrence of CRC, which may occur very early in the process of carcinogenesis. The earliest report supporting the relationship between the KRAS mutations and the progression of colorectal carcinogenesis was published in 1988 KRAS gene in the codons 12 and 13 was documented as one of the predictive markers in the assessment of the competency of targeted therapy for patients of progressive CRC, when using cetuximab or panitumumab as therapeutic monoclonal antibodies KRAS gene serves as a valuable positive predictive biomarker KRAS may exhibit no or worse response to the aforementioned therapy, especially if they also carry mutations in codons 61 or 146 of KRAS, or mutations in the BRAF gene Predictive biomarkers play an important role in providing data about the expected and possible response to a given therapy ERCC1, a gene encoding an essential protein for DNA repair, is another predictive biomarker for response to targeted therapy in hepatic and lung cancer. It has been reported that high ERCC1 expression is correlated with a cisplatin resistance in patients with HCC and in patients with NSCLC mTOR and c-erb-B2 may indicate tumor aggressiveness as a result of the presence of these genes in hepatic carcinogenesis Moreover, CTCs could be considered as a valuable predicative tool as well. Detection of CTCs at different time points during the course of treatments as during, before, and after therapies enables prediction of therapeutic outcome BRCA1 and BRCA2, had higher risk for breast cancer Comprehensive understanding of carcinogenesis and hallmarks of cancer is increasingly important. Large-scale systematic sequencing endeavors have been implemented over the last decade RB1 in gastric, prostate, and lung cancers TGFBR2miRNAs have attracted tremendous attention during the last decade especially in the implementation era of cancer gene targets and in the new cancer classification. Large-scale miRNA expression profiling “miRNAome” studies have potentially identified miRNA signatures that were applicable to multiple cancers. Specifically, these miRNAs have clear interactions with specific tumor suppressor genes or oncogenes in cancers of different tissue origins Recently, miRNA has been extensively utilized as one of the promising predictive biomarkers through RNA expression analysis i.e., ER-negative, progesterone receptor (PR)-negative, and human epidermal growth factor receptor 2 -negative, and (4) HER2-like class that usually overexpresses erbB-2 and is HER2-positive. These four classes could be differentiated by microarray studies. Luminal cancers show increased expression of genetic biomarkers reminiscent of normal breast myoepithelial cells, such as luminal cytokeratin, whereas basal-like cancers do not overexpress such genes or E-cadherin either BRCA1 mutation-associated breast cancers possess a molecular signature of basal-like cancers ER, HER2, PR-regulated transcripts, and proliferation-linked genes, which have been very effective in assessing the probability of breast cancer recurrence and classifying patients accordingly into high-, intermediate-, or low-risk groups for recurrence CD44-positive and CD24-negative patients Breast cancer can be grouped into four classes based on gene expression profiling There is not much known about the molecular alterations associated with CRC and no novel molecular biomarkers have been validated for clinical practice of diagnosis or prognosis. The multistep progression of CRC may involve changes of genes encoding KRAS, APC, P53, and mismatch repair (MMR), as well as proteins in transforming growth factor (TGF) pathway PTEN) and translocations of the genes encoding E-twenty-six specific (ETS)-related gene (ERG) and transmembrane protease, serine 2 (TMPRSS2), leading to the generation and increased transcription of the TMPRSS2-ERG fusion gene c-MYC, as well as deletions of CDH1, RB1, RAF, SMAD4, and NKX3-1 genes PCA3) is a predictive biomarker that has been extensively studied recently. PCA3 is a ncRNA that is highly specific for prostate tissue and overexpressed in PCa, indicative aggressive tumors. Gene fusions TMPRSS2-ERG and CTC counts, which have been shown to correlate with prognosis in castration-resistant PCa, could be used as predictive biomarkers, providing more personalized therapeutic alternatives to individual patients Initiation and progression of prostate cancer is driven by genetic alterations and rearrangements that eventually lead to activation of oncogenes and inactivation of tumor suppressor genes A 5-gene signature profiling for lung cancer has been identified by combining microarray profiling and qRT-PCR and was implemented to predict overall survival and relapse-free survival time EGFR-mutated lung cancer are clinically established as examples of targeted therapy Identical alterations or similar molecular signatures of certain cancers may lead to dissimilar manifestations in different individuals owing to tumor heterogeneity, thus leading to variations in the efficacy of diagnostic or prognostic markers, choice of potential cancer therapy, treatment outcome, and survival duration of two seemingly identical types of cancer -positive breast cancer patients showed significant increase in overall survival and metastasis-free interval in two large American and European group studies Trastuzumab (herceptin) is an antibody therapy targeting HER2, which is amplified in about 10% of breast cancer by acting on its domain IV EGF R when taking cetuximab as monotherapy than those taking the combined therapy of cetuximab and irinotecan PDGF-RA) or oncogene KITABL1) by competing with ATP at its binding site on ABL1, thus inhibiting kinase activity of ABL1 EGFR is a tyrosine kinase receptor and gets involved in the key signaling pathway for initiation and progression of CRC. Imatinib, cetuximab, and panitumumab, which are TKIs against EGFR, are used for the treatment of metastatic CRC. Earlier studies showed lower response rate in metastatic CRC patients with overexpressed EGFR alone KRAS mutations could effectively predict resistance to both drugs KRAS-mutated tumors were responsive to cetuximab and panitumumab treatment KRAS mutations, EGFR gene copy number variations, as well as BRAF and PIK3CA mutations, could also be useful for the prediction of patients with low response rate or secondary resistance to anti-EGFR therapy Cetuximab and panitumumab are also EGFR-targeted monoclonal antibodies used for treatment of metastatic CRC. However, prediction of the outcome of both drugs can’t be achieved by relying on positive expression of BRAF, KRAS, HER2, and EGFR, as well as translocations of the gene encoding anaplastic lymphoma kinase (ALK), rearrangements of the gene encoding c-ros oncogene 1 receptor tyrosine kinase (ROS), and fusion of the gene encoding rearranged during transfection tyrosine kinase receptors (RET) EGFR and translocations of the oncogenes encoding echinoderm microtubule-associated protein-like 4 (EML4)-ALK had been identified as the most common ones ALK crizotinib , which targets EML4-ALK translocation, in patients with NSCLC showed promising results. 57% of patients responded to the drug treatment with 72% 6-month progression-free survival reported ALK translocation Numerous studies have demonstrated the inter-individual tumor heterogeneity of NSCLC Therapies targeting oncoproteins, such as anti-HER2 (trastuzumab), c-Kit inhibitor (imatinib), and ALK inhibitor (crizotinib), have been successfully developed and extensively used recently Recent advances in molecular diagnostics have offered essential tools allowing applications of personalized medicine in oncology. The fast development of sequencing and microarray methods may facilitate the emergence of new biomarkers and targeted therapies for individual cancer patients, paving the road toward the new era of personalized medicine. Comprehensive genomic studies on most of the common cancer types, such as breast, colon, lung, ovarian, and renal cancers, have been released recently. These studies aid in identifying most of the genomic alterations that may be targetable or associated with drug resistance, thus enabling individualized cancer therapy. Resistance to targeted therapies might be due to secondary genomic alterations or instability and intra-tumor heterogeneity. Therefore, overcoming resistance would involve the concomitant administration of targeted therapies and implementation of specifically employed panel of predictive biomarkers. Better comprehensive understanding and proper evaluation of the information offered synchronously by prognostic and predictive biomarkers would enable quicker and earlier diagnoses as well. Predictive markers are also beneficial in reducing the toxicity and resistance to treatments and in assessment of the suitability of patients to a targeted treatment, in another word, “individualized biomarker-driven cancer therapy” or “personalized medicine”.etc. enables the identification of promising prognostic and predictive cancer biomarkers for better assessment and follow up of cancer patients.Integrated omics studies provide better understanding and identification of the crucial molecules involved in cancer development and progression. In addition, Technological breakthrough in microarray, automated DNA and RNA-sequencing, mass spectrometry, comparative genomic hybridization, One of the major limitations of personalized medicine is the unique genomic profiling of each patient. In fact, the alterations in each gene occur with low incidence. Therefore, the medication development in cohorts driven by a genomic alteration is encountered by the low frequency of genomic alteration. To overcome this obstacle, scientists would need to develop genomic algorithms and implement highly specified and constructed software for personalized medicine, allowing prediction at the individual patient level.The authors have declared no competing interests.