Genetic and epigenetic markers of gliomas

ISSN 1990�519X, Cell and Tissue Biology, 2013, Vol. 7, No. 4, pp. 303–313. © Pleiades Publishing, Ltd., 2013.Original Russian Text © E.V. Semenova, M.V. Filatov, 2013, published in Tsitologiya, 2013, Vol. 55, No. 5, pp. 290–299.

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Great progress has been achieved in our under�standing of genetic, epigenetic, and cellular mecha�nisms underlying glioma development and invasion. Itis known that the glioma malignant phenotype is theresult of malfunction of several signaling pathways.Malignant transformation results from hyperexpres�sion and amplification of oncogenes, as well as inacti�vation oncosupressor genes. There is no doubt that theprocess also involves epigenetic factors. Epigeneticmodifications may appear at the early stages of car�cinogenesis and alter the expression of oncogenes andantioncogenes that impairs the genome integrityand/or chromosome segregation (Bannister andKouzarides, 2011).

Both genetic and epigenetic changes underlie themechanisms of the tumor initiation and progression.Carcinogenesis may be controlled epigenetically aloneor in cooperation with genetic mechanisms. More�over, an aberrant epigenetic profile increases the risk ofacquiring additional genetic defects (Gronbaek et al.,2007). It may be stated that oncology has entered anepigenetic era (Rutka et al., 2009).

Although there is progress in understanding thecauses and consequences of epigenetic changes forglioma malignant transformation, much remainsobscure and needs further investigation. Identificationof epigenetic determinates is very important for eluci�dation of molecular and cellular mechanisms underly�ing gliomàgenesis, as well for diagnostics of the diseaseand estimation of probable recurrences and therapyefficacy.

This review surveys the glioma major epigeneticmarkers: disturbances in DNA�methylation, modified

“histone code,” and aberrant expression ofmicroRNA. Potential epigenetic targets for new ther�apeutic approaches and optimization of treatmentstrategy are also discussed.

GLIOMA GENETIC SPECIFICITIES

Gliomas are widespread variable brain tumors ofneuroectodermal origin. These tumors deeply extendinto the adjacent brain tissue and are highly resistant tochemo� and radiotherapy. Radical surgical removal ofthese tumors type is a formidable task. Thereby, theyare considered barely treatable malignancies.

The basic glioma types include astrocytomas andglioblastomas (the malignant counterpart to astrocy�toma) that make up 60–70% of all primary brainmalignancies, oligodendrogliomas (8–10%), andmixed gliomas.

According to the World Health Organization(WHO) classification, glial tumors are grouped bymalignancy. Degree I: pylocytic astrocytoma (juve�nile), subependimal giant cell astorcytoma, and pleo�morphic xantoacrocytoma. Degree II: diffuse astrocy�toma (fiblillar, protoplasmic, hemocytic). Degree III:anaplastic astrocytoma. Degree IV: multiform glio�blastoma.

Multiform glioblastoma is the most aggressiveglioma type. Patents rarely live for longer than 1 yearafter a precise diagnosis. After surgery and applicationof radio and chemotherapy, only 42% of patients liveup to 6 months, 18% live about 1 year, and 3% about2 years (Stewart, 2002; Ohgaki et al., 2004). Thus, aprognosis of glioma is not optimistic, although clinical

Genetic and Epigenetic Markers of GliomasE. V. Semenova and M. V. Filatov

Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Russiae�mail: [email protected]

Received February 5, 2013

Abstract—Malignant gliomas are aggressive and highly invasive tumors. Various genetic and epigeneticchanges are common for these tumors. Mostly they concern the genes involved in cell�cycle regulation, apo�ptotic pathways, cell invasion, angiogenesis, and cell metabolism. The role of epigenetic mechanisms inglioma malignant transformation, despite recent progress, is uncertain and remains under intense study. Thisreview describes the mechanisms of epigenetic regulation of gene expression, including posttranslationalmodifications of histones, DNA methylation in promoter regions, and microRNA regulation. The geneticand epigenetic factors driving the pathogenesis of gliomas in their possible mutual influence and the potentialepigenetic targets that can be used for diagnostics and new therapeutic approaches are also discussed.

Keywords: genetic particularities, gliomas, epigenetic alterations

DOI: 10.1134/S1990519X13040123

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neurooncology has been progressed in recent years.Almost 70% astrocytomas are considered to havetransformed into gliomas with malignancy ofdegrees III and IV during 5–10 years (Burgess et al.,2008).

Oligodendrogliomas are divided into oligodendro�gliomas (gliomas with degree II malignancy) and ana�plastic oligodendrogliomas (gliomas with degree IIImalignancy). It should be noted that oligodendroglio�mas are of rare occurrence. Mostly, they are compo�nents of mixed gliomas.

Molecular and cellular analysis of glioma has iden�tified numerous genes underlying the malignant trans�formation. It was found that inactivation of RB, TP53,p16, CDK4/6, and some other genes deregulated thecell cycle, which resulted in uncontrolled cell prolifer�ation. Amplification and overexpression of genesencoding growth factor receptors (EGFR, PDGFRA,FGFR, and IGF�1R) activated signaling pathways,mostly Ras/MAPK regulating the cell proliferationand PI3K/Akt engaged in the cell division, apoptosis,invasion, angiogenesis and cellular metabolism(Knobbe et al., Gonzalez and de Groot, 2008; Naviset al., 2010). The protein oncosupressor PTEN is alsoinvolved in glioma development, because its dysfunc�tion results in Akt aberrant activation (Alexiou andVoulgaris, 2010; Kim et al., 2010; Cecener et al., 2009;Tunca et al., 2007; Navis et al., 2010).

Gliablastomas are divided into two subtypes: pri�mary and secondary. Primary glioblastoma, or glio�blastoma de novo, is a well�defined vast tumor with ashort clinical history (in most cases, less than3 months) and a lack of any indications regarding pre�liminary alterations. Primary glioblastoma is com�monly revealed in elderly people. This glioblastomasubtype is characterized by loss of heterozygosity(LOH) of chromosome 10q (70%), EGRF amplifica�tion, p16 deletion, and TP53 and PTEN mutationswith a frequency of 24–34%. Secondary glioma devel�ops from less�differentiated gliomas (diffuse and ana�plastic astrocytomas) in younger patients (about45 years old) and usually has a high frequency of TP53mutations (65%) and LOH 10q (63%) (Maher et al.,2001; Ohgaki et al., 2004).

Genetic differences in primary and secondary glio�mas are shown in various expression profiles. Hyper�expression of VEGF, Fas (APO�1/CD95), IGFB, andMMP�9 is more typical for primary than for secondarygliomas. MMP�9 hyperexpression is registered in 69%of primary and 14% of secondary gliomas (Choe et al.,2002; Godard et al., 2003; Ohgaki and Kleihues,2007). Hyperexpression of EGFR and mdm2 is morecommon for primary gliomas (Watanabe et al., 1996;Biernat et al., 1997). On the other hand, the ASCL1expression level is high in 86% diffuse astrocytomasand 88% secondary glioblastomas, whereas in mostprimary glioblastomas (67%) its level is similar to, oreven lower than, in normal brain cells (Somasundaram

et al., 2005). Centrosome�associated protein CEP350and enolase 1 are typical only for primary gliomas;ERCC6, DUOX2, HNPPA3, and ADAMTS�19 arecommon for the secondary gliomas (Furuta et al.,2004). EGF�A protein is frequently registered in pri�mary gliomas; growth factor AB in more common forthe secondary gliomas (Huang et al., 1997). It impliesthat primary and secondary gliomas are diverse onco�logical diseases in the genetic terms. The epigeneticprofiles of these tumor subtypes are also different (seebelow).

GENERAL EPIGENETIC MECHANISMS

The general mechanisms of epigenetic regulationof gene activity are histone posttranslational modifica�tions, methylation of DNA promoter regions, andexpression of microRNA.

NH2�terminals of core histones are substrates forvarious covalent modifications, such as acethylation,methylation, phosporylation, ubiquitination, sumoy�lation, biotinylation, ADP�ribozylation, etc. Thesemodifications alter the chromatin structure andchange the interaction between DNA and histonesand internucleosome interactions and interactionsbetween nonhistone regulatory proteins and chroma�tin (Turner, 2005). More than 60 histone posttransla�tional modifications are currently known. Specificcombinations of histone modifications, the so�called“histone code,” regulate the key DNA�involved cellu�lar processes, such as replication, repair, recombina�tion, and transcription, as well as chromatin conden�sation and nuclear organization (Berger, 2007;Kouzarides, 2007; Li et al., 2007).

Acethylation of lysine and methylation of lysineand arginine are the most examined modificationsinvolved in carcinogenesis. These modifications arereversible: there are enzymes catalyzing binding(acethyltransferases and methyltransferases) orremoval (deacethylases and demethylases) of func�tional groups. Acethylation facilitates the formation oftranscriptionally active euchramatin; deacethylationpromotes the formation of transcriptionally inert het�erochromatin structures. Histone methylation mayresult both in gene expression and transcription inac�tivation, depending on the histone type, position ofamino acid residues for methylation, amount of boundmethyl groups (Bhaumik et al., 2007). The various his�tone modifications may be considered the letters of thehistone alphabet; combinations of them create wordswith a particular biological sense.

Another important epigenetic marker is DNAmethylation. DNA methylation is the binding cova�lent of methyl groups to cytosines of CpG dinucle�otides. The process is catalyzing by DNA�methyltransferases. In human beings, 50–70% of all CpGsites are methylated mostly in heterochromatinregions. The modified DNA presumably inhibits gene


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expression averting transcription factor bindingand/or, to the contrary, promoting the binding of pro�teins repressing transcription (Bird, 2002; Kanwal andGupta, 2010). CpG islands in euchromatin regions, asa rule, are not methylated, which provides free accessof transcription factors and chromatin�binding pro�teins to most “housekeeping” and regulatory genes(Villa et al., 2004). CpG islands are DNA sites of 500–1000 bp with a CpG dinucleotide frequency five timeshigher that in other genome regions. In cancer cells,genome�wide hypomethylation is accompanied withlocal hypermethylation of CpG islands in gene�pro�moter areas that are usually not methylated in normalcells. This concerns mostly genes driving oncosupres�sor proteins (Baylin and Bestor, 2002; Jones and Bay�lin, 2002; van Noesel et al., 2003; Feinberg, 2004;Feinberg and Tycko, 2004; Laird, 2005).

Both mechanisms of epigenetic regulation (histonecovalent modifications and DNA�methylation) mayoperate in cooperation. For example, UHRF1 proteinbinds with the nucleosome in which H3 histone ismodified with H3K9me3 (marker of transcriptioninactivity). The binding is stronger if the DNA twistedon the histone octamer is methylated. On the otherhand, methylated DNA may inhibit the interaction ofchromatin�binding proteins with specifically modifiedcore histones. Thus, the protein factor KDM2A caninteract with nucleosomes enriched with H3K9memodification only if DNA is not methylated (Bannis�ter and Kouzarides, 2011). Methyl�CpG�binding pro�teins (MECP2, MBD1, MBD2, MBD3, MBD4, andKaiso) interacting with methylated cytosines producecomplexes with histone deacethylases that facilitateschromatin compaction and transcription inactivationof certain genes (Kanwal and Gupta, 2010).

Along with DNA�methylation and posttranslationmodifications of histones, the epigenetic regulation ofgene expression involves so�called microRNA(miRNA). miRNA fulfills both an oncosuppressivefunction, reducing oncogene expression, and onco�genic function, modifying oncosupressor gene expres�sion (Anguera et al., 2006; Costa, 2008; Gartel, Kan�del, 2008; He et al., 2007). miRNA are noncoding reg�ulatory 21� to 23�bp RNA. They play an importantrole in the regulation of mRNA translation and degra�dation. miRNA in complex with specific proteins rec�ognizes and degrades homologous mRNA via RNAinterference (Stefani and Slack, 2008). A singlemiRNA molecule can interact with a great number oftranscripts encoding various proteins (Griffiths�Joneset al., 2008; Kanwal and Gupta, 2010). It is knownthat the expression profile of various miRNA is pro�foundly altered during the carcinogenesis process(Calin and Croce, 2006; Esquela�Kerscher and Slack,2006; Hammond, 2006; Gartel and Kandel, 2008;Kanwal and Gupta, 2010).

The mechanisms of the epigenetic regulation ofgene activity may function in cooperation. There is

probably a certain hierarchical sequence of epigeneticchanges that stabilizes the acquired signs essential forthe property underlying the malignant transformation.It is highly probable that DNA methylation in car�cinogenesis is a secondary epigenetic modificationthat occurs after changes in the “histone code” (anincreased number of histone markers of transcriptioninactivation and histone deacethylation in promoterareas of suppressor genes) (Bachman et al., 2003).Aberrantly expressed miRNA are a result of alteredchromatin structure due to covalent modifications ofhistones and DNA and appear later (Saito and Jones,2006).

Numerous studies have showed that epigenetic reg�ulation of gene expression plays an important role inthe glioma pathogenesis. Moreover, it has been sug�gested that disturbed epigenetic mechanisms is themain defect of gliomagenesis (Nagarajan and Cos�tello, 2009).

THE ROLE OF DNA�METHYLATION IN GLIOMA PATHOGENESIS

The majority of investigations of epigeneticchanges in glioma, as in other oncological diseases, aredevoted to DNA�methylation. There is no doubt thatCpG�islands in promoter regions of hundreds of genesin astrocytomas and gliomas are hypermethylated(Nagarajan and Costello, 2009). This parameter helpsto identify many gene suppressors transcriptionallyinactivated in these tumors. On the other hand, locus�specific DNA�hypomethylation (decreased DNAmethylation level) has been registered in malignantgliomas (Gama�Sosa et al., 1983; Cadieux et al., 2006;Nagarajan and Costello, 2009). It has been demon�strated that various subtypes of gliomas exhibit distinctDNA�methylation profiles (Uhlmann et al., 2003).

DNA�Hypomethylation

Genome�wide hypomethylation is commonmostly for glioblastomas de novo: 80% of primary glio�blastomas exhibited DNA�hypomethylation (Gama�Sosa et al., 1983; Cadieux et al., 2006). The level ofmethylation is variable in different tumors: from a levelclose to normal brain tissues up to 50% from the nor�mal level; i.e., 10 million GpC sites per transformedcell are demethylated. Biological function of theseepigenetic alterations in the glioma pathogenesis isunclear. Both repeated DNA fragments (e.g., Sat2 andD4Z4) and single�copy loci (MAGEA1) may behypomethylated in glioblastomas. Hypomethylationof DNA tandem sequences in multiform glioblasto�mas makes the cells predisposed to chromosomebreaks and changes the copy number of thesesequences (Yu et al., 2004; Cadieux et al., 2006;Fanelli et al., 2008; Nagarajan and Costello, 2009).

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Hypermethylation of CpG Islands in Promoter Regions

Locus�specific DNA hypermethylation is a fre�quent event in gliomagenesis. Hypermethylation ofCpG islands is common for genes involved in tumori�genesis (cell�cycle regulation, DNA repair, prolifera�tion, apoptosis, angiogenesis and invasiveness) (Naga�rajan and Costello, 2009). The following genes are fre�quently hypermethylated in malignant gliomas: p16,RB, PTEN, TP53, p14, MGMT, EMP3, PCDH�γ�A11,SOCS1 (Costello et al., 1996; Park et al., 2000; Naka�mura et al., 2001b; Watanabe et al., 2001; Zardo et al.,2002; Baeza et al., 2003; Alaminos et al., 2005;Amatya et al., 2005; Hegi et al., 2005; Waha et al.,2005; Bello and Rey, 2006; Kunitz et al., 2007; Zhouet al., 2007). Epigenetic inactivation of various genesserves as a marker of molecular and cellular differ�ences between primary and secondary glioblastomas.The frequency of the promoter methylation is higherin the secondary than in primary glioblastomas(Ohgaki and Kleihues, 2007). Thus, the promoters ofp14, p16, RB1, PTEN, MGMT, and TIMP�3 genes aremore frequently hypermethylated in secondary glio�blastomas (Ohgaki and Kleihues, 2007). The level ofp16 protein is significantly decreased in 74% of sec�ondary glioblastomas; 77% of these cases had alteredchromatin structure and DNA methylation in the p16promoter region (Costello et al., 1996; Park et al.,2000). Hypermethylation of the p14 promoter is asso�ciated with malignant progression and shortening oflife expectancy (Watanabe et al., 2007). CpG methyla�tion in the promoter area of caspase 8 proapototicgenes is also an indication of a bad prognosis for thesecondary glioblastomas (Martinez et al., 2007b).

The protein PTEN is a molecular marker forglioma pathogenesis (Tunca et al., 2007; Gonzalez andde Groot, 2008; Cecener et al., 2009; Alexiou andVoulgaris, 2010; Kim et al., 2010; Navis et al., 2010).The PTEN promoter is enriched with CpG islandslocated between nucleotides –2420 and –2211, –2113and ⎯1775, –1018 and –389, and –372 and –155.This shows that DNA methylation is probablyinvolved in regulation of gene transcription. Numer�ous data have showed that epigenetic mechanisms ofPTEN inactivation play an important role in gliomamalignant transformation (Knobbe et al., 2002;Wiencke et al., 2007; Gonzalez and de Groot, 2008;Müller et al., 2010). It was proposed that Akt activa�tion in gliomas was preferentially regulated by inhibi�tion of PTEN transcription by methylation of the pro�moter rather than PTEN mutation (Wiencke et al.,2007). Indeed, hypermethylation of PTEN promoterregions and, consequently, activation of PI3K/Akt areregularly observed in low�grade gliomas and secondaryglioblastomas, whereas it rarely occurs in primaryglioblastomas (Wiencke et al., 2007). Epigeneticchanges in PTEN expression play an important role inoligodendroglioma development (Kuo et al., 2009).The authors found that 21 tumors of the 49 examined

(43%) exhibited methylation in the PTEN promoterand it was associated with the lethality rate.

Another example of epigenetically modified genesinvolved in glioma progression is EMP3 gene (epithe�lial membrane protein 3). DNA�methylation of EMP3promoter presumably takes place at early stages of theastrocytoma development and is considered anadverse prognostic factor (Alaminos et al., 2005).EMP3 hypermethylation was registered in 80% of ana�plastic and diffuse astrocytomas and secondary glio�blastomas and only in 17% of primary glioblastomas(Kunitz et al., 2007).

Forty�three percent of primary glioblastomas havehypermethylated CpG islands in the TMS1/ASC geneengaged in the regulation of apoptosis, NF�κB activa�tion, and cytokine maturation. They are regarded asimportant features of gliomagenesis (Stone et al.,2004). DNA�methylation of TMS1/ASC is oftensimultaneous with DNA methylation of MGMT pro�moter (Martinez et al., 2007a). Thus, various epige�netic events operate together during glioma malignanttransformation.

The loss of MGMT expression produced by methy�lation of CpG islands was registered in 75% of second�ary and only 36% of primary glioblastomas (Naka�mura et al., 2001a; Blanc et al., 2004). The proteinencoded by this gene is engaged in DNA repair, and itsinhibition increases the risk of malignant transforma�tion. The majority (92%) of astrocytomas at earlystages with methylated MGMT contain TP53 muta�tions (versus 39% of astrocytomas without methylatedMGMT). Moreover, G:C substitutions for A:T in CpGsites of TP53 occur more frequently in astrocytomaswith methylated MGMT (58%) than without (11%)(Nakamura et al., 2001a). These findings show theinteraction of genetic and epigenetic changes in glio�mas. It is possible that TP53 mutations are the result ofMGMT epigenetic inactivation. Some researchersbelieve that epimutations precede genetic mutationsin the glioma pathogenesis (Gronbaek et al., 2007;Wiencke et al., 2007).

Epigenetic alterations (hypermethylation of pro�moter regions of certain genes) arising at the earlieststages of gliomagenesis may not only interact witheach other enhancing the adverse effect, but also mayfacilitate the appearance of novel genetic changes.

MODIFICATIONS OF THE “HISTONE CODE” IN GLIOMAS

Changes in the profile of histone posttranslationalmodifications are other molecular markers for gliomapathology. It has been showed that the total level ofhistone H3 acethylationin was enhanced in multiformglioblastomas (Lucio�Eterovic et al., 2008) mostly dueto aberrant expression of histone deacethylases.Expression of mRNA for histone deacethylasesclasses II (HDAC5, HDAC6, HDAC7, HDAC9 and



HDAC10) and IV (HDAC11) is significantly lower inglioblastomas than in the case of diffuse astrocytomasand normal brain�tissue cells (Lucio�Eterovic et al.,2008). Down�regulation of histone deacethylaseclass III SIRT2 was observed in malignant gliomas(Fraga and Esteller, 2007; Kanwal and Gupta, 2010;He et al., 2012). However, expression of histone deac�ethylase class I (HDAC2) is several times higher inmedulloblastomas than in normal brain cells (Rutka etal., 2009). Glioblastomas contain mutations of histonedeacethlases class I (HDAC2) and II (HDAC9) (Par�sons et al., 2008). Aberrant expression and/or muta�tions of genes encoding other histone�modifyingenzymes; histone demethylases JMJD1A andJMJD1B; and histone methytransferases SET7,SETD7, MLL, and MLL4 have been reported forhighly malignant gliomas (Parsons et al., 2008). Dif�fuse and anaplastic astrocytomas and glioblastomashaving an altered copy number of Bmi1 gene encodingthe protein (which is a member of Polycomb Repres�sive Complex) regulated H3K27 methylation (Häyryet al., 2008). Bmi1 deletion is associated with a badprognosis for patients with glioblastomas.

It has been noted that reduced PTEN expressioncorrelates with glioma malignancy (Sano et al., 1999;Zhou et al., 2003; Johnston et al., 2006; Yakut et al.,2007; Cecener et al., 2009). PTEN malfunctioningdue to mutations and epigenetic changes and pheno�typic alterations has been observed in 60–70% of mul�tiform glioblastomas (Johnston et al., 2006). Reducedor lost PTEN expression was found in most gliomas(more than 70%) even in low�grade tumors (degree Iand II) (Cecener et al., 2009). PTEN mutations arefrequently revealed in multiform glioblastomas butrarely (7% tumors) in low�graded gliomas (Ceceneret al., 2009). PTEN expression in gliomas is deter�mined with high probability by epigenetic mecha�nisms. We investigated PTEN transcription in gliomaprimary cultures employing epigenetic markers ofposttranslational H3 histone modifications: marker oftranscription inertness H3K9me3 and marker ofactively transcribed chromatin H3K4ac.

Using chromatin immunoprecipitation and PCRanalysis, we registered H3K9me3 modifications closeto sites of PTEN initiation transcription in most (sixout of seven) cell cultures. Deacetylation of H3 his�tone (lack of H3K4ac modification) was observed inthis PTEN region. These findings show that the tran�scription activity of PTEN oncogene is inhibited inmost gliomas by the epigenetic mechanism of a modi�fied “histone code” (Semenova et al., 2012).

As was mentioned above, DNA�methylation inMGMT gene promoter has been revealed in 70% ofsecondary gliomas (Nakamura et al., 2001a; Blancet al., 2004). Two epigenetic markers of transcriptioninertness were revealed in the promoter region ofMGMT gene: H3K9me2 and H3 histone deacethyla�tion. It is likely that several epigenetic mechanisms are

engaged in MGMT gene inactivation in glioblastomas(Nakagawachi et al., 2003). These epigenetic changesare considered adverse prognostic biomarkers, sincethe MGMT gene is involved in DNA repair and itsinactivation increases the number of mutations(Komine et al., 2003).

ABERRANT EXPRESSION OF MICRORNAIN GLIOMAS

Histone posttranslational modifications and meth�ylation of DNA promoter regions are currently con�sidered to be two classical epigenetic mechanisms ofthe regulation of the chromatin structure and geneexpression. Recently, it has been demonstrated thatnoncoding RNA molecules, microRNA (miRNA),are also involved in these processes in normal and can�cer cells and coordinate key cellular processes, such asdifferentiation, proliferation, and apoptosis (Bartel,2004). There is ample evidence pointing to impairedmiRNA expression in malignant cells (Calin andCroce, 2006, Esquela�Kerscher and Slack, 2006;Hammond, 2006).

Aberrant expression of miRNA was also registeredin malignant gliomas (Nicoloso, Calin, 2008). Hyper�expression of miR�221 is common for primary glio�blastoma, whereas miR�128, miR�181a, miR�181b,and miR�181c actively expressed in normal brain cellsare down�regulated (Ciafrè et al., 2005; Godlewskiet al., 2008). The miR�124 and miR�137 levels aredecreased in primary glioblastomas and anaplasticastrocytomas, which, presumably, indicates theironcosupressor function in these tumors (Silber et al.,2008). It is believed that these miRNA inhibit cell pro�liferation in glioblastomas. miR�124 expression is alsodecreased in medulloblastomas. The artificial increaseof their copy number in glioma cell lines decreasedCDK6 expression and inhibited cell proliferation(Pierson et al., 2008).

Noncoding RNA miR�21 displays antiapoptoticand proinvasive functions in gliomas (Chan et al.,2005; Nagarajan, Costello, 2009). Moreover, miR�21probably regulates genes engaged in cell migration(Gabriely et al., 2008). The level of miR�21 is signifi�cantly higher in glioblastomas and glioblastoma celllines than in normal brain cells. The inhibition ofmiR�21 in glioblastoma cell lines activated caspasesand resulted in apoptosis (Chan et al., 2005; Corstenet al., 2007).

As mentioned above, miR128 is down�regulated inprimary glioblastomas. miR�128 deficiency negativelyaffected the cell division. It has been proposed that, inthese tumors, miR�128 plays the role of an oncosu�pressor inhibiting the oncogene Bmi1 (Godlewskiet al., 2008).

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EPIGENETIC THERAPY

Epigenetic changes are very important for gliomamalignant transformation. It should be noted that theepigenetic changes mentioned in the review are com�mon not only for gliomagenesis, but for the develop�ment of various cancer types. Thereby, the investiga�tion of epigenetic mechanisms improves our knowl�edge of carcinogenesis as a whole, allows identifyingnovel epigenetic determinates in the glioma pathogen�esis and determining new molecular targets for drugtherapy. Analysis of epigenetic modifications is ofgreat practical interest, because the impairments, suchas DNA�methylation and modified “histone code,”unlike mutations, presumably are reversible (Jonesand Yoo, 2006). Theoretically, epimutations may beeliminated and genome normal functions restoredwith specific drugs and, probably, particular diets. Themain obstacle is our limited knowledge of specificmolecular targets. Recently, the search for potentialepigenetic markers of aberrant signaling in glioblasto�mas has been intensified to optimize current medicaltreatment and develop new therapeutic approach(Ohgaki and Kleihues, 2007). Much attention is paidto the search for inhibitors of histone deacethylasesand methyltransferases for reestablishing transcrip�tional activity of tumor�suppressor genes and genesencoding cell�cycle regulators (Minucci and Pelicci,2006; Yoo and Jones, 2006).

The following inhibitors of histone deacethylasesare the most promising for clinical practice: SAHA(vorinostat), TSA (Trichostatin A), butyrates (sodiumbutyrate, AN�9, VPA, valproic acid, and some otherderivates of butyric acid effective in non�toxic milli�molar doses) (Sawa et al., 2002; Haggarty et al., 2003;Ugur et al., 2007; Yin et al., 2007; Burgess et al., 2008;Egler et al., 2008; Guo et al., 2011). It has been pro�posed that inhibitors of histone deacethylases facilitatethe reexpression of genes epigenetically repressed inmalignant gliomas, resulting in irreversible cell�cyclearrest and apoptosis induction with DNA�damagedagents (Sathornsumetee et al., 2007). Although themechanisms of each particular inhibitor are not quiteclear, all of them result in a less condensed chromatinstructure, facilitating the access of DNA�damagedagents and increasing the sensitivity to radio� and che�motherapy. Normal cells are more resistant to inhibi�tors of histone deacethylases than are transformedcells (Qiu et al., 1999; Lee et al., 2010). Unfortunately,the reasons for this selective sensitivity are unknown.It has been proposed that the chromatin structure insites of epigenetically inactivated genes is more acces�sible to medical drugs. Thereby, the functions of thesegenes should recover more easily (with smaller dosesof drugs) that do genes that are transcriptionally inac�tive in accordance with the genetic program of thenormal cell functioning.

SAHA, a derivative of hydroxamic acid, has beensuccessfully used in vitro and in vivo. It is effective fortreatment of gliomas of various malignancies, includ�ing glioblastomas (Galanis et al., 1998; Ugur et al.,2007). The inhibitor blocks the cell�cycle transition,induces apoptosis, and inhibits tumor growth. How�ever, a molecular target for this inhibitor of histonedeacethylases has not yet been identified (Eyüpogluet al., 2005; Ugur et al., 2007; Yin et al., 2007).

Sodium butyrate, a short chain fatty acid salt, is aninhibitor of deacethlases classes I and II. Applicationof sodium butyrate together with other anticancerdrugs activates apoptosis and cell�cycle arrest inglioma cells (Haggarty et al., 2003; Kim et al., 2005;Guo et al., 2011). The strategy based on application ofsodium butyrate together with TRIAL in vitro resultsin up�regulation of p21 expression and decline in thecontent of such proteins as cyclin A and cyclin B andmajor caspase inhibitors XIAP and survivin (Kimet al., 2005). Increased transcription of the TP53 geneby sodium butyrate is considered the main factor thatcauses cell�cycle blocking in tumor cells (Bukreevaet al., 2009; Guo et al., 2011).

The novel inhibitor of histone deacetylases MS275promotes the activation of apoptosis in glioblastomacells increasing the cell sensibility to anticancer drugs(Bangert et al., 2011). Another novel inhibitor of his�tone deacetylases with antitumor activity is NBM�HD�1. Application of this drug in nontoxic millimolardoses in cell cultures (including glioma cells) signifi�cantly increases expression of TP53 and p21 genes(Huang et al., 2012).

In experiments on glioblastoma cell lines and labo�ratory animals, it was demonstrated that FK228induced apoptosis, suppressed cell proliferation andincreased expression of genes encoding the proteinsinvolved in the cell�cycle regulation, e.g., p21 (Sawaet al., 2004).

Inhibitors of histone methyltransferases and deme�thylases seem very promising for clinics, because theseenzymes possess superior selectivity compared to his�tone acethylases and may be more specific when inter�acting with strictly defined modifications of core his�tones. However, there are no reported data ontheir application for glioblastoma treatment. DZnep(S�adenosylhomocysteine hydrolase inhibitor 3�Dea�zaneplanocin A) may be regarded as a candidate. Pre�liminary data show that DZNep inhibits covalentbinding to histone H3 modification H3K27me3, anepigenetic marker of gene transcription and, there�fore, promotes the recovery of normal oncogeneexpression (Tan et al., 2007).

CONCLUSIONS

Analysis of epigenetic changes in the gene expres�sion is very important for understanding malignanttransformations, gliomagenesis in particular. Further



efforts should be concentrated on identification anddetailed description of various epigenetic changes thatresult in the development of particular oncologicaldiseases and the search of key molecular targets foreffective therapy. The knowledge gained will deter�mine if there is a successful treatment of this fatal dis�ease.

REFERENCES

Alaminos, M., Dävalos, V., Ropero, S., Setién, F.,Paz, M.F., Herranz, M., Fraga, M.F., Mora, J.,Cheung, N.K., Gerald, W.L., and Esteller, M., EMP3, amyelin�related gene located in the critical 19q13.3 region, isepigenetically silenced and exhibits features of a candidatetumor suppressor in glioma and neuroblastoma, CancerRes., 2005, vol. 65, pp. 2565–2571.

Alexiou, G.A. and Voulgaris, S., The role of the PTEN genein malignant gliomas, Neurol. Neurochir. Pol., 2010, vol. 44,pp. 80–86.

Amatya, V.J., Naumann, U., Weller, M., and Ohgaki, H.,TP53 promoter methylation in human gliomas, Acta Neuro�pathol., 2005, vol. 110, pp. 178–184.

Anguera, M.C., Sun, B.K., Xu, N., and Lee, J.T., X�chro�mosome kiss and tell: how the Xs go their separate ways,Cold Spring Harb. Symp. Quant. Biol., 2006, vol. 71,pp. 429–437.

Bachman, K.E., Park, B.H., Rhee, I., Rajagopalan, H.,Herman, J.G., Baylin, S.B., Kinzler, K.W., andVogelstein, B., Histone modifications and silencing prior toDNA methylation of a tumor suppressor gene, Cancer Cell,2003, vol. 3, pp. 89–95.

Baeza, N., Weller, M., Yonekawa, Y., Kleihues, P., andOhgaki, H., PTEN methylation and expression in glioblas�tomas, Acta Neuropathol., 2003, vol. 106, pp. 479–485.

Bangert, A., Häcker, S., Cristofanon, S., Debatin, K.M.,and Fulda, S., Chemosensitization of glioblastoma cells bythe histone deacetylase inhibitor MS275, Anticancer Drugs,2011, vol. 22, pp. 494–499.

Bannister, A.J. and Kouzarides, T., Regulation of chroma�tin by histone modifications, Cell Res., 2011, vol. 21,pp. 381–395.

Bartel, D.P., microRNAs: genomics, biogenesis, mecha�nism, and function, Cell, 2004, vol. 116, pp. 281–297.

Baylin, S. and Bestor, T.H., Altered methylation patterns incancer cell genomes: cause or consequence? Cancer Cell,2002, vol. 1, pp. 299–305.

Bello, M.J. and Rey, J.A., The p53/Mdm2/p14ARF cellcycle control pathway genes may be inactivated by geneticand epigenetic mechanisms in gliomas, Cancer Genet. Cyto�genet., 2006, vol. 164, pp. 172–173.

Berger, S.L., The complex language of chromatin regula�tion during transcription, Nature, 2007, vol. 447, pp. 407–412.

Bhaumik, S.R., Smith, E., and Shilatifard, A., Covalentmodifications of histones during development and diseasepathogenesis, Nat. Struct. Mol. Biol., 2007, vol. 14,pp. 1008–1016.

Biernat, W., Kleihues, P., Yonekawa, Y., and Ohgaki, H.,Amplification and overexpression of MDM2 in primary(de novo) glioblastomas, J. Neuropathol. Exp. Neurol., 1997,vol. 56, pp. 180–185.Bird, A., DNA methylation patterns and epigenetic mem�ory, Genes Dev., 2002, vol. 16, pp. 6–21.Blanc, J.L., Wager, M., Guilhot, J., Kusy, S., Bataille, B.,Chantereau, T., Lapierre, F., Larsen, C.J., and Karayan�Tapon, L., Correlation of clinical features and methylationstatus of MGMT gene promoter in glioblastomas, J. Neu�rooncol., 2004, vol. 68, pp. 275–283.Bukreeva, E.I., Aksenov, N.D., Bardin, A.A.,Pospelov, V.A., and Pospelova, T.V., Effect of histonedeacetylase inhibitor sodium butyrate (NaB) on transfor�mants E1A+cHa�Ras expressing wild type p53 with sup�pressed transactivation function, Cell Tiss. Biol., 2009,vol. 3, no. 5, pp. 445–453.Burgess, R., Jenkins, R., and Zhang, Z., Epigeneticchanges in gliomas, Cancer Biol. Ther., 2008, vol. 7,pp. 1326–1334.Cadieux, B., Ching, T.T., VandenBerg, S.R., andCostello, J.F., Genome�wide hypomethylation in humanglioblastomas associated with specific copy number alter�ation, methylenetetrahydrofolate reductase allele status,and increased proliferation, Cancer Res., 2006, vol. 66,pp. 8469–8476.Calin, G.A. and Croce, C.M., microRNA signatures inhuman cancers, Nat. Rev. Cancer., 2006, vol. 6, pp. 857–866.Cecener, G., Tunca, B., Egeli, U., Bekar, A., Guler, G.,Vatan, O., and Tolunay, S., Investigation of MMAC/PTENgene mutations and protein expression in low grade glio�mas, Cell Mol. Neurobiol., 2009, vol. 29, pp. 733–738.Chan, J.A., Krichevsky, A.M., and Kosik, K.S.,microRNA�21 is an antiapoptotic factor in human glioblas�toma cells, Cancer Res., 2005, vol. 65, pp. 6029–6033.Choe, G., Park, J.K., Jouben�Steele, L., Kremen, T.J.,Liau, L.M., Vinters, H.V., Cloughesy, T.F., andMischel, P.S., Active matrix metalloproteinase 9 expressionis associated with primary glioblastoma subtype, Clin. Can�cer Res., 2002, vol. 8, pp. 2894–2901.Ciafrè, S.A., Galardi, S., Mangiola, A., Ferracin, M.,Liu, C.G., Sabatino, G., Negrini, M., Maira, G.,Croce, C.M., and Farace, M.G., Extensive modulation of aset of microRNAs in primary glioblastoma, Biochem. Bio�phys. Res. Commun., 2005, vol. 334, pp. 1351–1358.Corsten, M.F., Miranda, R., Kasmieh, R., Krichevsky, A.M.,Weissleder, R., and Shah, K., MicroRNA�21 knockdowndisrupts glioma growth in vivo and displays synergistic cyto�toxicity with neural precursor cell delivered S�TRAIL inhuman gliomas, Cancer Res., 2007, vol. 67, pp. 8994–9000.Costa, F.F., Non�coding RNAs, epigenetics and complex�ity, Gene, 2008, vol. 410, pp. 9–17.Costello, J.F., Berger, M.S., Huang, H.S., andCavenee, W.K., Silencing of p16/CDKN2 expression inhuman gliomas by methylation and chromatin condensa�tion, Cancer Res., 1996, vol. 56, pp. 2405–2410.Egler, V., Korur, S., Failly, M., Boulay, J.L., Imber, R.,Lino, M.M., and Merlo, A., Histone deacetylase inhibitionand blockade of the glycolytic pathway synergistically

310


SEMENOVA, FILATOV

induce glioblastoma cell death, Clin. Cancer Res., 2008,vol. 14, pp. 3132–3140.Esquela�Kerscher, A., and Slack, F.J., Oncomirs—microRNAs with a role in cancer, Nat. Rev. Cancer, 2006,vol. 6, pp. 259–269.Eyüpoglu, I.Y., Hahnen, E., Buslei, R., Siebzehnrübl, F.A.,Savaskan, N.E., Lüders, M., Tränkle, C., Wick, W.,Weller, M., Fahlbusch, R., and Blümcke, I., Suberoylanil�ide hydroxamic acid (SAHA) has potent anti�glioma prop�erties in vitro, ex vivo and in vivo, J. Neurochem., 2005,vol. 93, pp. 992–999.Fanelli, M., Caprodossi, S., Ricci�Vitiani, L., Porcellini, A.,Tomassoni�Ardori, F., Amatori, S., Andreoni, F., Magnani, M.,De Maria, R., Santoni, A., Minucci, S., and Pelicci, P.G.,Loss of pericentromeric DNA methylation pattern inhuman glioblastoma is associated with altered DNA meth�yltransferases expression and involves the stem cell com�partment, Oncogene, 2008, vol. 27, pp. 358–365.Feinberg, A.P. and Tycko, B., The history of cancer epige�netics, Nat. Rev. Cancer, 2004, vol. 4, pp. 143–153.Feinberg, A.P., The epigenetics of cancer etiology, Semin.Cancer Biol., 2004, vol. 14, pp. 427–432.Fraga, M.F. and Esteller, M., Epigenetics and aging: thetargets and the marks, Trends Genet., 2007, vol. 23,pp. 413–418.Furuta, M., Weil, R.J., Vortmeyer, A.O., Huang, S., Lei, J.,Huang, T.N., Lee, Y.S., Bhowmick, D.A, Lubensky, I.A.,Oldfield, E.H., and Zhuang, Z., Protein patterns and pro�teins that identify subtypes of glioblastoma multiforme,Oncogene, 2004, vol. 23, pp. 6806–6814.Gabriely, G., Wurdinger, T., Kesari, S., Esau, C.C., Bur�chard, J., Linsley, P.S., and Krichevsky, A.M., microRNA21 promotes glioma invasion by targeting matrix metallo�proteinase regulators, Mol. Cell Biol., 2008, vol. 28,pp. 5369–5380.Galanis, E., Buckner, J.C., Burch, P.A., Schaefer, P.L.,Dinapoli, R.P., Novotny, P.J., Scheithauer, B.W.,Rowland, K.M., Vukov, A.M., Mailliard, J.A., andMorton, R.F., Phase II trial of nitrogen mustard, vincris�tine, and procarbazine in patients with recurrent glioma:north central cancer treatment group results, J. Clin. Oncol.,1998, vol. 16, pp. 2953–2958.Gama�Sosa, M.A., Slagel, V.A., Trewyn, R.W., Oxenhan�dler, R., Kuo, K.C., Gehrke, C.W., and Ehrlich, M., The5�methylcytosine content of DNA from human tumors,Nucleic Acids Res., 1983, vol. 11, pp. 6883–6894.Gartel, A.L. and Kandel, E.S., miRNAs: little knownmediators of oncogenesis, Semin. Cancer Biol., 2008,vol. 18, pp. 103–110.Godard, S., Getz, G., Delorenzi, M., Farmer, P., Koba�yashi, H., Desbaillets, I., Nozaki, M., Diserens, A.C.,Hamou, M.F., Dietrich, P.Y., Regli, L., Janzer, R.C.,Bucher, P., Stupp, R., de Tribolet, N., Domany, E., andHegi, M.E., Classification of human astrocytic gliomas onthe basis of gene expression: a correlated group of geneswith angiogenic activity emerges as a strong predictor ofsubtypes, Cancer Res., 2003, vol. 63, pp. 6613–6625.Godlewski, J., Nowicki, M.O., Bronisz, A., Williams, S.,Otsuki, A., Nuovo, G., Raychaudhury, A., Newton, H.B.,Chiocca, E.A., and Lawler, S., Targeting of the Bmi�1

oncogene/stem cell renewal factor by microRNA�128inhibits glioma proliferation and self�renewal, Cancer Res.,2008, vol. 68, pp. 9125–9130.Gonzalez, J. and de Groot, J., Combination therapy formalignant glioma based on PTEN status, Expert Rev. Anti�cancer Ther., 2008, vol. 8, pp. 1767–1779.Griffiths�Jones, S., Saini, H.K., van Dongen, S., andEnright, A.J., miRBase: tools for microRNA genomics,Nucleic Acids Res., 2008, vol. 36, pp. D154–D158.Gronbaek, K., Hother, C., and Jones, P.A., Epigeneticchanges in cancer, APMIS, 2007, vol. 115, pp. 1039–1059.Guo, H., Choudhury, Y., Yang, J., Chen, C., Tay, F.C.,Lim, T.M., and Wang, S., Antiglioma effects of combineduse of a baculovirual vector expressing wild�type p53 andsodium butyrate, J. Gene Med., 2011, vol. 13, pp. 26–36.Häyry, V., Tanner, M., Blom, T., Tynninen, O., Roselli, A.,Ollikainen, M., Sariola, H., Wartiovaara, K., and Nup�ponen, N.N., Copy number alterations of the polycombgene BMI1 in gliomas, Acta Neuropathol., 2008, vol. 116,pp. 97–102.Haggarty, S.J., Koeller, K.M., Wong, J.C., Grozinger, C.M.,and Schreiber, S.L., Domain�selective small�molecule inhib�itor of histone deacetylase 6 (HDAC6)�mediated tubulindeacetylation, Proc. Natl. Acad. Sci. USA, 2003, vol. 100,pp. 4389–4394.Hammond, S.M., microRNAs as oncogenes, Curr. Opin.Genet. Dev., 2006, vol. 16, pp. 4–9.He, L., He, X., Lowe, S.W., and Hannon, G.J., ÌicroRNAsjoin the p53 network—another piece in the tumour�sup�pression puzzle, Nat. Rev. Cancer, 2007, vol. 7, pp. 819–822.He, X., Nie, H., Hong, Y., Sheng, C., Xia, W., and Ying, W.,SIRT2 activity is required for the survival of C6 glioma cells,Biochem. Biophys. Res. Commun., 2012, vol. 417, pp. 468–472.Hegi, M.E., Diserens, A.C., Gorlia, T., Hamou, M.F.,de Tribolet, N., Weller, M., Kros, J.M., Hainfellner, J.A.,Mason, W., Mariani, L., Bromberg, J.E., Hau, P., Miri�manoff, R.O., Cairncross, J.G., Janzer, R.C., andStupp, R., MGMT gene silencing and benefit from temozo�lomide in glioblastoma, N. Engl. J. Med., 2005, vol. 352,pp. 997–1003.Huang, H.S., Nagane, M., Klingbeil, C.K., Lin, H., Nish�ikawa, R., Ji, X.D., Huang, C.M., Gill, G.N., Wiley, H.S.,and Cavenee, W.K., The enhanced tumorigenic activity of amutant epidermal growth factor receptor common inhuman cancers is mediated by threshold levels of constitu�tive tyrosine phosphorylation and unattenuated signaling, J.Biol. Chem., 1997, vol. 272, pp. 2927–2935.Huang, W.J., Liang, Y.C., Chuang, S.E., Chi, L.L.,Lee, C.Y., Lin, C.W., Chen, A.L., Huang, J.S., Chiu, C.J.,Lee, C.F., Huang, C.Y., and Chen, C.N., NBM�HD�1: anovel histone deacetylase inhibitor with anticancer activity,Evid. Based Complement. Alternat. Med., 2012, vol. 2012,pp. 781417–781428.Johnston, J.B., Navaratnam, S., Pitz, M.W., Maniate, J.M.,Wiechec, E., Baust, H., Gingerich, J., Skliris, G.P., Mur�phy, L.C., and Los, M., Targeting the EGFR pathway forcancer therapy, Curr. Med. Chem., 2006, vol. 13, pp. 483–492.



Jones, P.A. and Baylin, S.B., The fundamental role of epi�genetic events in cancer, Nat. Rev. Genet., 2002, vol. 3,pp. 415–428.Jones, P.A. and Yoo, C.B., Epigenetic therapy of cancer:past, present and future, Nat. Rev. Drug Discov., 2006,vol. 5, pp. 37–50.Kanwal, R. and Gupta, S., Epigenetics and cancer, J. Appl.Physiol., 2010, vol. 109, pp. 598–605.Kim, B., Myung, J.K., Seo, J.H., Park, C.K., Paek, S.H.,Kim, D.G., Jung, H.W., and Park, S.H., The clinicopatho�logic values of the molecules associated with the mainpathogenesis of the glioblastoma, J. Neurol. Sci., 2010,vol. 294, pp. 112–118.Kim, E.H., Kim, H.S., Kim, S.U., Noh, E.J., Lee, J.S.,and Choi, K.S., Sodium butyrate sensitizes human gliomacells to TRAIL�mediated apoptosis through inhibition ofCdc2 and the subsequent downregulation of surviving andXIAP, Oncogene, 2005, vol. 24, pp. 6877–6889.Knobbe, C.B., Merlo, A., and Reifenberger, G., Pten sig�naling in gliomas, Neuro�Oncol. 2002, vol. 4, pp. 196–211.Komine, C., Watanabe, T., Katayama, Y., Yoshino, A.,Yokoyama, T., and Fukushima, T., Promoter hypermethy�lation of the DNA repair gene O6�methylguanine�DNAmethyltransferase is an independent predictor of shortenedprogression free survival in patients with low�grade diffuseastrocytomas, Brain Pathol., 2003, vol. 13, pp. 176–184.Kouzarides, T., Chromatin modifications and their func�tion, Cell, 2007, vol. 128, pp. 693–705.Kunitz, A., Wolter, M., van den Boom, J., Felsberg, J.,Tews, B., Hahn, M., Benner, A., Sabel, M., Lichter, P.,Reifenberger, G., von, Deimling, A., and Hartmann, C.,DNA hypermethylation and aberrant expression of theEMP3 gene at 19q13.3 in human gliomas, Brain Pathol.,2007, vol. 17, pp. 363–370.Kuo, L.T., Kuo, K.T., Lee, M.J., Wei, C.C., Scaravilli, F.,Tsai, J.C., Tseng, H.M., Kuo, M.F., and Tu, Y.K., Correla�tion among pathology, genetic and epigenetic profiles andclinical outcome in oligodendroglial tumors, Int. J. Cancer,2009, vol. 124, pp. 2872–2879.Laird, P.W., Cancer epigenetics, Hum. Mol. Genet., 2005,vol. 14, spec. no. 1, pp. R65–R76.Lee, J.H., Choy, M.L., Ngo, L., Foster, S.S., andMarks, P.A., Histone deacetylase inhibitor induces DNAdamage, which normal but not transformed cells can repair,Proc. Natl. Acad. Sci. USA, 2010, vol. 107, pp. 14639–14644.Li, B., Carey, M., and Workman, J.L., The role of chroma�tin during transcription, Cell, 2007, vol. 128, pp. 707–719.Lim, L.P., Lau, N.C., Garrett�Engele, P., Grimson, A.,Schelter, J.M., Castle, J., Bartel, D.P., Linsley, P.S., andJohnson, J.M., Microarray analysis shows that somemicroRNAs downregulate large numbers of target mRNAs,Nature, 2005, vol. 433, pp. 769–773.Lucio�Eterovic, A.K., Cortez, M.A., Valera, E.T.,Motta, F.J., Queiroz, R.G., Machado, H.R., Car�lotti, C.G., Jr., Neder, L., Scrideli, C.A., and Tone, L.G.,Differential expression of 12 histone deacetylase (HDAC)genes in astrocytomas and normal brain tissue: class II andIV are hypoexpressed in glioblastomas, BMC Cancer, 2008,vol. 8, pp. 243–253.

Müller, I., Wischnewski, F., Pantel, K., and Schwarzen�bach, H., Promoter� and cell�specific epigenetic regulationof CD44, Cyclin D2, GLIPR1 and PTEN by methyl�CpGbinding proteins and histone modifications, BMC Cancer,2010, vol. 10, pp. 297.Maher, E.A., Furnari, F.B., Bachoo, R.M., Rowitch, D.H.,Louis, D.N., Cavenee, W.K., and DePinho, R.A., Malig�nant glioma: genetics and biology of a grave matter, GenesDev., 2001, vol. 15, pp. 1311–1333.Martinez, R., Schackert, G., and Esteller, M., Hypermeth�ylation of the proapoptotic gene TMS1/ASC: prognosticimportance in glioblastoma multiforme, J. Neurooncol.,2007b, vol. 82, pp. 133–139.Martinez, R., Setien, F., Voelter, C., Casado, S.,Quesada, M.P., Schackert, G., and Esteller, M., CpGisland promoter hypermethylation of the pro�apoptoticgene caspase�8 is a common hallmark of relapsed glioblas�toma multiforme, Carcinogenesis, 2007a, vol. 28, pp. 1264–1268.Minucci, S. and Pelicci, P.G., Histone deacetylase inhibi�tors and the promise of epigenetic (and more) treatmentsfor cancer, Nat. Rev. Cancer, 2006, vol. 6, pp. 38–51.Nagarajan, R.P. and Costello, J.F., Epigenetic mechanismsin glioblastoma multiforme, Semin. Cancer Biol., 2009,vol. 19, pp. 188–197.Nakagawachi, T., Soejima, H., Urano, T., Zhao, W.,Higashimoto, K., Satoh, Y., Matsukura, S., Kudo, S., Kita�jima, Y., Harada, H., Furukawa, K., Matsuzaki, H.,Emi, M., Nakabeppu, Y., Miyazaki, K., Sekiguchi, M., andMukai, T., Silencing effect of CpG island hypermethylationand histone modifications on O6�methylguanine�DNAmethyltransferase (MGMT) gene expression in human can�cer, Oncogene, 2003, vol. 22, pp. 8835–8844.Nakamura, M., Watanabe, T., Yonekawa, Y., Kleihues, P.,and Ohgaki, H., Promoter hypermethylation of the DNArepair gene MGMT in astrocytomas is frequently associatedwith G:C A:T mutations of the TP53 tumor suppressorgene, Carcinogenesis, 2001a, vol. 22, pp. 1715–1719.Nakamura, M., Yonekawa, Y., Kleihues, P., andOhgaki, H., Promoter hypermethylation of the RB1 gene inglioblastomas, Lab. Invest., 2001b, vol. 81, pp. 77–82.Navis, A.C., van den Eijnden, M., Schepens, J.T., Hooft,van Huijsduijnen, R., Wesseling, P., and Hendriks, W.J.,Protein tyrosine phosphatases in glioma biology, Acta Neu�ropathol., 2010, vol. 119, pp. 157–175.Nicoloso, M.S. and Calin, G.A., microRNA involvementin brain tumors: from bench to bedside, Brain Pathol., 2008,vol. 18, pp. 122–129.van Noesel, M.M., van Bezouw, S., Voute, P.A., Herman, J.G.,Pieters, R., and Versteeg, R., Clustering of hypermethylatedgenes in neuroblastoma, Genes Chromosomes Cancer, 2003,vol. 38, pp. 226–233.Ohgaki, H. and Kleihues, P., Genetic pathways to primaryand secondary glioblastoma, Am. J. Pathol., 2007, vol. 170,pp. 1445–1453.Ohgaki, H., Dessen, P., Jourde, B., Horstmann, S., Nishi�kawa, T., Di Patre, P.L., Burkhard, C., Schüler, D., Probst�Hensch, N.M., Maiorka, P.C., Baeza, N., Pisani, P., Yone�kawa, Y., Yasargil, M.G., Lütolf, U.M., and Kleihues, P.,Pathways to glioblastoma: a population based study on inci�

312


SEMENOVA, FILATOV

dence, survival rates, and genetic alterations, Cancer Res.2004, vol. 64, pp. 6892–6899.

Park, S.H., Jung, K.C., Ro, J.Y., Kang, G.H., andKhang, S.K., 5' CpG island methylation of p16 is associatedwith absence of p16 expression in glioblastomas, J. KoreanMed. Sci., 2000, vol. 15, pp. 555–559.

Parsons, D.W., Jones, S., Zhang, X., Lin, J.C., Leary, R.J.,Angenendt, P., Mankoo, P., Carter, H., Siu, I.M.,Gallia, G.L., Olivi, A., McLendon, R., Rasheed, B.A.,Keir, S., Nikolskaya, T., Nikolsky, Y., Busam, D.A., Tek�leab, H., Diaz, L.A., Jr., Hartigan, J., Smith, D.R., Straus�berg, R.L., Marie, S.K., Shinjo, S.M., Yan, H.,Riggins, G.J., Bigner, D.D., Karchin, R., Papadopoulos, N.,Parmigiani, G., Vogelstein, B., Velculescu, V.E., and Kin�zler, K.W., An integrated genomic analysis of human glio�blastoma multiforme, Science, 2008, vol. 321, pp. 1807–1812.

Pierson, J., Hostager, B., Fan, R., and Vibhakar, R., Regu�lation of cyclin dependent kinase 6 by microRNA 124 inmedulloblastoma, J. Neurooncol., 2008, vol. 90, pp. 1–7.

Qiu, L., Kelso, M.J., Hansen, C., West, M.L., Fairlie, D.P.,and Parsons, P.G., Anti�tumour activity in vitro and in vivoof selective differentiating agents containing hydroxamate,Br. J. Cancer, 1999, vol. 80, pp. 1252–1258.

Rutka, J.T., Kongkham, P., Northcott, P., Carlotti, C.,Guduk, M., Osawa, H., Moreno, O., Seol, H.J.,Restrepo, A., Weeks, A., Nagai, S., and Smith, C., Theevolution and application of techniques in molecular biol�ogy to human brain tumors: a 25 year perspective, J. Neu�rooncol., 2009, vol. 92, pp. 261–273.

Saito, Y. and Jones, P.A., Epigenetic activation of tumorsuppressor microRNAs in human cancer cells, Cell Cycle,2006, vol. 5, pp. 2220–2222.

Sano, T., Lin, H., Chen, X., Langford, L.A., Koul, D.,Bondy, M.L., Hess, K.R., Myers, J.N., Hong, Y.K.,Yung, W.K., and Steck, P.A., Differential expression ofMMAC/PTEN in glioblastoma multiforme: relationship tolocalization and prognosis, Cancer Res., 1999, vol. 59,pp. 1820–1824.

Sathornsumetee, S., Reardon, D.A., Desjardins, A.,Quinn, J.A., Vredenburgh, J.J., and Rich, J.N., Molecu�larly targeted therapy for malignant glioma, Cancer, 2007,vol. 110, pp. 13–24.

Sawa, H., Murakami, H., Kumagai, M., Nakasato, M.,Yamauchi, S., Matsuyama, N., Tamura, Y., Satone, A.,Ide, W., Hashimoto, I., and Kamada, H., Histone deacety�lase inhibitor, FK228, induces apoptosis and suppresses cellproliferation of human glioblastoma cells in vitro andin vivo, Acta Neuropathol., 2004, vol. 107, pp. 523–531.

Sawa, H., Murakami, H., Ohshima, Y., Murakami, M.,Yamazaki, I., Tamura, Y., Mima, T., Satone, A., Ide, W.,Hashimoto, I., and Kamada, H., Histone deacetylaseinhibitors such as sodium butyrate and trichostatin a inhibitvascular endothelial growth factor (VEGF) secretion fromhuman glioblastoma cells, Brain Tumor Pathol., 2002,vol. 19, pp. 77–81.

Semenova, E.V., Volnitsky, A.V., and Filatov, M.V., Histonecode and epigenetic regulation of the PTEN gene in malig�nant gliomas, Sib. Onkol. Zh., 2012, vol. 3, no. 51, pp. 74–78.

Silber, J., Lim, D.A., Petritsch, C., Persson, A.I.,Maunakea, A.K., Yu, M., Vandenberg, S.R., Ginzinger, D.G.,James, C.D., Costello, J.F., Bergers, G., Weiss, W.A., Alva�rez�Buylla, A., and Hodgson, J.G., miR�124 and miR�137inhibit proliferation of glioblastoma multiforme cells andinduce differentiation of brain tumor stem cells, BMC Med.,2008, vol. 6, p. 14.Somasundaram, K., Reddy, S.P., Vinnakota, K., Britto, R.,Subbarayan, M., Nambiar, S., Hebbar, A., Samuel, C.,Shetty, M., Sreepathi, H.K., Santosh, V., Hegde, A.S.,Hegde, S., Kondaiah, P., and Rao, M.R., Upregulation ofASCL1 and inhibition of notch signaling pathway charac�terize progressive astrocytoma, Oncogene, 2005, vol. 24,pp. 7073–7083.Stefani, G. and Slack, F.J., Small non�coding RNAs in ani�mal development, Nat. Rev. Mol. Cell Biol., 2008, vol. 9,pp. 219–230.Stewart, L.A., Chemotherapy in adult high�grade glioma: asystematic review and meta�analysis of individual patientdata from 12 randomised trials, Lancet. 2002, vol. 359,pp. 1011–1018.Stone, A.R., Bobo, W., Brat, D.J., Devi, N.S.,Van Meir, E.G., and Vertino, P.M., Aberrant methylationand down�regulation of TMS1/ASC in human glioblas�toma, Am. J. Pathol., 2004, vol. 165, pp. 1151–1161.Tan, J., Yang, X., Zhuang, L., Jiang, X., Chen, W.,Lee, P.L., Karuturi, R.K., Tan, P.B., Liu, E.T., and Yu, Q.,Pharmacologic disruption of polycomb�repressive complex2�mediated gene repression selectively induces apoptosis incancer cells, Genes Dev., 2007, vol. 21, pp. 1050–1063.Tunca, B., Bekar, A., Cecener, G., Egeli, U., Vatan, O.,Tolunay, S., Kocaeli, H., and Aksoy, K., Impact of novelPTEN mutations in turkish patients with glioblastoma mul�tiforme, J. Neurooncol., 2007, vol. 82, pp. 263–269.Turner, B.M., Reading signals on the nucleosome with anew nomenclature for modified histones, Nat. Struct. Mol.Biol., 2005, vol. 12, pp. 110–112.Ugur, H.C., Ramakrishna, N., Bello, L., Menon, L.G.,Kim, S.K., Black, P.M., and Carroll, R.S., Continuousintracranial administration of suberoylanilide hydroxamicacid (SAHA) inhibits tumor growth in an orthotopic gliomamodel, J. Neurooncol., 2007, vol. 83, pp. 267–275.Uhlmann, K., Rohde, K., Zeller, C., Szymas, J., Vogel, S.,Marczinek, K., Thiel, G., Nürnberg, P., and Laird, P.W.,Distinct methylation profiles of glioma subtypes, Int. J.Cancer., 2003, vol. 106, pp. 52–59.Villa, R., De Santis, F., Gutierrez, A., Minucci, S.,Pelicci, P.G., and Di Croce, L., Epigenetic gene silencingin acute promyelocytic leukemia, Biochem. Pharmacol.,2004, vol. 68, pp. 1247–1254.Waha, A., Güntner, S., Huang, T.H., Yan, P.S., Arslan, B.,Pietsch, T., Wiestler, O.D., and Waha, A., Epigeneticsilencing of the protocadherin family member PCDH�gamma�A11 in astrocytomas, Neoplasia, 2005, vol. 7,pp. 193–199.Watanabe, K., Tachibana, O., Sato, K., Yonekawa, Y.,Kleihues, P., and Ohgaki, H., Overexpression of the EGFreceptor and p53 mutations are mutually exclusive in theevolution of primary and secondary glioblastomas, BrainPathol., 1996, vol. 6, pp. 217–224.



Watanabe, T., Katayama, Y., Yoshino, A., Yachi, K.,Ohta, T., Ogino, A., Komine, C., and Fukushima, T., Aber�rant hypermethylation of p14ARF and O6�methylguanine�DNA methyltransferase genes in astrocytoma progression,Brain Pathol., 2007, vol. 17, pp. 5–10.Watanabe, T., Yokoo, H., Yokoo, M., Yonekawa, Y.,Kleihues, P., and Ohgaki, H., Concurrent inactivation ofRB1 and TP53 pathways in anaplastic oligodendrogliomas,J. Neuropathol. Exp. Neurol., 2001, vol. 60, pp. 1181–1189.Wiencke, J.K., Zheng, S., Jelluma, N., Tihan, T., Vanden�berg, S., Tamgüney, T., Baumber, R., Parsons, R., Lam�born, K.R., Berger, M.S., Wrensch, M.R., Haas�Kogan, D.A., and Stokoe, D., Methylation of the PTENpromoter defines low�grade gliomas and secondary glio�blastoma, Neuro Oncol., 2007, vol. 9, pp. 271–279.Yakut, T., Gutenberg, A., Bekar, A., Egeli, U., Gunawan, B.,Ercan, I., Tolunay, S., Doygun, M., and Schulten, H.J.,Correlation of chromosomal imbalances by comparativegenomic hybridization and expression of EGFR, PTEN,p53, and MIB�1 in diffuse gliomas, Oncol. Rep., 2007,vol. 17, pp. 1037–1043.Yin, D., Ong, J.M., Hu, J., Desmond, J.C., Kawamata, N.,Konda, B.M., Black, K.L., and Koeffler, H.P., Suberoyla�nilide hydroxamic acid, a histone deacetylase inhibitor:effects on gene expression and growth of glioma cells invitro and in vivo, Clin. Cancer. Res., 2007, vol. 13, pp. 1045–1052.

Yoo, C.B. and Jones, P.A., Epigenetic therapy of cancer:past, present and future, Nat. Rev. Drug Discov., 2006,vol. 5, pp. 37–50.

Yu, J., Zhang, H., Gu, J., Lin, S., Li, J., Lu, W., Wang, Y.,and Zhu, J., Methylation profiles of thirty four promoter�CpG islands and concordant methylation behaviours of six�teen genes that may contribute to carcinogenesis of astrocy�toma, BMC Cancer, 2004, vol. 4, p. 65.

Zardo, G., Tiirikainen, M.I., Hong, C., Misra, A., Feuer�stein, B.G., Volik, S., Collins, C.C., Lamborn, K.R., Bol�len, A., Pinkel, D., Albertson, D.G., and Costello, J.F.,Integrated genomic and epigenomic analyses pinpoint bial�lelic gene inactivation in tumors, Nat. Genet., 2002, vol. 32,pp. 453–458.

Zhou, H., Miki, R., Eeva, M., Fike, F.M., Seligson, D.,Yang, L., Yoshimura, A., Teitell, M.A., Jamieson, C.A., andCacalano, N.A., Reciprocal regulation of SOCS1 andSOCS3 enhances resistance to ionizing radiation in glio�blastoma multiforme, Clin. Cancer Res., 2007, vol. 13,pp. 2344–2353.

Zhou, Y.H., Tan, F., Hess, K.R., and Yung, W.K., Theexpression of PAX6, PTEN, vascular endothelial growthfactor, and epidermal growth factor receptor in gliomas:relationship to tumor grade and survival, Clin. Cancer Res.,2003, vol. 9, pp. 3369–3375.

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Genetic and epigenetic markers of gliomas