The most common chromosomal abnormality in diffuse astrocytomas of WHO grade II is trisomy 7 or at least a gain of 7q, which has been detected by comparative genomic hybridization in 50% of the cases [5, 6]. However, the relevant target genes on chromosome 7 have not yet been identified. Further chromosomal aberrations comprise losses on 22q, 19q, 13q, 10p, 6 and the sex chromosomes as well as gains on 5p, 9 and 19p [7].

The most common molecular alterations are mutations of the TP53 tumor suppressor gene at 17q13.1 in about 60% of cases as well as the just recently identified codon 132 mutations of the isocitrate dehydrogenase 1 (IDH1) gene in about 70% of diffuse astrocytomas [8–10] (Figure 1).

Even higher frequencies of TP53 mutations of up to 80% are detectable in the gemistocytic astrocytoma variant [11]. TP53 mutations are regarded as one of the earliest events in the tumorigenesis of diffuse astrocytomas, since in most cases they are already present in the first biopsy and their frequency does not increase in recurrences. TP53 mutations in diffuse astrocytomas are commonly associated with loss of heterozygosity (LOH) at polymorphic loci on 17p resulting in complete loss of wild-type p53 in the tumor cells.

In tumors without TP53 alterations, the p14^ARF gene at 9p21, the gene product of which regulates MDM2-mediated degradation of p53, is frequently methylated and transcriptionally downregulated [12]. Other genes that are frequently epigenetically silenced in diffuse astrocytomas include the MGMT gene at 10q26 [12], the protocadherin-gamma subfamily A11 (PCDH-gamma-A11) gene at 5q31 [13], and the EMP3 gene at 19q13 [14]. Interestingly, MGMT hypermethylation was found to be associated with TP53 mutation but is mutually exclusive to p14^ARF hypermethylation [12].

Another common alteration in diffuse astrocytomas is overexpression of the platelet-derived growth factor receptor alpha (PDGFRA) and its ligand PDGFalpha [15]; PDGFRA amplification, however, is restricted to a small subset of high-grade gliomas, in particular glioblastomas [16] (Figure 1).

Anaplastic astrocytomas show gains of chromosome 7 and TP53 mutations as well as IDH1 mutations at a similar frequency as diffuse astrocytomas. In addition, these tumors bear frequent allelic losses on chromosomes 6, 9p, 11p, 19q and 22q. The CDKN2A, p14^ARF and CDKN2B tumor suppressor genes are important targets for genetic and or epigenetic inactivation, with inactivation of p14^ARF serving as an alternative means to impair the p53 pathway in cases without TP53 mutations [8]. The gene products of CDKN2A, i.e. p16^INK4a, and CDKN2B, i.e. p15^INK4b, function as negative regulators of the cell cycle at the G1/S-phase transition by inhibiting the formation of complexes between D-type cyclins and the cyclin dependent kinases Cdk4 or Cdk6. The CDK4 gene at 12q13–q14 is amplified and overexpressed in about 10% of anaplastic astrocytomas [17], preferentially in tumors without CDKN2A deletion or mutation [18, 19].

In addition, about 25% of anaplastic astrocytomas carry mutations in the retinoblastoma gene (RB1) [18] (Figure 1). In contrast to glioblastomas, allelic losses on 10q and mutation of the PTEN tumor suppressor gene on 10q23 are rare in anaplastic astrocytomas (<10% of cases). However, when present, PTEN mutation indicates a poor prognosis [20].

Glioblastomas usually carry multiple chromosomal and genetic aberrations. In addition to the above listed aberrations found in diffuse and anaplastic astrocytomas, glioblastomas typically exhibit loss of genetic material from chromosome 10. Interestingly, molecular genetic analyses over the past years have shed light on two different genetic pathways in glioblastoma formation establishing the concept of primary and secondary glioblastomas [21] (Figure 1). Primary glioblastomas arise de novo without the clinical history of a lower grade precursor lesion. Primary glioblastomas exhibit frequent EGFR amplification, homozygous deletion of CDKN2A and p14^ARF, CDK4 amplification, MDM2 or MDM4 amplification, RB1 mutation/homozygous deletion, monosomy 10 and PTEN mutation [21–25]. EGFR amplification is particularly frequent in primary glioblastomas with a small cell, highly anaplastic histological phenotype [26]. TP53 mutation is found in less than 30% of primary glioblastomas. In contrast, secondary glioblastomas arise from a lower-grade precursor lesion and carry TP53 and IDH1 mutations in more than two thirds of the cases [10, 21]. Also, allelic losses on 19q and 13q, promoter hypermethylation of the RB1 gene, and overexpression of PDGFRA are more common in secondary glioblastomas [21, 22, 27]. Amplification of EGFR or MDM2, PTEN mutation as well as homozygous CDKN2A or p14^ARF deletions are all rare in secondary glioblastomas. Also epigenetic silencing of various genes has been described as overrepresented in either primary (NDRG2) or secondary (MGMT and EMP3) glioblastomas [21, 28, 29]. Taken together, these data clearly indicate that primary and secondary glioblastomas represent genetically different disease entities (Figure 1). Nevertheless, both entities share comparable histological features and an equally poor prognosis. The fact that the different molecular alterations converge on the same downstream cellular pathways, namely the p53, pRb1, PTEN/PI3K/AKT and mitogen-activated protein kinase pathways, and thereby lead to similar functional consequences, may explain this phenomenon [7, 30, 31].

Giant cell glioblastomas carry TP53 mutations in up to 90% and PTEN mutations in 30–40% of cases, thus combining molecular features of both primary and secondary glioblastoma. EGFR amplification and homozygous deletions of CDKN2A and p14^ARF are usually absent [36, 37].

The molecular genetics of gliosarcoma is fairly similar to that of primary glioblastoma, except for EGFR amplification, which seems to be less frequent [38]. Microdissection of the gliomatous and sarcomatous tumor components followed by CGH analysis revealed common genetic aberrations in both components, thus arguing for a monoclonal origin of both histological aspects of gliosarcomas [39].

Rare glioblastomas may exhibit metaplastic histologic features with adenoid or squamous cell epithelial differentiation, bone or cartilage formation as well as xanthomatous or adipocytic changes. However, none of these alterations are as yet known to be reflected by distinct alterations on the molecular level [40–44].

In pilocytic astrocytomas molecular and cytogenetic investigations have identified far less chromosomal and genetic alterations than in the diffusely infiltrating astrocytomas described above. Chromosomal comparative genomic hybridization (CGH) studies in 48 pilocytic astrocytomas revealed chromosomal imbalances only in a small subgroup of seven neoplasms [45] with gain of 9q34.1-qter constituting the most common abnormality. Recurrent trisomies of chromosomes 5 and chromosome 7 have been reported in another study employing array-CGH on 53 pilocytic astrocytomas [46] (Figure 2).

In patients with neurofibromatosis type 1 (NF1) pilocytic astrocytomas are the most common gliomas. In this setting, pilocytic astrocytomas are typically located in the optic nerve, often bilaterally, and carry allelic losses at the NF1 tumor suppressor gene locus at 17q11.2 [47]. Sporadic pilocytic astrocytomas, in contrast, rarely demonstrate allelic loss at the NF1 locus [47]. Furthermore, neither NF1 mutations nor loss of NF1 mRNA expression were found in sporadic pilocytic astrocytomas [48]. Losses on 17p and mutations in the TP53 tumor suppressor genes that are observed in diffuse astrocytomas are not a common feature in pilocytic astrocytomas [47, 49, 50]. In contrast, circumscribed duplication of the BRAF gene at 7q34 resulting in increased BRAF expression has been identified as a common aberration [46, 51–53]. BRAF duplication results in an in-frame fusion gene incorporating the kinase domain of the BRAF oncogene with constitutive BRAF kinase activity. A small subset of tumors alternatively carries activating BRAF mutations, thus implicating this gene as an important proto-oncogene in these tumors (Figure 2).

Recently, the pilomyxoid astrocytoma has been recognized as a histologically and clinically distinct variant of pilocytic astrocytoma with a less favorable prognosis [54]. Local recurrences as well as cerebrospinal spread occur more often in pilomyxoid tumors than in pilocytic astrocytomas. The WHO classification thus assigns these tumors to WHO grade II. Data on whether the histological and prognostic differences between pilocytic and pilomyxoid astrocytomas are also reflected by different genetic alterations at the molecular level are still scarce. A recent study employing gene expression profiling of NF1-associated and sporadic pilocytic and pilomyxoid astrocytomas identified aldehyde dehydrogenase 1 family member L1 (ALDH1L1) as an underexpressed candidate biomarker in more aggressive tumor subtypes [55].

Loss on chromosome 9 is the most common genomic imbalance in pleomorphic xanthoastrocytoma (PXA), which is detectable by CGH analysis in 50% of cases. Other losses affect chromosomes 17 (10%), 8, 18 and 22 (4% each). Chromosomal gains could be identified on chromosomes X (16%), 7, 9q, 20 (8% each), 4, 5 and 19 (4% each) [56].

TP53 mutations are seen in a small fraction of tumors (<10% of cases), while 1p/19q losses as well as amplification of EGFR, CDK4 and MDM2 are absent [57, 58]. In contrast, homozygous deletion of the tumor suppressor genes CDKN2A, p14^ARF and CDKN2B on 9p21.3 is common in PXA [56]. Interestingly, transcript levels of the TSC1 gene on 9q were found to be consistently low in PXA; however, the causative mechanism still remains unclear, as there was no evidence for TSC1 mutations or promoter methylation [56].

Biallelic inactivation of either the TSC1 or the TSC2 tumor suppressor gene is a hallmark for these tumors [59]. Since the corresponding gene products have an inhibitory function on the mTOR pathway, their mutational inactivation leads to aberrant activation of mTOR signaling, which in turn represents an interesting novel target for specific pharmacologic inhibition. A comparative genomic hybridization study on subependymal giant cell astrocytomas indicated that chromosomal imbalances are either rare or completely absent [40].

Despite extensive research efforts, oligodendroglioma-specific immunohistochemical markers could not yet be identified [60–62]. However, the most characteristic genetic feature of oligodendroglial tumors is the combined loss of alleles on 1p and 19q, which may be detected in up to two thirds of the cases [63] (Figure 3).

Two independent studies reported that an unbalanced t(1;19)(q10;p10) translocation, with the chromosomal breakpoints located close to the centromers of both chromosomes, serves as the cytogenetic mechanism responsible for the frequent co-deletions of both chromosome arms in oligodendrogliomas [64, 65]. The oligodendroglioma-associated tumor suppressor genes on 1p and 19q, however, have not yet been identified. Recent studies indicate that more than one gene from 1p may be aberrant in oligodendrogliomas. The NOTCH2 gene maps closest to the breakpoint region on 1p13–p11 and may function as a putative oligodendroglioma-associated tumor suppressor gene considering that intragenic homozygous deletions have been found in two tumors [66]. But also a number of other candidate tumor suppressor genes from different regions on 1p have been proposed, including TP73 (1p36.3), the calmodulin-binding transcription activator 1 gene (CAMTA1, 1p36), the DNA fragmentation factor subunit ß gene (DFFB, 1p36), SHREW1 (1p36.32), CITED4 (1p34.2), RAD54 (1p32), CDKN2C (1p32), and DIRAS3 (1p31) [67–73]. Candidate tumor suppressor genes on 19q include the p190RhoGAP gene at 19q13.3 [74], the myelin-related epithelial membrane protein gene 3 (EMP3) at 19q13.3 [75], ZNF342, a zinc-finger transcription factor gene at 19q13 [76], and the maternally imprinted PEG3 gene at 19q13.4 [77].

In addition to 1p/19q deletions, several other genetic and epigenetic alterations have been described in oligodendrogliomas (Figure 3). Less frequent cytogenetic alterations are gains on chromosomes 7 and 19p as well as losses on chromosomes 4, 6, 9p, 10q, 11p, 14, 18q, and 22q [71, 78]. Some of these chromosomal imbalances have been suggested as being linked to poor outcome, including gain of 7p and 8q as well as losses on 9p and 18q [79]. Both oligodendrogliomas of WHO grade II as well as anaplastic oligodendrogliomas (WHO grade III) share the high frequency of IDH1 mutations (~70%) with astrocytic gliomas [9]. Allelic losses on 17p and TP53 gene mutations are rare in low-grade oligodendrogliomas as they are mutually exclusive to the frequent 1p/19q losses. Nevertheless functional inactivation of the p53 pathway in oligodendrogliomas may be achieved by means of epigenetic silencing of the p14^ARF gene, which thereby loses its ability to bind Mdm2 and to prevent the Mdm2-mediated degradation of p53 [80, 81].

Other genes hypermethylated in oligodendrogliomas include the tumor suppressors CDKN2A, CDKN2B and RB1, as well as DAPK1 (death-associated protein kinase 1), ESR1 (estrogen receptor 1), THBS (thrombospondin 1) and TIMP3 (tissue inhibitor of metalloproteinase 3) [81–83]. Frequent promoter hypermethylation and reduced expression of the MGMT gene in oligodendrogliomas and consecutive impairment of MGMT-mediated DNA repair might in part contribute to the chemosensitivity of these neoplasms [84, 85].

Finally, oligodendrogliomas frequently demonstrate increased expression of growth factor receptors, such as EGFR and PDGFR [71, 86]. Platelet-derived growth factors A and B, as well as the corresponding receptors (PDGFR-alpha and PDGFR-beta) have been reported as constantly co-expressed in oligodendrogliomas suggesting an auto- and/or paracrine growth stimulatory activity of this signaling pathway [86] (Figure 3).

Malignant progression of oligodendroglial tumors is associated with the accumulation of multiple genetic abnormalities. Anaplastic oligodendrogliomas share the frequent loss of alleles on 1p and 19q with low-grade oligodendrogliomas, but additionally show frequent deletions on 9p and/or on chromosome 10 [87–89] (Figure 3). On 9p21, the tumor suppressor genes CDKN2A, p14^ARF and CDKN2B are homozygously deleted in up to one third of anaplastic oligodendrogliomas [71, 78]. Such deletions are particularly common in anaplastic oligodendrogliomas without 1p and 19q losses, but may also be present in 1p/19q-deleted cases. PTEN mutations occur in only about half of the cases with 10q loss, suggesting that there might be another progression-related target gene in this region [88, 89]. PTEN mutations and 10q deletions are more common in anaplastic oligodendrogliomas without 1p and 19q losses. Rare anaplastic oligodendrogliomas carry activating mutations in the PIK3CA gene [90].

Comparative genomic hybridization studies have uncovered that chromosomal imbalances on several other chromosomes occur at more than random frequency in anaplastic oligodendrogliomas, most notably losses on chromosomes 4, 6, 11, 13q, 18 and 22q as well as gains on chromosomes 7, 15 and 20 [71, 78]. Gene amplifications affecting the EGFR, PDGFRA, CDK4, MDM4, MYC or MYCN are uncommon (generally <10%) [71, 78].

Oligoastrocytomas are histologically mixed glial neoplasms with oligodendroglial as well as astrocytic features. The oligodendroglial and astroglial tumor components may either be diffusely intermingled or separated into distinct tumor areas. Genetic alterations that would separate oligoastrocytomas from oligodendrogliomas on the one hand and diffuse astrocytomas on the other hand have not been detected. Roughly half of the oligoastrocytomas show allelic losses on 1p and 19q [71]. While in one study these aberrations were identical in oligodendroglial and astrocytic tumor parts, indicating a monoclonal origin of oligoastrocytomas, other authors reported genetically distinct astrocytic and oligodendroglial components in a subset of oligoastrocytomas [99, 100]. About 30% of oligoastrocytomas carry genetic aberrations typical for diffuse astrocytomas, i.e. TP53 mutation and loss of heterozygosity on 17p [71]. Those oligoastrocytomas with TP53 mutation and 17p loss do not have LOH on 1p and 19q, and vice versa. Taken together, these data indicate that oligoastrocytomas are genetically heterogeneous with one subset being genetically related to oligodendrogliomas and another subset corresponding genetically to diffuse astrocytomas (Figure 4).

Oligoastrocytomas that are histologically highly anaplastic and contain areas of necrosis are referred to as “glioblastomas with oligodendroglial component, WHO grade IV”. While rare in classic glioblastomas (less than 10% of the cases), 1p/19q deletions may be more common in glioblastomas with an oligodendroglial component, which in part may account for the better survival associated with this particular glioblastoma subgroup [101].

The most common cytogenetic aberrations in ependymomas are losses of chromosomes 6q, 10, 13, 14, and 22q, as well as gains of chromosomes 1q, 7, 9, 12q, 15q, and 18. Recent studies using CGH analysis reported on distinct patterns of chromosomal aberrations being linked to certain clinical and pathological features of ependymomas, such as patient age, tumor location, and histological subtype or WHO grade [102–106]. Losses on 22q and gains of chromosome 4 were more common in adult tumors [105]. Gains on 1q correlated with the presence of structural chromosomal aberrations, pediatric age, high-grade histology and aggressive clinical behavior [102, 103, 105]. While spinal intramedullary ependymomas preferentially demonstrated losses of chromosomes 22q and 14q as well as gains on chromosomes 7q, 9p and 16, intracranial ependymomas frequently carried gains of 1q and losses on 6q (Figure 5). The distinct genetic profiles associated with tumor location were also reflected in regionally different mRNA expression signatures. Supratentorial ependymomas, for example, expressed elevated levels of members of the EPHB-EPHRIN and NOTCH families, whereas spinal ependymomas showed up-regulated expression of multiple HOX gene family members [106].

Molecular genetic studies on selected candidate genes revealed frequent NF2 gene mutations in intramedullary spinal ependymomas, while deletions of the CDKN2A gene were frequent in intracranial supratentorial ependymomas but rare in ependymomas from other locations [106] (Figure 5). Mutations in the TP53, PTEN and INI1 tumor suppressor genes are not a common feature in ependymomas [107–109]. The tumors suppressor genes RASSF1, CDKN2A, CDKN2B, p14^ARF and TP73, as well as other genes potentially involved in the tumorigenesis of ependymomas, such as CASP1, MGMT, TIMP3 and THBS1 are epigenetically silenced by aberrant promoter methylation in subsets of ependymomas [110, 111]. As in other gliomas, growth factor receptors, such as EGFR and the related ERBB2 and ERBB4 receptors, are commonly upregulated in ependymal tumors; amplifications of the respective genes, however, do not usually occur in low-grade ependymomas [105, 112].

The molecular changes observed in anaplastic ependymomas are fairly similar to those observed in their low-grade counterparts. Though to a certain extent malignant progression in ependymomas may occur, only few molecular changes have been pinpointed that are more or less exclusively associated with a high-grade ependymoma phenotype. In an analysis of 23 anaplastic ependymomas, loss of chromosome arm 10q appeared overrepresented [107]. Also, gain of 1q, with DUSP12 on 1q23 as a potential target gene [105], as well as losses of 9 and 13 were associated with WHO grade III lesions [113] (Figure 5). In regard to tumor location, mRNA expression analysis distinguished between supratentorial WHO grade II and III tumors. In contrast, infratentorial ependymomas could not that easily be graded by their mRNA expression profiles, suggesting that in this location WHO grade III tumors differ by relatively few genetic changes from WHO grade II tumors [114].

In spite of their benign clinical behavior, myxopapillary ependymomas are often aneuploid or tetraploid and carry numerous chromosomal imbalances, as determined by CGH analysis. In fact, the average number of chromosomal aberrations per tumor is considerably higher than that in ependymomas and anaplastic ependymomas [115]. The most common imbalances are concurrent gains of chromosomes 9 and 18 [116]. Additional recurrent alterations include gains of chromosomes 3, 4, 7, 8, 11, 13, 17q, 20 and X, as well as losses of chromosomes 10 and 22. Also, cDNA profiles with high expression levels of HOXB5, PLA2G5 and ITH2 in myxopapillary ependymomas clearly differed from those in intracranial ependymomas [114], thus indicating that myxopapillary ependymomas are molecularly distinct from other ependymal tumors.

Molecular genetic data on subependymomas are scarce. Cytogenetic investigation of two tumors revealed no structural or numerical abnormalities [117]. Individual cases studied for allelic losses on chromosome arms 10q and 22q, as well as for mutations in the hSNF5/INI1, NF2 and PTEN genes also did not show any aberrations [117].