Gliomas are the most common primary brain tumor in adults (incidence 5.97 per 100,000, CBTRUS statistical report 2010, http://www.cbtrus.org/) and can be subdivided based on their histological appearance into an astrocytic (A), oligodendroglial (OD), or oligoastrocytic (OA) lineage. They can be further subclassified into grades: I (pilocytic astrocytomas, PA), II (low grade), III (anaplastic) and IV (glioblastoma, GBM), depending on the number of malignant features present (high cellularity, nuclear atypia, mitosis, necrosis, and endothelial proliferation). Secondary GBMs are those that have progressed from lower grade gliomas, whereas primary GBMs arise de novo.

The prognosis of glioma patients varies between the different histological subtypes and grades; for example, patients with grade II OD have the longest survival (median survival 11.5 years) whereas patients with a glioblastoma (the most common subtype of glioma) have a median survival of only 4.9 months [1]. Pilocytic astrocytomas are the only subtype of glioma with a favorable prognosis (94–96% five year survival) (CBTRUS statistical report 2010; [1]).

Current treatment options involve a combination of surgical resection, radiotherapy and chemotherapy. Complete surgical resection of gliomas is virtually impossible due to their invasive growth pattern. Radiotherapy is effective. However, the infiltrating cells can only be reached by whole brain irradiation where the benefits of radiotherapy may not outweigh the side effects caused by radiation damage. Temozolomide has thusfar proven effective in improving the median overall survival in glioblastoma by three months [2], and is most effective in those in which the MGMT promoter is hypermethylated [3]. Adjuvant procarbazine, CCNU (lomustine) and vincristine (PCV) improved progression free survival but not overall survival in anaplastic oligodendrogliomas and oligoastrocytomas [4,5]. In these studies, tumors harboring loss of 1p and 19q chromosomal arms comprise a favorable subgroup. In spite of these advances, the prognosis of gliomas remains poor and therefore other strategies have to be developed. A better understanding of the genes (and their associated molecular pathways) involved in gliomagenesis and/or progression may reveal new options for targeted therapy.

The Cancer Genome Atlas project has published mRNA expression data and DNA copy number alteration data of 206 GBMs and has sequenced >600 genes in 91 GBMs [6]. The project is still ongoing and ultimately aims to include data from 500 gliomas, but already has shown the importance of a systematical approach and high sample numbers. Combining all detected homozygous deletions, focal amplifications and validated somatic nucleotide substitutions, they found three major pathways affected in a high percentage of glioblastomas: receptor tyrosine kinase signaling (altered in 88% of the GBMs), TP53 signaling (altered in 87%) and the pRB tumor suppressor pathway (altered in 78%). Novel genes in those pathways include the NF1 tumor suppressor gene and PIK3R1. Another large study on 22 GBMs sequenced all protein coding genes and performed copy number analysis and expression data analysis on these tumors [7]. All genes affected in more than two tumors were validated in a set of 80 GBMs. Besides confirmation of affected oncogenes and tumor suppressor genes in the formerly mentioned three pathways (50%, 64% and 68%, respectively) (see Scheme 1 and Table 1), they found the IDH1 gene to be mutated in 12% of the GBMs [7]. These mutations occurred in younger patients with mostly secondary GBMs and such tumors had a relatively favorable prognosis [7,8]. (For a more elaborate discussion on IDH1 see below).

In general, only few frequent genetic changes have been identified in lower grade gliomas (Table 1). Larger chromosomal aberrations include combined loss of 1p19q in grade II and III oligodendroglioma (40–69%) and oligoastrocytoma (44–48%). Such losses are far less common in astrocytoma (0–11%) [1,26,27]. The remarkably high frequency of LOH of 1p and 19q suggests the remaining arms harbor yet to be identified tumor suppressor genes (Knudson two-hit hypothesis [28]). Frequent mutations have been identified in IDH1 (all grade II and III gliomas, see below) and TP53 genes (predominantly astrocytic). TP53 mutations and LOH of 1p 19q are mutually exclusive [1], thereby distinguishing two different pathways of glioma development. Complete hemizygous losses of 1p are tightly associated with 19q loss and oligodendroglial phenotype and predict longer overall and progression free survival [29]. However, partial 1p deletions are mainly observed in astrocytic tumors, are not associated with 19q loss and have a negative prognostic value [29].

Based on these genetic changes, three large groups can be genetically characterized in low grade and anaplastic gliomas: tumors with TP53 mutations and IDH1/2 mutations (32%), tumors with LOH 1p19q and IDH1/2 mutations (37%) and tumors with only IDH1/2 mutations (17%) [30]. These molecular changes segregate with the distinct histological subgroups of glioma: for example, most of the diffuse astrocytoma have TP53 and IDH1/2 mutation and most of the oligodendrogliomas have LOH 1p19q and IDH1/2 mutation. The oligoastrocytomas were more equally distributed among the three different groups (33%, 34% and 19% respectively) [30].

The majority of pilocytic astrocytomas are cytogenetically normal [41] except for a small tandem dulication of 2 Mb at 7q34 (66%) [42]. This duplication results in a fusion gene incorporating the kinase domain of BRAF to KIAA1549 (exon 1-16/15) [42]. This fusion gene produces a constitutively active BRAF, which is able to transform NIH3T3 cells [42]. Activating BRAF point mutations (V600E/ins 3 bp at 598) can also occur in pilocytic astrocytoma [42,43].

Current classification of gliomas is largely based on histological appearance. However, histological classification of gliomas is troublesome and subject to interobserver-variation [44-47]. Gliomas may also be classified based on their similarities in gene expression profiles [48-50]. Such classification correlates better with survival than histological classification of gliomas [48]. Distinct genetic changes also segregate into the different molecular subtypes of glioma [48,50]. For example, EGFR amplifications are predominantly found in classical and neural subtypes [50] or in cluster 18 gliomas [48]. IDH1 mutations segregate in proneural type GBMs [50] or in gliomas containing predominantly secondary GBMs (Cluster 22) as well as in gliomas with more favorable prognosis (Clusters 9 and 17) [48].

Methylation in cancer often occurs in the promoter regions of tumor suppressor genes [51,52]. Inactivation of gene expression by promoter methylation thus contributes to tumor formation as the second “hit” in tumor suppressor genes (Knudson's two-hit hypothesis [28]). Several groups have therefore performed genome wide methylation profiling in GBMs and have identified a subset of tumors that have more favorable prognosis [40,53]. These tumors show an overall increase in DNA methylation at CpG sites (CIMP; CpG island methylator phenotype) [40]. It remains to be determined whether reversal of CIMP status can be used as a treatment for gliomas.

Large scale sequencing efforts, such as those described in this review, have revealed an unprecedented insight into the biology of gliomas. The rapid development of novel sequencing techniques will lead to even more genetic data in the next decade. It can therefore be expected that virtually all genetic changes in all glioma subtypes will be identified in the near future. However, not all genetic changes in gliomas (or other tumors) are causal for the disease; mutations can arise during cell division and are then found throughout the tumor due to clonal expansion [54]. In fact, the majority of somatic mutations in cancer may be such “passenger” mutations [54]. Distinguishing such “passenger” mutations from the causal “driver” mutations is therefore required.

One way to distinguish driver from passenger mutations is by frequency analysis: causal genetic changes are thought to occur at a higher incidence than predicted by chance. However, few genetic changes are recurrent events (so-called “mountains” in the genomic landscape of [55]); only a handful of genes are mutated at frequencies >10% not only in gliomas [6,7,54] but also in many other cancer types [56,57]. These studies show that many more genes are mutated at low frequencies (so-called “hills”). Such infrequent candidates have been demonstrated to contribute to tumor formation and/or progression (see e.g., [58]). Future research will thus require distinguishing “drivers” from “passengers” on infrequently mutated genes.

Eventually, the knowledge of these genetic alterations can be used for the development of targeted therapy. However, many infrequent “hills” could indicate that each tumor has its own unique spectrum of causal genetic changes. Treatments aimed at targeting these individual genetic changes may therefore be difficult. Nevertheless, it is likely that different genetic changes are part of a select set of molecular pathways. Therefore, pathway inhibition or reactivation can be used to target a broader range of tumors. In the future, it is likely that individual cancer genomes will therefore be sequenced to direct targeted therapies. Such practice does require a further increase in sequencing capacity and speed and dedicated data analysis pipelines.