IDH1 and IDH2 Mutations in Gliomas
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- Cohen, A.L., Holmen, S.L. & Colman, H. Curr Neurol Neurosci Rep (2013) 13: 345. doi:10.1007/s11910-013-0345-4
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Mutations in isocitrate dehydrogenase (IDH) 1 and 2, originally discovered in 2008, occur in the vast majority of low-grade gliomas and secondary high-grade gliomas. These mutations, which occur early in gliomagenesis, change the function of the enzymes, causing them to produce 2-hydroxyglutarate, a possible oncometabolite, and to not produce NADPH. IDH mutations are oncogenic, although whether the mechanism is through alterations in hydroxylases, redox potential, cellular metabolism, or gene expression is not clear. The mutations also drive increased methylation in gliomas. Gliomas with mutated IDH1 and IDH2 have improved prognosis compared with gliomas with wild-type IDH. Mutated IDH can now be detected by immunohistochemistry and magnetic resonance spectroscopy. No drugs currently target mutated IDH, although this remains an area of active research.
Diffuse gliomas are the commonest primary brain tumor in adults, affecting about 20,000 people in the USA each year . Most gliomas are astrocytic (70 %) or oligodendroglial (9 %) tumors, which include classic oligodendrogliomas and mixed oligoastrocytomas . Three pathways of glioma development have been identified: primary glioblastomas (GBMs), which arise de novo without lower-grade precursors; astrocytomas, which start as grade 2 or 3 and then transform into secondary GBMs; or oligodendrogliomas, which can transform into anaplastic oligodendrogliomas. Infiltrating gliomas are incurable with current treatment modalities: surgery, radiation therapy, and chemotherapy. Although several important genetic alterations in gliomas have been known for some time, new technologies have allowed much deeper genetic and epigenetic analyses of larger numbers of glioma samples, leading to a number of novel discoveries in the past few years. One of the most exciting and clinically relevant observations was the discovery that a high percentage of lower-grade gliomas (and a lower percentage of higher-grade gliomas) harbor mutations in the genes isocitrate dehydrogenase (IDH) 1 and 2. Growing data indicate that these mutations play a causal role in gliomagenesis, have a major impact on tumor biology, and also have clinical and prognostic importance.
Glioma Histopathologic and Molecular Classification
Diffuse gliomas can be categorized according to grade; low grade (grade 2), anaplastic (grade 3), and GBM (grade 4). Traditionally, GBMs have been classified as primary or secondary on the basis of clinical presentation . Secondary GBMs display evidence of progression from a lower-grade tumor, whereas primary GBMs present as advanced cancers at diagnosis. Secondary GBMs are predominantly found in younger patients (median age of approximately 45 years compared with median age of approximately 60 years for primary GBMs) and tend to occur less frequently than primary GBMs, making up approximately 5 % of all GBMs . Despite the differences in their ontology, these high-grade tumors are histopathologically indistinguishable .
Recently, large-scale efforts have been made to identify the major genetic and epigenetic alterations and to define important molecular subtypes in GBM and lower-grade gliomas [4, 5]. Publications from the Cancer Genome Atlas effort have identified four subgroups of GBM on the basis of dominant gene expression patterns, which were called proneural, neural, mesenchymal, and classic . Individual gene expression subtypes were associated with specific genetic and epigenetic alterations. Secondary GBMs are virtually always proneural, whereas primary GBMs can be any of the subtypes.
As discussed later, mutations in one of the IDH genes are tightly linked with the proneural phenotype and secondary GBMs. Virtually all tumors with IDH mutation are of the proneural gene expression subtype. In addition, IDH mutation was observed to be associated with increased DNA methylation, called G-CIMP for “glioma CpG island methylation phenotype” . Thus, both IDH mutation and G-CIMP are seen almost exclusively in secondary GBMs. Developing data regarding the metabolic and biologic consequences of IDH mutation have led to significant increases in our understanding of the development and clinical behavior of these different molecular subtypes of glioma.
IDH Mutations and Alterations in IDH Function
In 2008, a multigroup collaboration sequenced over 20,000 genes in 22 GBMs and identified a common point mutation in the metabolic gene IDH1 in 12 % of the samples analyzed . Further studies found that this mutation is present in approximately 80 % of grade 2 and grade 3 gliomas and secondary GBMs [8, 9, 10•, 11, 12•, 13••, 14••]. Mutations in IDH2 have also been identified in gliomas, although they are much less common and are mutually exclusive with mutations in IDH1 [10•, 14••, 15]. All mutations identified to date have been a single amino acid missense mutation in IDH1 at arginine 132 (R132) or the analogous residue in IDH2 (R172). Before these observations, mutation of IDH genes had never been linked to cancer. However, subsequent studies have identified IDH mutations in acute myelogenous leukemia, cholangiocarcinoma, cartilaginous tumors, prostate cancer, papillary breast carcinoma, acute lymphoblastic leukemia, angioimmunoblastic T-cell lymphoma, and primary myelofibrosis, indicating that these genes may be important players in multiple tumor types [16–23].
Five genes encode three human IDH catalytic isozymes: IDH1, IDH2, and IDH3. IDH1 and IDH2 form homodimers, whereas IDH3 forms a heterotetramer containing two α subunits, one β subunit, and one γ subunit . IDH3 functions in the Krebs cycle to convert isocitrate to α-ketoglutarate (α-KG) and NAD+ to NADH. The IDH1 and IDH2 proteins in the cytosol and mitochondria, respectively, generate reduced nicotinamide adenine dinucleotide phosphate (NADPH) from NADP+ by catalyzing the oxidative decarboxylation of isocitrate to α-KG outside the Krebs cycle . NADPH is mainly produced by glucose 6-phosphate dehydrogenase, malate dehydrogenase, and IDH. On exposure to free radicals and reactive oxygen species (ROS), cells with low levels of IDH became more sensitive to oxidative damage . These studies demonstrated that in addition to IDH being a major enzyme in the citric acid cycle, it may also function to maintain the cellular redox state and suggest that IDH plays an important role in cellular defense against oxidative stress.
All mutations in IDH1 in glioma appear to affect amino acid residue 132, with the vast majority (more than 85 %) containing a heterozygous missense mutation of arginine to histidine (R132H) . This residue is located in the active site of the enzyme and is critical for isocitrate binding . The mutation at R132 inactivates the protein’s ability to bind isocitrate and abolishes its normal catalytic activity. The net result is reduced levels of α-KG and NADPH, which is an important cofactor that is necessary to maintain normal levels of reduced glutathione to combat ROS [29, 30].
IDH Mutations and Oncogenesis
One question that always arises in studies of gene mutations in cancer is whether that specific gene is a key driver of tumor formation (oncogenesis), whether the mutation arises as a step in tumor progression, or whether it is an incidental consequence of impaired DNA repair in tumors (e.g., a carrier mutation). Two lines of evidence support the concept that IDH mutation is a direct driver of oncogenesis. First, somatic mosaicism for IDH1 or IDH2 at R132 causes the enchondromatosis syndromes Ollier’s disease and Maffucci syndrome, which are characterized by hemangiomas and cartilaginous tumors and which carry an increased risk of gliomas [18, 31, 32]. Second, introduction of mutated IDH into normal cells causes increased proliferation, increased colony formation, and inability to differentiate [33•, 34, 35].
Exactly how IDH mutation contributes to oncogenic transformation remains controversial. Initial reports suggested that the mutant protein functions in a dominate-negative fashion by heterodimerizing to wild-type IDH1 and impairing its activity [36–38]; however, more recent in vitro studies have shown that the mutated IDH1 protein acquires the ability to convert α-KG to (R)-2-hydroxyglutarate [39••, 40]. This is supported by the findings that 2-hydroxyglutarate (2-HG) levels are elevated in gliomas containing an IDH1 mutation [39••]. These findings led to the hypothesis that mutant IDH is an oncogene and 2-HG is an “oncometabolite” .
Whether it is 2-HG or mutated IDH or both that promote cancer remains unclear. An increased risk of gliomas has been observed for patients with inborn errors of metabolism that result in increased levels of (S)-2-HG but not (R)-2-HG, although interestingly people with (R)-2-hydroxyglutaric aciduria can have IDH2 mutations but never IDH1 mutations [42, 43]. Furthermore, it was recently discovered that the wild-type IDH1 can also catalyze the conversion of α-KG to 2-HG, albeit less efficiently than mutant IDH .
New evidence suggests that by antagonizing α-KG, 2-HG competitively inhibits the activity of many α-KG-dependent dioxygenases, including but not limited to histone demethylases, e.g., collagen prolyl 4-hydroxylase, prolyl hydroxylases, and the ten–eleven translocation (TET) family of DNA hydroxylases [35, 45, 46]. As described earlier, profiling of GBM from the Cancer Genome Atlas demonstrated an association between IDH mutation and increased promoter methylation (G-CIMP) , which generally results in transcriptional silencing of the associated genes .
Two recent independent studies demonstrated that the G-CIMP was not only correlated with IDH mutation but that IDH mutation alone is actually the cause of the G-CIMP hypermethylation phenotype in diffuse gliomas [48, 49]. In these studies, introduction of mutant IDH1 into immortalized primary human astrocytes was found to be sufficient to cause the hypermethylator phenotype [50••]. One possible implication of these findings is that reduced α-KG and increased 2-HG levels (from IDH mutation) may predispose cells harboring mutant IDH to malignant transformation via genome-wide epigenetic changes. However, further studies are needed to determine the precise link between these effects of IDH mutation and actual oncogenic transformation because development of G-CIMP in astrocytes after introduction of IDH mutations did not result in tumor formation.
IDH Mutations and the Hypoxia Pathway
Prolyl hydroxylase domain enzymes are important for the hydroxylation and degradation of hypoxia-inducible factor (HIF)-1α. These enzymes require α-KG and divalent ferrous iron (Fe2+). One of the effects of IDH mutation is the depletion of α-KG and oxidation of ferrous iron by ROS. Reduced levels of α-KG and Fe2+ in mutant IDH cells may therefore promote cellular accumulation of HIF-1α. Activation of this pathway leads to the induction of HIF-1α target genes that affect angiogenesis, metabolism, growth and differentiation, apoptosis, and autophagy, as well as cell motility. Zhao et al.  found that overexpression of mutant IDH in U87MG glioma cells increased HIF-1α protein levels and induced HIF-1α target gene expression. This effect was abolished after exogenous administration of α-KG. In addition, HIF-1α protein expression was found to be higher in gliomas with IDH1 mutations compared with those containing wild-type IDH . These observations suggest that IDH mutation can lead to activation of the hypoxia pathways in the presence of normoxia, a process termed “pseudohypoxia.” However, Koivunen et al. [33•] found that (R)-2-HG, could substitute for α-KG in late passage immortalized astrocytes expressing mutant IDH to stimulate the activity of the HIF-1α prolyl hydroxylase domain proteins EGLN1, EGLN2, and EGLN3, which promote the degradation of HIF-1α. Furthermore, analysis of gene expression data from the Cancer Genome Atlas showed that tumors harboring mutant IDH had reduced expression of HIF target genes relative to tumors containing wild-type IDH. Inconsistencies in these findings suggest that the effects of IDH mutation on the hypoxia pathway may be context-dependent, and further studies are required to determine the association between mutant IDH expression and HIF activity in gliomas.
IDH Mutation Distribution and Significance in Human Glioma
Several lines of evidence suggest that IDH1 mutations are an early event in glioma development. As described already, IDH1 mutations are seen in a high percentage of grade 2 and grade 3 astrocytomas and oligodendrogliomas and secondary GBMs. Mutations in IDH2 have been found in fewer than 3 % of glial tumors, with similar distributions related to grade. IDH mutations are rare in primary GBM [14••]. In lower-grade gliomas with a high percentage of IDH mutation, differences in other tumor mutations and copy number alterations have been found associated with histologic subtypes. IDH1 mutations often occur with a TP53 mutation in astrocytic tumors, and these tumors rarely demonstrate loss of chromosome arms 1p and 19q. On the other hand, IDH mutation is seen in virtually all oligodendrogliomas with 1p/19q codeletion, and these tumors rarely demonstrate p53 mutation [13••, 14••, 52]. Thus, even though IDH1 is highly associated with both TP53 mutation and loss of 1p/19q, these alterations are generally mutually exclusive in gliomas. These findings suggest that IDH mutation is an early event in glioma formation and occurs prominently in low-grade tumors of both astrocytic and oligodendroglial lineage. Indeed, studies of the timing of IDH1 mutations relative to others in gliomas indicate that IDH mutations precede TP53 mutations in 63 % of diffuse astrocytomas [13••, 30], and 80 % of GBMs and anaplastic astrocytomas with IDH mutations also had a mutation of TP53 [14••]. Mutations in the TP53 tumor suppressor gene were first implicated in gliomagenesis 20 years ago when an increased incidence of gliomas was observed in patients with Li–Fraumeni syndrome, a rare cancer-predisposing disorder caused by mutations in TP53 . Interestingly, IDH mutations found in astrocytomas that developed in Li–Fraumeni syndrome families contained the less common R132C substitution, suggesting a difference in selection in cells that already harbor TP53 mutations . Although commonly seen with alterations associated with low-grade glioma, IDH mutation is rarely observed with genetic alterations commonly seen in high frequency in primary GBMs (e.g., EGFR), supporting the idea that IDH mutation is not a driver of tumor initiation in these GBM subtypes [13••].
People with gliomas with mutated IDH are, on average, several years younger than people with gliomas with wild-type IDH. On the other hand, IDH mutations are rare in gliomas in young children, although they are common in gliomas in adolescents aged 14 years or older [54, 55]. About 20-25 % of people with IDH-mutated gliomas carry the rs55705857 single-nucleotide polymorphism (SNP) on chromosome band 8q24, compared with 5 % of the general population . In a prospective analysis, grade 2–4 glioma patients whose tumors harbored mutant IDH1 or IDH2 had significantly longer overall survival than patients without IDH mutation [12•]. This finding has been confirmed independently by others [14••, 57, 58]. The prognostic importance of IDH mutation is independent of other known prognostic factors, including age, grade, and O6-methylguanine-DNA methyltransferase methylation status [12•].
However, it remains to be determined whether IDH mutation is a prognostic factor only or whether it is predictive of outcome from specific treatments or is mechanistically related to treatment response. In vitro, induction of mutated IDH increased the sensitivity of gliomas to radiation . Small retrospective series have suggested that the rate of response to alkylating chemotherapy is also higher in IDH-mutated grade 2 tumors than in wild-type tumors and that progression-free survival after radiation therapy or alkylating chemotherapy is higher for people with IDH-mutated tumors than for people with wild-type tumors [60–62]. In the German Glioma Group retrospective study, IDH mutation influenced survival only in those patients who received radiation therapy or chemotherapy immediately after surgery . The presence of IDH mutation did not predict progression-free survival for temozolomide treatment in low-grade astrocytomas that had previously received radiation therapy . However, their retrospective nature and lack of control groups limits the conclusions that can be drawn from these studies.
In EORTC 26951, a randomized trial comparing the addition of chemotherapy with procarbazine, lomustine, and vincristine to adjuvant radiation therapy in anaplastic oligodendrogliomas, the presence of IDH mutation predicted prolonged survival in the chemotherapy group, but the presence of IDH mutation nearly completely overlapped with 1p/19q deletion, so the independent effect of these genetic alterations in grade 3 oligondendrogliomas cannot be determined . The NOA-04 trial compared radiation therapy with alkylating chemotherapy as up-front treatment of grade 3 gliomas. IDH mutation was associated with improved progression-free survival in both treatment groups approximately equally . The ongoing CATNON trial should provide important additional data to address the question of the predictive association with IDH mutation and specific treatments in non-1p/19q-deleted grade 3 gliomas.
Detection of IDH Mutation in Glioma
Initial studies of IDH mutations used direct sequencing [14••]. Pyrosequencing has remained clinically valuable for detection of IDH mutations in hematologic malignant diseases, particularly acute myelogenous leukemia. Although sequencing remains the gold standard for IDH mutation testing, more rapid and easier to apply methods have been developed for initial screening in gliomas. The development of a monoclonal antibody against IDH1 R132H allows the detection of the commonest mutation seen in gliomas by immunohistochemistry from paraffin-embedded sections, and this method is being used with increasing frequency for clinical classification of tumors [67•].
In addition to detection of IDH mutation in tissue, the increased levels of 2-HG in IDH-mutated tumors have led several groups to develop noninvasive imaging methods for detection of IDH-mutated gliomas. Indeed, 2-HG has a distinctive magnetic resonance spectrum that is detectable by in vivo magnetic resonance spectroscopy [68••]. Magnetic resonance spectroscopy may therefore be useful for distinguishing gliosis from low-grade gliomas, potentially avoiding biopsy in ambiguous cases. However, additional prospective studies are needed to further define the sensitivity and specificity of these imaging approaches.
Models of IDH-Mutated Glioma
Study of IDH-mutated gliomas has been limited by a lack of appropriate mouse models. There are no models of spontaneous IDH-mutated glioma-producing mice. Expression of mutated IDH1 in the brains of transgenic mice causes death soon after birth because of intercerebral hemorrhage . In vitro cell lines with IDH mutation can be transiently produced but do not persist in nonimmortalized cells. In standard cell culture conditions, IDH-mutated gliomas cells from IDH-mutated patient tumors generally do not grow well . Moreover, there may be a selection pressure against IDH-mutated glioma cells in culture because, in contrast to the effect on normal cells, introduction of mutated IDH into wild-type IDH glioma cells decreases the proliferation rate . Despite these challenges, IDH-mutated primary glioma neurospheres have been isolated from a human tumor and propagated in stem cell conditions by at least one group .
Targeting IDH Mutations
The discovery of IDH mutation in glioma has resulted in a number of novel ideas for therapeutic approaches. The concept of 2-HG being an oncometabolite has led several investigators to try to devise strategies to either restore normal IDH function or block production or downstream effects of 2-HG. Indeed, in an in vitro model, suppression of expression of mutated IDH decreases growth and clone formation in an IDH-mutated fibrosarcoma cell line . Although there are currently no direct IDH inhibitors in clinical trials, a number of investigators and drug companies are working on bringing specific inhibitors to the clinic. In vitro, the production of 2-HG by mutated IDH2 can be inhibited by metabolites such as oxaloacetate .
Another approach that is being considered is targeting the downstream signaling pathway alterations and epigenetic changes that are induced by IDH mutation. For example, IDH-mutated GBMs have increased activation of the hedgehog pathway, so use of a hedgehog inhibitor is of potential interest in these tumors . Alternatively, hypomethylating agents or other epigenetic modifiers may be rational to try to target the G-CIMP hypermethylation phenotype induced by mutated IDH . One potential caveat of this approach is that the general activation of expression of many genes through a decrease in methylation could also increase expression of deleterious ones such as oncogenes.
The story of IDH mutations in gliomas is one of the successes of mapping the human genome. In the 5 years since their discovery, our understanding of the biochemistry, genetics, and epigenetics of IDH mutations has grown. It is now clear that mutations in IDH1 and IDH2 are driver mutations in low-grade gliomas, likely through 2-HG production. These mutations lead to a hypermethylation phenotype as well as changes in cellular metabolism and response to hypoxic and oxidative stress. IDH mutations have a definite effect on prognosis and may be predictive of response to radiation therapy and/or alkylating chemotherapy. Our ability to target gliomas with IDH mutations remains limited, however. Thus, although our understanding of IDH mutation and its biology has increased dramatically in a relatively short time, it is clear more investigation is necessary to determine optimal therapeutic strategies to target the IDH-mutated subsets of gliomas.
The authors thank Rowan Arave for assistance with preparation of the figure.
Conflict of Interest
Adam Cohen declares no conflict of interest.
Sheri Holmen declares no conflict of interest.
Howard Colman has been a consultant to Roche and has received royalties from Castle Biosciences.