|Home | About | Journals | Submit | Contact Us | Français|
Mutations of arginine 132 (R132) in the enzyme isocitrate dehydrogenase-1 (IDH1) are present in up to 86% of grade II and III gliomas and secondary glioblastoma. R132 mutations in IDH1 result in excess production of the metabolite 2-hydroxyglutarate (2HG), which could be used as a biomarker for this subset of gliomas. Here, we use optimized spectral-editing and two-dimensional (2D) correlation magnetic resonance spectroscopy (MRS) methods to unambiguously detect 2HG non-invasively in glioma patients with IDH1 mutations. By comparison, fitting of conventional 1D MR spectra can provide false-positive readouts owing to spectral overlap of 2HG and chemically similar brain metabolites, such as glutamate and glutamine. 2HG has been found also by 2D high-resolution magic angle spinning MRS performed ex vivo on a separate set of glioma biopsy samples. 2HG detection by in vivo or ex vivo MRS enabled detailed molecular characterization of a clinically important subset of human gliomas. This has implications for diagnosis as well as monitoring of treatments targeting IDH mutations.
Isocitrate degydrogenase 1 (IDH1) is an intracellular enzyme that catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate in the cytoplasm and in peroxisomes. Recent genomic studies have identified heterozygous point mutations in arginine 132 (R132) of the IDH1 enzyme (1, 2). These mutations result in a neomorphic activity leading to overproduction and accumulation of the R (also D) enantiomer of the metabolite 2-hydroxglutarate (2HG) in 68 to 86% of grade II-III astrocytic and oligodendroglial tumors, as well as grade IV secondary glioblastoma, having higher frequency in young patients (3-5). Glioma patients with IDH1 mutations have a greater 5-year survival rate than patients with wild-type IDH1 gliomas (93% versus 51%) when correcting for age (3), suggesting that IDH1 mutations represent a clinically distinct subset of patients. In addition to glioma, mutations in IDH1 have also been found in patients with acute myelogenous leukemia and various other tumors, but at lower frequency than in glioma (6).
The full impact of the R132 mutation is not yet fully understood, but a major consequence of mutating this residue in IDH1 is a gain-of-function enzymatic activity favoring reduction of α-ketoglutarate to 2HG (7). This neomorphic activity leads to the accumulation of 2HG, a metabolite usually present in low levels in vivo as an error product of normal metabolism. Analogous mutations in the mitochondrial IDH2 isoform also result in 2HG production, but IDH2 mutations are found less frequently than IDH1 in various tumors, including gliomas (4).
2HG is a small biomolecule that has been shown ex vivo to identify IDH1/2-mutant tumors in humans (8). In transfected U87MG glioblastoma cell cultures, the intracellular concentration of 2HG can increase over 100-fold (7), up to 5-35 μmol/g (or 5-35 mM, assuming tissue density of 1.05 g/ml), after introduction of R132 mutated IDH1 in the U87MG genome. Accumulation of 2HG to similar levels as in U87MG cell cultures was measured in human glioma biopsy samples with IDH1R132 mutations (7, 9). This high concentration of 2HG (5-35 mM) is suitable for detection by in vivo magnetic resonance spectroscopy (MRS). Because the sensitivity threshold of in vivo MRS is roughly 1 mM, 2HG is not expected to be visible under normal conditions; but, 2HG might become measurable upon local accumulation owing to IDH mutation. Thus, the presence or absence of 2HG in the MR spectrum of glioma patients could effectively genotype tumors as being positive or negative for IDH1 or IDH2 mutations.
The S (also L) enantiomer of 2HG (L-2HG) has been detected using MRS in vivo in patients with hydroxyglutaric aciduria (10, 11). The detection challenge arises from the fact that the 2HG spectrum is largely overlapping with glutamate (Glu) and glutamine (Gln) — both abundant brain metabolites that have a similar five-spin system. Peaks in the region of 2.6 to 2.4 ppm that were previously indicated (10, 11) for L-2HG are shared with Glu, Gln, and also by N-acetyl-L-aspartate (NAA). With the limited in vivo spectral resolution (0.1 ppm) present in most clinical settings, these overlapping species are not easily resolved using conventional one-dimensional (1D) MRS, especially if spectral fitting was not used, as in these earlier reports (10, 11). Spectral fitting programs (12, 13) try to model the in vivo MR spectrum as a combination of modeled spectra (basis set) from all detectable metabolites. This approach might fail at clinically available fields when there is severe overlap as it is well known for GABA (14), or as we show in this paper for 2HG.
Two-dimensional (2D) correlation spectroscopy (COSY) (15) can potentially differentiate the overlapping metabolite spectra, because correlating two chemical shifts of coupled spins creates specific patterns of signals (crosspeaks) for each metabolite that are better separated in the plane of the 2D spectrum than spectral lines in a 1D spectrum. The 2D COSY exploits the idea that there is less likelihood for two metabolites to have two identical shifts, even if they might share a common chemical shift in the 1D spectrum. In particular, the crosspeaks involving Hα protons of 2HG appears in a region of the 2D COSY spectra where no other metabolite is found in healthy tissue or tumors without IDH mutations. Hence, although in 1D spectra the signals of 2HG appear in a region where other metabolites normally contribute, in 2D COSY spectra the crosspeaks involving Hα protons of 2HG can be uniquely identified. Alternatively, spectral-editing of 1D MRS, such as J-difference spectroscopy (14), can be tuned to detect a specific metabolite by removing the contribution of unwanted overlapping metabolites. The spectral-editing experiment can be easier to run on clinical scanners but offers limited metabolite information, while on the other hand the 2D COSY retains the full spectral information at the expense of complexity of the experiment.
In this work, we show that 2HG can be detected unambiguously in glioma patients using an optimized in vivo adiabatic 2D COSY method, developed previously for studying brain metabolism (16), or by spectral-editing MRS. We also find that fitting conventional 1D spectra might provide false positive results. In vivo measurements were compared with ex vivo high resolution magic angle spinning (HR-MAS) 2D MRS and liquid chromatography-mass spectrometry (LC-MS) of glioma biopsy samples. Results from brain phantoms, two glioma patients harboring the IDH1 R132 mutation, and eight control cases, including primary glioblastoma (n = 4) and healthy volunteers (n = 4) with wild-type IDH1, demonstrate that non-invasive detection of 2HG using 1D spectral-editing and 2D correlation MRS is feasible and may allow stratification of patients on the basis of IDH1 mutation.
We performed phantom experiments at 3T on clinical scanners to establish that 2HG can be distinguished from other metabolites by localized 2D correlation MRS as well as localized spectral-editing 1D MRS. 2HG was added to a phantom containing a mixture of brain metabolites, and a recently developed 2D LASER-COSY sequence (16) with improved in vivo performance based on localized adiabatic selective refocusing (LASER) was used as described in Methods. An adiabatic spectral-editing sequence (MEGA-LASER) was newly designed in this paper specifically for the purpose of 2HG detection (Methods and supplementary figs. S1, S3). A series of phantoms with a range of 2HG concentrations expected to be present in IDH-mutant tumors were also investigated to test the sensitivity limit of MRS. Assignments of 2HG (17) and other metabolites, such as myo-inositol (Myo), choline (Cho), N-acetylaspartic acid (NAA), glutamate (Glu), glutamine (Gln), and γ-amino-butyric acid GABA were made (Fig. 1) according to published literature values (18).
Fig. 1A shows the overlay of 2D LASER-COSY spectra recorded in a phantom containing a mixture of 2HG and brain metabolites (blue contours), and a phantom that contains only normal brain metabolites (red contours). The normal brain metabolites are at physiological concentrations in both phantoms. The Hα-Hβ crosspeak of 2HG located at 4.02/1.91 (δ2/δ1) ppm is well-separated from other metabolites, including the chemically similar metabolite glutamate, with Hα-Hβ correlation located at 3.75/2.12 ppm. Detailed information of the overlap between 2HG and other metabolites can be gleaned from spectra simulations (fig. S2). The strongly coupled five-spin system of 2HG, Glu, and Gln are very similar, and a large overlap is observed in the 2.6-2.0 ppm region for Hβ and Hγ protons. Additionally, GABA overlaps 2HG between 2.0-1.8 ppm and 2.4-2.2 ppm. As expected from the chemical structure, the largest separation between 2HG, Glu, and Gln is noticed for Hα protons owing to attached hydroxyl and amino moieties at Cα on 2HG and Glu/Gln, respectively. This Hα separation can be exploited in spectral-editing MRS.
Fig. 1B shows the edited 1D spectra obtained with the MEGA-LASER sequence on the same phantom as Fig. 1A. The Hα multiplet signal of 2HG at 4.02 ppm (Fig. 1B, blue) is aligned with the 2HG crosspeak from the 2D LASER-COSY spectrum. The signal at 4.02 ppm is missing in the brain phantom that does not contain 2HG (Fig. 1B, red). In addition to 2HG, the multiplet signals of Glu at 3.75 ppm and GABA at 3.01 ppm are co-edited, and their multiplets can be better observed in the inset of Fig. 1B. By comparison, in conventional 1D spectra obtained with LASER, the Hα proton of 2HG is largely overlapped by the strong Hβ peak of myo-inositol at 4.05 ppm (fig. S2). For in vivo spectroscopy, which typically has lower spectral resolution owing to susceptibility anisotropy of tissues, the Hα proton of 2HG might be obscured more even by the neighboring peaks of lactate (4.09 ppm) and both creatine and phosphocreatine (3.91 ppm).
MEGA-LASER showed excellent localization when compared to MEGA-PRESS in fig. S3, with no contamination of lipid signal from outside the voxel. The echo time of MEGA-LASER was optimized around the value of 1/2J (J, scalar coupling) for maximizing Hα signal of 2HG. The maximum was found for TE = 75 ms.
Calibration measurements were made for a series of 2HG phantoms with concentrations in the range of 0 to 16 mM (Fig. 1C). A strong correlation (R = 0.992) was found between 2D LASER-COSY crosspeak volume and 2HG concentration. A sensitivity limit of 2 mM 2HG was calculated for 2D LASER-COSY, with a voxel of 27 cm3, measurement time of 12.8 min, and a minimum signal-to-noise ratio (SNR) of 5, for reliable identification of the Hα crosspeaks. Similar strong correlation (R = 0.995) was found between 2HG concentration and the area of 2HG peak in spectral-editing MEGA-LASER. The SNR of 5 for 2 mM 2HG concentration and 27 cm3 voxel can be reached by MEGA-LASER with a shorter acquisition time of 5 min..
To ensure that 2HG measurements were possible in human tissue, we measured brain biopsy samples (n = 10, Table 1) prior to in vivo experiments. Biopsies were used because they contain the full set of metabolites and tumor metabolic profiles that are hard to replicate in phantoms. 2D spectra were obtained with HR-MAS conditions at 14 T from brain biopsies representing varied pathologies and IDH1 mutation status (Fig. 2). The 1H-1H 2D TOBSY [Total Through Bond Spectroscopy (18)] spectra of an IDH1-mutated anaplastic astrocytoma contained well-resolved and separated 2HG crosspeaks involving the correlations of Hα with Hβ (4.02/1.91 ppm) and Hγ (4.02/2.24 ppm) (Fig. 2A). The 2HG crosspeaks from biopsy spectrum overlaid entirely with the corresponding 2HG crosspeaks of the phantom spectrum (Fig. 2A). Projections along δ1 and δ2 spectral dimensions through the 2HG crosspeaks of the anaplastic astrocytoma biopsy are shown along axes of the 2D TOBSY. Importantly, 2HG signals are not present in the 2D TOBSY spectra from both primary glioblastoma (Fig. 2B) and non-tumor control (Fig. 2C) tissues, which were both wild-type IDH1. Of notice though, our 2HG findings from HRMAS measurements are based on the single biopsy that had mutant IDH1.
In addition to 2HG, large qualitative and quantitative differences are easily observed among different biopsy samples; most notably the presence of lipids, L-fucose, and β-glucose, as well as the absence of glutathione (GSH) in glioblastoma; the increased GPC (glycerophosphocholine) to PC (phosphocholine) ratio in anaplastic astrocytoma compared to non-tumor control biopsy; and a decreased GPC to PC ratio in glioblastoma compared to non-tumor control biopsy (Fig. 2). Similar finding have been previously reported, regarding increased lipids (19) and the presence of L-fucose in glioblastoma (20), and increased GPC in low grade glioma versus increased PC in high grade glioma (21-23). For comparison, 1D HRMAS spectra acquired on the anaplastic astrocytoma biopsy are shown in fig. S4. Because no tissue is destroyed during HR-MAS measurements, further assays are possible, such as histology, genomics, or mass spectrometry, to fully characterize the tumors. LC-MS was performed on the same biopsies and 2HG levels were measured to be 151.58 ng 2HG per mg tissue (wet weight) for IDH1R132H anaplastic astrocytoma, 2.39 ng/mg for wt-IDH1 glioblastoma, and 1.79 ng/mg for wt-IDH1 non-tumor control. The 2HG level in IDH1R132H anaplastic astrocytoma was 1.02 μmol/g-tissue, which is an order of magnitude above the 0.1 μmol/g lower sensitivity limit of HR-MAS (24); whereas the wt-IDH1 tissues had almost 100-fold less 2HG (0.01-0.015 μmol/g), concordant with previous results (7). The 2HG levels in wt-IDH1 biopsies are <0.1 μmol/g (detection threshold of HR-MAS) and hence not visible in Fig. 2, B and C.
After confirming MRS detection of 2HG in biopsy tissue ex vivo, MRS spectroscopy was performed in vivo in a separate set of human subjects (n = 10, Table 2). The results obtained on biopsies were important to identify the 2HG peaks that have the best chances to be detected in vivo and helped us select the appropriate in vivo methods. Two glioma patients (n = 2) with known IDH1 mutations (R132C and R132H), as well as two control groups, including primary glioblastoma patients without IDH1 mutations (n = 4) and healthy, non-tumor volunteers (n = 4) were investigated. Single voxels were prescribed based on fluid attenuation inversion recovery (FLAIR) image abnormalities in tumor patients, and magnetization prepared by rapid acquisition of gradient echo (MEMPRAGE) images in volunteers. 2D LASER-COSY, 1D MEGA-LASER, and 1D LASER spectra were acquired from the tumor patients and volunteers.
2D LASER-COSY results from a patient with anaplastic astrocytoma confirmed by tumor DNA sequencing to have R132C mutation of IDH1 are shown in Fig. 3A. A 27 cm3 voxel (3×3×3 cm3) was placed on the FLAIR images to include most of the solid tumor located in the splenium of the corpus callosum and the tail of the left hippocampus. The Hα-Hβ crosspeak of 2HG was present in the 2D LASER-COSY spectrum at 4.02/1.91 ppm (δ2/δ1), with δ2 and δ1 projections well above the baseline noise level (Fig. 3A). Similar 2HG projections can be observed in the phantom spectrum (fig. S2A). Crosspeaks of several other metabolites can be identified (Fig. 3A). Results from LCModel fitting of 1D LASER spectra are shown in fig. S5. Considering a basis set of spectra formed by the 20 most abundant metabolites in addition to 2HG, the fitting algorithm estimated the contribution of each metabolite so that the computed spectrum overlaps as best as possible with the measured spectrum (fig. S5).
An example of 2D LASER-COSY from a primary glioblastoma patient (wt-IDH1 by tumor DNA sequencing) is shown (Fig. 3B). A slightly bigger voxel (3.5×3.5×3.5 cm3) was chosen owing to the extension of the tumor into the left occipital lobe. The 2D LASER-COSY does not contain any 2HG crosspeak in the Hα region outlined by the green rectangle. Fitting methods applied to conventional 1D MRS (fig. S6) erroneously suggest the large presence of 2HG within confidence limits for goodness of fit (16% Cramer-Rao bounds), and that the level of 2HG is higher than NAA or GPC. These latter metabolites are both present in the 2D LASER-COSY spectrum; therefore, if the computed 1D MRS results in fig. S6 were true, the 2HG should be also visible in the 2D spectrum in Fig. 3B. This contradiction suggests that, in this case, the fitted 1D MRS result represents a false-positive. Fitting programs, such as LCModel, assume that the composite spectrum can be obtained by a unique combination of individual metabolite spectra. However, this is known to fail for in vivo spectra due to adverse combination of lower resolution and severe overlap of weaker metabolite signals by stronger metabolite signals. The most known example is erroneous GABA measurement by fitting conventional 1D spectra (25). On the other hand, 2D LASER-COSY is more in line with the genetic analysis that showed no IDH1 mutations in this patient.
Fig. 3C shows data from a healthy volunteer with wild-type IDH1. A 27 cm3 voxel was placed in the white matter of the left occipital lobe similar to the patient tumor positions. 2HG is absent, as expected, from the 2D LASER-COSY spectrum with the Hα crosspeak region outlined in green. 2D spectral quality is indicated by projections through the glutamate and glutamine crosspeak (Glu+Gln, 3.75/2.12 ppm). The fitting of the 1D MRS from the healthy volunteer is shown in fig. S7. The Cramer-Rao lower bound (23%) for 2HG fit is only slightly above the accepted limit (20%) for goodness of fit. However, 2HG was not expected to be found in a healthy control (see fig. S9 where the LCModel fits 2HG with 17% Cramer-Rao bounds in the healthy contralateral hemisphere of the glioblastoma patient).
Results obtained with the spectral-editing 1D MEGA-LASER sequence are presented in Fig. 4. Overlay of spectra acquired from tumor and the healthy contralateral side in a secondary glioblastoma patient with IDH1R132H mutation is shown in Fig. 4A. Importantly, the Hα multiplet signal of 2HG around 4.02 ppm is found only in the tumor spectrum and not on the healthy side. The multiplets of glutamate and glutamine (Glu+Gln), and GABA [+macromolecules (MM)] are present in both voxels. LCModel fitting of the corresponding non-edited 1D LASER spectra showed 2HG in tumor (Cramer-Rao 15%) (fig. S8) and also in the healthy voxel (Cramer-Rao 17%) (fig. S9), contrary to expectations.
Spectra from the control primary glioblastoma patient (wt-IDH1) (Fig. 4B) and from the healthy volunteer (wt-IDH1) (Fig. 4C) do not contain any 2HG; but they do show Glu+Gln and GABA+MM peaks. Interestingly, the Glu+Gln peaks in tumor voxels seem to be shifted slightly upfield compared to healthy side spectra (Fig. 4, A and B). The shift can be caused by different pH conditions in tumors compared to healthy brain tissue, and by different Glu and Gln relative contributions. There is no shift for Glu+Gln peaks between right and left sides in the healthy volunteer (Fig. 4C). No shift was observed for the GABA+MM peaks in any subject (Fig. 4).
Quantitative analysis of 2D LASER-COSY, 1D MEGA-LASER, and 1D LASER spectra was performed using the ratio of 2HG to the sum of Glu+Gln for reasons outlined in Methods. Volumes of crosspeaks at 4.02/1.91 ppm for 2HG and 3.75/2.12 ppm for Glu+Gln were used to calculate the 2HG/(Glu+Gln) ratio from 2D LASER-COSY (Fig. 5A). Areas of peaks at 4.02 ppm for 2HG and 3.75 ppm for Glu+Gln were used to estimate the 2HG/(Gln+Glu) ratio from 1D MEGA-LASER (Fig. 5B). For 1D LASER, the values fitted by LCModel (Fig. 5, A and B) were used to calculate the ratio.
The 2HG/(Glu+Gln) ratios are plotted for phantoms (n = 2), mutant IDH1R132H glioma patients (n = 2), wt-IDH1 glioblastoma patients (n = 4), and healthy volunteers (n = 4) (Fig. 5). In the case of phantoms, there is very good agreement between 2D correlation (LASER-COSY) MRS, 1D spectral-editing (MEGA-LASR) MRS, and 1D conventional (LASER) MRS for the 2HG/(Glu+Gln) ratio, which was close to 0.4, as expected from their respective concentrations: 2HG (3 mM), Glu (7.5 mM), Gln (0 mM). Because of similar spin systems, the ratio of crosspeak volumes was determined by their concentrations (assuming similar T2 and T1 times), without the need to correct for number of protons and build-up rates.
In the case of mutant R132-IDH1 glioma patients estimation of 2HG/(Glu+Gln) ratio showed slight differences which, however, are not statistical significant (P = 0.28). 2D LASER-COSY and 1D MEGA-LASER found an average ratio of 1.27, whereas LCModel fitting estimated an average ratio of 1.11 (Fig. 5). In the wt-IDH1 primary glioblastoma and non-tumor controls there was significant difference (P = 0.03) between the 2HG/(Glu+Gln) ratios obtained by LCModel fitting (ratios 0.33 and 0.57), and 2D LASER-COSY (ratio 0.04) and 1D MEGA-LASER (ratio 0.03), respectively.
The discovery that mutated IDH1/2 in gliomas can be correlated with survival benefit (3) has generated interest in using this mutation for diagnostic and prognostic purposes. 2HG is a metabolite that accumulates in human gliomas that harbor IDH1 mutations. Here, we preliminarily show that 2HG can be detected unambiguously and non-invasively by localized 2D correlation and 1D spectral-editing MRS in patients with mutated IDH1.
In vivo MRS detection of 2HG in gliomas has been suggested previously (7). Our results show that 2D LASER-COSY and 1D MEGA-LASER can reliably identify 2HG. The sensitivity of 2D LASER-COSY was approximately 2 mM (or 10 mg) for a 3×3×3 cm3 voxel, using a 13-min in vivo acquisition time and a minimum SNR of 5. The same sensitivity can be achieved by 1D MEGA-LASER in 5-min scan for the same voxel size. This is sufficient for the range (5 to 35 mM) of 2HG concentrations reported in IDH1-mutant tumors. Although the voxels used seem to be pretty large, several aspects besides maximizing sensitivity may justify this choice. First, gliomas are very infiltrative tumors with ill-defined margins, and active tumor exceeds the contours of the T1-weighted post-contrast images, which are mostly used to report tumor diameters or volumes. Second, IDH1 mutations seem to be uniformly expressed in tumors when present (26), so a large tumor volume could be included in the voxel. Finally, our method can separate or remove the contribution of normal metabolite; hence the inclusion of healthy tissue, which we showed does not contain 2HG, does not alter 2HG estimation. Further improvements in spatial resolution and multivoxel acquisitions of 2D LASER-COSY (27) or spectral-editing MRS (28) are possible. In addition, the sensitivity of ex vivo HRMAS approaches 1 μM and may therefore be employed as a non-destructive method for more detailed metabolite profiling in tumor samples.
Relative quantification of in vivo MRS data indicated that a 2HG/(Glu+Gln) ratio >1 could be specific for IDH1 mutations. Moreover, existing data indicate that 2HG and Glu might be inversely proportional: a slight decrease of Glu together with a large increase of 2HG in IDH1R132H (9), compared with a slight increase of Glu (20) with virtually undetectable 2HG (7) in wild-type IDH1 gliomas. These results suggests that the 2HG/(Glu+Gln) ratio might have increased dynamic range for detecting IDH1 mutations compared with either metabolite alone.
Comparing 2D correlation and 1D spectral-editing MRS, each method has its own strengths and limitations. For example, all metabolites are preserved and identified by two well-defined chemical shifts in 2D COSY, whereas in 1D spectral-editing, there is only one well-defined chemical shift in addition to a range of possible chemical shifts given by the bandwidth of the selective pulse (fig. S1). Conversely, spectral-editing experiments are easier to run and may require shorter scan times or smaller voxel sizes to detect the same concentration.
In addition to using 2HG as a biomarker, there is mounting interest in deciphering the biological mechanisms that link IDH mutations, 2HG production, and tumorigenesis. 2HG might act as an oncometabolite by competitive inhibition of α-ketoglutarate–dependent dioxygenases (29). This includes inhibition of histone demethylases and 5-methlycytosine (5 mC) hydroxylases, leading to genome-wide alterations in histone and DNA methylation, as well as inhibition of hydroxylases resulting in up-regulation of hypoxia-inducible factor 1 (HIF-1) (30). Hence, a large interest exists from pharmacological companies and research groups to develop inhibitors of mutated IDH1R132. The ability to objectively and non-invasively follow the effects of these compounds in animals and patients is a pre-requisite for successful drug development.
The importance of a reliable method for a novel noninvasive method of detecting 2HG in vivo is underscored by the fact that no report exists about increased D-2HG in the blood, cerebrospinal fluid, or urine of glioma patients with IDH1 mutations. This situation is different from hydroxyglutaric aciduria metabolic disorders, which show high levels of L-2HG in body fluids. Therefore, other than tumor biopsy, no assay currently exists to probe 2HG in IDH-mutated gliomas. Although a biopsy might be necessary for the initial diagnosis, multiple serial brain biopsies are generally not feasible. Moreover, MRS methods could map 2HG distribution and identify 2HG hot spots, guiding biopsy procedures to increase the chances for correct typing of the tumor, since it is known that biopsy based on conventional CT or MRI is suboptimal and subject to undergrading (31).
The in vivo 2D correlation and 1D spectral-editing MRS methods that we demonstrated can be repeated noninvasively, without harmful effects to patients, and might facilitate preclinical or clinical studies of new therapies, as well as assist with initial diagnostic workup. With further validation in humans, this approach could even allow molecular typing of IDH-mutant tumor using magnetic resonance imaging (MRI) investigations, which are already included in most patients’ diagnostic work-up, resulting in cost-effective and rapid genotyping of IDH mutations.
Complete details for all the methods are given in the Supplementary Material.
Patients and healthy volunteers (n = 10 total) listed in Table 2 were scanned with informed consent approved by the Internal Review Board at Massachusetts General Hospital.
Biopsies (n= 10, Table 1) were collected at the time of surgery and snap frozen in liquid nitrogen.
A multiplexed allele-specific assay (32) was used to detect somatic mutations in tumor DNA extracted from formalin-fixed paraffin-embedded samples.
Two phantoms with a mixture of metabolites were prepared for the initial assessment of unambiguous 2HG detection with MRS. One phantom contained normal brain metabolites at physiological concentrations. Another phantom contained the same brain metabolites as the first phantom, but also had 3 mM of D-2HG (D-α-hydroxyglutaric acid disodium salt, Sigma Aldrich). A series of phantoms containing only 2HG at different concentrations were prepared for calibration and sensitivity tests.
Quantum mechanical simulations were done in GAMMA [General Approach To Magnetic Resonance Mathematical Analysis (33)] for spectra of 2HG and the overlapping brain metabolites Glu, Gln, and GABA.
All HR-MAS experiments were conducted on a wide-bore 14.1 T (600 MHz 1H) Bruker Avance spectrometer using a 4 mm double channel HR-MAS probehead (Bruker). 2D spectra were measured at 3 kHz MAS using a 2D TOBSY (20) sequence.
The same biopsies measured by HRMAS were used for LC-MS metabolic profiling (7). Eluted metabolite ions were detected using a triple-quadrupole mass spectrometer, tuned to detect eight known central metabolites, including 2-HG.
All in vivo MR scans were performed on 3 T Tim Trio scanners (Siemens, Erlangen), using a head 32-channel phased array for receive and body radio-frequency (RF) coil for transmit. Single voxel spectroscopy was performed using recently optimized 1D LASER (34) and the 2D LASER-COSY (16) sequences. In addition, a newly designed 1D MEGA-LASER was used for spectral-editing (fig. S1). Typical voxel sizes were 27 cm3 (3×3×3 cm3) or 42.8 cm3 (3.5×3.5×3.5 cm3), in case of large tumors. A repetition time (TR) of 1.5s was used for all acquisitions. For 1D LASER and 2D LASER-COSY an echo time (TE) of 45 ms was used. The 1D MEGA-LASER spectra were acquired with TE of 75 ms.
Raw data were exported from the Siemens scanners for subsequent processing and analysis. The 1D LASER data (FID) were processed and quantified with LCModel (12) using a GAMMA-simulated basis set for LASER. For 1D MEGA-LASER data fitting was done in jMRUI (13). For 2D LASER-COSY, the FIDs of all t1 increments were imported in Matlab (The Mathworks) and futher processed. For quantification and comparison of methods and subjects, the 2HG/(Glu+Gln) ratio was chosen.
2-Hydroxyglutarate, a metabolite overproduced in IDH-mutated gliomas, can be detected noninvasively in vivo in patients with brain tumors by optimized MRS methods.
We thank M. Malgorzata and M. Garwood from the Center for Magnetic Resonance Research at University of Minnesota for help with building the LCModel basis set for LASER excitation. Funding: NIH grants R01 1200-206456, S10RR013026, S10RR021110, and S10RR023401
Author contributions: O.C.A.: conceptual design, measurements, data analysis, and manuscript drafting; G.K.: experimental measurements; E.G.: patient recruitment, clinical guidance, and manuscript review; T.B: patient recruitment, clinical guidance, and manuscript review; A.A.T: support for biopsy measurements and manuscript review; V.R.F.: LC-MS measurements, literature review, and manuscript editing; M.G.V.H.: literature review and manuscript editing; A.G.S.: initiated project, funding support, and manuscript review.
Competing interests: O.C.A. and A.G.S have applied for a patent for the 2D COSY-LASER method that is used in the paper.