1
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Sun Y, Zhang Y, Gan J, Zhou H, Guo S, Wang X, Zhang C, Zheng W, Zhao X, Li X, Wang L, Ning S. Comprehensive quantitative radiogenomic evaluation reveals novel radiomic subtypes with distinct immune pattern in glioma. Comput Biol Med 2024; 177:108636. [PMID: 38810473 DOI: 10.1016/j.compbiomed.2024.108636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 04/07/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Accurate classification of gliomas is critical to the selection of immunotherapy, and MRI contains a large number of radiomic features that may suggest some prognostic relevant signals. We aim to predict new subtypes of gliomas using radiomic features and characterize their survival, immune, genomic profiles and drug response. METHODS We initially obtained 341 images of 36 patients from the CPTAC dataset for the development of deep learning models. Further 1812 images of 111 patients from TCGA_GBM and 152 images of 53 patients from TCGA_LGG were collected for testing and validation. A deep learning method based on Mask R-CNN was developed to identify new subtypes of glioma patients and compared the survival status, immune infiltration patterns, genomic signatures, specific drugs, and predictive models of different subtypes. RESULTS 200 glioma patients (mean age, 33 years ± 19 [standard deviation]) were enrolled. The accuracy of the deep learning model for identifying tumor regions achieved 88.3 % (98/111) in the test set and 83 % (44/53) in the validation set. The sample was divided into two subtypes based on radiomic features showed different prognostic outcomes (hazard ratio, 2.70). According to the results of the immune infiltration analysis, the subtype with a poorer prognosis was defined as the immunosilencing radiomic (ISR) subtype (n = 43), and the other subtype was the immunoactivated radiomic (IAR) subtype (n = 53). Subtype-specific genomic signatures distinguished celllines into ISR celllines (n = 9) and control celllines (n = 13), and identified eight ISR-specific drugs, four of which were validated by the OCTAD database. Three machine learning-based classifiers showed that radiomic and genomic co-features better predicted the radiomic subtypes of gliomas. CONCLUSIONS These findings provide insights into how radiogenomic could identify specific subtypes that predict prognosis, immune and drug sensitivity in a non-invasive manner.
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Affiliation(s)
- Yue Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yakun Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jing Gan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xinyue Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Caiyu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Wen Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xiaoxi Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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2
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Two Patterns of White Matter Connection in Multiple Gliomas: Evidence from Probabilistic Fiber Tracking. J Clin Med 2022; 11:jcm11133693. [PMID: 35806978 PMCID: PMC9267772 DOI: 10.3390/jcm11133693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 02/05/2023] Open
Abstract
Background: Multiple lesions are uncommon in brain gliomas, and their pathophysiology is poorly understood. Invasive growth along white matter tracts is an important clinicopathological characteristic of gliomas, and a major factor in a poor therapeutic outcome. Here, we used probabilistic fiber tracking and cluster analysis to investigate the inter-focal connectivity relationships of multiple gliomas, in order to seek inferential evidence of common origin. Methods: MRI scans of 46 patients with multiple gliomas were retrospectively analyzed. Before surgery, all patients underwent multimodal functional MR imaging, including diffusion tensor imaging, enhanced 3D T1-weighted imaging, diffusion-weighted imaging, 1H MR spectroscopy, and dynamic susceptibility contrast perfusion-weighted imaging. Probabilistic fiber tracking was used to quantify white matter connectivity between neoplastic foci. Hierarchical cluster analysis was performed to identify patterns of white matter connection. Results: Cluster analysis reveals two patterns of connectivity, one with smaller, and one with greater, connectivity (2675 ± 1098 versus 30432 ± 22707, p < 0.0001). The two subgroups show significant differences in relative cerebral blood volume (2.31 ± 0.95 versus 1.73 ± 0.48, p = 0.002) and lipid/creatine ratio (0.32 ± 0.22 versus 0.060 ± 0.051, p = 0.006). Conclusion: Two distinct patterns of white matter connection exist in multiple gliomas. Those with lower connectivity tend to have independent origins, and can be termed true multicentric glioma, whereas those with greater connectivity tend to share common origin, and spread along white matter tracts. True multicentric gliomas have higher vascularity and more intratumoral necrosis. These findings may help to develop personalized therapeutic strategies for multiple gliomas.
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3
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Nuechterlein N, Shapiro LG, Holland EC, Cimino PJ. Machine learning modeling of genome-wide copy number alteration signatures reliably predicts IDH mutational status in adult diffuse glioma. Acta Neuropathol Commun 2021; 9:191. [PMID: 34863298 PMCID: PMC8645099 DOI: 10.1186/s40478-021-01295-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022] Open
Abstract
Knowledge of 1p/19q-codeletion and IDH1/2 mutational status is necessary to interpret any investigational study of diffuse gliomas in the modern era. While DNA sequencing is the gold standard for determining IDH mutational status, genome-wide methylation arrays and gene expression profiling have been used for surrogate mutational determination. Previous studies by our group suggest that 1p/19q-codeletion and IDH mutational status can be predicted by genome-wide somatic copy number alteration (SCNA) data alone, however a rigorous model to accomplish this task has yet to be established. In this study, we used SCNA data from 786 adult diffuse gliomas in The Cancer Genome Atlas (TCGA) to develop a two-stage classification system that identifies 1p/19q-codeleted oligodendrogliomas and predicts the IDH mutational status of astrocytic tumors using a machine-learning model. Cross-validated results on TCGA SCNA data showed near perfect classification results. Furthermore, our astrocytic IDH mutation model validated well on four additional datasets (AUC = 0.97, AUC = 0.99, AUC = 0.95, AUC = 0.96) as did our 1p/19q-codeleted oligodendroglioma screen on the two datasets that contained oligodendrogliomas (MCC = 0.97, MCC = 0.97). We then retrained our system using data from these validation sets and applied our system to a cohort of REMBRANDT study subjects for whom SCNA data, but not IDH mutational status, is available. Overall, using genome-wide SCNAs, we successfully developed a system to robustly predict 1p/19q-codeletion and IDH mutational status in diffuse gliomas. This system can assign molecular subtype labels to tumor samples of retrospective diffuse glioma cohorts that lack 1p/19q-codeletion and IDH mutational status, such as the REMBRANDT study, recasting these datasets as validation cohorts for diffuse glioma research.
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Affiliation(s)
- Nicholas Nuechterlein
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Linda G Shapiro
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick J Cimino
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, Division of Neuropathology, University of Washington, 325 9th Avenue, Box 359791, Seattle, WA, 98104, USA.
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4
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Palpan Flores A, Vivancos Sanchez C, Roda JM, Cerdán S, Barrios AJ, Utrilla C, Royo A, Gandía González ML. Assessment of Pre-operative Measurements of Tumor Size by MRI Methods as Survival Predictors in Wild Type IDH Glioblastoma. Front Oncol 2020; 10:1662. [PMID: 32984040 PMCID: PMC7492614 DOI: 10.3389/fonc.2020.01662] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Abstract
Objective: We evaluate the performance of three MRI methods to determine non-invasively tumor size, as overall survival (OS) and Progression Free Survival (PFS) predictors, in a cohort of wild type, IDH negative, glioblastoma patients. Investigated protocols included bidimensional (2D) diameter measurements, and three-dimensional (3D) estimations by the ellipsoid or semi-automatic segmentation methods. Methods: We investigated OS in a cohort of 44 patients diagnosed with wild type IDH glioblastoma (58.2 ± 11.4 years, 1.9/1 male/female) treated with neurosurgical resection followed by adjuvant chemo and radiotherapy. Pre-operative MRI images were evaluated to determine tumor mass area and volume, gadolinium enhancement volume, necrosis volume, and FLAIR-T2 hyper-intensity area and volume. We implemented then multivariate Cox statistical analysis to select optimal predictors for OS and PFS. Results: Median OS was 16 months (1–42 months), ranging from 9 ± 2.4 months in patients over 65 years, to 18 ± 1.6 months in younger ones. Patients with tumors carrying O6-methylguanin-DNA-methyltransferase (MGMT) methylation survived 30 ± 5.2 vs. 13 ± 2.5 months in non-methylated. Our study evidenced high and positive correlations among the results of the three methods to determine tumor size. FLAIR-T2 hyper-intensity areas (2D) and volumes (3D) were also similar as determined by the three methods. Cox proportional hazards analysis with the 2D and 3D methods indicated that OS was associated to age ≥ 65 years (HR 2.70, 2.94, and 3.16), MGMT methylation (HR 2.98, 3.07, and 2.90), and FLAIR-T2 ≥ 2,000 mm2 or ≥60 cm3 (HR 4.16, 3.93, and 3.72), respectively. Other variables including necrosis, tumor mass, necrosis/tumor ratio, and FLAIR/tumor ratio were not significantly correlated with OS. Conclusion: Our results reveal a high correlation among measurements of tumor size performed with the three methods. Pre-operative FLAIR-T2 hyperintensity area and volumes provided, independently of the measurement method, the optimal neuroimaging features predicting OS in primary glioblastoma patients, followed by age ≥ 65 years and MGMT methylation.
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Affiliation(s)
| | | | - José M Roda
- Department of Neurosurgery, University Hospital La Paz, Madrid, Spain
| | - Sebastian Cerdán
- Institute of Biomedical Research "Alberto Sols" CSIC/UAM, Madrid, Spain
| | | | - Cristina Utrilla
- Department of Neuroradiology, University Hospital La Paz, Madrid, Spain
| | - Aranzazu Royo
- Department of Neuroradiology, University Hospital La Paz, Madrid, Spain
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5
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Recent Trends of microRNA Significance in Pediatric Population Glioblastoma and Current Knowledge of Micro RNA Function in Glioblastoma Multiforme. Int J Mol Sci 2020; 21:ijms21093046. [PMID: 32349263 PMCID: PMC7246719 DOI: 10.3390/ijms21093046] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Central nervous system tumors are a significant problem for modern medicine because of their location. The explanation of the importance of microRNA (miRNA) in the development of cancerous changes plays an important role in this respect. The first papers describing the presence of miRNA were published in the 1990s. The role of miRNA has been pointed out in many medical conditions such as kidney disease, diabetes, neurodegenerative disorder, arthritis and cancer. There are several miRNAs responsible for invasiveness, apoptosis, resistance to treatment, angiogenesis, proliferation and immunology, and many others. The research conducted in recent years analyzing this group of tumors has shown the important role of miRNA in the course of gliomagenesis. These particles seem to participate in many stages of the development of cancer processes, such as proliferation, angiogenesis, regulation of apoptosis or cell resistance to cytostatics.
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6
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Liu X, Li Y, Li S, Fan X, Sun Z, Yang Z, Wang K, Zhang Z, Jiang T, Liu Y, Wang L, Wang Y. IDH mutation-specific radiomic signature in lower-grade gliomas. Aging (Albany NY) 2020; 11:673-696. [PMID: 30696801 PMCID: PMC6366985 DOI: 10.18632/aging.101769] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/06/2019] [Indexed: 12/16/2022]
Abstract
Unravelling the heterogeneity is the central challenge for glioma precession oncology. In this study, we extracted quantitative image features from T2-weighted MR images and revealed that the isocitrate dehydrogenase (IDH) wild type and mutant lower grade gliomas (LGGs) differed in their expression of 146 radiomic descriptors. The logistic regression model algorithm further reduced these to 86 features. The classification model could discriminate the two types in both the training and validation sets with area under the curve values of 1.0000 and 0.9932, respectively. The transcriptome-radiomic analysis revealed that these features were associated with the immune response, biological adhesion, and several malignant behaviors, all of which are consistent with biological processes that are differentially expressed in IDH wild type and IDH mutant LGGs. Finally, a prognostic signature showed an ability to stratify IDH mutant LGGs into high and low risk groups with distinctive outcomes. By extracting a large number of radiomic features, we identified an IDH mutation-specific radiomic signature with prognostic implications. This radiomic signature may provide a way to non-invasively discriminate lower-grade gliomas as with or without the IDH mutation.
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Affiliation(s)
- Xing Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yiming Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shaowu Li
- Neurological Imaging Center, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xing Fan
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhiyan Sun
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhengyi Yang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Kai Wang
- Department of Nuclear Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhong Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)
| | - Yong Liu
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Lei Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yinyan Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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7
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Tompa M, Nagy A, Komoly S, Kalman B. Wnt pathway markers in molecular subgroups of glioblastoma. Brain Res 2019; 1718:114-125. [DOI: 10.1016/j.brainres.2019.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022]
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8
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Perrech M, Dreher L, Röhn G, Stavrinou P, Krischek B, Toliat M, Goldbrunner R, Timmer M. Qualitative and Quantitative Analysis of IDH1 Mutation in Progressive Gliomas by Allele-Specific qPCR and Western Blot Analysis. Technol Cancer Res Treat 2019; 18:1533033819828396. [PMID: 30943868 PMCID: PMC6457076 DOI: 10.1177/1533033819828396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To date, diagnosis of IDH1 mutation is based on DNA sequencing and immunohistochemistry, methods limited in terms of sensitivity and ease of use. Recently, the diagnosis of IDH1 mutation by real-time polymerase chain reaction was introduced as an alternative method. In this study, real-time polymerase chain reaction was validated as a tool for detection of IDH1 mutation, and expression levels were analyzed for correlation with course of the disease. A total of 113 tumor samples were obtained intraoperatively from 84 patients with glioma having a diagnosis of diffuse glioma (World Health Organization II), anaplastic glioma (World Health Organization III), secondary glioblastoma ± chemotherapy, primary glioblastoma ± chemotherapy (World Health Organization IV). Tumor samples were snap frozen and processed for sectioning and RNA and protein isolation. Presence of IDH1 mutation was determined by DNA sequencing. Hereafter, quantitative expression of IDH1 messenger RNA was assessed using real-time polymerase chain reaction with specific primers for IDH1 mutation and -wt; protein expression was verified by Western Blot analysis and immunohistochemistry. Additionally, 19 samples of low-grade glioma and their consecutive high-grade glioma were analyzed at different time points of the disease. IDH1 mutation was identified in 63% of samples by DNA sequencing. In correlation with the real-time polymerase chain reaction results, a cutoff value was determined. Above this threshold, sensitivity and specificity of real-time polymerase chain reaction in detecting IDH1 mutation were 98% and 94%, respectively. Quantitative analysis revealed that IDH1 mutation expression is upregulated in secondary glioblastoma (mean ± standard error of mean: 3.52 ± 0.55) compared to lower grade glioma (II = 1.54 ± 0.22; III = 1.67 ± 0.23). In contrast, IDH1 wt expression is upregulated in all glioma grades (concentration >0.1) compared to control brain tissue (0.007 ± 0.0016). Western Blot analysis showed a high concordance to both sequencing and real-time polymerase chain reaction results in qualitative analysis of IDH1 mutation status (specificity 100% and sensitivity 100%). Moreover, semiquantitative protein expression analysis also showed higher expression levels of mutated IDH1 in secondary glioblastoma. In our study, real-time polymerase chain reaction and Western Blot analysis were found to be highly efficient methods in detecting IDH1 mutation in glioma samples. As cost-effective and time-saving methods, real-time polymerase chain reaction and Western Blot analysis may therefore play an important role in IDH1 mutation analysis in the future. IDH1 mutation expression level was found to correlate with the course of disease to a certain extent. Yet, clinical factors as recurrent disease or prior radiochemotherapy did not alter IDH1 mutation expression level.
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Affiliation(s)
- Moritz Perrech
- 1 Laboratory of Neuro-oncology and Experimental Neurosurgery, Department of General Neurosurgery, Center for Neurosurgery, University Hospital Cologne, Cologne, Germany
| | - Lena Dreher
- 1 Laboratory of Neuro-oncology and Experimental Neurosurgery, Department of General Neurosurgery, Center for Neurosurgery, University Hospital Cologne, Cologne, Germany
| | - Gabriele Röhn
- 1 Laboratory of Neuro-oncology and Experimental Neurosurgery, Department of General Neurosurgery, Center for Neurosurgery, University Hospital Cologne, Cologne, Germany
| | - Pantelis Stavrinou
- 1 Laboratory of Neuro-oncology and Experimental Neurosurgery, Department of General Neurosurgery, Center for Neurosurgery, University Hospital Cologne, Cologne, Germany
| | - Boris Krischek
- 1 Laboratory of Neuro-oncology and Experimental Neurosurgery, Department of General Neurosurgery, Center for Neurosurgery, University Hospital Cologne, Cologne, Germany
| | - Mohammad Toliat
- 2 Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Roland Goldbrunner
- 1 Laboratory of Neuro-oncology and Experimental Neurosurgery, Department of General Neurosurgery, Center for Neurosurgery, University Hospital Cologne, Cologne, Germany
| | - Marco Timmer
- 1 Laboratory of Neuro-oncology and Experimental Neurosurgery, Department of General Neurosurgery, Center for Neurosurgery, University Hospital Cologne, Cologne, Germany
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9
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Burford C, Laxton R, Sidhu Z, Aizpurua M, King A, Bodi I, Ashkan K, Al-Sarraj S. ATRX immunohistochemistry can help refine 'not elsewhere classified' categorisation for grade II/III gliomas. Br J Neurosurg 2019; 33:536-540. [PMID: 31018710 DOI: 10.1080/02688697.2019.1600657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Purpose: The 2016 WHO tumour classification highlights the role of IDH1/2 gene mutation and 1p/19q co-deletion in classifying grade II/III gliomas. A recent cIMPACT-NOW update proposes the use of the term 'Not Elsewhere Classified' (NEC) for IDH-mutant, non co-deleted tumours. Here we show how the incorporation of ATRX immunohistochemistry can be used to better delineate the NEC group. Methods: Clinical data was collected for 112 patients (59% male) treated at our unit. Mutations in IDH1/2 genes were detected by pyrosequencing or immunohistochemistry, 1p/19q co-deletion was assessed with fluorescence in situ hybridisation and ATRX status was determined using immunohistochemical techniques. Tumours were grouped on the basis of molecular markers and outcomes compared. Results: The mean age of diagnosis was 42.6 years (20-73 years). There were 88 oligodendrogliomas (II = 47, III = 41), 18 diffuse astrocytomas (II = 9, III = 9) and 6 oligoastrocytomas (II = 4, III = 2). The majority of gliomas (87.5%) had mutations in IDH1/2. 1p/19q co-deletion was significantly associated with oligodendroglial morphology (p = < 0.001) and was mutually exclusive with ATRX mutation. Classification on the basis of molecular information showed a significant different in survival between the groups. Conclusions: ATRX immunohistochemisty is a useful adjunct which can be used with IDH mutation status, 1p/19q co-deletion and histological findings to further define tumour groups. More work is needed to understand the molecular profiles and prognostic implications for non co-deletion, ATRX preserved cases.
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Affiliation(s)
- C Burford
- Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London , London , UK
| | - R Laxton
- Department of Neuropathology, King's College Hospital , London , UK
| | - Z Sidhu
- Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London , London , UK
| | - M Aizpurua
- Department of Neuropathology, King's College Hospital , London , UK
| | - A King
- Department of Neuropathology, King's College Hospital , London , UK
| | - I Bodi
- Department of Neuropathology, King's College Hospital , London , UK
| | - K Ashkan
- Department of Neurosurgery, King's College Hospital , London , UK
| | - S Al-Sarraj
- Department of Neuropathology, King's College Hospital , London , UK
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10
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Picca A, Berzero G, Di Stefano AL, Sanson M. The clinical use of IDH1 and IDH2 mutations in gliomas. Expert Rev Mol Diagn 2018; 18:1041-1051. [PMID: 30427756 DOI: 10.1080/14737159.2018.1548935] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Mutations in the genes isocitrate dehydrogenase (IDH) 1 and 2 have been reported in a limited number of tumors. In gliomas, IDH mutations are primarily detected in WHO grade II-III tumors and represent a major biomarker with diagnostic, prognostic, and predictive implications. The recent development of IDH inhibitors and vaccines suggests that the IDH mutation is also an appealing target for therapy. Areas covered: This review focuses on the role of IDH mutations in diffuse gliomas. Besides discussing their role in gliomagenesis, we will emphasize the role of IDH mutations in clinical practice as a diagnostic, prognostic and predictive biomarker, and as a potential therapeutic target. Noninvasive detection of the IDH mutation by means of liquid biopsy and MR spectroscopy will also be discussed. Expert commentary: While IDH mutation is a consolidated diagnostic and prognostic biomarker in clinical practice, its role in oncogenesis is far from being elucidated, and there are several pending issues. The routine use of noninvasive techniques for detection and monitoring of the IDH status remains challenging. Although the IDH mutation is a very early alteration in gliomagenesis, it may then be omitted during tumor progression. This observation has important implications when designing targeted clinical trials.
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Affiliation(s)
- Alberto Picca
- a Neuroscience Consortium , University of Pavia , Pavia , Italy
| | - Giulia Berzero
- b Neuroncology Unit , IRCCS Mondino Foundation , Pavia , Italy.,c Biomedical Sciences , University of Pavia , Pavia , Italy
| | - Anna Luisa Di Stefano
- d Sorbonne Universités , Paris , France.,e Department of Neurology , Foch Hospital , Suresnes, Paris , France
| | - Marc Sanson
- d Sorbonne Universités , Paris , France.,f Service de Neurologie 2 , AP-HP, Hôpital de la Pitié-Salpêtrière , Paris , France
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11
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Benesova L, Belsanova B, Kramar F, Halkova T, Benes V, Minarik M. Application of denaturing capillary electrophoresis for the detection of prognostic mutations in isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 genes in brain tumors. J Sep Sci 2018; 41:2819-2827. [PMID: 29791066 DOI: 10.1002/jssc.201701473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 12/12/2022]
Abstract
Malignant transformation in gliomas is frequently supplemented by somatic mutations in isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 genes. It has recently emerged that mutations in these genes are associated with prolonged survival and should be used as prognostic factor in management of brain cancer patients. There are several approaches in use for the detection of isocitrate dehydrogenase 1 and 2 mutations; however, these often exhibit shortcomings such as convoluted protocols with long processing time, complex (and costly) dedicated fluorescent probes, and/or demand on amounts of input DNA. Therefore, a simple and rapid method would be highly desired. Here, we present development and validation of simple and reliable isocitrate dehydrogenase 1 and 2 mutation detection assay using denaturing capillary electrophoresis. The detection sensitivity in terms of the limiting mutated allele fraction detectable estimated from a series of dilution runs was 2.9%. The method was validated by comparing to results obtained by a widely accepted detection technique, the multiplex ligation-dependent probe amplification, on a set of 85 brain tumors. The concordance of both methods was 100%, but denaturing capillary electrophoresis assay required fivefold lower input of DNA (1 versus 5 μL of DNA at concentrations typically between 10 and 30 ng/μL).
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Affiliation(s)
- Lucie Benesova
- Center for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Prague, Czech Republic
| | - Barbora Belsanova
- Center for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Prague, Czech Republic
| | - Filip Kramar
- Department of Neurosurgery, First Faculty of Medicine, Military University Hospital and Charles University, Prague, Czech Republic
| | - Tereza Halkova
- Center for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Prague, Czech Republic
| | - Vladimir Benes
- Department of Neurosurgery, First Faculty of Medicine, Military University Hospital and Charles University, Prague, Czech Republic
| | - Marek Minarik
- Center for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Prague, Czech Republic.,Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
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12
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Urbanovska I, Megova MH, Dwight Z, Kalita O, Uvirova M, Simova J, Tuckova L, Buzrla P, Palecek T, Hajduch M, Dvorackova J, Drabek J. IDH Mutation Analysis in Glioma Patients by CADMA Compared with SNaPshot Assay and two Immunohistochemical Methods. Pathol Oncol Res 2018; 25:971-978. [PMID: 29556922 PMCID: PMC6614140 DOI: 10.1007/s12253-018-0413-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/08/2018] [Indexed: 02/02/2023]
Abstract
Mutations in IDH1/2 genes are a marker of good prognosis for glioma patients, associated with low grade gliomas and secondary glioblastomas. Immunohistochemistry and Sanger sequencing are current standards for IDH1/2 genotyping while many other methods exist. The aim of this study was to validate Competitive amplification of differentially melting amplicons (CADMA) PCR for IDH genotyping by comparison with SNaPshot assay and two immunohistochemical methods. In our study, 87 glioma patients (46 from Olomouc and 41 from Ostrava) were analyzed. IDH1/2 mutations in native bioptical samples were analyzed at DNA level by CADMA and SNaPshot while IDH1 mutations in FFPE samples were analyzed at protein level by two IHC methods. CADMA PCR sensitivity for IDH1 was 96.4% and specificity 100% for 86 concluded samples. SNaPshot assay sensitivity was 92.9% and specificity of 100% for 85 concluded samples. IHC in the laboratory no. 2 reached sensitivity 85.7% and specificity 100% for 86 concluded samples. IHC in the laboratory no. 4 reached sensitivity of 96.4% and specificity of 79.7% in 74 concluded samples. Only one IDH2 mutation was found by SNaPshot while CADMA yielded false negative result. In conclusion, CADMA is a valid method for IDH1 p.(R132H) testing with higher sensitivity than SNaPshot assay. Also, molecular genetic methods of IDH1 testing from native samples were more robust than IHC from FFPE.
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Affiliation(s)
- Irena Urbanovska
- CGB Laboratory Inc., Ostrava, Czech Republic.,Department of Biomedical Sciences, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Magdalena Houdova Megova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 779 00, Olomouc, Czech Republic
| | - Zachary Dwight
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Ondrej Kalita
- Department of Neurosurgery, University Hospital Olomouc, Olomouc, Czech Republic
| | | | | | - Lucie Tuckova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - Petr Buzrla
- Institute of Pathology, Faculty of Medicine and University Hospital, University of Ostrava, Syllabova 19, 703 00, Ostrava - Zábřeh, Czech Republic
| | - Tomas Palecek
- Neurosurgery Clinic, University Hospital Ostrava, Ostrava, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 779 00, Olomouc, Czech Republic
| | - Jana Dvorackova
- Department of Biomedical Sciences, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic. .,Institute of Pathology, Faculty of Medicine and University Hospital, University of Ostrava, Syllabova 19, 703 00, Ostrava - Zábřeh, Czech Republic.
| | - Jiri Drabek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 779 00, Olomouc, Czech Republic.
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13
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Visani M, Acquaviva G, Marucci G, Paccapelo A, Mura A, Franceschi E, Grifoni D, Pession A, Tallini G, Brandes AA, de Biase D. Non-canonical IDH1 and IDH2 mutations: a clonal and relevant event in an Italian cohort of gliomas classified according to the 2016 World Health Organization (WHO) criteria. J Neurooncol 2017; 135:245-254. [PMID: 28748342 DOI: 10.1007/s11060-017-2571-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/13/2017] [Indexed: 02/05/2023]
Abstract
According to the 2016 World Health Organization (WHO) classification of tumors of the central nervous system, assessment of exon 4 mutations in isocitrate dehydrogenase 1 or 2 genes (IDH1 or IDH2) is an essential step in the characterization of gliomas. The p.R132H mutation is the most frequent alteration in IDH genes, however other non-canonical IDH mutations can be identified. The aim of this study is to investigate in depth the prevalence of non-R132H IDH ("non-canonical") mutations in brain tumors classified according to the 2016 WHO scheme and their clonal distribution in neoplastic cells. A total of 288 consecutive cases of brain gliomas (grade II-IV) were analyzed for exon 4 IDH1 and IDH2 mutations. IDH1 and IDH2 analysis was performed using next generation sequencing. Non-canonical IDH mutations were identified in 13/52 (25.0%) grade II gliomas (astrocytomas: 8/31, 25.8%; oligodendrogliomas: 5/21, 23.8%) and in 5/40 (12.5%) grade III gliomas (astrocytomas: 3/25, 12.0%; oligodendrogliomas: 2/15, 13.3%). They were not identified in 196 grade IV gliomas (192 glioblastomas, 4 gliosarcomas). In the large majority (>80%) of tumors IDH mutations, both IDH1-R132H and the non-canonical ones, were present in the large majority (>80%) of neoplastic cells. Our data highlight the importance of investigating not only the IDH1-R132H mutation but also the non-canonical ones. These mutations are clonally distributed, with proportions of mutated neoplastic cells overlapping with those of p.R132H, a finding consistent with their driver role in gliomagenesis.
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Affiliation(s)
- Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Gianluca Marucci
- Anatomic Pathology Unit, AUSL of Bologna, Via Altura 3, 40139, Bologna, Italy
- Department of Neuropathology, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Alexandro Paccapelo
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Antonella Mura
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Enrico Franceschi
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Daniela Grifoni
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy.
- Anatomia Patologica, ASL Bologna, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Scuola di Medicina e Chirurgia, Università di Bologna, Via Altura 3, 40139, Bologna, Italy.
| | - Alba A Brandes
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
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14
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Nagy Á, Garzuly F, Padányi G, Szűcs I, Feldmann Á, Murnyák B, Hortobágyi T, Kálmán B. Molecular Subgroups of Glioblastoma- an Assessment by Immunohistochemical Markers. Pathol Oncol Res 2017; 25:21-31. [PMID: 28948518 DOI: 10.1007/s12253-017-0311-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/15/2017] [Indexed: 12/11/2022]
Abstract
Comprehensive molecular characterization of and novel therapeutic approaches to glioblastoma have been explored as a result of advancements in biotechnologies. In this study, we aimed to bring basic research discoveries closer to clinical practice and ultimately incorporate molecular classification into the routine histopathological evaluation of grade IV gliomas. Integrated results of genome-wide sequencing, transcriptomic and epigenomic analyses by The Cancer Genome Atlas Network defined the classic, proneural, neural and mesenchymal subtypes of this tumor. In a retrospective cohort, we analyzed selected subgroup-defining molecular markers in formalin-fixed paraffin-embedded surgical specimens by immunohistochemistry. Quantitative and qualitative scores of marker expression were tested in hierarchical cluster analyses to evaluate segregations of the molecular subgroups, which then were correlated with clinical parameters including patients' age, gender and overall survival. Our study has confirmed the separation of molecular glioblastoma subgroups with clear trends regarding clinical correlations. Future analyses in a larger, prospective cohort using similar methods are expected to facilitate the development of a molecular diagnostic panel that may complement routine histological work up and support prognostication as well as treatment decisions in glioblastoma.
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Affiliation(s)
- Ádám Nagy
- Faculty of Health Sciences, School of Graduate Studies, University of Pécs, Pécs, Hungary
| | - Ferenc Garzuly
- Markusovszky University Teaching Hospital, University of Pecs, 5. Markusovszky Street, Szombathely, 9700, Hungary
| | - Gergely Padányi
- Markusovszky University Teaching Hospital, University of Pecs, 5. Markusovszky Street, Szombathely, 9700, Hungary
| | | | - Ádám Feldmann
- Faculty of Medicine, Institute of Behavioral Sciences, University of Pécs, Pécs, Hungary
| | - Balázs Murnyák
- Department of Pathology, Division of Neuropathology, University of Debrecen, Debrecen, Hungary
| | - Tibor Hortobágyi
- Department of Pathology, Division of Neuropathology, University of Debrecen, Debrecen, Hungary
| | - Bernadette Kálmán
- Faculty of Health Sciences, School of Graduate Studies, University of Pécs, Pécs, Hungary. .,Markusovszky University Teaching Hospital, University of Pecs, 5. Markusovszky Street, Szombathely, 9700, Hungary.
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15
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Pediatric high-grade glioma: current molecular landscape and therapeutic approaches. J Neurooncol 2017; 134:541-549. [PMID: 28357536 DOI: 10.1007/s11060-017-2393-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/24/2017] [Indexed: 01/06/2023]
Abstract
High-grade pediatric central nervous system glial tumors are comprised primarily of anaplastic astrocytomas (AA, WHO grade III) and glioblastomas (GBM, WHO grade IV). High-grade gliomas are most commonly diagnosed in the primary setting in children, but as in adults, they can also arise as a result of transformation of a low-grade malignancy, though with limited frequency in the pediatric population. The molecular genetics of high-grade gliomas in the pediatric population are distinct from their adult counterparts. In contrast to the adult population, high-grade gliomas in children are relatively infrequent, representing less than 20% of cases.
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16
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Sirirat T, Chuncharunee S, Nipaluk P, Siriboonpiputtana T, Chareonsirisuthigul T, Limsuwannachot N, Rerkamnuaychoke B. Mutation Analysis of Isocitrate Dehydrogenase (IDH1/2) and DNA Methyltransferase 3A (DNMT3A) in Thai Patients with Newly Diagnosed Acute Myeloid Leukemia. Asian Pac J Cancer Prev 2017; 18:413-420. [PMID: 28345823 PMCID: PMC5454736 DOI: 10.22034/apjcp.2017.18.2.413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Acute myeloid leukemia (AML) is a clonal hematopoietic stem/progenitor cell disorder which features several genetic mutations. Recurrent genetic alterations identified in AML are recognized as causes of the disease, finding application as diagnostic, prognostic and monitoring markers, with potential use as targets for cancer therapy. Here, we performed a pyrosequencing technique to investigate common mutations of IDH1, IDH2 and DNMT3A in 81 newly diagnosed AML patients. The prevalences of IDH1, IDH2 and DNMT3A mutations were 6.2%, 18.5%, and 7.4%, respectively. In addition, exclusive mutations in IDH1 codon 132 (R132H, R132C, R132G and R132S) were identified in all IDH1-mutated cases indicating that these are strongly associated with AML. Interestingly, higher median blast cell counts were significantly associated with IDH1/2 and DNMT3A mutations. In summary, we could establish a routine robust pyrosequencing method to detect common mutations in IDH1/2 and DNMT3A and demonstrate the frequency of those mutations in adult Thai AML patients.
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Affiliation(s)
- Tanasan Sirirat
- Doctoral Program in Clinical Pathology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University. Bangkok, 10400, Thailand.
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17
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Luxen D, Gielen GH, Waha A, Isselstein L, Müller T, Koch P, Hammes J, Becker A, Simon M, Wurst P, Endl E, Pietsch T, Gessi M, Waha A. MTSS1 is epigenetically regulated in glioma cells and inhibits glioma cell motility. Transl Oncol 2017; 10:70-79. [PMID: 27988423 PMCID: PMC5167248 DOI: 10.1016/j.tranon.2016.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 11/18/2016] [Accepted: 11/22/2016] [Indexed: 12/23/2022] Open
Abstract
Epigenetic silencing by DNA methylation in brain tumors has been reported for many genes, however, their function on pathogenesis needs to be evaluated. We investigated the MTSS1 gene, identified as hypermethylated by differential methylation hybridization (DMH). Fifty-nine glioma tissue samples and seven glioma cell lines were examined for hypermethylation of the MTSS1 promotor, MTSS1 expression levels and gene dosage. GBM cell lines were treated with demethylating agents and interrogated for functional consequences of MTSS1 expression after transient transfection. Hypermethylation was significantly associated with IDH1/2 mutation. Comparative SNP analysis indicates higher incidence of loss of heterozygosity of MTSS1 in anaplastic astrocytomas and secondary glioblastomas as well as hypermethylation of the remaining allele. Reversal of promoter hypermethylation results in an increased MTSS1 expression. Cell motility was significantly inhibited by MTSS1 overexpression without influencing cell growth or apoptosis. Immunofluorescence analysis of MTSS1 in human astrocytes indicates co-localization with actin filaments. MTSS1 is down-regulated by DNA methylation in glioblastoma cell lines and is part of the G-CIMP phenotype in primary glioma tissues. Our data on normal astrocytes suggest a function of MTSS1 at focal contact structures with an impact on migratory capacity but no influence on apoptosis or cellular proliferation.
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Affiliation(s)
- Daniel Luxen
- Department of Neuropathology, University of Bonn, Germany
| | | | - Anke Waha
- Department of Neuropathology, University of Bonn, Germany
| | | | - Tim Müller
- Department of Neuropathology, University of Bonn, Germany
| | - Philipp Koch
- Institute of Reconstructive Neurobiology, LIFE & BRAIN, University of Bonn, Germany
| | | | - Albert Becker
- Department of Neuropathology, University of Bonn, Germany
| | | | - Peter Wurst
- Department of Molecular Medicine and Experimental Immunology, (Core Facility Flow Cytometry) University of Bonn, Germany
| | - Elmar Endl
- Department of Molecular Medicine and Experimental Immunology, (Core Facility Flow Cytometry) University of Bonn, Germany
| | | | - Marco Gessi
- Department of Neuropathology, University of Bonn, Germany
| | - Andreas Waha
- Department of Neuropathology, University of Bonn, Germany.
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18
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Precise Detection of IDH1/2 and BRAF Hotspot Mutations in Clinical Glioma Tissues by a Differential Calculus Analysis of High-Resolution Melting Data. PLoS One 2016; 11:e0160489. [PMID: 27529619 PMCID: PMC4987040 DOI: 10.1371/journal.pone.0160489] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/20/2016] [Indexed: 01/08/2023] Open
Abstract
High resolution melting (HRM) is a simple and rapid method for screening mutations. It offers various advantages for clinical diagnostic applications. Conventional HRM analysis often yields equivocal results, especially for surgically obtained tissues. We attempted to improve HRM analyses for more effective applications to clinical diagnostics. HRM analyses were performed for IDH1R132 and IDH2R172 mutations in 192 clinical glioma samples in duplicate and these results were compared with sequencing results. BRAFV600E mutations were analyzed in 52 additional brain tumor samples. The melting profiles were used for differential calculus analyses. Negative second derivative plots revealed additional peaks derived from heteroduplexes in PCR products that contained mutations; this enabled unequivocal visual discrimination of the mutations. We further developed a numerical expression, the HRM-mutation index (MI), to quantify the heteroduplex-derived peak of the mutational curves. Using this expression, all IDH1 mutation statuses matched those ascertained by sequencing, with the exception of three samples. These discordant results were all derived from the misinterpretation of sequencing data. The effectiveness of our approach was further validated by analyses of IDH2R172 and BRAFV600E mutations. The present analytical method enabled an unequivocal and objective HRM analysis and is suitable for reliable mutation scanning in surgically obtained glioma tissues. This approach could facilitate molecular diagnostics in clinical environments.
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19
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Zhang J, Yang JH, Quan J, Kang X, Wang HJ, Dai PG. Identification of MGMT promoter methylation sites correlating with gene expression and IDH1 mutation in gliomas. Tumour Biol 2016; 37:13571-13579. [PMID: 27468718 DOI: 10.1007/s13277-016-5153-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/12/2016] [Indexed: 12/30/2022] Open
Abstract
O6-methylguanine-DNA methyltransferase (MGMT) gene promoter methylation was reported to be an independent prognostic and predictive factor in glioma patients who received temozolomide treatment. However, the predictive value of MGMT methylation was recently questioned by several large clinical studies. The purpose of this study is to identify MGMT gene promoter CpG sites or region whose methylation were closely correlated with its gene expression to elucidate this contradictory clinical observations. The methylation status for all CpG dinucleotides in MGMT promoter and first exon region were determined in 42 Chinese glioma patients, which were then correlated with MGMT gene expression, IDH1 mutation, and tumor grade. In whole 87 CpG dinucleotides analyzed, three distinct CpG regions covering 28 CpG dinucleotides were significantly correlated with MGMT gene expression; 10 CpG dinucleotides were significantly correlated with glioma classification (p < 0.05). Isocitrate dehydrogenase 1 (IDH1) mutation and MGMT gene hypermethylation significantly co-existed, but not for MGMT gene expression. The validation cohort of gliomas treated with standard of care and comparison of the CpGs we identified with the current CpGs used in clinical setting will be very important for gliomas individual medicine in the future.
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Affiliation(s)
- Jie Zhang
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, China
| | - Jian-Hui Yang
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, China
| | - Jia Quan
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, China
| | - Xing Kang
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, China
| | - Hui-Juan Wang
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, China
| | - Peng-Gao Dai
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, China.
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20
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Kang X, Chen R, Zhang J, Li G, Dai PG, Chen C, Wang HJ. Expression Profile Analysis of Zinc Transporters (ZIP4, ZIP9, ZIP11, ZnT9) in Gliomas and their Correlation with IDH1 Mutation Status. Asian Pac J Cancer Prev 2016; 16:3355-60. [PMID: 25921144 DOI: 10.7314/apjcp.2015.16.8.3355] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zinc transporters have been considered as essential regulators in many cancers; however, their mechanisms remain unknown, especially in gliomas. Isocitrate dehydrogenase 1(IDH1) mutation is crucial to glioma. This study aimed to investigate whether zinc transporters are correlated with glioma grade and IDH1 mutation status. MATERIALS AND METHODS IDH1 mutation status and mRNA expression of four zinc transporters (ZIP4, ZIP9, ZIP11, and ZnT9) were determined by subjecting a panel of 74 glioma tissue samples to quantitative real-time PCR and pyrosequencing. The correlations between the expression levels of these zinc transporter genes and the grade of glioma, as well as IDH1 mutation status, were investigated. RESULTS Among the four zinc transporter genes, high ZIP4 expression and low ZIP11 expression were significantly associated with higher grade (grades III and IV) tumors compared with lower grade (grades I and II) counterparts (p<0.0001). However, only ZIP11 exhibited weak correlation with IDH1 mutation status (p=0.045). Samples with mutations in IDH1 displayed higher ZIP11 expression than those without IDH1 mutations. CONCLUSIONS This finding indicated that zinc transporters may interact with IDH1 mutation by direct modulation or action in some shared pathways or genes to promote the development of glioma. Zinc transporters may play an important role in glioma. ZIP4 and ZIP11 are promising molecular diagnostic markers and novel therapeutic targets. Nevertheless, the detailed biological function of zinc transporters and the mechanism of the potential interaction between ZIP11 and IDH1 mutation in gliomagenesis should be further investigated.
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Affiliation(s)
- Xing Kang
- School of Life Sciences, Northwest University, Xi'an, China E-mail : ,
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21
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Liu A, Hou C, Chen H, Zong X, Zong P. Genetics and Epigenetics of Glioblastoma: Applications and Overall Incidence of IDH1 Mutation. Front Oncol 2016; 6:16. [PMID: 26858939 PMCID: PMC4731485 DOI: 10.3389/fonc.2016.00016] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 01/16/2016] [Indexed: 12/02/2022] Open
Abstract
Glioblastoma is the most fatal brain cancer found in humans. Patients suffering from glioblastoma have a dismal prognosis, with a median survival of 15 months. The tumor may develop rapidly de novo in older patients or through progression from anaplastic astrocytomas in younger patients if glioblastoma is primary or secondary, respectively. During the past decade, significant advances have been made in the understanding of processes leading to glioblastoma, and several important genetic defects that appear to be important for the development and progression of this tumor have been identified. Particularly, the discovery of recurrent mutations in the isocitrate dehydrogenase 1 (IDH1) gene has shed new light on the molecular landscape in glioblastoma. Indeed, emerging research on the consequences of mutant IDH1 protein expression suggests that its neomorphic enzymatic activity catalyzing the production of the oncometabolite 2-hydroxyglutarate influences a range of cellular programs that affect the epigenome and contribute to glioblastoma development. One of the exciting observations is the presence of IDH1 mutation in the vast majority of secondary glioblastoma, while it is almost absent in primary glioblastoma. Growing data indicate that this particular mutation has clinical and prognostic importance and will become a critical early distinction in diagnosis of glioblastoma.
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Affiliation(s)
- Aizhen Liu
- Department of Oncology, Yidu Central Hospital , Jinan , China
| | - Chunfeng Hou
- Department of Oncology Nursing, Yidu Central Hospital , Jinan , China
| | - Hongfang Chen
- Department of Oncology, Yidu Central Hospital , Jinan , China
| | - Xuan Zong
- Department of Oncology, Shandong University School of Medicine , Jinan , China
| | - Peijun Zong
- Department of Oncology, Yidu Central Hospital , Jinan , China
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22
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Molecular heterogeneity characterizes glioblastoma with lipoblast/adipocyte-like cytology. Virchows Arch 2015; 467:105-9. [PMID: 25896447 DOI: 10.1007/s00428-015-1774-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/24/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
Glioblastoma, the most common primary brain tumor in adults, may rarely show among unusual histological patterns lipoblast/adipocyte-like features. The genetic features of such cases are not yet well characterized, and molecular data are available for only few cases. In order to further expand our knowledge about their molecular profile, we analyzed four cases of glioblastoma with adipocyte-like features. Multiplex ligation-dependent probe amplification (MLPA) revealed loss of PTEN and MDM2 amplification in two cases while another case was characterized by CDKN2A deletion. Conversely, we did not find any evidence of EGFR amplification, BRAF (V600E) or IDH1/2 mutations. Our results, along with data published in previous studies, showed that glioblastoma with lipoblast/adipocyte-like cytology present a heterogeneous genetic background and therefore seem to represent more a rare phenotypic variant than a specific tumor subtype.
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23
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Mendez G, Ozpinar A, Raskin J, Gultekin SH, Ross DA. Case comparison and literature review of glioblastoma: A tale of two tumors. Surg Neurol Int 2014; 5:121. [PMID: 25140280 PMCID: PMC4135538 DOI: 10.4103/2152-7806.138034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/11/2014] [Indexed: 11/25/2022] Open
Abstract
Background: Diagnosis of glioblastoma multiforme (GBM) includes a heterogeneous group of tumors. We describe two cases with histopathologically and molecularly similar tumors, but very different outcomes. We attempt to illustrate the need for improved prognostic markers for GBM. Case Description: Two patients with similar molecular profiles were retrospectively identified. The following markers were assessed: O6-methylguanine DNA methyltransferase (MGMT) methylation, isocitrate dehydrogenase (IDH) 1 and 2 status, epidermal growth factor receptor (EGFR) amplification, phosphatase and tensin homolog (PTEN) status, Ki-67, p53, and 1p/19q status. Each patient was assigned a Karnofsky performance score at presentation. Case 1 (62-year-old male) was a right temporal lobe glioblastoma with a molecular profile of amplified EGFR, normal PTEN, no IDH1/2 mutation, 28.7% MGMT promoter methylation, 5-20% Ki-67, 1p deletion, and 19q intact. The patient underwent resection followed by radiation therapy and 2 years of chemotherapy, and was asymptomatic and tumor free 5 years post diagnosis. Tumor eventually recurred and the patient expired 72 months after initial diagnosis. Case 2 (63-year-old male) was a right frontal white matter mass consistent with glioblastoma with a molecular profile of amplified EGFR, absent PTEN, no IDH1/2 mutation, 9.9% MGMT promoter methylation, 5-10% Ki-67, and 1p/19q status inconclusive. A radical subtotal resection was performed; however, 2 weeks later symptoms had returned. Subsequent imaging revealed a tumor larger than at diagnosis. The patient expired 3 months after initial diagnosis. Conclusion: The need for formulating more robust means to classify GBM tumor subtypes is paramount. Standard histopathologic and molecular analyses are costly and did not provide either of these patients with a realistic appraisal of their prognosis. Individualized whole genome testing similar to that being reported for medulloblastoma and other tumors may be preferable to the array of tests as currently utilized.
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Affiliation(s)
- Gustavo Mendez
- Department of Neurological Surgery, Oregon Health & Science University, Portland, OR, USA
| | - Alp Ozpinar
- Department of Neurological Surgery, Oregon Health & Science University, Portland, OR, USA
| | - Jeffrey Raskin
- Department of Neurological Surgery, Oregon Health & Science University, Portland, OR, USA
| | - Sakir H Gultekin
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Donald A Ross
- Department of Neurological Surgery, Oregon Health & Science University, Portland, OR, USA ; Section of Neurological Surgery, Operative Care Division, Portland Veterans Administration Hospital, Portland, OR, USA
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Arita H, Narita Y, Yoshida A, Hashimoto N, Yoshimine T, Ichimura K. IDH1/2 mutation detection in gliomas. Brain Tumor Pathol 2014; 32:79-89. [PMID: 25008158 DOI: 10.1007/s10014-014-0197-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/17/2014] [Indexed: 12/25/2022]
Abstract
Somatic mutations of isocitrate dehydrogenase 1 and 2 (IDH1/2) are strongly associated with pathological subtypes, genetic profiles, and clinical features in gliomas. The IDH1/2 status is currently regarded as one of the most important molecular markers in gliomas and should be assessed accurately and robustly. However, the methods used for IDH1/2 testing are not fully standardized. The purpose of this paper is to review the clinical significance of IDH1/2 mutations and the methods used for IDH1/2 testing. The optimal method for IDH1/2 testing varies depending on a number of factors, including the purpose, sample types, sample number, or laboratory equipment. It is therefore important to acknowledge the advantages and disadvantages of each method.
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Affiliation(s)
- Hideyuki Arita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan,
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A new sensitive PCR assay for one-step detection of 12 IDH1/2 mutations in glioma. Acta Neuropathol Commun 2014; 2:58. [PMID: 24889502 PMCID: PMC4229941 DOI: 10.1186/2051-5960-2-58] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/23/2014] [Indexed: 01/13/2023] Open
Abstract
INTRODUCTION Mutations in isocitrate dehydrogenase genes IDH1 or IDH2 are frequent in glioma, and IDH mutation status is a strong diagnostic and prognostic marker. Current IDH mutation screening is performed with an immunohistochemistry (IHC) assay specific for IDH1 R132H, the most common mutation. Sequencing is recommended as a second-step test for IHC-negative or -equivocal cases. We developed and validated a new real-time quantitative polymerase chain reaction (PCR) assay for single-step detection of IDH1 R132H and 11 rare IDH1/2 mutations in formalin-fixed paraffin-embedded (FFPE) glioma samples. Performance of the IDH1/2 PCR assay was compared to IHC and Sanger sequencing. RESULTS The IDH1/2 PCR assay combines PCR clamping for detection of 7 IDH1 and 5 IDH2 mutations, and Amplification Refractory Mutation System technology for specific identification of the 3 most common mutations (IDH1 R132H, IDH1 R132C, IDH2 R172K). Analytical sensitivity of the PCR assay for mutation detection was <5% for 11/12 mutations (mean: 3.3%), and sensitivity for mutation identification was very high (0.8% for IDH1 R132H; 1.2% for IDH1 R132C; 0.6% for IDH2 R172K). Assay performance was further validated on 171 clinical glioma FFPE samples; of these, 147 samples met the selection criteria and 146 DNA samples were successfully extracted. IDH1/2 status was successfully obtained in 91% of cases. All but one positive IDH1 R132H-IHC cases were concordantly detected by PCR and 3 were not detected by sequencing. Among the IHC-negative cases (n = 72), PCR detected 12 additional rare mutations (10 IDH1, 2 IDH2). All mutations detected by sequencing (n = 67) were concordantly detected by PCR and 5/66 sequencing-negative cases were PCR-positive (overall concordance: 96%). Analysis of synthetic samples representative of the 11 rare IDH1/2 mutations detected by the assay produced 100% correct results. CONCLUSIONS The new IDH1/2 PCR assay has a high technical success rate and is more sensitive than Sanger sequencing. Positive concordance was 98% with IHC for IDH1 R132H detection and 100% with sequencing. The PCR assay can reliably be performed on FFPE samples and has a faster turnaround time than current IDH mutation detection algorithms. The assay should facilitate implementation of a comprehensive IDH1/2 testing protocol in routine clinical practice.
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Arita H, Narita Y, Matsushita Y, Fukushima S, Yoshida A, Takami H, Miyakita Y, Ohno M, Shibui S, Ichimura K. Development of a robust and sensitive pyrosequencing assay for the detection of IDH1/2 mutations in gliomas. Brain Tumor Pathol 2014; 32:22-30. [PMID: 24748374 DOI: 10.1007/s10014-014-0186-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/30/2014] [Indexed: 10/25/2022]
Abstract
Assessment of the mutational status of the isocitrate dehydrogenase 1/2 (IDH1/2) gene has become an integral part of the standard diagnostic procedure and, therefore, needs to be accurate. This may, however, be compromised by various factors including the method of analysis and a low tumor cell content. We have developed a rapid, sensitive and robust assay to detect all types of mutation in either IDH1 or IDH2 using pyrosequencing. The efficacy of detecting mutation was evaluated using a panel of control plasmids representing all the different types of IDH1/2 mutation and a set of 160 tumor specimens. The sensitivity of the assays was examined by a serial dilution analysis performed on samples containing various ratios of wild-type and mutant alleles. The pyrosequencing assay detected as little as 5 % of mutant alleles for most mutation types, while conventional Sanger sequencing required the presence of at least 20 % of mutant alleles for identifying mutations. The pyrosequencing assay detected IDH1/2 mutations in three samples which were missed by Sanger sequencing due to their low tumor cell contents. Our assay is particularly useful for the analysis of a large number of specimens as in a retrospective clinical study for example.
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Affiliation(s)
- Hideyuki Arita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
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Bodi I, Curran O, Selway R, Elwes R, Burrone J, Laxton R, Al-Sarraj S, Honavar M. Two cases of multinodular and vacuolating neuronal tumour. Acta Neuropathol Commun 2014; 2:7. [PMID: 24444358 PMCID: PMC3899932 DOI: 10.1186/2051-5960-2-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/13/2013] [Indexed: 01/09/2023] Open
Abstract
An unusual multinodular and vacuolating neuronal tumour (MVNT) has been described in the cerebral hemispheres of ten patients with adult-onset seizures. We report the findings in two cases with similar features, a surgical resection and the other an autopsy specimen. Case 1, a 34-year-old female, underwent surgical resection for a multinodular non-enhancing frontal white matter lesion causing intractable epilepsy. Case 2, presented with motor neurone disease (MND) at the age of 71 and MRI scanning revealed extensive multinodular non-enhancing white matter lesions in the temporal lobe. There was no history of epilepsy and post mortem histology confirmed MND. Macroscopically multiple small grey well-formed, discrete and coalescent nodules were seen in the deep cortex and subcortical white matter. On histology, mature-looking neurons with large cytoplasmic vacuoles were distributed in a fibrillary background, where vacuoles were also noted. In the resected tumour scattered oligodendroglia-like cells were present. No ganglion cells were seen. The vacuolated cells exhibited immunopositivity for synaptophysin, HuC/HuD and p62 but were negative for NeuN, neurofilament, GFAP, IDH1, nestin and CD34. Electron microscopy showed non-membrane bound cytoplasmic vacuoles in the neurons and in some neuronal processes. The seizures recurred in Case 1. Some clinicopathological features of this lesion suggest a possible relationship with dysembryoplastic neuroepithelial tumour (DNT) although the morphological features are not typical of DNT. Case 2 demonstrates that MVNT may remain asymptomatic.
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Gliomatosis Cerebri Type 1 with Extensive Involvement of the Spinal Cord and BRAF V600E Mutation. Pathol Oncol Res 2013; 20:215-20. [PMID: 24353007 DOI: 10.1007/s12253-013-9732-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 12/04/2013] [Indexed: 11/26/2022]
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Zhang C, Moore LM, Li X, Yung WKA, Zhang W. IDH1/2 mutations target a key hallmark of cancer by deregulating cellular metabolism in glioma. Neuro Oncol 2013; 15:1114-26. [PMID: 23877318 DOI: 10.1093/neuonc/not087] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) enzymes have recently become a focal point for research aimed at understanding the biology of glioma. IDH1 and IDH2 are mutated in 50%-80% of astrocytomas, oligodendrogliomas, oligoastrocytomas, and secondary glioblastomas but are seldom mutated in primary glioblastomas. Gliomas with IDH1/2 mutations always harbor other molecular aberrations, such as TP53 mutation or 1p/19q loss. IDH1 and IDH2 mutations may serve as prognostic factors because patients with an IDH-mutated glioma survive significantly longer than those with an IDH-wild-type tumor. However, the molecular pathogenic role of IDH1/2 mutations in the development of gliomas is unclear. The production of 2-hydroxyglutarate and enhanced NADP+ levels in tumor cells with mutant IDH1/2 suggest mechanisms through which these mutations contribute to tumorigenesis. Elucidating the pathogenesis of IDH mutations will improve understanding of the molecular mechanisms of gliomagenesis and may lead to development of a new molecular classification system and novel therapies.
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Affiliation(s)
- Chunzhi Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Abstract
Mutations in isocitrate dehydrogenase -1 or -2 (IDH1 or IDH2) are found in the majority of WHO grade II and III diffuse gliomas and secondary glioblastomas. IDH mutation screening is rapidly becoming part of the routine pathological work up of human brain tumors, providing both diagnostic and prognostic information. Here, we characterize four rare and novel IDH1 mutations identified in surgical human glioma samples: two instances of an IDH1 p.R132S mutation caused by a previously undescribed dinucleotide deletion/insertion mutation, a novel homozygous somatic IDH1 p.R132L mutation, and an IDH1 p.R100Q mutation. Characterization of novel and rare IDH mutations may provide additional insight into the mechanisms of mutant IDH in neoplasia. Furthermore, given the clinical import of IDH status, these results highlight the need for comprehensive mutation screening, beyond the targeted identification of common pathogenic variants.
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Gessi M, Hammes J, Lauriola L, Dörner E, Kirfel J, Kristiansen G, zur Muehlen A, Denkhaus D, Waha A, Pietsch T. GNA11andN-RASmutations: alternatives for MAPK pathway activating GNAQ mutations in primary melanocytic tumours of the central nervous system. Neuropathol Appl Neurobiol 2013; 39:417-25. [DOI: 10.1111/j.1365-2990.2012.01288.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Cykowski MD, Allen RA, Fung KM, Harmon MA, Dunn ST. Pyrosequencing of IDH1 and IDH2 mutations in brain tumors and non-neoplastic conditions. ACTA ACUST UNITED AC 2013; 21:214-20. [PMID: 23111198 DOI: 10.1097/pdm.0b013e31825d802b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The molecular profiling of brain tumors, including testing for MGMT promoter methylation and chromosome 1p/19q deletion, can provide both diagnostic and prognostic information that may guide treatment. Isocitrate dehydrogenase (IDH) mutation testing is a recent addition to this armamentarium of molecular pathology tools that similarly provides both diagnostic (eg, glioma vs. gliosis) and prognostic information. Herein, we describe a pyrosequencing-based approach to IDH1 and IDH2 mutation testing and its application to 139 neoplastic and non-neoplastic central nervous system specimens. Several technical issues encountered in the development of the assay, particularly with regard to the optimization of the sequencing reaction, are described. Mutations in IDH1 codon 132 or IDH2 codon 172 were identified in 31.2% of all screened cases and 46.2% of screened World Health Organization grade I to IV gliomas (n=93), with mutations arising exclusively in grade II to IV oligodendroglial, astrocytic, or mixed oligoastrocytic neoplasms. Examination of the relationship between the mutation status and other pertinent variables demonstrated a significant male predominance among IDH1-mutated gliomas, most notably in grade III to IV astrocytic neoplasms. A significant association between IDH1/IDH2 mutation and 1p/19q deletion was also seen (Kendall τ coefficient=0.26, P=0.018), although several cases with 1p/19q deletion were IDH1/IDH2 wild type.
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Affiliation(s)
- Matthew D Cykowski
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, USA
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Choi J, Lee EY, Shin KJ, Minn YK, Kim J, Kim SH. IDH1 mutation analysis in low cellularity specimen: a limitation of diagnostic accuracy and a proposal for the diagnostic procedure. Pathol Res Pract 2013; 209:284-90. [PMID: 23561624 DOI: 10.1016/j.prp.2013.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/02/2013] [Accepted: 02/03/2013] [Indexed: 11/16/2022]
Abstract
Recently, new techniques for detecting IDH1 mutations have been developed. Most studies assessed the mutation status in glioma tissue without consideration of the size of the samples. We assessed the mutation status of IDH1 in simulated small biopsied tissue from 5 low grade gliomas, prepared by grid cutting procedure with direct sequencing, IDH1 immunohistochemistry (IHC), multiplex PCR with single base extension (SBE) assay and PNA-clamping method, and then analyzed the agreement between the methods. Kappa values were 0.53 (direct sequencing), 0.59 (multiplex PCR with SBE assay), and 0.69 (PNA-clamping method). Discrepant results between the methods were observed in lower cellularity samples. Twelve out of 25 cases were classified as wild type by direct sequencing, even with IDH1 IHC-positive cells, whereas 6, 8, and 11 of IHC-negative cases were classified as mutant cases by other 3 methods. In conclusion, newly developed sensitive methods, such as the PNA-clamping method and multiplex PCR with SBE assay, are practically useful in addition to the conventional IDH1 IHC in small biopsied samples.
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Affiliation(s)
- Junjeong Choi
- Department of Pathology, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
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Gielen GH, Gessi M, Hammes J, Kramm CM, Waha A, Pietsch T. H3F3A K27M mutation in pediatric CNS tumors: a marker for diffuse high-grade astrocytomas. Am J Clin Pathol 2013; 139:345-9. [PMID: 23429371 DOI: 10.1309/ajcpabohbc33fvmo] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Brain tumors are one of the most common childhood malignancies. Diffuse high-grade gliomas represent approximately 10% of pediatric brain tumors. Exon sequencing has identified a mutation in K27M of the histone H3.3 gene (H3F3A K27M and G34R/V) in about 20% of pediatric glioblastomas, but it remains to be seen whether these mutations can be considered specific for pediatric diffuse high-grade astrocytomas or also occur in other pediatric brain tumors. We performed a pyrosequencing-based analysis for the identification of H3F3A codon 27 and codon 34 mutations in 338 pediatric brain tumors. The K27M mutation occurred in 35 of 129 glioblastomas (27.1%) and in 5 of 28 (17.9%) anaplastic astrocytomas. None of the other tumor entities showed H3F3A K27M mutation. Because H3F3A K27M mutations occur exclusively in pediatric diffuse high-grade astrocytomas, analysis of codon 27 mutational status could be useful in the differential diagnosis of these neoplasms.
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Affiliation(s)
- Gerrit H. Gielen
- Institute of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Marco Gessi
- Institute of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Jennifer Hammes
- Institute of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Christof M. Kramm
- University Children's Hospital, Martin-Luther-University Medical Center, Halle, Germany
| | - Andreas Waha
- Institute of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Torsten Pietsch
- Institute of Neuropathology, University of Bonn Medical Center, Bonn, Germany
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Leu S, von Felten S, Frank S, Vassella E, Vajtai I, Taylor E, Schulz M, Hutter G, Hench J, Schucht P, Boulay JL, Mariani L. IDH/MGMT-driven molecular classification of low-grade glioma is a strong predictor for long-term survival. Neuro Oncol 2013; 15:469-79. [PMID: 23408861 DOI: 10.1093/neuonc/nos317] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Low-grade gliomas (LGGs) are rare brain neoplasms, with survival spanning up to a few decades. Thus, accurate evaluations on how biomarkers impact survival among patients with LGG require long-term studies on samples prospectively collected over a long period. METHODS The 210 adult LGGs collected in our databank were screened for IDH1 and IDH2 mutations (IDHmut), MGMT gene promoter methylation (MGMTmet), 1p/19q loss of heterozygosity (1p19qloh), and nuclear TP53 immunopositivity (TP53pos). Multivariate survival analyses with multiple imputation of missing data were performed using either histopathology or molecular markers. Both models were compared using Akaike's information criterion (AIC). The molecular model was reduced by stepwise model selection to filter out the most critical predictors. A third model was generated to assess for various marker combinations. RESULTS Molecular parameters were better survival predictors than histology (ΔAIC = 12.5, P< .001). Forty-five percent of studied patients died. MGMTmet was positively associated with IDHmut (P< .001). In the molecular model with marker combinations, IDHmut/MGMTmet combined status had a favorable impact on overall survival, compared with IDHwt (hazard ratio [HR] = 0.33, P< .01), and even more so the triple combination, IDHmut/MGMTmet/1p19qloh (HR = 0.18, P< .001). Furthermore, IDHmut/MGMTmet/TP53pos triple combination was a significant risk factor for malignant transformation (HR = 2.75, P< .05). CONCLUSION By integrating networks of activated molecular glioma pathways, the model based on genotype better predicts prognosis than histology and, therefore, provides a more reliable tool for standardizing future treatment strategies.
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Affiliation(s)
- Severina Leu
- Department of Biomedicine, University Hospital of Basel, Spitalstrasse 21, CH-4031 Basel, Switzerland
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Sturm D, Witt H, Hovestadt V, Khuong-Quang DA, Jones DTW, Konermann C, Pfaff E, Tönjes M, Sill M, Bender S, Kool M, Zapatka M, Becker N, Zucknick M, Hielscher T, Liu XY, Fontebasso AM, Ryzhova M, Albrecht S, Jacob K, Wolter M, Ebinger M, Schuhmann MU, van Meter T, Frühwald MC, Hauch H, Pekrun A, Radlwimmer B, Niehues T, von Komorowski G, Dürken M, Kulozik AE, Madden J, Donson A, Foreman NK, Drissi R, Fouladi M, Scheurlen W, von Deimling A, Monoranu C, Roggendorf W, Herold-Mende C, Unterberg A, Kramm CM, Felsberg J, Hartmann C, Wiestler B, Wick W, Milde T, Witt O, Lindroth AM, Schwartzentruber J, Faury D, Fleming A, Zakrzewska M, Liberski PP, Zakrzewski K, Hauser P, Garami M, Klekner A, Bognar L, Morrissy S, Cavalli F, Taylor MD, van Sluis P, Koster J, Versteeg R, Volckmann R, Mikkelsen T, Aldape K, Reifenberger G, Collins VP, Majewski J, Korshunov A, Lichter P, Plass C, Jabado N, Pfister SM. Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell 2012; 22:425-37. [PMID: 23079654 DOI: 10.1016/j.ccr.2012.08.024] [Citation(s) in RCA: 1325] [Impact Index Per Article: 110.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/03/2012] [Accepted: 08/24/2012] [Indexed: 12/30/2022]
Abstract
Glioblastoma (GBM) is a brain tumor that carries a dismal prognosis and displays considerable heterogeneity. We have recently identified recurrent H3F3A mutations affecting two critical amino acids (K27 and G34) of histone H3.3 in one-third of pediatric GBM. Here, we show that each H3F3A mutation defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and that they are mutually exclusive with IDH1 mutations, which characterize a third mutation-defined subgroup. Three further epigenetic subgroups were enriched for hallmark genetic events of adult GBM and/or established transcriptomic signatures. We also demonstrate that the two H3F3A mutations give rise to GBMs in separate anatomic compartments, with differential regulation of transcription factors OLIG1, OLIG2, and FOXG1, possibly reflecting different cellular origins.
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Affiliation(s)
- Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) Heidelberg, 69120 Heidelberg, Germany
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Szuhai K, Cleton-Jansen AM, Hogendoorn PCW, Bovée JVMG. Molecular pathology and its diagnostic use in bone tumors. Cancer Genet 2012; 205:193-204. [PMID: 22682618 DOI: 10.1016/j.cancergen.2012.04.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 03/30/2012] [Accepted: 04/04/2012] [Indexed: 12/22/2022]
Abstract
Bone tumors are considered by most pathologists difficult to diagnose as they are rare, have overlapping morphology, need radiological correlation, and the usefulness of immunohistochemistry is limited, making conventional morphology the cornerstone of the diagnosis. Over the past decade, more and more has become known of the molecular background of bone tumors. Three groups of bone tumors are recognized, namely, tumors with specific translocations combined with a relatively simple karyotype involving chromosomal translocations (Ewing sarcoma, aneurysmal bone cyst), tumors with specific gene mutations or amplifications (chondrosarcoma, fibrous dysplasia, chordoma), and sarcomas with genetic instability and as a consequence complex karyotypes (osteosarcoma). Technical advancements will rapidly reveal new alterations in the more rare sarcoma subtypes for which the molecular background has remained enigmatic. Opening the archives and using new technologies, as well as refinement of existing technologies for decalcified paraffin-embedded tissue, may bring to light more specific genetic aberrations in bone tumors that can be applied in molecular diagnostics in the near future.
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Affiliation(s)
- Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, The Netherlands
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Müller T, Gessi M, Waha A, Isselstein LJ, Luxen D, Freihoff D, Freihoff J, Becker A, Simon M, Hammes J, Denkhaus D, zur Mühlen A, Pietsch T, Waha A. Nuclear Exclusion of TET1 Is Associated with Loss of 5-Hydroxymethylcytosine in IDH1 Wild-Type Gliomas. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 181:675-83. [DOI: 10.1016/j.ajpath.2012.04.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/23/2012] [Accepted: 04/24/2012] [Indexed: 10/28/2022]
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Mascelli S, Raso A, Biassoni R, Severino M, Sak K, Joost K, Milanaccio C, Barra S, Grillo-Ruggieri F, Vanni I, Consales A, Cama A, Capra V, Nozza P, Garrè ML. Analysis of NADP+-dependent isocitrate dehydrogenase-1/2 gene mutations in pediatric brain tumors: report of a secondary anaplastic astrocytoma carrying the IDH1 mutation. J Neurooncol 2012; 109:477-84. [PMID: 22821382 DOI: 10.1007/s11060-012-0925-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 06/22/2012] [Indexed: 11/28/2022]
Abstract
Somatic mutations of the isocitrate dehydrogenase-1 gene (IDH1), most commonly resulting in replacement of arginine at position 132 by histidine (p.R132H), have been reported for WHO grade II and III diffuse gliomas and secondary glioblastomas. We investigated IDH1/2 mutations in a retrospective series of 165 pediatric brain tumors, including atypical teratoid/rhabdoid tumors (AT/RT) and choroid plexus tumors, which had not previously been investigated. Mutation analysis was performed by use of pyrosequencing and, additionally, data were validated for a cohort of 70 gliomas from among the series by use of the arrayed primer extension technique. We identified one tumor which harbored mutation of IDH1 at codon 132 and no alteration was identified in the matched-germline DNA. No IDH2 mutations were detected. Most noteworthy, the IDH1 mutant tumor was an anaplastic astrocytoma involving the cortex in the left frontal lobe which appeared seven years after radiation treatment for an extensive sellar/suprasellar craniopharyngioma. This anaplastic astrocytoma was regarded as secondary to radiation treatment because it seemed to originate within the irradiation field that received a dose varying from a maximum of 30.6 Gy of 4 MV X-rays down to very few Gy of lower-energy scattered radiation. In this work our observations agree with those in previous reports showing the rarity of IDH1/2 mutations in childhood tumors. The interesting identification of an IDH1 mutation in a radiation-induced secondary malignant glioma raises the likelihood that these types of tumor may develop IDH1/2 mutations. Thus, caution is needed when dealing with these tumors, and further genetic analysis is warranted.
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Affiliation(s)
- Samantha Mascelli
- Neurosurgery Unit, IRCCS Giannina Gaslini Children's Research Hospital, Genoa, Italy.
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Abstract
A novel mutation of isocitrate dehydrogenase-1 (IDH1) was recently found in a large percentage of secondary human gliomas. Unlike previously discovered prognostic molecular characteristics, IDH1 mutations were found across gliomas of many different grades and histologies. Further studies have illuminated its utility as a prognostic marker in low-grade and high-grade gliomas and its ability to aid the differentiation and diagnosis of various tumors with histologic ambiguity. As a metabolic enzyme, its inhibitory actions and neomorphic activity present a unique avenue in the understanding of these tumors and potentially a novel mechanism through which they may be treated.
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Affiliation(s)
- Won Kim
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA 90095-6901, USA.
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Current world literature. Curr Opin Pediatr 2012; 24:134-44. [PMID: 22245849 DOI: 10.1097/mop.0b013e328350498a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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MacDonald TJ, Aguilera D, Kramm CM. Treatment of high-grade glioma in children and adolescents. Neuro Oncol 2011; 13:1049-58. [PMID: 21784756 PMCID: PMC3177659 DOI: 10.1093/neuonc/nor092] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 05/20/2011] [Indexed: 12/15/2022] Open
Abstract
Pediatric high-grade gliomas (HGGs)--including glioblastoma multiforme, anaplastic astrocytoma, and diffuse intrinsic pontine glioma--are difficult to treat and are associated with an extremely poor prognosis. There are no effective chemotherapeutic regimens for the treatment of pediatric HGG, but many new treatment options are in active investigation. There are crucial molecular differences between adult and pediatric HGG such that results from adult clinical trials cannot simply be extrapolated to children. Molecular markers overexpressed in pediatric HGG include PDGFRα and P53. Amplification of EGFR is observed, but to a lesser degree than in adult HGG. Potential molecular targets and new therapies in development for pediatric HGG are described in this review. Research into bevacizumab in pediatric HGG indicates that its activity is less than that observed in adult HGG. Similarly, tipifarnib was found to have minimal activity in pediatric HGG, whereas gefitinib has shown greater effects. After promising phase I findings in children with primary CNS tumors, the integrin inhibitor cilengitide is being investigated in a phase II trial in pediatric HGG. Studies are also ongoing in pediatric HGG with 2 EGFR inhibitors: cetuximab and nimotuzumab. Other novel treatment modalities under investigation include dendritic cell-based vaccinations, boron neutron capture therapy, and telomerase inhibition. While the results of these trials are keenly awaited, the current belief is that multimodal therapy holds the greatest promise. Research efforts should be directed toward building multitherapeutic regimens that are well tolerated and that offer the greatest antitumor activity in the setting of pediatric HGG.
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Affiliation(s)
- T J MacDonald
- Aflac Cancer Center and Blood Disorders Service, Children's Healthcare of Atlanta, Emory University School of Medicine, Emory Children's Center, 2015 Uppergate Drive, Suite 442, Atlanta, GA 30322 USA.
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Song X, Andrew Allen R, Terence Dunn S, Fung KM, Farmer P, Gandhi S, Ranjan T, Demopoulos A, Symons M, Schulder M, Li JY. Glioblastoma with PNET-like components has a higher frequency of isocitrate dehydrogenase 1 (IDH1) mutation and likely a better prognosis than primary glioblastoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2011; 4:651-660. [PMID: 22076165 PMCID: PMC3209605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 09/06/2011] [Indexed: 05/31/2023]
Abstract
Glioblastoma with primitive neuroectodermal tumor-like components (GBM-PNET), a rare variant of glioblastoma, poses both diagnostic and therapeutic challenges. Ten patients with GBM-PNET were investigated with a median age of 51.5 years and the male to female ratio of 4:1. The majority of patients (7 out of 10) showed ring-enhancing lesions on magnetic resonance imaging (MRI), which is classic for GBMs. Restricted diffusion was noted in 7 cases where diffusion weighted imaging (DWI) was performed, which correlates with the presence of PNET-like components. CD56 and vimentin immunostaining made the diagnosis of GBM-PNET much easier. Vimentin strongly and diffusely highlighted the astrocytic components and was negative in PNET-like components, while CD56 was strongly and diffusely positive in both astrocytic and PNET-like components. Seven out of 9 cases were positive for p53 in both astrocytic and PNET-like components. Two out of 8 cases harbored isocitrate dehydrogenase 1 (IDH1) R132H mutation, while IDH2 R172 mutations were not identified. Three out of 10 patients had a median survival time of 17 months while the two patients, whose tumor carried IDH1 mutation, were still alive after 15 and 31 months of follow-up. Compared to primary GBMs, GBM-PNETs might have a better prognosis. Further large scale studies are necessary to confirm this observation.
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Affiliation(s)
- Xianyuan Song
- Department of Pathology, Hartford HospitalHartford, CT
| | - R Andrew Allen
- Department of Pathology, The University of Oklahoma Health Sciences CenterOklahoma City, OK
| | - S Terence Dunn
- Department of Pathology, The University of Oklahoma Health Sciences CenterOklahoma City, OK
| | - Kar-Ming Fung
- Department of Pathology, The University of Oklahoma Health Sciences CenterOklahoma City, OK
| | - Peter Farmer
- Department of Pathology and Lab. Medicine, North Shore-Long Island Jewish Health System, Lake Success, Hofstra North Shore-LU School of MedicineNY
| | - Shital Gandhi
- Department of Radiology, North Shore University HospitalManhasset, NY
| | - Tulika Ranjan
- Department of Neurology, North Shore University HospitalManhasset, NY
| | | | - Marc Symons
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical ResearchManhasset, NY, USA
| | - Michael Schulder
- Department of Neurosurgery, North Shore University HospitalManhasset, NY
| | - Jian Yi Li
- Department of Pathology and Lab. Medicine, North Shore-Long Island Jewish Health System, Lake Success, Hofstra North Shore-LU School of MedicineNY
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Value and limitations of immunohistochemistry and gene sequencing for detection of the IDH1-R132H mutation in diffuse glioma biopsy specimens. J Neuropathol Exp Neurol 2011; 70:715-23. [PMID: 21760534 DOI: 10.1097/nen.0b013e31822713f0] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
To assess the value of anti-isocitrate dehydrogenase 1 (IDH1) immunohistochemistry for evaluating diffuse gliomas, we analyzed anti-IDH1-R132H immunohistochemistry using monoclonal antibodies DIA-H09 and IMab-1 and IDH1 gene sequencing in formalin-fixed and paraffin-embedded biopsy samples of 95 diffuse gliomas. We found concordant immunostaining results using the 2 antibodies in 94 (98.9%) of the 95 cases, but DIA-H09 generally showed a higher signal-to-background ratio than IMab-1 did. Fifty-five percent of cases showed anti-IDH1-R132H immunostaining of virtually all tumor cells and 15% of only a fraction of tumor cells. All cases with complete or partial immunostaining of the tumor tissue carried the IDH1-R132H mutation. In all cases with negative immunostaining results (approximately 30%), genetic analysis showed IDH1 wild-type or non-R132H-IDH1 mutations. In a single tiny biopsy, both anti-IDH1-R132H antibodies showed immunoreactivity, but genetic testing was inconclusive. Our data confirm anti-IDH1-R132H immunostaining as a reliable method for evaluation of IDH1 gene mutation status. They also suggest the following: (i) in some cases, nonspecific background staining or regional heterogeneity of IDH1-R132H protein expression may necessitate confirmatory genetic analysis; (ii) for individual cases, anti-IDH1-R132H immunostaining may not reliably identify infiltrating tumor cells admixed with preexisting or reactive glial cells; and (iii) in tiny biopsies, immunohistochemistry may be more sensitive for detection of IDH1-R132H mutation than genetic analysis.
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Gupta R, Webb-Myers R, Flanagan S, Buckland ME. Isocitrate dehydrogenase mutations in diffuse gliomas: clinical and aetiological implications. J Clin Pathol 2011; 64:835-44. [PMID: 21752797 DOI: 10.1136/jclinpath-2011-200227] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The discovery of isocitrate dehydrogenase (IDH) mutations in gliomas is one example of the large impact that next-generation sequencing is having on the understanding of tumour biology and human disease in general. IDH mutations are early and common events in the development of astrocytomas, oligodendrogliomas and oligoastrocytomas. IDH mutations are also found in some myeloid malignancies and soft tissue tumours, but are rare in other malignancies. IDH mutation detection can be incorporated into routine pathology practice via immunohistochemistry and/or standard sequencing techniques and has great diagnostic value. An emerging theme is that IDH mutation status in gliomas is of great prognostic relevance, and there are proposals to include IDH mutation status in the next iteration of the WHO classification of gliomas. The mechanisms of action(s) of mutant IDH are not fully understood, but the understanding is progressing rapidly, and may provide a mechanism to link diverse proneoplastic processes such as oxidative damage and epigenetic dysregulation. There are exciting prospects of novel therapies for glioma patients emerging from the elucidation of these mechanisms. Given the diagnostic and prognostic implications of IDH mutation, and the potential for new therapies, all gliomas should be assessed for IDH mutation status in the future.
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Affiliation(s)
- R Gupta
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, Australia
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Abstract
CONTEXT Gliomas are the most common primary brain tumors of adults and include a variety of histologic types and morphologies. Histologic evaluation remains the gold standard for glioma diagnosis; however, diagnostic difficulty may arise from tumor heterogeneity, overlapping morphologic features, and tumor sampling. Recently, our knowledge about the genetics of these tumors has expanded, and new molecular markers have been developed. Some of these markers have shown diagnostic value, whereas others are useful prognosticators for patient survival and therapeutic response. OBJECTIVE To review the most clinically useful molecular markers and their detection techniques in gliomas. DATA SOURCES Review of the pertinent literature and personal experience with the molecular testing in gliomas. CONCLUSIONS This article provides an overview of the most common molecular markers in neurooncology, including 1p/19q codeletion in oligodendroglial tumors, mutations in the isocitrate dehydrogenase 1 and 2 genes in diffuse gliomas, hypermethylation of the O(6)-methylguanine-DNA methyltransferase gene promoter in glioblastomas and anaplastic gliomas, alterations in the epidermal growth factor receptor and phosphatase and tensin homolog genes in high-grade gliomas, as well as BRAF alterations in pilocytic astrocytomas. Molecular testing of gliomas is increasingly used in routine clinical practice and requires that neuropathologists be familiar with these genetic markers and the molecular diagnostic techniques for their detection.
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Affiliation(s)
- Marina N Nikiforova
- Department of Pathology, University of Pittsburgh, 200 Lothrop Ave, Pittsburgh, PA 15213, USA.
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Lin J, Qian J, Yao DM, Li Y, Yang J, Chen Q, Chai HY, Xiao GF, Xu WR. Rapid and reliable detection of IDH1 R132 mutations in acute myeloid leukemia using high-resolution melting curve analysis. Clin Biochem 2011; 44:779-83. [PMID: 21539821 DOI: 10.1016/j.clinbiochem.2011.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/13/2011] [Accepted: 04/17/2011] [Indexed: 10/18/2022]
Abstract
OBJECTIVE The mutations of isocitrate dehydrogenase 1 (IDH1) gene have been identified in a proportion of hematologic malignancies including acute myeloid leukemia (AML). The aim of the present study was to explore the reliability of the high-resolution melting analysis (HRMA) for the identification of IDH1 R132 mutations in AML. DESIGNS AND METHODS We evaluated the sensitivity of HRMA in the detection of IDH1 R132 mutation and screened IDH1 mutations in 110 AML patients using HRMA. The results of HRMA were validated by direct DNA sequencing. RESULTS The reproducible sensitivity of HRMA was 5% for the detection of IDH1 R132 mutation, higher than 10% of direct DNA sequencing. Heterozygous IDH1 mutations were identified in 4 (3.6%) AML cases, which were R132H in 3 cases and R132S in 1 case confirmed by DNA sequencing. CONCLUSION The HRMA is a rapid, accurate, reliable, high-throughput method to screen IDH1 gene mutations.
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Affiliation(s)
- Jiang Lin
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, PR China
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von Deimling A, Korshunov A, Hartmann C. The next generation of glioma biomarkers: MGMT methylation, BRAF fusions and IDH1 mutations. Brain Pathol 2011; 21:74-87. [PMID: 21129061 PMCID: PMC8094257 DOI: 10.1111/j.1750-3639.2010.00454.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 10/11/2010] [Indexed: 01/12/2023] Open
Abstract
For some, glioma biomarkers have been expected to solve common diagnostic problems in routine neuropathology service caused by insufficient material, technical shortcomings or lack of experience. Further, biomarkers should predict patient outcome and direct optimal therapy for the individual patient. Unfortunately, current biomarkers still fall somewhat short of these grand expectations. While there has been some progress, it has generally been slow and in small steps. In this review, the newest set of glioma biomarkers: O(6) -methylguanine-DNA methyltransferase (MGMT) methylation, BRAF fusion and IDH1 mutation are discussed. MGMT methylation is well established as a prognostic/predictive marker for glioblastoma; however, technical questions regarding testing remain, it is not currently utilized widely in guiding patient management, and it has proven to be of no assistance in diagnostics. In contrast, BRAF fusion and IDH1 mutation analyses promise to be very helpful for classifying and grading gliomas, while their potential predictive value has yet to be established.
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Affiliation(s)
- Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, and Clinical Cooperation Unit Neuropathology, German Cancer Research Center, Heidelberg, Germany.
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