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Ji Q, Zheng Y, Zhou L, Chen F, Li W. Unveiling divergent treatment prognoses in IDHwt-GBM subtypes through multiomics clustering: a swift dual MRI-mRNA model for precise subtype prediction. J Transl Med 2024; 22:578. [PMID: 38890658 PMCID: PMC11186189 DOI: 10.1186/s12967-024-05401-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND IDH1-wildtype glioblastoma multiforme (IDHwt-GBM) is a highly heterogeneous and aggressive brain tumour characterised by a dismal prognosis and significant challenges in accurately predicting patient outcomes. To address these issues and personalise treatment approaches, we aimed to develop and validate robust multiomics molecular subtypes of IDHwt-GBM. Through this, we sought to uncover the distinct molecular signatures underlying these subtypes, paving the way for improved diagnosis and targeted therapy for this challenging disease. METHODS To identify stable molecular subtypes among 184 IDHwt-GBM patients from TCGA, we used the consensus clustering method to consolidate the results from ten advanced multiomics clustering approaches based on mRNA, lncRNA, and mutation data. We developed subtype prediction models using the PAM and machine learning algorithms based on mRNA and MRI data for enhanced clinical utility. These models were validated in five independent datasets, and an online interactive system was created. We conducted a comprehensive assessment of the clinical impact, drug treatment response, and molecular associations of the IDHwt-GBM subtypes. RESULTS In the TCGA cohort, two molecular subtypes, class 1 and class 2, were identified through multiomics clustering of IDHwt-GBM patients. There was a significant difference in survival between Class 1 and Class 2 patients, with a hazard ratio (HR) of 1.68 [1.15-2.47]. This difference was validated in other datasets (CGGA: HR = 1.75[1.04, 2.94]; CPTAC: HR = 1.79[1.09-2.91]; GALSS: HR = 1.66[1.09-2.54]; UCSF: HR = 1.33[1.00-1.77]; UPENN HR = 1.29[1.04-1.58]). Additionally, class 2 was more sensitive to treatment with radiotherapy combined with temozolomide, and this sensitivity was validated in the GLASS cohort. Correspondingly, class 2 and class 1 exhibited significant differences in mutation patterns, enriched pathways, programmed cell death (PCD), and the tumour immune microenvironment. Class 2 had more mutation signatures associated with defective DNA mismatch repair (P = 0.0021). Enriched pathways of differentially expressed genes in class 1 and class 2 (P-adjust < 0.05) were mainly related to ferroptosis, the PD-1 checkpoint pathway, the JAK-STAT signalling pathway, and other programmed cell death and immune-related pathways. The different cell death modes and immune microenvironments were validated across multiple datasets. Finally, our developed survival prediction model, which integrates molecular subtypes, age, and sex, demonstrated clinical benefits based on the decision curve in the test set. We deployed the molecular subtyping prediction model and survival prediction model online, allowing interactive use and facilitating user convenience. CONCLUSIONS Molecular subtypes were identified and verified through multiomics clustering in IDHwt-GBM patients. These subtypes are linked to specific mutation patterns, the immune microenvironment, prognoses, and treatment responses.
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Affiliation(s)
- Qiang Ji
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- National Institute for Data Science in Health and Medicine, Capital Medical University, Beijing, China
| | - Yi Zheng
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Lili Zhou
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Feng Chen
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Wenbin Li
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- National Institute for Data Science in Health and Medicine, Capital Medical University, Beijing, China.
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Dono A, Zhu P, Takayasu T, Arevalo O, Riascos R, Tandon N, Ballester LY, Esquenazi Y. Extent of Resection Thresholds in Molecular Subgroups of Newly Diagnosed Isocitrate Dehydrogenase-Wildtype Glioblastoma. Neurosurgery 2024:00006123-990000000-01153. [PMID: 38687046 DOI: 10.1227/neu.0000000000002964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/05/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Maximizing the extent of resection (EOR) improves outcomes in glioblastoma (GBM). However, previous GBM studies have not addressed the EOR impact in molecular subgroups beyond IDH1/IDH2 status. In the current article, we evaluate whether EOR confers a benefit in all GBM subtypes or only in particular molecular subgroups. METHODS A retrospective cohort of newly diagnosed GBM isocitrate dehydrogenase (IDH)-wildtype undergoing resection were prospectively included in a database (n = 138). EOR and residual tumor volume (RTV) were quantified with semiautomated software. Formalin-fixed paraffin-embedded tumor tissues were analyzed by targeted next-generation sequencing. The association between recurrent genomic alterations and EOR/RTV was evaluated using a recursive partitioning analysis to identify thresholds of EOR or RTV that may predict survival. The Kaplan-Meier methods and multivariable Cox proportional hazards regression methods were applied for survival analysis. RESULTS Patients with EOR ≥88% experienced 44% prolonged overall survival (OS) in multivariable analysis (hazard ratio: 0.56, P = .030). Patients with alterations in the TP53 pathway and EOR <89% showed reduced OS compared to TP53 pathway altered patients with EOR>89% (10.5 vs 18.8 months; HR: 2.78, P = .013); however, EOR/RTV was not associated with OS in patients without alterations in the TP53 pathway. Meanwhile, in all patients with EOR <88%, PTEN-altered had significantly worse OS than PTEN-wildtype (9.5 vs 15.4 months; HR: 4.53, P < .001). CONCLUSION Our results suggest that a subset of molecularly defined GBM IDH-wildtype may benefit more from aggressive resections. Re-resections to optimize EOR might be beneficial in a subset of molecularly defined GBMs. Molecular alterations should be taken into consideration for surgical treatment decisions in GBM IDH-wildtype.
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Affiliation(s)
- Antonio Dono
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ping Zhu
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Octavio Arevalo
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Roy Riascos
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital - TMC, Houston, Texas, USA
| | - Nitin Tandon
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital - TMC, Houston, Texas, USA
| | - Leomar Y Ballester
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital - TMC, Houston, Texas, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, Texas, USA
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Lim-Fat MJ, Iorgulescu JB, Rahman R, Bhave V, Muzikansky A, Woodward E, Whorral S, Allen M, Touat M, Li X, Xy G, Patel J, Gerstner ER, Kalpathy-Cramer J, Youssef G, Chukwueke U, McFaline-Figueroa JR, Nayak L, Lee EQ, Reardon DA, Beroukhim R, Huang RY, Bi WL, Ligon KL, Wen PY. Clinical and Genomic Predictors of Adverse Events in Newly Diagnosed Glioblastoma. Clin Cancer Res 2024; 30:1327-1337. [PMID: 38252427 DOI: 10.1158/1078-0432.ccr-23-3018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/01/2023] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
PURPOSE Adverse clinical events cause significant morbidity in patients with GBM (GBM). We examined whether genomic alterations were associated with AE (AE) in patients with GBM. EXPERIMENTAL DESIGN We identified adults with histologically confirmed IDH-wild-type GBM with targeted next-generation sequencing (OncoPanel) at Dana Farber Cancer Institute from 2013 to 2019. Seizure at presentation, lymphopenia, thromboembolic events, pseudoprogression, and early progression (within 6 months of diagnosis) were identified as AE. The biologic function of genetic variants was categorized as loss-of-function (LoF), no change in function, or gain-of-function (GoF) using a somatic tumor mutation knowledge base (OncoKB) and consensus protein function predictions. Associations between functional genomic alterations and AE were examined using univariate logistic regressions and multivariable regressions adjusted for additional clinical predictors. RESULTS Our study included 470 patients diagnosed with GBM who met the study criteria. We focused on 105 genes that had sequencing data available for ≥ 90% of the patients and were altered in ≥10% of the cohort. Following false-discovery rate (FDR) correction and multivariable adjustment, the TP53, RB1, IGF1R, and DIS3 LoF alterations were associated with lower odds of seizures, while EGFR, SMARCA4, GNA11, BRD4, and TCF3 GoF and SETD2 LoF alterations were associated with higher odds of seizures. For all other AE of interest, no significant associations were found with genomic alterations following FDR correction. CONCLUSIONS Genomic biomarkers based on functional variant analysis of a routine clinical panel may help identify AE in GBM, particularly seizures. Identifying these risk factors could improve the management of patients through better supportive care and consideration of prophylactic therapies.
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Affiliation(s)
- Mary Jane Lim-Fat
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - J Bryan Iorgulescu
- Molecular Diagnostics Laboratory, Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rifaquat Rahman
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Varun Bhave
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Alona Muzikansky
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Eleanor Woodward
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sydney Whorral
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Marie Allen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mehdi Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | | | | | - Jay Patel
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Elizabeth R Gerstner
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jayashree Kalpathy-Cramer
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Gilbert Youssef
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ugonma Chukwueke
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - J Ricardo McFaline-Figueroa
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lakshmi Nayak
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Eudocia Q Lee
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Rameen Beroukhim
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Raymond Y Huang
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Keith L Ligon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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Dono A, Torres J, Nunez L, Arevalo O, Rodriguez-Quinteros JC, Riascos RF, Kamali A, Tandon N, Ballester LY, Esquenazi Y. Imaging predictors of 4q12 amplified and RB1 mutated glioblastoma IDH-wildtype. J Neurooncol 2024; 167:99-109. [PMID: 38351343 PMCID: PMC11227885 DOI: 10.1007/s11060-024-04575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/16/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION Recent studies have identified that glioblastoma IDH-wildtype consists of different molecular subgroups with distinct prognoses. In order to accurately describe and classify gliomas, the Visually AcceSAble Rembrandt Images (VASARI) system was developed. The goal of this study was to evaluate the VASARI characteristics in molecular subgroups of IDH-wildtype glioblastoma. METHODS A retrospective analysis of glioblastoma IDH- wildtype with comprehensive next-generation sequencing and pre-operative and post-operative MRI was performed. VASARI characteristics and 205 genes were evaluated. Multiple comparison adjustment by the Bejamin-Hochberg false discovery rate (BH-FDR) was performed. A 1:3 propensity score match (PSM) with a Caliper of 0.2 was done. RESULTS 178 patients with GBM IDH-WT met the inclusion criteria. 4q12 amplified patients (n = 20) were associated with cyst presence (30% vs. 12%, p = 0.042), decreased hemorrhage (35% vs. 62%, p = 0.028), and non-restricting/mixed (35%/60%) rather than restricting diffusion pattern (5%), meanwhile, 4q12 non-amplified patients had mostly restricting (47.4%) rather than a non-restricting/mixed diffusion pattern (28.4%/23.4%). This remained statistically significant after BH-FDR adjustment (p = 0.002). PSM by 4q12 amplification showed that diffusion characteristics continued to be significantly different. Among RB1-mutant patients, 96% had well-defined enhancing margins vs. 70.6% of RB1-WT (p = 0.018), however, this was not significant after BH-FDR or PSM. CONCLUSIONS Patients with glioblastoma IDH-wildtype harboring 4q12 amplification rarely have restricting DWI patterns compared to their wildtype counterparts, in which this DWI pattern is present in ~ 50% of patients. This suggests that some phenotypic imaging characteristics can be identified among molecular subtypes of IDH-wildtype glioblastoma.
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Affiliation(s)
- Antonio Dono
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Jose Torres
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Luis Nunez
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Octavio Arevalo
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Department of Radiology, LSU Health Shreveport, 71103, Shreveport, LA, USA
| | - Juan Carlos Rodriguez-Quinteros
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Roy F Riascos
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA
| | - Arash Kamali
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA
| | - Nitin Tandon
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA
| | - Leomar Y Ballester
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA.
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA.
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, 77030, Houston, TX, USA.
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Yu F, Wang R, Chaudhari P, Davatzikos C. Investigating Causal Genetic Effects on Overall Survival of Glioblastoma Patients using Normalizing Flow and Structural Causal Model. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2024; 12927:129271F. [PMID: 38650741 PMCID: PMC11034818 DOI: 10.1117/12.3005434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Glioblastoma (GBM) is the most common and aggressive brain tumor with short overall survival (OS) of about 15 months. Understanding the causal factors affecting the patient survival is crucial for disease prognosis and treatment planning. Although previous efforts on survival prediction using multi-omics data has yielded useful predictive models, the causation of the correlated genetic risk factors has not been addressed. Recent advances in causal deep learning models enable the study of causality from complex dataset. In this paper, we leverage the recently proposed structural causal model (SCM) with normalizing flows parameterized by deep networks to perform the counterfactual query to investigate the causal relationship between gene mutation and OS with the presence of other confounders including sex, age and radiomics features. The query amounts to the question that what the survival days will be if the gene mutation status has been changed, i.e., from mutant to non-mutant and vice versa. The trained causal model will infer the counterfactual outcome given the intervention on specific gene mutation. We apply multivariate Cox-PH model to find the genes associated with survival, and investigate the causal genetic effect by comparing the original and counterfactual survival days in a bi-directional fashion. Particularly, the following two scenarios are considered: (1) intervention on a specific gene with non-mutant status to generate the counterfactual survival days as if the gene is mutant, with which the original survival days of the subjects with that mutant gene will be compared; (2) intervention on the gene with mutant status and perform the comparison with survival days of subjects with that non-mutant gene. Our experimental results show that no causation of two correlated genes (NF1, RB1) was revealed in the cohort (n=181), while their genetic effects on OS in terms of prolonging or shortening are generally in accordance with clinical findings.
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Affiliation(s)
- Fanyang Yu
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rongguang Wang
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pratik Chaudhari
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Carlotto BS, Trevisan P, Provenzi VO, Soares FP, Rosa RFM, Varella-Garcia M, Zen PRG. PDGFRA, KIT, and KDR Gene Amplification in Glioblastoma: Heterogeneity and Clinical Significance. Neuromolecular Med 2023; 25:441-450. [PMID: 37610648 PMCID: PMC10514169 DOI: 10.1007/s12017-023-08749-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/30/2023] [Indexed: 08/24/2023]
Abstract
Glioblastoma (GBM) is the most frequent tumor of the central nervous system, and its heterogeneity is a challenge in treatment. This study examined tumoral heterogeneity involving PDGFRA, KIT, and KDR gene amplification (GA) in 4q12 and its association with clinical parameters. Specimens from 22 GBM cases with GA for the 4q12 amplicon detected by FISH were investigated for homogeneous or heterogeneous coamplification patterns, diffuse or focal distribution of cells harboring GA throughout tumor sections, and pattern of clustering of fluorescence signals. Sixteen cases had homogenously amplification for all three genes (45.5%), for PDGFRA and KDR (22.7%), or only for PDGFRA (4.6%); six cases had heterogeneous GA patterns, with subpopulations including GA for all three genes and for two genes - PDGFRA and KDR (13.6%), or GA for all three and for only one gene - PDGFRA (9.1%) or KIT (4.6%). In 6 tumors (27.3%), GA was observed in focal tumor areas, while in the remaining 16 tumors (72.7%) it was diffusely distributed throughout the pathological specimen. Amplification was universally expressed as double minutes and homogenously stained regions. Coamplification of all three genes PDGFRA, KIT, and KDR, age ≥ 60 years, and total tumor resection were statistically associated with poor prognosis. FISH proved effective for detailed interpretation of molecular heterogeneity. The study uncovered an even more diverse range of amplification patterns involving the 4q12 oncogenes in GBM than previously described, thus highlighting a complex tumoral heterogeneity to be considered when devising more effective therapies.
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Affiliation(s)
- Bianca Soares Carlotto
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS Brazil
| | - Patricia Trevisan
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS Brazil
- Colorado Genetics Laboratory, Department of Pathology, School of Medicine, University of Colorado, Aurora, CO USA
| | | | | | - Rafael Fabiano Machado Rosa
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS Brazil
- Department of Internal Medicine, Clinical Genetics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS Brazil
- Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS Brazil
| | - Marileila Varella-Garcia
- Department of Medicine, Medical Oncology Division, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Paulo Ricardo Gazzola Zen
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS Brazil
- Department of Internal Medicine, Clinical Genetics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS Brazil
- Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS Brazil
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Parker M, Kalluri A, Materi J, Gujar SK, Schreck K, Mukherjee D, Weingart J, Brem H, Redmond KJ, Lucas CHG, Bettegowda C, Rincon-Torroella J. Management and Molecular Characterization of Intraventricular Glioblastoma: A Single-Institution Case Series. Int J Mol Sci 2023; 24:13285. [PMID: 37686092 PMCID: PMC10488126 DOI: 10.3390/ijms241713285] [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: 07/01/2023] [Revised: 08/13/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
While the central nervous system (CNS) tumor classification has increasingly incorporated molecular parameters, there is a paucity of literature reporting molecular alterations found in intraventricular glioblastoma (IVGBM), which are rare. We present a case series of nine IVGBMs, including molecular alterations found in standardized next-generation sequencing (NGS). We queried the clinical charts, operative notes, pathology reports, and radiographic images of nine patients with histologically confirmed IVGBM treated at our institution (1995-2021). Routine NGS was performed on resected tumor tissue of two patients. In this retrospective case series of nine patients (22% female, median (range) age: 64.3 (36-85) years), the most common tumor locations were the atrium of the right lateral ventricle (33%) and the septum pellucidum (33%). Five patients had preoperative hydrocephalus, which was managed with intraoperative external ventricular drains in three patients and ventriculoperitoneal shunts in one patient. Hydrocephalus was managed with subtotal resection of a fourth ventricular IVGBM in one patient. The most common surgical approach was transcortical intraventricular (56%). Gross total resection was achieved in two patients, subtotal resection was achieved in six patients, and one patient received a biopsy only. Immunohistochemistry for IDH1 R132H mutant protein was performed in four cases and was negative in all four. Genetic alterations common in glioblastoma, IDH-wildtype, were seen in two cases with available NGS data, including EGFR gene amplification, TERT promoter mutation, PTEN mutation, trisomy of chromosome 7, and monosomy of chromosome 10. Following surgical resection, four patients received adjuvant chemoradiation. Median survival among our cohort was 4.7 months (IQR: 0.9-5.8 months). Management of IVGBM is particularly challenging due to their anatomical location, presentation with obstructive hydrocephalus, and fast growth, necessitating prompt intervention. Additional studies are needed to better understand the genetic landscape of IVGBM compared to parenchymal glioblastoma and may further elucidate the unique pathophysiology of these rare tumors.
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Affiliation(s)
- Megan Parker
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anita Kalluri
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joshua Materi
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sachin K. Gujar
- Division of Neuroradiology, The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Karisa Schreck
- Department of Neurology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Debraj Mukherjee
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jon Weingart
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Henry Brem
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kristin J. Redmond
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Calixto-Hope G. Lucas
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jordina Rincon-Torroella
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Dono A, Alfaro-Munoz K, Yan Y, Lopez-Garcia CA, Soomro Z, Williford G, Takayasu T, Robell L, Majd NK, de Groot J, Esquenazi Y, Kamiya-Matsuoka C, Ballester LY. Molecular, Histological, and Clinical Characteristics of Oligodendrogliomas: A Multi-Institutional Retrospective Study. Neurosurgery 2022; 90:515-522. [PMID: 35179134 PMCID: PMC9514747 DOI: 10.1227/neu.0000000000001875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Reports suggest that phosphatidylinositol 3-kinase pathway alterations confer increased risk of progression and poor prognosis in oligodendroglioma, IDH-mutant, and 1p/19q-codeleted molecular oligodendrogliomas (mODG). However, factors that affect prognosis in mODG have not been thoroughly studied. In addition, the benefits of adjuvant radiation and temozolomide (TMZ) in mODGs remain to be determined. OBJECTIVE To evaluate the role of PIK3CA mutations in mODGs. METHODS One hundred seven mODGs (2008-2019) diagnosed at 2 institutions were included. A retrospective review of clinical characteristics, molecular alterations, treatments, and outcomes was performed. RESULTS The median age was 37 years, and 61 patients (57%) were male. There were 64 (60%) World Health Organization (WHO) grade 2 and 43 (40%) WHO grade 3 tumors. Eighty-two patients (77%) were stratified as high risk (age 40 years or older and/or subtotal resection per Radiation Treatment Oncology Group-9802). Gross-total resection was achieved in 47 patients (45%). Treatment strategies included observation (n = 15), TMZ (n = 11), radiation (n = 13), radiation/TMZ (n = 62), and others (n = 6). Our results show a benefit of TMZ vs observation in progression-free survival (PFS). No difference in PFS or overall survival (OS) was observed between radiation and radiation/TMZ. PIK3CA mutations were detected in 15 (14%) mODG, and shorter OS was observed in PIK3CA-mutant compared with PIK3CA wild-type mODGs (10.7 years vs 15.1 years, P = .009). WHO grade 3 tumors showed a shorter PFS, but no significant difference in OS was observed between WHO grades. CONCLUSION Our findings suggest that mODGs harboring PIK3CA mutations have worse OS. Except for an advantage in PFS with TMZ treatment, adjuvant TMZ, radiation, or a combination of the two showed no significant improvement in OS.
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Affiliation(s)
- Antonio Dono
- Vivian L. Smith Department of Neurosurgery, School of Biomedical Informatics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, School of Biomedical Informatics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Yuanqing Yan
- Vivian L. Smith Department of Neurosurgery, School of Biomedical Informatics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Carlos A. Lopez-Garcia
- Department of Pathology and Laboratory Medicine, School of Biomedical Informatics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Zaid Soomro
- Department of Neuro-Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Garret Williford
- Department of Neuro-Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Takeshi Takayasu
- Department of Pathology and Laboratory Medicine, School of Biomedical Informatics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Lindsay Robell
- Department of Neuro-Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Nazanin K. Majd
- Department of Neuro-Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - John de Groot
- Department of Neuro-Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, School of Biomedical Informatics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Center of Precision Health, School of Biomedical Informatics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital, Houston, Texas, USA
| | | | - Leomar Y. Ballester
- Vivian L. Smith Department of Neurosurgery, School of Biomedical Informatics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, School of Biomedical Informatics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital, Houston, Texas, USA
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Dono A, Zhu P, Holmes E, Takayasu T, Zhu JJ, Blanco AI, Hsu S, Bhattacharjee MB, Ballester LY, Kim DH, Esquenazi Y, Tandon N. Impacts of genotypic variants on survival following reoperation for recurrent glioblastoma. J Neurooncol 2022; 156:353-363. [PMID: 34997451 PMCID: PMC9338692 DOI: 10.1007/s11060-021-03917-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/29/2021] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Recurrent glioblastoma (rGBM) prognosis is dismal. In the absence of effective adjuvant treatments for rGBM, re-resections remain prominent in our arsenal. This study evaluates the impact of reoperation on post-progression survival (PPS) considering rGBM genetic makeup. METHODS To assess the genetic heterogeneity and treatment-related changes (TRC) roles in re-operated or medically managed rGBMs, we compiled demographic, clinical, histopathological, and next-generation genetic sequencing (NGS) characteristics of these tumors from 01/2005 to 10/2019. Survival data and reoperation were analyzed using conventional and random survival forest analysis (RSF). RESULTS Patients harboring CDKN2A/B loss (p = 0.017) and KDR mutations (p = 0.031) had notably shorter survival. Reoperation or bevacizumab were associated with longer PPS (11.2 vs. 7.4-months, p = 0.006; 13.1 vs 6.2, p < 0.001). Reoperated patients were younger, had better performance status and greater initial resection. In 136/273 (49%) rGBMs undergoing re-operation, CDKN2A/B loss (p = 0.03) and KDR mutations (p = 0.02) were associated with shorter survival. In IDH-WT rGBMs with NGS data (n = 166), reoperation resulted in 7.0-month longer survival (p = 0.004) than those managed medically. This reoperation benefit was independently identified by RSF analysis. Stratification analysis revealed that EGFR-mutant, CDKN2A/B-mutant, NF1-WT, and TP53-WT rGBM IDH-WT subgroups benefit most from reoperation (p = 0.03). Lastly, whether or not TRC was prominent at re-operation does not have any significant impact on PPS (10.5 vs. 11.5-months, p = 0.77). CONCLUSIONS Maximal safe re-resection significantly lengthens PPS regardless of genetic makeup, but reoperations are especially beneficial for IDH-WT rGBMs with EGFR and CDKN2A/B mutations with TP53-WT, and NF1-WT. Histopathology at recurrence may be an imperfect gauge of disease severity at progression and the imaging progression may be more reflective of the prognosis.
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Affiliation(s)
- Antonio Dono
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA,Department of Pathology and Laboratory Medicine, McGovern Medical School at UT Health, Houston, TX, USA
| | - Ping Zhu
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA
| | - Emma Holmes
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA
| | - Takeshi Takayasu
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UT Health, Houston, TX, USA
| | - Jay-jiguang Zhu
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA,Memorial Hermann Hospital-TMC, Houston, TX, USA
| | - Angel I. Blanco
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA,Memorial Hermann Hospital-TMC, Houston, TX, USA
| | - Sigmund Hsu
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA,Memorial Hermann Hospital-TMC, Houston, TX, USA
| | - Meenakshi B. Bhattacharjee
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UT Health, Houston, TX, USA,Memorial Hermann Hospital-TMC, Houston, TX, USA
| | - Leomar Y. Ballester
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UT Health, Houston, TX, USA,Memorial Hermann Hospital-TMC, Houston, TX, USA
| | - Dong H. Kim
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA,Memorial Hermann Hospital-TMC, Houston, TX, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA,Memorial Hermann Hospital-TMC, Houston, TX, USA
| | - Nitin Tandon
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA,Memorial Hermann Hospital-TMC, Houston, TX, USA,Texas Institute for Restorative Neurotechnologies, UT Health, Houston, TX, USA,Department of Neurosurgery, Texas Institute of Restorative Neurotechnology, McGovern Medical School at UT Health, 6400 Fannin Street, Suite 2800, Houston, TX 77030, USA
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