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Batsios G, Udutha S, Taglang C, Gillespie AM, Lau B, Ji S, Phoenix T, Mueller S, Venneti S, Koschmann C, Viswanath P. GABA production induced by imipridones is a targetable and imageable metabolic alteration in diffuse midline gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597982. [PMID: 38915617 PMCID: PMC11195108 DOI: 10.1101/2024.06.07.597982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Diffuse midline gliomas (DMGs) are lethal primary brain tumors in children. The imipridones ONC201 and ONC206 induce mitochondrial dysfunction and have emerged as promising therapies for DMG patients. However, efficacy as monotherapy is limited, identifying a need for strategies that enhance response. Another hurdle is the lack of biomarkers that report on drug-target engagement at an early timepoint after treatment onset. Here, using 1 H-magnetic resonance spectroscopy, which is a non-invasive method of quantifying metabolite pool sizes, we show that accumulation of ψ-aminobutyric acid (GABA) is an early metabolic biomarker that can be detected within a week of ONC206 treatment, when anatomical alterations are absent, in mice bearing orthotopic xenografts. Mechanistically, imipridones activate the mitochondrial protease ClpP and upregulate the stress-responsive transcription factor ATF4. ATF4, in turn, upregulates glutamate decarboxylase, which synthesizes GABA, and downregulates ABAT , which degrades GABA, leading to GABA accumulation in DMG cells and tumors. Functionally, GABA secreted by imipridone-treated cells acts in an autocrine manner via the GABAB receptor to induce expression of superoxide dismutase (SOD1), which mitigates imipridone-induced oxidative stress and, thereby, curbs apoptosis. Importantly, blocking autocrine GABA signaling using the clinical stage GABAB receptor antagonist SGS-742 exacerbates oxidative stress and synergistically induces apoptosis in combination with imipridones in DMG cells and orthotopic tumor xenografts. Collectively, we identify GABA as a unique metabolic adaptation to imipridones that can be leveraged for non-invasive assessment of drug-target engagement and therapy. Clinical translation of our studies has the potential to enable precision metabolic therapy and imaging for DMG patients. One Sentence Summary Imipridones induce GABA accumulation in diffuse midline gliomas, an effect that can be leveraged for therapy and non-invasive imaging.
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Mikolajewicz N, Yee PP, Bhanja D, Trifoi M, Miller AM, Metellus P, Bagley SJ, Balaj L, de Macedo Filho LJM, Zacharia BE, Aregawi D, Glantz M, Weller M, Ahluwalia MS, Kislinger T, Mansouri A. Systematic Review of Cerebrospinal Fluid Biomarker Discovery in Neuro-Oncology: A Roadmap to Standardization and Clinical Application. J Clin Oncol 2024; 42:1961-1974. [PMID: 38608213 DOI: 10.1200/jco.23.01621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/17/2024] [Accepted: 02/26/2024] [Indexed: 04/14/2024] Open
Abstract
Effective diagnosis, prognostication, and management of CNS malignancies traditionally involves invasive brain biopsies that pose significant risk to the patient. Sampling and molecular profiling of cerebrospinal fluid (CSF) is a safer, rapid, and noninvasive alternative that offers a snapshot of the intracranial milieu while overcoming the challenge of sampling error that plagues conventional brain biopsy. Although numerous biomarkers have been identified, translational challenges remain, and standardization of protocols is necessary. Here, we systematically reviewed 141 studies (Medline, SCOPUS, and Biosis databases; between January 2000 and September 29, 2022) that molecularly profiled CSF from adults with brain malignancies including glioma, brain metastasis, and primary and secondary CNS lymphomas. We provide an overview of promising CSF biomarkers, propose CSF reporting guidelines, and discuss the various considerations that go into biomarker discovery, including the influence of blood-brain barrier disruption, cell of origin, and site of CSF acquisition (eg, lumbar and ventricular). We also performed a meta-analysis of proteomic data sets, identifying biomarkers in CNS malignancies and establishing a resource for the research community.
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Affiliation(s)
- Nicholas Mikolajewicz
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Patricia P Yee
- Medical Scientist Training Program, Penn State College of Medicine, Hershey, PA
| | - Debarati Bhanja
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Mara Trifoi
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Alexandra M Miller
- Departments of Neurology and Pediatrics, Memorial Sloan Kettering Cancer Center, Manhattan, NY
| | - Philippe Metellus
- Department of Neurosurgery, Ramsay Santé, Hôpital Privé Clairval, Marseille, France
| | - Stephen J Bagley
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | - Brad E Zacharia
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Dawit Aregawi
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Michael Glantz
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zurich, Zurich, Switzerland
| | - Manmeet S Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Alireza Mansouri
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
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Ortega-Martorell S, Olier I, Hernandez O, Restrepo-Galvis PD, Bellfield RAA, Candiota AP. Tracking Therapy Response in Glioblastoma Using 1D Convolutional Neural Networks. Cancers (Basel) 2023; 15:4002. [PMID: 37568818 PMCID: PMC10417313 DOI: 10.3390/cancers15154002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/26/2023] [Accepted: 08/05/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Glioblastoma (GB) is a malignant brain tumour that is challenging to treat, often relapsing even after aggressive therapy. Evaluating therapy response relies on magnetic resonance imaging (MRI) following the Response Assessment in Neuro-Oncology (RANO) criteria. However, early assessment is hindered by phenomena such as pseudoprogression and pseudoresponse. Magnetic resonance spectroscopy (MRS/MRSI) provides metabolomics information but is underutilised due to a lack of familiarity and standardisation. METHODS This study explores the potential of spectroscopic imaging (MRSI) in combination with several machine learning approaches, including one-dimensional convolutional neural networks (1D-CNNs), to improve therapy response assessment. Preclinical GB (GL261-bearing mice) were studied for method optimisation and validation. RESULTS The proposed 1D-CNN models successfully identify different regions of tumours sampled by MRSI, i.e., normal brain (N), control/unresponsive tumour (T), and tumour responding to treatment (R). Class activation maps using Grad-CAM enabled the study of the key areas relevant to the models, providing model explainability. The generated colour-coded maps showing the N, T and R regions were highly accurate (according to Dice scores) when compared against ground truth and outperformed our previous method. CONCLUSIONS The proposed methodology may provide new and better opportunities for therapy response assessment, potentially providing earlier hints of tumour relapsing stages.
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Affiliation(s)
- Sandra Ortega-Martorell
- Data Science Research Centre, Liverpool John Moores University, Liverpool L3 3AF, UK; (I.O.); (R.A.A.B.)
| | - Ivan Olier
- Data Science Research Centre, Liverpool John Moores University, Liverpool L3 3AF, UK; (I.O.); (R.A.A.B.)
| | - Orlando Hernandez
- Escuela Colombiana de Ingeniería Julio Garavito, Bogota 111166, Colombia; (O.H.); (P.D.R.-G.)
| | | | - Ryan A. A. Bellfield
- Data Science Research Centre, Liverpool John Moores University, Liverpool L3 3AF, UK; (I.O.); (R.A.A.B.)
| | - Ana Paula Candiota
- Centro de Investigación Biomédica en Red: Bioingeniería, Biomateriales y Nanomedicina, 08193 Cerdanyola del Vallès, Spain
- Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
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Dubey R, Sinha N, Jagannathan NR. Potential of in vitro nuclear magnetic resonance of biofluids and tissues in clinical research. NMR IN BIOMEDICINE 2023; 36:e4686. [PMID: 34970810 DOI: 10.1002/nbm.4686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/18/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Body fluids, cells, and tissues contain a wide variety of metabolites that consist of a mixture of various low-molecular-weight compounds, including amino acids, peptides, lipids, nucleic acids, and organic acids, which makes comprehensive analysis more difficult. Quantitative nuclear magnetic resonance (NMR) spectroscopy is a well-established analytical technique for analyzing the metabolic profiles of body fluids, cells, and tissues. It enables fast and comprehensive detection, characterization, a high level of experimental reproducibility, minimal sample preparation, and quantification of various endogenous metabolites. In recent times, NMR-based metabolomics has been appreciably utilized in diverse branches of medicine, including microbiology, toxicology, pathophysiology, pharmacology, nutritional intervention, and disease diagnosis/prognosis. In this review, the utility of NMR-based metabolomics in clinical studies is discussed. The significance of in vitro NMR-based metabolomics as an effective tool for detecting metabolites and their variations in different diseases are discussed, together with the possibility of identifying specific biomarkers that can contribute to early detection and diagnosis of disease.
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Affiliation(s)
- Richa Dubey
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, India
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, India
| | - Naranamangalam R Jagannathan
- Department of Radiology, Chettinad Hospital & Research Institute, Chettinad Academy of Research & Education, Kelambakkam, India
- Department of Radiology, Sri Ramachandra Institute of Higher Education & Research, Chennai, India
- Department of Electrical Engineering, Indian Institute Technology, Madras, Chennai, India
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Molecular MRI-Based Monitoring of Cancer Immunotherapy Treatment Response. Int J Mol Sci 2023; 24:ijms24043151. [PMID: 36834563 PMCID: PMC9959624 DOI: 10.3390/ijms24043151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Immunotherapy constitutes a paradigm shift in cancer treatment. Its FDA approval for several indications has yielded improved prognosis for cases where traditional therapy has shown limited efficiency. However, many patients still fail to benefit from this treatment modality, and the exact mechanisms responsible for tumor response are unknown. Noninvasive treatment monitoring is crucial for longitudinal tumor characterization and the early detection of non-responders. While various medical imaging techniques can provide a morphological picture of the lesion and its surrounding tissue, a molecular-oriented imaging approach holds the key to unraveling biological effects that occur much earlier in the immunotherapy timeline. Magnetic resonance imaging (MRI) is a highly versatile imaging modality, where the image contrast can be tailored to emphasize a particular biophysical property of interest using advanced engineering of the imaging pipeline. In this review, recent advances in molecular-MRI based cancer immunotherapy monitoring are described. Next, the presentation of the underlying physics, computational, and biological features are complemented by a critical analysis of the results obtained in preclinical and clinical studies. Finally, emerging artificial intelligence (AI)-based strategies to further distill, quantify, and interpret the image-based molecular MRI information are discussed in terms of perspectives for the future.
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Jiang S, Chai H, Tang Q. Advances in the intraoperative delineation of malignant glioma margin. Front Oncol 2023; 13:1114450. [PMID: 36776293 PMCID: PMC9909013 DOI: 10.3389/fonc.2023.1114450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Surgery plays a critical role in the treatment of malignant glioma. However, due to the infiltrative growth and brain shift, it is difficult for neurosurgeons to distinguish malignant glioma margins with the naked eye and with preoperative examinations. Therefore, several technologies were developed to determine precise tumor margins intraoperatively. Here, we introduced four intraoperative technologies to delineate malignant glioma margin, namely, magnetic resonance imaging, fluorescence-guided surgery, Raman histology, and mass spectrometry. By tracing their detecting principles and developments, we reviewed their advantages and disadvantages respectively and imagined future trends.
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Batsios G, Taglang C, Gillespie AM, Viswanath P. Imaging telomerase reverse transcriptase expression in oligodendrogliomas using hyperpolarized δ-[1- 13C]-gluconolactone. Neurooncol Adv 2023; 5:vdad092. [PMID: 37600229 PMCID: PMC10433788 DOI: 10.1093/noajnl/vdad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023] Open
Abstract
Background Telomere maintenance by telomerase reverse transcriptase (TERT) is essential for immortality in most cancers, including oligodendrogliomas. Agents that disrupt telomere maintenance such as the telomere uncapping agent 6-thio-2'-deoxyguanosine (6-thio-dG) are in clinical trials. We previously showed that TERT expression in oligodendrogliomas is associated with upregulation of glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the pentose phosphate pathway (PPP). We also showed that hyperpolarized δ-[1-13C]-gluconolactone metabolism to 6-phosphogluconate (6-PG) can be used to probe the PPP in glioblastomas. The goal of this study was to determine whether hyperpolarized 13C imaging using δ-[1-13C]-gluconolactone can monitor TERT expression and response to 6-thio-dG in oligodendrogliomas. Methods We examined patient-derived oligodendroglioma cells and orthotopic tumors to assess the link between TERT and hyperpolarized δ-[1-13C]-gluconolactone metabolism. We performed in vivo imaging to assess the ability of hyperpolarized δ-[1-13C]-gluconolactone to report on TERT and response to 6-thio-dG in rats bearing orthotopic oligodendrogliomas in vivo. Results Doxycycline-inducible TERT silencing abrogated 6-PG production from hyperpolarized δ-[1-13C]-gluconolactone in oligodendroglioma cells, consistent with the loss of G6PD activity. Rescuing TERT expression by doxycycline removal restored G6PD activity and, concomitantly, 6-PG production. 6-PG production from hyperpolarized δ-[1-13C]-gluconolactone demarcated TERT-expressing tumor from surrounding TERT-negative normal brain in vivo. Importantly, 6-thio-dG abrogated 6-PG production at an early timepoint preceding MRI-detectable alterations in rats bearing orthotopic oligodendrogliomas in vivo. Conclusions These results indicate that hyperpolarized δ-[1-13C]-gluconolactone reports on TERT expression and early response to therapy in oligodendrogliomas. Our studies identify a novel agent for imaging tumor proliferation and treatment response in oligodendroglioma patients.
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Affiliation(s)
- Georgios Batsios
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Celine Taglang
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Pavithra Viswanath
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
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Wang H, Zhang S, Xing X, Yue Q, Feng W, Chen S, Zhang J, Xie D, Chen N, Liu Y. Radiomic study on preoperative multi-modal magnetic resonance images identifies IDH-mutant TERT promoter-mutant gliomas. Cancer Med 2022; 12:2524-2537. [PMID: 36176070 PMCID: PMC9939206 DOI: 10.1002/cam4.5097] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/20/2022] [Accepted: 07/13/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES Gliomas with comutations of isocitrate dehydrogenase (IDH) genes and telomerase reverse transcriptase (TERT) gene promoter (IDHmut pTERTmut) show distinct biological features and respond to first-line treatment differently in comparison with other gliomas. This study aimed to characterize the IDHmut pTERTmut gliomas in multimodal MRI using the radiomic method and establish a precise diagnostic model identifying this group of gliomas. METHODS A total of 140 patients with untreated primary gliomas were admitted between 2016 and 2020 to West China Hospital as a discovery cohort, including 22 IDHmut pTERTmut patients. Thirty-four additional cases from a different hospital were included in the study as an independent validation cohort. A total of 3654 radiomic features were extracted from the preoperative multimodal MRI images (T1c, FLAIR, and ADC maps) and filtered in a data-driven approach. The discovery cohort was split into training and test sets by a 4:1 ratio. A diagnostic model (multilayer perceptron classifier) for detecting the IDHmut pTERTmut gliomas was trained using an automatic machine-learning algorithm named tree-based pipeline optimization tool (TPOT). The most critical radiomic features in the model were identified and visualized. RESULTS The model achieved an area under the receiver-operating curve (AUROC) of 0.971 (95% CI, 0.902-1.000), the sensitivity of 0.833 (95% CI, 0.333-1.000), and the specificity of 0.966 (95% CI, 0.931-1.000) in the test set. The area under the precision-recall curve (AUCPR) was 0.754 (95% CI, 0.572-0.833) and the F1 score was 0.833 (95% CI, 0.500-1.000). In the independent validation set, the model reached 0.952 AUROC, 0.714 sensitivity, 0.963 specificity, 0.841 AUCPR, and 0.769 F1 score. MR radiomic features of the IDHmut pTERTmut gliomas represented homogenous low-complexity texture in three modalities. CONCLUSIONS An accurate diagnostic model was constructed for detecting IDHmut pTERTmut gliomas using multimodal radiomic features. The most important features were associated with the homogenous simple texture of IDHmut pTERTmut gliomas in MRI images transformed using Laplacian of Gaussian and wavelet filters.
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Affiliation(s)
- Haoyu Wang
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina,Department of NeurosurgeryXinhua Hospital, Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Shuxin Zhang
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina,Department of Head and Neck Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of MedicineUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xiang Xing
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina
| | - Qiang Yue
- Department of RadiologyWest China Hospital of Sichuan UniversityChengduChina
| | - Wentao Feng
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina
| | - Siliang Chen
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina
| | - Jun Zhang
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Dan Xie
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Ni Chen
- Department of Pathology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yanhui Liu
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina
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Batsios G, Taglang C, Tran M, Stevers N, Barger C, Gillespie AM, Ronen SM, Costello JF, Viswanath P. Deuterium Metabolic Imaging Reports on TERT Expression and Early Response to Therapy in Cancer. Clin Cancer Res 2022; 28:3526-3536. [PMID: 35679032 PMCID: PMC9378519 DOI: 10.1158/1078-0432.ccr-21-4418] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Telomere maintenance is a hallmark of cancer. Most tumors maintain telomere length via reactivation of telomerase reverse transcriptase (TERT) expression. Identifying clinically translatable imaging biomarkers of TERT can enable noninvasive assessment of tumor proliferation and response to therapy. EXPERIMENTAL DESIGN We used RNAi, doxycycline-inducible expression systems, and pharmacologic inhibitors to mechanistically delineate the association between TERT and metabolism in preclinical patient-derived tumor models. Deuterium magnetic resonance spectroscopy (2H-MRS), which is a novel, translational metabolic imaging modality, was used for imaging TERT in cells and tumor-bearing mice in vivo. RESULTS Our results indicate that TERT expression is associated with elevated NADH in multiple cancers, including glioblastoma, oligodendroglioma, melanoma, neuroblastoma, and hepatocellular carcinoma. Mechanistically, TERT acts via the metabolic regulator FOXO1 to upregulate nicotinamide phosphoribosyl transferase, which is the key enzyme for NAD+ biosynthesis, and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase, which converts NAD+ to NADH. Because NADH is essential for pyruvate flux to lactate, we show that 2H-MRS-based assessment of lactate production from [U-2H]-pyruvate reports on TERT expression in preclinical tumor models in vivo, including at clinical field strength (3T). Importantly, [U-2H]-pyruvate reports on early response to therapy in mice bearing orthotopic patient-derived gliomas at early timepoints before radiographic alterations can be visualized by MRI. CONCLUSIONS Elevated NADH is a metabolic consequence of TERT expression in cancer. Importantly, [U-2H]-pyruvate reports on early response to therapy, prior to anatomic alterations, thereby providing clinicians with a novel tool for assessment of tumor burden and treatment response in cancer.
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Affiliation(s)
- Georgios Batsios
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Céline Taglang
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Meryssa Tran
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Nicholas Stevers
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Carter Barger
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Joseph F Costello
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Pavithra Viswanath
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
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Rehman AU, Khan P, Maurya SK, Siddiqui JA, Santamaria-Barria JA, Batra SK, Nasser MW. Liquid biopsies to occult brain metastasis. Mol Cancer 2022; 21:113. [PMID: 35538484 PMCID: PMC9088117 DOI: 10.1186/s12943-022-01577-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/19/2022] [Indexed: 02/08/2023] Open
Abstract
Brain metastasis (BrM) is a major problem associated with cancer-related mortality, and currently, no specific biomarkers are available in clinical settings for early detection. Liquid biopsy is widely accepted as a non-invasive method for diagnosing cancer and other diseases. We have reviewed the evidence that shows how the molecular alterations are involved in BrM, majorly from breast cancer (BC), lung cancer (LC), and melanoma, with an inception in how they can be employed for biomarker development. We discussed genetic and epigenetic changes that influence cancer cells to breach the blood-brain barrier (BBB) and help to establish metastatic lesions in the uniquely distinct brain microenvironment. Keeping abreast with the recent breakthroughs in the context of various biomolecules detections and identifications, the circulating tumor cells (CTC), cell-free nucleotides, non-coding RNAs, secretory proteins, and metabolites can be pursued in human body fluids such as blood, serum, cerebrospinal fluid (CSF), and urine to obtain potential candidates for biomarker development. The liquid biopsy-based biomarkers can overlay with current imaging techniques to amplify the signal viable for improving the early detection and treatments of occult BrM.
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Affiliation(s)
- Asad Ur Rehman
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Jawed A Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | | | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA. .,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA.
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Yuan Y, Quan T, Song Y, Guan J, Zhou T, Wu R. Noise-immune Extreme Ensemble Learning for Early Diagnosis of Neuropsychiatric Systemic Lupus Erythematosus. IEEE J Biomed Health Inform 2022; 26:3495-3506. [PMID: 35380977 DOI: 10.1109/jbhi.2022.3164937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Early diagnosis is currently the most effective way of saving the life of patients with neuropsychiatric systemic lupus erythematosus (NPSLE). However, it is rather difficult to detect this terrible disease at the early stage, due to the subtle and elusive symptomatic signals. Recent studies show that the 1H-MRS (proton magnetic resonance spectroscopy) imaging technique can capture more information reflecting the early appearance of this disease than conventional magnetic resonance imaging techniques. 1H-MRS data, however, also presents more noises that can bring serious diagnosis bias. We hence proposed a noise-immune extreme ensemble learning technique for effectively leveraging 1H-MRS data for advancing the early diagnosis of NPSLE. Our main results are that 1) by developing generalized maximum correntropy criterion in the kernel extreme learning setting, many types of non-Gaussian noises can be distinguished, and 2) weighted recursive feature elimination, using maximal information coefficient to weight feature's importance, helps to further alleviate the bad impact of noises on the diagnosis performance. The proposed method is assessed on a publicly available dataset with 97.5% accuracy, 95.8% sensitivity, and 99.9% specificity, which well demonstrates its efficacy.
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12
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Epigenetic MRI: Noninvasive imaging of DNA methylation in the brain. Proc Natl Acad Sci U S A 2022; 119:e2119891119. [PMID: 35235458 PMCID: PMC8915962 DOI: 10.1073/pnas.2119891119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Dynamic epigenetic activity is a fundamental mechanism underpinning how the brain changes its function during development and aging and in response to environmental and disease stimuli. We developed a technology called epigenetic MRI (eMRI) that enables noninvasive imaging of DNA methylation in the brain, a major epigenetic mechanism. eMRI reveals strong regional differences in global DNA methylation in pig brains, a model with stronger resemblance to human brains than are rodents. Given the noninvasive nature of eMRI, our results pave the way for a DNA-methylation imaging paradigm for living human brains. We expect eMRI to enable many studies to unravel the molecular control of brain function and disease. Both neuronal and genetic mechanisms regulate brain function. While there are excellent methods to study neuronal activity in vivo, there are no nondestructive methods to measure global gene expression in living brains. Here, we present a method, epigenetic MRI (eMRI), that overcomes this limitation via direct imaging of DNA methylation, a major gene-expression regulator. eMRI exploits the methionine metabolic pathways for DNA methylation to label genomic DNA through 13C-enriched diets. A 13C magnetic resonance spectroscopic imaging method then maps the spatial distribution of labeled DNA. We validated eMRI using pigs, whose brains have stronger similarity to humans in volume and anatomy than rodents, and confirmed efficient 13C-labeling of brain DNA. We also discovered strong regional differences in global DNA methylation. Just as functional MRI measurements of regional neuronal activity have had a transformational effect on neuroscience, we expect that the eMRI signal, both as a measure of regional epigenetic activity and as a possible surrogate for regional gene expression, will enable many new investigations of human brain function, behavior, and disease.
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Taglang C, Batsios G, Mukherjee J, Tran M, Gillespie AM, Hong D, Ronen SM, Artee Luchman H, Pieper RO, Viswanath P. Deuterium magnetic resonance spectroscopy enables noninvasive metabolic imaging of tumor burden and response to therapy in low-grade gliomas. Neuro Oncol 2022; 24:1101-1112. [PMID: 35091751 PMCID: PMC9248401 DOI: 10.1093/neuonc/noac022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The alternative lengthening of telomeres (ALT) pathway is essential for tumor proliferation in astrocytomas. The goal of this study was to identify metabolic alterations linked to the ALT pathway that can be exploited for noninvasive magnetic resonance spectroscopy (MRS)-based imaging of astrocytomas in vivo. METHODS Genetic and pharmacological methods were used to dissect the association between the ALT pathway and glucose metabolism in genetically engineered and patient-derived astrocytoma models. 2H-MRS was used for noninvasive imaging of ALT-linked modulation of glycolytic flux in mice bearing orthotopic astrocytomas in vivo. RESULTS The ALT pathway was associated with higher activity of the rate-limiting glycolytic enzyme phosphofructokinase-1 and concomitantly elevated flux of glucose to lactate in astrocytoma cells. Silencing the ALT pathway or treating with the poly(ADP-ribose) polymerase inhibitor niraparib that induces telomeric fusion in ALT-dependent astrocytoma cells abrogated glycolytic flux. Importantly, this metabolic reprogramming could be non-invasively visualized by 2H-MRS. Lactate production from [6,6'-2H]-glucose was higher in ALT-dependent astrocytoma tumors relative to the normal brain in vivo. Furthermore, treatment of orthotopic astrocytoma-bearing mice with niraparib reduced lactate production from [6,6'-2H]-glucose at early timepoints when alterations in tumor volume could not be detected by anatomical imaging, pointing to the ability of [6,6'-2H]-glucose to report on pseudoprogression in vivo. CONCLUSIONS We have mechanistically linked the ALT pathway to elevated glycolytic flux and demonstrated the ability of [6,6'-2H]-glucose to non-invasively assess tumor burden and response to therapy in astrocytomas. Our findings point to a novel, clinically translatable method for metabolic imaging of astrocytoma patients.
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Affiliation(s)
- Céline Taglang
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
| | - Georgios Batsios
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
| | - Joydeep Mukherjee
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Meryssa Tran
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
| | - Donghyun Hong
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
| | - Hema Artee Luchman
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute and Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Russell O Pieper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Pavithra Viswanath
- Corresponding Author: Pavithra Viswanath, PhD, Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1700 4th St, San Francisco, CA 94143, USA ()
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Zhu XH, Lee BY, Tuite P, Coles L, Sathe AG, Chen C, Cloyd J, Low WC, Steer CJ, Chen W. Quantitative Assessment of Occipital Metabolic and Energetic Changes in Parkinson's Patients, Using In Vivo 31P MRS-Based Metabolic Imaging at 7T. Metabolites 2021; 11:metabo11030145. [PMID: 33804401 PMCID: PMC8000945 DOI: 10.3390/metabo11030145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
Abnormal energy metabolism associated with mitochondrial dysfunction is thought to be a major contributor to the progression of neurodegenerative diseases such as Parkinson's disease (PD). Recent advancements in the field of magnetic resonance (MR) based metabolic imaging provide state-of-the-art technologies for non-invasively probing cerebral energy metabolism under various brain conditions. In this proof-of-principle clinical study, we employed quantitative 31P MR spectroscopy (MRS) imaging techniques to determine a constellation of metabolic and bioenergetic parameters, including cerebral adenosine triphosphate (ATP) and other phosphorous metabolite concentrations, intracellular pH and nicotinamide adenine dinucleotide (NAD) redox ratio, and ATP production rates in the occipital lobe of cognitive-normal PD patients, and then we compared them with age-sex matched healthy controls. Small but statistically significant differences in intracellular pH, NAD and ATP contents and ATPase enzyme activity between the two groups were detected, suggesting that subtle defects in energy metabolism and mitochondrial function are quantifiable before regional neurological deficits or pathogenesis begin to occur in these patients. Pilot data aiming to evaluate the bioenergetic effect of mitochondrial-protective bile acid, ursodeoxycholic acid (UDCA) were also obtained. These results collectively demonstrated that in vivo 31P MRS-based neuroimaging can non-invasively and quantitatively assess key metabolic-energetic metrics in the human brain. This provides an exciting opportunity to better understand neurodegenerative diseases, their progression and response to treatment.
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Affiliation(s)
- Xiao-Hong Zhu
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence: (X.-H.Z.); (W.C.); Tel.: +1-(612) 626-2001 (X.-H.Z.); Fax: +1-(612) 626-2004 (X.-H.Z.)
| | - Byeong-Yeul Lee
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Paul Tuite
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Lisa Coles
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA; (L.C.); (A.G.S.); (J.C.)
| | - Abhishek G. Sathe
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA; (L.C.); (A.G.S.); (J.C.)
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Jim Cloyd
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA; (L.C.); (A.G.S.); (J.C.)
| | - Walter C. Low
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Clifford J. Steer
- Departments of Medicine and Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Wei Chen
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence: (X.-H.Z.); (W.C.); Tel.: +1-(612) 626-2001 (X.-H.Z.); Fax: +1-(612) 626-2004 (X.-H.Z.)
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