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Ruiz-Rodado V, Brender JR, Cherukuri MK, Gilbert MR, Larion M. Magnetic resonance spectroscopy for the study of cns malignancies. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 122:23-41. [PMID: 33632416 PMCID: PMC7910526 DOI: 10.1016/j.pnmrs.2020.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 05/04/2023]
Abstract
Despite intensive research, brain tumors are amongst the malignancies with the worst prognosis; therefore, a prompt diagnosis and thoughtful assessment of the disease is required. The resistance of brain tumors to most forms of conventional therapy has led researchers to explore the underlying biology in search of new vulnerabilities and biomarkers. The unique metabolism of brain tumors represents one potential vulnerability and the basis for a system of classification. Profiling this aberrant metabolism requires a method to accurately measure and report differences in metabolite concentrations. Magnetic resonance-based techniques provide a framework for examining tumor tissue and the evolution of disease. Nuclear Magnetic Resonance (NMR) analysis of biofluids collected from patients suffering from brain cancer can provide biological information about disease status. In particular, urine and plasma can serve to monitor the evolution of disease through the changes observed in the metabolic profiles. Moreover, cerebrospinal fluid can be utilized as a direct reporter of cerebral activity since it carries the chemicals exchanged with the brain tissue and the tumor mass. Metabolic reprogramming has recently been included as one of the hallmarks of cancer. Accordingly, the metabolic rewiring experienced by these tumors to sustain rapid growth and proliferation can also serve as a potential therapeutic target. The combination of 13C tracing approaches with the utilization of different NMR spectral modalities has allowed investigations of the upregulation of glycolysis in the aggressive forms of brain tumors, including glioblastomas, and the discovery of the utilization of acetate as an alternative cellular fuel in brain metastasis and gliomas. One of the major contributions of magnetic resonance to the assessment of brain tumors has been the non-invasive determination of 2-hydroxyglutarate (2HG) in tumors harboring a mutation in isocitrate dehydrogenase 1 (IDH1). The mutational status of this enzyme already serves as a key feature in the clinical classification of brain neoplasia in routine clinical practice and pilot studies have established the use of in vivo magnetic resonance spectroscopy (MRS) for monitoring disease progression and treatment response in IDH mutant gliomas. However, the development of bespoke methods for 2HG detection by MRS has been required, and this has prevented the wider implementation of MRS methodology into the clinic. One of the main challenges for improving the management of the disease is to obtain an accurate insight into the response to treatment, so that the patient can be promptly diverted into a new therapy if resistant or maintained on the original therapy if responsive. The implementation of 13C hyperpolarized magnetic resonance spectroscopic imaging (MRSI) has allowed detection of changes in tumor metabolism associated with a treatment, and as such has been revealed as a remarkable tool for monitoring response to therapeutic strategies. In summary, the application of magnetic resonance-based methodologies to the diagnosis and management of brain tumor patients, in addition to its utilization in the investigation of its tumor-associated metabolic rewiring, is helping to unravel the biological basis of malignancies of the central nervous system.
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Affiliation(s)
- Victor Ruiz-Rodado
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institute of Health, Bethesda, United States.
| | - Jeffery R Brender
- Radiation Biology Branch, Center for Cancer Research, National Institute of Health, Bethesda, United States
| | - Murali K Cherukuri
- Radiation Biology Branch, Center for Cancer Research, National Institute of Health, Bethesda, United States
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institute of Health, Bethesda, United States
| | - Mioara Larion
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institute of Health, Bethesda, United States.
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Urman JM, Herranz JM, Uriarte I, Rullán M, Oyón D, González B, Fernandez-Urién I, Carrascosa J, Bolado F, Zabalza L, Arechederra M, Alvarez-Sola G, Colyn L, Latasa MU, Puchades-Carrasco L, Pineda-Lucena A, Iraburu MJ, Iruarrizaga-Lejarreta M, Alonso C, Sangro B, Purroy A, Gil I, Carmona L, Cubero FJ, Martínez-Chantar ML, Banales JM, Romero MR, Macias RI, Monte MJ, Marín JJG, Vila JJ, Corrales FJ, Berasain C, Fernández-Barrena MG, Avila MA. Pilot Multi-Omic Analysis of Human Bile from Benign and Malignant Biliary Strictures: A Machine-Learning Approach. Cancers (Basel) 2020; 12:cancers12061644. [PMID: 32575903 PMCID: PMC7352944 DOI: 10.3390/cancers12061644] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022] Open
Abstract
Cholangiocarcinoma (CCA) and pancreatic adenocarcinoma (PDAC) may lead to the development of extrahepatic obstructive cholestasis. However, biliary stenoses can also be caused by benign conditions, and the identification of their etiology still remains a clinical challenge. We performed metabolomic and proteomic analyses of bile from patients with benign (n = 36) and malignant conditions, CCA (n = 36) or PDAC (n = 57), undergoing endoscopic retrograde cholangiopancreatography with the aim of characterizing bile composition in biliopancreatic disease and identifying biomarkers for the differential diagnosis of biliary strictures. Comprehensive analyses of lipids, bile acids and small molecules were carried out using mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (1H-NMR) in all patients. MS analysis of bile proteome was performed in five patients per group. We implemented artificial intelligence tools for the selection of biomarkers and algorithms with predictive capacity. Our machine-learning pipeline included the generation of synthetic data with properties of real data, the selection of potential biomarkers (metabolites or proteins) and their analysis with neural networks (NN). Selected biomarkers were then validated with real data. We identified panels of lipids (n = 10) and proteins (n = 5) that when analyzed with NN algorithms discriminated between patients with and without cancer with an unprecedented accuracy.
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Affiliation(s)
- Jesús M. Urman
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
| | - José M. Herranz
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Iker Uriarte
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - María Rullán
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - Daniel Oyón
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - Belén González
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - Ignacio Fernandez-Urién
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
| | - Juan Carrascosa
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
| | - Federico Bolado
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - Lucía Zabalza
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - María Arechederra
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Gloria Alvarez-Sola
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Leticia Colyn
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - María U. Latasa
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Leonor Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | - Antonio Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
- Program of Molecular Therapeutics, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
| | - María J. Iraburu
- Department of Biochemistry and Genetics, School of Sciences; University of Navarra, 31008 Pamplona, Spain;
| | | | - Cristina Alonso
- OWL Metabolomics, Bizkaia Technology Park, 48160 Derio, Spain; (M.I.-L.); (C.A.)
| | - Bruno Sangro
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Hepatology Unit, Department of Internal Medicine, University of Navarra Clinic, 31008 Pamplona, Spain
| | - Ana Purroy
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- Navarrabiomed Biobank Unit, IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Isabel Gil
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- Navarrabiomed Biobank Unit, IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Lorena Carmona
- Proteomics Unit, Centro Nacional de Biotecnología (CNB) Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
| | - Francisco Javier Cubero
- Department of Immunology, Ophtalmology & Ear, Nose and Throat (ENT), Complutense University School of Medicine and 12 de Octubre Health Research Institute (Imas12), 28040 Madrid, Spain;
| | - María L. Martínez-Chantar
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Jesús M. Banales
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, 20014 San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Marta R. Romero
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Rocio I.R. Macias
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Maria J. Monte
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Jose J. G. Marín
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Juan J. Vila
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
| | - Fernando J. Corrales
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Proteomics Unit, Centro Nacional de Biotecnología (CNB) Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
| | - Carmen Berasain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Maite G. Fernández-Barrena
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Matías A. Avila
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
- Correspondence: ; Tel.: +34-948-194700 (ext. 4003)
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Dietz C, Ehret F, Palmas F, Vandergrift LA, Jiang Y, Schmitt V, Dufner V, Habbel P, Nowak J, Cheng LL. Applications of high-resolution magic angle spinning MRS in biomedical studies II-Human diseases. NMR IN BIOMEDICINE 2017; 30:10.1002/nbm.3784. [PMID: 28915318 PMCID: PMC5690552 DOI: 10.1002/nbm.3784] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/21/2017] [Accepted: 07/10/2017] [Indexed: 05/06/2023]
Abstract
High-resolution magic angle spinning (HRMAS) MRS is a powerful method for gaining insight into the physiological and pathological processes of cellular metabolism. Given its ability to obtain high-resolution spectra of non-liquid biological samples, while preserving tissue architecture for subsequent histopathological analysis, the technique has become invaluable for biochemical and biomedical studies. Using HRMAS MRS, alterations in measured metabolites, metabolic ratios, and metabolomic profiles present the possibility to improve identification and prognostication of various diseases and decipher the metabolomic impact of drug therapies. In this review, we evaluate HRMAS MRS results on human tissue specimens from malignancies and non-localized diseases reported in the literature since the inception of the technique in 1996. We present the diverse applications of the technique in understanding pathological processes of different anatomical origins, correlations with in vivo imaging, effectiveness of therapies, and progress in the HRMAS methodology.
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Affiliation(s)
- Christopher Dietz
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Faculty of Medicine, Julius Maximilian University of Würzburg, 97080 Würzburg, Germany
| | - Felix Ehret
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Faculty of Medicine, Julius Maximilian University of Würzburg, 97080 Würzburg, Germany
| | - Francesco Palmas
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Department of Chemical and Geological Sciences, University of Cagliari, Cagliari, Sardinia, 09042 Italy
| | - Lindsey A. Vandergrift
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
| | - Yanni Jiang
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Department of Radiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029 China
| | - Vanessa Schmitt
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Faculty of Medicine, Julius Maximilian University of Würzburg, 97080 Würzburg, Germany
| | - Vera Dufner
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Department of Hematology and Oncology, Charité Medical University of Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Piet Habbel
- Department of Hematology and Oncology, Charité Medical University of Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Johannes Nowak
- Department of Diagnostic and Interventional Radiology, University Hospital of Würzburg, 97080 Würzburg, Germany
| | - Leo L. Cheng
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
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Constantin A, Elkhaled A, Jalbert L, Srinivasan R, Cha S, Chang SM, Bajcsy R, Nelson SJ. Identifying malignant transformations in recurrent low grade gliomas using high resolution magic angle spinning spectroscopy. Artif Intell Med 2012; 55:61-70. [PMID: 22387185 DOI: 10.1016/j.artmed.2012.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 12/12/2011] [Accepted: 01/17/2012] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The objective of this study was to determine whether metabolic parameters derived from ex vivo analysis of tissue samples are predictive of biologic characteristics of recurrent low grade gliomas (LGGs). This was achieved by exploring the use of multivariate pattern recognition methods to generate statistical models of the metabolic characteristics of recurrent LGGs that correlate with aggressive biology and poor clinical outcome. METHODS Statistical models were constructed to distinguish between patients with recurrent gliomas that had undergone malignant transformation to a higher grade and those that remained grade 2. The pattern recognition methods explored in this paper include three filter-based feature selection methods (chi-square, gain ratio, and two-way conditional probability), a genetic search wrapper-based feature subset selection algorithm, and five classification algorithms (linear discriminant analysis, logistic regression, functional trees, support vector machines, and decision stump logit boost). The accuracy of each pattern recognition framework was evaluated using leave-one-out cross-validation and bootstrapping. MATERIALS The population studied included fifty-three patients with recurrent grade 2 gliomas. Among these patients, seven had tumors that transformed to grade 4, twenty-four had tumors that transformed to grade 3, and twenty-two had tumors that remained grade 2. Image-guided tissue samples were obtained from these patients using surgical navigation software. Part of each tissue sample was examined by a pathologist for histological features and for consistency with the tumor grade diagnosis. The other part of the tissue sample was analyzed with ex vivo nuclear magnetic resonance (NMR) spectroscopy. RESULTS Distinguishing between recurrent low grade gliomas that transformed to a higher grade and those that remained grade 2 was achieved with 96% accuracy, using areas of the ex vivo NMR spectrum corresponding to myoinositol, 2-hydroxyglutarate, hypo-taurine, choline, glycerophosphocholine, phosphocholine, glutathione, and lipid. Logistic regression and decision stump boosting models were able to distinguish between recurrent gliomas that transformed to a higher grade and those that did not with 100% training accuracy (95% confidence interval [93-100%]), 96% leave-one-out cross-validation accuracy (95% confidence interval [87-100%]), and 96% bootstrapping accuracy (95% confidence interval [95-97%]). Linear discriminant analysis, functional trees, and support vector machines were able to achieve leave-one-out cross-validation accuracy above 90% and bootstrapping accuracy above 85%. The three feature ranking methods were comparable in performance. CONCLUSIONS This study demonstrates the feasibility of using quantitative pattern recognition methods for the analysis of metabolic data from brain tissue obtained during the surgical resection of gliomas. All pattern recognition techniques provided good diagnostic accuracies, though logistic regression and decision stump boosting slightly outperform the other classifiers. These methods identified biomarkers that can be used to detect malignant transformations in individual low grade gliomas, and can lead to a timely change in treatment for each patient.
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Affiliation(s)
- Alexandra Constantin
- Electrical Engineering and Computer Science, Sutardja Dai Hall, University of California, Berkeley, Berkeley, CA 94709, USA.
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