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Cheng LL, Zhong AB, Muti IH, Eyles SJ, Vachet RW, Stopka SA, Sikora KN, Bobst CE, Agar JN, Mino-Kenudson MA, Wu CL, Christiani DC, Kaltashov IA, Agar NY. Abstract 2322: Multiplatform metabolomics studies of human cancers with NMR and mass spectrometry imaging. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Unfortunately, at present, there is no single technique that possesses all the characteristics needed to be considered an ideal global metabolite profiling tool. Thus, the use of multiple analytical platforms, such as combining the strengths of Mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR), for metabolic profiling can maximize coverage and generate more global metabolomic profiles. In this study, we demonstrate the utilities of the combined NMR and MSI multiplatform in our metabolomics results on human prostate and lung cancers.
Statistical data on the natural history of prostate cancer (PCa) show that >70% of patients diagnosed by PSA screening will likely experience indolent disease with little impact on well-being. For about 17% of newly PSA-diagnosed patients, however, aggressive PCa proliferation ensues, truncating life expectancy. At present, no reliable clinical test can differentiate between these two groups. Using HRMAS 1HNMR followed by quantitative histology, we showed statistically significant correlations between concentrations of Spm and the amount of histologically-benign epithelial (Hb Epi) prostatic cells and glands in human cancerous prostates. However, as above discussed that using HRMAS NMR alone we cannot prove that Spm was indeed generated or resided in the Hb Epi cells. Nevertheless, using MALDI MSI, we were able to locate Spm (m/z: 203.223 ± 0.001Da) onto Hb Epi, where spermine on the PCa lesions appeared below detection limits. From these maps, for the first time, we could visualize and confirm the differential localizations of Spm in prostates. This proof of Sym relationship to prostate pathologies and its proposed PCa inhibitory effects may support further studies that are critical in differentiating aggressive from indolent PCa for disease evaluations and patient personalized treatment strategies.
To search for such screening metabolomics biomarkers in lung cancer, we used HRMAS NMR to analyze 93 pairs of human LuCa tissue and serum samples, and 29 healthy human sera. A number of potential metabolite candidates capable to differentiate LuCa characteristics were identified, including glutamate, lipids, alanine, glycerylphosphorylcholine, glutamine, phosphorylcholine, etc. This list can be further expanded by analyzing metabolite composition in the serum of cancer patients and control healthy subjects using LC-MS, which offers a dramatic increase in sensitivity compared to HRMAS NMR and, therefore, is better suited for the biomarker discovery. In addition to acquiring high-resolution mass data, the high data acquisition rate allows the fragment ion mass spectra (MS/MS) to be generated for the most abundant ionic species in each chromatographic peak. This feature allows specific classes of tumor-attenuated metabolites to be identified based on the presence of unique structurally diagnostic fragment ions in MS/MS spectra.
Citation Format: Leo L. Cheng, Anya B. Zhong, Isabella H. Muti, Stephen J. Eyles, Richard W. Vachet, Sylwia A. Stopka, Kristen N. Sikora, Cedric E. Bobst, Jeffrey N. Agar, Mari A. Mino-Kenudson, Chin-Lee Wu, David C. Christiani, Igor A. Kaltashov, Nathalie Y. Agar. Multiplatform metabolomics studies of human cancers with NMR and mass spectrometry imaging [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2322.
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Affiliation(s)
- Leo L. Cheng
- 1Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
| | - Anya B. Zhong
- 1Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
| | - Isabella H. Muti
- 1Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
| | | | | | - Sylwia A. Stopka
- 3Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | | | | | | | - Chin-Lee Wu
- 5Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | | | - Nathalie Y. Agar
- 3Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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Calligaris D, Clark A, Kallay L, Krummel DP, Agar J, Schniederjan M, Pomeroy S, Agar NY, Sengupta S. PATH-04. DISTINGUISHING PINEOBLASTOMA FROM MEDULLOBLASTOMAS USING TISSUE MASS SPECTROMETRY IMAGING. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox168.695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Sun Y, Alberta JA, Pilarz C, Calligaris D, Chadwick EJ, Ramkissoon SH, Ramkissoon LA, Garcia VM, Mazzola E, Goumnerova L, Kane M, Yao Z, Kieran MW, Ligon KL, Hahn WC, Garraway LA, Rosen N, Gray NS, Agar NY, Buhrlage SJ, Segal RA, Stiles CD. A brain-penetrant RAF dimer antagonist for the noncanonical BRAF oncoprotein of pediatric low-grade astrocytomas. Neuro Oncol 2017; 19:774-785. [PMID: 28082416 PMCID: PMC5464455 DOI: 10.1093/neuonc/now261] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Activating mutations or structural rearrangements in BRAF are identified in roughly 75% of all pediatric low-grade astrocytomas (PLGAs). However, first-generation RAF inhibitors approved for adult melanoma have poor blood-brain penetrance and are only effective on tumors that express the canonical BRAFV600E oncoprotein, which functions as a monomer. These drugs (type I antagonists that target the "DFG-in" conformation of the kinase) fail to block signaling via KIAA1549:BRAF, a truncation/fusion BRAF oncoprotein which functions as a dimer and is found in the most common form of PLGA. Methods A panel of small molecule RAF inhibitors (including type II inhibitors, targeting the "DFG-out" conformation of the kinase) was screened for drugs showing efficacy on murine models of PLGA and on authentic human PLGA cells expressing KIAA1549:BRAF. Results We identify a type II RAF inhibitor that serves as an equipotent antagonist of BRAFV600E, KIAA1549:BRAF, and other noncanonical BRAF oncoproteins that function as dimers. This drug (MLN2480, also known as TAK-580) has good brain penetrance and is active on authentic human PLGA cells in brain organotypic cultures. Conclusion MLN2480 may be an effective therapeutic for BRAF mutant pediatric astrocytomas.
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Affiliation(s)
- Yu Sun
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - John A Alberta
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Catherine Pilarz
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David Calligaris
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily J Chadwick
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shakti H Ramkissoon
- Center for Molecular Oncologic Pathology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lori A Ramkissoon
- Center for Molecular Oncologic Pathology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Veronica Matia Garcia
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Emanuele Mazzola
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Liliana Goumnerova
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Kane
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Zhan Yao
- Program in Molecular Pharmacology, Department of Medicine, and Center for Mechanism Based Therapeutics Memorial Sloan Kettering Cancer Center, New York, USA
| | - Mark W Kieran
- Division of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Keith L Ligon
- Center for Molecular Oncologic Pathology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Neal Rosen
- Program in Molecular Pharmacology, Department of Medicine, and Center for Mechanism Based Therapeutics Memorial Sloan Kettering Cancer Center, New York, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nathalie Y Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Departments of Neurosurgery and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rosalind A Segal
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Charles D Stiles
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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Kieran MW, Sun Y, Pilarz C, Calligaris D, Chadwick EJ, Alberta JA, Ramkissoon SH, Ramkissoon LA, Garcia VM, Wilkinson K, Kane M, Goumnerova L, Chi SN, Manley P, Wright KD, Agar NY, Ligon KL, Beroukhim R, Bandopadhayay P, Kannan G, Segal RA, Garraway LA, Gray NS, Eck M, Stiles CD, Buhrlage SJ. LG-47TYPE II RAF INHIBITORS INHIBIT BRAF MUTATIONS AND TRUNCATED FUSIONS IN PEDIATRIC LOW-GRADE GLIOMAS. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now075.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Li H, Jiang X, Yu Y, Huang W, Xing H, Agar NY, Yang HW, Yang B, Carroll RS, Johnson MD. KAP regulates ROCK2 and Cdk2 in an RNA-activated glioblastoma invasion pathway. Oncogene 2014; 34:1432-41. [PMID: 24704824 DOI: 10.1038/onc.2014.49] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/13/2013] [Accepted: 01/06/2014] [Indexed: 12/30/2022]
Abstract
Aberrant splicing of the cyclin-dependent kinase-associated phosphatase, KAP, promotes glioblastoma invasion in a Cdc2-dependent manner. However, the mechanism by which this occurs is unknown. Here we show that miR-26a, which is often amplified in glioblastoma, promotes invasion in phosphatase and tensin homolog (PTEN)-competent and PTEN-deficient glioblastoma cells by directly downregulating KAP expression. Mechanistically, we find that KAP binds and activates ROCK2. Thus, RNA-mediated downregulation of KAP leads to decreased ROCK2 activity and this, in turn, increases Rac1-mediated invasion. In addition, the decrease in KAP expression activates the cyclin-dependent kinase, Cdk2, and this directly promotes invasion by increasing retinoblastoma phosphorylation, E2F-dependent Cdc2 expression and Cdc2-mediated inactivation of the actomyosin inhibitor, caldesmon. Importantly, glioblastoma cell invasion mediated by this pathway can be antagonized by Cdk2/Cdc2 inhibitors in vitro and in vivo. Thus, two distinct RNA-based mechanisms activate this novel KAP/ROCK2/Cdk2-dependent invasion pathway in glioblastoma.
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Affiliation(s)
- H Li
- 1] Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA [2] Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - X Jiang
- Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Y Yu
- Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - W Huang
- Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - H Xing
- Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - N Y Agar
- Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - H W Yang
- Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - B Yang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - R S Carroll
- Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - M D Johnson
- 1] Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA [2] Program in Neuro-Oncology, Dana Farber/Brigham and Women's Cancer Center, Boston, MA, USA
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Calligaris D, Norton I, Feldman DR, Ide JL, Dunn IF, Eberlin LS, Cooks RG, Jolesz FA, Golby AJ, Santagata S, Agar NY. Mass spectrometry imaging as a tool for surgical decision-making. J Mass Spectrom 2013; 48:1178-87. [PMID: 24259206 PMCID: PMC3957233 DOI: 10.1002/jms.3295] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/03/2013] [Accepted: 10/10/2013] [Indexed: 05/18/2023]
Abstract
Despite significant advances in image-guided therapy, surgeons are still too often left with uncertainty when deciding to remove tissue. This binary decision between removing and leaving tissue during surgery implies that the surgeon should be able to distinguish tumor from healthy tissue. In neurosurgery, current image-guidance approaches such as magnetic resonance imaging (MRI) combined with neuronavigation offer a map as to where the tumor should be, but the only definitive method to characterize the tissue at stake is histopathology. Although extremely valuable information is derived from this gold standard approach, it is limited to very few samples during surgery and is not practically used for the delineation of tumor margins. The development and implementation of faster, comprehensive, and complementary approaches for tissue characterization are required to support surgical decision-making--an incremental and iterative process with tumor removed in multiple and often minute biopsies. The development of atmospheric pressure ionization sources makes it possible to analyze tissue specimens with little to no sample preparation. Here, we highlight the value of desorption electrospray ionization as one of many available approaches for the analysis of surgical tissue. Twelve surgical samples resected from a patient during surgery were analyzed and diagnosed as glioblastoma tumor or necrotic tissue by standard histopathology, and mass spectrometry results were further correlated to histopathology for critical validation of the approach. The use of a robust statistical approach reiterated results from the qualitative detection of potential biomarkers of these tissue types. The correlation of the mass spectrometry and histopathology results to MRI brings significant insight into tumor presentation that could not only serve to guide tumor resection, but that is also worthy of more detailed studies on our understanding of tumor presentation on MRI.
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Affiliation(s)
- David Calligaris
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Isaiah Norton
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Daniel R. Feldman
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115
| | - Jennifer L. Ide
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Ian F. Dunn
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Livia S. Eberlin
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN 47907
| | - R. Graham Cooks
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN 47907
| | - Ferenc A. Jolesz
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Alexandra J. Golby
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115
| | - Nathalie Y. Agar
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN 47907
- Corresponding author: Dr. Nathalie Y.R. Agar Departments of Neurosurgery and Radiology, Brigham and Women’s Hospital, and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115. , +1617/525-7374
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