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Daneshmandi S, Choi JE, Yan Q, MacDonald CR, Pandey M, Goruganthu M, Roberts N, Singh PK, Higashi RM, Lane AN, Fan TWM, Wang J, McCarthy PL, Repasky EA, Mohammadpour H. Myeloid-derived suppressor cell mitochondrial fitness governs chemotherapeutic efficacy in hematologic malignancies. Nat Commun 2024; 15:2803. [PMID: 38555305 PMCID: PMC10981707 DOI: 10.1038/s41467-024-47096-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 03/28/2023] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
Myeloid derived suppressor cells (MDSCs) are key regulators of immune responses and correlate with poor outcomes in hematologic malignancies. Here, we identify that MDSC mitochondrial fitness controls the efficacy of doxorubicin chemotherapy in a preclinical lymphoma model. Mechanistically, we show that triggering STAT3 signaling via β2-adrenergic receptor (β2-AR) activation leads to improved MDSC function through metabolic reprograming, marked by sustained mitochondrial respiration and higher ATP generation which reduces AMPK signaling, altering energy metabolism. Furthermore, induced STAT3 signaling in MDSCs enhances glutamine consumption via the TCA cycle. Metabolized glutamine generates itaconate which downregulates mitochondrial reactive oxygen species via regulation of Nrf2 and the oxidative stress response, enhancing MDSC survival. Using β2-AR blockade, we target the STAT3 pathway and ATP and itaconate metabolism, disrupting ATP generation by the electron transport chain and decreasing itaconate generation causing diminished MDSC mitochondrial fitness. This disruption increases the response to doxorubicin and could be tested clinically.
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Affiliation(s)
- Saeed Daneshmandi
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Jee Eun Choi
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Qi Yan
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Cameron R MacDonald
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Manu Pandey
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Mounika Goruganthu
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Nathan Roberts
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Prashant K Singh
- Department of Cancer Genetics & Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Richard M Higashi
- Department of Toxicology and Cancer Biology, Markey Cancer Center, Center for Environmental and Systems Biochemistry (CESB), Lexington, KY, USA
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, Markey Cancer Center, Center for Environmental and Systems Biochemistry (CESB), Lexington, KY, USA
| | - Teresa W-M Fan
- Department of Toxicology and Cancer Biology, Markey Cancer Center, Center for Environmental and Systems Biochemistry (CESB), Lexington, KY, USA
| | - Jianmin Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Philip L McCarthy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Elizabeth A Repasky
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA
| | - Hemn Mohammadpour
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, USA.
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W-M Fan T, Islam JMM, Higashi RM, Lin P, Brainson CF, Lane AN. Metabolic reprogramming driven by EZH2 inhibition depends on cell-matrix interactions. J Biol Chem 2024; 300:105485. [PMID: 37992808 PMCID: PMC10770523 DOI: 10.1016/j.jbc.2023.105485] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 05/11/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023] Open
Abstract
EZH2 (Enhancer of Zeste Homolog 2), a subunit of Polycomb Repressive Complex 2 (PRC2), catalyzes the trimethylation of histone H3 at lysine 27 (H3K27me3), which represses expression of genes. It also has PRC2-independent functions, including transcriptional coactivation of oncogenes, and is frequently overexpressed in lung cancers. Clinically, EZH2 inhibition can be achieved with the FDA-approved drug EPZ-6438 (tazemetostat). To realize the full potential of EZH2 blockade, it is critical to understand how cell-cell/cell-matrix interactions present in 3D tissue and cell culture systems influences this blockade in terms of growth-related metabolic functions. Here, we show that EZH2 suppression reduced growth of human lung adenocarcinoma A549 cells in 2D cultures but stimulated growth in 3D cultures. To understand the metabolic underpinnings, we employed [13C6]-glucose stable isotope-resolved metabolomics to determine the effect of EZH2 suppression on metabolic networks in 2D versus 3D A549 cultures. The Krebs cycle, neoribogenesis, γ-aminobutyrate metabolism, and salvage synthesis of purine nucleotides were activated by EZH2 suppression in 3D spheroids but not in 2D cells, consistent with the growth effect. Using simultaneous 2H7-glucose + 13C5,15N2-Gln tracers and EPZ-6438 inhibition of H3 trimethylation, we delineated the effects on the Krebs cycle, γ-aminobutyrate metabolism, gluconeogenesis, and purine salvage to be PRC2-dependent. Furthermore, the growth/metabolic effects differed for mouse Matrigel versus self-produced A549 extracellular matrix. Thus, our findings highlight the importance of the presence and nature of extracellular matrix in studying the function of EZH2 and its inhibitors in cancer cells for modeling the in vivo outcomes.
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Affiliation(s)
- Teresa W-M Fan
- Center for Environmental and System Biochemistry, University of Kentucky, Lexington, Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA; Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA.
| | - Jahid M M Islam
- Center for Environmental and System Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Richard M Higashi
- Center for Environmental and System Biochemistry, University of Kentucky, Lexington, Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA; Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
| | - Penghui Lin
- Center for Environmental and System Biochemistry, University of Kentucky, Lexington, Kentucky, USA; Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
| | - Christine F Brainson
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA; Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
| | - Andrew N Lane
- Center for Environmental and System Biochemistry, University of Kentucky, Lexington, Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA; Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
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Gnanaprakasam JNR, Kushwaha B, Liu L, Chen X, Kang S, Wang T, Cassel TA, Adams CM, Higashi RM, Scott DA, Xin G, Li Z, Yang J, Lane AN, Fan TWM, Zhang J, Wang R. Asparagine restriction enhances CD8 + T cell metabolic fitness and antitumoral functionality through an NRF2-dependent stress response. Nat Metab 2023; 5:1423-1439. [PMID: 37550596 PMCID: PMC10447245 DOI: 10.1038/s42255-023-00856-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 07/05/2023] [Indexed: 08/09/2023]
Abstract
Robust and effective T cell immune surveillance and cancer immunotherapy require proper allocation of metabolic resources to sustain energetically costly processes, including growth and cytokine production. Here, we show that asparagine (Asn) restriction on CD8+ T cells exerted opposing effects during activation (early phase) and differentiation (late phase) following T cell activation. Asn restriction suppressed activation and cell cycle entry in the early phase while rapidly engaging the nuclear factor erythroid 2-related factor 2 (NRF2)-dependent stress response, conferring robust proliferation and effector function on CD8+ T cells during differentiation. Mechanistically, NRF2 activation in CD8+ T cells conferred by Asn restriction rewired the metabolic program by reducing the overall glucose and glutamine consumption but increasing intracellular nucleotides to promote proliferation. Accordingly, Asn restriction or NRF2 activation potentiated the T cell-mediated antitumoral response in preclinical animal models, suggesting that Asn restriction is a promising and clinically relevant strategy to enhance cancer immunotherapy. Our study revealed Asn as a critical metabolic node in directing the stress signaling to shape T cell metabolic fitness and effector functions.
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Affiliation(s)
- J N Rashida Gnanaprakasam
- Center for Childhood Cancer, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Bhavana Kushwaha
- Center for Childhood Cancer, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Lingling Liu
- Center for Childhood Cancer, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Xuyong Chen
- Center for Childhood Cancer, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Siwen Kang
- Center for Childhood Cancer, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Tingting Wang
- Center for Childhood Cancer, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Teresa A Cassel
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Christopher M Adams
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - David A Scott
- Cancer Metabolism Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Gang Xin
- Department of Microbial Infection and Immunity, Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, USA
| | - Zihai Li
- Department of Microbial Infection and Immunity, Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, USA
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Ji Zhang
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ruoning Wang
- Center for Childhood Cancer, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA.
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Fan TWM, Sun Q, Higashi RM. Ultrahigh resolution MS 1/MS 2-based reconstruction of metabolic networks in mammalian cells reveals changes for selenite and arsenite action. J Biol Chem 2022; 298:102586. [PMID: 36223837 PMCID: PMC9667311 DOI: 10.1016/j.jbc.2022.102586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Metabolic networks are complex, intersecting, and composed of numerous enzyme-catalyzed biochemical reactions that transfer various molecular moieties among metabolites. Thus, robust reconstruction of metabolic networks requires metabolite moieties to be tracked, which cannot be readily achieved with mass spectrometry (MS) alone. We previously developed an Ion Chromatography-ultrahigh resolution-MS1/data independent-MS2 method to track the simultaneous incorporation of the heavy isotopes 13C and 15N into the moieties of purine/pyrimidine nucleotides in mammalian cells. Ultrahigh resolution-MS1 resolves and counts multiple tracer atoms in intact metabolites, while data independent-tandem MS (MS2) determines isotopic enrichment in their moieties without concern for the numerous mass isotopologue source ions to be fragmented. Together, they enabled rigorous MS-based reconstruction of metabolic networks at specific enzyme levels. We have expanded this approach to trace the labeled atom fate of [13C6]-glucose in 3D A549 spheroids in response to the anticancer agent selenite and that of [13C5,15N2]-glutamine in 2D BEAS-2B cells in response to arsenite transformation. We deduced altered activities of specific enzymes in the Krebs cycle, pentose phosphate pathway, gluconeogenesis, and UDP-GlcNAc synthesis pathways elicited by the stressors. These metabolic details help elucidate the resistance mechanism of 3D versus 2D A549 cultures to selenite and metabolic reprogramming that can mediate the transformation of BEAS-2B cells by arsenite.
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Affiliation(s)
- Teresa W-M Fan
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA; Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA.
| | - Qiushi Sun
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky, USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA; Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
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5
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Fan TWM, Daneshmandi S, Cassel TA, Uddin MB, Sledziona J, Thompson PT, Lin P, Higashi RM, Lane AN. Polarization and β-Glucan Reprogram Immunomodulatory Metabolism in Human Macrophages and Ex Vivo in Human Lung Cancer Tissues. J Immunol 2022; 209:1674-1690. [PMID: 36150727 PMCID: PMC9588758 DOI: 10.4049/jimmunol.2200178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/16/2022] [Accepted: 08/23/2022] [Indexed: 11/06/2022]
Abstract
Immunomodulatory (IM) metabolic reprogramming in macrophages (Mϕs) is fundamental to immune function. However, limited information is available for human Mϕs, particularly in response plasticity, which is critical to understanding the variable efficacy of immunotherapies in cancer patients. We carried out an in-depth analysis by combining multiplex stable isotope-resolved metabolomics with reversed phase protein array to map the dynamic changes of the IM metabolic network and key protein regulators in four human donors' Mϕs in response to differential polarization and M1 repolarizer β-glucan (whole glucan particles [WGPs]). These responses were compared with those of WGP-treated ex vivo organotypic tissue cultures (OTCs) of human non-small cell lung cancer. We found consistently enhanced tryptophan catabolism with blocked NAD+ and UTP synthesis in M1-type Mϕs (M1-Mϕs), which was associated with immune activation evidenced by increased release of IL-1β/CXCL10/IFN-γ/TNF-α and reduced phagocytosis. In M2a-Mϕs, WGP treatment of M2a-Mϕs robustly increased glucose utilization via the glycolysis/oxidative branch of the pentose phosphate pathway while enhancing UDP-N-acetyl-glucosamine turnover and glutamine-fueled gluconeogenesis, which was accompanied by the release of proinflammatory IL-1β/TNF-α to above M1-Mϕ's levels, anti-inflammatory IL-10 to above M2a-Mϕ's levels, and attenuated phagocytosis. These IM metabolic responses could underlie the opposing effects of WGP, i.e., reverting M2- to M1-type immune functions but also boosting anti-inflammation. Variable reprogrammed Krebs cycle and glutamine-fueled synthesis of UTP in WGP-treated OTCs of human non-small cell lung cancer were observed, reflecting variable M1 repolarization of tumor-associated Mϕs. This was supported by correlation with IL-1β/TNF-α release and compromised tumor status, making patient-derived OTCs unique models for studying variable immunotherapeutic efficacy in cancer patients.
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Affiliation(s)
- Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY;
- Markey Cancer Center, University of Kentucky, Lexington, KY; and
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY
| | - Saeed Daneshmandi
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY
| | - Teresa A Cassel
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY
| | - Mohammad B Uddin
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY
| | - James Sledziona
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY
| | - Patrick T Thompson
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY
| | - Penghui Lin
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY
- Markey Cancer Center, University of Kentucky, Lexington, KY; and
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY;
- Markey Cancer Center, University of Kentucky, Lexington, KY; and
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY
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Lin P, W-M Fan T, Lane AN. NMR-based isotope editing, chemoselection and isotopomer distribution analysis in stable isotope resolved metabolomics. Methods 2022; 206:8-17. [PMID: 35908585 PMCID: PMC9539636 DOI: 10.1016/j.ymeth.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 05/24/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022] Open
Abstract
NMR is a very powerful tool for identifying and quantifying compounds within complex mixtures without the need for individual standards or chromatographic separation. Stable Isotope Resolved Metabolomics (or SIRM) is an approach to following the fate of individual atoms from precursors through metabolic transformation, producing an atom-resolved metabolic fate map. However, extracts of cells or tissue give rise to very complex NMR spectra. While multidimensional NMR experiments may partially overcome the spectral overlap problem, additional tools may be needed to determine site-specific isotopomer distributions. NMR is especially powerful by virtue of its isotope editing capabilities using NMR active nuclei such as 13C, 15N, 19F and 31P to select molecules containing just these atoms in a complex mixture, and provide direct information about which atoms are present in identified compounds and their relative abundances. The isotope-editing capability of NMR can also be employed to select for those compounds that have been selectively derivatized with an NMR-active stable isotope at particular functional groups, leading to considerable spectral simplification. Here we review isotope analysis by NMR, and methods of chemoselection both for spectral simplification, and for enhanced isotopomer analysis.
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Affiliation(s)
- Penghui Lin
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA.
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Kang S, Liu L, Wang T, Cannon M, Lin P, Fan TWM, Scott DA, Wu HJJ, Lane AN, Wang R. GAB functions as a bioenergetic and signalling gatekeeper to control T cell inflammation. Nat Metab 2022; 4:1322-1335. [PMID: 36192601 PMCID: PMC9584824 DOI: 10.1038/s42255-022-00638-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/12/2022] [Indexed: 01/20/2023]
Abstract
γ-Aminobutyrate (GAB), the biochemical form of (GABA) γ-aminobutyric acid, participates in shaping physiological processes, including the immune response. How GAB metabolism is controlled to mediate such functions remains elusive. Here we show that GAB is one of the most abundant metabolites in CD4+ T helper 17 (TH17) and induced T regulatory (iTreg) cells. GAB functions as a bioenergetic and signalling gatekeeper by reciprocally controlling pro-inflammatory TH17 cell and anti-inflammatory iTreg cell differentiation through distinct mechanisms. 4-Aminobutyrate aminotransferase (ABAT) funnels GAB into the tricarboxylic acid (TCA) cycle to maximize carbon allocation in promoting TH17 cell differentiation. By contrast, the absence of ABAT activity in iTreg cells enables GAB to be exported to the extracellular environment where it acts as an autocrine signalling metabolite that promotes iTreg cell differentiation. Accordingly, ablation of ABAT activity in T cells protects against experimental autoimmune encephalomyelitis (EAE) progression. Conversely, ablation of GABAA receptor in T cells worsens EAE. Our results suggest that the cell-autonomous control of GAB on CD4+ T cells is bimodal and consists of the sequential action of two processes, ABAT-dependent mitochondrial anaplerosis and the receptor-dependent signalling response, both of which are required for T cell-mediated inflammation.
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Affiliation(s)
- Siwen Kang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Lingling Liu
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Tingting Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Matthew Cannon
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA
| | - Penghui Lin
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - David A Scott
- Cancer Metabolism Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Hsin-Jung Joyce Wu
- Division of Rheumatology and Immunology, Department of Internal Medicine at The Ohio State University, Columbus, OH, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Ruoning Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH, USA.
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Lin P, Crooks DR, Linehan WM, Fan TWM, Lane AN. Resolving Enantiomers of 2-Hydroxy Acids by Nuclear Magnetic Resonance. Anal Chem 2022; 94:12286-12291. [PMID: 36040304 PMCID: PMC9539631 DOI: 10.1021/acs.analchem.2c00490] [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: 11/30/2022]
Abstract
Biologically important 2-hydroxy carboxylates such as lactate, malate, and 2-hydroxyglutarate exist in two enantiomeric forms that cannot be distinguished under achiral conditions. The D and L (or R, S) enantiomers have different biological origins and functions, and therefore, there is a need for a simple method for resolving, identifying, and quantifying these enantiomers. We have adapted and improved a chiral derivatization technique for nuclear magnetic resonance (NMR), which needs no chromatography for enantiomer resolution, with greater than 90% overall recovery. This method was developed for 2-hydroxyglutarate (2HG) to produce diastereomers resolvable by column chromatography. We have applied the method to lactate, malate, and 2HG. The limit of quantification was determined to be about 1 nmol for 2HG with coefficients of variation of less than 5%. We also demonstrated the method on an extract of a renal carcinoma bearing an isocitrate dehydrogenase-2 (IDH2) variant that produces copious quantities of 2HG and showed that it is the D enantiomer that was exclusively produced. We also demonstrated in the same experiment that the lactate produced in the same sample was the L enantiomer.
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Affiliation(s)
- Penghui Lin
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, United States
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Lane AN, Scott TL, Zhu J, Cassel TA, Vicente-Munoz S, Lin P, Higashi RM, Fan TWM. Abstract 2324: Small-scale microwave-assisted acid hydrolysis method for glycogen determination and turnover in tumors using Stable Isotope Resolved Metabolomics. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2324] [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
Introduction: Glycogen is a readily deployed intracellular energy storage macromolecule composed of branched chains of glucose. Although glycogen primarily occurs in the liver and muscle, it can be found in most tissues throughout the body, and its metabolism has been shown to be important in cancers and immune cells. Robust analysis of glycogen turnover requires stable isotope tracing plus a reliable means of quantifying total and labeled glycogen derived from precursors such as 13C6-glucose. Current methods for analyzing glycogen are time- and sample-consuming, at best semi-quantitative, and unable to measure stable isotope enrichment.
Methods: We have developed a microscale method for quantifying both intact and acid-hydrolyzed glycogen by ultra-high-resolution Fourier transform mass spectrometric (UHR-FTMS) and/or NMR analysis in stable isotope resolved metabolomics (SIRM) studies. Polar metabolites, including intact glycogen and their 13C positional isotopomer distributions were first measured in crude biological extracts by high resolution NMR, followed by rapid and efficient acid hydrolysis to glucose in 1 N HCl for 10 minutes at 110 °C under a N2 atmosphere in a microwave-assisted synthesis reactor. The resulting glucose and its 13C isotopologues were then analyzed by UHR-FTMS and/or NMR.
Results: We optimized the microwave digestion time, temperature, and oxygen purging in terms of recovery versus degradation and found 10 minutes at 110-115 °C to give > 90% recovery. The method was applied to track the fate of 13C6-glucose in primary human lung BEAS-2B cells, human macrophages, murine liver and patient-derived tumor xenograft (PDTX) in vivo, and the fate of 2H7-glucose in ex vivo lung organotypic tissue cultures of a lung cancer patient. We showed the incorporation of 13C6-glucose into glycogen and its metabolic intermediates, UDP-Glucose and glucose-1-phosphate, both in terms of the 13C levels and fractional enrichment, thereby demonstrating the utility of the method in tracing glycogen turnover in cells and tissues.
Conclusions: The method offers a quantitative, sensitive, and convenient means to analyze glycogen turnover in mg amounts of complex biological materials.
Keywords: glycogen turnover; 13C6-glucose, stable isotope resolved metabolomics (SIRM); microwave-assisted hydrolysis.
Citation Format: Andrew N. Lane, Timothy L. Scott, Juan Zhu, Teresa A. Cassel, Sara Vicente-Munoz, Penghui Lin, Richard M. Higashi, Teresa W-M Fan. Small-scale microwave-assisted acid hydrolysis method for glycogen determination and turnover in tumors using Stable Isotope Resolved Metabolomics [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 2324.
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Affiliation(s)
| | | | - Juan Zhu
- 1University of Kentucky, Lexington, KY
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10
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Daneshmandi S, Cassel T, Higashi RM, Fan TWM, Seth P. 6-Phosphogluconate dehydrogenase (6PGD), a key checkpoint in reprogramming of regulatory T cells metabolism and function. eLife 2021; 10:e67476. [PMID: 34709178 PMCID: PMC8553335 DOI: 10.7554/elife.67476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 10/17/2021] [Indexed: 12/29/2022] Open
Abstract
Cellular metabolism has key roles in T cells differentiation and function. CD4+ T helper-1 (Th1), Th2, and Th17 subsets are highly glycolytic while regulatory T cells (Tregs) use glucose during expansion but rely on fatty acid oxidation for function. Upon uptake, glucose can enter pentose phosphate pathway (PPP) or be used in glycolysis. Here, we showed that blocking 6-phosphogluconate dehydrogenase (6PGD) in the oxidative PPP resulted in substantial reduction of Tregs suppressive function and shifts toward Th1, Th2, and Th17 phenotypes which led to the development of fetal inflammatory disorder in mice model. These in turn improved anti-tumor responses and worsened the outcomes of colitis model. Metabolically, 6PGD blocked Tregs showed improved glycolysis and enhanced non-oxidative PPP to support nucleotide biosynthesis. These results uncover critical role of 6PGD in modulating Tregs plasticity and function, which qualifies it as a novel metabolic checkpoint for immunotherapy applications.
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Affiliation(s)
- Saeed Daneshmandi
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBostonUnited States
- Division of Interdisciplinary Medicine, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBostonUnited States
| | - Teresa Cassel
- Center for Environmental and Systems Biochemistry, University of KentuckyLexingtonUnited States
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, University of KentuckyLexingtonUnited States
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of KentuckyLexingtonUnited States
| | - Pankaj Seth
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBostonUnited States
- Division of Interdisciplinary Medicine, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBostonUnited States
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11
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Vicente-Muñoz S, Lin P, Fan TWM, Lane AN. NMR Analysis of Carboxylate Isotopomers of 13C-Metabolites by Chemoselective Derivatization with 15N-Cholamine. Anal Chem 2021; 93:6629-6637. [PMID: 33880916 DOI: 10.1021/acs.analchem.0c04220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A substantial fraction of common metabolites contains carboxyl functional groups. Their 13C isotopomer analysis by nuclear magnetic resonance (NMR) is hampered by the low sensitivity of the 13C nucleus, the slow longitudinal relaxation for the lack of an attached proton, and the relatively low chemical shift dispersion of carboxylates. Chemoselective (CS) derivatization is a means of tagging compounds in a complex mixture via a specific functional group. 15N1-cholamine has been shown to be a useful CS agent for carboxylates, producing a peptide bond that can be detected via 15N-attached H with high sensitivity in heteronuclear single quantum coherence experiments. Here, we report an improved method of derivatization and show how 13C-enrichment at the carboxylate and/or the adjacent carbon can be determined via one- and two-bond coupling of the carbons adjacent to the cholamine 15N atom in the derivatives. We have applied this method for the determination of 13C isotopomer distribution in the extracts of A549 cell culture and liver tissue from a patient-derived xenograft mouse.
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Affiliation(s)
- Sara Vicente-Muñoz
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Dept. of Toxicology & Cancer Biology, University of Kentucky, 789 S. Limestone Street, Lexington, Kentucky 40536, United States
| | - Penghui Lin
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Dept. of Toxicology & Cancer Biology, University of Kentucky, 789 S. Limestone Street, Lexington, Kentucky 40536, United States
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Dept. of Toxicology & Cancer Biology, University of Kentucky, 789 S. Limestone Street, Lexington, Kentucky 40536, United States
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Dept. of Toxicology & Cancer Biology, University of Kentucky, 789 S. Limestone Street, Lexington, Kentucky 40536, United States
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12
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Daneshmandi S, Cassel T, Lin P, Higashi RM, Wulf GM, Boussiotis VA, Fan TWM, Seth P. Blockade of 6-phosphogluconate dehydrogenase generates CD8 + effector T cells with enhanced anti-tumor function. Cell Rep 2021; 34:108831. [PMID: 33691103 PMCID: PMC8051863 DOI: 10.1016/j.celrep.2021.108831] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/07/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Although T cell expansion depends on glycolysis, T effector cell differentiation requires signaling via the production of reactive oxygen species (ROS). Because the pentose phosphate pathway (PPP) regulates ROS by generating nicotinamide adenine dinucleotide phosphate (NADPH), we examined how PPP blockade affects T cell differentiation and function. Here, we show that genetic ablation or pharmacologic inhibition of the PPP enzyme 6-phosphogluconate dehydrogenase (6PGD) in the oxidative PPP results in the generation of superior CD8+ T effector cells. These cells have gene signatures and immunogenic markers of effector phenotype and show potent anti-tumor functions both in vitro and in vivo. In these cells, metabolic reprogramming occurs along with increased mitochondrial ROS and activated antioxidation machinery to balance ROS production against oxidative damage. Our findings reveal a role of 6PGD as a checkpoint for T cell effector differentiation/survival and evidence for 6PGD as an attractive metabolic target to improve tumor immunotherapy.
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Affiliation(s)
- Saeed Daneshmandi
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Division of Interdisciplinary Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Teresa Cassel
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Penghui Lin
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Gerburg M Wulf
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Vassiliki A Boussiotis
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA.
| | - Pankaj Seth
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Division of Interdisciplinary Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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13
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Sun Q, Fan TWM, Lane AN, Higashi RM. An Ion Chromatography-Ultrahigh-Resolution-MS 1/Data-Independent High-Resolution MS 2 Method for Stable Isotope-Resolved Metabolomics Reconstruction of Central Metabolic Networks. Anal Chem 2021; 93:2749-2757. [PMID: 33482055 DOI: 10.1021/acs.analchem.0c03070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The metabolome comprises a complex network of interconnecting enzyme-catalyzed reactions that involve transfers of numerous molecular subunits. Thus, the reconstruction of metabolic networks requires metabolite substructures to be tracked. Subunit tracking can be achieved by tracing stable isotopes through metabolic transformations using NMR and ultrahigh -resolution (UHR)-mass spectrometry (MS). UHR-MS1 readily resolves and counts isotopic labels in metabolites but requires tandem MS to help identify isotopic enrichment in substructures. However, it is challenging to perform chromatography-based UHR-MS1 with its long acquisition time, while acquiring MS2 data on many coeluting labeled isotopologues for each metabolite. We have developed an ion chromatography (IC)-UHR-MS1/data-independent(DI)-HR-MS2 method to trace the fate of 13C atoms from [13C6]-glucose ([13C6]-Glc) in 3D A549 spheroids in response to anticancer selenite and simultaneously 13C/15N atoms from [13C5,15N2]-glutamine ([13C5,15N2]-Gln) in 2D BEAS-2B cells in response to arsenite transformation. This method retains the complete isotopologue distributions of metabolites via UHR-MS1 while simultaneously acquiring substructure label information via DI-MS2. These details in metabolite labeling patterns greatly facilitate rigorous reconstruction of multiple, intersecting metabolic pathways of central metabolism, which are illustrated here for the purine/pyrimidine nucleotide biosynthesis. The pathways reconstructed based on subunit-level isotopologue analysis further reveal specific enzyme-catalyzed reactions that are impacted by selenite or arsenite treatments.
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Affiliation(s)
- Qiushi Sun
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky 40536, United States
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky 40536, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, United States.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky 40536, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, United States.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky 40536, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, United States.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, United States
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Crooks DR, Maio N, Lang M, Ricketts CJ, Vocke CD, Gurram S, Turan S, Kim YY, Cawthon GM, Sohelian F, De Val N, Pfeiffer RM, Jailwala P, Tandon M, Tran B, Fan TWM, Lane AN, Ried T, Wangsa D, Malayeri AA, Merino MJ, Yang Y, Meier JL, Ball MW, Rouault TA, Srinivasan R, Linehan WM. Mitochondrial DNA alterations underlie an irreversible shift to aerobic glycolysis in fumarate hydratase-deficient renal cancer. Sci Signal 2021; 14:14/664/eabc4436. [PMID: 33402335 DOI: 10.1126/scisignal.abc4436] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the mechanisms of the Warburg shift to aerobic glycolysis is critical to defining the metabolic basis of cancer. Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is an aggressive cancer characterized by biallelic inactivation of the gene encoding the Krebs cycle enzyme fumarate hydratase, an early shift to aerobic glycolysis, and rapid metastasis. We observed impairment of the mitochondrial respiratory chain in tumors from patients with HLRCC. Biochemical and transcriptomic analyses revealed that respiratory chain dysfunction in the tumors was due to loss of expression of mitochondrial DNA (mtDNA)-encoded subunits of respiratory chain complexes, caused by a marked decrease in mtDNA content and increased mtDNA mutations. We demonstrated that accumulation of fumarate in HLRCC tumors inactivated the core factors responsible for replication and proofreading of mtDNA, leading to loss of respiratory chain components, thereby promoting the shift to aerobic glycolysis and disease progression in this prototypic model of glucose-dependent human cancer.
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Affiliation(s)
- Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Martin Lang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Cathy D Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sandeep Gurram
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sevilay Turan
- Sequencing Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Yun-Young Kim
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - G Mariah Cawthon
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ferri Sohelian
- Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Natalia De Val
- Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Ruth M Pfeiffer
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Parthav Jailwala
- CCR Collaborative Bioinformatics Resource (CCBR), Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource (CCBR), Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Bao Tran
- Sequencing Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ashkan A Malayeri
- Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria J Merino
- Genitourinary Pathology Section, Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Youfeng Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jordan L Meier
- Epigenetics and Metabolism Section, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Mark W Ball
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Ramaprasad Srinivasan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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Yang JS, Fan TWM, Lane AN, Brandon JA, Higashi RM. Abstract PO-006: Tracking S-Adenosylmethionine (SAM) and S-Adenosylhomocysteine (SAH) biosynthesis pathway using stable isotope-resolved metabolomics (SIRM). Cancer Res 2020. [DOI: 10.1158/1538-7445.epimetab20-po-006] [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
S-Adenosylmethionine (SAM) and S-Adenosylhomocysteine (SAH) are low abundance, key metabolites in one-carbon metabolism. The ratio of SAM/SAH controls epigenetic DNA and histone methylation, which is central to regulating gene expression in both normal and disease states including cancers (1,2). Stable isotope resolved metabolomics (SIRM) is a powerful approach for mapping metabolic networks in cells and tissues, which employs untargeted ultrahigh resolution MS1 to quantify a full set of isotopologues for a large number of metabolites (3). This demand makes it difficult to implement liquid chromatography (LC)-based analysis. We have developed a simple, rapid and robust LC-free method for analyzing SAM and SAH in mouse tissue, A549 cells, and human plasma. This method has sub nmol detection and is fully compatible with SIRM analysis of many other metabolites. Flash frozen mouse liver tissues or A549 cells were quenched and extracted with ice-cold acetonitrile:water:chloroform (2:0.75:1, v/v). Prior to extraction, A549 cells were grown for 24 h in the presence of either 13C6-glucose or 13CH3-methionine. No extraction was applied to human plasmas. SAM and SAH were captured by solid phase extraction (SPE) using a Bond-Elut phenylboronic acid (PBA) column (Agilent). SAM and SAH levels in liver tissues and plasma obtained by our method was comparable to those found by other methods (4). Tracing with 13C6 glucose showed extensive incorporation of label into the ribose ring and purine of the adenosyl subunit in both SAM and SAH. In contrast, tracing with 13CH3-methioinine showed predominant, single carbon label in SAM and none in SAH, suggesting the prevalence in the incorporation of exogenous methionine into SAM and turnover into SAH. Thus, it is practical to determine SAM and SAH turnover in the methionine cycle in various biological samples, which provides important insights into epigenetic metabolism. Funding: This work was supported in part by grants: 1R01ES022191-01 (to TWMF and RMH), 1P01CA163223-01A1 (to ANL and TWMF), and 1U24DK097215-01A1 (to RMH, TWMF, and ANL). References 1. Cheng et al. (2019) Targeting epigenetic regulators for cancer therapy:mechanisms and advances in clinical trials. Signal Transduction and Targeted Therapy 4:622. 2. U. Hübner, et al. (2007) Stability of Plasma Homocysteine, S-Adenosylmethionine, and S-Adenosylhomocysteine in EDTA, Acidic Citrate, and Primavette™Collection Tubes. Clinical Chemistry 53, 2217-2218. 3. Q. Sun, T. W-M. Fan, A. N. Lane, R. M. Higashi (2019). Applications of Chromatography-Ultra High-resolution MS for Stable Isotope-Resolved Metabolomics (SIRM) Reconstruction of Metabolic Networks. TrAC 123, 115676 4. H. Gellekink, D. et al. (2005) Stable-isotope dilution liquid chromatography-electrospray injection tandem mass spectrometry method for fast, selective measurement of S-adenosylmethionine and S-adenosylhomocysteine in plasma, Clin Chem, 51, 1487-1492.
Citation Format: Joon S Yang, Teresa W-M Fan, Andrew N. Lane, Jason A. Brandon, Richard M. Higashi. Tracking S-Adenosylmethionine (SAM) and S-Adenosylhomocysteine (SAH) biosynthesis pathway using stable isotope-resolved metabolomics (SIRM) [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-006.
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Fan TWM, Lane AN, Brandon JA, Yang J, Dang CV, Higashi RM. Abstract IA22: Tracking metabolic compartmentation and epigenetic metabolism in human lung cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.epimetab20-ia22] [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
Although metabolic reprogramming has been recognized as a hallmark of human cancers, our understanding of metabolic heterogeneities/compartmentation and regulation of epigenetics in human tumors is largely unknown. This is crucial to elucidating metabolic checkpoints and strategizing therapeutic target(s) for human cancer. The slow progress is at least in part due to the lack of relevant models and tools for studying these processes. We have established patient-derived organotypic tissue cultures (OTC) that recapitulate the in vivo metabolic reprogramming of human cancer while retaining native patient tumor microenvironment and 3D architecture 1,2. The matched pairs of cancerous (CA) and non-cancerous (NC) lung OTC from the same patient enable reprogrammed cancer tissue metabolism and on-/off-target drug responses for individual patients to be defined. We have deployed this system along with multiplexed Stable Isotope-Resolved Metabolomics (mSIRM) to probe the efficiency of different substates that fuel de novo synthesis of purine nucleotides in matched patients’ CA versus NC lung OTC 3. We found for seven non-small cell lung cancer (NSCLC) patients that 13C6-glucose was the preferred substrate over D3-serine, D2-glycine, or 13C2-glycine in supporting purine synthesis in CA tissues but not or less so in matched NC tissues. Kinetic modeling of the tracer data along with gene/protein expression data suggests that cytoplasmic activation and dynamic compartmentation of the glucose-to-serine pathway as well as reversal of mitochondrial serine to glycine fluxes can account for this preference for glucose. In all seven patients’ CA tissues, c-MYC was overexpressed and its suppression in NSCLC PC9 cells blocked de novo serine synthesis from glucose, enhanced serine-glycine exchanges, and reduced the efficiency of glucose versus serine incorporation into ATP/GTP. However, serine rather than glucose was the preferred substrate for purine synthesis in NSCLC cell lines but c-MYC could alter this preference for serine towards glucose in fueling purine synthesis. This tissue and cell line difference should be considered in designing serine starvation-based cancer therapy. To track metabolism that modulates epigenetic regulation, we employed a fast, sensitive, and robust Fourier transform-mass spectrometric method to analyze S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) levels in A549 cells under anti-cancer methylseleninic acid (MSA) and selenite treatments. We found that SAM/SAH levels were reduced by both treatments and MSA but not selenite increased the SAM to SAH ratio. These changes were accompanied by reduced proliferation, central metabolism, and H3K27Me3 levels in MSA and less so in selenite-treated A549 cells. Thus, the tool for tracking SAM/SAH metabolism along with the SIRM approach opens the opportunity for interrogating epigenetic metabolism and its regulation of growth-promoting central metabolic events. Funding: This work was supported in part by grants: 1R01ES022191-01 (to TWMF and RMH), 1P01CA163223-01A1 (to ANL and TWMF), and 1U24DK097215-01A1 (to RMH, TWMF, and ANL). Refs: 1 Sellers, K. et al. Pyruvate carboxylase is critical for non–small-cell lung cancer proliferation. The Journal of Clinical Investigation 125, 687-698, doi:10.1172/JCI72873 (2015). 2 Fan, T. W., Lane, A. N. & Higashi, R. M. Stable Isotope Resolved Metabolomics Studies in ex vivo Tissue Slices. Bio-protocol 6, e1730 (2016). 3 Fan, T. W. M. et al. De novo synthesis of serine and glycine fuels purine nucleotide biosynthesis in human lung cancer tissues. The Journal of biological chemistry 294, 13464-13477, doi:10.1074/jbc.RA119.008743 (2019).
Citation Format: Teresa W-M Fan, Andrew N. Lane, Jason A. Brandon, Joonseon Yang, Chi V. Dang, Richard M. Higashi. Tracking metabolic compartmentation and epigenetic metabolism in human lung cancer [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr IA22.
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Affiliation(s)
| | | | | | | | - Chi V. Dang
- 2Ludwig Institute for Cancer Research, New York, NY
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Panarsky R, Crooks DR, Lane AN, Yang Y, Cassel TA, Fan TWM, Linehan WM, Moscow JA. Fumarate hydratase-deficient renal cell carcinoma cells respond to asparagine by activation of the unfolded protein response and stimulation of the hexosamine biosynthetic pathway. Cancer Metab 2020; 8:7. [PMID: 32774853 PMCID: PMC7397616 DOI: 10.1186/s40170-020-00214-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/10/2020] [Indexed: 12/03/2022] Open
Abstract
Background The loss-of-function mutation of fumarate hydratase (FH) is a driver of hereditary leiomyomatosis and renal cell carcinoma (HLRCC). Fumarate accumulation results in activation of stress-related mechanisms leading to upregulation of cell survival-related genes. To better understand how cells compensate for the loss of FH in HLRCC, we determined the amino acid nutrient requirements of the FH-deficient UOK262 cell line (UOK262) and its FH-repleted control (UOK262WT). Methods We determined growth rates and survival of cell lines in response to amino acid depletion and supplementation. RNAseq was used to determine the transcription changes contingent on Asn and Gln supplementation, which was further followed with stable isotope resolved metabolomics (SIRM) using both [U- 13C,15N] Gln and Asn. Results We found that Asn increased the growth rate of both cell lines in vitro. Gln, but not Asn, increased oxygen consumption rates and glycolytic reserve of both cell lines. Although Asn was taken up by the cells, there was little evidence of Asn-derived label in cellular metabolites, indicating that Asn was not catabolized. However, Asn strongly stimulated Gln labeling of uracil and precursors, uridine phosphates and hexosamine metabolites in the UOK262 cells and to a much lesser extent in the UOK262WT cells, indicating an activation of the hexosamine biosynthetic pathway (HBP) by Asn. Asn in combination with Gln, but not Asn or Gln alone, stimulated expression of genes associated with the endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) in UOK262 to a greater extent than in FH-restored cells. The changes in expression of these genes were confirmed by RT-PCR, and the stimulation of the UPR was confirmed orthogonally by demonstration of an increase in spliced XBP1 (sXBP1) in UOK262 cells under these conditions. Asn exposure also increased both the RNA and protein expression of the HBP regulator GFPT2, which is a transcriptional target of sXBP1. Conclusions Asn in the presence of Gln induces an ER stress response in FH-deficient UOK262 cells and stimulates increased synthesis of UDP-acetyl glycans indicative of HBP activity. These data demonstrate a novel effect of asparagine on cellular metabolism in FH-deficient cells that could be exploited therapeutically.
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Affiliation(s)
- Rony Panarsky
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NCI Shady Grove Room 5 W460, 9609 Medical Center Drive, Bethesda, MD 20892-9739 USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NCI Shady Grove Room 5 W460, 9609 Medical Center Drive, Bethesda, MD 20892-9739 USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY USA.,Markey Cancer Center and Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY USA
| | - Youfeng Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NCI Shady Grove Room 5 W460, 9609 Medical Center Drive, Bethesda, MD 20892-9739 USA
| | - Teresa A Cassel
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY USA.,Markey Cancer Center and Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NCI Shady Grove Room 5 W460, 9609 Medical Center Drive, Bethesda, MD 20892-9739 USA
| | - Jeffrey A Moscow
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NCI Shady Grove Room 5 W460, 9609 Medical Center Drive, Bethesda, MD 20892-9739 USA
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18
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Wang T, Gnanaprakasam JNR, Chen X, Kang S, Xu X, Sun H, Liu L, Rodgers H, Miller E, Cassel TA, Sun Q, Vicente-Muñoz S, Warmoes MO, Lin P, Piedra-Quintero ZL, Guerau-de-Arellano M, Cassady KA, Zheng SG, Yang J, Lane AN, Song X, Fan TWM, Wang R. Inosine is an alternative carbon source for CD8 +-T-cell function under glucose restriction. Nat Metab 2020; 2:635-647. [PMID: 32694789 PMCID: PMC7371628 DOI: 10.1038/s42255-020-0219-4] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/30/2020] [Indexed: 12/15/2022]
Abstract
T cells undergo metabolic rewiring to meet their bioenergetic, biosynthetic and redox demands following antigen stimulation. To fulfil these needs, effector T cells must adapt to fluctuations in environmental nutrient levels at sites of infection and inflammation. Here, we show that effector T cells can utilize inosine, as an alternative substrate, to support cell growth and function in the absence of glucose in vitro. T cells metabolize inosine into hypoxanthine and phosphorylated ribose by purine nucleoside phosphorylase. We demonstrate that the ribose subunit of inosine can enter into central metabolic pathways to provide ATP and biosynthetic precursors, and that cancer cells display diverse capacities to utilize inosine as a carbon source. Moreover, the supplementation with inosine enhances the anti-tumour efficacy of immune checkpoint blockade and adoptive T-cell transfer in solid tumours that are defective in metabolizing inosine, reflecting the capability of inosine to relieve tumour-imposed metabolic restrictions on T cells.
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Affiliation(s)
- Tingting Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - J N Rashida Gnanaprakasam
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Xuyong Chen
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Siwen Kang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Xuequn Xu
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Hua Sun
- The Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Lingling Liu
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Hayley Rodgers
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Ethan Miller
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Teresa A Cassel
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Qiushi Sun
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Sara Vicente-Muñoz
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Marc O Warmoes
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Penghui Lin
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Zayda Lizbeth Piedra-Quintero
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center, Ohio State University, Columbus, OH, USA
| | - Mireia Guerau-de-Arellano
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center, Ohio State University, Columbus, OH, USA
| | - Kevin A Cassady
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Song Guo Zheng
- Division of Rheumatology and Immunology, Department of Internal Medicine at Ohio State University of Medicine and Wexner Medical Center, Columbus, OH, USA
| | - Jun Yang
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Xiaotong Song
- The Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
- Icell Kealex Therapeutics, Houston, TX, USA.
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
| | - Ruoning Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA.
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19
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Palmieri EM, Gonzalez-Cotto M, Baseler WA, Davies LC, Ghesquière B, Maio N, Rice CM, Rouault TA, Cassel T, Higashi RM, Lane AN, Fan TWM, Wink DA, McVicar DW. Nitric oxide orchestrates metabolic rewiring in M1 macrophages by targeting aconitase 2 and pyruvate dehydrogenase. Nat Commun 2020; 11:698. [PMID: 32019928 PMCID: PMC7000728 DOI: 10.1038/s41467-020-14433-7] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/16/2019] [Indexed: 01/24/2023] Open
Abstract
Profound metabolic changes are characteristic of macrophages during classical activation and have been implicated in this phenotype. Here we demonstrate that nitric oxide (NO) produced by murine macrophages is responsible for TCA cycle alterations and citrate accumulation associated with polarization. 13C tracing and mitochondrial respiration experiments map NO-mediated suppression of metabolism to mitochondrial aconitase (ACO2). Moreover, we find that inflammatory macrophages reroute pyruvate away from pyruvate dehydrogenase (PDH) in an NO-dependent and hypoxia-inducible factor 1α (Hif1α)-independent manner, thereby promoting glutamine-based anaplerosis. Ultimately, NO accumulation leads to suppression and loss of mitochondrial electron transport chain (ETC) complexes. Our data reveal that macrophages metabolic rewiring, in vitro and in vivo, is dependent on NO targeting specific pathways, resulting in reduced production of inflammatory mediators. Our findings require modification to current models of macrophage biology and demonstrate that reprogramming of metabolism should be considered a result rather than a mediator of inflammatory polarization. Production of inflammatory mediators by M1-polarized macrophages is thought to rely on suppression of mitochondrial metabolism in favor of glycolysis. Refining this concept, here the authors define metabolic targets of nitric oxide as responsible for the mitochondrial rewiring resulting from polarization.
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Affiliation(s)
- Erika M Palmieri
- Leukocyte Signaling Section, Cancer & Inflammation Program, National Cancer Institute, Frederick, MD, USA
| | - Marieli Gonzalez-Cotto
- Leukocyte Signaling Section, Cancer & Inflammation Program, National Cancer Institute, Frederick, MD, USA
| | - Walter A Baseler
- Leukocyte Signaling Section, Cancer & Inflammation Program, National Cancer Institute, Frederick, MD, USA
| | - Luke C Davies
- Leukocyte Signaling Section, Cancer & Inflammation Program, National Cancer Institute, Frederick, MD, USA.,Division of Infection & Immunity, School of Medicine, Cardiff University, Tenovus Building, Heath Park, Cardiff, CF14 4XN, UK
| | - Bart Ghesquière
- Metabolomics Expertise Center, Vesalius Research Center, VIB, 3000, Leuven, Belgium.,Metabolomics Expertise Center, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Christopher M Rice
- Leukocyte Signaling Section, Cancer & Inflammation Program, National Cancer Institute, Frederick, MD, USA.,School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Teresa Cassel
- Department of Toxicology and Cancer Biology and Markey Cancer Center and Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Richard M Higashi
- Department of Toxicology and Cancer Biology and Markey Cancer Center and Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology and Markey Cancer Center and Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Teresa W-M Fan
- Department of Toxicology and Cancer Biology and Markey Cancer Center and Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, USA
| | - David A Wink
- Chemical and Molecular Inflammation Section, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA
| | - Daniel W McVicar
- Leukocyte Signaling Section, Cancer & Inflammation Program, National Cancer Institute, Frederick, MD, USA.
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20
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Huang Z, Lane AN, Fan TWM, Higashi RM, Weiss HL, Yin X, Wang C. Differential Abundance Analysis with Bayes Shrinkage Estimation of Variance (DASEV) for Zero-Inflated Proteomic and Metabolomic Data. Sci Rep 2020; 10:876. [PMID: 31964922 PMCID: PMC6972855 DOI: 10.1038/s41598-020-57470-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/20/2019] [Indexed: 11/09/2022] Open
Abstract
Mass spectrometry (MS) is frequently used for proteomic and metabolomic profiling of biological samples. Data obtained by MS are often zero-inflated. Those zero values are called point mass values (PMVs). Zero values can be further grouped into biological PMVs and technical PMVs. The former type is caused by true absence of a compound and the later type is caused by a technical detection limit. Methods based on a mixture model have been developed to separate the two types of zeros and to perform differential abundance analysis comparing proteomic/metabolomic profiles between different groups of subjects. However, we notice that those methods may give unstable estimate of the model variance, and thus lead to false positive and false negative results when the number of non-zero values is small. In this paper, we propose a new differential abundance analysis method, DASEV, which uses an empirical Bayes shrinkage method to more robustly estimate the variance and enhance the accuracy of differential abundance analysis. Simulation studies and real data analysis show that DASEV substantially improves parameter estimation of the mixture model and outperforms current methods in identifying differentially abundant features.
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Affiliation(s)
- Zhengyan Huang
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, 40536, USA
| | - Andrew N Lane
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky, 40536, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky, 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA
| | - Teresa W-M Fan
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky, 40536, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky, 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA
| | - Richard M Higashi
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky, 40536, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky, 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA
| | - Heidi L Weiss
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky, 40536, USA
| | - Xiangrong Yin
- Department of Statistics, University of Kentucky, Lexington, Kentucky, 40536, USA
| | - Chi Wang
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, 40536, USA. .,Markey Cancer Center, University of Kentucky, Lexington, Kentucky, 40536, USA.
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21
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Sengupta D, Cassel T, Teng KY, Aljuhani M, Chowdhary VK, Hu P, Zhang X, Fan TWM, Ghoshal K. Regulation of hepatic glutamine metabolism by miR-122. Mol Metab 2020; 34:174-186. [PMID: 32180557 PMCID: PMC7044666 DOI: 10.1016/j.molmet.2020.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/18/2019] [Accepted: 01/03/2020] [Indexed: 01/17/2023] Open
Abstract
Objective It is well established that the liver-specific miR-122, a bona fide tumor suppressor, plays a critical role in lipid homeostasis. However, its role, if any, in amino acid metabolism has not been explored. Since glutamine (Gln) is a critical energy and anaplerotic source for mammalian cells, we assessed Gln metabolism in control wild type (WT) mice and miR-122 knockout (KO) mice by stable isotope resolved metabolomics (SIRM) studies. Methods Six-to eight-week-old WT and KO mice and 12- to 15-month-old liver tumor-bearing mice were injected with [U–13C5,15N2]-L-Gln, and polar metabolites from the liver tissues were analyzed by nuclear magnetic resonance (NMR) imaging and ion chromatography-mass spectrometry (IC-MS). Gln-metabolism was also assessed in a Gln-dependent hepatocellular carcinoma (HCC) cell line (EC4). Expressions of glutaminases (Gls and Gls2) were analyzed in mouse livers and human primary HCC samples. Results The results showed that loss of miR-122 promoted glutaminolysis but suppressed gluconeogenesis in mouse livers as evident from the buildup of 13C- and/or 15N-Glu and decrease in glucose-6-phosphate (G6P) levels, respectively, in KO livers. Enhanced glutaminolysis is consistent with the upregulation of expressions of Gls (kidney-type glutaminase) and Slc1a5, a neutral amino acid transporter in KO livers. Both Gls and Slc1a5 were confirmed as direct miR-122 targets by the respective 3′-UTR-driven luciferase assays. Importantly, expressions of Gls and Slc1a5 as well as glutaminase activity were suppressed in a Gln-dependent HCC (EC4) cell line transfected with miR-122 mimic that resulted in decreased 13C-Gln, 13C-á-ketoglutarate, 13C-isocitrate, and 13C-citrate levels. In contrast, 13C-phosphoenolpyruvate and 13C-G6P levels were elevated in cells expressing ectopic miR-122, suggesting enhanced gluconeogenesis. Finally, The Cancer Genome Atlas—Liver Hepatocellular Carcinoma (TCGA-LIHC) database analysis showed that expression of GLS is negatively correlated with miR-122 in primary human HCCs, and the upregulation of GLS RNA is associated with higher tumor grade. More importantly, patients with higher expressions of GLS or SLC1A5 in tumors exhibited poor survival compared with those expressing lower levels of these proteins. Conclusions Collectively, these results show that miR-122 modulates Gln metabolism both in vitro and in vivo, implicating the therapeutic potential of miR-122 in HCCs that exhibit relatively high GLS levels. miR-122, the most abundant liver specific microRNA and a potent tumor suppressor, regulates glutamine metabolism. SIRM analysis showed enhanced glutaminolysis and impeded gluconeogenesis in the livers of miR-122 KO mice. Gls, a key enzyme involved in glutaminolysis and a miR-122 target is upregulated in miR-122 KO livers. Ectopic miR-122 expression suppressed glutaminolysis but enhanced gluconeogenesis in a glutamine dependent HCC cell line. Expression of MIR-122 negatively correlated with that of GLS in human primary HCCs.
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Affiliation(s)
- Dipanwita Sengupta
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Teresa Cassel
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Kun-Yu Teng
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Mona Aljuhani
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Vivek K Chowdhary
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Peng Hu
- Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Xiaoli Zhang
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Dept. Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40536, USA.
| | - Kalpana Ghoshal
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA.
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22
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Selivanov VA, Marin S, Tarragó-Celada J, Lane AN, Higashi RM, Fan TWM, de Atauri P, Cascante M. Software Supporting a Workflow of Quantitative Dynamic Flux Maps Estimation in Central Metabolism from SIRM Experimental Data. Methods Mol Biol 2020; 2088:271-298. [PMID: 31893378 DOI: 10.1007/978-1-0716-0159-4_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stable isotope-resolved metabolomics (SIRM), based on the analysis of biological samples from living cells incubated with artificial isotope enriched substrates, enables mapping the rates of biochemical reactions (metabolic fluxes). We developed software supporting a workflow of analysis of SIRM data obtained with mass spectrometry (MS). The evaluation of fluxes starting from raw MS recordings requires at least three steps of computer support: first, extraction of mass spectra of metabolites of interest, then correction of the spectra for natural isotope abundance, and finally, evaluation of fluxes by simulation of the corrected spectra using a corresponding mathematical model. A kinetic model based on ordinary differential equations (ODEs) for isotopomers of metabolites of the corresponding biochemical network supports the final part of the analysis, which provides a dynamic flux map.
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Affiliation(s)
- Vitaly A Selivanov
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain. .,INB-Bioinformatics Platform Metabolomics Node, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Josep Tarragó-Celada
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Andrew N Lane
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Richard M Higashi
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Teresa W-M Fan
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,INB-Bioinformatics Platform Metabolomics Node, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain. .,INB-Bioinformatics Platform Metabolomics Node, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
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23
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Reyes-Caballero H, Rao X, Sun Q, Warmoes MO, Lin P, Sussan TE, Park B, Fan TWM, Maiseyeu A, Rajagopalan S, Girnun GD, Biswal S. Air pollution-derived particulate matter dysregulates hepatic Krebs cycle, glucose and lipid metabolism in mice. Sci Rep 2019; 9:17423. [PMID: 31757983 PMCID: PMC6874681 DOI: 10.1038/s41598-019-53716-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/01/2019] [Indexed: 12/12/2022] Open
Abstract
Exposure to ambient air particulate matter (PM2.5) is well established as a risk factor for cardiovascular and pulmonary disease. Both epidemiologic and controlled exposure studies in humans and animals have demonstrated an association between air pollution exposure and metabolic disorders such as diabetes. Given the central role of the liver in peripheral glucose homeostasis, we exposed mice to filtered air or PM2.5 for 16 weeks and examined its effect on hepatic metabolic pathways using stable isotope resolved metabolomics (SIRM) following a bolus of 13C6-glucose. Livers were analyzed for the incorporation of 13C into different metabolic pools by IC-FTMS or GC-MS. The relative abundance of 13C-glycolytic intermediates was reduced, suggesting attenuated glycolysis, a feature found in diabetes. Decreased 13C-Krebs cycle intermediates suggested that PM2.5 exposure led to a reduction in the Krebs cycle capacity. In contrast to decreased glycolysis, we observed an increase in the oxidative branch of the pentose phosphate pathway and 13C incorporations suggestive of enhanced capacity for the de novo synthesis of fatty acids. To our knowledge, this is one of the first studies to examine 13C6-glucose utilization in the liver following PM2.5 exposure, prior to the onset of insulin resistance (IR).
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Affiliation(s)
- Hermes Reyes-Caballero
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, Baltimore, MD, 21205, USA.
| | - Xiaoquan Rao
- Cardiovascular Research Institute, Case Western Reserve School of Medicine, 11100 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Qiushi Sun
- Department of Toxicology and Cancer Biology, Markey Cancer Center, Center for Environmental and Systems Biochemistry, University of Kentucky, 1095V.A. Drive, Lexington, KY, 40536, USA
| | - Marc O Warmoes
- Department of Toxicology and Cancer Biology, Markey Cancer Center, Center for Environmental and Systems Biochemistry, University of Kentucky, 1095V.A. Drive, Lexington, KY, 40536, USA
| | - Penghui Lin
- Department of Toxicology and Cancer Biology, Markey Cancer Center, Center for Environmental and Systems Biochemistry, University of Kentucky, 1095V.A. Drive, Lexington, KY, 40536, USA
| | - Tom E Sussan
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, Baltimore, MD, 21205, USA.,Public Health Center, Toxicology Directorate, Aberdeen Proving Ground, Aberdeen, MD, USA
| | - Bongsoo Park
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Teresa W-M Fan
- Department of Toxicology and Cancer Biology, Markey Cancer Center, Center for Environmental and Systems Biochemistry, University of Kentucky, 1095V.A. Drive, Lexington, KY, 40536, USA
| | - Andrei Maiseyeu
- Cardiovascular Research Institute, Case Western Reserve School of Medicine, 11100 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Sanjay Rajagopalan
- Cardiovascular Research Institute, Case Western Reserve School of Medicine, 11100 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Geoffrey D Girnun
- Department of Pharmacological Sciences, Stony Brook University, BST 8-140, Stony Brook, NY, 11794, USA.,Department of Pathology, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Shyam Biswal
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, Baltimore, MD, 21205, USA.
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24
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Rao TN, Hansen N, Hilfiker J, Rai S, Majewska JM, Leković D, Gezer D, Andina N, Galli S, Cassel T, Geier F, Delezie J, Nienhold R, Hao-Shen H, Beisel C, Di Palma S, Dimeloe S, Trebicka J, Wolf D, Gassmann M, Fan TWM, Lane AN, Handschin C, Dirnhofer S, Kröger N, Hess C, Radimerski T, Koschmieder S, Čokić VP, Skoda RC. JAK2-mutant hematopoietic cells display metabolic alterations that can be targeted to treat myeloproliferative neoplasms. Blood 2019; 134:1832-1846. [PMID: 31511238 PMCID: PMC6872961 DOI: 10.1182/blood.2019000162] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/17/2019] [Indexed: 12/20/2022] Open
Abstract
Increased energy requirement and metabolic reprogramming are hallmarks of cancer cells. We show that metabolic alterations in hematopoietic cells are fundamental to the pathogenesis of mutant JAK2-driven myeloproliferative neoplasms (MPNs). We found that expression of mutant JAK2 augmented and subverted metabolic activity of MPN cells, resulting in systemic metabolic changes in vivo, including hypoglycemia, adipose tissue atrophy, and early mortality. Hypoglycemia in MPN mouse models correlated with hyperactive erythropoiesis and was due to a combination of elevated glycolysis and increased oxidative phosphorylation. Modulating nutrient supply through high-fat diet improved survival, whereas high-glucose diet augmented the MPN phenotype. Transcriptomic and metabolomic analyses identified numerous metabolic nodes in JAK2-mutant hematopoietic stem and progenitor cells that were altered in comparison with wild-type controls. We studied the consequences of elevated levels of Pfkfb3, a key regulatory enzyme of glycolysis, and found that pharmacological inhibition of Pfkfb3 with the small molecule 3PO reversed hypoglycemia and reduced hematopoietic manifestations of MPNs. These effects were additive with the JAK1/2 inhibitor ruxolitinib in vivo and in vitro. Inhibition of glycolysis by 3PO altered the redox homeostasis, leading to accumulation of reactive oxygen species and augmented apoptosis rate. Our findings reveal the contribution of metabolic alterations to the pathogenesis of MPNs and suggest that metabolic dependencies of mutant cells represent vulnerabilities that can be targeted for treating MPNs.
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Affiliation(s)
- Tata Nageswara Rao
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Nils Hansen
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Julian Hilfiker
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Shivam Rai
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Julia-Magdalena Majewska
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Danijela Leković
- Clinic of Hematology, Clinical Center of Serbia, Belgrade, Serbia
| | - Deniz Gezer
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Nicola Andina
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Serena Galli
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Teresa Cassel
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Florian Geier
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | | | - Ronny Nienhold
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Hui Hao-Shen
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Serena Di Palma
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Sarah Dimeloe
- Immunobiology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jonel Trebicka
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
- European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain
- Department of Gastroenterology, Odense Hospital, University of Southern Denmark, Odense, Denmark
- Institute for Bioengineering of Catalonia, Barcelona, Spain
| | - Dominik Wolf
- Internal Medicine V, Department of Hematology and Oncology, Medical University Innsbruck, Innsbruck, Austria
- Medical Clinic III for Oncology, Hematology, Immunoncology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Max Gassmann
- Institute of Veterinary Physiology, Vetsuisse Faculty and Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY
| | | | - Stefan Dirnhofer
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Hospital Eppendorf, Hamburg, Germany
| | - Christoph Hess
- Immunobiology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Thomas Radimerski
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland; and
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Vladan P Čokić
- Institute for Medical Research, University of Belgrade, Belgrade, Serbia
| | - Radek C Skoda
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
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Bruntz RC, Belshoff AC, Zhang Y, Macedo JKA, Higashi RM, Lane AN, Fan TWM. Inhibition of Anaplerotic Glutaminolysis Underlies Selenite Toxicity in Human Lung Cancer. Proteomics 2019; 19:e1800486. [PMID: 31298457 DOI: 10.1002/pmic.201800486] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/04/2019] [Indexed: 01/01/2023]
Abstract
Large clinical trials and model systems studies suggest that the chemical form of selenium dictates chemopreventive and chemotherapeutic efficacy. Selenite induces excess ROS production, which mediates autophagy and eventual cell death in non-small cell lung cancer adenocarcinoma A549 cells. As the mechanisms underlying these phenotypic effects are unclear, the clinical relevance of selenite for cancer therapy remains to be determined. The authors' previous stable isotope-resolved metabolomics and gene expression analysis showed that selenite disrupts glycolysis, the Krebs cycle, and polyamine metabolism in A549 cells, potentially through perturbed glutaminolysis, a vital anaplerotic process for proliferation of many cancer cells. Herein, the role of the glutaminolytic enzyme glutaminase 1 (GLS1) in selenite's toxicity in A549 cells and in patient-derived lung cancer tissues is investigated. Using [13 C6 ]-glucose and [13 C5 ,15 N2 ]-glutamine tracers, selenite's action on metabolic networks is determined. Selenite inhibits glutaminolysis and glutathione synthesis by suppressing GLS1 expression, and blocks the Krebs cycle, but transiently activates pyruvate carboxylase activity. Glutamate supplementation partially rescues these anti-proliferative and oxidative stress activities. Similar metabolic perturbations and necrosis are observed in selenite-treated human patients' cancerous lung tissues ex vivo. The results support the hypothesis that GLS1 suppression mediates part of the anti-cancer activity of selenite both in vitro and ex vivo.
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Affiliation(s)
- Ronald C Bruntz
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Alex C Belshoff
- Department of Chemistry, University of Louisville, Louisville, KY, 40292, USA
| | - Yan Zhang
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Jessica K A Macedo
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40536-0596, USA
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Crooks DR, Fan TWM, Linehan WM. Metabolic Labeling of Cultured Mammalian Cells for Stable Isotope-Resolved Metabolomics: Practical Aspects of Tissue Culture and Sample Extraction. Methods Mol Biol 2019; 1928:1-27. [PMID: 30725447 PMCID: PMC8195444 DOI: 10.1007/978-1-4939-9027-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 06/09/2023]
Abstract
Stable isotope-resolved metabolomics (SIRM) methods are used increasingly by cancer researchers to probe metabolic pathways and identify vulnerabilities in cancer cells. Analytical and computational advances are being made constantly, but tissue culture and sample extraction procedures are often variable and not elaborated in the literature. This chapter discusses basic aspects of tissue culture practices as they relate to the use of stable isotope tracers and provides a detailed metabolic labeling and metabolite extraction procedure designed to maximize the amount of information that can be obtained from a single tracer experiment.
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Affiliation(s)
- Daniel R Crooks
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Teresa W-M Fan
- Department of Toxicology and Cancer Biology, Center for Environmental and Systems Biochemistry, Markey Cancer Center, and University of Kentucky, Lexington, KY, USA.
| | - W Marston Linehan
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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27
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Yang Y, Fan TWM, Lane AN, Higashi RM. Quantification of Isotopologues of Amino Acids by Multiplexed Stable Isotope-Resolved Metabolomics Using Ultrahigh-Resolution Mass Spectrometry Coupled with Direct Infusion. Methods Mol Biol 2019; 2030:57-68. [PMID: 31347110 DOI: 10.1007/978-1-4939-9639-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Stable isotope-resolved metabolomics (SIRM) is increasingly used among researchers for metabolic studies including amino acid metabolism. However, the classical GC- or HPLC-based methods for amino acid quantification do not meet the needs for multiplexed stable isotope-enriched analysis by ultrahigh-resolution Fourier transform mass spectrometry (UHR-FTMS). This is due to insufficient acquisition time during chromatographic separations and large dynamic range in concentrations of analytes, which compromises detection and quantification of the numerous metabolite isotopologues present in crude extracts. This chapter discusses a modified ethyl chloroformate derivatization method to enable rapid quantitative analysis of stable isotope-enriched amino acids using direct infusion ion introduction coupled with UHR-FTMS.
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Affiliation(s)
- Ye Yang
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Teresa W-M Fan
- Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA. .,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, USA.
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Richard M Higashi
- Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, USA
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Abstract
There is considerable interest in defining metabolic reprogramming in human diseases, which is recognized as a hallmark of human cancer. Although radiotracers have a long history in specific metabolic studies, stable isotope-enriched precursors coupled with modern high resolution mass spectrometry and NMR spectroscopy have enabled systematic mapping of metabolic networks and fluxes in cells, tissues and living organisms including humans. These analytical platforms are high in information content, are complementary and cross-validating in terms of compound identification, quantification, and isotope labeling pattern analysis of a large number of metabolites simultaneously. Furthermore, new developments in chemoselective derivatization and in vivo spectroscopy enable tracking of labile/low abundance metabolites and metabolic kinetics in real-time. Here we review developments in Stable Isotope Resolved Metabolomics (SIRM) and recent applications in cancer metabolism using a wide variety of stable isotope tracers that probe both broad and specific aspects of cancer metabolism required for proliferation and survival.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
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Mitchell JM, Flight RM, Wang QJ, Higashi RM, Fan TWM, Lane AN, Moseley HNB. New methods to identify high peak density artifacts in Fourier transform mass spectra and to mitigate their effects on high-throughput metabolomic data analysis. Metabolomics 2018; 14:125. [PMID: 30830442 PMCID: PMC6153687 DOI: 10.1007/s11306-018-1426-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/05/2018] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Direct injection Fourier-transform mass spectrometry (FT-MS) allows for the high-throughput and high-resolution detection of thousands of metabolite-associated isotopologues. However, spectral artifacts can generate large numbers of spectral features (peaks) that do not correspond to known compounds. Misassignment of these artifactual features creates interpretive errors and limits our ability to discern the role of representative features within living systems. OBJECTIVES Our goal is to develop rigorous methods that identify and handle spectral artifacts within the context of high-throughput FT-MS-based metabolomics studies. RESULTS We observed three types of artifacts unique to FT-MS that we named high peak density (HPD) sites: fuzzy sites, ringing and partial ringing. While ringing artifacts are well-known, fuzzy sites and partial ringing have not been previously well-characterized in the literature. We developed new computational methods based on comparisons of peak density within a spectrum to identify regions of spectra with fuzzy sites. We used these methods to identify and eliminate fuzzy site artifacts in an example dataset of paired cancer and non-cancer lung tissue samples and evaluated the impact of these artifacts on classification accuracy and robustness. CONCLUSION Our methods robustly identified consistent fuzzy site artifacts in our FT-MS metabolomics spectral data. Without artifact identification and removal, 91.4% classification accuracy was achieved on an example lung cancer dataset; however, these classifiers rely heavily on artifactual features present in fuzzy sites. Proper removal of fuzzy site artifacts produces a more robust classifier based on non-artifactual features, with slightly improved accuracy of 92.4% in our example analysis.
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Affiliation(s)
- Joshua M Mitchell
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA
| | - Robert M Flight
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA
| | - Qing Jun Wang
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY, USA
| | - Richard M Higashi
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA
- Department of Toxicology & Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Teresa W-M Fan
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA
- Department of Toxicology & Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Andrew N Lane
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA
- Department of Toxicology & Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Hunter N B Moseley
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
- Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY, USA.
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Deng P, Higashi RM, Lane AN, Bruntz RC, Sun RC, Ramakrishnam Raju MV, Nantz MH, Qi Z, Fan TWM. Quantitative profiling of carbonyl metabolites directly in crude biological extracts using chemoselective tagging and nanoESI-FTMS. Analyst 2018; 143:311-322. [PMID: 29192912 DOI: 10.1039/c7an01256j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The extensive range of chemical structures, wide range of abundances, and chemical instability of metabolites present in the metabolome pose major analytical challenges that are difficult to address with existing technologies. To address these issues, one approach is to target a subset of metabolites that share a functional group, such as ketones and aldehydes, using chemoselective tagging. Here we report a greatly improved chemoselective method for the quantitative analysis of hydrophilic and hydrophobic carbonyl-containing metabolites directly in biological samples. This method is based on direct tissue or cells extraction with simultaneous derivatization of stable and labile carbonylated metabolites using N-[2-(aminooxy)ethyl]-N,N-dimethyl-1-dodecylammonium (QDA) and 13CD3 labeled QDA. We combined innovations of direct quenching of biological sample with frozen derivatization conditions under the catalyst N,N-dimethyl-p-phenylenediamine, which facilitated the formation of oxime stable-isotope ion pairs differing by m/z 4.02188 while minimizing metabolite degradation. The resulting oximes were extracted by HyperSep C8 tips to remove interfering compounds, and the products were detected using nano-electrospray ionization interfaced with a Thermo Fusion mass spectrometer. The quaternary ammonium tagging greatly increased electrospray MS detection sensitivity and the signature ions pairs enabled simple identification of carbonyl compounds. The improved method showed the lower limits of quantification for carbonyl standards to be in the range of 0.20-2 nM, with linearity of R2 > 0.99 over 4 orders of magnitude. We have applied the method to assign 66 carbonyls in mouse tumor tissues, many of which could not be assigned solely by accurate mass and tandem MS. Fourteen of the metabolites were quantified using authentic standards. We also demonstrated the suitability of this method for determining 13C labeled isotopologues of carbonyl metabolites in 13C6-glucose-based stable isotope-resolved metabolomic (SIRM) studies.
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Affiliation(s)
- Pan Deng
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Dept. Toxicology & Cancer Biology, University of Kentucky, Lexington, Kentucky 40536-0596, USA.
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Crooks DR, Maio N, Lane AN, Jarnik M, Higashi RM, Haller RG, Yang Y, Fan TWM, Linehan WM, Rouault TA. Acute loss of iron-sulfur clusters results in metabolic reprogramming and generation of lipid droplets in mammalian cells. J Biol Chem 2018. [PMID: 29523684 DOI: 10.1074/jbc.ra118.001885] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are ancient cofactors in cells and participate in diverse biochemical functions, including electron transfer and enzymatic catalysis. Although cell lines derived from individuals carrying mutations in the Fe-S cluster biogenesis pathway or siRNA-mediated knockdown of the Fe-S assembly components provide excellent models for investigating Fe-S cluster formation in mammalian cells, these experimental strategies focus on the consequences of prolonged impairment of Fe-S assembly. Here, we constructed and expressed dominant-negative variants of the primary Fe-S biogenesis scaffold protein iron-sulfur cluster assembly enzyme 2 (ISCU2) in human HEK293 cells. This approach enabled us to study the early metabolic reprogramming associated with loss of Fe-S-containing proteins in several major cellular compartments. Using multiple metabolomics platforms, we observed a ∼12-fold increase in intracellular citrate content in Fe-S-deficient cells, a surge that was due to loss of aconitase activity. The excess citrate was generated from glucose-derived acetyl-CoA, and global analysis of cellular lipids revealed that fatty acid biosynthesis increased markedly relative to cellular proliferation rates in Fe-S-deficient cells. We also observed intracellular lipid droplet accumulation in both acutely Fe-S-deficient cells and iron-starved cells. We conclude that deficient Fe-S biogenesis and acute iron deficiency rapidly increase cellular citrate concentrations, leading to fatty acid synthesis and cytosolic lipid droplet formation. Our findings uncover a potential cause of cellular steatosis in nonadipose tissues.
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Affiliation(s)
- Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Nunziata Maio
- Section on Human Iron Metabolism, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536
| | - Michal Jarnik
- Section on Cell Biology and Metabolism, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536
| | - Ronald G Haller
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Veterans Affairs North Texas Medical Center, Dallas, Texas 75216; Neuromuscular Center, Institute for Exercise and Environmental Medicine, Dallas, Texas 75231
| | - Ye Yang
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Tracey A Rouault
- Section on Human Iron Metabolism, National Institutes of Health, Bethesda, Maryland 20892.
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Kuperman RG, Checkai RT, Simini M, Phillips CT, Higashi RM, Fan TWM, Sappington K. Selenium toxicity to survival and reproduction of Collembola and Enchytraeids in a sandy loam soil. Environ Toxicol Chem 2018; 37:846-853. [PMID: 29078251 DOI: 10.1002/etc.4017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/04/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
We investigated the toxicity of selenium (Se) to the soil invertebrates Folsomia candida (Collembola) and Enchytraeus crypticus (potworm). Studies were designed to generate ecotoxicological benchmarks for developing ecological soil screening levels (Eco-SSLs) for risk assessments of contaminated soils. For the present studies, we selected Sassafras sandy loam, an aerobic upland soil with soil characteristics (low levels of clay and organic matter, soil pH adjusted from 5.2 to 7.1) that support high relative bioavailability of the anionic Se species that is typically found in aerobic soil. The Se was amended into soil as sodium selenate, subjected to weathering and aging using 21 d of alternating cycles of air-drying/rehydration to 60% of the water-holding capacity of the Sassafras sandy loam soil, under ambient greenhouse conditions. Effective concentrations at 20 and 50% (EC20 and EC50) levels for production of juveniles (reproduction) were 4.7 and 10.9 mg of Se/kg of soil (dry mass basis), respectively, for Collembola, and 4.4 and 6.2 mg/kg, respectively, for the potworms. The data enabled the derivation of toxicity benchmarks, contributing to the development of a soil invertebrate-based Eco-SSL of 4.1 mg/kg for Se. Environ Toxicol Chem 2018;37:846-853. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
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Affiliation(s)
- Roman G Kuperman
- US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Ronald T Checkai
- US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Michael Simini
- US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Carlton T Phillips
- US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | | | | | - Keith Sappington
- US Environmental Protection Agency, Office of Research and Development, Washington, DC, USA
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Deng P, Higashi RM, Lane AN, Bruntz RC, Sun RC, Raju MVR, Nantz MH, Qi Z, Fan TWM. Correction: Quantitative profiling of carbonyl metabolites directly in crude biological extracts using chemoselective tagging and nanoESI-FTMS. Analyst 2018; 143:999. [PMID: 29359211 DOI: 10.1039/c8an90009d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for 'Quantitative profiling of carbonyl metabolites directly in crude biological extracts using chemoselective tagging and nanoESI-FTMS' by Pan Deng, et al., Analyst, 2018, 143, 311-322.
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Affiliation(s)
- Pan Deng
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, and Dept. Toxicology & Cancer Biology, University of Kentucky, Lexington, Kentucky 40536-0596, USA.
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Dent LL, Mandape SN, Pratap S, Dong J, Davis J, Gaddy JA, Amoah K, Damo S, Marshall DR, Jones J, Brandt T, Diaz G, Wang Q, Gary T, Yenamandra A, Ghattas MZ, Elrakaiby M, Aziz RK, Zedan HH, Elmassry M, ElRakaiby M, Aziz RK, Lotfy M, Elmassry M, Marcel J, Khattab RA, Abdelfattah MM, Gilbert JA, Aziz RK, Dini P, Loux SC, Scoggin KE, Esteller-Vico A, Squires EL, Troedsson MHT, Daels P, Ball BA, De Silva K, Bailey E, Stephens JC, Kalbfleisch TS, Dolin CE, Poole LG, Wilkey DW, Rouchka EC, Arteel GE, Barati MT, Merchant ML, Higashi RM, Fan TWM, Moseley H, Lane AN. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings. BMC Proc 2017. [PMCID: PMC5667591 DOI: 10.1186/s12919-017-0078-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Rouchka EC, Chariker JH, Tieri DA, Park JW, Rajurkar S, Singh V, Verma NK, Cui Y, Farman M, Condon B, Moore N, Jaromczyk J, Jaromczyk J, Harris D, Calie P, Shin EK, Davis RL, Shaban-Nejad A, Mitchell JM, Flight RM, Wang QJ, Higashi RM, Fan TWM, Lane AN, Moseley HNB, Lu L, Daigle BJ, Chen X, Smelter A, Moseley HNB, Jaromczyk JW, Farman M, Chen L, Moore N, Phan BK, Serpico NJ, Toney EG, Melton CE, Mandel JR, Daigle BJ, Chen H, Zaman KI, Homayouni R, Trainor PJ, Carlisle SM, DeFilippis AP, Rai SN. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics. BMC Bioinformatics 2017. [PMCID: PMC5647556 DOI: 10.1186/s12859-017-1781-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Abstract
Metabolic reprogramming is a hallmark of cancer. The changes in metabolism are adaptive to permit proliferation, survival, and eventually metastasis in a harsh environment. Stable isotope-resolved metabolomics (SIRM) is an approach that uses advanced approaches of NMR and mass spectrometry to analyze the fate of individual atoms from stable isotope-enriched precursors to products to deduce metabolic pathways and networks. The approach can be applied to a wide range of biological systems, including human subjects. This review focuses on the applications of SIRM to cancer metabolism and its use in understanding drug actions.
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Affiliation(s)
- Ronald C Bruntz
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506.
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506.
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Sun RC, Warmoes MO, Yang Y, Deng P, Sun Q, Lane AN, Higashi RM, Fan TWM. Abstract 2502: Liquid diet introduction of tracers into mice for stable isotope-resolved metabolomics (SIRM) investigations. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2502] [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
Tracer-based mapping of metabolic networks in vivo is a powerful approach for revealing metabolic reprogramming in human cancer. However, current in vivo labeling techniques for model animals face important challenges including insufficient depth of pathway coverage (e.g. inability to detect labeled nucleotides, proteins, and lipids) and stress-related artifacts. Here, we report stress-free administration of 13C6-glucose via liquid diet into mice. 13C enrichment was observed in metabolites of glycolysis, the Krebs cycle, the pentose phosphate pathway, nucleobases, UDP-sugars, as well as macromolecules glycogen, lipids, and proteins from major organs in NSG mice. We have applied the liquid diet method to map the glucose metabolic networks in NSCLC tumors in a patient-derived xenograft (PDX) model. We observed a high enrichment in the metabolites of glycolysis, Krebs cycle, and PPP as well as de novo synthesized nucleotides and amino acids by IC-UHR-FTMS analysis. Lung PDX displayed unexpected metabolic complexity, such as the use of pyruvate to fuel anaplerosis as well as gluconeogenesis. We also found high 13C enrichment in both tumor and plasma glutamine, which implies that glutamine in the PDX tumors largely came from other organs via the blood rather than being synthesized in situ. Our data showed that liquid diet is an effective and noninvasive means for comprehensive analysis of glucose-associated metabolic networks in human tumor xenografts, which can also be extended to SIRM studies with other fuel sources.
Acknowledgements: This work was supported in part by grants: 1R01ES022191-01 (to TWMF and RMH), 1P01CA163223-01A1 (to ANL and TWMF), and 1U24DK097215-01A1 (to RMH, TWMF, and ANL)
R.C. Sun was supported by a T32 training grant to M. Vore (5T32ES007266-25)
Citation Format: Ramon C. Sun, Marc O. Warmoes, Ye Yang, Pan Deng, Qiushi Sun, Andrew N. Lane, Richard M. Higashi, Teresa W-M Fan. Liquid diet introduction of tracers into mice for stable isotope-resolved metabolomics (SIRM) investigations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2502. doi:10.1158/1538-7445.AM2017-2502
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Affiliation(s)
| | | | - Ye Yang
- University of Kentucky, Lexington, KY
| | - Pan Deng
- University of Kentucky, Lexington, KY
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Yang Y, Fan TWM, Lane AN, Higashi RM. Chloroformate derivatization for tracing the fate of Amino acids in cells and tissues by multiple stable isotope resolved metabolomics (mSIRM). Anal Chim Acta 2017; 976:63-73. [PMID: 28576319 DOI: 10.1016/j.aca.2017.04.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/02/2017] [Accepted: 04/03/2017] [Indexed: 12/29/2022]
Abstract
Amino acids have crucial roles in central metabolism, both anabolic and catabolic. To elucidate these roles, steady-state concentrations of amino acids alone are insufficient, as each amino acid participates in multiple pathways and functions in a complex network, which can also be compartmentalized. Stable Isotope-Resolved Metabolomics (SIRM) is an approach that uses atom-resolved tracking of metabolites through biochemical transformations in cells, tissues, or whole organisms. Using different elemental stable isotopes to label multiple metabolite precursors makes it possible to resolve simultaneously the utilization of these precursors in a single experiment. Conversely, a single precursor labeled with two (or more) different elemental isotopes can trace the allocation of e.g. C and N atoms through the network. Such dual-label experiments however challenge the resolution of conventional mass spectrometers, which must distinguish the neutron mass differences among different elemental isotopes. This requires ultrahigh resolution Fourier transform mass spectrometry (UHR-FTMS). When combined with direct infusion nano-electrospray ion source (nano-ESI), UHR-FTMS can provide rapid, global, and quantitative analysis of all possible mass isotopologues of metabolites. Unfortunately, very low mass polar metabolites such as amino acids can be difficult to analyze by current models of UHR-FTMS, plus the high salt content present in typical cell or tissue polar extracts may cause unacceptable ion suppression for sources such as nano-ESI. Here we describe a modified method of ethyl chloroformate (ECF) derivatization of amino acids to enable rapid quantitative analysis of stable isotope labeled amino acids using nano-ESI UHR-FTMS. This method showed excellent linearity with quantifiable limits in the low nanomolar range represented in microgram quantities of biological specimens, which results in extracts with total analyte abundances in the low to sub-femtomole range. We have applied this method to profile amino acids and their labeling patterns in 13C and 2H doubly labeled PC9 cell extracts, cancerous and non-cancerous tissue extracts from a lung cancer patient and their protein hydrolysates as well as plasma extracts from mice fed with a liquid diet containing 13C6-glucose (Glc). The multi-element isotopologue distributions provided key insights into amino acid metabolism and intracellular pools in human lung cancer tissues in high detail. The 13C labeling of Asp and Glu revealed de novo synthesis of these amino acids from 13C6-Glc via the Krebs cycle, specifically the elevated level of 13C3-labeled Asp and Glu in cancerous versus non-cancerous lung tissues was consistent with enhanced pyruvate carboxylation. In addition, tracking the fate of double tracers, (13C6-Glc + 2H2-Gly or 13C6-Glc + 2H3-Ser) in PC9 cells clearly resolved pools of Ser and Gly synthesized de novo from 13C6-Glc (13C3-Ser and 13C2-Gly) versus Ser and Gly derived from external sources (2H3-Ser, 2H2-Gly). Moreover the complex 2H labeling patterns of the latter were results of Ser and Gly exchange through active Ser-Gly one-carbon metabolic pathway in PC9 cells.
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Affiliation(s)
- Ye Yang
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40539, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40539, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA.
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40539, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40539, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA.
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Lane AN, Fan TWM. NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry. Arch Biochem Biophys 2017; 628:123-131. [PMID: 28263717 DOI: 10.1016/j.abb.2017.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 01/23/2023]
Abstract
Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA.
| | - Teresa W-M Fan
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA
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Lane AN, Tan J, Wang Y, Yan J, Higashi RM, Fan TWM. Probing the metabolic phenotype of breast cancer cells by multiple tracer stable isotope resolved metabolomics. Metab Eng 2017; 43:125-136. [PMID: 28163219 DOI: 10.1016/j.ymben.2017.01.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 12/12/2022]
Abstract
Breast cancers vary by their origin and specific set of genetic lesions, which gives rise to distinct phenotypes and differential response to targeted and untargeted chemotherapies. To explore the functional differences of different breast cell types, we performed Stable Isotope Resolved Metabolomics (SIRM) studies of one primary breast (HMEC) and three breast cancer cells (MCF-7, MDAMB-231, and ZR75-1) having distinct genotypes and growth characteristics, using 13C6-glucose, 13C-1+2-glucose, 13C5,15N2-Gln, 13C3-glycerol, and 13C8-octanoate as tracers. These tracers were designed to probe the central energy producing and anabolic pathways (glycolysis, pentose phosphate pathway, Krebs Cycle, glutaminolysis, nucleotide synthesis and lipid turnover). We found that glycolysis was not associated with the rate of breast cancer cell proliferation, glutaminolysis did not support lipid synthesis in primary breast or breast cancer cells, but was a major contributor to pyrimidine ring synthesis in all cell types; anaplerotic pyruvate carboxylation was activated in breast cancer versus primary cells. We also found that glucose metabolism in individual breast cancer cell lines differed between in vitro cultures and tumor xenografts, but not the metabolic distinctions between cell lines, which may reflect the influence of tumor architecture/microenvironment.
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Affiliation(s)
- Andrew N Lane
- J.G. Brown Cancer Center, University of Louisville, Louisville, KY, United States; Dept. Chemistry and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY, United States.
| | - Julie Tan
- J.G. Brown Cancer Center, University of Louisville, Louisville, KY, United States.
| | - Yali Wang
- J.G. Brown Cancer Center, University of Louisville, Louisville, KY, United States.
| | - Jun Yan
- J.G. Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - Richard M Higashi
- Dept. Chemistry and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY, United States
| | - Teresa W-M Fan
- J.G. Brown Cancer Center, University of Louisville, Louisville, KY, United States; Dept. Chemistry and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY, United States.
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Fan TWM, Warmoes MO, Sun Q, Song H, Turchan-Cholewo J, Martin JT, Mahan A, Higashi RM, Lane AN. Distinctly perturbed metabolic networks underlie differential tumor tissue damages induced by immune modulator β-glucan in a two-case ex vivo non-small-cell lung cancer study. Cold Spring Harb Mol Case Stud 2016; 2:a000893. [PMID: 27551682 PMCID: PMC4990809 DOI: 10.1101/mcs.a000893] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cancer and stromal cell metabolism is important for understanding tumor development, which highly depends on the tumor microenvironment (TME). Cell or animal models cannot recapitulate the human TME. We have developed an ex vivo paired cancerous (CA) and noncancerous (NC) human lung tissue approach to explore cancer and stromal cell metabolism in the native human TME. This approach enabled full control of experimental parameters and acquisition of individual patient's target tissue response to therapeutic agents while eliminating interferences from genetic and physiological variations. In this two-case study of non-small-cell lung cancer, we performed stable isotope-resolved metabolomic (SIRM) experiments on paired CA and NC lung tissues treated with a macrophage activator β-glucan and (13)C6-glucose, followed by ion chromatography-Fourier transform mass spectrometry (IC-FTMS) and nuclear magnetic resonance (NMR) analyses of (13)C-labeling patterns of metabolites. We demonstrated that CA lung tissue slices were metabolically more active than their NC counterparts, which recapitulated the metabolic reprogramming in CA lung tissues observed in vivo. We showed β-glucan-enhanced glycolysis, Krebs cycle, pentose phosphate pathway, antioxidant production, and itaconate buildup in patient UK021 with chronic obstructive pulmonary disease (COPD) and an abundance of tumor-associated macrophages (TAMs) but not in UK049 with no COPD and much less macrophage infiltration. This metabolic response of UK021 tissues was accompanied by reduced mitotic index, increased necrosis, and enhaced inducible nitric oxide synthase (iNOS) expression. We surmise that the reprogrammed networks could reflect β-glucan M1 polarization of human macrophages. This case study presents a unique opportunity for investigating metabolic responses of human macrophages to immune modulators in their native microenvironment on an individual patient basis.
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Affiliation(s)
- Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Marc O Warmoes
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Qiushi Sun
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Huan Song
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Jadwiga Turchan-Cholewo
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Jeremiah T Martin
- Department of Surgery and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Angela Mahan
- Department of Surgery and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
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Fan TWM, Lane AN, Yan J, Higashi RM, Martin JT, Bousamra M. Abstract 4271: Beta-glucan activates macrophages in human NSCLC demonstrated by Stable Isotope Resolved Metabolomics (SIRM). Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4271] [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
Introduction: We use SIRM to evaluate metabolic reprogramming of lung cancer cells in monoculture, in mouse xenograft/explant models, and in NSCLC patients in situ (1,2). We have now extended the range of models to fresh human tissue slices, which retain the original tissue architecture and heterogeneity with a paired benign versus cancer tissue design under defined cell culture conditions. β-glucan is a polysaccharide that repolarizes tumor-associated macrophages (TAMs) from the M2 to the M1 phenotype in mice (3). Here we report the activation of TAMs in human NSCLC tissue slices.
Experimental: Freshly resected paired tissue slices from individual patients (approx. 1 mm or less thick and 5-40 mg wet weight) were incubated ± particulate β-glucan in standard cell culture conditions, with gentle rocking to enable efficient gas, nutrient, and waste product exchange. Tissue slices could be maintained metabolically viable for at least 48 h of incubation. The metabolic activity was determined by measuring the uptake and transformation of 13C and/or 15N-enriched common nutrient tracers such as glucose and glutamine, using high resolution mass spectrometry, GC-MS, and NMR after a period of incubation (2).
Findings: Time-course analysis of the slices by NMR, MS, and histology revealed that NSCLC tissue slices, both benign and tumorous, retained their architecture and a broad spectrum of metabolic activities. Glucose and glutamine metabolism was reprogrammed in the tumor relative to the paired benign tissues ex vivo, as the in vivo case. The paired tissues from different patients showed significantly different metabolic responses to β-glucan, as expected
Conclusions: This platform offers a human tissue model for preclinical studies on metabolic reprogramming of human cancer and stromal cells in their tissue context, and response to drug treatment (4). As the microenvironment of the target human tissue is maintained, including the resident immune cells, individualized response to immune-active agents can be determined in a clinically relevant setting.
Supported by NCI P01CA163223-01 and NIEHS 1R01ES022191-01
1. Lane, A.N., Fan, T.W.-M., Bousamra II, M., et al. (2011) Clinical Applications of Stable Isotope-Resolved Metabolomics (SIRM) in Non-Small Cell Lung Cancer. Omics, 15, 173-182.
2. Sellers, K., Fox, M.P., Bousamra, M., II, et al. (2015) Pyruvate carboxylase is critical for non-small-cell lung cancer proliferation. Journal of Clinical Investigation, 125, 687-698.
3. Liu, M., Luo, F., Ding, C., et al. (2015) Particulate β-Glucan Converts Immunosuppressive Macrophages into M1 Phenotype Through Dectin-1-induced Syk-Card9-Erk Pathway and Raf-1-c-Maf Pathway. J. Immunol., 195, 5055-5065.
4. Xie, H., Hanai, J., Ren, et al. (2014) Targeting lactate dehydrogenase-A (LDH-A) inhibits tumorigenesis and tumor progression in mouse models of lung cancer and impacts tumor initiating cells. Cell Metabolism 19, 795-809
Citation Format: Teresa W-M Fan, Andrew N. Lane, Jun Yan, Richard M. Higashi, Jeremiah T. Martin, Michael Bousamra. Beta-glucan activates macrophages in human NSCLC demonstrated by Stable Isotope Resolved Metabolomics (SIRM). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4271.
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Affiliation(s)
| | | | - Jun Yan
- 2University of Louisville, Louisville, KY
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Abstract
AIMS In this review we compare the advantages and disadvantages of different model biological systems for determining the metabolic functions of cells in complex environments, how they may change in different disease states, and respond to therapeutic interventions. BACKGROUND All preclinical drug-testing models have advantages and drawbacks. We compare and contrast established cell, organoid and animal models with ex vivo organ or tissue culture and in vivo human experiments in the context of metabolic readout of drug efficacy. As metabolism reports directly on the biochemical state of cells and tissues, it can be very sensitive to drugs and/or other environmental changes. This is especially so when metabolic activities are probed by stable isotope tracing methods, which can also provide detailed mechanistic information on drug action. We have developed and been applying Stable Isotope-Resolved Metabolomics (SIRM) to examine metabolic reprogramming of human lung cancer cells in monoculture, in mouse xenograft/explant models, and in lung cancer patients in situ (Lane et al. 2011; T. W. Fan et al. 2011; T. W-M. Fan et al. 2012; T. W. Fan et al. 2012; Xie et al. 2014b; Ren et al. 2014a; Sellers et al. 2015b). We are able to determine the influence of the tumor microenvironment using these models. We have now extended the range of models to fresh human tissue slices, similar to those originally described by O. Warburg (Warburg 1923), which retain the native tissue architecture and heterogeneity with a paired benign versus cancer design under defined cell culture conditions. This platform offers an unprecedented human tissue model for preclinical studies on metabolic reprogramming of human cancer cells in their tissue context, and response to drug treatment (Xie et al. 2014a). As the microenvironment of the target human tissue is retained and individual patient's response to drugs is obtained, this platform promises to transcend current limitations of drug selection for clinical trials or treatments. CONCLUSIONS AND FUTURE WORK Development of ex vivo human tissue and animal models with humanized organs including bone marrow and liver show considerable promise for analyzing drug responses that are more relevant to humans. Similarly using stable isotope tracer methods with these improved models in advanced stages of the drug development pipeline, in conjunction with tissue biopsy is expected significantly to reduce the high failure rate of experimental drugs in Phase II and III clinical trials.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, University of Kentucky
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky
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Li J, Song J, Zaytseva YY, Liu Y, Rychahou P, Jiang K, Starr ME, Kim JT, Harris JW, Yiannikouris FB, Katz WS, Nilsson PM, Orho-Melander M, Chen J, Zhu H, Fahrenholz T, Higashi RM, Gao T, Morris AJ, Cassis LA, Fan TWM, Weiss HL, Dobner PR, Melander O, Jia J, Evers BM. An obligatory role for neurotensin in high-fat-diet-induced obesity. Nature 2016; 533:411-5. [PMID: 27193687 PMCID: PMC5484414 DOI: 10.1038/nature17662] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/10/2016] [Indexed: 12/15/2022]
Abstract
Obesity and its associated comorbidities (e.g., diabetes mellitus and hepatic steatosis) contribute to approximately 2.5 million deaths annually1 and are among the most prevalent and challenging conditions confronting the medical profession2,3. Neurotensin (NT), a 13-amino acid peptide predominantly localized in specialized enteroendocrine (EE) cells of the small bowel4 and released by fat ingestion5, facilitates fatty acid (FA) translocation in rat intestine6, and stimulates growth of various cancers7; the effects of NT are mediated through three known NT receptors (NTR1, 2 and 3)8. Increased fasting plasma levels of pro-NT (a stable NT precursor fragment produced in equimolar amounts relative to NT) are associated with increased risk of diabetes, cardiovascular disease and mortality9; however, a role for NT as a causative factor in these diseases is unknown. Here, we show that NT-deficient mice demonstrate significantly reduced intestinal fat absorption and are protected from obesity, hepatic steatosis and insulin resistance associated with high fat consumption. We further demonstrate that NT attenuates the activation of AMP-activated protein kinase (AMPK) and stimulates FA absorption in mice and in cultured intestinal cells, and that this occurs through a mechanism involving NTR1 and NTR3/sortilin. Consistent with the findings in mice, expression of NT in Drosophila midgut EE cells results in increased lipid accumulation in the midgut, fat body, and oenocytes (specialized hepatocyte-like cells) and decreased AMPK activation. Remarkably, in humans, we show that both obese and insulin-resistant subjects have elevated plasma concentrations of pro-NT, and in longitudinal studies among non-obese subjects, high levels of pro-NT denote a doubling of the risk of developing obesity later in life. Our findings directly link NT with increased fat absorption and obesity and suggest that NT may provide a prognostic marker of future obesity and a potential target for prevention and treatment.
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Affiliation(s)
- Jing Li
- Department of Surgery, University of Kentucky, Lexington, Kentucky 40536, USA.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Jun Song
- Department of Surgery, University of Kentucky, Lexington, Kentucky 40536, USA.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Yekaterina Y Zaytseva
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Yajuan Liu
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Piotr Rychahou
- Department of Surgery, University of Kentucky, Lexington, Kentucky 40536, USA.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Kai Jiang
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Marlene E Starr
- Department of Surgery, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Ji Tae Kim
- Department of Surgery, University of Kentucky, Lexington, Kentucky 40536, USA.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Jennifer W Harris
- Department of Surgery, University of Kentucky, Lexington, Kentucky 40536, USA.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Frederique B Yiannikouris
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Wendy S Katz
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Peter M Nilsson
- Department of Clinical Sciences, Lund University, Malmö, 221 00 Lund, Sweden.,Department of Internal Medicine, Skåne University Hospital, Malmö, 205 02 Malmö, Sweden
| | - Marju Orho-Melander
- Department of Clinical Sciences, Lund University, Malmö, 221 00 Lund, Sweden
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA.,Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA.,Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Timothy Fahrenholz
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Richard M Higashi
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Tianyan Gao
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA.,Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Andrew J Morris
- Division of Cardiovascular Medicine, Gill Heart Institute, University of Kentucky and Lexington Veterans Affairs Medical Center, Lexington, Kentucky 40536, USA
| | - Lisa A Cassis
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Teresa W-M Fan
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Heidi L Weiss
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA.,Department of Biostatistics, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Paul R Dobner
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, 221 00 Lund, Sweden.,Department of Internal Medicine, Skåne University Hospital, Malmö, 205 02 Malmö, Sweden
| | - Jianhang Jia
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA.,Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | - B Mark Evers
- Department of Surgery, University of Kentucky, Lexington, Kentucky 40536, USA.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
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Liu M, Luo F, Ding C, Albeituni S, Hu X, Ma Y, Cai Y, McNally L, Sanders MA, Jain D, Kloecker G, Bousamra M, Zhang HG, Higashi RM, Lane AN, Fan TWM, Yan J. Correction: Dectin-1 Activation by a Natural Product β-Glucan Converts Immunosuppressive Macrophages into an M1-like Phenotype. J Immunol 2016; 196:3968. [PMID: 27183653 DOI: 10.4049/jimmunol.1600345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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Saxena N, Maio N, Crooks DR, Ricketts CJ, Yang Y, Wei MH, Fan TWM, Lane AN, Sourbier C, Singh A, Killian JK, Meltzer PS, Vocke CD, Rouault TA, Linehan WM. SDHB-Deficient Cancers: The Role of Mutations That Impair Iron Sulfur Cluster Delivery. J Natl Cancer Inst 2016; 108:djv287. [PMID: 26719882 DOI: 10.1093/jnci/djv287] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Mutations in the Fe-S cluster-containing SDHB subunit of succinate dehydrogenase cause familial cancer syndromes. Recently the tripeptide motif L(I)YR was identified in the Fe-S recipient protein SDHB, to which the cochaperone HSC20 binds. METHODS In order to characterize the metabolic basis of SDH-deficient cancers we performed stable isotope-resolved metabolomics in a novel SDHB-deficient renal cell carcinoma cell line and conducted bioinformatics and biochemical screening to analyze Fe-S cluster acquisition and assembly of SDH in the presence of other cancer-causing SDHB mutations. RESULTS We found that the SDHBR46Q mutation in UOK269 cells disrupted binding of HSC20, causing rapid degradation of SDHB. In the absence of SDHB, respiration was undetectable in UOK269 cells, succinate was elevated to 351.4 ± 63.2 nmol/mg cellular protein, and glutamine became the main source of TCA cycle metabolites through reductive carboxylation.Furthermore, HIF1α, but not HIF2α, increased markedly and the cells showed a strong DNA CpG island methylatorphenotype (CIMP). Biochemical and bioinformatic screening revealed that 37% of disease-causing missense mutations in SDHB were located in either the L(I)YR Fe-S transfer motifs or in the 11 Fe-S cluster-ligating cysteines. CONCLUSIONS These findings provide a conceptual framework for understanding how particular mutations disproportionately cause the loss of SDH activity, resulting in accumulation of succinate and metabolic remodeling in SDHB cancer syndromes.
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Fan TWM, Lane AN. Applications of NMR spectroscopy to systems biochemistry. Prog Nucl Magn Reson Spectrosc 2016; 92-93:18-53. [PMID: 26952191 PMCID: PMC4850081 DOI: 10.1016/j.pnmrs.2016.01.005] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [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: 10/14/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 05/05/2023]
Abstract
The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective in vivo imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied in vitro, ex vivo, or in vivo in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other 'omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.
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Affiliation(s)
- Teresa W-M Fan
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
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Abstract
An important component of this methodology is to assess the role of the tumor microenvironment on tumor growth and survival. To tackle this problem, we have adapted the original approach of Warburg 1, by combining thin tissue slices with Stable Isotope Resolved Metabolomics (SIRM) to determine detailed metabolic activity of human tissues. SIRM enables the tracing of metabolic transformations of source molecules such as glucose or glutamine over defined time periods, and is a requirement for detailed pathway tracing and flux analysis. In our approach, we maintain freshly resected tissue slices (both cancerous and non- cancerous from the same organ of the same subject) in cell culture media, and treat with appropriate stable isotope-enriched nutrients, e.g.13C6-glucose or 13C5, 15N2 -glutamine. These slices are viable for at least 24 h, and make it possible to eliminate systemic influence on the target tissue metabolism while maintaining the original 3D cellular architecture. It is therefore an excellent pre-clinical platform for assessing the effect of therapeutic agents on target tissue metabolism and their therapeutic efficacy on individual patients 2,3.
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Affiliation(s)
- Teresa W-M Fan
- Center for Environmental Systems Biochemistry, Dept. Toxicology and Cancer Biology and Markey Cancer Center, 789 S. Limestone St., Lexington KY
| | - Andrew N Lane
- Center for Environmental Systems Biochemistry, Dept. Toxicology and Cancer Biology and Markey Cancer Center, 789 S. Limestone St., Lexington KY
| | - Richard M Higashi
- Center for Environmental Systems Biochemistry, Dept. Toxicology and Cancer Biology and Markey Cancer Center, 789 S. Limestone St., Lexington KY
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Liu M, Luo F, Ding C, Albeituni S, Hu X, Ma Y, Cai Y, McNally L, Sanders MA, Jain D, Kloecker G, Bousamra M, Zhang HG, Higashi RM, Lane AN, Fan TWM, Yan J. Dectin-1 Activation by a Natural Product β-Glucan Converts Immunosuppressive Macrophages into an M1-like Phenotype. J Immunol 2015; 195:5055-65. [PMID: 26453753 DOI: 10.4049/jimmunol.1501158] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/10/2015] [Indexed: 12/15/2022]
Abstract
Tumor-associated macrophages (TAM) with an alternatively activated phenotype have been linked to tumor-elicited inflammation, immunosuppression, and resistance to chemotherapies in cancer, thus representing an attractive target for an effective cancer immunotherapy. In this study, we demonstrate that particulate yeast-derived β-glucan, a natural polysaccharide compound, converts polarized alternatively activated macrophages or immunosuppressive TAM into a classically activated phenotype with potent immunostimulating activity. This process is associated with macrophage metabolic reprograming with enhanced glycolysis, Krebs cycle, and glutamine utilization. In addition, particulate β-glucan converts immunosuppressive TAM via the C-type lectin receptor dectin-1-induced spleen tyrosine kinase-Card9-Erk pathway. Further in vivo studies show that oral particulate β-glucan treatment significantly delays tumor growth, which is associated with in vivo TAM phenotype conversion and enhanced effector T cell activation. Mice injected with particulate β-glucan-treated TAM mixed with tumor cells have significantly reduced tumor burden with less blood vascular vessels compared with those with TAM plus tumor cell injection. In addition, macrophage depletion significantly reduced the therapeutic efficacy of particulate β-glucan in tumor-bearing mice. These findings have established a new paradigm for macrophage polarization and immunosuppressive TAM conversion and shed light on the action mode of β-glucan treatment in cancer.
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Affiliation(s)
- Min Liu
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202; Department of Immunology, Wuhan University School of Medicine, Wuhan 430072, China
| | - Fengling Luo
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202; Department of Immunology, Wuhan University School of Medicine, Wuhan 430072, China
| | - Chuanlin Ding
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - Sabrin Albeituni
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY 40202
| | - Xiaoling Hu
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - Yunfeng Ma
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - Yihua Cai
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - Lacey McNally
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - Mary Ann Sanders
- Department of Pathology, University of Louisville School of Medicine, Louisville, KY 40202
| | - Dharamvir Jain
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - Goetz Kloecker
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - Michael Bousamra
- Department of Cardiovascular Thoracic Surgery, University of Louisville, Louisville, KY 40202
| | - Huang-ge Zhang
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY 40202
| | - Richard M Higashi
- Department of Chemistry, University of Louisville, Louisville, KY 40202; and
| | - Andrew N Lane
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202; Department of Chemistry, University of Louisville, Louisville, KY 40202; and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40202
| | - Teresa W-M Fan
- Department of Chemistry, University of Louisville, Louisville, KY 40202; and Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40202
| | - Jun Yan
- Division of Hematology/Oncology, Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202; Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY 40202;
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Lane AN, Fan TWM, Belshoff AC, Higashi RM, Martin J, Bousamra M. Abstract 3199: Stable isotope resolved metabolomics (SIRM) on fresh human tissues as a preclinical drug testing platform. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3199] [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
Introduction: All preclinical drug testing models have advantages and drawbacks. We have been using SIRM to evaluate metabolic reprogramming of lung cancer cells in monoculture, in mouse xenograft/explant models, and in NSCLC patients in situ (1), and to determine the influence of the tumor microenvironment using these models. We have now extended the range of models to fresh human tissue slices, similar to those originally described by Warburg (2), which retain the original tissue architecture and heterogeneity with a paired benign versus cancer design under controlled cell culture conditions.
Experimental: Freshly resected tissue slices from individuals (ca. 1 mm or less thick and 5-40 mg wet weight) were incubated in standard cell culture conditions with gentle rocking for efficient gas, nutrient and waste product exchange. The metabolic activity was determined by measuring the uptake and transformation of 13C and/or 15N-enriched nutrient tracers such as glucose and glutamine, using high-resolution MS, GC-MS, and NMR after a period of incubation. Acute metabolic and histologic response to inhibitors or drugs was readily detected in treated tissue slices.
Findings: Analysis at different time points by NMR, MS and histology shows that the NSCLC tissue slices, both benign and tumorous, retained their architecture and remained metabolically viable for at least 48 h of incubation. Glucose and glutamine metabolism was reprogrammed in the tumor relative to the paired benign tissues. The paired tissue also showed very different responses to Se-containing compounds when incubated at the IC50 established for cell lines. After 24 h of incubation, large scale necrosis was evident in the tumor, but not in the benign slices, which was accompanied by large changes in metabolic activities observed by SIRM analysis.
Conclusions: This platform offers a human tissue model for preclinical studies on metabolic reprogramming of human cancer cells in their tissue context, and response to drug treatment (3). As the microenvironment of the target human tissue is retained and individualized response to drugs is obtained, this platform promises to transcend current limitations of drug selection for clinical trials or treatments.
Supported by NCI P01CA163223-01A1 and NIEHS 1R01ES022191-01
1. Lane, A.N., Fan, T.W.-M., Bousamra II, M., Higashi, R.M., Yan, J. and Miller, D.M. (2011) Clinical Applications of Stable Isotope-Resolved Metabolomics (SIRM) in Non-Small Cell Lung Cancer. Omics, 15, 173-182.
2. Warburg, O. (1923) Versuche an überlebendem Carcinomgewebe (Methoden). Biochem. Zeitschr., 142, 317-333.
3. Xie, H., Hanai, J., Ren, J.-G., Kats, L., Burgess, K., Bhargava, P., Signoretti, S., Billiard, J., Duffy, K.J., Grant, A. et al. (2014) Targeting lactate dehydrogenase-A (LDH-A) inhibits tumorigenesis and tumor progression in mouse models of lung cancer and impacts tumor initiating cells. Cell Metabolism 19, 795-809.
Citation Format: Andrew N. Lane, Teresa W-M Fan, Alexander C. Belshoff, Richard M. Higashi, Jeremiah Martin, Michael Bousamra. Stable isotope resolved metabolomics (SIRM) on fresh human tissues as a preclinical drug testing platform. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3199. doi:10.1158/1538-7445.AM2015-3199
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